US20160017358A1

US20160017358A1 - Plants having modified growth characteristics and a method for making the same

Info

Publication number: US20160017358A1
Application number: US14/722,254
Authority: US
Inventors: Kristiina Himanen; Maria van Lijsebettens; Christophe Reuzeau; Tommaso Matteo Boccardi
Original assignee: Universiteit Gent; Vlaams Instituut voor Biotechnologie VIB; BASF Plant Science GmbH
Current assignee: Universiteit Gent; Vlaams Instituut voor Biotechnologie VIB; BASF Plant Science GmbH
Priority date: 2008-07-31
Filing date: 2015-05-27
Publication date: 2016-01-21
Also published as: EP2669379A2; EP2669379A3; MX2011000778A; CA2731038A1; AR075545A1; WO2010012760A2; US20110162109A1; EP2318535A2; BRPI0916530A8; BRPI0916530A2; AU2009275889A1; DE112009001860T5; US9074006B2; CN102144033A; WO2010012760A3

Abstract

The present invention relates generally to the field of molecular biology and concerns a method for improving various economically important growth characteristics in plants. More specifically, the present invention concerns inter alia a method for modifying growth characteristics in plants by modulating expression in a plant of a nucleic acid encoding a HUB1 (Histone Monoubiquitination 1) polypeptide or encoding another protein useful in the methods of the present invention. The modified growth characteristics comprise a modification of light regulated phenotypes, such as modified circadian clock and/or circadian clock responses, or modified plant architecture.

Description

RELATED APPLICATIONS

This application is a divisional application of U.S. application Ser. No. 13/056,534 filed Jan. 28, 2011, which is a national stage application (under 35 U.S.C. §371) of PCT/EP2009/059790, filed Jul. 29, 2009, which claims benefit of European application 08161540.3, filed Jul. 31, 2008; European Application 08161514.8, filed Jul. 31, 2008; U.S. Provisional Application 61/085,046, filed Jul. 31, 2008 and U.S. Provisional Application 61/085,431, filed Aug. 1, 2008. The entire contents of each of these applications are hereby incorporated by reference herein in their entirety.

SUBMISSION OF SEQUENCE LISTING

The Sequence Listing associated with this application is filed in electronic format via EFS-Web and hereby incorporated by reference into the specification in its entirety. The name of the text file containing the Sequence Listing is Sequence_Listing_—074021_—0138_—01. The size of the text file is 3,366 KB, and the text file was created on May 26, 2015.
The present invention relates generally to the field of molecular biology and concerns a method for modifying various plant growth characteristics by modulating expression in a plant of a nucleic acid encoding a HUB1 (Histone Monoubiquitination 1) or encoding another protein useful in the methods of the present invention. The present invention also concerns plants having modulated expression of a nucleic acid encoding a HUB1 or of a nucleic acid encoding another protein useful in the methods of the present invention, which plants have modified growth characteristics relative to corresponding wild type plants or other control plants. The invention also provides hitherto unknown HUB1-encoding nucleic acids, and constructs useful in the methods of the invention.
The ever-increasing world population and the dwindling supply of arable land available for agriculture fuels research towards increasing the efficiency of agriculture. Conventional means for crop and horticultural improvements utilise selective breeding techniques to identify plants having desirable characteristics. However, such selective breeding techniques have several drawbacks, namely that these techniques are typically labour intensive and result in plants that often contain heterogeneous genetic components that may not always result in the desirable trait being passed on from parent plants. Advances in molecular biology have allowed mankind to modify the germplasm of animals and plants. Genetic engineering of plants entails the isolation and manipulation of genetic material (typically in the form of DNA or RNA) and the subsequent introduction of that genetic material into a plant. Such technology has the capacity to deliver crops or plants having various improved economic, agronomic or horticultural traits.
A trait of particular economic interest is increased yield. Yield is normally defined as the measurable produce of economic value from a crop. This may be defined in terms of quantity and/or quality. Yield is directly dependent on several factors, for example, the number and size of the organs, plant architecture (for example, the number of branches), seed production, leaf senescence and more. Root development, nutrient uptake, stress tolerance and early vigour may also be important factors in determining yield. Optimizing the abovementioned factors may therefore contribute to increasing crop yield.
Seed yield is a particularly important trait, since the seeds of many plants are important for human and animal nutrition. Crops such as corn, rice, wheat, canola and soybean account for over half the total human caloric intake, whether through direct consumption of the seeds themselves or through consumption of meat products raised on processed seeds. They are also a source of sugars, oils and many kinds of metabolites used in industrial processes. Seeds contain an embryo (the source of new shoots and roots) and an endosperm (the source of nutrients for embryo growth during germination and during early growth of seedlings). The development of a seed involves many genes, and requires the transfer of metabolites from the roots, leaves and stems into the growing seed. The endosperm, in particular, assimilates the metabolic precursors of carbohydrates, oils and proteins and synthesizes them into storage macromolecules to fill out the grain.
Another important trait for many crops is early vigour. Improving early vigour is an important objective of modern rice breeding programs in both temperate and tropical rice cultivars. Long roots are important for proper soil anchorage in water-seeded rice. Where rice is sown directly into flooded fields, and where plants must emerge rapidly through water, longer shoots are associated with vigour. Where drill-seeding is practiced, longer mesocotyls and coleoptiles are important for good seedling emergence. The ability to engineer early vigour into plants would be of great importance in agriculture. For example, poor early vigour has been a limitation to the introduction of maize (Zea mays L.) hybrids based on Corn Belt germplasm in the European Atlantic.
A further interesting trait is the flowering time of a plant. The life span of a plant can be divided in phases such as germination, vegetative growth, reproductive growth and senescence. The flowering time is the time elapsed between sowing and start of reproductive growth. It is a crucial moment in the life of a plant that determines the transition from vegetative to reproductive growth, which in some plants coincides with the start of senescence. In many plants, this is the point in time at which the shoot apical meristem stops making leaves and starts making flowers which has a great impact on morphogenesis affecting, for example, the number of organs formed and the overall size and shape of the plant. The flowering time also impacts other yield-related traits in plants. Typically an early flowering variety shows less branching or tillering and therefore is less bushy. Such traits may be advantageous to the farmer to, for example, simplify crop management. On the other hand, delayed flowering may result in plants with more vegetative organs, for example more leaves which is a desirable trait in many crops, particularly in crops where the vegetative organs are harvested, such as lettuce. The relative duration of vegetative and reproductive phase of a plant directly affects its seed yield. In some plants, control of flowering time is a mechanism used to avoid negative impact of stresses such as drought. Flowering time may also affect quality traits of crops, for example herbage quality in forage crops, where delay in flowering may result in higher digestibility. The flowering time affects the length of the cultivation season. Modification of flowering time of a crop may result in the possibility to extend the geographic area of cultivation and therefore increase the cultivated acreage. It may also result in plants being more amenable to agriculture in a given environment, for example early flowering may allow late planting in areas where crop establishment may be negatively affected by low temperatures or may allow early harvest to avoid biotic and abiotic pressure at the end of the season, resulting therefore in an increase in the yield of the crop. Therefore, the ability to control flowering time is an important factor with many industrial applications in the field of agriculture.
For crop plants it is also important to respond adequately to the daily rhythms they are exposed to. Anticipation to regular changes in the environment gives plants a growth advantage by shortening the delay between the environmental change and the physiological response thereto. For example, activation of the photosynthesis pathways before daybreak allows optimal use of the light period, or timely activation of drought stress responses protects plants from water shortage during warm summer afternoons.
A further important trait is that of improved abiotic stress tolerance. Abiotic stress is a primary cause of crop loss worldwide, reducing average yields for most major crop plants by more than 50% (Wang et al., Planta (2003) 218: 1-14). Abiotic stresses may be caused by drought, salinity, extremes of temperature, chemical toxicity and oxidative stress. The ability to improve plant tolerance to abiotic stress would be of great economic advantage to farmers worldwide and would allow for the cultivation of crops during adverse conditions and in territories where cultivation of crops may not otherwise be possible.
Crop yield may therefore be increased by optimising one of the above-mentioned factors.
Depending on the end use, the modification of certain yield traits may be favoured over others. For example for applications such as forage or wood production, or bio-fuel resource, an increase in the vegetative parts of a plant may be desirable, and for applications such as flour, starch or oil production, an increase in seed parameters may be particularly desirable. Even amongst the seed parameters, some may be favoured over others, depending on the application. Various mechanisms may contribute to increasing seed yield, whether that is in the form of increased seed size or increased seed number.
One approach to increasing yield (seed yield and/or biomass) in plants may be through modification of the inherent growth mechanisms of a plant, such as the cell cycle, circadian rhythm or various signalling pathways involved in plant growth or in defence mechanisms.
Circadian rhythms control many aspects of plant metabolism, physiology and development. Plants make use of environmental signals such as the daily light-dark cycle or regular temperature variations to maintain a biological time-keeping mechanism. This mechanism, known as the circadian clock, is commonly represented as a so-called oscillator that consists of a set of proteins which interact in a complex pattern of positive and negative transcriptional feedback loops, for a review see McClung (Plant Cell 18, 792-803, 2006) and Gardner et al (Biochemical Journal 397, 15-24, 2006). The oscillator is calibrated by external signals (such as light, perceived by phytochromes and cryptochromes) which are transmitted via the “input pathways” to the oscillator. The oscillator on its turn controls a number of pathways (the “output pathways”) which regulate physiological processes that are influenced by the daily environmental changes. An overview is given in Barak et al. (Trends in Plant Science 5, 517-522, 2000) and include for example induction of flowering, opening of petals, opening or closure of stomata, growth of the hypocotyl, movement of cotyledons and leaves, movement of chloraplasts, expression of genes associated with photosynthesis and related biochemical and physiological processes, cytoplasmic calcium concentrations, and the phosphorylation status of proteins like phosphoenol pyruvate carboxylase.
It has now been found that various growth characteristics may be altered in plants by modulating expression in a plant of a nucleic acid encoding a HUB1 (Histone Monoubiquitination 1) in a plant.

BACKGROUND

Ubiquitination plays a central role in regulating protein turnover. Ubiquitin is a highly conserved 76-amino acid protein and one of the most abundant proteins in cells. Ubiquitin proteins are found linked to other proteins as post-translational modification. Polyubiquitination, attachment of more than 4 ubiquitins has been shown to direct proteins for degradation. Ubiquitin conjugation requires sequential action of three enzymes or protein complexes, namely ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2), and ubiquitin-protein ligase (E3). Ubiquitin is initially attached to E1 enzyme in an ATP dependent reaction. After ubiquitin activation, it is transferred to the E2 enzyme via thiolester linkage. Finally, the E3 ligase enzyme brings together the substrate and the E2 with attached ubiquitin. Once a polyubiquitin chain is assembled on a substrate, the substrate is captured and degraded by 26S proteasomes. The step of substrate recognition is mediated by E3 ligases, which typically contain a RING domain as a ‘docking site’ for E2s. The E3 ligase proteins appear in two forms: as single chain E3s that bind directly E2 and their substrate, and as multisubunit complexes in which a RING finger protein is an essential component. The classification of E3 ligases is based on the presence of domains like E6-AP C-terminus, U-box or the Really Interesting Gene (RING) domain. The RING domain is a particular type of Zinc-finger domain that binds two zinc atoms and that is involved in protein-protein interactions. Ubiquitin dependent protein degradation has been acknowledged as an important regulatory means of cell cycle, DNA repair, transcription, protein quality control and immune response.
The hub1 (histone monoubiquitination 1) mutant, also known as hub1-1, ang4-1 or rdo4, belongs to the angusta class of recessive mutants characterised by a reduced leaf size and narrow lamina (Berná et al., Genetics 152, 729-742, 1999), and reduced seed dormancy (Peeters et al., Physiol. Plant. 115, 604-612, 2002; Liu et al., Plant Cell 19, 433-444, 2007). Germination tests (wherein the percentage of germinated seeds was scored after 7 days) showed that this percentage was higher compared to the wild type seeds. However, seedling growth was dependent on the presence of sucrose in the medium (Liu et al., 2007). The mutant plants are small compared to wild type and have narrow leaves, and also root growth is negatively affected (Fleury et al., Plant Cell 19, 417-432, 2007). Overexpression of the HUB1 gene under control of the strong CaMV35S promoter in Arabidopsis resulted in plants having increased leaf size (Cnops et al., WO 2006/027310). It is postulated (Liu et al., 2007 and Fleury et al., 2007) that HUB1 is involved chromatin remodelling, but HUB1 may also be involved in protein degradation: BRE1, the yeast homologue of HUB1, is shown to interact with RAD6 and the proteasome (Xiao et al., Mol. Cell. Biol. 25, 637-651, 2005) and HUB1 or HUB2 furthermore aligns with Staring, a protein which is also involved in protein degradation (Chin et al., J. Biol. Chem. 277, 35071-35079, 2002).

SUMMARY

Surprisingly, it has now been found that modulating expression of a nucleic acid encoding a HUB1 polypeptide gives plants having modified growth characteristics, in particular modified light regulated phenotypes, increased seed yield, increased stress resistance, increased early vigour relative to control plants.
According one embodiment, there is provided a method for modifying growth characteristics of a plant relative to control plants, comprising modulating expression of a nucleic acid encoding a HUB1 polypeptide in a plant. The modified growth characteristics comprise increased seed yield, increased stress resistance, increased early vigour and modified light regulated phenotypes relative to control plants, but do not comprise increased vegetative biomass.
The invention also encompasses the construction of a dominant positive mutant of HUB1; therefore, in another embodiment, there is provided a dominant positive mutant form of HUB1 and its use for improving growth characteristics of plants.

DEFINITIONS

Polypeptide(s)/Protein(s)

The terms “polypeptide” and “protein” are used interchangeably herein and refer to amino acids in a polymeric form of any length, linked together by peptide bonds.

Polynucleotide(s)/Nucleic Acid(s)/Nucleic Acid Sequence(s)/Nucleotide Sequence(s)

The terms “polynucleotide(s)”, “nucleic acid sequence(s)”, “nucleotide sequence(s)”, “nucleic acid(s)”, “nucleic acid molecule” are used interchangeably herein and refer to nucleotides, either ribonucleotides or deoxyribonucleotides or a combination of both, in a polymeric unbranched form of any length.

Control Plant(s)

The choice of suitable control plants is a routine part of an experimental setup and may include corresponding wild type plants or corresponding plants without the gene of interest. The control plant is typically of the same plant species or even of the same variety as the plant to be assessed. The control plant may also be a nullizygote of the plant to be assessed. Nullizygotes are individuals missing the transgene by segregation. A “control plant” as used herein refers not only to whole plants, but also to plant parts, including seeds and seed parts.

Homologue(s)

“Homologues” of a protein encompass peptides, oligopeptides, polypeptides, proteins and enzymes having amino acid substitutions, deletions and/or insertions relative to the unmodified protein in question and having similar biological and functional activity as the unmodified protein from which they are derived.
A deletion refers to removal of one or more amino acids from a protein.
An insertion refers to one or more amino acid residues being introduced into a predetermined site in a protein. Insertions may comprise N-terminal and/or C-terminal fusions as well as intra-sequence insertions of single or multiple amino acids. Generally, insertions within the amino acid sequence will be smaller than N- or C-terminal fusions, of the order of about 1 to 10 residues. Examples of N- or C-terminal fusion proteins or peptides include the binding domain or activation domain of a transcriptional activator as used in the yeast two-hybrid system, phage coat proteins, (histidine)-6-tag, glutathione S-transferase-tag, protein A, maltose-binding protein, dihydrofolate reductase, Tag•100 epitope, c-myc epitope, FLAG® epitope tag, lacZ, CMP (calmodulin-binding peptide), HA epitope, protein C epitope and VSV epitope.
A substitution refers to replacement of amino acids of the protein with other amino acids having similar properties (such as similar hydrophobicity, hydrophilicity, antigenicity, propensity to form or break α-helical structures or β-sheet structures). Amino acid substitutions are typically of single residues, but may be clustered depending upon functional constraints placed upon the polypeptide; insertions will usually be of the order of about 1 to 10 amino acid residues. The amino acid substitutions are preferably conservative amino acid substitutions. Conservative substitution tables are well known in the art (see for example Creighton (1984) Proteins. W.H. Freeman and Company (Eds) and Table 1 below).

TABLE 1

Examples of conserved amino acid substitutions

	Residue	Conservative Substitutions

	Ala	Ser
	Arg	Lys
	Asn	Gln; His
	Asp	Glu
	Gln	Asn
	Cys	Ser
	Glu	Asp
	Gly	Pro
	His	Asn; Gln
	Ile	Leu, Val
	Leu	Ile; Val
	Lys	Arg; Gln
	Met	Leu; Ile
	Phe	Met; Leu; Tyr
	Ser	Thr; Gly
	Thr	Ser; Val
	Trp	Tyr
	Tyr	Trp; Phe
	Val	Ile; Leu

Amino acid substitutions, deletions and/or insertions may readily be made using peptide synthetic techniques well known in the art, such as solid phase peptide synthesis and the like, or by recombinant DNA manipulation. Methods for the manipulation of DNA sequences to produce substitution, insertion or deletion variants of a protein are well known in the art. For example, techniques for making substitution mutations at predetermined sites in DNA are well known to those skilled in the art and include M13 mutagenesis, T7-Gen in vitro mutagenesis (USB, Cleveland, Ohio), QuickChange Site Directed mutagenesis (Stratagene, San Diego, Calif.), PCR-mediated site-directed mutagenesis or other site-directed mutagenesis protocols.
Derivatives “Derivatives” include peptides, oligopeptides, polypeptides which may, compared to the amino acid sequence of the naturally-occurring form of the protein, such as the protein of interest, comprise substitutions of amino acids with non-naturally occurring amino acid residues, or additions of non-naturally occurring amino acid residues. “Derivatives” of a protein also encompass peptides, oligopeptides, polypeptides which comprise naturally occurring altered (glycosylated, acylated, prenylated, phosphorylated, myristoylated, sulphated etc.) or non-naturally altered amino acid residues compared to the amino acid sequence of a naturally-occurring form of the polypeptide. A derivative may also comprise one or more non-amino acid substituents or additions compared to the amino acid sequence from which it is derived, for example a reporter molecule or other ligand, covalently or non-covalently bound to the amino acid sequence, such as a reporter molecule which is bound to facilitate its detection, and non-naturally occurring amino acid residues relative to the amino acid sequence of a naturally-occurring protein. Furthermore, “derivatives” also include fusions of the naturally-occurring form of the protein with tagging peptides such as FLAG, HIS6 or thioredoxin (for a review of tagging peptides, see Terpe, Appl. Microbiol. Biotechnol. 60, 523-533, 2003).

Orthologue(s)/Paralogue(s)

Orthologues and paralogues encompass evolutionary concepts used to describe the ancestral relationships of genes. Paralogues are genes within the same species that have originated through duplication of an ancestral gene; orthologues are genes from different organisms that have originated through speciation, and are also derived from a common ancestral gene.

Domain

The term “domain” refers to a set of amino acids conserved at specific positions along an alignment of sequences of evolutionarily related proteins. While amino acids at other positions can vary between homologues, amino acids that are highly conserved at specific positions indicate amino acids that are likely essential in the structure, stability or function of a protein. Identified by their high degree of conservation in aligned sequences of a family of protein homologues, they can be used as identifiers to determine if any polypeptide in question belongs to a previously identified polypeptide family.

Motif/Consensus Sequence/Signature

The term “motif” or “consensus sequence” or “signature” refers to a short conserved region in the sequence of evolutionarily related proteins. Motifs are frequently highly conserved parts of domains, but may also include only part of the domain, or be located outside of conserved domain (if all of the amino acids of the motif fall outside of a defined domain).

Hybridisation

The term “hybridisation” as defined herein is a process wherein substantially homologous complementary nucleotide sequences anneal to each other. The hybridisation process can occur entirely in solution, i.e. both complementary nucleic acids are in solution. The hybridisation process can also occur with one of the complementary nucleic acids immobilised to a matrix such as magnetic beads, Sepharose beads or any other resin. The hybridisation process can furthermore occur with one of the complementary nucleic acids immobilised to a solid support such as a nitro-cellulose or nylon membrane or immobilised by e.g. photolithography to, for example, a siliceous glass support (the latter known as nucleic acid arrays or microarrays or as nucleic acid chips). In order to allow hybridisation to occur, the nucleic acid molecules are generally thermally or chemically denatured to melt a double strand into two single strands and/or to remove hairpins or other secondary structures from single stranded nucleic acids.
The term “stringency” refers to the conditions under which a hybridisation takes place. The stringency of hybridisation is influenced by conditions such as temperature, salt concentration, ionic strength and hybridisation buffer composition. Generally, low stringency conditions are selected to be about 30° C. lower than the thermal melting point (T_m) for the specific sequence at a defined ionic strength and pH. Medium stringency conditions are when the temperature is 20° C. below T_m, and high stringency conditions are when the temperature is 10° C. below T_m. High stringency hybridisation conditions are typically used for isolating hybridising sequences that have high sequence similarity to the target nucleic acid sequence. However, nucleic acids may deviate in sequence and still encode a substantially identical polypeptide, due to the degeneracy of the genetic code. Therefore medium stringency hybridisation conditions may sometimes be needed to identify such nucleic acid molecules.
The Tm is the temperature under defined ionic strength and pH, at which 50% of the target sequence hybridises to a perfectly matched probe. The T_mis dependent upon the solution conditions and the base composition and length of the probe. For example, longer sequences hybridise specifically at higher temperatures. The maximum rate of hybridisation is obtained from about 16° C. up to 32° C. below T_m. The presence of monovalent cations in the hybridisation solution reduce the electrostatic repulsion between the two nucleic acid strands thereby promoting hybrid formation; this effect is visible for sodium concentrations of up to 0.4M (for higher concentrations, this effect may be ignored). Formamide reduces the melting temperature of DNA-DNA and DNA-RNA duplexes with 0.6 to 0.7° C. for each percent formamide, and addition of 50% formamide allows hybridisation to be performed at 30 to 45° C., though the rate of hybridisation will be lowered. Base pair mismatches reduce the hybridisation rate and the thermal stability of the duplexes. On average and for large probes, the Tm decreases about 1° C. per % base mismatch. The Tm may be calculated using the following equations, depending on the types of hybrids:
1) DNA-DNA hybrids (Meinkoth and Wahl, Anal. Biochem., 138: 267-284, 1984):
T _m=81.5° C.+16.6×log₁₀[Na⁺]^a+0.41×%[G/C ^b]−500×[L ^c]⁻¹−0.61×% formamide
2) DNA-RNA or RNA-RNA hybrids:
Tm=79.8+18.5(log₁₀[Na⁺]^a)+0.58(% G/C ^b)+11.8(% G/C ^b)²−820/L ^c
3) oligo-DNA or oligo-RNAs hybrids:
For <20 nucleotides: T _m=2(l _n)
For 20-35 nucleotides: T _m=22+1.46(l _n)
^aor for other monovalent cation, but only accurate in the 0.01-0.4 M range.
^bonly accurate for % GC in the 30% to 75% range.
^cL=length of duplex in base pairs.
^doligo, oligonucleotide; l_n, =effective length of primer=2×(no. of G/C)+(no. of A/T).
Non-specific binding may be controlled using any one of a number of known techniques such as, for example, blocking the membrane with protein containing solutions, additions of heterologous RNA, DNA, and SDS to the hybridisation buffer, and treatment with Rnase. For non-homologous probes, a series of hybridizations may be performed by varying one of (i) progressively lowering the annealing temperature (for example from 68° C. to 42° C.) or (ii) progressively lowering the formamide concentration (for example from 50% to 0%). The skilled artisan is aware of various parameters which may be altered during hybridisation and which will either maintain or change the stringency conditions.
Besides the hybridisation conditions, specificity of hybridisation typically also depends on the function of post-hybridisation washes. To remove background resulting from non-specific hybridisation, samples are washed with dilute salt solutions. Critical factors of such washes include the ionic strength and temperature of the final wash solution: the lower the salt concentration and the higher the wash temperature, the higher the stringency of the wash. Wash conditions are typically performed at or below hybridisation stringency. A positive hybridisation gives a signal that is at least twice of that of the background. Generally, suitable stringent conditions for nucleic acid hybridisation assays or gene amplification detection procedures are as set forth above. More or less stringent conditions may also be selected. The skilled artisan is aware of various parameters which may be altered during washing and which will either maintain or change the stringency conditions.
For example, typical high stringency hybridisation conditions for DNA hybrids longer than 50 nucleotides encompass hybridisation at 65° C. in 1×SSC or at 42° C. in 1×SSC and 50% formamide, followed by washing at 65° C. in 0.3×SSC. Examples of medium stringency hybridisation conditions for DNA hybrids longer than 50 nucleotides encompass hybridisation at 50° C. in 4×SSC or at 40° C. in 6×SSC and 50% formamide, followed by washing at 50° C. in 2×SSC. The length of the hybrid is the anticipated length for the hybridising nucleic acid. When nucleic acids of known sequence are hybridised, the hybrid length may be determined by aligning the sequences and identifying the conserved regions described herein. 1×SSC is 0.15M NaCl and 15 mM sodium citrate; the hybridisation solution and wash solutions may additionally include 5×Denhardt's reagent, 0.5-1.0% SDS, 100 μg/ml denatured, fragmented salmon sperm DNA, 0.5% sodium pyrophosphate.
For the purposes of defining the level of stringency, reference can be made to Sambrook et al. (2001) Molecular Cloning: a laboratory manual, 3^rdEdition, Cold Spring Harbor Laboratory Press, CSH, New York or to Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989 and yearly updates).

Splice Variant

The term “splice variant” as used herein encompasses variants of a nucleic acid sequence in which selected introns and/or exons have been excised, replaced, displaced or added, or in which introns have been shortened or lengthened. Such variants will be ones in which the biological activity of the protein is substantially retained; this may be achieved by selectively retaining functional segments of the protein. Such splice variants may be found in nature or may be manmade. Methods for predicting and isolating such splice variants are well known in the art (see for example Foissac and Schiex (2005) BMC Bioinformatics 6: 25).

Allelic Variant

Alleles or allelic variants are alternative forms of a given gene, located at the same chromosomal position. Allelic variants encompass Single Nucleotide Polymorphisms (SNPs), as well as Small Insertion/Deletion Polymorphisms (INDELs). The size of INDELs is usually less than 100 bp. SNPs and INDELs form the largest set of sequence variants in naturally occurring polymorphic strains of most organisms.

Gene Shuffling/Directed Evolution

Gene shuffling or directed evolution consists of iterations of DNA shuffling followed by appropriate screening and/or selection to generate variants of nucleic acids or portions thereof encoding proteins having a modified biological activity (Castle et al., (2004) Science 304(5674): 1151-4; U.S. Pat. Nos. 5,811,238 and 6,395,547).

Regulatory Element/Control Sequence/Promoter

The terms “regulatory element”, “control sequence” and “promoter” are all used interchangeably herein and are to be taken in a broad context to refer to regulatory nucleic acid sequences capable of effecting expression of the sequences to which they are ligated.
The term “promoter” typically refers to a nucleic acid control sequence located upstream from the transcriptional start of a gene and which is involved in recognising and binding of RNA polymerase and other proteins, thereby directing transcription of an operably linked nucleic acid. Encompassed by the aforementioned terms are transcriptional regulatory sequences derived from a classical eukaryotic genomic gene (including the TATA box which is required for accurate transcription initiation, with or without a CCAAT box sequence) and additional regulatory elements (i.e. upstream activating sequences, enhancers and silencers) which alter gene expression in response to developmental and/or external stimuli, or in a tissue-specific manner. Also included within the term is a transcriptional regulatory sequence of a classical prokaryotic gene, in which case it may include a −35 box sequence and/or −10 box transcriptional regulatory sequences. The term “regulatory element” also encompasses a synthetic fusion molecule or derivative that confers, activates or enhances expression of a nucleic acid molecule in a cell, tissue or organ.
A “plant promoter” comprises regulatory elements, which mediate the expression of a coding sequence segment in plant cells. Accordingly, a plant promoter need not be of plant origin, but may originate from viruses or micro-organisms, for example from viruses which attack plant cells. The “plant promoter” can also originate from a plant cell, e.g. from the plant which is transformed with the nucleic acid sequence to be expressed in the inventive process and described herein. This also applies to other “plant” regulatory signals, such as “plant” terminators. The promoters upstream of the nucleotide sequences useful in the methods of the present invention can be modified by one or more nucleotide substitution(s), insertion(s) and/or deletion(s) without interfering with the functionality or activity of either the promoters, the open reading frame (ORF) or the 3′-regulatory region such as terminators or other 3′ regulatory regions which are located away from the ORF. It is furthermore possible that the activity of the promoters is increased by modification of their sequence, or that they are replaced completely by more active promoters, even promoters from heterologous organisms. For expression in plants, the nucleic acid molecule must, as described above, be linked operably to or comprise a suitable promoter which expresses the gene at the right point in time and with the required spatial expression pattern.
For the identification of functionally equivalent promoters, the promoter strength and/or expression pattern of a candidate promoter may be analysed for example by operably linking the promoter to a reporter gene and assaying the expression level and pattern of the reporter gene in various tissues of the plant. Suitable well-known reporter genes include for example beta-glucuronidase or beta-galactosidase. The promoter activity is assayed by measuring the enzymatic activity of the beta-glucuronidase or beta-galactosidase. The promoter strength and/or expression pattern may then be compared to that of a reference promoter (such as the one used in the methods of the present invention). Alternatively, promoter strength may be assayed by quantifying mRNA levels or by comparing mRNA levels of the nucleic acid used in the methods of the present invention, with mRNA levels of housekeeping genes such as 18S rRNA, using methods known in the art, such as Northern blotting with densitometric analysis of autoradiograms, quantitative real-time PCR or RT-PCR (Heid et al., 1996 Genome Methods 6: 986-994). Generally by “weak promoter” is intended a promoter that drives expression of a coding sequence at a low level. By “low level” is intended at levels of about 1/10,000 transcripts to about 1/100,000 transcripts, to about 1/500,0000 transcripts per cell. Conversely, a “strong promoter” drives expression of a coding sequence at high level, or at about 1/10 transcripts to about 1/100 transcripts to about 1/1000 transcripts per cell. Generally, by “medium strength promoter” is intended a promoter that drives expression of a coding sequence at a lower level than a strong promoter, in particular at a level that is in all instances below that obtained when under the control of a 35S CaMV promoter.

Operably Linked

The term “operably linked” as used herein refers to a functional linkage between the promoter sequence and the gene of interest, such that the promoter sequence is able to initiate transcription of the gene of interest.

Constitutive Promoter

A “constitutive promoter” refers to a promoter that is transcriptionally active during most, but not necessarily all, phases of growth and development and under most environmental conditions, in at least one cell, tissue or organ. Table 2a below gives examples of constitutive promoters.

TABLE 2a

Examples of constitutive promoters

Gene Source	Reference

Actin	McElroy et al, Plant Cell, 2: 163-171, 1990
HMGP	WO 2004/070039
CAMV 35S	Odell et al, Nature, 313: 810-812, 1985
CaMV 19S	Nilsson et al., Physiol. Plant. 100: 456-462, 1997
GOS2	de Pater et al, Plant J Nov; 2(6): 837-44, 1992, WO 2004/065596
Ubiquitin	Christensen et al, Plant Mol. Biol. 18: 675-689, 1992
Rice cyclophilin	Buchholz et al, Plant Mol Biol. 25(5): 837-43, 1994
Maize H3 histone	Lepetit et al, Mol. Gen. Genet. 231: 276-285, 1992
Alfalfa H3 histone	Wu et al. Plant Mol. Biol. 11: 641-649, 1988
Actin 2	An et al, Plant J. 10(1); 107-121, 1996
34S FMV	Sanger et al., Plant. Mol. Biol., 14, 1990: 433-443
Rubisco small subunit	U.S. Pat. No. 4,962,028
OCS	Leisner (1988) Proc Natl Acad Sci USA 85(5): 2553
SAD1	Jain et al., Crop Science, 39 (6), 1999: 1696
SAD2	Jain et al., Crop Science, 39 (6), 1999: 1696
nos	Shaw et al. (1984) Nucleic acid sequences Res. 12(20): 7831-7846
V-ATPase	WO 01/14572
Super promoter	WO 95/14098
G-box proteins	WO 94/12015

Ubiquitous Promoter

A ubiquitous promoter is active in substantially all tissues or cells of an organism.

Developmentally-Regulated Promoter

A developmentally-regulated promoter is active during certain developmental stages or in parts of the plant that undergo developmental changes.

Inducible Promoter

An inducible promoter has induced or increased transcription initiation in response to a chemical (for a review see Gatz 1997, Annu. Rev. Plant Physiol. Plant Mol. Biol., 48:89-108), environmental or physical stimulus, or may be “stress-inducible”, i.e. activated when a plant is exposed to various stress conditions, or a “pathogen-inducible” i.e. activated when a plant is exposed to exposure to various pathogens.

Organ-Specific/Tissue-Specific Promoter

An organ-specific or tissue-specific promoter is one that is capable of preferentially initiating transcription in certain organs or tissues, such as the leaves, roots, seed tissue etc. For example, a “root-specific promoter” is a promoter that is transcriptionally active predominantly in plant roots, substantially to the exclusion of any other parts of a plant, whilst still allowing for any leaky expression in these other plant parts. Promoters able to initiate transcription in certain cells only are referred to herein as “cell-specific”.
Examples of root-specific promoters are listed in Table 2b below:

TABLE 2b

Examples of root-specific promoters

Gene Source	Reference

RCc3	Plant Mol Biol. 1995 January; 27(2): 237-48
Arabidopsis PHT1	Kovama et al., 2005; Mudge et al. (2002, Plant J. 31: 341)
Medicago phosphate transporter	Xiao et al., 2006
Arabidopsis Pyk10	Nitz et al. (2001) Plant Sci 161(2): 337-346
root-expressible genes	Tingey et al., EMBO J. 6: 1, 1987.
tobacco auxin-inducible gene	Van der Zaal et al., Plant Mol. Biol. 16, 983, 1991.
β-tubulin	Oppenheimer, et al., Gene 63: 87, 1988.
tobacco root-specific genes	Conkling, et al., Plant Physiol. 93: 1203, 1990.
B. napus G1-3b gene	U.S. Pat. No. 5,401,836
SbPRP1	Suzuki et al., Plant Mol. Biol. 21: 109-119, 1993.
LRX1	Baumberger et al. 2001, Genes & Dev. 15: 1128
BTG-26 Brassica napus	US 20050044585
LeAMT1 (tomato)	Lauter et al. (1996, PNAS 3: 8139)
The LeNRT1-1 (tomato)	Lauter et al. (1996, PNAS 3: 8139)
class I patatin gene (potato)	Liu et al., Plant Mol. Biol. 153: 386-395, 1991.
KDC1 (Daucus carota)	Downey et al. (2000, J. Biol. Chem. 275: 39420)
TobRB7 gene	W Song (1997) PhD Thesis, North Carolina State
	University, Raleigh, NC USA
OsRAB5a (rice)	Wang et al. 2002, Plant Sci. 163: 273
ALF5 (Arabidopsis)	Diener et al. (2001, Plant Cell 13: 1625)
NRT2; 1Np (N. plumbaginifolia)	Quesada et al. (1997, Plant Mol. Biol. 34: 265)

A seed-specific promoter is transcriptionally active predominantly in seed tissue, but not necessarily exclusively in seed tissue (in cases of leaky expression). The seed-specific promoter may be active during seed development and/or during germination. The seed specific promoter may be endosperm-, aleurone-, and/or embryo-specific. Examples of seed-specific promoters are shown in Table 2c below. Further examples of seed-specific promoters are given in Qing Qu and Takaiwa (Plant Biotechnol. J. 2, 113-125, 2004), which disclosure is incorporated by reference herein as if fully set forth.

TABLE 2c

Examples of seed-specific promoters

Gene source	Reference

seed-specific genes	Simon et al., Plant Mol. Biol. 5: 191, 1985;
	Scofield et al., J. Biol. Chem. 262: 12202, 1987.;
	Baszczynski et al., Plant Mol. Biol. 14: 633, 1990.
Brazil Nut albumin	Pearson et al., Plant Mol. Biol. 18: 235-245, 1992.
legumin	Ellis et al., Plant Mol. Biol. 10: 203-214, 1988.
glutelin (rice)	Takaiwa et al., Mol. Gen. Genet. 208: 15-22, 1986;
	Takaiwa et al., FEBS Letts. 221: 43-47, 1987.
zein	Matzke et al Plant Mol Biol, 14(3): 323-32 1990
napA	Stalberg et al, Planta 199: 515-519, 1996.
wheat LMW and HMW glutenin-1	Mol Gen Genet 216: 81-90, 1989; NAR 17: 461-2, 1989
wheat SPA	Albani et al, Plant Cell, 9: 171-184, 1997
wheat α, β, γ-gliadins	EMBO J. 3: 1409-15, 1984
barley ltr1 promoter	Diaz et al. (1995) Mol Gen Genet 248(5): 592-8
barley B1, C, D, hordein	Theor Appl Gen 98: 1253-62, 1999; Plant J 4: 343-55, 1993;
	Mol Gen Genet 250: 750-60, 1996
barley DOF	Mena et al, The Plant Journal, 116(1): 53-62, 1998
blz2	EP99106056.7
synthetic promoter	Vicente-Carbajosa et al., Plant J. 13: 629-640, 1998.
rice prolamin NRP33	Wu et al, Plant Cell Physiology 39(8) 885-889, 1998
rice a-globulin Glb-1	Wu et al, Plant Cell Physiology 39(8) 885-889, 1998
rice OSH1	Sato et al, Proc. Natl. Acad. Sci. USA, 93: 8117-8122,
	1996
rice α-globulin REB/OHP-1	Nakase et al. Plant Mol. Biol. 33: 513-522, 1997
rice ADP-glucose pyrophos-	Trans Res 6: 157-68, 1997
phorylase
maize ESR gene family	Plant J 12: 235-46, 1997
sorghum α-kafirin	DeRose et al., Plant Mol. Biol 32: 1029-35, 1996
KNOX	Postma-Haarsma et al, Plant Mol. Biol. 39: 257-71, 1999
rice oleosin	Wu et al, J. Biochem. 123: 386, 1998
sunflower oleosin	Cummins et al., Plant Mol. Biol. 19: 873-876, 1992
PRO0117, putative rice 40S	WO 2004/070039
ribosomal protein
PRO0136, rice alanine	unpublished
aminotransferase
PRO0147, trypsin inhibitor ITR1	unpublished
(barley)
PRO0151, rice WSI18	WO 2004/070039
PRO0175, rice RAB21	WO 2004/070039
PRO005	WO 2004/070039
PRO0095	WO 2004/070039
α-amylase (Amy32b)	Lanahan et al, Plant Cell 4: 203-211, 1992; Skriver et al,
	Proc Natl Acad Sci USA 88: 7266-7270, 1991
cathepsin β-like gene	Cejudo et al, Plant Mol Biol 20: 849-856, 1992
Barley Ltp2	Kalla et al., Plant J. 6: 849-60, 1994
Chi26	Leah et al., Plant J. 4: 579-89, 1994
Maize B-Peru	Selinger et al., Genetics 149; 1125-38, 1998

A green tissue-specific promoter as defined herein is a promoter that is transcriptionally active predominantly in green tissue, substantially to the exclusion of any other parts of a plant, whilst still allowing for any leaky expression in these other plant parts.
Examples of green tissue-specific promoters which may be used to perform the methods of the invention are shown in Table 2d below.

TABLE 2d

Examples of green tissue-specific promoters

Gene	Expression	Reference

Maize Orthophosphate dikinase	Leaf specific	Fukavama et al., 2001
Maize Phosphoenolpyruvate	Leaf specific	Kausch et al., 2001
carboxylase
Rice Phosphoenolpyruvate	Leaf specific	Liu et al., 2003
carboxylase
Rice small subunit Rubisco	Leaf specific	Nomura et al., 2000
rice beta expansin EXBP9	Shoot specific	WO 2004/070039
Pigeonpea small subunit Rubisco	Leaf specific	Panguluri et al., 2005
Pea RBCS3A	Leaf specific

Another example of a tissue-specific promoter is a meristem-specific promoter, which is transcriptionally active predominantly in meristematic tissue, substantially to the exclusion of any other parts of a plant, whilst still allowing for any leaky expression in these other plant parts. Examples of green meristem-specific promoters which may be used to perform the methods of the invention are shown in Table 2e below.

TABLE 2e

Examples of meristem-specific promoters

Gene source	Expression pattern	Reference

rice OSH1	Shoot apical meristem,	Sato et al. (1996)
	from embryo globular	Proc. Natl. Acad. Sci.
	stage to seedling stage	USA, 93: 8117-8122
Rice metallothionein	Meristem specific	BAD87835.1
WAK1 & WAK 2	Shoot and root apical	Wagner & Kohorn
	meristems, and in ex-	(2001) Plant Cell
	panding leaves and sepals	13(2): 303-318

Terminator

The term “terminator” encompasses a control sequence which is a DNA sequence at the end of a transcriptional unit which signals 3′ processing and polyadenylation of a primary transcript and termination of transcription. The terminator can be derived from the natural gene, from a variety of other plant genes, or from T-DNA. The terminator to be added may be derived from, for example, the nopaline synthase or octopine synthase genes, or alternatively from another plant gene, or less preferably from any other eukaryotic gene.

Modulation

The term “modulation” means in relation to expression or gene expression, a process in which the expression level is changed by said gene expression in comparison to the control plant, the expression level may be increased or decreased. The original, unmodulated expression may be of any kind of expression of a structural RNA (rRNA, tRNA) or mRNA with subsequent translation. The term “modulating the activity” shall mean any change of the expression of the inventive nucleic acid sequences or encoded proteins, which leads to increased yield and/or increased growth of the plants.

Expression

The term “expression” or “gene expression” means the transcription of a specific gene or specific genes or specific genetic construct. The term “expression” or “gene expression” in particular means the transcription of a gene or genes or genetic construct into structural RNA (rRNA, tRNA) or mRNA with or without subsequent translation of the latter into a protein. The process includes transcription of DNA and processing of the resulting mRNA product.

Increased Expression/Overexpression

The term “increased expression” or “overexpression” as used herein means any form of expression that is additional to the original wild-type expression level.
Methods for increasing expression of genes or gene products are well documented in the art and include, for example, overexpression driven by appropriate promoters, the use of transcription enhancers or translation enhancers. Isolated nucleic acids which serve as promoter or enhancer elements may be introduced in an appropriate position (typically upstream) of a non-heterologous form of a polynucleotide so as to upregulate expression of a nucleic acid encoding the polypeptide of interest. For example, endogenous promoters may be altered in vivo by mutation, deletion, and/or substitution (see, Kmiec, U.S. Pat. No. 5,565,350; Zarling et al., WO9322443), or isolated promoters may be introduced into a plant cell in the proper orientation and distance from a gene of the present invention so as to control the expression of the gene.
If polypeptide expression is desired, it is generally desirable to include a polyadenylation region at the 3′-end of a polynucleotide coding region. The polyadenylation region can be derived from the natural gene, from a variety of other plant genes, or from T-DNA. The 3′ end sequence to be added may be derived from, for example, the nopaline synthase or octopine synthase genes, or alternatively from another plant gene, or less preferably from any other eukaryotic gene.
An intron sequence may also be added to the 5′ untranslated region (UTR) or the coding sequence of the partial coding sequence to increase the amount of the mature message that accumulates in the cytosol. Inclusion of a spliceable intron in the transcription unit in both plant and animal expression constructs has been shown to increase gene expression at both the mRNA and protein levels up to 1000-fold (Buchman and Berg (1988) Mol. Cell biol. 8: 4395-4405; Callis et al. (1987) Genes Dev 1:1183-1200). Such intron enhancement of gene expression is typically greatest when placed near the 5′ end of the transcription unit. Use of the maize introns Adh1- S intron 1, 2, and 6, the Bronze-1 intron are known in the art. For general information see: The Maize Handbook, Chapter 116, Freeling and Walbot, Eds., Springer, N.Y. (1994).

Endogenous Gene

Reference herein to an “endogenous” gene not only refers to the gene in question as found in a plant in its natural form (i.e., without there being any human intervention), but also refers to that same gene (or a substantially homologous nucleic acid/gene) in an isolated form subsequently (re)introduced into a plant (a transgene). For example, a transgenic plant containing such a transgene may encounter a substantial reduction of the transgene expression and/or substantial reduction of expression of the endogenous gene. The isolated gene may be isolated from an organism or may be manmade, for example by chemical synthesis.

Decreased Expression

Reference herein to “decreased expression” or “reduction or substantial elimination” of expression is taken to mean a decrease in endogenous gene expression and/or polypeptide levels and/or polypeptide activity relative to control plants. The reduction or substantial elimination is in increasing order of preference at least 10%, 20%, 30%, 40% or 50%, 60%, 70%, 80%, 85%, 90%, or 95%, 96%, 97%, 98%, 99% or more reduced compared to that of control plants.
For the reduction or substantial elimination of expression an endogenous gene in a plant, a sufficient length of substantially contiguous nucleotides of a nucleic acid sequence is required. In order to perform gene silencing, this may be as little as 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10 or fewer nucleotides, alternatively this may be as much as the entire gene (including the 5′ and/or 3′ UTR, either in part or in whole). The stretch of substantially contiguous nucleotides may be derived from the nucleic acid encoding the protein of interest (target gene), or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of the protein of interest. Preferably, the stretch of substantially contiguous nucleotides is capable of forming hydrogen bonds with the target gene (either sense or antisense strand), more preferably, the stretch of substantially contiguous nucleotides has, in increasing order of preference, 50%, 60%, 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100% sequence identity to the target gene (either sense or antisense strand). A nucleic acid sequence encoding a (functional) polypeptide is not a requirement for the various methods discussed herein for the reduction or substantial elimination of expression of an endogenous gene.
This reduction or substantial elimination of expression may be achieved using routine tools and techniques. A preferred method for the reduction or substantial elimination of endogenous gene expression is by introducing and expressing in a plant a genetic construct into which the nucleic acid (in this case a stretch of substantially contiguous nucleotides derived from the gene of interest, or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of any one of the protein of interest) is cloned as an inverted repeat (in part or completely), separated by a spacer (non-coding DNA).
In such a preferred method, expression of the endogenous gene is reduced or substantially eliminated through RNA-mediated silencing using an inverted repeat of a nucleic acid or a part thereof (in this case a stretch of substantially contiguous nucleotides derived from the gene of interest, or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of the protein of interest), preferably capable of forming a hairpin structure. The inverted repeat is cloned in an expression vector comprising control sequences. A non-coding DNA nucleic acid sequence (a spacer, for example a matrix attachment region fragment (MAR), an intron, a polylinker, etc.) is located between the two inverted nucleic acids forming the inverted repeat. After transcription of the inverted repeat, a chimeric RNA with a self-complementary structure is formed (partial or complete). This double-stranded RNA structure is referred to as the hairpin RNA (hpRNA). The hpRNA is processed by the plant into siRNAs that are incorporated into an RNA-induced silencing complex (RISC). The RISC further cleaves the mRNA transcripts, thereby substantially reducing the number of mRNA transcripts to be translated into polypeptides. For further general details see for example, Grierson et al. (1998) WO 98/53083; Waterhouse et al. (1999) WO 99/53050).
Performance of the methods of the invention does not rely on introducing and expressing in a plant a genetic construct into which the nucleic acid is cloned as an inverted repeat, but any one or more of several well-known “gene silencing” methods may be used to achieve the same effects.
One such method for the reduction of endogenous gene expression is RNA-mediated silencing of gene expression (downregulation). Silencing in this case is triggered in a plant by a double stranded RNA sequence (dsRNA) that is substantially similar to the target endogenous gene. This dsRNA is further processed by the plant into about 20 to about 26 nucleotides called short interfering RNAs (siRNAs). The siRNAs are incorporated into an RNA-induced silencing complex (RISC) that cleaves the mRNA transcript of the endogenous target gene, thereby substantially reducing the number of mRNA transcripts to be translated into a polypeptide. Preferably, the double stranded RNA sequence corresponds to a target gene.
Another example of an RNA silencing method involves the introduction of nucleic acid sequences or parts thereof (in this case a stretch of substantially contiguous nucleotides derived from the gene of interest, or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of the protein of interest) in a sense orientation into a plant. “Sense orientation” refers to a DNA sequence that is homologous to an mRNA transcript thereof. Introduced into a plant would therefore be at least one copy of the nucleic acid sequence. The additional nucleic acid sequence will reduce expression of the endogenous gene, giving rise to a phenomenon known as co-suppression. The reduction of gene expression will be more pronounced if several additional copies of a nucleic acid sequence are introduced into the plant, as there is a positive correlation between high transcript levels and the triggering of co-suppression.
Another example of an RNA silencing method involves the use of antisense nucleic acid sequences. An “antisense” nucleic acid sequence comprises a nucleotide sequence that is complementary to a “sense” nucleic acid sequence encoding a protein, i.e. complementary to the coding strand of a double-stranded cDNA molecule or complementary to an mRNA transcript sequence. The antisense nucleic acid sequence is preferably complementary to the endogenous gene to be silenced. The complementarity may be located in the “coding region” and/or in the “non-coding region” of a gene. The term “coding region” refers to a region of the nucleotide sequence comprising codons that are translated into amino acid residues. The term “non-coding region” refers to 5′ and 3′ sequences that flank the coding region that are transcribed but not translated into amino acids (also referred to as 5′ and 3′ untranslated regions).
Antisense nucleic acid sequences can be designed according to the rules of Watson and Crick base pairing. The antisense nucleic acid sequence may be complementary to the entire nucleic acid sequence (in this case a stretch of substantially contiguous nucleotides derived from the gene of interest, or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of the protein of interest), but may also be an oligonucleotide that is antisense to only a part of the nucleic acid sequence (including the mRNA 5′ and 3′ UTR). For example, the antisense oligonucleotide sequence may be complementary to the region surrounding the translation start site of an mRNA transcript encoding a polypeptide. The length of a suitable antisense oligonucleotide sequence is known in the art and may start from about 50, 45, 40, 35, 30, 25, 20, 15 or 10 nucleotides in length or less. An antisense nucleic acid sequence according to the invention may be constructed using chemical synthesis and enzymatic ligation reactions using methods known in the art. For example, an antisense nucleic acid sequence (e.g., an antisense oligonucleotide sequence) may be chemically synthesized using naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed between the antisense and sense nucleic acid sequences, e.g., phosphorothioate derivatives and acridine substituted nucleotides may be used. Examples of modified nucleotides that may be used to generate the antisense nucleic acid sequences are well known in the art. Known nucleotide modifications include methylation, cyclization and ‘caps’ and substitution of one or more of the naturally occurring nucleotides with an analogue such as inosine. Other modifications of nucleotides are well known in the art.
The antisense nucleic acid sequence can be produced biologically using an expression vector into which a nucleic acid sequence has been subcloned in an antisense orientation (i.e., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest). Preferably, production of antisense nucleic acid sequences in plants occurs by means of a stably integrated nucleic acid construct comprising a promoter, an operably linked antisense oligonucleotide, and a terminator.
The nucleic acid molecules used for silencing in the methods of the invention (whether introduced into a plant or generated in situ) hybridize with or bind to mRNA transcripts and/or genomic DNA encoding a polypeptide to thereby inhibit expression of the protein, e.g., by inhibiting transcription and/or translation. The hybridization can be by conventional nucleotide complementarity to form a stable duplex, or, for example, in the case of an antisense nucleic acid sequence which binds to DNA duplexes, through specific interactions in the major groove of the double helix. Antisense nucleic acid sequences may be introduced into a plant by transformation or direct injection at a specific tissue site. Alternatively, antisense nucleic acid sequences can be modified to target selected cells and then administered systemically. For example, for systemic administration, antisense nucleic acid sequences can be modified such that they specifically bind to receptors or antigens expressed on a selected cell surface, e.g., by linking the antisense nucleic acid sequence to peptides or antibodies which bind to cell surface receptors or antigens. The antisense nucleic acid sequences can also be delivered to cells using the vectors described herein.
According to a further aspect, the antisense nucleic acid sequence is an a-anomeric nucleic acid sequence. An a-anomeric nucleic acid sequence forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual b-units, the strands run parallel to each other (Gaultier et al. (1987) Nucl Ac Res 15: 6625-6641). The antisense nucleic acid sequence may also comprise a 2′-o-methylribonucleotide (Inoue et al. (1987) Nucl Ac Res 15, 6131-6148) or a chimeric RNA-DNA analogue (Inoue et al. (1987) FEBS Lett. 215, 327-330).
The reduction or substantial elimination of endogenous gene expression may also be performed using ribozymes. Ribozymes are catalytic RNA molecules with ribonuclease activity that are capable of cleaving a single-stranded nucleic acid sequence, such as an mRNA, to which they have a complementary region. Thus, ribozymes (e.g., hammerhead ribozymes (described in Haselhoff and Gerlach (1988) Nature 334, 585-591) can be used to catalytically cleave mRNA transcripts encoding a polypeptide, thereby substantially reducing the number of mRNA transcripts to be translated into a polypeptide. A ribozyme having specificity for a nucleic acid sequence can be designed (see for example: Cech et al. U.S. Pat. No. 4,987,071; and Cech et al. U.S. Pat. No. 5,116,742). Alternatively, mRNA transcripts corresponding to a nucleic acid sequence can be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules (Bartel and Szostak (1993) Science 261, 1411-1418). The use of ribozymes for gene silencing in plants is known in the art (e.g., Atkins et al. (1994) WO 94/00012; Lenne et al. (1995) WO 95/03404; Lutziger et al. (2000) WO 00/00619; Prinsen et al. (1997) WO 97/13865 and Scott et al. (1997) WO 97/38116).
Gene silencing may also be achieved by insertion mutagenesis (for example, T-DNA insertion or transposon insertion) or by strategies as described by, among others, Angell and Baulcombe ((1999) Plant J 20(3): 357-62), (Amplicon VIGS WO 98/36083), or Baulcombe (WO 99/15682).
Gene silencing may also occur if there is a mutation on an endogenous gene and/or a mutation on an isolated gene/nucleic acid subsequently introduced into a plant. The reduction or substantial elimination may be caused by a non-functional polypeptide. For example, the polypeptide may bind to various interacting proteins; one or more mutation(s) and/or truncation(s) may therefore provide for a polypeptide that is still able to bind interacting proteins (such as receptor proteins) but that cannot exhibit its normal function (such as signalling ligand).
A further approach to gene silencing is by targeting nucleic acid sequences complementary to the regulatory region of the gene (e.g., the promoter and/or enhancers) to form triple helical structures that prevent transcription of the gene in target cells. See Helene, C., Anticancer Drug Res. 6, 569-84, 1991; Helene et al., Ann. N.Y. Acad. Sci. 660, 27-36 1992; and Maher, L. J. Bioassays 14, 807-15, 1992.
Other methods, such as the use of antibodies directed to an endogenous polypeptide for inhibiting its function in planta, or interference in the signalling pathway in which a polypeptide is involved, will be well known to the skilled man. In particular, it can be envisaged that manmade molecules may be useful for inhibiting the biological function of a target polypeptide, or for interfering with the signalling pathway in which the target polypeptide is involved.
Alternatively, a screening program may be set up to identify in a plant population natural variants of a gene, which variants encode polypeptides with reduced activity. Such natural variants may also be used for example, to perform homologous recombination.
Artificial and/or natural microRNAs (miRNAs) may be used to knock out gene expression and/or mRNA translation. Endogenous miRNAs are single stranded small RNAs of typically 19-24 nucleotides long. They function primarily to regulate gene expression and/or mRNA translation. Most plant microRNAs (miRNAs) have perfect or near-perfect complementarity with their target sequences. However, there are natural targets with up to five mismatches. They are processed from longer non-coding RNAs with characteristic fold-back structures by double-strand specific RNases of the Dicer family. Upon processing, they are incorporated in the RNA-induced silencing complex (RISC) by binding to its main component, an Argonaute protein. MiRNAs serve as the specificity components of RISC, since they base-pair to target nucleic acids, mostly mRNAs, in the cytoplasm. Subsequent regulatory events include target mRNA cleavage and destruction and/or translational inhibition. Effects of miRNA overexpression are thus often reflected in decreased mRNA levels of target genes.
Artificial microRNAs (amiRNAs), which are typically 21 nucleotides in length, can be genetically engineered specifically to negatively regulate gene expression of single or multiple genes of interest. Determinants of plant microRNA target selection are well known in the art. Empirical parameters for target recognition have been defined and can be used to aid in the design of specific amiRNAs, (Schwab et al., Dev. Cell 8, 517-527, 2005). Convenient tools for design and generation of amiRNAs and their precursors are also available to the public (Schwab et al., Plant Cell 18, 1121-1133, 2006).
For optimal performance, the gene silencing techniques used for reducing expression in a plant of an endogenous gene requires the use of nucleic acid sequences from monocotyledonous plants for transformation of monocotyledonous plants, and from dicotyledonous plants for transformation of dicotyledonous plants. Preferably, a nucleic acid sequence from any given plant species is introduced into that same species. For example, a nucleic acid sequence from rice is transformed into a rice plant. However, it is not an absolute requirement that the nucleic acid sequence to be introduced originates from the same plant species as the plant in which it will be introduced. It is sufficient that there is substantial homology between the endogenous target gene and the nucleic acid to be introduced.
Described above are examples of various methods for the reduction or substantial elimination of expression in a plant of an endogenous gene. A person skilled in the art would readily be able to adapt the aforementioned methods for silencing so as to achieve reduction of expression of an endogenous gene in a whole plant or in parts thereof through the use of an appropriate promoter, for example.

Selectable Marker (Gene)/Reporter Gene

“Selectable marker”, “selectable marker gene” or “reporter gene” includes any gene that confers a phenotype on a cell in which it is expressed to facilitate the identification and/or selection of cells that are transfected or transformed with a nucleic acid construct of the invention. These marker genes enable the identification of a successful transfer of the nucleic acid molecules via a series of different principles. Suitable markers may be selected from markers that confer antibiotic or herbicide resistance, that introduce a new metabolic trait or that allow visual selection. Examples of selectable marker genes include genes conferring resistance to antibiotics (such as nptII that phosphorylates neomycin and kanamycin, or hpt, phosphorylating hygromycin, or genes conferring resistance to, for example, bleomycin, streptomycin, tetracyclin, chloramphenicol, ampicillin, gentamycin, geneticin (G418), spectinomycin or blasticidin), to herbicides (for example bar which provides resistance to Basta®; aroA or gox providing resistance against glyphosate, or the genes conferring resistance to, for example, imidazolinone, phosphinothricin or sulfonylurea), or genes that provide a metabolic trait (such as manA that allows plants to use mannose as sole carbon source or xylose isomerase for the utilisation of xylose, or antinutritive markers such as the resistance to 2-deoxyglucose). Expression of visual marker genes results in the formation of colour (for example β-glucuronidase, GUS or β-galactosidase with its coloured substrates, for example X-Gal), luminescence (such as the luciferin/luceferase system) or fluorescence (Green Fluorescent Protein, GFP, and derivatives thereof). This list represents only a small number of possible markers. The skilled worker is familiar with such markers. Different markers are preferred, depending on the organism and the selection method.
It is known that upon stable or transient integration of nucleic acids into plant cells, only a minority of the cells takes up the foreign DNA and, if desired, integrates it into its genome, depending on the expression vector used and the transfection technique used. To identify and select these integrants, a gene coding for a selectable marker (such as the ones described above) is usually introduced into the host cells together with the gene of interest. These markers can for example be used in mutants in which these genes are not functional by, for example, deletion by conventional methods. Furthermore, nucleic acid molecules encoding a selectable marker can be introduced into a host cell on the same vector that comprises the sequence encoding the polypeptides of the invention or used in the methods of the invention, or else in a separate vector. Cells which have been stably transfected with the introduced nucleic acid can be identified for example by selection (for example, cells which have integrated the selectable marker survive whereas the other cells die).
Since the marker genes, particularly genes for resistance to antibiotics and herbicides, are no longer required or are undesired in the transgenic host cell once the nucleic acids have been introduced successfully, the process according to the invention for introducing the nucleic acids advantageously employs techniques which enable the removal or excision of these marker genes. One such a method is what is known as co-transformation. The co-transformation method employs two vectors simultaneously for the transformation, one vector bearing the nucleic acid according to the invention and a second bearing the marker gene(s). A large proportion of transformants receives or, in the case of plants, comprises (up to 40% or more of the transformants), both vectors. In case of transformation with Agrobacteria, the transformants usually receive only a part of the vector, i.e. the sequence flanked by the T-DNA, which usually represents the expression cassette. The marker genes can subsequently be removed from the transformed plant by performing crosses. In another method, marker genes integrated into a transposon are used for the transformation together with desired nucleic acid (known as the Ac/Ds technology). The transformants can be crossed with a transposase source or the transformants are transformed with a nucleic acid construct conferring expression of a transposase, transiently or stable. In some cases (approx. 10%), the transposon jumps out of the genome of the host cell once transformation has taken place successfully and is lost. In a further number of cases, the transposon jumps to a different location. In these cases the marker gene must be eliminated by performing crosses. In microbiology, techniques were developed which make possible, or facilitate, the detection of such events. A further advantageous method relies on what is known as recombination systems; whose advantage is that elimination by crossing can be dispensed with. The best-known system of this type is what is known as the Cre/lox system. Cre1 is a recombinase that removes the sequences located between the loxP sequences. If the marker gene is integrated between the loxP sequences, it is removed once transformation has taken place successfully, by expression of the recombinase. Further recombination systems are the HIN/HIX, FLP/FRT and REP/STB system (Tribble et al., J. Biol. Chem., 275, 2000: 22255-22267; Velmurugan et al., J. Cell Biol., 149, 2000: 553-566). A site-specific integration into the plant genome of the nucleic acid sequences according to the invention is possible. Naturally, these methods can also be applied to microorganisms such as yeast, fungi or bacteria.

Transgenic/Transgene/Recombinant

For the purposes of the invention, “transgenic”, “transgene” or “recombinant” means with regard to, for example, a nucleic acid sequence, an expression cassette, gene construct or a vector comprising the nucleic acid sequence or an organism transformed with the nucleic acid sequences, expression cassettes or vectors according to the invention, all those constructions brought about by recombinant methods in which either

- (a) the nucleic acid sequences encoding proteins useful in the methods of the invention, or
- (b) genetic control sequence(s) which is operably linked with the nucleic acid sequence according to the invention, for example a promoter, or
- (c) a) and b)
  are not located in their natural genetic environment or have been modified by recombinant methods, it being possible for the modification to take the form of, for example, a substitution, addition, deletion, inversion or insertion of one or more nucleotide residues. The natural genetic environment is understood as meaning the natural genomic or chromosomal locus in the original plant or the presence in a genomic library. In the case of a genomic library, the natural genetic environment of the nucleic acid sequence is preferably retained, at least in part. The environment flanks the nucleic acid sequence at least on one side and has a sequence length of at least 50 bp, preferably at least 500 bp, especially preferably at least 1000 bp, most preferably at least 5000 bp. A naturally occurring expression cassette—for example the naturally occurring combination of the natural promoter of the nucleic acid sequences with the corresponding nucleic acid sequence encoding a polypeptide useful in the methods of the present invention, as defined above—becomes a transgenic expression cassette when this expression cassette is modified by non-natural, synthetic (“artificial”) methods such as, for example, mutagenic treatment. Suitable methods are described, for example, in U.S. Pat. No. 5,565,350 or WO 00/15815.

A transgenic plant for the purposes of the invention is thus understood as meaning, as above, that the nucleic acids used in the method of the invention are not at their natural locus in the genome of said plant, it being possible for the nucleic acids to be expressed homologously or heterologously. However, as mentioned, transgenic also means that, while the nucleic acids according to the invention or used in the inventive method are at their natural position in the genome of a plant, the sequence has been modified with regard to the natural sequence, and/or that the regulatory sequences of the natural sequences have been modified. Transgenic is preferably understood as meaning the expression of the nucleic acids according to the invention at an unnatural locus in the genome, i.e. homologous or, preferably, heterologous expression of the nucleic acids takes place. Preferred transgenic plants are mentioned herein.

Transformation

The term “introduction” or “transformation” as referred to herein encompasses the transfer of an exogenous polynucleotide into a host cell, irrespective of the method used for transfer. Plant tissue capable of subsequent clonal propagation, whether by organogenesis or embryogenesis, may be transformed with a genetic construct of the present invention and a whole plant regenerated there from. The particular tissue chosen will vary depending on the clonal propagation systems available for, and best suited to, the particular species being transformed. Exemplary tissue targets include leaf disks, pollen, embryos, cotyledons, hypocotyls, megagametophytes, callus tissue, existing meristematic tissue (e.g., apical meristem, axillary buds, and root meristems), and induced meristem tissue (e.g., cotyledon meristem and hypocotyl meristem). The polynucleotide may be transiently or stably introduced into a host cell and may be maintained non-integrated, for example, as a plasmid. Alternatively, it may be integrated into the host genome. The resulting transformed plant cell may then be used to regenerate a transformed plant in a manner known to persons skilled in the art.
The transfer of foreign genes into the genome of a plant is called transformation. Transformation of plant species is now a fairly routine technique. Advantageously, any of several transformation methods may be used to introduce the gene of interest into a suitable ancestor cell. The methods described for the transformation and regeneration of plants from plant tissues or plant cells may be utilized for transient or for stable transformation. Transformation methods include the use of liposomes, electroporation, chemicals that increase free DNA uptake, injection of the DNA directly into the plant, particle gun bombardment, transformation using viruses or pollen and microprojection. Methods may be selected from the calcium/polyethylene glycol method for protoplasts (Krens, F. A. et al., (1982) Nature 296, 72-74; Negrutiu I et al. (1987) Plant Mol Biol 8: 363-373); electroporation of protoplasts (Shillito R. D. et al. (1985) Bio/Technol 3, 1099-1102); microinjection into plant material (Crossway A et al., (1986) Mol. Gen Genet 202: 179-185); DNA or RNA-coated particle bombardment (Klein T M et al., (1987) Nature 327: 70) infection with (non-integrative) viruses and the like. Transgenic plants, including transgenic crop plants, are preferably produced via Agrobacterium-mediated transformation. An advantageous transformation method is the transformation in planta. To this end, it is possible, for example, to allow the agrobacteria to act on plant seeds or to inoculate the plant meristem with agrobacteria. It has proved particularly expedient in accordance with the invention to allow a suspension of transformed agrobacteria to act on the intact plant or at least on the flower primordia. The plant is subsequently grown on until the seeds of the treated plant are obtained (Clough and Bent, Plant J. (1998) 16, 735-743). Methods for Agrobacterium-mediated transformation of rice include well known methods for rice transformation, such as those described in any of the following: European patent application EP 1198985 A1, Aldemita and Hodges (Planta 199: 612-617, 1996); Chan et al. (Plant Mol Biol 22 (3): 491-506, 1993), Hiei et al. (Plant J 6 (2): 271-282, 1994), which disclosures are incorporated by reference herein as if fully set forth. In the case of corn transformation, the preferred method is as described in either Ishida et al. (Nat. Biotechnol 14(6): 745-50, 1996) or Frame et al. (Plant Physiol 129(1): 13-22, 2002), which disclosures are incorporated by reference herein as if fully set forth. Said methods are further described by way of example in B. Jenes et al., Techniques for Gene Transfer, in: Transgenic Plants, Vol. 1, Engineering and Utilization, eds. S. D. Kung and R. Wu, Academic Press (1993) 128-143 and in Potrykus Annu. Rev. Plant Physiol. Plant Molec. Biol. 42 (1991) 205-225). The nucleic acids or the construct to be expressed is preferably cloned into a vector, which is suitable for transforming Agrobacterium tumefaciens, for example pBin19 (Bevan et al., Nucl. Acids Res. 12 (1984) 8711). Agrobacteria transformed by such a vector can then be used in known manner for the transformation of plants, such as plants used as a model, like Arabidopsis (Arabidopsis thaliana is within the scope of the present invention not considered as a crop plant), or crop plants such as, by way of example, tobacco plants, for example by immersing bruised leaves or chopped leaves in an agrobacterial solution and then culturing them in suitable media. The transformation of plants by means of Agrobacterium tumefaciens is described, for example, by Höfgen and Willmitzer in Nucl. Acid Res. (1988) 16, 9877 or is known inter alia from F. F. White, Vectors for Gene Transfer in Higher Plants; in Transgenic Plants, Vol. 1, Engineering and Utilization, eds. S. D. Kung and R. Wu, Academic Press, 1993, pp. 15-38.
In addition to the transformation of somatic cells, which then have to be regenerated into intact plants, it is also possible to transform the cells of plant meristems and in particular those cells which develop into gametes. In this case, the transformed gametes follow the natural plant development, giving rise to transgenic plants. Thus, for example, seeds of Arabidopsis are treated with agrobacteria and seeds are obtained from the developing plants of which a certain proportion is transformed and thus transgenic [Feldman, K A and Marks M D (1987). Mol Gen Genet 208:274-289; Feldmann K (1992). In: C Koncz, N-H Chua and J Shell, eds, Methods in Arabidopsis Research. Word Scientific, Singapore, pp. 274-289]. Alternative methods are based on the repeated removal of the inflorescences and incubation of the excision site in the center of the rosette with transformed agrobacteria, whereby transformed seeds can likewise be obtained at a later point in time (Chang (1994). Plant J. 5: 551-558; Katavic (1994). Mol Gen Genet, 245: 363-370). However, an especially effective method is the vacuum infiltration method with its modifications such as the “floral dip” method. In the case of vacuum infiltration of Arabidopsis, intact plants under reduced pressure are treated with an agrobacterial suspension [Bechthold, N (1993). C R Acad Sci Paris Life Sci, 316: 1194-1199], while in the case of the “floral dip” method the developing floral tissue is incubated briefly with a surfactant-treated agrobacterial suspension [Clough, S J and Bent A F (1998) The Plant J. 16, 735-743]. A certain proportion of transgenic seeds are harvested in both cases, and these seeds can be distinguished from non-transgenic seeds by growing under the above-described selective conditions. In addition the stable transformation of plastids is of advantages because plastids are inherited maternally is most crops reducing or eliminating the risk of transgene flow through pollen. The transformation of the chloroplast genome is generally achieved by a process which has been schematically displayed in Klaus et al., 2004 [Nature Biotechnology 22 (2), 225-229]. Briefly the sequences to be transformed are cloned together with a selectable marker gene between flanking sequences homologous to the chloroplast genome. These homologous flanking sequences direct site specific integration into the plastome. Plastidal transformation has been described for many different plant species and an overview is given in Bock (2001) Transgenic plastids in basic research and plant biotechnology. J Mol Biol. 2001 Sep. 21; 312 (3):425-38 or Maliga, P (2003) Progress towards commercialization of plastid transformation technology. Trends Biotechnol. 21, 20-28. Further biotechnological progress has recently been reported in form of marker free plastid transformants, which can be produced by a transient co-integrated maker gene (Klaus et al., 2004, Nature Biotechnology 22(2), 225-229).

T-DNA Activation Tagging

T-DNA activation tagging (Hayashi et al. Science (1992) 1350-1353), involves insertion of T-DNA, usually containing a promoter (may also be a translation enhancer or an intron), in the genomic region of the gene of interest or 10 kb up- or downstream of the coding region of a gene in a configuration such that the promoter directs expression of the targeted gene. Typically, regulation of expression of the targeted gene by its natural promoter is disrupted and the gene falls under the control of the newly introduced promoter. The promoter is typically embedded in a T-DNA. This T-DNA is randomly inserted into the plant genome, for example, through Agrobacterium infection and leads to modified expression of genes near the inserted T-DNA. The resulting transgenic plants show dominant phenotypes due to modified expression of genes close to the introduced promoter.

TILLING

The term “TILLING” is an abbreviation of “Targeted Induced Local Lesions In Genomes” and refers to a mutagenesis technology useful to generate and/or identify nucleic acids encoding proteins with modified expression and/or activity. TILLING also allows selection of plants carrying such mutant variants. These mutant variants may exhibit modified expression, either in strength or in location or in timing (if the mutations affect the promoter for example). These mutant variants may exhibit higher activity than that exhibited by the gene in its natural form. TILLING combines high-density mutagenesis with high-throughput screening methods. The steps typically followed in TILLING are: (a) EMS mutagenesis (Redei G P and Koncz C (1992) In Methods in Arabidopsis Research, Koncz C, Chua N H, Schell J, eds. Singapore, World Scientific Publishing Co, pp. 16-82; Feldmann et al., (1994) In Meyerowitz E M, Somerville C R, eds, Arabidopsis. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., pp 137-172; Lightner J and Caspar T (1998) In J Martinez-Zapater, J Salinas, eds, Methods on Molecular Biology, Vol. 82. Humana Press, Totowa, N.J., pp 91-104); (b) DNA preparation and pooling of individuals; (c) PCR amplification of a region of interest; (d) denaturation and annealing to allow formation of heteroduplexes; (e) DHPLC, where the presence of a heteroduplex in a pool is detected as an extra peak in the chromatogram; (f) identification of the mutant individual; and (g) sequencing of the mutant PCR product. Methods for TILLING are well known in the art (McCallum et al., (2000) Nat Biotechnol 18: 455-457; reviewed by Stemple (2004) Nat Rev Genet 5(2): 145-50).

Homologous Recombination

Homologous recombination allows introduction in a genome of a selected nucleic acid at a defined selected position. Homologous recombination is a standard technology used routinely in biological sciences for lower organisms such as yeast or the moss Physcomitrella. Methods for performing homologous recombination in plants have been described not only for model plants (Offringa et al. (1990) EMBO J 9(10): 3077-84) but also for crop plants, for example rice (Terada et al. (2002) Nat Biotech 20(10): 1030-4; Iida and Terada (2004) Curr Opin Biotech 15(2): 132-8), and approaches exist that are generally applicable regardless of the target organism (Miller et al, Nature Biotechnol. 25, 778-785, 2007).

Yield

The term “yield” in general means a measurable produce of economic value, typically related to a specified crop, to an area, and to a period of time. Individual plant parts directly contribute to yield based on their number, size and/or weight, or the actual yield is the yield per square meter for a crop and year, which is determined by dividing total production (includes both harvested and appraised production) by planted square meters. The term “yield” of a plant may relate to vegetative biomass (root and/or shoot biomass), to reproductive organs, and/or to propagules (such as seeds) of that plant.

Early Vigour

“Early vigour” refers to active healthy well-balanced growth especially during early stages of plant growth, and may result from increased plant fitness due to, for example, the plants being better adapted to their environment (i.e. optimizing the use of energy resources and partitioning between shoot and root). Plants having early vigour also show increased seedling survival and a better establishment of the crop, which often results in highly uniform fields (with the crop growing in uniform manner, i.e. with the majority of plants reaching the various stages of development at substantially the same time), and often better and higher yield. Therefore, early vigour may be determined by measuring various factors, such as thousand kernel weight, percentage germination, percentage emergence, seedling growth, seedling height, root length, root and shoot biomass and many more.

Increase/Improve/Enhance

The terms “increase”, “improve” or “enhance” are interchangeable and shall mean in the sense of the application at least a 3%, 4%, 5%, 6%, 7%, 8%, 9% or 10%, preferably at least 15% or 20%, more preferably 25%, 30%, 35% or 40% more yield and/or growth in comparison to control plants as defined herein.

Seed Yield

Increased seed yield may manifest itself as one or more of the following: a) an increase in seed biomass (total seed weight) which may be on an individual seed basis and/or per plant and/or per square meter; b) increased number of flowers per plant; c) increased number of (filled) seeds; d) increased seed filling rate (which is expressed as the ratio between the number of filled seeds divided by the total number of seeds); e) increased harvest index, which is expressed as a ratio of the yield of harvestable parts, such as seeds, divided by the total biomass; and f) increased thousand kernel weight (TKW), which is extrapolated from the number of filled seeds counted and their total weight. An increased TKW may result from an increased seed size and/or seed weight, and may also result from an increase in embryo and/or endosperm size.
An increase in seed yield may also be manifested as an increase in seed size and/or seed volume. Furthermore, an increase in seed yield may also manifest itself as an increase in seed area and/or seed length and/or seed width and/or seed perimeter. Increased yield may also result in modified architecture, or may occur because of modified architecture.

Greenness Index

The “greenness index” as used herein is calculated from digital images of plants. For each pixel belonging to the plant object on the image, the ratio of the green value versus the red value (in the RGB model for encoding color) is calculated. The greenness index is expressed as the percentage of pixels for which the green-to-red ratio exceeds a given threshold. Under normal growth conditions, under salt stress growth conditions, and under reduced nutrient availability growth conditions, the greenness index of plants is measured in the last imaging before flowering. In contrast, under drought stress growth conditions, the greenness index of plants is measured in the first imaging after drought.

Plant

The term “plant” as used herein encompasses whole plants, ancestors and progeny of the plants and plant parts, including seeds, shoots, stems, leaves, roots (including tubers), flowers, and tissues and organs, wherein each of the aforementioned comprise the gene/nucleic acid of interest. The term “plant” also encompasses plant cells, suspension cultures, callus tissue, embryos, meristematic regions, gametophytes, sporophytes, pollen and microspores, again wherein each of the aforementioned comprises the gene/nucleic acid of interest.
Plants that are particularly useful in the methods of the invention include all plants which belong to the superfamily Viridiplantae, in particular monocotyledonous and dicotyledonous plants including fodder or forage legumes, ornamental plants, food crops, trees or shrubs selected from the list comprising Acer spp., Actinidia spp., Abelmoschus spp., Agave sisalana, Agropyron spp., Agrostis stolonifera, Allium spp., Amaranthus spp., Ammophila arenaria, Ananas comosus, Annona spp., Apium graveolens, Arachis spp, Artocarpus spp., Asparagus officinaks, Avena spp. (e.g. Avena sativa, Avena fatua, Avena byzantina, Avena fatua var. sativa, Avena hybrida), Averrhoa carambola, Bambusa sp., Benincasa hispida, Bertholletia excelsea, Beta vulgaris, Brassica spp. (e.g. Brassica napus, Brassica raga ssp. [canola, oilseed rape, turnip rape]), Cadaba farinosa, Camellia sinensis, Canna indica, Cannabis sativa, Capsicum spp., Carex elata, Carica papaya, Carissa macrocarpa, Carya spp., Carthamus tinctorius, Castanea spp., Ceiba pentandra, Cichorium endivia, Cinnamomum spp., Citrullus lanatus, Citrus spp., Cocos spp., Coffea spp., Colocasia esculenta, Cola spp., Corchorus sp., Coriandrum sativum, Corylus spp., Crataegus spp., Crocus sativus, Cucurbita spp., Cucumis spp., Cynara spp., Daucus carota, Desmodium spp., Dimocarpus longan, Dioscorea spp., Diospyros spp., Echinochloa spp., Elaeis (e.g. Elaeis guineensis, Elaeis oleifera), Eleusine coracana, Eragrostis tef, Erianthus sp., Eriobotrya japonica, Eucalyptus sp., Eugenia uniflora, Fagopyrum spp., Fagus spp., Festuca arundinacea, Ficus carica, Fortunella spp., Fragaria spp., Ginkgo biloba, Glycine spp. (e.g. Glycine max, Soja hispida or Soja max), Gossypium hirsutum, Helianthus spp. (e.g. Helianthus annuus), Hemerocallis fulva, Hibiscus spp., Hordeum spp. (e.g. Hordeum vulgare), Ipomoea batatas, Juglans spp., Lactuca sativa, Lathyrus spp., Lens culinaris, Linum usllagssimum, Litchi chinensis, Lotus spp., Luffa acutangula, Lupinus spp., Luzula sylvatica, Lycopersicon spp. (e.g. Lycopersicon esculentum, Lycopersicon lycopersicum, Lycopersicon pyriforme), Macrotyloma spp., Malus spp., Malpighia emarginata, Mammea americana, Mangifera indica, Manihot spp., Manilkara zapota, Medicago sativa, Melilotus spp., Mentha spp., Miscanthus sinensis, Momordica spp., Morus nigra, Musa spp., Nicotiana spp., Olea spp., Opuntia spp., Ornithopus spp., Oryza spp. (e.g. Oryza sativa, Oryza latifolia), Panicum miliaceum, Panicum virgatum, Passiflora edulis, Pastinaca sativa, Pennisetum sp., Persea spp., Petroselinum crispum, Phalaris arundinacea, Phaseolus spp., Phleum pratense, Phoenix spp., Phragmites australis, Physalis spp., Pinus spp., Pistacia vera, Pisum spp., Poa spp., Populus spp., Prosopis spp., Prunus spp., Psidium spp., Punica granatum, Pyrus communis, Quercus spp., Raphanus sativus, Rheum rhabarbarum, Ribes spp., Ricinus communis, Rubus spp., Saccharum spp., Salix sp., Sambucus spp., Secale cereale, Sesamum spp., Sinapis sp., Solanum spp. (e.g. Solanum tuberosum, Solanum integrifolium or Solanum lycopersicum), Sorghum bicolor, Spinacia spp., Syzygium spp., Tagetes spp., Tamarindus indica, Theobroma cacao, Trifolium spp., Tripsacum dactyloides, Triticosecale rimpaui Triticum spp. (e.g. Triticum aestivum, Triticum durum, Triticum turgidum, Triticum hybernum, Triticum macha, Triticum sativum, Triticum monococcum or Triticum vulgare), Tropaeolum minus, Tropaeolum majus, Vaccinium spp., Viola spp., Vigna spp., Viola odorata, Vitis spp., Zea mays, Zizania palustris, Ziziphus spp., amongst others.

DETAILED DESCRIPTION OF THE INVENTION

Surprisingly, it has now been found that modulating expression in a plant of a nucleic acid encoding a HUB1 polypeptide gives plants having modified growth characteristics relative to control plants. According to a first embodiment, the present invention provides a method for altering growth characteristics in plants relative to control plants and in particular for modifying light regulated phenotypes, comprising modulating expression in a plant of a nucleic acid encoding a HUB1 polypeptide or a part thereof. In one particular embodiment, wherein HUB1 is misexpressed, the modified light regulated phenotypes encompass a modification of the circadian clock of the plant, a modification of the circadian clock downstream pathways, such as modified photosynthetic capacity (exemplified by reduced photosynthetic pigments, defects in plastid structure), a modified expression pattern of developmental genes, and/or modified plant development, exemplified by altered flowering time or a modified plant architecture (including leaf morphology, flower morphology or hypocotyl length). According to another embodiment, the present invention provides a method for improving growth characteristics in plants, in particular increased early vigour, increased germination vigour and/or increased yield (biomass and/or seed yield) relative to control plants, comprising modulating expression in a plant of a nucleic acid encoding a HUB1 polypeptide, and/or comprising modulating expression of genes encoding target proteins of HUB1 and/or proteins interacting with HUB1.
A preferred method for modulating (increasing or decreasing) expression of a nucleic acid encoding a HUB1 polypeptide is by introducing and expressing in a plant a nucleic acid encoding a HUB1 polypeptide or a part thereof. The tem “misexpression” of a gene as used in the present invention comprises downregulated expression of the gene as well as reduced activity of the protein encoded by the gene by for example reducing the concentration of the protein (reduced synthesis or increased degradation) or by introducing mutations in the protein for decreasing the intrinsic activity or the capability to interact with ligands, cofactors or other interactors. Methods for downregulating expression are provided in the definitions section.
Any reference hereinafter to a “protein useful in the methods of the invention” is taken to mean a HUB1 polypeptide as defined herein. Any reference hereinafter to a “nucleic acid useful in the methods of the invention” is taken to mean a nucleic acid capable of encoding such a HUB1 polypeptide or a part thereof. The nucleic acid to be introduced into a plant (and therefore useful in performing the methods of the invention) is any nucleic acid encoding the type of protein which will now be described, hereafter also named “HUB1 nucleic acid” or “HUB1 gene”.
A “HUB1 polypeptide” as defined herein refers to a ubiquitin-protein ligase (E3 ligase) comprising a RING domain. E3 ligases mediate ubiquitination of substrate proteins. Preferably, the HUB1 polypeptide belongs to the RING HCa class of E3 ligase proteins (Stone et al., Plant Physiol. 137, 13-30, 2005). The RING domain is a special type of Zn-finger domains and is involved in protein-protein interactions. Preferably, the RING domain is a C3HC4 type RING domain and corresponds to Pfam entry PF00097. C3HC4 domains have the following consensus sequence (Lorick et al., Proc. Natl. Acad. Sci. USA 96, 11364-11369, 1999): C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-{right arrow over (C)} (the cofactor coordination residues are indicated in bold underlined, see also the multiple alignment in FIG. 2). Preferably, the consensus sequence is C-X2-C-X11-C-X-H-X2-C-X2-C-X11-C-X2-C. The C3HC4 domains are reported to bind 2 metal cofactors, in particular zinc; the first cofactor is putatively bound by the first four coordination residues (numbers 1 to 4 in FIG. 1B(i) and the second cofactor is putatively bound by the last four coordination residues (numbers 5 to 8 in FIG. 1B(i)).
The term “HUB1 polypeptide” as used in the present invention also encompasses mutant forms with reduced autopolyubiquitination but with normal, reduced or completely eliminated substrate ubiquitination activity (dominant positive forms of a HUB1 polypeptide). In one such dominant positive form, the Cys residues nr 1 and 2 of the C3HC4 domain (FIG. 1B(i)) were mutated into Ser residues (FIG. 1B(ii) and (iii)).
Alternatively, the homologue of a HUB1 protein has in increasing order of preference at least 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% overall sequence identity to the amino acid represented by SEQ ID NO: 2, provided that the homologous protein comprises the conserved motif as outlined above. The overall sequence identity is determined using a global alignment algorithm, such as the Needleman Wunsch algorithm in the program GAP (GCG Wisconsin Package, Accelrys), preferably with default parameters. Compared to overall sequence identity, the sequence identity will generally be higher when only conserved domains or motifs (such as the RING domain, see Example 3) are considered.
Preferably, the polypeptide sequence which when used in the construction of a phylogenetic tree, such as the one depicted in FIG. 3, clusters with the group of HUB1 polypeptides comprising the amino acid sequence represented by SEQ ID NO: 2 (At2g44950) rather than with any other group of proteins comprising a RING domain.
The terms “domain”, “signature” and “motif” are defined in the “definitions” section herein. Specialist databases exist for the identification of domains, for example, SMART (Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864; Letunic et al. (2002) Nucleic Acids Res 30, 242-244), InterPro (Mulder et al., (2003) Nucl. Acids. Res. 31, 315-318), Prosite (Bucher and Bairoch (1994), A generalized profile syntax for biomolecular sequences motifs and its function in automatic sequence interpretation. (In) ISMB-94; Proceedings 2nd International Conference on Intelligent Systems for Molecular Biology. Altman R., Brutlag D., Karp P., Lathrop R., Searls D., Eds., pp 53-61, AAAI Press, Menlo Park; Hulo et al., Nucl. Acids. Res. 32:D134-D137, (2004)), or Pfam (Bateman et al., Nucleic Acids Research 30(1): 276-280 (2002)). A set of tools for in silico analysis of protein sequences is available on the ExPASy proteomics server (Swiss Institute of Bioinformatics (Gasteiger et al., ExPASy: the proteomics server for in-depth protein knowledge and analysis, Nucleic Acids Res. 31:3784-3788(2003)). Domains or motifs may also be identified using routine techniques, such as by sequence alignment.
Methods for the alignment of sequences for comparison are well known in the art, such methods include GAP, BESTFIT, BLAST, FASTA and TFASTA. GAP uses the algorithm of Needleman and Wunsch ((1970) J Mol Biol 48: 443-453) to find the global (i.e. spanning the complete sequences) alignment of two sequences that maximizes the number of matches and minimizes the number of gaps. The BLAST algorithm (Altschul et al. (1990) J Mol Biol 215: 403-10) calculates percent sequence identity and performs a statistical analysis of the similarity between the two sequences. The software for performing BLAST analysis is publicly available through the National Centre for Biotechnology Information (NCBI). Homologues may readily be identified using, for example, the ClustalW multiple sequence alignment algorithm (version 1.83), with the default pairwise alignment parameters, and a scoring method in percentage. Global percentages of similarity and identity may also be determined using one of the methods available in the MatGAT software package (Campanella et al., BMC Bioinformatics. 2003 Jul. 10; 4:29. MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences.). Minor manual editing may be performed to optimise alignment between conserved motifs, as would be apparent to a person skilled in the art. Furthermore, instead of using full-length sequences for the identification of homologues, specific domains may also be used. The sequence identity values may be determined over the entire nucleic acid or amino acid sequence or over selected domains or conserved motif(s), using the programs mentioned above using the default parameters. For local alignments, the Smith-Waterman algorithm is particularly useful (Smith T F, Waterman M S (1981) J. Mol. Biol 147(1); 195-7).
Furthermore, HUB1 polypeptides (at least in their native form) typically mediate monoubiquitination of Histone H2B. Tools and techniques for measuring in vitro ubiquitination are well known in the art, see for example Fleury et al (2007) or Liu et al (2007). Further details are provided in Example 6.
In addition, HUB1 polypeptides, when expressed in rice or Arabidopsis according to the methods of the present invention as outlined in the Examples section, give plants having amongst other, modified light regulated phenotypes, increased early vigour, increased germination vigour and/or increased seed yield related traits, including (but not limited to) total number of seeds, number of filled seeds or total seed weight.
The invention also provides dominant positive forms of a HUB1 polypeptide. In one dominant positive form (HUB1pm), the Cys residues nr 1 and 2 of the C3HC4 domain (FIG. 1B(i)) were mutated into Ser residues (FIG. 1B(ii) and (iii)). Surprisingly, the H2B monoubiquitination was not influenced by these point mutations (FIG. 5, HA-Ab) whereas the autopolyubiquitination activity of HUB1 was negatively affected. Also the presence of the substrate reduced the autopolyubiquitination activity, suggesting that in the absence of substrate HUB1 protein may be removed through protein degradation. This reduced autoregulation may lead to stabilization of the protein, thereby creating a dominant positive form of the protein with enhanced activity.
The overexpression of wild type HUB1 has positive influence on plant growth, therefore it is expected that a dominant positive or stabilized form of HUB1 may allow further improvement these growth effects (See Example 16). It is also postulated that other mutations substantially preventing cofactor binding in one of both Zn-binding sites will have a comparable effect on the protein function; these other mutations encompass any type of mutation(s), including insertion mutagenesis to disrupt or increase the open reading frame. The term “HUB1 polypeptide” as used in the present invention thus also encompasses mutant forms with reduced autopolyubiquitination but with normal, reduced or completely eliminated substrate ubiquitination activity.
Therefore, according to a further embodiment of the present invention, there is provided an isolated polypeptide selected from:

- (i) a polypeptide sequence encoding a HUB1 protein as defined above, comprising in its RING domain one or more mutations that substantially prevent cofactor binding in the Zn-binding sites and wherein said one or more mutations reduce autopolyubiquitination without affecting substrate ubiquitination;
- (ii) a HUB1 polypeptide sequence represented by SEQ ID NO: 28;
- (iii) a polypeptide sequence having, in increasing order of preference, at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid sequence represented by SEQ ID NO: 28, and comprising a RING domain, which RING domain comprises one or more mutations as defined in (i);
- (iv) functional fragments of any of the amino acid sequences given in (i), (ii), or (iii) above, provided that the functional fragment comprises a RING domain, which RING domain comprises one or more mutations as defined in (i).

Preferably, the HUB1 polypeptide sequence as defined in (i) above is a HUB1 polypeptide wherein binding of one cofactor is substantially prevented, more preferably binding of the first cofactor is prevented.
According to a further embodiment of the present invention, there is also provided an isolated nucleic acid molecule encoding a HUB1 polypeptide as defined in (i) to (iv) above, or a nucleic acid capable of hybridising under stringent conditions to the complement of an isolated nucleic acid encoding a HUB1 polypeptide as defined in (i) to (iv) above; preferably the isolated nucleic acid is as represented by SEQ ID NO: 49.
In a further embodiment, the invention provides genes having altered expression levels in plants overexpressing a HUB1 polypeptide relative to expression levels in corresponding wild type plants. Furthermore, the present invention provides means to modulate expression of these genes, which in turn allows for modulation of the biological processes that they control. The present invention provides methods to mimic HUB1 polypeptide level and/or activity by manipulating downstream factors involved in HUB1 polypeptide regulated pathways. This strategy allows a fine-tuning of the effects of the HUB1 polypeptide. Whereas overexpression or downregulation of a HUB1 polypeptide can be pleiotropic and/or can have pleiotropic effects, the invention provides methods to alter plant characteristics in a more controlled and targeted way, by using the HUB1 polypeptide target genes as defined by the present invention. Modulation of particular biological processes is now possible and may give rise to plants having altered characteristics, which may have particularly useful applications in agriculture and horticulture, such as improved yield-related traits for plants grown under normal or under stress conditions.
Therefore, according to the present invention, there is provided a method to enhance one or more yield-related traits in plants, comprising modifying in a plant expression of one or more nucleic acids and/or modifying level and/or activity of one or more proteins, which nucleic acids or proteins are essentially similar to any one of the genes listed in Tables G to K, and wherein said one or more yield-related traits are altered relative to corresponding wild type plants. Furthermore, the present invention provides methods for modifying the circadian clock in plants, for modifying the photosynthetic capacity and/or for modifying plant development.
The present invention is illustrated by transforming plants with the nucleic acid sequence represented by SEQ ID NO: 1, encoding the polypeptide sequence of SEQ ID NO: 2 and with plants comprising a mutation in the HUB1 gene (hub1-1, Fleury et al, 2007). However, performance of the invention is not restricted to these sequences; the methods of the invention may advantageously be performed using any HUB1-encoding nucleic acid or HUB1 polypeptide as defined herein, or any dominant positive mutant of HUB1. Alternatively, plants may be subjected to mutagenesis to generate a mutant form of the endogenous HUB1 gene that has the same functional characteristics as the dominant positive mutant or the hub1-1 mutant. Techniques for generating such type of mutations are known in the art (such as TILLING or site-specific recombination (Thomson and Ow, Genesis 44, 465-476, 2006)). Furthermore, any of the genes listed in Table G to K (which include SEQ ID NO: 50 to SEQ ID NO: 243), or the orthologues of such genes, can be used in the methods of the present invention.
Examples of nucleic acids encoding HUB1 polypeptides are given in Table A of Example 1 herein. Such nucleic acids are useful in performing the methods of the invention. The amino acid sequences given in Table A of Example 1 are example sequences of orthologues and paralogues of the HUB1 polypeptide represented by SEQ ID NO: 2, the terms “orthologues” and “paralogues” being as defined herein. Further orthologues and paralogues may readily be identified by performing a so-called reciprocal blast search. Typically, this involves a first BLAST involving BLASTing a query sequence (for example using any of the sequences listed in Table A of Example 1) against any sequence database, such as the publicly available NCBI database. BLASTN or TBLASTX (using standard default values) are generally used when starting from a nucleotide sequence, and BLASTP or TBLASTN (using standard default values) when starting from a protein sequence. The BLAST results may optionally be filtered. The full-length sequences of either the filtered results or non-filtered results are then BLASTed back (second BLAST) against sequences from the organism from which the query sequence is derived (where the query sequence is SEQ ID NO: 1 or SEQ ID NO: 2, the second BLAST would therefore be against Arabidopsis sequences). The results of the first and second BLASTs are then compared. A paralogue is identified if a high-ranking hit from the first blast is from the same species as from which the query sequence is derived, a BLAST back then ideally results in the query sequence amongst the highest hits; an orthologue is identified if a high-ranking hit in the first BLAST is not from the same species as from which the query sequence is derived, and preferably results upon BLAST back in the query sequence being among the highest hits.
High-ranking hits are those having a low E-value. The lower the E-value, the more significant the score (or in other words the lower the chance that the hit was found by chance). Computation of the E-value is well known in the art. In addition to E-values, comparisons are also scored by percentage identity. Percentage identity refers to the number of identical nucleotides (or amino acids) between the two compared nucleic acid (or polypeptide) sequences over a particular length. In the case of large families, ClustalW may be used, followed by a neighbour joining tree, to help visualize clustering of related genes and to identify orthologues and paralogues.
Examples of proteins involved in the circadian clock, in the output response of the circadian clock and or in development are provided in Table G, H and I. Examples of proteins that interact with HUB1 are listed in Tables J, K and L. All these proteins (including orthologues) are useful in the methods of the present invention, hereafter referred to as “other proteins useful in the methods of the present invention”.
Nucleic acid variants may also be useful in practising the methods of the invention. Examples of such variants include nucleic acids encoding homologues and derivatives of any one of the amino acid sequences given in Table A of Example 1 or of other proteins useful in the methods of the present invention, the terms “homologue” and “derivative” being as defined herein. Also useful in the methods of the invention are nucleic acids encoding homologues and derivatives of orthologues or paralogues of any one of the amino acid sequences given in Table A of Example 1 or of other proteins useful in the methods of the present invention. Homologues and derivatives useful in the methods of the present invention have substantially the same biological and functional activity as the unmodified protein from which they are derived.
Further nucleic acid variants useful in practising the methods of the invention include portions of nucleic acids encoding HUB1 polypeptides, nucleic acids hybridising to nucleic acids encoding HUB1 polypeptides, splice variants of nucleic acids encoding HUB1 polypeptides, allelic variants of nucleic acids encoding HUB1 polypeptides and variants of nucleic acids encoding HUB1 polypeptides obtained by gene shuffling. The terms hybridising sequence, splice variant, allelic variant and gene shuffling are as described herein. Also nucleic acid variants of nucleic acids encoding other proteins useful in the methods of the present invention, nucleic acids hybridising to nucleic acids encoding other proteins useful in the methods of the present invention, splice variants of nucleic acids encoding other proteins useful in the methods of the present invention, allelic variants of nucleic acids encoding other proteins useful in the methods of the present invention, and variants of nucleic acids encoding other proteins useful in the methods of the present invention obtained by gene shuffling are useful in practising the methods of the invention.
Nucleic acids encoding HUB1 polypeptides or other proteins useful in the methods of the present invention need not be full-length nucleic acids, since performance of the methods of the invention does not rely on the use of full-length nucleic acid sequences. According to the present invention, there is provided a method for modifying growth characteristics in plants, comprising introducing and expressing in a plant a portion of any one of the nucleic acid sequences given in Table A of Example 1 or in Tables G to K, or a portion of a nucleic acid encoding an orthologue, paralogue or homologue of any of the amino acid sequences given in Table A of Example 1 or in Tables G to K.
A portion of a nucleic acid may be prepared, for example, by making one or more deletions to the nucleic acid. The portions may be used in isolated form or they may be fused to other coding (or non-coding) sequences in order to, for example, produce a protein that combines several activities. When fused to other coding sequences, the resultant polypeptide produced upon translation may be bigger than that predicted for the protein portion.
Portions useful in the methods of the invention, encode a HUB1 polypeptide as defined herein, and have substantially the same biological activity as the amino acid sequences given in Table A of Example 1 or in Tables G to K. Preferably, the portion is a portion of any one of the nucleic acids given in Table A of Example 1, or is a portion of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A of Example 1. Preferably the portion is at least 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2700, 2800, 2900, 3000 consecutive nucleotides in length, the consecutive nucleotides being of any one of the nucleic acid sequences given in Table A of Example 1 or in Tables G to K, or of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A of Example 1 or in Tables G to K. Most preferably the portion is a portion of the nucleic acid of SEQ ID NO: 1 or of a nucleic encoding a protein given in Tables G to K. Preferably, the portion encodes a fragment of a HUB1 polypeptide sequence which when used in the construction of a phylogenetic tree, such as the one depicted in FIG. 3, clusters with the group of HUB1 polypeptides comprising the amino acid sequence represented by SEQ ID NO: 2 (At2g44950) rather than with any other group of proteins comprising a RING domain.
Another nucleic acid variant useful in the methods of the invention is a nucleic acid capable of hybridising, under reduced stringency conditions, preferably under stringent conditions, with a nucleic acid encoding a HUB1 polypeptide as defined herein or with a nucleic acid encoding a protein as given in any of Tables G to K, or with a portion as defined herein.
According to the present invention, there is provided a method for modifying growth characteristics in plants, comprising introducing and expressing in a plant a nucleic acid capable of hybridizing to any one of the nucleic acids given in Table A of Example 1 or in Tables G to K, or comprising introducing and expressing in a plant a nucleic acid capable of hybridising to a nucleic acid encoding an orthologue, paralogue or homologue of any of the nucleic acid sequences given in Table A of Example 1 or in Tables G to K.
Hybridising sequences useful in the methods of the invention encode a HUB1 polypeptide as defined herein, having substantially the same biological activity as the amino acid sequences given in Table A of Example 1 or in Tables G to K. Preferably, the hybridising sequence is capable of hybridising to the complement of any one of the nucleic acids given in Table A of Example 1 or in Tables G to K, or to a portion of any of these sequences, a portion being as defined above, or the hybridising sequence is capable of hybridising to the complement of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A of Example 1 or in Tables G to K. Most preferably, the hybridising sequence is capable of hybridising to the complement of a nucleic acid as represented by SEQ ID NO: 1 or to a portion thereof.
For HUB1, the hybridising sequence preferably encodes a polypeptide with an amino acid sequence which, when full-length and used in the construction of a phylogenetic tree, such as the one depicted in FIG. 3, clusters with the group of HUB1 polypeptides comprising the amino acid sequence represented by SEQ ID NO: 2 (At2g44950) rather than with any other group of proteins comprising a RING domain. Preferably, the hybridising sequence encodes a protein having a C3HC4 type RING domain.
Another nucleic acid variant useful in the methods of the invention is a splice variant encoding a HUB1 polypeptide as defined hereinabove or encoding other proteins useful in the methods of the present invention, a splice variant being as defined herein.
According to the present invention, there is provided a method for modifying growth characteristics in plants, comprising introducing and expressing in a plant a splice variant of any one of the nucleic acid sequences given in Table A of Example 1 or in Tables G to K, or a splice variant of a nucleic acid encoding an orthologue, paralogue or homologue of any of the amino acid sequences given in Table A of Example 1 or in Tables G to K.
Preferred splice variants are splice variants of a nucleic acid represented by SEQ ID NO: 1, or a splice variant of a nucleic acid encoding an orthologue or paralogue of SEQ ID NO: 2. Preferably, the HUB1 amino acid sequence encoded by the splice variant, when used in the construction of a phylogenetic tree, such as the one depicted in FIG. 3, clusters with the group of HUB1 polypeptides comprising the amino acid sequence represented by SEQ ID NO: 2 (At2g44950) rather than with any other group of proteins comprising a RING domain. Preferably, the splice variant encodes a protein having a C3HC4 type RING domain.
Another nucleic acid variant useful in performing the methods of the invention is an allelic variant of a nucleic acid encoding a HUB1 polypeptide as defined hereinabove or encoding other proteins useful in the methods of the present invention, an allelic variant being as defined herein.
According to the present invention, there is provided a method for modifying growth characteristics in plants, comprising introducing and expressing in a plant an allelic variant of any one of the nucleic acids given in Table A of Example 1 or in Tables G to K, or comprising introducing and expressing in a plant an allelic variant of a nucleic acid encoding an orthologue, paralogue or homologue of any of the amino acid sequences given in Table A of Example 1 or in Tables G to K.
The polypeptides encoded by allelic variants useful in the methods of the present invention have substantially the same biological activity as the HUB1 polypeptide of SEQ ID NO: 2 and any of the amino acids depicted in Table A of Example 1 or in Tables G to K. Allelic variants exist in nature, and encompassed within the methods of the present invention is the use of these natural alleles. Preferably, the allelic variant is an allelic variant of SEQ ID NO: 1 or an allelic variant of a nucleic acid encoding an orthologue or paralogue of SEQ ID NO: 2 or of a protein given in Tables G to K. Preferably, the HUB1 amino acid sequence encoded by the allelic variant, when used in the construction of a phylogenetic tree, such as the one depicted in FIG. 3, clusters with the group of HUB1 polypeptides comprising the amino acid sequence represented by SEQ ID NO: 2 (At2g44950) rather than with any other group of proteins comprising a RING domain. Preferably, the allelic variant encodes a protein having a C3HC4 type RING domain.
Gene shuffling or directed evolution may also be used to generate variants of nucleic acids encoding HUB1 polypeptides as defined above or encoding other proteins useful in the methods of the present invention; the term “gene shuffling” being as defined herein.
According to the present invention, there is provided a method for modifying growth characteristics in plants, comprising introducing and expressing in a plant a variant of any one of the nucleic acid sequences given in Table A of Example 1 or in Tables G to K, or comprising introducing and expressing in a plant a variant of a nucleic acid encoding an orthologue, paralogue or homologue of any of the amino acid sequences given in Table A of Example 1 or in Tables G to K, which variant nucleic acid is obtained by gene shuffling.
Preferably, the HUB1 amino acid sequence encoded by the variant nucleic acid obtained by gene shuffling, when used in the construction of a phylogenetic tree such as the one depicted in FIG. 3, clusters with the group of HUB1 polypeptides comprising the amino acid sequence represented by SEQ ID NO: 2 (At2g44950) rather than with any other group of proteins comprising a RING domain.
Furthermore, nucleic acid variants may also be obtained by site-directed mutagenesis. Several methods are available to achieve site-directed mutagenesis, the most common being PCR based methods (Current Protocols in Molecular Biology. Wiley Eds.).
Nucleic acids encoding HUB1 polypeptides or other proteins useful in the methods of the present invention may be derived from any natural or artificial source. The nucleic acid may be modified from its native form in composition and/or genomic environment through deliberate human manipulation. Preferably the HUB1 polypeptide-encoding nucleic acid or nucleic acids encoding other proteins useful in the methods of the present invention are from a plant, further preferably from a dicotyledonous or a monocotyledonous plant. The HUB1 polypeptide-encoding nucleic acid from a dicotyledonous plant is preferably from the family Brassicaceae, more preferably from Arabidopsis thaliana.
Performance of the methods of the invention gives plants having modified growth characteristics. In particular performance of the methods of the invention gives plants having modified light regulated phenotypes, increased germination vigour, increased early vigour, increased stress resistance, altered fruit shape and/or increased seed yield relative to control plants. The term “seed yield” is described in more detail in the “definitions” section herein. It should be noted that the terms “modified growth characteristics” or “yield” as used in the present invention do not encompass vegetative biomass (such as roots, leaves, stems) except where a dominant positive mutant of HUB1 is used in the methods of the present invention.
Reference herein to modified growth characteristics also encompasses a modification of light regulated phenotypes, which include, but are not limited to, an alteration of the circadian clock, and a modification of the pathways downstream of the circadian clock (the circadian clock output responses). The modified downstream pathways encompass one or more of a modified photosynthetic capacity, altered expression of genes involved in plant development and modified plant development. The modification of the circadian clock comprises modified expression of the circadian clock input genes as well as oscillator genes and output genes. The “modified circadian clock output response” or the “modified downstream pathways” as used in the present invention encompasses a modification of the photosynthetic capacity, such as a modification in the concentration of photosynthetic pigments (chlorophyll a and b and total carotenoids) in a plant cell, modified plastid structure, or modified chloroplast structure. The “modified circadian clock output response” or the “modified downstream pathways” as used in the present invention also encompasses altered expression of genes involved in plant development and modifications in plant development such as altered architecture (including reduced hypocotyl length, modified leaf morphology, altered flower morphology) and/or altered flowering time.
Therefore the present invention provides a method for modifying expression of circadian clock input genes, of oscillator genes, of output genes and/or of developmental genes, which method preferably comprises modulating expression of a HUB1 polypeptide. Some of these genes are located close to each other on the chromosome. Therefore, HUB1 can be used as a transcriptional regulator for synchronisation of the transcription of genes that form a cluster. Examples of such clusters are photosynthetic genes, circadian clock genes or developmental genes. The modified expression of the circadian clock input genes, oscillator genes, output genes, developmental genes and/or genes listed in any of Tables G to K (or the orthologues thereof) as the result of modulated HUB1 expression may on its turn result in improved plant growth characteristics such as increased yield or increased stress tolerance. Therefore the present invention provides a method for improving plant growth characteristics which method comprises modulated expression of circadian clock input genes, oscillator genes, output genes and/or developmental genes as the result of modulated HUB1 expression. The present invention also provides a method for improving growth characteristics comprising modulated expression of any of the genes listed in Table G to K, or the orthologue of such a gene. Methods for identifying the orthologue of a gene are described above. The modulated expression may be increased or decreased expression.
The present invention also provides a method for altering plant development, in particular for altering flowering time and/or for modifying plant architecture.
The flowering time is the time elapsed between sowing and start of reproductive growth. Conventional methods for determining the start of flowering include dissecting plants under magnification to determine the presence of either a vegetative or reproductive structure at the meristem; to monitor emergence of the inflorescence, otherwise known as “emergence” or “heading time”, or to monitor anthesis. A widely used method for determining the start of flowering in crops in the field involves repeated visual inspection of plots to estimate the number of flowering plants present in a plot. It is conventionally accepted in agronomics that a plot is “flowering” when 50% of plants in a plot exhibit emerged inflorescences. Yet another method is described in WO 2007/093444, this method is based on computer analysis of digital images take from the growing plants.
The term plant architecture encompasses the appearance or morphology of a plant, including any one or more structural features or combination of structural features thereof. Such structural features include the shape, size, number, position, texture, arrangement, and pattern of any cell, tissue or organ or groups of cells, tissues or organs of a plant, including the root, leaf, shoot, stem or tiller, petiole, trichome, flower, inflorescence (for monocotyledonous and dicotyledonous plants), panicles, petal, stigma, style, stamen, pollen, ovule, seed, embryo, endosperm, seed coat, aleurone, fibre, cambium, wood, heartwood, parenchyma, aerenchyma, sieve elements, phloem or vascular tissue, amongst others. Modified architecture therefore includes all aspects of modified growth of the plant.
Preferably, the plants according to the invention exhibit modified architecture, which modified architecture includes one or more of stunted growth, modified leaf morphology, modified hypocotyl morphology, altered flower morphology, relative to control plants. Therefore, according to the present invention, there is provided a method for modifying the architecture of plants, particularly one or more of stunted growth, modified leaf morphology, modified hypocotyl morphology, altered flower morphology, which method comprises modulating expression of a nucleic acid sequence encoding a HUB1 polypeptide as defined herein. The term “stunted growth” as used herein is taken to mean a reduction in plant height without affecting organ size, giving the plant a bushy phenotype, in contrast to dwarfism or miniature growth in which the proportions are maintained but overall plant growth is reduced.
The RING domain in HUB1 proteins is known to be involved in protein-protein interactions. In the present invention, it is shown that HUB1 interacts with various proteins (Example 22). Besides homodimerisation and dimerisation with its paralogue HUB2, HUB1 also interacts with GCN5, a histone acylation enzyme that is involved in stress response, defence, signal transduction, transcription, metabolism, transport. GCN5 is also involved in flower development by affecting expression of WUSCHEL and AGAMOUS. The MYB transcription factor At1g58220, another interactor of HUB1, is involved in responses to plant hormone stimuli (such as abscisic acid, jasmonic acid and salicylic acid). The present invention thus also provides a method for altering responses to one or more of stress responses, defence responses, hormonal signal transduction, and flower development, said method comprising modulation of HUB1 expression.
Reference herein to improved growth characteristics is also taken to mean an increase in biomass (weight) of one or more harvestable parts of a plant, in particular, such harvestable parts are seeds, and performance of the methods of the invention results in plants having increased seed yield relative to the seed yield of control plants. The improved growth characteristics also encompasses increased germination vigour (increased speed of germination), increased early vigour, and increased resistance to stress, in particular abiotic stress. It was furthermore observed that the cell size was increased compared to control plants, particularly in leaves.
Taking corn as an example, a yield increase may be manifested as one or more of the following: increase in the number of plants established per square meter, an increase in the number of ears per plant, an increase in the number of rows, number of kernels per row, kernel weight, thousand kernel weight, ear length/diameter, increase in the seed filling rate (which is the number of filled seeds divided by the total number of seeds and multiplied by 100), among others. Taking rice as an example, a yield increase may manifest itself as an increase in one or more of the following: number of plants per square meter, number of panicles per plant, number of spikelets per panicle, number of flowers (florets) per panicle (which is expressed as a ratio of the number of filled seeds over the number of primary panicles), increase in the seed filling rate (which is the number of filled seeds divided by the total number of seeds and multiplied by 100), increase in thousand kernel weight, among others.
The present invention provides a method for increasing yield, especially seed yield of plants, relative to control plants, which method comprises modulating expression in a plant of a nucleic acid encoding a HUB1 polypeptide as defined herein or encoding another protein useful in the methods of the present invention.
Since the transgenic plants according to the present invention have increased yield, it is likely that these plants exhibit an increased growth rate (during at least part of their life cycle), relative to the growth rate of control plants at a corresponding stage in their life cycle.
The increased growth rate may be specific to one or more parts of a plant (including seeds), or may be throughout substantially the whole plant. Plants having an increased growth rate may have a shorter life cycle. The life cycle of a plant may be taken to mean the time needed to grow from a dry mature seed up to the stage where the plant has produced dry mature seeds, similar to the starting material. This life cycle may be influenced by factors such as speed of germination (germination vigour), early vigour, growth rate, greenness index, flowering time and speed of seed maturation. The increase in growth rate may take place at one or more stages in the life cycle of a plant or during substantially the whole plant life cycle. Increased growth rate during the early stages in the life cycle of a plant may reflect enhanced vigour. The increase in growth rate may alter the harvest cycle of a plant allowing plants to be sown later and/or harvested sooner than would otherwise be possible (a similar effect may be obtained with earlier flowering time). If the growth rate is sufficiently increased, it may allow for the further sowing of seeds of the same plant species (for example sowing and harvesting of rice plants followed by sowing and harvesting of further rice plants all within one conventional growing period). Similarly, if the growth rate is sufficiently increased, it may allow for the further sowing of seeds of different plants species (for example the sowing and harvesting of corn plants followed by, for example, the sowing and optional harvesting of soybean, potato or any other suitable plant). Harvesting additional times from the same rootstock in the case of some crop plants may also be possible. Altering the harvest cycle of a plant may lead to an increase in annual biomass production per square meter (due to an increase in the number of times (say in a year) that any particular plant may be grown and harvested). An increase in growth rate may also allow for the cultivation of transgenic plants in a wider geographical area than their wild-type counterparts, since the territorial limitations for growing a crop are often determined by adverse environmental conditions either at the time of planting (early season) or at the time of harvesting (late season). Such adverse conditions may be avoided if the harvest cycle is shortened. The growth rate may be determined by deriving various parameters from growth curves, such parameters may be: T-Mid (the time taken for plants to reach 50% of their maximal size) and T-90 (time taken for plants to reach 90% of their maximal size), amongst others.
According to a preferred feature of the present invention, performance of the methods of the invention gives plants having an increased growth rate relative to control plants. Therefore, according to the present invention, there is provided a method for increasing the growth rate of plants, which method comprises modulating expression in a plant of a nucleic acid encoding a HUB1 polypeptide as defined herein or encoding another protein useful in the methods of the present invention.
An increase in yield and/or growth rate occurs whether the plant is under non-stress conditions or whether the plant is exposed to various stresses compared to control plants. Plants typically respond to exposure to stress by growing more slowly. In conditions of severe stress, the plant may even stop growing altogether. Mild stress on the other hand is defined herein as being any stress to which a plant is exposed which does not result in the plant ceasing to grow altogether without the capacity to resume growth. Mild stress in the sense of the invention leads to a reduction in the growth of the stressed plants of less than 40%, 35% or 30%, preferably less than 25%, 20% or 15%, more preferably less than 14%, 13%, 12%, 11% or 10% or less in comparison to the control plant under non-stress conditions. Due to advances in agricultural practices (irrigation, fertilization, pesticide treatments) severe stresses are not often encountered in cultivated crop plants. As a consequence, the compromised growth induced by mild stress is often an undesirable feature for agriculture. Mild stresses are the everyday biotic and/or abiotic (environmental) stresses to which a plant is exposed. Abiotic stresses may be due to drought or excess water, anaerobic stress, salt stress, chemical toxicity, oxidative stress and hot, cold or freezing temperatures. The abiotic stress may be an osmotic stress caused by a water stress (particularly due to drought), salt stress, oxidative stress or an ionic stress. Biotic stresses are typically those stresses caused by pathogens, such as bacteria, viruses, fungi, nematodes and insects.
In particular, the methods of the present invention may be performed under non-stress conditions or under conditions of mild drought to give plants having improved growth characteristics relative to control plants. As reported in Wang et al. (Planta (2003) 218: 1-14), abiotic stress leads to a series of morphological, physiological, biochemical and molecular changes that adversely affect plant growth and productivity. Drought, salinity, extreme temperatures and oxidative stress are known to be interconnected and may induce growth and cellular damage through similar mechanisms. Rabbani et al. (Plant Physiol (2003) 133: 1755-1767) describes a particularly high degree of “cross talk” between drought stress and high-salinity stress. For example, drought and/or salinisation are manifested primarily as osmotic stress, resulting in the disruption of homeostasis and ion distribution in the cell. Oxidative stress, which frequently accompanies high or low temperature, salinity or drought stress, may cause denaturing of functional and structural proteins. As a consequence, these diverse environmental stresses often activate similar cell signalling pathways and cellular responses, such as the production of stress proteins, up-regulation of anti-oxidants, accumulation of compatible solutes and growth arrest. The term “non-stress” conditions as used herein are those environmental conditions that allow optimal growth of plants. Persons skilled in the art are aware of normal soil conditions and climatic conditions for a given location.
Performance of the methods of the invention gives plants grown under non-stress conditions or under mild drought conditions improved growth characteristics relative to control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for improving growth characteristics in plants grown under non-stress conditions or under mild drought conditions, which method comprises modulating expression in a plant of a nucleic acid encoding a HUB1 polypeptide or encoding another protein useful in the methods of the present invention. In addition, performance of the methods of the invention also gives plants grown under severe drought conditions improved growth characteristics relative to control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for improving growth characteristics in plants grown under severe drought conditions, which method comprises modulating expression in a plant of a nucleic acid encoding a HUB1 polypeptide or encoding another protein useful in the methods of the present invention.
Performance of the methods of the invention gives plants grown under conditions of salt stress, improved growth characteristics relative to control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for improving growth characteristics in plants grown under conditions of salt stress, which method comprises modulating expression in a plant of a nucleic acid encoding a HUB1 polypeptide or encoding another protein useful in the methods of the present invention. The term salt stress is not restricted to common salt (NaCl), but may be any one or more of: NaCl, KCl, LiCl, MgCl₂, CaCl₂, amongst others.
Performance of the methods of the invention gives plants grown under conditions of nutrient deficiency, particularly under conditions of nitrogen deficiency, improved growth characteristics relative to control plants grown under comparable conditions, in other words, the plants according to the invention have an increased efficiency in nutrient uptake. Therefore, according to the present invention, there is provided a method for improving growth characteristics in plants grown under conditions of nutrient deficiency, which method comprises modulating expression in a plant of a nucleic acid encoding a HUB1 polypeptide or encoding another protein useful in the methods of the present invention. Nutrient deficiency may result from a lack of nutrients such as nitrogen, phosphates and other phosphorous-containing compounds, potassium, calcium, magnesium, manganese, iron and boron, amongst others.
The present invention encompasses plants or parts thereof (including seeds) obtainable by the methods according to the present invention. The plants or parts thereof comprise a nucleic acid transgene encoding a HUB1 polypeptide as defined above or encoding another protein useful in the methods of the present invention.
The invention also provides genetic constructs and vectors to facilitate introduction and/or expression in plants of nucleic acids encoding HUB1 polypeptides or encoding another protein useful in the methods of the present invention. The gene constructs may be inserted into vectors, which may be commercially available, suitable for transforming into plants and suitable for expression of the gene of interest in the transformed cells. The invention also provides use of a gene construct as defined herein in the methods of the invention.
More specifically, the present invention provides a construct comprising:

- (a) a nucleic acid encoding a HUB1 polypeptide as defined above or encoding another protein useful in the methods of the present invention;
- (b) one or more control sequences capable of driving expression of the nucleic acid sequence of (a); and optionally
- (c) a transcription termination sequence.

Preferably, the nucleic acid encoding a HUB1 polypeptide is as defined above. The proteins useful in the methods of the present invention are as described above and encompass the proteins listed in Table G to K and the orthologues thereof. The term “control sequence” and “termination sequence” are as defined herein.
Plants are transformed with a vector comprising any of the nucleic acids described above. The skilled artisan is well aware of the genetic elements that must be present on the vector in order to successfully transform, select and propagate host cells containing the sequence of interest. The sequence of interest is operably linked to one or more control sequences (at least to a promoter).
Advantageously, any type of promoter, whether natural or synthetic, may be used to drive expression of the nucleic acid sequence, but preferably the promoter is of plant origin. A constitutive promoter is particularly useful in the methods. Preferably the constitutive promoter is also a ubiquitous promoter. The rice GOS2 promoter may be useful in monocot plants and a CaMV35S promoter may be useful in dicot plants. In some instances, the constitutive promoter is preferably not a strong constitutive promoter (such as the CaMV35S promoter) and is less strong than the rice GOS2 promoter. However, for obtaining increased early vigour and/or germination vigour, a strong constitutive promoter is useful too. In other instances, an organ specific, a tissue specific or a cell specific promoter is more suitable. See the “Definitions” section herein for definitions of the various promoter types.
It should be clear that the applicability of the present invention is not restricted to the HUB1 polypeptide-encoding nucleic acid represented by SEQ ID NO: 1, nor is the applicability of the invention restricted to expression of a HUB1 polypeptide-encoding nucleic acid when driven by a constitutive promoter, or when driven by a seed-specific promoter.
In one embodiment of this invention, the constitutive promoter is preferably a medium strength promoter that is weaker than the rice GOS2 promoter and the CaMV35S promoter, such as a High Mobility Group Protein (HMGP) promoter, preferably the promoter is a HMGP promoter from rice. Further preferably the constitutive promoter is represented by a nucleic acid sequence substantially similar to SEQ ID NO: 6, most preferably the constitutive promoter is as represented by SEQ ID NO: 6. See Table 2a in the “Definitions” section herein for further examples of constitutive promoters.
According to another embodiment of the invention, the nucleic acid encoding a HUB1 polypeptide is operably linked to a seed-specific promoter. The seed-specific promoter is preferably a WSI18 promoter, more preferably the WSI18 promoter is from rice, further preferably the WSI18 promoter is represented by a nucleic acid sequence substantially similar to SEQ ID NO: 7, most preferably the promoter is as represented by SEQ ID NO: 7. Examples of other seed-specific promoters which may also be used to perform the methods of the invention are shown in Table 2c in the “Definitions” section above.
Optionally, one or more terminator sequences may be used in the construct introduced into a plant.
Additional regulatory elements may include transcriptional as well as translational enhancers. Those skilled in the art will be aware of terminator and enhancer sequences that may be suitable for use in performing the invention. An intron sequence may also be added to the 5′ untranslated region (UTR) or in the coding sequence to increase the amount of the mature message that accumulates in the cytosol, as described in the definitions section. Other control sequences (besides promoter, enhancer, silencer, intron sequences, 3′UTR and/or 5′UTR regions) may be protein and/or RNA stabilizing elements. Such sequences would be known or may readily be obtained by a person skilled in the art.
The genetic constructs of the invention may further include an origin of replication sequence that is required for maintenance and/or replication in a specific cell type. One example is when a genetic construct is required to be maintained in a bacterial cell as an episomal genetic element (e.g. plasmid or cosmid molecule). Preferred origins of replication include, but are not limited to, the f1-ori and colE1.
For the detection of the successful transfer of the nucleic acid sequences as used in the methods of the invention and/or selection of transgenic plants comprising these nucleic acids, it is advantageous to use marker genes (or reporter genes). Therefore, the genetic construct may optionally comprise a selectable marker gene. Selectable markers are described in more detail in the “definitions” section herein. The marker genes may be removed or excised from the transgenic cell once they are no longer needed. Techniques for marker removal are known in the art, useful techniques are described above in the definitions section.
The invention also provides a method for the production of transgenic plants having modified growth characteristics relative to control plants, comprising introduction and expression in a plant of any nucleic acid encoding a HUB1 polypeptide as defined hereinabove or encoding another protein useful in the methods of the present invention.
More specifically, the present invention provides a method for the production of transgenic plants having modified growth characteristics, particularly increased (seed) yield, which method comprises:

- (i) introducing and expressing in a plant or plant cell a HUB1 polypeptide-encoding nucleic acid or encoding another protein useful in the methods of the present invention; and
- (ii) cultivating the plant cell under conditions promoting plant growth and development.

The nucleic acid of (i) may be any of the nucleic acids capable of encoding a HUB1 polypeptide as defined herein or encoding another protein useful in the methods of the present invention.
The nucleic acid may be introduced directly into a plant cell or into the plant itself (including introduction into a tissue, organ or any other part of a plant). According to a preferred feature of the present invention, the nucleic acid is preferably introduced into a plant by transformation. The term “transformation” is described in more detail in the “definitions” section herein.
The genetically modified plant cells can be regenerated via all methods with which the skilled worker is familiar. Suitable methods can be found in the abovementioned publications by S. D. Kung and R. Wu, Potrykus or Hofgen and Willmitzer.
Generally after transformation, plant cells or cell groupings are selected for the presence of one or more markers which are encoded by plant-expressible genes co-transferred with the gene of interest, following which the transformed material is regenerated into a whole plant. To select transformed plants, the plant material obtained in the transformation is, as a rule, subjected to selective conditions so that transformed plants can be distinguished from untransformed plants. For example, the seeds obtained in the above-described manner can be planted and, after an initial growing period, subjected to a suitable selection by spraying. A further possibility consists in growing the seeds, if appropriate after sterilization, on agar plates using a suitable selection agent so that only the transformed seeds can grow into plants. Alternatively, the transformed plants are screened for the presence of a selectable marker such as the ones described above.
Following DNA transfer and regeneration, putatively transformed plants may also be evaluated, for instance using Southern analysis, for the presence of the gene of interest, copy number and/or genomic organisation. Alternatively or additionally, expression levels of the newly introduced DNA may be monitored using Northern and/or Western analysis, both techniques being well known to persons having ordinary skill in the art.
The generated transformed plants may be propagated by a variety of means, such as by clonal propagation or classical breeding techniques. For example, a first generation (or T1) transformed plant may be selfed and homozygous second-generation (or T2) transformants selected, and the T2 plants may then further be propagated through classical breeding techniques. The generated transformed organisms may take a variety of forms. For example, they may be chimeras of transformed cells and non-transformed cells; clonal transformants (e.g., all cells transformed to contain the expression cassette); grafts of transformed and untransformed tissues (e.g., in plants, a transformed rootstock grafted to an untransformed scion).
The present invention clearly extends to any plant cell or plant produced by any of the methods described herein, and to all plant parts and propagules thereof. The present invention extends further to encompass the progeny of a primary transformed or transfected cell, tissue, organ or whole plant that has been produced by any of the aforementioned methods, the only requirement being that progeny exhibit the same genotypic and/or phenotypic characteristic(s) as those produced by the parent in the methods according to the invention.
The invention also includes host cells containing an isolated nucleic acid encoding a HUB1 polypeptide as defined hereinabove or encoding another protein useful in the methods of the present invention. Preferred host cells according to the invention are plant cells. Host plants for the nucleic acids or the vector used in the method according to the invention, the expression cassette or construct or vector are, in principle, advantageously all plants, which are capable of synthesizing the polypeptides used in the inventive method.
The methods of the invention are advantageously applicable to any plant. Plants that are particularly useful in the methods of the invention include all plants which belong to the superfamily Viridiplantae, in particular monocotyledonous and dicotyledonous plants including fodder or forage legumes, ornamental plants, food crops, trees or shrubs. According to a preferred embodiment of the present invention, the plant is a crop plant. Examples of crop plants include soybean, sunflower, canola, alfalfa, rapeseed, linseed, cotton, tomato, potato and tobacco. Further preferably, the plant is a monocotyledonous plant. Examples of monocotyledonous plants include sugarcane. More preferably the plant is a cereal. Examples of cereals include rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, secale, einkorn, teff, milo and oats.
The invention also extends to harvestable parts of a plant such as, seeds, fruits, flowers, which harvestable parts comprise a recombinant nucleic acid encoding a HUB1 polypeptide or encoding another protein useful in the methods of the present invention. The invention furthermore relates to products derived, preferably directly derived, from a harvestable part of such a plant, such as dry pellets or powders, oil, fat and fatty acids, starch or proteins.
According to a preferred feature of the invention, the modulated expression is increased expression. Methods for increasing expression of nucleic acids or genes, or gene products, are well documented in the art and examples are provided in the definitions section.
As mentioned above, a preferred method for modulating expression of a nucleic acid encoding a HUB1 polypeptide or encoding another protein useful in the methods of the present invention is by introducing and expressing in a plant a nucleic acid encoding a HUB1 polypeptide or encoding another protein useful in the methods of the present invention; however the effects of performing the method, i.e. modifying growth characteristics may also be achieved using other well known techniques, including but not limited to T-DNA activation tagging, TILLING, homologous recombination or mutagenesis. A description of these techniques is provided in the definitions section.
The present invention also encompasses use of nucleic acids encoding HUB1 polypeptides or other proteins useful in the methods of the present invention, as described herein and use of these HUB1 polypeptides or other proteins useful in the methods of the present invention in modifying any of the aforementioned growth characteristics in plants.
Nucleic acids encoding HUB1 polypeptide described herein or encoding another protein useful in the methods of the present invention, or the HUB1 polypeptides themselves or another protein useful in the methods of the present invention, may find use in breeding programmes in which a DNA marker is identified which may be genetically linked to a HUB1 polypeptide-encoding gene or linked to a gene encoding another protein useful in the methods of the present invention. The nucleic acids/genes, or the HUB1 polypeptides themselves, or other polypeptides useful in the methods of this invention may be used to define a molecular marker. This DNA or protein marker may then be used in breeding programmes to select plants having modified growth characteristics as defined hereinabove in the methods of the invention.
Allelic variants of a HUB1 polypeptide-encoding nucleic acid/gene or of a nucleic acid/gene encoding another protein useful in the methods of the present invention may also find use in marker-assisted breeding programmes. Such breeding programmes sometimes require introduction of allelic variation by mutagenic treatment of the plants, using for example EMS mutagenesis; alternatively, the programme may start with a collection of allelic variants of so called “natural” origin caused unintentionally. Identification of allelic variants then takes place, for example, by PCR. This is followed by a step for selection of superior allelic variants of the sequence in question and which give increased yield. Selection is typically carried out by monitoring growth performance of plants containing different allelic variants of the sequence in question. Growth performance may be monitored in a greenhouse or in the field. Further optional steps include crossing plants in which the superior allelic variant was identified with another plant. This could be used, for example, to make a combination of interesting phenotypic features.
Nucleic acids encoding HUB1 polypeptides or encoding another protein useful in the methods of the present invention may also be used as probes for genetically and physically mapping the genes that they are a part of, and as markers for traits linked to those genes. Such information may be useful in plant breeding in order to develop lines with desired phenotypes. Such use of HUB1 polypeptide-encoding nucleic acids or use of nucleic acids encoding another protein useful in the methods of the present invention requires only a nucleic acid sequence of at least 15 nucleotides in length. The HUB1 polypeptide-encoding nucleic acids or nucleic acids encoding another protein useful in the methods of the present invention may be used as restriction fragment length polymorphism (RFLP) markers. Southern blots (Sambrook J, Fritsch E F and Maniatis T (1989) Molecular Cloning, A Laboratory Manual) of restriction-digested plant genomic DNA may be probed with the HUB1-encoding nucleic acids. The resulting banding patterns may then be subjected to genetic analyses using computer programs such as MapMaker (Lander et al. (1987) Genomics 1: 174-181) in order to construct a genetic map. In addition, the nucleic acids may be used to probe Southern blots containing restriction endonuclease-treated genomic DNAs of a set of individuals representing parent and progeny of a defined genetic cross. Segregation of the DNA polymorphisms is noted and used to calculate the position of the HUB1 polypeptide-encoding nucleic acid in the genetic map previously obtained using this population (Botstein et al. (1980) Am. J. Hum. Genet. 32:314-331).
The production and use of plant gene-derived probes for use in genetic mapping is described in Bernatzky and Tanksley (1986) Plant Mol. Biol. Reporter 4: 37-41. Numerous publications describe genetic mapping of specific cDNA clones using the methodology outlined above or variations thereof. For example, F2 intercross populations, backcross populations, randomly mated populations, near isogenic lines, and other sets of individuals may be used for mapping. Such methodologies are well known to those skilled in the art.
The nucleic acid probes may also be used for physical mapping (i.e., placement of sequences on physical maps; see Hoheisel et al. In: Non-mammalian Genomic Analysis: A Practical Guide, Academic press 1996, pp. 319-346, and references cited therein).
In another embodiment, the nucleic acid probes may be used in direct fluorescence in situ hybridisation (FISH) mapping (Trask (1991) Trends Genet. 7:149-154). Although current methods of FISH mapping favour use of large clones (several kb to several hundred kb; see Laan et al. (1995) Genome Res. 5:13-20), improvements in sensitivity may allow performance of FISH mapping using shorter probes.
A variety of nucleic acid amplification-based methods for genetic and physical mapping may be carried out using the nucleic acids. Examples include allele-specific amplification (Kazazian (1989) J. Lab. Clin. Med 11:95-96), polymorphism of PCR-amplified fragments (CAPS; Sheffield et al. (1993) Genomics 16:325-332), allele-specific ligation (Landegren et al. (1988) Science 241:1077-1080), nucleotide extension reactions (Sokolov (1990) Nucleic Acid Res. 18:3671), Radiation Hybrid Mapping (Walter et al. (1997) Nat. Genet. 7:22-28) and Happy Mapping (Dear and Cook (1989) Nucleic Acid Res. 17:6795-6807). For these methods, the sequence of a nucleic acid is used to design and produce primer pairs for use in the amplification reaction or in primer extension reactions. The design of such primers is well known to those skilled in the art. In methods employing PCR-based genetic mapping, it may be necessary to identify DNA sequence differences between the parents of the mapping cross in the region corresponding to the instant nucleic acid sequence. This, however, is generally not necessary for mapping methods.
The methods according to the present invention result in plants having modified growth characteristics, as described hereinbefore. These traits may also be combined with other economically advantageous traits, such as further yield-enhancing traits, tolerance to other abiotic and biotic stresses, traits modifying various architectural features and/or biochemical and/or physiological features.

DESCRIPTION OF FIGURES

The present invention will now be described with reference to the following figures in which:

FIG. 1A represents the amino acid sequence of SEQ ID NO: 2, the RING domain is indicated in bold; FIG. 1B shows the mutagenesis strategy for generating HUB1pm. (i) Wild type HUB1 RING domain with 8 Zinc binding residues in which X is any amino acid. (ii) Strategy of the mutagenesis on HUB1 gene sequence wherein two Cys residues were selected for mutagenesis (italics & underlined) into Ser. Sequences shown are: DNA (found within SEQ ID NO: 1) and aa (found within SEQ ID NO: 2). (iii) Mutagenised HUB1 RING domain of HUB1pm with two Serine residues.

FIG. 2 represents a multiple alignment of HUB1 proteins. The N-terminal part (600 amino acids) of CAO22034 is not shown in the alignment. Sequences shown are: XP_—001754625 (SEQ ID NO: 13); XP_—001777122 (SEQ ID NO: 14); EDQ74097 (SEQ ID NO: 12); CAO22034 (SEQ ID NO: 15); AAG51572 (SEQ ID NO: 17); ABB47997 (SEQ ID NO: 20); LOC_Os04g46450 (SEQ ID NO: 10); CAD41603 (SEQ ID NO: 19); At2g44950 (SEQ ID NO: 28); AAL91211 (SEQ ID NO: 16); scaff_—40.53 (SEQ ID NO: 8); CAO70576 (SEQ ID NO: 11); TA45131_—4081 (SEQ ID NO: 9); AC144591 (SEQ ID NO: 27); ABE92765 (SEQ ID NO: 18); BAB14005 (SEQ ID NO: 25); AAH18647 (SEQ ID NO: 26); AAF50744 (SEQ ID NO: 24); AAK21443 (SEQ ID NO: 23); CAA98640 (SEQ ID NO: 21); NP_—587845 (SEQ ID NO: 22).

FIG. 3 shows a phylogenetic tree of HUB1 proteins. The tree was constructed as described in Example 2.

FIG. 4 represents the binary vector for increased expression in Oryza sativa of a HUB1-encoding nucleic acid under the control of a rice HMGP promoter (pHMGP)

FIG. 5 HUB1 mediated monoubiquitination of histone H2B (HA antibody) and HUB1 autoubiquitination activity (HA antibody).

FIG. 6 Rosettes of Ler, hub1-1 and OE-HUB1 lines in short day, long day and continuous light conditions after 21 days of growth.

FIG. 7 Measurements of chlorophyll a and b from in vitro grown samples from short day (SD), long day (LD) and continuous light (CL). Both “hub1-1” and “hub1-1 pale” samples were growing on same plates.

FIG. 8 TEM images of SD grown Ler and hub1-1 leaves.

FIG. 9 Extracted hypocotyls of short day grown 21 days old Ler, OE-HUB1 and hub1-1 plants.

FIG. 10 Leaf area measurements of Ler, hub1-1 and OE-HUB1 in vitro grown seedlings under long day conditions.

FIG. 11 Leaf area measurements of Ler, hub1-1 and OE-HUB1 in vitro grown seedlings under short day conditions.

FIG. 12 Spike-like structures (arrow) on the abaxial side of narrow hub1-1 leaves from SD grown in vitro plants.

FIG. 13 Diagrams of hub1-1 and wild type Ler flowers.

FIG. 14 organ specific expression patterns of differentially expressed developmental genes in HUB1.

FIG. 15 Germination vigour in Arabidopsis HUB1 lines. DAV=days after vernalisation. (n=30). OE7a and OE17×5 are HUB1 overexpressing lines, Ler and hub1 (mutant) are controls.

FIG. 16 Epidermal cell size in Arabidopsis Ler wild type and OE-HUB1 lines presented as log 2 transformed values.

FIG. 17 Silique area measurements of Arabidopsis Ler wild type, hub1-1 mutant and two overexpression HUB1 lines.

FIG. 18 Siliques of Ler wild type, hub1-1 mutant and HUB1 overexpression lines.

FIG. 19 Seed area measurements of Ler wild type, hub1-1 mutant and two HUB1 overexpression lines.

FIG. 20 Seed yield (grams of seeds per plant) for Ler wild type, the hub1-1 mutant and two HUB1 overexpression lines

FIG. 21A shows the effect on leaf width of HUB1 and HUB1pm overexpression in wild type (Ler) background; #1247 represents a HUB1 overexpressing line and #1249 is the HUB1pm overexpressing line. Untransformed Ler served as control. FIG. 21B shows that mature leaf width is affected by overexpressing HUB1pm in the hub1-1 mutant background. #1248 represents a WT HUB1 overexpressing line in a hub1-1 background, #1250 represent the HUB1pm overexpressing line in a hub1-1 background. Untransformed hub1-1 served as control. Numbers 1 to 11 represent the two cotyls and leaves 1 to 9 of the rosette.

FIGS. 22A-D Phenotypic characterization of sl-1 and sl-2 T-DNA insertion lines in comparison with Col-0 and hub1-4 mutant. FIG. 22A—Whole plant picture of all the four genotypes at WT, sl-1 and sl-2 flowering time (28 DAS). FIG. 22B—The flowering time analysis of the four lines evidences that hub1-4 flowers much earlier than the other ones (also shown in A) except for a very slight reduction in sl-2 On the other hand, the number of rosette leaves at flowering has a different trend for all the mutant lines since a significant reduction of it is reported for sl-1, sl-2 and hub1-4. FIG. 22C—Leaf area of sl-1 is severely reduced for almost all leaves whereas in the case of sl-2 the reduction is much less as just in few leaves the reduction was shown to be significant. Upper panel: bars in black are Col-0, bars in white are sl-1; bottom panel: bars in black are Col-0, bars in grey are sl-2. FIG. 22D—The flower stem diameter of sl-1 and sl-2 is also reduced compared to wild type plants. All Student's T-test performed with a level of significance of 5% (p=0.05).

EXAMPLES

The present invention will now be described with reference to the following examples, which are by way of illustration alone. The following examples are not intended to completely define or otherwise limit the scope of the invention.
DNA manipulation: unless otherwise stated, recombinant DNA techniques are performed according to standard protocols described in (Sambrook (2001) Molecular Cloning: a laboratory manual, 3rd Edition Cold Spring Harbor Laboratory Press, CSH, New York) or in Volumes 1 and 2 of Ausubel et al. (1994), Current Protocols in Molecular Biology, Current Protocols. Standard materials and methods for plant molecular work are described in Plant Molecular Biology Labfax (1993) by R. D. D. Croy, published by BIOS Scientific Publications Ltd (UK) and Blackwell Scientific Publications (UK).

Example 1

Identification of Sequences Related to the Nucleic Acid Sequence of SEQ ID NO: 1 or the Protein of SEQ ID NO: 2

Sequences (full length cDNA, ESTs or genomic) related to the nucleic acid sequence used in the methods of the present invention were identified amongst those maintained in the Entrez Nucleotides database at the National Center for Biotechnology Information (NCBI) using database sequence search tools, such as the Basic Local Alignment Tool (BLAST) (Altschul et al. (1990) J. Mol. Biol. 215:403-410; and Altschul et al. (1997) Nucleic Acids Res. 25:3389-3402). The program is used to find regions of local similarity between sequences by comparing nucleic acid or polypeptide sequences to sequence databases and by calculating the statistical significance of matches. For example, the polypeptide encoded by the nucleic acid used in the present invention was used for the TBLASTN algorithm, with default settings and the filter to ignore low complexity sequences set off. The output of the analysis was viewed by pairwise comparison, and ranked according to the probability score (E-value), where the score reflect the probability that a particular alignment occurs by chance (the lower the E-value, the more significant the hit). In addition to E-values, comparisons were also scored by percentage identity. Percentage identity refers to the number of identical nucleotides (or amino acids) between the two compared nucleic acid (or polypeptide) sequences over a particular length. In some instances, the default parameters may be adjusted to modify the stringency of the search. For example the E-value may be increased to show less stringent matches. This way, short nearly exact matches may be identified.
Table A provides a list of nucleic acid sequences related to the nucleic acid sequence of SEQ ID NO: 1 and the protein of SEQ ID NO: 2.

TABLE A

Examples of HUB1 polypeptides:

Identifier, Plant Source	Nucleic acid	Protein

At2g44950, Arabidopsis thaliana (HUB1)	SEQ ID NO: 1	SEQ ID NO: 2
scaff_40.53#1, Populus sp.	SEQ ID NO: 29	SEQ ID NO: 8
TA45131_4081#1, Solanum lycopersicum	SEQ ID NO: 30	SEQ ID NO: 9
LOC_Os04g46450.1#1, Oryza sativa	SEQ ID NO: 31	SEQ ID NO: 10
CAO70576.1, Vitis vinifera	SEQ ID NO: 32	SEQ ID NO: 11
EDQ74097.1, Physcomitrella patens subsp. patens	SEQ ID NO: 33	SEQ ID NO: 12
XP_001754625.1, Physcomitrella patens subsp. patens	SEQ ID NO: 34	SEQ ID NO: 13
XP_001777122.1, Physcomitrella patens subsp. patens	SEQ ID NO: 35	SEQ ID NO: 14
CAO22034.1, Vitis vinifera	SEQ ID NO: 36	SEQ ID NO: 15
AAL91211, Arabidopsis thaliana	SEQ ID NO: 37	SEQ ID NO: 16
AAG51572.1, Arabidopsis thaliana (HUB2)	SEQ ID NO: 38	SEQ ID NO: 17
ABE92765.2, Medicago truncatula	SEQ ID NO: 39	SEQ ID NO: 18
CAD41603.3, Oryza sativa (japonica cultivar-group)	SEQ ID NO: 40	SEQ ID NO: 19
ABB47997.1, Oryza sativa (japonica cultivar-group)	SEQ ID NO: 41	SEQ ID NO: 20
CAA98640.1, Saccharomyces cerevisiae (BRE1)	SEQ ID NO: 42	SEQ ID NO: 21
NP_587845.1, Schizosaccharomyces pombe	SEQ ID NO: 43	SEQ ID NO: 22
AAK21443.1, Caenorhabditis elegans	SEQ ID NO: 44	SEQ ID NO: 23
AAF50744.2, Drosophila melanogaster	SEQ ID NO: 45	SEQ ID NO: 24
BAB14005.1, Homo sapiens	SEQ ID NO: 46	SEQ ID NO: 25
AAH18647.1, Homo sapiens	SEQ ID NO: 47	SEQ ID NO: 26
AC144591, Medicago truncatula	SEQ ID NO: 48	SEQ ID NO: 27
At2g44950 Arabidopsis thaliana point mutation	SEQ ID NO: 49	SEQ ID NO: 28

In some instances, related sequences have tentatively been assembled and publicly disclosed by research institutions, such as The Institute for Genomic Research (TIGR). The Eukaryotic Gene Orthologs (EGO) database may be used to identify such related sequences, either by keyword search or by using the BLAST algorithm with the nucleic acid or polypeptide sequence of interest.

Example 2

Alignment of HUB1 Polypeptide Sequences

Alignment of polypeptide sequences was performed using the ClustalW 2.0 algorithm of progressive alignment (Larkin et al., Bioinformatics 23, 2947-2948, 2007). Default values are for the gap open penalty of 10, for the gap extension penalty of 0.1 and the selected weight matrix is Gonnet (if polypeptides are aligned). Minor manual editing may be done to further optimise the alignment. Sequence conservation among HUB1 polypeptides is essentially in the C-terminal RING domain of the polypeptides, the N-terminal domain usually being more variable in sequence length and composition. The HUB1 polypeptides are aligned in FIG. 2.
A phylogenetic tree of HUB1 polypeptides (FIG. 3) was constructed from the alignment using a neighbour-joining clustering algorithm as provided in the ClustalW 2.0 program. The figures give the bootstrap values for 1000 repetitions.

Example 3

Calculation of Global Percentage Identity Between HUB1 Polypeptide Sequences

Global percentages of similarity and identity between full length polypeptide sequences useful in performing the methods of the invention were determined using one of the methods available in the art, the MatGAT (Matrix Global Alignment Tool) software (BMC Bioinformatics. 2003 4:29. MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences. Campanella J J, Bitincka L, Smalley J; software hosted by Ledion Bitincka). MatGAT software generates similarity/identity matrices for DNA or protein sequences without needing pre-alignment of the data. The program performs a series of pair-wise alignments using the Myers and Miller global alignment algorithm (with a gap opening penalty of 12, and a gap extension penalty of 2), calculates similarity and identity using for example Blosum 62 (for polypeptides), and then places the results in a distance matrix. Sequence similarity is shown in the bottom half of the dividing line and sequence identity is shown in the top half of the diagonal dividing line.
Parameters used in the comparison were:

- Scoring matrix: Blosum62
- First Gap: 12
- Extending gap: 2

Results of the software analysis are shown in Table B1 for the global similarity and identity over the full length of the polypeptide sequences. Percentage identity is given above the diagonal and percentage similarity is given below the diagonal.
The percentage identity between the HUB1 polypeptide sequences useful in performing the methods of the invention can be as low as 18% amino acid identity compared to SEQ ID NO: 2 (At2g44950); however, when only the RING domains are compared the identity is much higher (Table B2). It should be noted however that yeast BRE1 (CAA98640), the functional orthologue of HUB1 (At2g44950) has only 18.6% sequence identity with HUB1.

TABLE B1

MatGAT results for global similarity and identity over
the full length of the HUB1 polypeptide sequences.

	1	2	3	4	5	6	7	8	9	10	11

1. At2g44950		54.5	37.0	43.2	33.1	56.2	35.3	35.1	34.5	19.0	99.9
2. scaff_40.53	72.8		40.3	45.5	37.0	66.2	35.7	35.4	34.5	21.2	54.5
3. TA45131_4081	49.2	52.3		33.1	54.2	46.1	29.2	25.4	25.2	15.2	37.1
4. LOC_Os04g46450	63.3	65.8	47.2		30.7	49.0	32.6	33.2	31.8	19.1	43.3
5. AC144591	47.7	48.6	71.4	45.6		39.9	26.8	24.0	24.5	14.0	33.1
6. CAO70576	73.9	81.5	54.7	69.3	51.3		36.6	35.9	33.8	21.3	56.2
7. EDQ74097	58.8	58.8	46.8	55.4	43.7	59.1		47.2	47.4	23.5	35.2
8. XP_001754625	58.0	57.6	42.1	55.4	38.9	59.0	66.6		64.2	22.0	35.0
9. XP_001777122	59.0	56.6	41.4	54.6	39.6	58.4	66.4	77.3		20.6	34.5
10. CAO22034	30.6	32.6	23.4	30.3	22.3	33.2	33.9	33.3	32.9		19.1
11. AAL91211	100.0	72.8	49.2	63.3	47.7	73.9	58.8	57.8	59.0	30.6
12. AAG51572	52.4	55.5	39.7	52.3	37.5	57.0	57.5	56.5	55.5	43.0	52.4
13. ABE92765	49.7	50.1	71.9	46.7	95.3	52.4	45.5	40.5	40.6	23.4	49.7
14. CAD41603	59.7	61.4	44.4	94.1	43.6	64.9	52.0	53.1	51.6	28.8	59.7
15. ABB47997	50.9	54.8	42.7	51.8	39.3	55.9	65.0	57.2	56.8	40.1	50.9
16. CAA98640	38.7	38.6	40.4	38.0	39.6	38.0	37.6	36.2	37.3	23.2	38.7
17. NP_587845	38.2	37.1	41.3	37.4	42.1	36.0	39.4	38.9	37.3	21.4	38.6
18. AAK21443	42.4	41.0	37.6	39.1	34.2	41.9	42.2	42.1	42.6	25.7	42.4
19. AAF50744	40.4	40.2	31.3	39.7	29.6	41.4	38.3	40.9	40.1	29.7	40.4
20. BAB14005	39.3	41.4	40.3	40.4	38.5	41.6	42.1	41.7	41.3	24.7	39.3
21. AAH18647	40.9	41.8	32.1	41.1	29.1	41.9	41.2	43.3	43.2	28.7	40.9

	12	13	14	15	16	17	18	19	20	21

1. At2g44950	29.3	34.4	38.2	29.4	18.6	18.2	20.5	19.9	20.6	22.7
2. scaff_40.53	31.9	38.2	40.4	32.3	19.4	18.7	20.1	21.4	21.6	21.9
3. TA45131_4081	24.4	53.3	29.3	26.4	18.1	19.0	19.6	17.8	21.6	18.9
4. LOC_Os04g46450	30.5	31.4	89.0	30.9	19.6	19.3	19.3	19.1	21.0	21.7
5. AC144591	21.6	94.5	28.9	23.6	19.5	20.0	16.7	15.6	22.2	17.2
6. CAO70576	33.4	40.9	43.7	34.2	18.9	19.2	20.4	21.0	22.0	21.7
7. EDQ74097	38.4	27.7	29.3	41.5	17.8	20.6	19.7	22.3	23.5	24.1
8. XP_001754625	34.7	25.0	30.8	36.0	18.9	20.0	21.6	23.8	22.9	24.8
9. XP_001777122	32.1	25.3	28.9	33.3	16.6	17.0	21.2	20.2	22.0	23.8
10. CAO22034	34.4	14.9	17.8	30.1	13.6	12.5	13.5	16.1	14.0	16.4
11. AAL91211	29.3	34.4	38.4	29.4	18.6	18.5	20.6	19.8	20.5	22.6
12. AAG51572		23.7	27.3	46.4	19.0	19.0	21.2	21.2	21.4	20.8
13. ABE92765	39.0		29.6	25.1	18.6	20.4	18.1	15.7	23.2	19.3
14. CAD41603	49.3	44.3		27.5	19.1	18.7	20.2	19.1	20.1	21.3
15. ABB47997	67.6	41.2	49.2		18.5	20.1	18.7	20.2	21.3	20.9
16. CAA98640	37.9	39.6	37.4	37.7		23.8	19.5	18.4	20.2	18.3
17. NP_587845	36.4	39.1	37.5	39.8	45.6		19.2	18.4	19.2	17.5
18. AAK21443	39.4	35.4	39.4	41.9	38.4	38.1		22.8	24.3	22.9
19. AAF50744	40.6	30.0	39.9	38.9	33.7	33.7	41.9		36.2	43.8
20. BAB14005	41.7	39.1	38.8	43.1	41.7	39.8	43.5	50.6		47.3
21. AAH18647	41.1	30.8	40.0	40.5	35.3	33.3	42.4	61.9	58.5

TABLE B2

MatGAT results for similarity and identity over the RING domains of the HUB1 polypeptide sequences.

	1	2	3	4	5	6	7	8	9	10	11

1. XP_001754625		73.7	81.6	81.6	78.9	86.8	65.8	65.8	63.2	63.2	76.3
2. XP_001777122	86.8		71.1	68.4	65.8	71.1	55.3	55.3	50.0	50.0	68.4
3. EDQ74097	92.1	81.6		81.6	73.7	84.2	63.2	63.2	57.9	57.9	71.1
4. CAO22034	86.8	76.3	86.8		89.5	89.5	68.4	68.4	65.8	65.8	76.3
5. AAG51572	84.2	76.3	81.6	92.1		86.8	71.1	71.1	60.5	60.5	71.1
6. ABB47997	92.1	81.6	86.8	94.7	92.1		65.8	65.8	63.2	63.2	73.7
7. LOC_Os04g46450	78.9	76.3	81.6	81.6	78.9	81.6		100.0	68.4	68.4	65.8
8. CAD41603	78.9	76.3	81.6	81.6	78.9	81.6	100.0		68.4	68.4	65.8
9. At2g44950	73.7	71.1	73.7	73.7	68.4	76.3	81.6	81.6		100.0	65.8
10. AAL91211	73.7	71.1	73.7	73.7	68.4	76.3	81.6	81.6	100.0		65.8
11. scaff_40.53	84.2	84.2	81.6	81.6	76.3	84.2	76.3	76.3	78.9	78.9
12. CAO70576	84.2	81.6	84.2	86.8	81.6	89.5	81.6	81.6	81.6	81.6	92.1
13. TA45131_4081	78.9	76.3	76.3	78.9	73.7	78.9	71.1	71.1	71.1	71.1	84.2
14. AC144591	81.6	71.1	73.7	71.1	68.4	73.7	81.6	81.6	81.6	81.6	78.9
15. ABE92765	81.6	71.1	73.7	71.1	68.4	73.7	81.6	81.6	81.6	81.6	78.9
16. BAB14005	63.2	65.8	65.8	60.5	63.2	63.2	71.1	71.1	68.4	68.4	68.4
17. AAH18647	63.2	65.8	65.8	60.5	63.2	63.2	71.1	71.1	65.8	65.8	68.4
18. AAF50744	65.8	63.2	63.2	60.5	60.5	63.2	65.8	65.8	68.4	68.4	68.4
19. AAK21443	63.2	57.9	60.5	65.8	68.4	63.2	60.5	60.5	71.1	71.1	68.4
20. CAA98640	52.6	50.0	55.3	50.0	52.6	50.0	55.3	55.3	52.6	52.6	52.6
21. NP_587845	66.7	66.7	69.2	64.1	66.7	66.7	69.2	69.2	64.1	64.1	71.8

	12	13	14	15	16	17	18	19	20	21

1. XP_001754625	68.4	65.8	68.4	68.4	44.7	47.4	42.1	47.4	42.1	48.7
2. XP_001777122	57.9	52.6	55.3	55.3	39.5	42.1	36.8	44.7	34.2	43.6
3. EDQ74097	65.8	60.5	63.2	63.2	50.0	52.6	47.4	47.4	42.1	51.3
4. CAO22034	73.7	68.4	65.8	65.8	42.1	44.7	42.1	50.0	39.5	48.7
5. AAG51572	68.4	63.2	63.2	63.2	42.1	44.7	42.1	50.0	39.5	51.3
6. ABB47997	71.1	63.2	63.2	63.2	47.4	50.0	44.7	47.4	39.5	48.7
7. LOC_Os04g46450	68.4	60.5	76.3	76.3	44.7	44.7	39.5	47.4	36.8	51.3
8. CAD41603	68.4	60.5	76.3	76.3	44.7	44.7	39.5	47.4	36.8	51.3
9. At2g44950	68.4	60.5	71.1	71.1	52.6	50.0	42.1	50.0	36.8	46.2
10. AAL91211	68.4	60.5	71.1	71.1	52.6	50.0	42.1	50.0	36.8	46.2
11. scaff_40.53	78.9	76.3	76.3	76.3	47.4	50.0	44.7	50.0	39.5	46.2
12. CAO70576		65.8	68.4	68.4	47.4	52.6	42.1	47.4	39.5	46.2
13. TA45131_4081	81.6		68.4	68.4	42.1	42.1	44.7	44.7	31.6	46.2
14. AC144591	78.9	73.7		100.0	47.4	47.4	42.1	50.0	39.5	48.7
15. ABE92765	78.9	73.7	100.0		47.4	47.4	42.1	50.0	39.5	48.7
16. BAB14005	65.8	60.5	68.4	68.4		86.8	71.1	63.2	42.1	43.6
17. AAH18647	68.4	57.9	68.4	68.4	92.1		71.1	55.3	42.1	46.2
18. AAF50744	63.2	63.2	71.1	71.1	94.7	86.8		60.5	39.5	51.3
19. AAK21443	65.8	60.5	73.7	73.7	76.3	73.7	81.6		39.5	46.2
20. CAA98640	55.3	50.0	57.9	57.9	50.0	52.6	50.0	47.4		43.6
21. NP_587845	69.2	69.2	66.7	66.7	69.2	66.7	66.7	56.4	64.1

Example 4

Identification of Domains Comprised in HUB1 Polypeptide Sequences

The Integrated Resource of Protein Families, Domains and Sites (InterPro) database is an integrated interface for the commonly used signature databases for text- and sequence-based searches. The InterPro database combines these databases, which use different methodologies and varying degrees of biological information about well-characterized proteins to derive protein signatures. Collaborating databases include SWISS-PROT, PROSITE, TrEMBL, PRINTS, ProDom and Pfam, Smart and TIGRFAMs. Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families. Pfam is hosted at the Sanger Institute server in the United Kingdom. Interpro is hosted at the European Bioinformatics Institute in the United Kingdom.
The results of the InterPro scan of the polypeptide sequence as represented by SEQ ID NO: 2 are presented in Table C.

TABLE C

InterPro scan results (major accession numbers) of the
polypeptide sequence as represented by SEQ ID NO: 2.

			Amino acid
	Accession		coordinates on
Database	number	Accession name	SEQ ID NO 2

InterPro	IPR001093	IMP dehydrogenase/GMP
		reductase
HMMPfam	PF00478.12	IMP dehydrogenase/GMP	368-761
		reductase domainT
InterPro	IPR001841	Zn-finger, RING
HMMPfam	PF00097.11	Zinc finger, C3HC4 type	826-864
		(RING finger)
HMMSmart	SM00184	no description	826-864
ProfileScan	PS50089	ZF_RING_2	826-865
ScanRegExp	PS00518	ZF_RING_1	841-850
InterPro	IPR009054	Eukaryotic DNA
		topoisomerases I,
		dispensable insert
superfamily	SSF46596	Eukaryotic DNA	598-664
		topoisomerase I,
		dispensable insert domainT
InterPro	IPR011072	Protein kinase PKN/PRK1,
		effector
superfamily	SSF46585	Effector domain of the	394-477
		protein kinase pkn/prk1T
superfamily	SSF57850	RING/U-box	803-877

Example 5

Topology Prediction of the HUB1 Polypeptide Sequences

TargetP 1.1 predicts the subcellular location of eukaryotic proteins. The location assignment is based on the predicted presence of any of the N-terminal pre-sequences: chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP) or secretory pathway signal peptide (SP). Scores on which the final prediction is based are not really probabilities, and they do not necessarily add to one. However, the location with the highest score is the most likely according to TargetP, and the relationship between the scores (the reliability class) may be an indication of how certain the prediction is. The reliability class (RC) ranges from 1 to 5, where 1 indicates the strongest prediction. TargetP is maintained at the server of the Technical University of Denmark.
For the sequences predicted to contain an N-terminal presequence a potential cleavage site can also be predicted.
A number of parameters were selected, such as organism group (non-plant or plant), cutoff sets (none, predefined set of cutoffs, or user-specified set of cutoffs), and the calculation of prediction of cleavage sites (yes or no).
The results of TargetP 1.1 analysis of the polypeptide sequence as represented by SEQ ID NO: 2 are presented Table D. The “plant” organism group has been selected, no cutoffs defined, and the predicted length of the transit peptide requested. The subcellular localization of the polypeptide sequence as represented by SEQ ID NO: 2 may be the cytoplasm or nucleus, no transit peptide is predicted. Localisation experiments revealed that HUB1 is present in the nucleus (Liu et al., 2007).

TABLE D

TargetP 1.1 analysis of the polypeptide
sequence as represented by SEQ ID NO: 2

	Length (AA)	878
	Chloroplastic transit peptide	0.133
	Mitochondrial transit peptide	0.342
	Secretory pathway signal peptide	0.017
	Other subcellular targeting	0.635
	Predicted Location	/
	Reliability class	4
	Predicted transit peptide length	/

Many other algorithms can be used to perform such analyses, including:

- ChloroP 1.1 hosted on the server of the Technical University of Denmark;
- Protein Prowler Subcellular Localisation Predictor version 1.2 hosted on the server of the Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia;
- PENCE Proteome Analyst PA-GOSUB 2.5 hosted on the server of the University of Alberta, Edmonton, Alberta, Canada;
- TMHMM, hosted on the server of the Technical University of Denmark
- PSORT (URL: psort.org)
- PLOC (Park and Kanehisa, Bioinformatics, 19, 1656-1663, 2003).

Example 6

Functional Assay for the HUB1 Polypeptide

Based on sequence homologies, HUB1 had been previously identified as a BRE1 homolog (Hwang et al., 2003; Stone et al., 2005, Fleury et al., 2007). To confirm the suggested function as H2B monoubiquitinating E3 ligase, a series of in vitro ubiquitination assays were performed with epitope tagged recombinant HUB1 protein. In such type of assay, functional BRE1 E3 ligase is expected to ligate one ubiquitin molecule on histone H2B, causing a corresponding increase in H2B molecular weight (Zhu et al., Molecular Cell 20, 601-611, 2005).
cDNAs encoding HUB1 and the point mutated from (HUB1pm) were cloned into recombinant expression vectors with a GST or His epitope tags to allow purification with affinity chromatography. The GST-tagged protein was expressed in many fragments by E coil and the His-tagged protein was precipitated in inclusion bodies. The insoluble His-tagged protein fraction was purified and refolded through a dialysis series with decreasing urea concentrations and bound to NiNTA beads (Invitrogen) in refolding buffer. During the HUB1 refolding the protein formed high molecular weight complexes suggesting that it forms dimers. This data is indicative that also in plants HUB1 activity may depend on homo- or heterodimerization as described for human Bret homologs (Zhu et al., 2005).
The purified proteins were subjected for self-ubiquitination assays in in vitro (auto)ubiquitination assays as well as histone H2B ubiquitination assays as described in Fleury et al., (2007). In this assay the purified HUB1 E3 ligase was combined with ubiquitin activating and conjugating enzymes (E1 and E2, respectively) and Ubiquitin in ATP containing buffer and was incubated for 1 hr at 37° C. with agitation. The reactions were stopped by boiling in SDS loading buffer and separated on 6% SDS-PAGE and transferred on membranes for hybridization with anti histone H2B or anti HA (against HA tagged ubiquitin) antibodies. The hybridization signals were detected by ECL (GE Healthcare) reagents and visualized on autoradiographic film (Amersham Hyperfilm ECL, GE Healthcare). Both His and GST protein fractions were enzymatically active and mediated histone H2B monoubiquitination in the in vitro ubiquitination assays (FIG. 5).
Both HUB1 and HUB1pm mediated monoubiquitination of histone H2B (17 kDa) that was seen as shift of H2B by 10 kDa in the protein gel blot (FIG. 5, HA-Ab below). This band of 27 kDa was reactive to both the H2B specific antibody and the HA antibody that detected the HA tagged ubiquitin. In the absence of E1, E2 or Ub, no shift in H2B migration was observed. Similar results were obtained in ubiquitination reactions with His tagged HUB1. Taken together these data confirmed that HUB1 is a functional homolog of human and yeast BRE1 proteins. Interestingly the point mutations (HUBpm) in the RING domain did not abolish the H2B monoubiquitination activity of HUB1.
In the histone H2B monoubiquitination assays with full length HUB1 and the point mutated form autoregulation of HUB1 was observed as high molecular weight modifications of the protein (FIG. 5, HA-Ab, above). These modifications were reactive to ubiquitin antibody suggesting that HUB1 has autopolyubiquitination activity. The pointmutations in the RING domain appeared to reduce the autopolyubiquitination activity as indicated by reduced levels of these modifications on the western blots (FIG. 5, HA-Ab, above). The equal loading of GST-HUB1 is shown by GST Ab (FIG. 5, GST-Ab). These data confirmed that the RING domain was required for the autoubiquitination activity.

Example 7

Cloning of the Nucleic Acid Sequence of SEQ ID NO: 1 for Rice Transformation

The HUB1 encoding nucleic acid sequence used in the methods of the invention was amplified by PCR using as template a custom-made Arabidopsis thaliana seedlings cDNA library (in pCMV Sport 6.0; Invitrogen, Paisley, UK). PCR was performed using Hifi Taq DNA polymerase in standard conditions, using 200 ng of template in a 50 μl PCR mix. The primers used were prm09774 (SEQ ID NO: 3; sense, start codon in bold): 5′-ggggacaagtttg tacaaaaaagcaggcttaaacaatggcgagcacaggcg-3′ and prm09775 (SEQ ID NO: 4; reverse, complementary): 5′-ggggaccactttgtacaagaaagctgggttcatatgtagatag gtttaatatcattt-3′, which include the AttB sites for Gateway recombination. The amplified PCR fragment was purified also using standard methods. The first step of the Gateway procedure, the BP reaction, was then performed, during which the PCR fragment recombines in vivo with the pDONR201 plasmid to produce, according to the Gateway terminology, an “entry clone”, pHUB1. Plasmid pDONR201 was purchased from Invitrogen, as part of the Gateway® technology.
The entry clone comprising SEQ ID NO: 1 was then used in an LR reaction with a destination vector used for Oryza sativa transformation. This vector contained as functional elements within the T-DNA borders: a plant selectable marker; a screenable marker expression cassette; and a Gateway cassette intended for LR in vivo recombination with the nucleic acid sequence of interest already cloned in the entry clone. A rice HMGP promoter (SEQ ID NO: 6) for constitutive expression was located upstream of this Gateway cassette.
After the LR recombination step, the resulting expression vector pHMGP::HUB1 (FIG. 4) was transformed into Agrobacterium strain LBA4044 according to methods well known in the art.
In a similar way, other genes disclosed in this invention can be cloned using primers comprising AttB sites for Gateway recombination. Design of such primers is known to persons skilled in the art.

Example 8

Plant Transformation

Rice Transformation

The Agrobacterium containing the expression vector was used to transform Oryza sativa plants. Mature dry seeds of the rice japonica cultivar Nipponbare were dehusked. Sterilization was carried out by incubating for one minute in 70% ethanol, followed by 30 minutes in 0.2% HgCl₂, followed by a 6 times 15 minutes wash with sterile distilled water. The sterile seeds were then germinated on a medium containing 2,4-D (callus induction medium). After incubation in the dark for four weeks, embryogenic, scutellum-derived calli were excised and propagated on the same medium. After two weeks, the calli were multiplied or propagated by subculture on the same medium for another 2 weeks. Embryogenic callus pieces were sub-cultured on fresh medium 3 days before co-cultivation (to boost cell division activity).
Agrobacterium strain LBA4404 containing the expression vector was used for co-cultivation. Agrobacterium was inoculated on AB medium with the appropriate antibiotics and cultured for 3 days at 28° C. The bacteria were then collected and suspended in liquid co-cultivation medium to a density (OD₆₀₀) of about 1. The suspension was then transferred to a Petri dish and the calli immersed in the suspension for 15 minutes. The callus tissues were then blotted dry on a filter paper and transferred to solidified, co-cultivation medium and incubated for 3 days in the dark at 25° C. Co-cultivated calli were grown on 2,4-D-containing medium for 4 weeks in the dark at 28° C. in the presence of a selection agent. During this period, rapidly growing resistant callus islands developed. After transfer of this material to a regeneration medium and incubation in the light, the embryogenic potential was released and shoots developed in the next four to five weeks. Shoots were excised from the calli and incubated for 2 to 3 weeks on an auxin-containing medium from which they were transferred to soil. Hardened shoots were grown under high humidity and short days in a greenhouse.
Approximately 35 independent T0 rice transformants were generated for one construct. The primary transformants were transferred from a tissue culture chamber to a greenhouse. After a quantitative PCR analysis to verify copy number of the T-DNA insert, only single copy transgenic plants that exhibit tolerance to the selection agent were kept for harvest of T1 seed. Seeds were then harvested three to five months after transplanting. The method yielded single locus transformants at a rate of over 50% (Aldemita and Hodges 1996, Chan et al. 1993, Hiei et al. 1994).

Corn Transformation

Transformation of maize (Zea mays) is performed with a modification of the method described by Ishida et al. (1996) Nature Biotech 14(6): 745-50. Transformation is genotype-dependent in corn and only specific genotypes are amenable to transformation and regeneration. The inbred line A188 (University of Minnesota) or hybrids with A188 as a parent are good sources of donor material for transformation, but other genotypes can be used successfully as well. Ears are harvested from corn plant approximately 11 days after pollination (DAP) when the length of the immature embryo is about 1 to 1.2 mm. Immature embryos are cocultivated with Agrobacterium tumefaciens containing the expression vector, and transgenic plants are recovered through organogenesis. Excised embryos are grown on callus induction medium, then maize regeneration medium, containing the selection agent (for example imidazolinone but various selection markers can be used). The Petri plates are incubated in the light at 25° C. for 2-3 weeks, or until shoots develop. The green shoots are transferred from each embryo to maize rooting medium and incubated at 25° C. for 2-3 weeks, until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Wheat Transformation

Transformation of wheat is performed with the method described by Ishida et al. (1996) Nature Biotech 14(6): 745-50. The cultivar Bobwhite (available from CIMMYT, Mexico) is commonly used in transformation. Immature embryos are co-cultivated with Agrobacterium tumefaciens containing the expression vector, and transgenic plants are recovered through organogenesis. After incubation with Agrobacterium, the embryos are grown in vitro on callus induction medium, then regeneration medium, containing the selection agent (for example imidazolinone but various selection markers can be used). The Petri plates are incubated in the light at 25° C. for 2-3 weeks, or until shoots develop. The green shoots are transferred from each embryo to rooting medium and incubated at 25° C. for 2-3 weeks, until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Soybean Transformation

Soybean is transformed according to a modification of the method described in the Texas A&M patent U.S. Pat. No. 5,164,310. Several commercial soybean varieties are amenable to transformation by this method. The cultivar Jack (available from the Illinois Seed foundation) is commonly used for transformation. Soybean seeds are sterilised for in vitro sowing. The hypocotyl, the radicle and one cotyledon are excised from seven-day old young seedlings. The epicotyl and the remaining cotyledon are further grown to develop axillary nodes. These axillary nodes are excised and incubated with Agrobacterium tumefaciens containing the expression vector. After the cocultivation treatment, the explants are washed and transferred to selection media. Regenerated shoots are excised and placed on a shoot elongation medium. Shoots no longer than 1 cm are placed on rooting medium until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Rapeseed/Canola Transformation

Cotyledonary petioles and hypocotyls of 5-6 day old young seedling are used as explants for tissue culture and transformed according to Babic et al. (1998, Plant Cell Rep 17: 183-188). The commercial cultivar Westar (Agriculture Canada) is the standard variety used for transformation, but other varieties can also be used. Canola seeds are surface-sterilized for in vitro sowing. The cotyledon petiole explants with the cotyledon attached are excised from the in vitro seedlings, and inoculated with Agrobacterium (containing the expression vector) by dipping the cut end of the petiole explant into the bacterial suspension. The explants are then cultured for 2 days on MSBAP-3 medium containing 3 mg/l BAP, 3% sucrose, 0.7% Phytagar at 23° C., 16 hr light. After two days of co-cultivation with Agrobacterium, the petiole explants are transferred to MSBAP-3 medium containing 3 mg/l BAP, cefotaxime, carbenicillin, or timentin (300 mg/l) for 7 days, and then cultured on MSBAP-3 medium with cefotaxime, carbenicillin, or timentin and selection agent until shoot regeneration. When the shoots are 5-10 mm in length, they are cut and transferred to shoot elongation medium (MSBAP-0.5, containing 0.5 mg/l BAP). Shoots of about 2 cm in length are transferred to the rooting medium (MS0) for root induction. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Alfalfa Transformation

A regenerating clone of alfalfa (Medicago sativa) is transformed using the method of (McKersie et al., 1999 Plant Physiol 119: 839-847). Regeneration and transformation of alfalfa is genotype dependent and therefore a regenerating plant is required. Methods to obtain regenerating plants have been described. For example, these can be selected from the cultivar Rangelander (Agriculture Canada) or any other commercial alfalfa variety as described by Brown D C W and A Atanassov (1985. Plant Cell Tissue Organ Culture 4: 111-112). Alternatively, the RA3 variety (University of Wisconsin) has been selected for use in tissue culture (Walker et al., 1978 Am J Bot 65:654-659). Petiole explants are cocultivated with an overnight culture of Agrobacterium tumefaciens C58C1 pMP90 (McKersie et al., 1999 Plant Physiol 119: 839-847) or LBA4404 containing the expression vector. The explants are cocultivated for 3 d in the dark on SH induction medium containing 288 mg/L Pro, 53 mg/L thioproline, 4.35 g/L K2SO4, and 100 μm acetosyringinone. The explants are washed in half-strength Murashige-Skoog medium (Murashige and Skoog, 1962) and plated on the same SH induction medium without acetosyringinone but with a suitable selection agent and suitable antibiotic to inhibit Agrobacterium growth. After several weeks, somatic embryos are transferred to BOi2Y development medium containing no growth regulators, no antibiotics, and 50 g/L sucrose. Somatic embryos are subsequently germinated on half-strength Murashige-Skoog medium. Rooted seedlings were transplanted into pots and grown in a greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Cotton Transformation

Cotton is transformed using Agrobacterium tumefaciens according to the method described in U.S. Pat. No. 5,159,135. Cotton seeds are surface sterilised in 3% sodium hypochlorite solution during 20 minutes and washed in distilled water with 500 μg/ml cefotaxime. The seeds are then transferred to SH-medium with 50 μg/ml benomyl for germination. Hypocotyls of 4 to 6 days old seedlings are removed, cut into 0.5 cm pieces and are placed on 0.8% agar. An Agrobacterium suspension (approx. 108 cells per ml, diluted from an overnight culture transformed with the gene of interest and suitable selection markers) is used for inoculation of the hypocotyl explants. After 3 days at room temperature and lighting, the tissues are transferred to a solid medium (1.6 g/l Gelrite) with Murashige and Skoog salts with B5 vitamins (Gamborg et al., Exp. Cell Res. 50:151-158 (1968)), 0.1 mg/l 2,4-D, 0.1 mg/l 6-furfurylaminopurine and 750 μg/ml MgCL2, and with 50 to 100 μg/ml cefotaxime and 400-500 μg/ml carbenicillin to kill residual bacteria. Individual cell lines are isolated after two to three months (with subcultures every four to six weeks) and are further cultivated on selective medium for tissue amplification (30° C., 16 hr photoperiod). Transformed tissues are subsequently further cultivated on non-selective medium during 2 to 3 months to give rise to somatic embryos. Healthy looking embryos of at least 4 mm length are transferred to tubes with SH medium in fine vermiculite, supplemented with 0.1 mg/l indole acetic acid, 6 furfurylaminopurine and gibberellic acid. The embryos are cultivated at 30° C. with a photoperiod of 16 hrs, and plantlets at the 2 to 3 leaf stage are transferred to pots with vermiculite and nutrients. The plants are hardened and subsequently moved to the greenhouse for further cultivation.

Example 9

Phenotypic Evaluation Procedure for Rice Transformed with SEQ ID NO: 1

9.1 Evaluation Setup

Approximately 35 independent T0 rice transformants were generated. The primary transformants were transferred from a tissue culture chamber to a greenhouse for growing and harvest of T1 seed. Six events, of which the T1 progeny segregated 3:1 for presence/absence of the transgene, were retained. For each of these events, approximately 10 T1 seedlings containing the transgene (hetero- and homo-zygotes) and approximately 10 T1 seedlings lacking the transgene (nullizygotes) were selected by monitoring visual marker expression. The transgenic plants and the corresponding nullizygotes were grown side-by-side at random positions. Greenhouse conditions were of shorts days (12 hours light), 28° C. in the light and 22° C. in the dark, and a relative humidity of 70%. Plants grown under non-stress conditions were watered at regular intervals to ensure that water and nutrients were not limiting to satisfy plant needs to complete growth and development.
Four T1 events were further evaluated in the T2 generation following the same evaluation procedure as for the T1 generation but with more individuals per event. From the stage of sowing until the stage of maturity the plants were passed several times through a digital imaging cabinet. At each time point digital images (2048×1536 pixels, 16 million colours) were taken of each plant from at least 6 different angles.

Drought Screen

Plants from T2 seeds are grown in potting soil under normal conditions until they approach the heading stage. They are then transferred to a “dry” section where irrigation is withheld. Humidity probes are inserted in randomly chosen pots to monitor the soil water content (SWC). When SWC goes below certain thresholds, the plants are automatically re-watered continuously until a normal level is reached again. The plants are then re-transferred again to normal conditions. The rest of the cultivation (plant maturation, seed harvest) is the same as for plants not grown under abiotic stress conditions. Growth and yield parameters are recorded as detailed for growth under normal conditions.

Nitrogen Use Efficiency Screen

Rice plants from T2 seeds are grown in potting soil under normal conditions except for the nutrient solution. The pots are watered from transplantation to maturation with a specific nutrient solution containing reduced N nitrogen (N) content, usually between 7 to 8 times less. The rest of the cultivation (plant maturation, seed harvest) is the same as for plants not grown under abiotic stress. Growth and yield parameters are recorded as detailed for growth under normal conditions.

Salt Stress Screen

Plants are grown on a substrate made of coco fibers and argex (3 to 1 ratio). A normal nutrient solution is used during the first two weeks after transplanting the plantlets in the greenhouse. After the first two weeks, 25 mM of salt (NaCl) is added to the nutrient solution, until the plants are harvested. Growth and yield parameters are then measured.

9.2 Statistical Analysis: F Test

A two factor ANOVA (analysis of variants) was used as a statistical model for the overall evaluation of plant phenotypic characteristics. An F test was carried out on all the parameters measured of all the plants of all the events transformed with the gene of the present invention. The F test was carried out to check for an effect of the gene over all the transformation events and to verify for an overall effect of the gene, also known as a global gene effect. The threshold for significance for a true global gene effect was set at a 5% probability level for the F test. A significant F test value points to a gene effect, meaning that it is not only the mere presence or position of the gene that is causing the differences in phenotype.
Because two experiments with overlapping events were carried out, a combined analysis was performed. This is useful to check consistency of the effects over the two experiments, and if this is the case, to accumulate evidence from both experiments in order to increase confidence in the conclusion. The method used was a mixed-model approach that takes into account the multilevel structure of the data (i.e. experiment-event-segregants). P values were obtained by comparing likelihood ratio test to chi square distributions.

9.3 Parameters Measured

Biomass-Related Parameter Measurement

From the stage of sowing until the stage of maturity the plants were passed several times through a digital imaging cabinet. At each time point digital images (2048×1536 pixels, 16 million colours) were taken of each plant from at least 6 different angles.
The plant aboveground area (or leafy biomass) was determined by counting the total number of pixels on the digital images from aboveground plant parts discriminated from the background. This value was averaged for the pictures taken on the same time point from the different angles and was converted to a physical surface value expressed in square mm by calibration. Experiments show that the aboveground plant area measured this way correlates with the biomass of plant parts above ground. The above ground area is the area measured at the time point at which the plant had reached its maximal leafy biomass. The early vigour is the plant (seedling) aboveground area three weeks post-germination. Increase in root biomass is expressed as an increase in total root biomass (measured as maximum biomass of roots observed during the lifespan of a plant); or as an increase in the root/shoot index (measured as the ratio between root mass and shoot mass in the period of active growth of root and shoot).
Early vigour was determined by counting the total number of pixels from aboveground plant parts discriminated from the background. This value was averaged for the pictures taken on the same time point from different angles and was converted to a physical surface value expressed in square mm by calibration. The results are for plants three weeks post-germination. Germination vigour is measured as the number of germinating seeds after one, two or three days after sowing, compared to control plants.

Seed-Related Parameter Measurements

The mature primary panicles were harvested, counted, bagged, barcode-labelled and then dried for three days in an oven at 37° C. The panicles were then threshed and all the seeds were collected and counted. The filled husks were separated from the empty ones using an air-blowing device. The empty husks were discarded and the remaining fraction was counted again. The filled husks were weighed on an analytical balance. The number of filled seeds was determined by counting the number of filled husks that remained after the separation step. The total seed yield was measured by weighing all filled husks harvested from a plant. Total seed number per plant was measured by counting the number of husks harvested from a plant. Thousand Kernel Weight (TKW) is extrapolated from the number of filled seeds counted and their total weight. The Harvest Index (HI) in the present invention is defined as the ratio between the total seed yield and the above ground area (mm²), multiplied by a factor 10⁶. The total number of flowers per panicle as defined in the present invention is the ratio between the total number of seeds and the number of mature primary panicles. The seed fill rate as defined in the present invention is the proportion (expressed as a %) of the number of filled seeds over the total number of seeds (or florets).

Example 10

Results of the Phenotypic Evaluation of the Transgenic Rice Plants

The results of the evaluation of transgenic rice plants expressing a HUB1 nucleic acid under non-stress conditions are presented below in Table E. An increase of more than 5% was observed for emergence vigour (early vigour), total weight of seeds (total seed yield), number of filled seeds, and total number of seeds.

TABLE E

improved growth parameters in transgenic rice expressing
HUB1 under control of a medium strength promoter (HMGP):

	% increase in	% increase in	p-value
Parameter	T1 generation	T2 generation	combined analysis

Emergence vigour	18.9	35.8	0.007
Total weight of	21.6	24.6	0.006
seeds
Nr filled seeds	20.6	24.6	0.006
Total nr seeds	13.8	22.7	0.021

When grown under stress conditions, the transgenic rice plants expressing HUB1 show, compared to control plants, in increase in one or more of the following parameters: aboveground area (or leafy biomass), early vigour, germination vigour, root biomass, total number of seeds, number of filled seeds, total seed yield (total weight of seeds), Thousand Kernel Weight, Harvest Index, number of flowers per panicle.

Example 11

Comparison of Promoter Activity in Rice

Rice plants were transformed with the GUS gene under control of the CaMV35S promoter, the rice GOS2 promoter, or the rice HMGP promoter. Plant transformation was as described above and six single copy (or low copy) events per construct were selected. Sixty T1 seeds per event were sown, and transgenic seedlings were picked up through visual marker selection. The integrity of the transgene was further confirmed by qPCR on the terminator. Seedling leaf, stem and root were sampled individually from nine 1 week-old plants per event (destructive sampling). Another nine transgenic plants per event were grown in the greenhouse until T2 seed harvesting, for later stage sampling. Samples included 6 week-old leaves, young inflorescences (1-2 days before flowering), and mature T2 seed. Two events of 35S-GUS transgenic rice were sown, sampled and analyzed in parallel to the lines with the GOS2 and the HMGP promoter, as reference and control. The promoter activities were determined by a standard quantitative GUS assay, results are shown in Table F.

TABLE F

Overview of promoter activity determined by quantitative GUS assay.
The scoring was based on the mean value of each construct (6 event,
54 samples). 1 W: one week old seedlings; 6 W: six weeks old plants.
The scoring system corresponds to GUS activity (U/mg total soluble
protein) as follows: −: <1; +: 1-10; ++: 10-100; +++: 100-1000;
++++: >1000.

		1 W	1 W	1 W	6 W	Inflores-	T2
Promoter	Specificity	Leaf	Root	Stem	Leaf	cence	Seed

PRO0170	constitutive	++	+	+	+	+	+
PRO0129	constitutive	++	++	++	++	+++	++
PRO35S	constitutive	++++	+++	++	+++	+++	++

Example 12

Arabidopsis Plant Material, Engineering and Growth Conditions

Seeds of Arabidopsis thaliana Ler were obtained from the Nottingham Arabidopsis Stock Centre. The hub1-1 mutant has been described previously as ang4-1 (Berná et al., 1999). The plants were generally grown in vitro on germination medium (Valvekens et al., 1988). For root growth experiments, a single row of five plants was sown in square plates (BD Falcon) in vertical position in germination medium containing 10 g/L plant tissue culture agar (Lab M). The growth chamber conditions were 16-h-light/8-h-dark photoperiod with white light (cool-white neon tubes; Radium Lampenwerken), 100 pEM⁻²h⁻¹photosynthetically active radiation, and 20° C. Plants were grown in a soil:vermiculite (3:1; v/v) mixture under greenhouse conditions with a setting temperature between 21 and 30° C., relative humidity of 50 to 60%, and the irradiance (natural light and fluorescent lamps) between 100 and 120 μE M⁻²h⁻¹photosynthetically active radiation in a 16-h-light/8-h-dark regime.
To obtain overexpression lines of HUB1 (OE-HUB1) the open reading frame (including ATG and stop codon) of HUB1 (2637 bp) was amplified by Pfu polymerase and cloned into the pDONRT221 vector using the GATEWAY recombination strategy (Invitrogen) to obtain ENTRY clones. The ENTRY clone was recombined with the pK7WG2 vector (Karimi et al., Trends Plant Sci. 7, 193-195, 2002) to obtain a DESTINATION vector with the ORF under the control of a 35S promotor. This construct was introduced into Agrobacterium tumefaciens and subsequently Ler plants were transformed with the Agrobacterium tumefaciens suspension through floral dip. The T0 seeds were grown in high density on growth medium containing Kanamycin (50 μg/ml), Nystatin (50 μg/ml) and Carbenicillin (250 μg/ml) to select the transformants. These T1 transformants were transferred to soil to obtain T2 seeds.
Ler wild type, hub1-1 mutant and OE-HUB1 seeds were sterilized and plated on MS media with 1% agar. After 2 nights of vernalisation in dark at 4° C. the plates were put in growth chambers at 21° C., with a relative humidity of 50-60%, PAR 100-120 μE/m²/hr and 16/8 hours day/night regime (Long Day (LD) growth conditions). Short Day (CD) growth conditions comprised an 8/16 hours day/night regime.

Example 13

Analysis of Arabidopsis Plants

Leaf lamina length, width and area of the hub1-1 mutant, HUB1 overexpression line and Ler wild type were measured during a time course of three weeks after sowing. The juvenile leaves one and two were sampled during this time course by initially clearing the chlorophyll in 70% ethanol overnight. The cleared samples were then transferred into 100% lactic acid for preservation. The cleared leaves were mounted on a microscope slide and photographed using a an Axiom video camera (ZEISS, USA) installed on the Bino-Leica microscope and the measurements of the lamina length, width and area was performed with ImageJ 1.34 software program. For statistical analysis, pair wise comparison of the data was done with an online statistical program (Uitenbroek, D. G, Binomial. SISA. 1997. quantitativeskills.com/sisa/distributions/binomial.htm).
Determination of flowering time: the start of bolting was observed visually and is expressed in days after vernalisation.
For determination of photosynthetic pigments, 50 mg leaf samples were harvested from 25 days old in vitro grown seedlings. The samples were submerged in 2 ml of cold 80% acetone and ground with glass beads. Samples were centrifuged (5′ at 4 C) and supernatant was transferred in fresh tubes and adjusted to 5 ml with 80% acetone. The pigments were extracted overnight in −20 C, centrifuged and analysed in a spectrophotometer in plastic cuvettes at 3 wave lengths (at 663, 646, and 470 nm).

- Chlorophyll a content was calculated from (12.21*A663)−(2.81*A646),
- Chlorophyll b content from (20.31*A646)−(5.03*A663),
- Total carotenoid content from (1000*A470)−(1.82*chl a)−(85.02*chl b).

For each case, the pigment content was calculated per 50 mg fresh weight. The experiment was repeated twice and each sample was analysed in triplicate.

Microarray Analysis:

Shoot apexes of seedlings of the three lines were harvested at developmental stage 1.02 and total RNA was extracted by RNeasy (Qiagen) according to the manual. The samples were hybridized on Agilent arrays and the data were normalised. All analyses were performed on the log base 2 foreground fluorescence intensity measurements. The expression data were analyzed in two steps: 1) a “within slide” analysis aimed at removing variation associated with differential dye responses to binding as noise; and 2) a “between slide” analysis aimed at estimating the mean differences between genotypes and their standard error. For the within slide analysis, a spatial linear fixed model of the form
response=μ+spline(intensity)+residual (1)
was applied, where the response variable is the log₂ratio of the foreground fluorescence intensities (M) measured at the 37971 gene spots. Within the model (1), the dye bias was represented by a cubic smoothing spline curve (spline(intensity)), as implemented in the GenStat menu for microarray data analysis. Once the adjusted log 2 ratios (M′) for each gene were obtained, adjusted log₂R and log₂G signal intensities were calculated. For the between slide analysis, a two step mixed model analysis of variance was used and performed with GenStat. Each of the 24 hybridization samples was subjected to a linear normalization model of the form (random terms underlined)
response=μ+array+residual (2)
where the response variable represents the corrected log₂transformed Cy3 and Cy5 fluorescence intensity measurements of the 37971 gene-specific tags. Array modeling the hybridization effects of each of the 12 microarrays, were added as random terms.
In a last step, the proportion of expressed genes was estimated for which a significant part of their variation can be attributed to genotypic differences, i.e., is genetic. The residuals from the model (2) were analyzed for each of the 37971 genes separately by a mixed model of the following form
residual=μ+dye+replicate+genotype_ij+array+error (3)
partitioning gene specific variation into gene specific fixed dye (Cy3 and Cy5), replicate (A and B) and genotypic effects, and random spot effects. The genotypic effect, genotype_ij, refers to the 3 genotypes Ler, hub1-1, OE-HUB1. The array term models the effects for each spot and equals the (Gene.Array) interaction effect. Random effects in the model were assumed to be independent and normally distributed with means zero and variance G?, where t=A (array) and E (error).
The linear mixed model (3) was fitted and, and a measure of variability in expression levels among the four genotypes, Wald statistics were calculated and significance was assigned to each of the six pair wise comparison between genotypes. The False Discovery Rates (FDRs) were subsequently estimated by modeling the adjusted P-values as a 2-component mixture of Uniform and Beta densities, as implemented in GenStat; default parameter settings were used to estimate π₀, the proportion of features that are truly null. Finally, a 2-fold change in genotype expression difference was imposed to further filter genes likely to have a statistically and biologically significant difference in genotype expression. BinGo analysis was performed on the data to identify the overrepresented and underrepresented biological processes affected in the different HUB1 misexpression lines (Maere et al., Bioinformatics 21, 3448-3449, 2005).

Example 14

Overexpression of HUB1 Under Control of the CaMV35S Promoter in Arabidopsis Results in Improved Growth Properties

Seeds of HUB1 overexpressing lines (OE-HUB1) showed enhanced germination vigour compared to wild type (Ler) or hub1-1 mutant lines: Ler wild type, hub1-1 mutant and OE-HUB1 seeds were sterilized and plated on MS media with 1% agar. After 2 nights of vernalisation in dark at 4° C. the plates were put in growth chambers at 21° C., with a relative humidity of 50-60%, PAR 100-120 ρE/m2/hr and 16/8 hours day/night condition. Germination was monitored daily and visible signs of germination were recorded. The growth promoting effect of HUB1 overexpression was observed as enhanced germination vigour of the transgenic seedlings compared to wild type or hub1-1 mutant. In wild type plants, the majority of the seedlings germinated two days after vernalisation (DAV) (FIG. 15). For 50% of OE-HUB1 seedlings germination was detected already on the first day after vernalisation and the other 50% germinated on the second day. In the hub1-1 mutant germination was delayed by one day and for 50% of the seedlings germination was observed only on the third day. To analyse the underlying mechanisms of the enhanced germination vigour cell areas of Ler and OE-HUB1 lines were measured during the juvenile leaf growth. In the beginning of the growth OE-HUB1 indeed shows an enhancement of cell growth which is however levelled out by the time leaves reach their mature size (FIG. 16). Thus the positive HUB1 effect on Arabidopsis growth takes place early in development.
Furthermore, it was investigated whether the hub1-1 mutation would lead to changes in silique and seed development. For the analysis fully grown green siliques (4 to 8 days after fertilization) were harvested and scanned for analysis or photographed for images. The ImageJ software program (Image Processing and Analysis in Java, developed at the Research Services Branch, National Institute of Mental Health, Bethesda, Md., USA) was used to calculate the area of the scanned siliques. The number of siliques per plant was counted from scanned whole plants.
Seeds were harvested from the dried siliques and scanned. The seed area was calculated from scans using the ImageJ program. Seed weight was determined by wrapping 200 seeds in an aluminium foil of known weight and measured. The seed yield per plant was subjected to t-test analyses. The area of hub1-1 siliques was found to be severely reduced (FIGS. 17 and 18). The hub1-1 siliques also contained fewer seeds with 50-80% unfertilized seeds, resulting in reduced total seed yield. The hub1-1 seeds were also smaller in size (FIG. 19). As a result the total seed yield of hub1-1 plants was dramatically reduced compared to Ler wild type (FIG. 20). While in hub1-1 mutant plants the silique and seed parameters were strongly affected, in the HUB1 overexpression lines no significant effects on the seed parameters were observed. This may be due to the fact that in Arabidopsis seed development is not dependent on cell growth or that the overexpression under control of the 35S CaMV promoter was not optimal. However, in the HUB1 overexpression lines the siliques (fruit) morphology was altered by increased area in width (FIG. 18).

Example 15

Mutagenesis of HUB1 and Functional Characterisation of the HUB1pm Mutant

The coding sequence of octamer of cysteines and histidines in the RING domain of HUB1 was mutagenised by PCR mediated site directed mutagenesis (QuickChange, Stratagene), such that Cys1 and Cys2 were changed into Ser residues (FIG. 1, panel B). The recombinant proteins were cloned as fusion proteins with His and GST epitope tags, expressed in E. coli and purified on affinity columns. The purified proteins were tested for histone H2B monoubiquitination and for self-ubiquitination activity in an in vitro (auto)ubiquitination assay as described by Fleury et al. (2007), see also Example 6.
The pointmutations in the RING domain reduced the autopolyubiquitination activity as indicated by reduced levels of these modifications on the western blots (FIG. 5, HA-Ab). The equal loading of GST-HUB1 is shown by GST Ab (FIG. 5, GST-Ab). These data confirmed that the RING domain was required for the autoubiquitination activity. Unexpectedly, histone H2B monoubiquitination was not affected by the point mutations (FIG. 5, HA-Ab). In addition, the presence of H2B substrate reduced the autopolyubiquitination activity suggesting that in the absence of substrate HUB1 protein may be removed through protein degradation. It is assumed that the point mutations render the protein to dominant positive by reducing the autoregulation and thereby stabilising the protein. However, in an initial test with proteasome inhibitor (MG132) treatment no accumulation of HUB1 protein was observed suggesting that it may not be an unstable protein but that the polyubiquitination may have an alternative yet to be identified regulatory function.
The RING domain is mainly involved in interaction with the E2 enzyme and it seems that the point mutations generated in this disclosure do not abolish this interaction or that a fully functional RING domain is not absolutely necessary for mediating the histone modifications. Other possible mutations of ubiquitin E3 ligases and RING domains would include targeting additional amino acids of the octamer of cysteins and histidines holding the two Zinc atoms. The possibilities include replacing one or two cysteines holding one Zn or replacing two or four cysteines holding the two Zn atoms. A more severe alteration is deletion of the whole RING domain, which would create a mutant comparable to the hub1-1 mutant. The hub1-1 phenotypes are uniquely strong as compared to the knockout alleles in Col-0 background (Fleury et al., 2007) and may suggest that the early stop codon in front of the RING domain causes the generation of a truncated protein with a dominant negative effect on the protein function. Antibodies are being generated to confirm the truncation of the HUB1 protein in hub1-1 lines. NTAP-tagged HUB1 and HUB1pm constructs were generated for Tandem Affinity Purification experiments for interactome studies. The RING domain of an ubiquitin E3 ligase usually mediates interactions with the E2 enzyme. The point mutations generated in the HUB1 RING domain however had an effect on the interactome. While the full length HUB1 was able to bind the homologous protein HUB2 the point mutations appeared to abolish this binding activity.
To further analyse the role of the RING domain in HUB1 (when functioning in protein degradation) towards plant growth regulation, the TAP tagged wild type and point mutant constructs were transformed in Arabidopsis plants. Western blot analysis was used for detecting the protein levels in plants and assessing the impact of proteasome inhibitor treatment on Hub1 protein levels. Usually point mutations in the RING domain generate dominant negative forms of the E3 ligases, which trap the substrates but do not mediate their ubiquitination and thus the targets are stabilized. The phenotypes of point mutant transgenic plants are expected to be milder than those of null mutants due to only a titration effect on the substrates. Molecular characterization of the point mutant protein in vitro however, suggests that HUB1 may be rather stabilized due to reduced autoregulation while no reduction in H2B monoubiquitination was observed.

Example 16

Overexpression of HUB1pm in Transgenic Arabidopsis Improves Plant Growth Properties

The Arabidopsis thaliana hub1-1 mutant or wild type Ler was transformed with the HUB1 or HUB1pm coding sequence, each under control of the CaMV35S promoter, and cultivated as described above. It was unexpectedly found that overexpression of the HUB1pm mutant in Ler background had an effect on leaf width, and the increased leaf width is more prominent for HUB1pm than for HUB1 (FIG. 21A); the same effect was observed in the mutant hub1-1 background, in particular leaves 3 to 9 of the HUB1pm transformant had increased leaf width, compared to the control or the HUB1 transformant (FIG. 21B).

Example 17

Overexpression of the HUB1pm Protein Under Control of a Medium Strength Promoter Increases Seed Yield

Oryza sativa is transformed with the HUB1pm coding sequence operably linked to a medium strength promoter (such as the HMGP promoter) and are cultivated as described above. The plants have improved growth characteristics, comprising one or more of: increased biomas, increased germination vigour, increased early vigour, increased seed yield, increased stress tolerance.

Example 18

Circadian Clock Gene Expression is Affected by Modulated HUB1 Expression

OE-HUB1 microarray data suggested that circadian clock is impaired in HUB1 misexpression lines. Input genes, clock oscillator genes as well as output genes were detected as up regulated in the HUB1 overexpression line. To identify true HUB1 target genes, oppositely regulated genes between hub1-1 mutant and OE-HUB1 lines were recorded from the microarray experiment. Table G shows a list of 43 genes that were significantly downregulated in the hub1-1 mutant and upregulated in the OE-HUB1 line, the data are ranked according to ascending log 2 ratios between hub1-1 and OE-HUB1. From the first 43 genes oppositely regulated between the overexpression (up) and mutant (down) lines 18 were diurnally regulated and 8 of these diurnally regulated genes were part of the top 10 (Table G). Among these genes the circadian clock oscillator components such as CCA1, LHY and APRR9 were detected. In addition, expression of the F-box family protein (FKF1)/adagio 3 (ADO3) E3 ubiquitin ligase SCF complex F-box subunit and ELF4 (respectively At1g68050 and At2g40080, both clock input genes), the clock oscillator genes APRR5 (pseudo-response regulator 5, At5g24470), APRR3 (pseudo-response regulator 3, At5g60100), and TOC1 were upregulated in the hub1-1 mutant, but downregulated in the OE-HUB1 plants. Several clock output genes, including chlorophyll A-B binding proteins (such as LHCB4.3, At2g40100), were upregulated OE-HUB1 plants. Taken together these data confirm that circadian clock is impacted by HUB1 misexpression. To further confirm whether the frequency or the amplitude of the circadian clock is affected in the hub1 lines a time course experiment with QPCR analysis of clock genes was carried out. To this end, in vitro grown seedlings were used that had germinated under short day conditions, after 12 to 14 days moved to continuous light conditions. Sampling started after 24 hrs in continuous light, above-ground parts were harvested every 4 hours during a 48 hour time period. RNA was extracted using RNeasy (Qiagen) followed by a DNase treatment. cDNA was prepared with a first strand synthesis kit (Invitrogen) starting from 3 ug of total RNA. 5 μl of diluted cDNA (20 ng/ul) was used in each reaction with SYBR Green and gene specific primers. QPCR was performed in a Bio Rad iCycler using standard techniques.
The first results showed that in the hub1-1 mutant CCA1 expression was reduced in amplitude with a shift in the wave.

TABLE G

Genes oppositely regulated between hub1-1 with negative
log2 values and OE-HUB1 (with positive log2 values).

name	hub1-1	Ler	OEHUB1	AGI code	Diurnal

CCA1	−1.9	1.5	4.6	At2g46830	D
LHY	−1.9	0.2	4.0	At1g01060	D
expressed prot.	−1.3	0.8	4.0	At3g12320	D
	−4.4	0.1	0.5	At2g18880
hypothetical prot.	−4.2	−1.6	0.8	At3g09450
APRR9	−3.5	−1.9	0.9	At2g46790	D
MYB TR F	−1.4	0.0	2.8	At3g09600	D
galactinol synth.	−1.1	0.5	2.9	At2g47180	D
CIPK20	−0.5	3.5	3.5	At5g45820	D
beta-carotenoid hydroxylase	−0.9	1.2	3.1	At5g52570	D
RCC1	−0.7	1.4	2.9	At3g53830
F-box	−2.8	0.6	0.7	At5g60610
LEA domain	−2.6	0.5	0.9	At4g13560
LHCB2	−2.7	−0.7	0.7	At2g05100	D
glycerophosphoryl diester	−1.7	−0.2	1.2	At5g08030
oxidoreductase	−0.4	1.2	2.5	At2g36690
expressed prot.	−2.8	0.2	0.0	At1g62190
DREB1C/CBF2	−1.2	0.5	1.6	At4g25470
leucine-rich repeat	−0.6	1.5	1.9	At1g51800
Zn finger B-box	−1.7	−1.7	0.8	At3g21150
transcription factor	−2.2	−1.9	0.3	At4g18650	D
expressed prot.	−1.4	1.3	1.1	At5g45830
transcription factor	−0.1	2.3	2.3	At2g35310
glycocyl transferase	−1.6	0.7	0.8	At2g13680
VSP1	−0.9	1.2	1.5	At5g24780	D
aminotransferase	−1.8	−0.4	0.6	At2g24850
protein	−2.2	0.0	0.1	AV786179
cytochrome P450	−0.1	1.8	2.1	At2g29090	D
TIR class protein	−1.5	−0.2	0.7	At1g65390
hydroxyproline rich prot	−2.2	−0.8	0.0	At1g11070
WRKY	−0.2	0.7	2.0	At1g80840
SUC5	−0.5	0.9	1.7	At1g71890
transcription factor	−1.1	0.5	1.1	At4g31680
jacalin lectin prot	−1.4	0.6	0.8	At5g35940
ABC transporter	−0.1	1.3	2.0	At1g15520
expressed prot.	−1.8	−0.4	0.3	At3g28270	D
DREB2A like	−0.3	0.3	1.8	At1g75490
NAM family	−1.7	−1.5	0.3	At1g69490	D
DOF zn finger protein	0.0	0.2	2.0	At1g69570	D
expressed prot.	−0.5	1.5	1.5	At3g17890
zinc finger B-box	−1.7	−1.5	0.3	At3g21890	D
DOF zn finger protein	−0.2	0.6	1.8	At5g62430	D
unknown	0.0	1.9	2.0	CHR3: 006127463-
				006127522
SAUR/AC1	−1.9	−0.7	0.1	At4g38850	D

Genes are ordered with ascending log2 ratios between hub1-1 and OE-HUB1 with a cut off log2 ratio at −1.99. D; diurnally regulated. Log2; expression values.

Example 19

Downstream Pathways of Circadian Clock are Affected by Modulated Expression of HUB1

Output genes of circadian clock include regulators of photosynthetic capacity and plastid development. To elucidate the light dependent phenotypes hub1-1 mutant, Ler wild type and HUB1 overexpression plants were grown in three different light conditions; long day (LD), short day (SD) and continuous light (CL) for phenotypic characterisation (FIG. 6). The hub1-1 mutant grown under short day light conditions clearly had a pale colour. In long day conditions hub1-1 growth phenotype was mildest and mainly as described in Fleury et al., (2007). In LD and CL conditions hub1-1 seedlings showed only occasionally a lack of pigments.
To confirm that hub1-1 mutant plants had reduced photosynthetic capacity the content of photosynthetic pigments namely, chlorophyll a and b and total carotenoid contents was analysed in plants grown under the three light regimes. In SD all pigments were reduced (FIG. 7). The pale leaf colouration and reduced pigment content predicts defects in plastid structures and this hypothesis is supported by the transcriptome data. This was confirmed upon investigating the subcellular characteristics underlying the light phenotypes by Transmission Electron Microscopy. The first images by TEM show altered thylacoid membrane structures for hub1-1 mutant (FIG. 8). The total amount of membranes and grana were reduced and there were more plastoglobuli present in the stroma.

Example 20

Light Dependent Phenotypes of Hub1-1 are Enhanced in Short Day Conditions

In addition to the reduced photosynthetic capacity, circadian clock regulated phenotypes in hub1-1 include reduced hypocotyl length, reduced leaf growth and early flowering time. We compared these clock related phenotypes in the HUB1 misexpression lines (OE and mutant) in comparison to wild type Ler. Plants were grown in short day conditions and their hypocotyl lengths were measured after 21 days of growth. Hub1-1 mutant hypocotyl lengths were reduced (FIG. 9). In dark grown seedlings no differences in hypocotyl length were observed.
It has also been suggested that impaired plastid development may affect leaf morphology. To compare the growth phenotypes in the three conditions the leaf area was measured of the 21 days old in vitro grown seedlings. While the growth of cotyledons of the hub1-1 mutant is not affected, the expansion growth of the true leaves is severely repressed in all conditions (FIGS. 6, 10 and 11).
Furthermore, new morphological effects were observed in the hub1-1 mutant grown under short day conditions. From the leaf three and four onwards some leaves only developed as spike like structures or had their mid vein protruding out from the abaxial side of a narrow leaf (FIG. 12). In addition to the spike-like structures, hub1-1 mutants showed altered leaf morphologies such as reduced growth, narrow leaf lamina and altered venation pattern. Also altered flower morphologies have been observed. Flower structures from hub1-1 mutant plants revealed that flower meristems and organs were missing and/or misplaced (FIG. 13).
Furthermore, hub1-1 mutant plants flower early in SD conditions as well as in both other growth conditions, based on the start of bolting.

Example 21

Altered Expression of Developmental Genes Correlates with Hub1-1 Phenotypes

hub1-1 mutant plants have severe leaf phenotypes with reduced growth, altered venation patterns and occasionally appearing protruding mid veins or spike-like true leaves. The microarray data of HUB1 misexpression lines has shown alterations of a number of developmental genes such as the KNAT, WUS, AP2, CLAVATA genes (Table H). FIG. 14 shows expression patterns of the developmental genes identified in HUB1 microarrays according to Genevestigator.

TABLE H

developmental genes differentially expressed
in hub1-1 and Ler wild type or OE-HUB1 lines.

		hub1/ler	hub1/OE17
NAME	AGI code	log2 ratio	x log2 ratio

MYB60	At1g08810.1	−1.65	−1.62
CLV1 like	At1g08590.1	−1.46	−1.18
MYB	At3g09600.1	−1.39	−4.20
MYB	At2g40260.1	−1.34	−1.40
MYB56	At5g17800.1	−1.32	−1.37
MYB	At1g18330.1	−1.10	−1.41
WUS like	At3g11260.1	−0.93
AP2 like	At5g67180.1	−0.89	−0.68
COL	At1g07050.1	−0.84	4.49
MADS	At1g26310.1	−0.84	−0.73
MYB	At5g44190.1	−0.74	−1.36
ARR7	At1g19050.1	−0.63	−0.73
WUS like	At3g18010.1	−0.54	−0.73
MYB	At1g01520.1	−0.49	−2.04
BEL1	At5g41410.1	−0.42	0.42
TCP3	At1g53230.1	−0.38
AP2	At4g36920.1	−0.33
CLV2	At1g65380.1	−0.29	−0.39
CLV1 like	At1g27190.1	−0.27	−0.22
ANT	At4g37750.1	0.33	0.32
AP2 like	At5g60120.1	0.36	0.44
LBD6	At1g65620.1	0.37	0.29
WER	At5g14750.1	0.39	0.53
WUS like	At1g46480.1	0.53	0.73
KNAT7	At1g62990.1	0.62	0.63
LFY	At5g61850.1	0.69	0.41
KNAT1	At4g08150.1	0.88	0.57
AP2 like	At3g54990.1	0.95	1.02
CCA1	At5g17300.1	1.56	−0.73
jmjC	At3g20810.1	2.07	6.66
MADS	At5g40220.1	4.69	4.39
CUC2 like	At5g14490.1	5.88	6.31
MYB15	At3g23250.1		−1.50
KNAT4	At5g11060.1		0.57
DRM1	At1g28330.1		4.27
DRM1	At1g28330.3		5.29

Missing values were not significant (p). Genes were sorted according ascending ratio btw hub1-1 and Ler wild type.

Example 22

Modulation of Biological Processes in Hub1-1 Compared to Ler Wild Type Plants and to HUB1 OE

A BiNGO analysis (a tool to determine which Gene Ontology (GO) terms are significantly overrepresented in a set of genes) was performed on the micro array data (Example 13) to indentify biological processes that were influenced by HUB1 misexpression. Tables I1 and I2 show a list of genes that were differentially expressed in hub1-1 compared to Ler WT plants:

TABLE I1

genes downregulated in hub1-1 vs Ler (SEQ ID NO: 244 to SEQ ID NO: 835)

AT1G01010	AT1G55670	AT2G26760	AT3G19820	AT4G18480	AT5G24400
AT1G02065	AT1G56200	AT2G26760	AT3G20070	AT4G18960	AT5G24400
AT1G02800	AT1G56200	AT2G27380	AT3G20070	AT4G19350	AT5G24400
AT1G03120	AT1G56200	AT2G27960	AT3G20070	AT4G19350	AT5G24470
AT1G03130	AT1G57770	AT2G27960	AT3G20440	AT4G19350	AT5G24470
AT1G04110	AT1G58290	AT2G27960	AT3G20440	AT4G19560	AT5G24470
AT1G05190	AT1G58290	AT2G27970	AT3G20440	AT4G19560	AT5G24470
AT1G05190	AT1G59940	AT2G28000	AT3G20780	AT4G19560	AT5G24470
AT1G05190	AT1G59940	AT2G29090	AT3G21640	AT4G20050	AT5G26742
AT1G06570	AT1G60600	AT2G29090	AT3G22200	AT4G20060	AT5G26742
AT1G06820	AT1G63260	AT2G29090	AT3G22780	AT4G20060	AT5G26742
AT1G07370	AT1G63970	AT2G30950	AT3G22880	AT4G20060	AT5G27720
AT1G07370	AT1G63970	AT2G30950	AT3G24560	AT4G20910	AT5G27720
AT1G07370	AT1G63970	AT2G32250	AT3G24560	AT4G20910	AT5G27720
AT1G08090	AT1G65470	AT2G32250	AT3G24560	AT4G21270	AT5G35220
AT1G08520	AT1G66330	AT2G32590	AT3G24730	AT4G24150	AT5G35520
AT1G08520	AT1G66650	AT2G33480	AT3G25980	AT4G25080	AT5G35630
AT1G08840	AT1G67440	AT2G33810	AT3G25980	AT4G25080	AT5G37630
AT1G08840	AT1G67440	AT2G33810	AT3G25980	AT4G25700	AT5G37630
AT1G08840	AT1G67440	AT2G34420	AT3G27920	AT4G26500	AT5G37630
AT1G09000	AT1G67740	AT2G34420	AT3G29290	AT4G26500	AT5G37630
AT1G10470	AT1G68050	AT2G34430	AT3G29290	AT4G26500	AT5G37780
AT1G10470	AT1G68050	AT2G34430	AT3G29290	AT4G27700	AT5G37780
AT1G10510	AT1G68480	AT2G34650	AT3G33520	AT4G28190	AT5G37890
AT1G10510	AT1G68900	AT2G34650	AT3G33520	AT4G28190	AT5G39820
AT1G10510	AT1G68900	AT2G34650	AT3G44560	AT4G28210	AT5G40280
AT1G11870	AT1G69040	AT2G37680	AT3G44880	AT4G28210	AT5G40600
AT1G12770	AT1G69040	AT2G37680	AT3G44880	AT4G28210	AT5G40600
AT1G12770	AT1G69040	AT2G37860	AT3G47500	AT4G28660	AT5G40600
AT1G12770	AT1G69440	AT2G37920	AT3G47500	AT4G28980	AT5G41480
AT1G13690	AT1G69440	AT2G37920	AT3G48110	AT4G29830	AT5G41480
AT1G13870	AT1G70210	AT2G37920	AT3G48110	AT4G29830	AT5G41480
AT1G14150	AT1G70210	AT2G38280	AT3G48190	AT4G30950	AT5G42190
AT1G15570	AT1G70210	AT2G38280	AT3G48470	AT4G30950	AT5G42190
AT1G15570	AT1G71230	AT2G38280	AT3G48470	AT4G31500	AT5G42190
AT1G15570	AT1G71230	AT2G39470	AT3G48470	AT4G31500	AT5G43080
AT1G15820	AT1G71230	AT2G40760	AT3G50210	AT4G31500	AT5G43080
AT1G18450	AT1G71230	AT2G41720	AT3G50790	AT4G32810	AT5G43080
AT1G19050	AT1G71230	AT2G41720	AT3G50790	AT4G33790	AT5G45930
AT1G20610	AT1G71230	AT2G41720	AT3G50790	AT4G34620	AT5G45930
AT1G20610	AT1G71440	AT2G41980	AT3G51160	AT4G34620	AT5G47110
AT1G20610	AT1G71440	AT2G43010	AT3G52430	AT4G34620	AT5G47110
AT1G20930	AT1G71440	AT2G43010	AT3G53130	AT4G35900	AT5G48150
AT1G20930	AT1G73590	AT2G43280	AT3G54420	AT4G35900	AT5G48150
AT1G20930	AT1G73590	AT2G43280	AT3G54420	AT4G36920	AT5G48150
AT1G21970	AT1G73590	AT2G45330	AT3G54420	AT4G36920	AT5G48150
AT1G21970	AT1G73590	AT2G45330	AT3G54720	AT4G36920	AT5G48150
AT1G21970	AT1G73590	AT2G45330	AT3G54720	AT4G37000	AT5G48630
AT1G22770	AT1G74470	AT2G45480	AT3G54720	AT4G37230	AT5G48630
AT1G22770	AT1G74470	AT2G46340	AT3G54720	AT4G37230	AT5G48630
AT1G22920	AT1G75350	AT2G46340	AT3G54720	AT4G37580	AT5G48820
AT1G22920	AT1G75350	AT2G46340	AT3G54720	AT4G37580	AT5G48820
AT1G22920	AT1G75350	AT2G46340	AT3G55330	AT4G37580	AT5G48820
AT1G22920	AT1G76570	AT2G46340	AT3G58780	AT4G37580	AT5G49030
AT1G22920	AT1G77080	AT2G46340	AT3G59400	AT4G37580	AT5G49555
AT1G22920	AT1G77080	AT2G46820	AT3G59400	AT4G37740	AT5G49880
AT1G23080	AT1G77850	AT2G48120	AT3G60370	AT4G39100	AT5G49880
AT1G23080	AT1G78630	AT2G48120	AT3G60830	AT4G39100	AT5G49880
AT1G23080	AT1G78630	AT3G02380	AT3G60830	AT4G39100	AT5G50280
AT1G24260	AT1G78630	AT3G02380	AT3G60830	AT4G39100	AT5G50280
AT1G24340	AT1G80080	AT3G02660	AT3G61470	AT4G39100	AT5G50280
AT1G24340	AT1G80370	AT3G02660	AT3G61470	AT4G39620	AT5G52570
AT1G24340	AT1G80370	AT3G02660	AT3G61780	AT4G39620	AT5G53090
AT1G25580	AT1G80370	AT3G02780	AT3G61780	AT4G39620	AT5G53660
AT1G26310	AT2G01420	AT3G02780	AT3G61780	AT5G01530	AT5G57030
AT1G26310	AT2G04160	AT3G03450	AT4G00180	AT5G02250	AT5G57030
AT1G29410	AT2G04842	AT3G03450	AT4G01710	AT5G02250	AT5G57030
AT1G30610	AT2G04842	AT3G04630	AT4G02560	AT5G02250	AT5G57050
AT1G30610	AT2G04842	AT3G06350	AT4G02560	AT5G04560	AT5G57050
AT1G30610	AT2G05620	AT3G06350	AT4G02770	AT5G04560	AT5G60540
AT1G32200	AT2G13680	AT3G06350	AT4G03270	AT5G04560	AT5G60540
AT1G32200	AT2G16500	AT3G06430	AT4G03270	AT5G06240	AT5G60540
AT1G32200	AT2G16500	AT3G06430	AT4G03270	AT5G06240	AT5G61510
AT1G33060	AT2G16500	AT3G06430	AT4G03280	AT5G06240	AT5G62430
AT1G33280	AT2G17620	AT3G07390	AT4G04350	AT5G07280	AT5G62430
AT1G42970	AT2G17620	AT3G07430	AT4G04350	AT5G08170	AT5G63050
AT1G43710	AT2G17620	AT3G07430	AT4G04350	AT5G08170	AT5G63050
AT1G43710	AT2G18020	AT3G07430	AT4G04900	AT5G08170	AT5G63050
AT1G43710	AT2G18020	AT3G07500	AT4G10180	AT5G10140	AT5G63790
AT1G44110	AT2G18020	AT3G07500	AT4G10180	AT5G10140	AT5G64050
AT1G44110	AT2G20000	AT3G10390	AT4G10180	AT5G10330	AT5G64520
AT1G44110	AT2G20000	AT3G10390	AT4G10180	AT5G10330	AT5G65060
AT1G44446	AT2G20000	AT3G10670	AT4G10180	AT5G10330	AT5G65060
AT1G44446	AT2G20000	AT3G10670	AT4G10180	AT5G10360	AT5G65070
AT1G45474	AT2G20000	AT3G10670	AT4G10350	AT5G10360	AT5G65070
AT1G45474	AT2G20000	AT3G11670	AT4G12550	AT5G10360	AT5G65080
AT1G47530	AT2G21710	AT3G11670	AT4G12980	AT5G10480	AT5G65080
AT1G47530	AT2G21710	AT3G13960	AT4G13560	AT5G10480	AT5G65930
AT1G48270	AT2G21710	AT3G14110	AT4G13560	AT5G12990	AT5G66055
AT1G48270	AT2G22840	AT3G14110	AT4G13560	AT5G16715	AT5G66055
AT1G48270	AT2G22870	AT3G15030	AT4G15090	AT5G16715	AT5G66055
AT1G48270	AT2G22870	AT3G15270	AT4G15090	AT5G16715	AT5G66570
AT1G48380	AT2G22870	AT3G15270	AT4G15510	AT5G17710	AT5G66570
AT1G49510	AT2G23430	AT3G16290	AT4G15560	AT5G17710	AT5G67030
AT1G49510	AT2G23430	AT3G16290	AT4G15560	AT5G17710	AT5G67180
AT1G49510	AT2G23430	AT3G16290	AT4G16110	AT5G18700	AT5G67260
AT1G50250	AT2G23430	AT3G18110	AT4G16250	AT5G18700	AT5G67260
AT1G50250	AT2G25660	AT3G18110	AT4G16250	AT5G18700	AT5G67260
AT1G51190	AT2G25660	AT3G18110	AT4G16280	AT5G22290	AT5G67570
AT1G52230	AT2G25660	AT3G18390	AT4G16280	AT5G22370	AT5G67570
AT1G52890	AT2G25840	AT3G18390	AT4G16750	AT5G22370	AT5G67570
AT1G53230	AT2G26760	AT3G18390	AT4G18480	AT5G22370

The genes in Table I1 are involved in photosynthesis (Gene Ontology (GO) ID nr 15979), regulation of photosynthesis, light reaction (GO ID nr 42548), chlorophyll biosynthesis (GO ID nr 15995), chlorophyll metabolism (GO ID nr 15994), carotenoid biosynthesis (GO ID nr 16117), response to red or far red light (GO ID nr 9639), photosynthesis, light harvesting (GO ID nr 9765), photomorphogenesis (GO ID nr 9640), regulation of development (GO ID nr 50793), seed development (GO ID nr 48316), development (GO ID nr 7275), cell cycle (GO ID nr 7049), regulation of cell cycle (GO ID nr 51726).

TABLE I2

genes upregulated in hub1-1 vs Ler (SEQ ID NO: 836 to SEQ ID NO: 961)

AT1G09570	AT1G70140	AT2G25930	AT3G46550	AT4G32880	AT5G20520
AT1G12840	AT1G70140	AT2G25930	AT3G54010	AT4G32880	AT5G20730
AT1G12840	AT1G70710	AT2G26710	AT3G54010	AT4G34490	AT5G25810
AT1G13180	AT1G70710	AT2G26890	AT3G54220	AT4G34490	AT5G25810
AT1G13180	AT1G70940	AT2G34710	AT3G54920	AT4G36380	AT5G26751
AT1G13980	AT1G72560	AT2G34710	AT3G54920	AT4G36380	AT5G39510
AT1G13980	AT1G75080	AT2G34710	AT3G61460	AT4G39400	AT5G49720
AT1G13980	AT1G75750	AT2G38120	AT4G02980	AT4G39400	AT5G49720
AT1G17060	AT1G75750	AT2G46920	AT4G02980	AT4G39400	AT5G52240
AT1G17060	AT1G75750	AT3G05840	AT4G12420	AT4G40060	AT5G52240
AT1G19350	AT1G75780	AT3G13870	AT4G12420	AT4G40060	AT5G53950
AT1G19850	AT1G75780	AT3G13870	AT4G18710	AT5G16490	AT5G53950
AT1G36160	AT1G76420	AT3G15170	AT4G18710	AT5G16490	AT5G62310
AT1G49040	AT2G06850	AT3G15170	AT4G18710	AT5G18580	AT5G62310
AT1G49040	AT2G06850	AT3G15170	AT4G23640	AT5G18580	AT5G64630
AT1G56010	AT2G18790	AT3G18730	AT4G23640	AT5G19280	AT5G66680
AT1G56010	AT2G20370	AT3G23050	AT4G30610	AT5G20350	AT5G66680
AT1G62360	AT2G20370	AT3G46550	AT4G32880	AT5G20350

The genes in Table I2 are involved in regulation of cell size (GO ID nr 8361), longitudinal axis specification (GO ID nr 9942), primary shoot apical meristem specification (GO ID nr 10072), cell morphogenesis (GO ID nr 7148), meristem organization (GO ID nr 9933, gravitropism (GO ID nr 9630), response to brassinosteroid stimulus (GO ID nr 9741).
Tables I3 and I4 show a list of genes that were differentially expressed in hub1-1 compared to HUB1 overexpressing plants (HUB1 OE):

TABLE I3

genes down in hub1-1 vs HUB OE (SEQ ID NO: 962 to SEQ ID NO: 1023)

AT1G07790	AT1G75600	AT2G46830	AT3G46030	AT5G10400	AT5G59870
AT1G07790	AT2G21660	AT2G46830	AT3G46320	AT5G10400	AT5G60100
AT1G09200	AT2G21660	AT3G09480	AT3G46320	AT5G12910	AT5G60100
AT1G09200	AT2G28720	AT3G09480	AT3G46640	AT5G12910	AT5G61380
AT1G22770	AT2G28720	AT3G20670	AT3G46640	AT5G22880	AT5G61380
AT1G22770	AT2G37470	AT3G20670	AT3G54560	AT5G22880	AT5G65360
AT1G28330	AT2G37470	AT3G27360	AT3G54560	AT5G24470	AT5G65360
AT1G28330	AT2G40080	AT3G27360	AT5G02560	AT5G24470
AT1G51060	AT2G40080	AT3G45980	AT5G02560	AT5G27670
AT1G51060	AT2G46790	AT3G45980	AT5G09230	AT5G27670
AT1G75600	AT2G46790	AT3G46030	AT5G09230	AT5G59870

The genes in Table I3 are involved in chromatin assembly (GO ID nr 31497), circadian rhythm (GO ID nr 7623).

TABLE I4

genes up in hub1-1 vs HUB OE (SEQ ID NO: 1024 to SEQ ID NO: 1045)

AT1G04550	AT1G56010	AT2G34710	AT4G08150	AT4G37650	AT5G53950
AT1G13980	AT1G56010	AT3G54220	AT4G24220	AT5G53950	AT5G63090
AT1G51190	AT2G34710

The genes in Table I4 are involved in pattern specification (GO ID nr 7389), primary shoot apical meristem specification (GO ID nr 10072).
From these data it can clearly be concluded that the circadian clock is under control of HUB1.

Example 23

Interactome of HUB1

First Experiment:

The role of HUB1 in histone H2B monoubiquitination suggested that HUB1 is a functional homolog of Bre1 E3 ligase. To identify HUB1 interacting proteins Tandem Affinity Purification (TAP) technology has been employed, which allows fast purification of protein complexes in their native conditions and which is based on the fusion of TAP-tags in the protein of interest (Puig et al., Methods. 24(3):218-29, 2001).
Because the RING proteins have their functionally important domain at the C-terminus, an N-terminal fusion was prepared instead of the traditional C-terminal fusion by cloning both full length and the point mutant form of HUB1 (HUB1pm, HUB1fl). The Arabidopsis cell cultures were transformed with the two constructs and cultivated on 10 litre scale, harvested and purified by TAP (Van Leene et al., Mol. Cell Proteomics 6, 1226-38, 2007). The protein extracts were separated on 1-D SDS-PAGE gels and isolated from gel for protein identification by mass spectrometry (Laukens et al., Proteomics. 4, 720-7, 2004, Van Leene et al., 2007). Two cut offs were used resulting in “confirmed” and “to be confirmed” candidate interactor lists (Table I).

TABLE J

All confirmed and a selection of to be confirmed
TAP identified HUB1 interactors. Confirmed

Confirmed	AGI code	To be confirmed	AGI code

GCN5	At5g11340	SEUSS	At1g43850
HUB1	At2g44950	SPT16	At4g10710
HUB2	At1g55250	NOP56	At1g56110
KH domain	At1g51580	MYB	At1g58220
protein
Spen like protein	At1g27750	FIBRILLARIN2	At4g25630
		Ulp1 protease	At1g34610
		Ulp1 protease	At3g09170
		PhyD	At4g16250
		ubiq protease	At5g22035
		U-BOX	At5g65920
		zinc finger	At1g18660
		BRCT	At4g02110
		SCL11	At5g59460

In the data set of confirmed interactors TAP HUB1 and HUB2 were present, confiming the dimer formation between the homologues. In addition, the acetyltransferase GCN5, RNA binding proteins and a KH domain protein were identified as HUB1 interacting proteins. Most of these proteins are known to be localized in nucleus or nucleoli. GFP constructs of HUB1 have also been localized to nucleus (Liu et al., 2007). When HUB1pm was used for TAP purification no HUB2 could be identified as an interacting protein. These data suggest that a functional RING domain is required for HUB1 and HUB2 dimerization. A selection of the proteins that interacted only once in the TAP purification experiments is listed in table as “to be confirmed”.
GCN5 is a histone acetylation enzyme involved in stress response, defense, signal transduction, transcription, metabolism, transport and in flower development where it affects two key genes such as WUSCHEL (WUS) and AGAMOUS (AG). NOP56 is required in ribosome biogenesis in yeast. Myb is a DNA binding protein with transcription factor activity involved in response to abscisic acid, jasmonic acid and salicylic acid stimuli. Fibrillarin 2 is an RNA methyltransferase and a potential substrate of AtPRMT1a and AtPRMT1b, two protein methyltransferases involved in mH4K3 among other post-translational modifications. Direct interactions with HUB1 were also shown for SEUSS and a spen-like nucleid acid binding protein. A number of the confirmed and to be confirmed interactors were tested by a Yeast two Hybrid assay to verify whether they directly interact with HUB1. Direct interaction with HUB1 was shown for HUB2, SEUSS and Spen-like proteins. Other confirmed interactors may require intermediating proteins for the interaction with HUB1.

Second Experiment:

Instead of using the original TAP tag, the optimised GS-TAP tag, developed by Van Leene et al. (Trends in Plant Science 13, 517-520, 2008), was N-terminally fused to the various bait proteins (see Table J). Constructs were transformed into Arabidopsis thaliana protoplast cells and expression of the fusion proteins was confirmed by Western analysis. Tagged proteins were produced in 5 litre scale cell cultures, extracted and the protein complexes were purified using the Tandem Affinity Purification protocol described by Van Leene et al. (2008). Bound complexes were eluted, precipitated and subjected to SDS-PAGE. Coomassie stained protein bands were extracted, trypsin digested and analysed by MALDI-TOF-TOF Mass Spectrometry.
For each experiment two independent purifications (a & b) from the same cell culture have been done and, in the case of HUB1, two different purifications have been performed in order to have a stronger support for its interaction network. The results of the different TAP purifications are listed in Table J. These data indicate the presence of a complex comprising HUB1, HUB2, SL and KH. Indeed all the TAP assays done using HUB1, HUB2 and SL as baits enabled to identify these three proteins together with KH. In addition, the results of HUB1 TAP were strengthened by purification with two different TAP tags.

TABLE K

List of proteins retrieved by TAP purification
with using fusions with the GS-TAP tag.

Bait	Prey Name	AGI Code	Expectance

HUB1 (a)	HUB1	AT2G44950	2.10E−19
	HUB2	AT1G55250	1.00E−20
HUB1 (b)	HUB1	AT2G44950	6.50E−29
	HUB2	AT1G55250	5.20E−22
	KH	AT1G51580	1.60E−08
HUB1 (a′)	HUB1	AT2G44950	2.10E−09
	HUB2	AT1G55250	1.00E−19
	SL	AT1G27750	6.50E−16
	KH	AT1G51580	2.10E−09
HUB1 (b′)	HUB1	AT2G44950	6.50E−16
	HUB2	AT1G55250	1.60E−11
	SL	AT1G27750	0.024
	KH	AT1G51580	3.30E−09
	K3K7	AT5G50990	/
HUB2 (a)	HUB2	AT1G55250	3.30E−99
	HUB1	AT2G44950	8.20E−85
	SL	AT1G27750	0.00097
	KH	AT1G51580	1.30E−08
HUB2 (b)	HUB2	AT1G55250	3.30E−99
	HUB1	AT2G44950	4.10E−68
	SL	AT1G27750	1.00E−24
	KH	AT1G51580	1.60E−09
SL (a)	SL	AT1G27750	8.20E−07
	HUB1	AT2G44950	0.0032
	HUB2	AT1G55250	0.005
	KH	AT1G51580	0.00054
SL (b)	SL	AT1G27750	3.30E−09
	HUB1	AT2G44950	0.0016
	HUB2	AT1G55250	0.0072
	KH	AT1G51580	2.60E−12
SEUSS (a)	SEUSS	At1g43850	6.50E−38
	LUG/RON2	At4G32551	1.30E−23
	LUH	At2G32700	3.30E−99
SEUSS (b)	SEUSS	At1g43850	3.30E−107
	LUG/RON2	At4G32551	5.20E−15
	LUH	At2G32700	2.10E−82
UBC2	UBC2	At2g02760	4.10E−15
	UBQs	14*	6.50E−14
UBC2	UBC2	At2g02760	1.60E−07
	UBQs	14*	3.30E−16
	SEUSS	At1g43850	1.00E−24
	UBC2	AT2G02760	5.20E−11
UBC2	UBC2	AT2G02760	6.50E−09
	AtUBA2	AT5G06460	0.00026
	AtUBA1	AT2G30110	0.00082

(a) and (b) represent independent purifications, the expectance value is based on homology between the peptide sequence and the protein.
*14 Ubiquitins having different accession numbers

In both of the TAP experiments involving HUB1 as bait, its homologue HUB2 has been retrieved as well as a K-homology motif containing protein (renamed KH), an uncharacterized molecule with five KH domains that are involved in RNA binding. Spen-Like (SL) is another uncharacterized protein that appeared in the two technical repeats of one experiment as well as in the experiments done with the original TAP tag. This protein also has an RNA-binding domain (RRM) in addition to a SPOC domain at its C-terminus. Comparable results were obtained by using HUB2 as bait. The reciprocal purification of HUB1 and HUB2 suggests the formation of a tetramere structure to control histone H2B monoubiquitination. K3K7 has been retrieved in one technical repeat of a TAP experiment with HUB1. This protein contains five pentatricopeptide repeats (PPR) that function in RNA stabilization since the same domain is present in Chloroplast RNA Processing 1 (Crp1), a protein involved in RNA processing. TAP using SL as bait showed how tight its association with HUB1, HUB2 and KH is. Combining the TAP experimental data for HUB1, HUB2 and SL (and KH will follow) as baits we can conclude that the so-called histone H2B monoubiquitination tetramere core complex composed by HUB1-HUB2 contains at least two additional proteins: SL and KH. Both proteins have RNA binding modules. This kind of proteins has never been associated with histone H2B monoubiquitination so far, however the fact that this process, like the other epigenetic marks, is tightly associated to DNA and to newly generated mRNA, propose these proteins to have crucial roles in histone H2B monoubiquitination where their affinity for RNA could lead to incorporate in the HUB1/HUB2 complex upstream or feedback information (e.g. from small RNA molecules). UBC2 allowed pulling down the other basic components of ubiquitination complex like ubiquitin, represented by 14 UBQ different accession numbers that cannot be distinguished due to the high homology among them, and two E1 activating enzymes AtUBA1 and AtUBA2.

Third Experiment:

In order to identify direct interactors of HUB1, a yeast-2-hybrid experiment was carried out.
For each of the selected proteins, AD and BD fusions were constructed whose expression was confirmed by Western blotting. HUB2, HUB1 truncated, SEUSS and KH strains showed self activation activity evidenced by a blue staining of colonies and were therefore not be used as prey in the Y2H experiment to avoid false positive results. Results are summarised in Table K:

TABLE L

Matrix with pair wise interactions.

pDEST32

pDEST22	HUB1	HUB2 no RING	SL

HUB1	++	++	++
HUB1 no RING	++	++	−
HUB2	++	++	−
HUB2 no RING	−	−
SL	++	−	++
SEUSS	+	+	−

++, strong interaction; +, mild interaction; −, no interactions; interaction among the different HUB1, HUB2 and SEUSS versions have been tested in two independent experiments.

Full length and truncated version of HUB1 and full length HUB2 interacted in vivo. The RING domain seemed to influence the interaction of the HUB1 interactome complex that was most evident in the case of HUB2 where the deletion of this domain abolished the interaction between HUB1 and HUB2. The strongest interaction of HUB1 was with SL.
To test which portion of SL binds HUB1, two different versions of the protein were generated. The results showed that only the N-terminal region but not the C-terminal part interacts with HUB1. SL also showed dimerization activity and both regions of the protein seemed to be involved. HUB1 and the truncated version of HUB2 showed also a mild interaction with SEUSS. In addition SEUSS showed a strong interaction with itself reflecting homodimerization. A strong interaction between SEUSS and LUG/RON2 was detected and, as reported in previous studies, supporting the reliability of the assay. Neither HUB1 nor HUB2 were shown to have a detectable interaction with the E2 conjugating enzymes involved in histone H2B monoubiquitination (UBC1, UBC2, UBC3) that are present in the Arabidopsis thaliana genome, however it is possible that the HUB1/HUB2 dimeric or tetrameric complex is essential for the interaction with one of the UBC polypeptides.

Example 24

Phenotypic Characterisation of Spen-Like Mutant Plants

The Spen-like protein comprises an RNA recognition motif (RRM) in the middle of the sequence and a “spen paralog and ortholog C-terminal” (SPOC) domain in the C-terminal region; which is the typical composition of Split Ends (Spen) proteins.
Arabidopsis thaliana sl-1 (SALK_—025388) and sl-2 (GABI_—461F01) seeds were obtained from the Nottingham Arabidopsis Stock Centre and GABI-Kat respectively. Homozygous seeds were sown on Jiffy-7 pellet (jiffypot.com), vernalized overnight and subsequently grown in growth chambers under long day conditions as described above. At the time of flowering (with inflorescence stem length approximately 0.5 cm) leaf series were prepared by aligning all the rosette leaves on 1% agar plates (n=10). Leaves were photographed and scanned to measure leaf area by ImageJ 1.41. The number of leaves at flowering was also scored on the entire population (n=25).
Twenty-five plants of wild type (Col-0), hub1-4 (SALK_—122512) (Fleury et al., 2007) and the two T-DNA lines (sl-1 and sl-2) were grown on soil for phenotypic analysis. Flowering time was slightly but significantly reduced in the case of sl-2 and highly altered in hub1-4. On the other hand, sl-1 shows a consistent reduction of the number of leaves at the moment of flowering while the time of this developmental switch was comparable to the one of Col-0 (FIGS. 22A and B). Ten plants of each genotype were grown until the flowering stem was approximately 0.5 mm tall and then analyzed for their leaf size, a measurement that gives a clear indication of the rosette size. The results of this analysis show that the area of almost all the leaves (cotyledons included) of sl-1 plants was significantly smaller than wild type. On the contrary, this reduction was milder in the sl-2 mutant and only few leaves were significantly smaller (FIG. 22C). The fifteen remaining plants were further grown to analyze the reproductive structures. The flower stem diameter of each genotype was measured and a significant reduction was observed in both sl-1 and sl-2 as well as for hub1-4. However, at the level of flower organs no obvious differences were noted among the sl alleles and with the wild type. These indications suggest that, unlike FPA (which comprises multiple RRM domains, in contrast to SL), SL is likely not involved in flower development as it has been shown by the absence of any flowering time phenotypes and alteration of flower structures (FIG. 22). SL does not show any flowering phenotype, but the alterations displayed by its mutants are restricted to growth. This is evident in FIG. 22B where, although flowering time is in line with the one of WT, sl-1 produces 1.3 leaves less than Col-0. In addition to this, traits clearly related to growth like leaf area and flowering stem diameter are significantly reduced. Flowers structures of sl-1 and sl-2 show no alterations and the production of siliques and therefore seeds is also not altered in any of the T-DNA lines. It has been shown in the previous examples that SL directly interacts with HUB1, an E3 ligase involved in histone H2B monoubiquitination that also has a function in plant growth (Fleury et al., 2007). According to these data, we therefore propose SL as a plant growth regulator by its influence on this epigenetic mark.

Claims

1. A method for improving growth characteristics in a plant relative to a control plant, comprising introducing and expressing in a plant a nucleic acid encoding a HUB1 polypeptide operably linked to a medium strength constitutive promoter, wherein the HUB1 polypeptide comprises a RING domain of a C3HC4 type.

2. The method of claim 1, wherein the nucleic acid encodes any one of the proteins listed in Table A or is a portion of such a nucleic acid, or a nucleic acid capable of hybridizing with such a nucleic acid.

3. The method of claim 1, wherein the improved growth characteristics comprise one or more of increased germination vigour, increased early vigour, increased yield, increased biomass, and/or increased seed yield relative to a control plant.

4. The method of claim 1, wherein the improved growth characteristics are obtained under non-stress conditions.

5. The method of claim 1, wherein the improved growth characteristics are obtained under conditions of drought stress, salt stress, or nitrogen deficiency.

6. The method of claim 1, wherein the medium strength constitutive promoter is a HMGP promoter or a HMGP promoter from rice.

7. A construct comprising:

(i) a nucleic acid encoding a HUB1 polypeptide as defined in claim 1;

(ii) one or more heterologous medium strength control sequences capable of driving expression of the nucleic acid of (i); and optionally

(iii) a transcription termination sequence.

8. The construct of claim 7, wherein one of the medium strength control sequences is a constitutive promoter, a HMGP promoter, or a HMGP promoter from rice.

9. A method for making a plant having one or more of increased germination vigour, increased early vigour, and increased yield, relative to a control plant, comprising transforming a plant, plant cell or plant part with the construct of claim 7.

10. A plant, plant cell or plant part comprising the construct of claim 7.

11. A method for the production of a transgenic plant having improved growth properties, increased germination vigour, increased early vigour, and/or increased yield relative to a control plant, comprising:

(i) introducing and expressing in a plant or plant cell a nucleic acid encoding a HUB1 polypeptide as defined in claim 1;

(ii) cultivating the plant or plant cell under conditions promoting plant growth and development; and

(iii) selecting for a plant having improved growth properties, increased germination vigour, increased early vigour, and/or increased yield relative to a control plant.

12. A transgenic plant obtained by the method of claim 11, or a plant cell, plant part, seed, or progeny of said plant, wherein said plant, plant cell, plant part, seed, or progeny comprises a recombinant nucleic acid encoding said HUB1 polypeptide.

13. A transgenic plant having improved growth properties, increased germination vigour, increased early vigour, and/or increased yield relative to a control plant, resulting from modulated expression of a nucleic acid encoding a HUB1 polypeptide as defined in claim 1, or a transgenic plant cell derived from said transgenic plant.

14. The transgenic plant of claim 13, or a transgenic plant cell derived therefrom, wherein said plant is a crop plant, a monocot, or a cereal, or wherein said plant is rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, secale, einkorn, teff, milo or oats.

15. Harvestable parts of the transgenic plant of claim 13, wherein the harvestable parts are shoot biomass and/or seeds and comprise a recombinant nucleic acid encoding said HUB1 polypeptide.

16. A product derived from the transgenic plant of claim 13 and/or from harvestable parts of said plant, wherein said product comprises a recombinant nucleic acid encoding said HUB1 polypeptide.

17. A method for modifying a light regulated phenotype in a plant, comprising expression in a plant of a nucleic acid encoding a HUB1 polypeptide.

18. A method for modifying plant growth characteristics relative to a control plant, comprising modulating expression in a plant of a nucleic acid encoding any of the proteins listed in Tables G to K, or an orthologue thereof, wherein the plant growth characteristics comprise increased yield and/or increased stress resistance.

19. The method of claim 18, wherein the modified growth characteristics comprise increased yield, increased stress resistance, and/or modified architecture.

20. The method of claim 19, wherein the increased yield comprises increased biomass and/or increased seed yield, or wherein the increased stress resistance is one or more of increased drought stress resistance, increased salt stress resistance, and/or improved growth under conditions of nutrient deficiency.