WO2024008752A1 - Methods to increase iron content in plants - Google Patents
Methods to increase iron content in plants Download PDFInfo
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- WO2024008752A1 WO2024008752A1 PCT/EP2023/068456 EP2023068456W WO2024008752A1 WO 2024008752 A1 WO2024008752 A1 WO 2024008752A1 EP 2023068456 W EP2023068456 W EP 2023068456W WO 2024008752 A1 WO2024008752 A1 WO 2024008752A1
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
- C07K14/415—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from plants
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- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
- C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
- C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
- C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
- C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
- C12N9/14—Hydrolases (3)
- C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
- C12N9/22—Ribonucleases [RNase]; Deoxyribonucleases [DNase]
Definitions
- the invention relates to genetically altered plants, parts thereof or plant cells, where the plants, parts thereof or plant cells are characterised by increased levels of iron. Also described are methods of increasing the levels of iron in a plant, particularly a crop plant as well as food compositions and nutritional supplements obtained from the plants or parts thereof.
- iron deficiency remains a significant global health problem. It detrimentally affects health outcomes for vulnerable populations including pregnant women and young children in developing countries with dire economic consequences.
- Gottschalk identified an X-ray induced mutant in the pea (Pisum sativum) cultivar Dippes Gelbe Viktoria characterised by premature senescence of leaves and stipules, leading to the associated mutant name degenerative leaves (dgl). Often the leaves display brown spots, although not in all growth conditions. Further work on this mutant demonstrated that the brown spots were a symptom of excessive iron accumulation in the leaves and that the seed also accumulate iron. However, attempts to identify the mutation or at least map it to a specific chromosome have failed (Kneen et al., 1990) and consequently the causative mutation has not been identified to date.
- the dgl mutation affects a motif that is thought to mediate iron sensing, leading to at least 25-fold more iron in young pea shoots and at least four-fold more iron in seeds.
- the plants have only minor growth defects, whereas null mutants in BTS homologs in model plant species are lethal.
- the BRUTUS polypeptide is highly conserved in both plants and algae. Therefore, introducing similar mutations into the BRUTUS polypeptide to reduce its iron-sensing function or reduce iron binding can be used to increase the iron content of any plant or alga.
- a genetically altered organism, part thereof or cell wherein the organism, part thereof or cell comprises one or more mutations in at least one nucleic acid sequence encoding a BRUTUS polypeptide, wherein when the organism is a plant, the BRUTUS polypeptide comprises an amino acid sequence as defined in SEQ ID NO: 4 or a functional variant or homologue thereof, wherein the functional variant has at least 30% overall amino acid sequence identity to SEQ ID NO: 4; and wherein when the organism is an alga, the BRUTUS polypeptide comprises an amino acid sequence as defined in SEQ ID NO: 15 or a functional variant or homologue thereof, wherein the functional variant has at least 30% overall amino acid sequence identity to SEQ ID NO: 15; and wherein the mutation reduces or abolishes binding of iron to the polypeptide, and wherein the organism is a plant or alga.
- the BRUTUS polypeptide comprises one or more hemerythrin domain(s), wherein there is at least one mutation in at least one hemerythrin domain, wherein the hemerythrin domain comprises a sequence selected from SEQ ID NO: 20, or 50 - 102 or a functional variant thereof. More preferably, the at least one mutation is in the first N- terminal hemerythrin domain.
- the at least one mutation is a deletion of one or more amino acids. More preferably, at least one mutation is a deletion of between 1 and 50 amino acids, preferably around 5 amino acids, or around 20 amino acids (specifically 22 amino acids in one embodiment).
- the mutation may be a deletion of SEQ ID NO: 1 , 22, 23, 24, 44, 47, 48, 49 or a variant thereof, wherein the variant has at least 80% overall sequence identity to SEQ ID NO: 1 , 22, 23,24, 44, 47, 48, or 49.
- the mutation does not significantly affect organism growth or yield.
- a method of increasing iron concentration in an organism, part thereof or cell comprising introducing at least one mutation into at least one nucleic acid sequence encoding BRUTUS wherein when the organism is a plant, the BRUTUS polypeptide comprises an amino acid sequence as defined in SEQ ID NO: 4 or a functional variant or homologue thereof, wherein the functional variant has at least 30% overall amino acid sequence identity to SEQ ID NO: 4; and wherein when the organism is an alga, the BRUTUS polypeptide comprises an amino acid sequence as defined in SEQ ID NO: 15 or a functional variant or homologue thereof, wherein the functional variant has at least 30% overall amino acid sequence identity to SEQ ID NO: 15; and wherein the mutation reduces or abolishes binding of iron to the polypeptide, and wherein the organism is a plant or alga.
- the method comprises introducing at least one mutation into at least one nucleic acid sequence encoding a BRUTUS polypeptide wherein when the organism is a plant, the BRUTUS polypeptide comprises an amino acid sequence as defined in SEQ ID NO: 4 or a functional variant or homologue thereof, wherein the functional variant has at least 30% overall amino acid sequence identity to SEQ ID NO: 4; and wherein when the organism is an alga, the BRUTUS polypeptide comprises an amino acid sequence as defined in SEQ ID NO: 15 or a functional variant or homologue thereof, wherein the functional variant has at least 30% overall amino acid sequence identity to SEQ ID NO: 15; and wherein the mutation reduces or abolishes binding of iron to the polypeptide, and wherein the organism is a plant or alga.
- the method comprises introducing a mutation into the BRUTUS polypeptide.
- the BRUTUS polypeptide comprises one or more hemerythrin domains, and the method comprises introducing at least one mutation in at least one hemerythrin domain, wherein the hemerythrin domain comprises a sequence selected from SEQ ID NO: 20, or 50 to 102 or a functional variant thereof.
- the method comprises introducing at least one mutation in the first N-terminal hemerythrin domain.
- the method comprises an organism wherein said organism is a plant, part thereof or cell is a plant
- the plant is selected from a monocot or dicot. More preferably the plant is selected from rice, wheat, maize, barley, Brassicas, Medicago soybean, potato and tomato, lettuce and beetroot.
- the organism is a plant, plant cell or plant part thereof
- said plant is a monocot or dicot. More preferably, when the organism is a plant, plant cell or plant part thereof, said plant is selected from rice, wheat, maize, barley, Brassicas, Medicago, soybean, potato and tomato and beetroot.
- the plant part thereof is a seed or a vegetative part of the plant, preferably selected from the root, shoot or leaves.
- the plant part of the invention may also comprise one or more mutations in a BRUTUS polypeptide as described herein. Preferably therefore the plant part has an increased iron content.
- the alga is selected from Chlorella (such as Auxenochlorella protothecoides), Porphyra, Dulse, Laminaria, Alaria, Nostoc, Monostroma, Ulva, Enteromorpha, Caulerpa racemose and Durvillaea antarctica.
- Chlorella such as Auxenochlorella protothecoides
- Porphyra Dulse
- Laminaria Alaria
- Nostoc Monostroma
- Ulva Monostroma
- Enteromorpha Caulerpa racemose and Durvillaea antarctica.
- a method of screening a population of plants and identifying and/or selecting an organism that will have an increased iron content comprising detecting in the organism or organism germplasm at least one polymorphism in a BRUTUS gene, wherein the BRUTUS gene encodes a polypeptide as defined in SEQ ID NO: 4 or 15 or a functional variant or homologue thereof, wherein the functional variant has at least 30% overall sequence identity to SEQ ID NO: 4 or 15; and wherein the BRUTUS polypeptide comprises at least one hemerythrin domain, and wherein the at least one polymorphism is in at least one hemerythrin domain.
- the polymorphism is a deletion of one or more, preferably around five amino acids, or around 20 amino acids (specifically 22 amino acids in one embodiment) in at least one hemerythrin domain of the BRUTUS polypeptide.
- a method of producing a food, vitamin or nutritional supplement comprising producing a genetically altered organism, and producing a food composition, vitamin or nutritional supplement from the organism or part thereof.
- a food, vitamin or nutritional supplement obtained or obtainable by the method of the invention.
- a method of treating anaemia in a patient in need of iron comprising consuming the seed or other plant part of the genetically altered plant or the food, vitamin or nutritional supplement derived from the genetically altered plant, part thereof or plant cell.
- Figure 1 shows the phenotypic characteristics associated with the dgl mutation.
- A The pea cultivar Sparkle, which serves as the wild-type line (left) and the same cultivar but carrying the dgl mutation (right).
- Upper panel 4-week-old plants grown on F2 Levington compost in the greenhouse.
- Lower panel Leaves consisting of two leaflets of Sparkle wild type (left) and the dgl mutant (right). Note the brown spots due to hyperaccumulation of iron (toxicity).
- B Iron staining using potassium ferrocyanide, known as Prussian Blue or Peris’ staining, in pieces of the leaf.
- C Iron concentration in leaflets, measured 2 weeks apart. Leaflets were dried, weighed and digested in nitric acid and hydrogen peroxide.
- the digest was diluted with milliQ water to 5% nitric acid and the pH was brought to 7 with ammonium acetate. After reduction of iron with ascorbic acid, ferrous iron was quantitatively detected using the colorimetric chelator ferene. Similar results were obtained with Inductively Coupled Plasma-Optical Emission Spectroscopy (ICP-OES).
- ICP-OES Inductively Coupled Plasma-Optical Emission Spectroscopy
- Figure 2 shows that the deletion is predicted to remove 5 amino acids from the Hr1 domain, likely affecting iron binding.
- A The 15 nucleotide deletion is located in exon 2 of the BRUTUS gene and removes 5 semi-conserved amino acids in the first hemerythrin (Hr) domain of the polypeptide. Each of the three Hr domains of BRUTUS harbours a diiron centre. Two iron-binding ligands, histidine (H) and glutamate (E) residues, are close to this deletion.
- B Modelling predicts that the position of 2 of the 7 iron ligands in the Hr1 domain are shifted, affecting the stability of the di-iron site.
- Figure 3 shows that the expression and iron storage in ferritin is highly upregulated in dgl mutant leaves.
- A Transcript abundance of the five ferritin genes found in the pea genome. No expression was observed for Psat15g171400 which is therefore likely to be a non-functional gene (pseudogene). The expression of the other 4 genes is significantly increased in dgl vs Sparkle leaves.
- B Protein levels of ferritin detected by antibodies using Western blot analysis. The two bands around 25 kDa correspond to two different isoforms of the monomer, processed to slightly different molecular weights after import into the chloroplasts.
- Figure 4 shows that a small deletion in BRUTUS co-segregates with the high-iron phenotype.
- A Detail of the RNA-seq mapping data, showing a 15 nucleotide deletion at the 5’ end of exon 2 (red) in the BRUTUS gene, Psat1g036240.
- B PCR analysis to detect the wild-type and dgl alleles. The shorter PCR product with the 15 nt deletion is associated with the dgl mutant and F2 segregates that displayed iron accumulation. A total of 44 sibling F2 plants were tested, of which 11 had the dgl phenotype and invariable the 15-nucleotide deletion in BRUTUS.
- Figure 5 shows an amino acid alignment of part of the first hemerythrin domain in the BRUTUS protein in several crops; the high conservation of this domain and the specific 5 amino acids deleted in the dgl mutant makes it a gene-editing target for increased iron.
- the shown sequence fragments are from Arabidopsis (Athal), Brassica, pea (Psat), rice (Os), tomato (Solyc), barley (Hovul), wheat (Traes) and alga (Auxchl).
- Figure 6 shows an amino acid alignment of BRUTUS proteins across different species. Sequences are shown for Arabidopsis (Athal), Brassica, pea (Psat), rice (Os), wheat (Traes) and green alga (chromochloris).
- FIG. 7 shows that the wild-type pea (Ps) BTS1 coding sequence genetically complements the iron accumulation phenotype of the Arabidopsis bts-3 mutant, but the pea BTS1-dgl sequence does not.
- Figure 8 shows the proposed mechanism of iron accumulation in dgl (bts1) mutants. Reduced function of the E3 ubiquitin ligase BRUTUS (BTS) leads to constitutive activity of the iron uptake pathway in roots.
- BTS E3 ubiquitin ligase BRUTUS
- the pea BTS1 gene is expressed predominantly in shoots in agreement with Arabidopsis BTS promoter activity and high transcript levels in leaves, root stele and embryo cotyledons.
- Arabidopsis BTS interacts with the transcription factor ILR3 to target it for degradation. Decreased activity of BTS leads to increased levels (and transcriptional activity) of ILR3, which indirectly leads to enhanced transcription of iron uptake genes. Iron accumulates in minor and major veins and also in seeds.
- Figure 9 shows an example of a gene-editing strategy in wheat based on the dgl mutation in pea.
- A. Two guide RNAs were designed, Guide 1 and Guide 2 (magenta), which are predicted to generate an in-frame deletion of 66 nucleotides in between histidine (H, orange) residues that bind the di-iron cofactor (based on homology) in the wheat HRZ1 protein, which is homologous to BTS.
- the target sequence of the guides is identical in all three gene copies of HRZ1 in bread wheat and is thus predicted to edit all three copies.
- B. 3D modelling using the neural network Alphafold2 shows that the deletion causes one of the histidine ligands to flip outwards, likely destabilizing the di-iron site (transparent pink spheres). In the pea dgl variant, two iron-binding ligands are predicted to rotated away (not shown here).
- FIG 10 shows selected first-generation (TO) wheat plants transformed with the HRZ gene editing constructs which have increased levels of iron in leaves and grains, as well as increased zinc.
- A Iron staining using the Peris’ method on leaf sectors and on mature grain cut transversely (top) and along the longitudinal plane (bottom). Iron is evenly distributed in leaves and barely detectable with Peris' staining in wild-type plants. The blue patches indicate significant iron accumulation which is only observed in a very limited number of iron homeostasis mutants.
- B Iron and zinc concentrations measured by ICP-OES. The grain of gene-edited wheat plants often have increased zinc levels as well as increased iron.
- HRZ genes act upstream of the NAS genes which are known to enhance both iron and zinc concentrations when overexpressed. It is important to note that the TO lines are chimeric and that Cas9 activity continues until this is crossed out.
- nucleic acid As used herein, the words “nucleic acid”, “nucleic acid sequence”, “nucleotide”, “nucleic acid molecule” or “polynucleotide” are intended to include DNA molecules (e.g., cDNA or genomic DNA), RNA molecules (e.g., mRNA), natural occurring, mutated, synthetic DNA or RNA molecules, and analogs of the DNA or RNA generated using nucleotide analogs. It can be single-stranded or double-stranded. Such nucleic acids or polynucleotides include, but are not limited to, coding sequences of structural genes, anti-sense sequences, and non-coding regulatory sequences that do not encode mRNAs or protein products.
- genes may include introns and exons as in the genomic sequence, or may comprise only a coding sequence as in cDNAs, and/or may include cDNAs in combination with regulatory sequences.
- polypeptide and “protein” are used interchangeably herein and refer to amino acids in a polymeric form of any length, linked together by peptide bonds.
- a “genetically altered organism” is a plant that has been genetically altered compared to a common, naturally occurring wild type (WT) plant.
- a genetically altered organism is an organism that has been altered compared to the naturally occurring wild type (WT) plant using a mutagenesis method, such as any of the mutagenesis methods described herein.
- the mutagenesis method is targeted genome modification or genome editing.
- the genome has been altered compared to wild type sequences using a mutagenesis method.
- Such organisms have an altered phenotype as described herein, such as an increased iron content. Therefore, in this example, increased iron content is conferred by the presence of an altered genome, for example, the presence of at least one of the described mutations in the BRUTUS gene.
- the aspects of the invention involve recombination DNA technology and exclude embodiments that are solely based on generating plants by traditional breeding methods.
- a genetically altered organism, part thereof or cell wherein the organism, part thereof or cell comprises one or more mutations in at least one nucleic acid sequence encoding a BRUTUS polypeptide.
- the mutation is in the endogenous gene.
- the organism is not a human.
- a plant comprising one of the described mutations in the BRUTUS polypeptide has an increased amount of iron, particularly in vegetative tissues such as the leaves and the roots or in the seeds. Accordingly, the genetically altered organism of the invention is characterised by having an increased amount of iron.
- a wheat plant altered to have one of the described mutations in the BRUTUS gene homolog (HRZ), or at least one of the three homeologsin hexapioid bread wheat has an increased amount of iron and/or zinc, particularly in the grain.
- the genetically altered organism of the invention can be characterised by having an increased amount of zinc.
- said genetically altered organism has increased levels of iron and zinc.
- a method of increasing the iron content in an organism comprising introducing at least one mutation into at least one nucleic acid sequence encoding a BRUTUS polypeptide.
- the organism is a plant or plant part thereof.
- a method of increasing the zinc content in an organism comprising introducing at least one mutation into at least one nucleic acid sequence encoding a BRUTUS polypeptide.
- the organism is a plant or plant part thereof.
- a method of increasing the iron and zinc content in an organism wherein the method comprises introducing at least one mutation into at least one nucleic acid sequence encoding a BRUTUS polypeptide.
- the organism is a plant or plant part thereof.
- a method of producing an organism, part thereof or cell wherein the organism, part thereof or cell has an increased iron content, and wherein the method comprises introducing at least one mutation into at least one nucleic acid sequence encoding a BRUTUS polypeptide.
- the organism is not a human
- a method of producing an organism, part thereof or cell, wherein the organism, part thereof or cell has an increased zinc content comprises introducing at least one mutation into at least one nucleic acid sequence encoding a BRUTUS polypeptide.
- the organism is not a human
- a method of producing an organism, part thereof or cell wherein the organism, part thereof or cell has an increased zinc and iron content, and wherein the method comprises introducing at least one mutation into at least one nucleic acid sequence encoding a BRUTUS polypeptide.
- the organism is not a human.
- the terms increased iron “content”, “level”, “concentration” or “amount” can be used interchangeably, and all refer to the amount of iron - preferably in the form of ferric or ferrous iron - or zinc in the genetically altered organism.
- the iron may be in the form of ferritin (ferric-oxyhydrite), as well as in other forms, for example ferric citrate2 malate2 and ferrous nicotianamine compounds.
- the genetically altered organism is a plant
- the amount of iron and/or zinc is preferably increased in vegetative tissues. This includes the roots, stems, shoot buds and leaves, and in particular in the shoots and leaves. Alternatively, or additionally, the amount of iron and/or zinc in the seeds is increased.
- Iron and/or zinc from either the seeds or vegetative tissue can be extracted and used, for example, as a nutritional supplement or in a food or feed formulation.
- the amount of iron and/or zinc in the genetically altered organism is increased compared to the amount of iron and/or zinc in a control or wild-type organism, as defined below.
- an increase may be between 5 and 50-fold more than the amount of iron and/or zinc in the wild-type or control organism.
- said increase is at least 5- fold, at least 10-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold or at least 50-fold more than the amount of iron and/or zinc in the control or wild-type plant.
- the level of increase is at least 5-fold in the leaves.
- the level of increase is at least 2- fold in the seeds or part of the seeds.
- said increase is around 25- fold as shown in Figure 1.
- the amount of iron in the organism or any part of the organism may be measured using standard techniques in the art.
- an iron leaf staining assay can be used (as described below and in Meguro et al., 2007).
- the leaf is incubated with potassium ferrous cyanide in an acid solution of 2% (weight/vol) hydrochloric acid, and left for 2 hours, after which leaf pigments such as chlorophyll are removed by incubation with ethanol.
- the first step is to digest the tissue in, for example, nitric acid and hydrogen peroxide, then either dilute the sample with water for Inductively Coupled Plasma-Optical Emission Spectroscopy, or neutralise the digested tissue with for example, ammonium acetate then reduce with, for example, ascorbic acid, and finally quantify the iron concentration with a colorimetric iron chelator and measure absorbance. This can be used to calculate the amount of iron in pg per g of dry weight.
- ICP Inductively Coupled Plasma-Optical Emission Spectroscopy
- This is used for a ‘broad-sweep’ element analysis (iron as well as other elements).
- ICP-OES is the gold standard for iron measurements in biological tissues.
- atomic absorption spectroscopy (AAS) or X-ray fluorescence (XRF) may be used.
- Inductively Coupled Plasma-Optical Emission Spectroscopy can be used for a ‘broad-sweep’ element analysis to measure zinc as well as other elements.
- the methods of the invention may further comprise the step of assessing the phenotype of the genetically altered organism, and specifically measuring the amount of iron in the organism, or part thereof or cell, preferably compared to the level in a wild-type or control organism.
- the BRUTUS polypeptide is an E3 ubiquitin ligase that negatively regulates the response to iron deficiency by promoting the degradation of iron-responsive transcription factors.
- BRUTUS polypeptides contain up to three iron-binding hemerythrin domains in the N- terminus and a CHY/RING-type Zn finger domain with ubiquitin E3 ligase activity in the C-terminus.
- HRZ refers to a BRUTUS orthologue, and the terms BRUTUS and HRZ are therefore used interchangeably herein.
- the BRUTUS polypeptide is characterised by one or more, but preferably three hemerythrin domains, required for sensing the amount of iron in the cell.
- Each hemerythrin domain is believed to bind to two iron atoms
- the hemerythrin domain or domains are found at the N-terminus of the protein. More preferably the domains are consecutive.
- the sequence of the hemerythrin domains are highly conserved in both plants and algae, as shown in Figure 3.
- the hemerythrin domain has four alpha-helices binding two iron ions.
- the sequence may be of a variable length, but contains histidine and glutamate residues required for iron binding spaced as follows: (H)-HxxxE-H-HxxxE.
- sequence of the hemerythin domain may comprise the following sequence (from the Hr1 domain of the pea BRUTUS protein). conserveed residues are underlined.
- the sequence of the hemerythin domain may comprise any of the sequences defined in SEQ ID NO: 50 to 102 or a functional variant thereof.
- a homologue or functional variant may be defined as comprising at least one hemerythin domain.
- This domain may comprise SEQ ID NO: 20, or any of SEQ ID NO: 50 to 102 or a functional variant thereof, preferably a sequence with at least 70%, more preferably 80%, even more preferably 90% or more overall sequence identity to SEQ ID NO: 20, or any of SEQ ID NO: 50 to 102.
- a functional variant of a hemerythrin domain is a domain that can bind iron as described herein.
- the CHY/RING-type Zn finger domain may comprise the following sequence or a functional variant thereof:
- a functional variant of a CHY/RING-type Zn finger domain retains the ability of the domain to mediate E3 ubiquitin ligase activity.
- the nucleic acid or gene sequence of the BRUTUS gene may comprise or consist of a nucleic acid sequence encoding a polypeptide as defined in SEQ ID NO: 4 or a functional variant or homologue thereof.
- the sequence of the homologue comprises or consists of a nucleic acid sequence as defined in SEQ ID NO: 2 to 3 and 5 to 19 or a functional variant thereof.
- the nucleic acid sequence may comprise or consist of SEQ ID NO: 42 or 43 or a functional variant or homologue thereof.
- the amino acid sequence of the BRUTUS protein comprises or consists of a sequence as defined in SEQ ID NO: 4 or a functional variant or homologue thereof.
- sequence of the homologue comprises or consists of a nucleic acid sequence as defined in SEQ ID NO: 2, 3 or 5 to 19 or a functional variant thereof.
- an ‘endogenous’ nucleic acid as used herein may refer to the native or natural sequence in the plant genome.
- the endogenous sequence of the BRUTUS gene comprises a sequence that encodes an amino acid sequence as defined in SEQ ID NO: 4.
- functional variants as defined herein
- homologs are shown in SEQ ID NOs: 2, 3 and 5 to 19 or functional variants thereof. Accordingly, in one embodiment, the homologue is selected from one of the above homologous sequences.
- the term “functional variant of a nucleic acid sequence” as used with reference to any SEQ ID NO described herein refers to a variant gene sequence or part of the gene sequence that retains the biological function of the full non-variant sequence (e.g. able to bind iron (e.g. one or more iron molecules) and/or has E3 ubiquitin ligase activity).
- a functional variant also comprises a variant of the gene of interest, which has sequence alterations that do not affect function, for example in non-conserved residues. Also encompassed is a variant that is substantially identical, i.e. has only some sequence variations, for example in non-conserved residues, compared to the wild type sequences as shown herein and is biologically active.
- a codon for the amino acid alanine, a hydrophobic amino acid may be substituted by a codon encoding another less hydrophobic residue, such as glycine, or a more hydrophobic residue, such as valine, leucine, or isoleucine.
- a codon encoding another less hydrophobic residue such as glycine
- a more hydrophobic residue such as valine, leucine, or isoleucine.
- changes which result in substitution of one negatively charged residue for another such as aspartic acid for glutamic acid, or one positively charged residue for another, such as lysine for arginine, can also be expected to produce a functionally equivalent product.
- a functional variant as used above also (or alternatively) refers to a variant sequence that has at least 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%,
- able to bind to iron is meant that the iron-binding amino acids/motif (e.g. (H)-HxxxE-H-HxxxE) need to be present in the functional variant, and that preferably the amino acids of the iron-binding motif are spaced such that iron can bind. Iron binding can be measured as described below.
- the overall sequence identity of a variant can be determined using any number of sequence alignment programs known in the art.
- the functional variant has at least 35 to 40% overall sequence identity to the non-variant sequence. In another embodiment, the functional variant has at least 70% overall sequence identity to the non-variant sequence.
- homolog also designates a gene orthologue from other plant or algae species.
- a homolog may have, in increasing order of preference, at least 25%, 26%, 27%, 28%, 29%, 30%, 31 %, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%,
- homolog may be functional, in that the homolog is able to bind iron (e.g. one or more iron atoms) and/or has E3 ubiquitin ligase activity and consequently negatively regulate iron responses.
- Functional variants of homologs as defined above are also within the scope of the invention.
- nucleic acid sequences or polypeptides are said to be “identical” if the sequence of nucleotides or amino acid residues, respectively, in the two sequences is the same when aligned for maximum correspondence as described below.
- the terms “identical” or percent “identity,” in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same, when compared and aligned for maximum correspondence over a comparison window, as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection.
- sequence identity When percentage of sequence identity is used in reference to proteins or peptides, it is recognised that residue positions that are not identical often differ by conservative amino acid substitutions, where amino acids residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule. Where sequences differ in conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Means for making this adjustment are well known to those of skill in the art. For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated.
- sequence comparison algorithm calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters.
- algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms.
- Suitable homologues can be identified by sequence comparisons and identifications of conserved domains, as described above. There are predictors in the art that can be used to identify such sequences.
- the function of the homologue can be identified as described herein and a skilled person would thus be able to confirm the function, for example when expressed in a plant and function is assessed (e.g. as described herein, some of the characterising features of BRUTUS include binding to iron and negatively regulating iron responses).
- nucleotide sequences of the invention and described herein can also be used to isolate corresponding sequences from other organisms, particularly other plants, particularly crop plants and algae.
- methods such as PCR, hybridization, and the like can be used to identify such sequences based on their sequence homology to the sequences described herein.
- Topology of the sequences and the characteristic domain structure can also be considered when identifying and isolating homologs.
- Sequences may be isolated based on their sequence identity to the entire sequence or to fragments thereof.
- hybridization techniques all or part of a known nucleotide sequence is used as a probe that selectively hybridizes to other corresponding nucleotide sequences present in a population of cloned genomic DNA fragments or cDNA fragments (i.e. , genomic or cDNA libraries) from a chosen plant.
- the hybridization probes may be genomic DNA fragments, cDNA fragments, RNA fragments, or other oligonucleotides, and may be labelled with a detectable group, or any other detectable marker.
- Hybridization of such sequences may be carried out under stringent conditions.
- stringent conditions or “stringent hybridization conditions” is intended conditions under which a probe will hybridize to its target sequence to a detectably greater degree than to other sequences (e.g., at least 2-fold over background).
- Stringent conditions are sequence dependent and will be different in different circumstances.
- target sequences that are 100% complementary to the probe can be identified (homologous probing).
- stringency conditions can be adjusted to allow some mismatching in sequences so that lower degrees of similarity are detected (heterologous probing).
- a probe is less than about 1000 nucleotides in length, preferably less than 500 nucleotides in length.
- stringent conditions will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30°C for short probes (e.g., 10 to 50 nucleotides) and at least about 60°C for long probes (e.g., greater than 50 nucleotides). Duration of hybridization is generally less than about 24 hours, usually about 4 to 12. Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide.
- a variant as used herein can comprise a nucleic acid sequence encoding a BRUTUS polypeptide as defined herein that is capable of hybridising under stringent conditions, for example as described above, to a nucleic acid sequence as defined in SEQ ID NO: 4.
- a genetically altered plant, part thereof or plant cell wherein the plant, part thereof or plant cell comprises at least one mutation in at least BRUTUS gene, wherein the BRUTUS gene comprises or consists of a. a nucleic acid sequence encoding a polypeptide as defined in one of SEQ ID NO: 4 or a functional variant or homolog thereof; or b. a nucleic acid sequence as defined in one of SEQ ID NO:42, SEQ ID NO:43 or a functional variant or homolog thereof; or c.
- nucleic acid sequence with at least 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 at least 99% overall sequence identity to either (a) or (b); or d. a nucleic acid sequence encoding a BRUTUS polypeptide as defined herein that is capable of hybridising under stringent conditions as defined herein to the nucleic acid sequence of any of (a) to (c).
- the mutation is in one or more of the hemerythrin domains.
- the mutation is in one or more of the hemerythin domains described in SEQ ID NO: 20, or 50 to 102 and functional variants thereof. That is, the mutation is in the nucleic acid sequence that encodes one or more of the hemerythrin domains.
- the one or more mutation prevents or reduces the binding of iron to the hemerythrin domain.
- the ability to bind iron may be measured experimentally by (1) purifying the protein from the plant and determining bound iron by (i) UV-visible spectroscopy, in combination with (ii) a valid method to measure iron, such as published colorimetric reagents and ICP- OES or ICP-MS.
- a valid method to measure iron such as published colorimetric reagents and ICP- OES or ICP-MS.
- the full length protein, or the full-length hemethryin domain sequences can also be expressed in the bacterium Escherichia coli and purified, for example by incorporating an affinity tag and affinity chromatography. The same methods (i) and (ii) can then be applied. In both cases, the native sequence must be expressed and purified alongside the altered sequence, to show that the method itself does not affect iron binding.
- “By at least one mutation in at least one copy” is meant that where the BRUTUS gene is present as more than one copy or homologue (with the same or slightly different sequence) there is at least one mutation in at least one gene. Preferably, only one copy of the gene is mutated. Alternatively, all genes are mutated.
- the genetically altered organism with at least one mutation in at least one copy of the BRUTUS gene can also act as an environmental iron sensor whereby brown spots appear on an organism with a mutation in the BRUTUS gene when there is sufficient bioavailable iron in the soil and brown spots do not appear on the organism when there is very little bioavailable iron. Accordingly, in another aspect of the invention, there is provided the use of the genetically altered organism of the invention as a biosensor for iron.
- the mutation that is introduced into the endogenous BRUTUS gene can be selected from the following mutation types
- a "missense mutation” which is a change in the nucleic acid sequence that results in the substitution of an amino acid for another amino acid
- a "nonsense mutation” or "STOP codon mutation” which is a change in the nucleic acid sequence that results in the introduction of a premature STOP codon and, thus, the termination of translation (resulting in a truncated protein); plant genes contain the translation stop codons "TGA” (UGA in RNA), "TAA” (UAA in RNA) and “TAG” (UAG in RNA); thus any nucleotide substitution, insertion, deletion which results in one of these codons to be in the mature mRNA being translated (in the reading frame) will terminate translation.
- splice site which is a mutation that results in the insertion, deletion or substitution of a nucleotide at the site of splicing.
- the mutation may be any of the above mutations that reduces or abolishes binding of iron to the polypeptide.
- the mutation may reduce the binding affinity, such that only one iron atom binds to the hemerythrin domain, or alternatively due to cooperativity no iron binds to the hemerythrin domain.
- the mutation is any mutation that prevents binding of iron to one or more hemerythrin domain(s).
- bolishing is meant that the mutated hemerythrin domain of the BRUTUS polypeptide cannot bind iron, or that binding of iron cannot be detected.
- the mutation may prevent binding of both atoms of iron to the hemerythrin domain. This may in turn result in a reduction in the amount of iron bound to a population of BRUTUS polypeptides. In other words, at the population level, the amount of iron bound to a population of BRUTUS polypeptides is reduced compared to the amount of iron bound to a population of BRUTUS polypeptides that do not contain one of the above-described mutations.
- the mutation is a deletion.
- a “deletion” may refer to the deletion of at least one nucleotide. More preferably, the deletion is in the hemerythin domain.
- the mutation is the deletion of one or more amino acids where the deletion is sufficient to reduce or abolish binding of iron to the hemerythrin domain(s).
- the mutation may be a substitution provided again that the substitution is sufficient to reduce or abolish binding of iron to the hemerythrin domain(s).
- the mutation is a deletion of at least one hemerythrin domain in its entirety. For example, the deletion of one more hemerythin domains as defined in any of SEQ ID NO: 20, or 50 to 102 and functional variants thereof.
- the mutation is the deletion of between 1 and 50 amino acid residues in at least one hemerythrin domain.
- the hemerythin domain is selected from any of SEQ ID NO: 20, or 50 to 102 and functional variants thereof.
- the mutation is the deletion of between 5 and 25 amino acids. More preferably, the mutation is the deletion of around five amino acid residues or around 20 amino acids (in one embodiment 22 amino acid residues).
- the mutation is the deletion of one or more amino acids between the third H and the fourth H in the (H)-HxxxE-H-HxxxE motif, as shown in Figure 10.
- the mutation is the deletion of the following amino acids in the hemerythrin domain(s):
- X can be any amino acid, but preferably selected form L, V or I.
- the mutation may be selected from the deletion of the following amino acid residues in one or more hemerythrin domains:
- CTSIS SEQ ID NO: 48
- RTFIT (SEQ ID NO: 49).
- the plant when the mutation is a deletion of QTSVS (SEQ ID NO: 22) preferably, the plant is Brassica.
- the plant when the mutation is a deletion of QTCLS (SEQ ID NO: 23), preferably the plant is rice.
- the plant when the mutation is a deletion of QTCLT (SEQ ID NO: 24), preferably the plant is selected from barley or wheat. In an embodiment, when the mutation is a deletion of QTFIT (SEQ ID NO: 47), preferably the plant is rice.
- the plant when the mutation is a deletion of CTSIS (SEQ ID NO: 48), preferably the plant is potato.
- the plant when the mutation is a deletion of RTFIT (SEQ ID NO: 49), preferably the plant is selected from barley or wheat.
- the dgl deletion identified in the pea ortholog of BRUTUS is located within the first hemerythrin domain, near to the second iron-binding HxxxE motif.
- the deletions described here are predicted to rotate this HxxxE motif away from the other two iron ligands, diminishing effective iron binding (Fig 2B). This in turn would directly or indirectly supress the ubiquitination activity of BRUTUS.
- the mutation may be the deletion of some or all of the following amino acids (or corresponding amino acids in a homologous sequence) in one or more of the hemerythrin domains:
- this mutation disrupts the orientation of the iron binding ligands in at least one hemerythrin domain. Preferably, this diminishes effective iron binding.
- the mutation disrupts the orientation of at least one histidine residue required for iron binding in the hemerythrin domain, preferably diminishing effective iron binding, as illustrated in Figure 6B.
- the mutation leads to increased iron and/or zinc content in an organism.
- the mutation does not affect the expression levels or preferably, transcript levels of the BRUTUS polypeptide. In a preferred embodiment the mutation does not significantly affect organism growth or yield. Preferably an effect on organism growth (such as height) or yield (such as seed yield, thousand grain weight etc.) cannot be detected.
- 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. 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 metres.
- yield may comprise a measurement of one or more of (a) biomass (weight) of one or more parts of a plant, aboveground (harvestable parts), or root biomass, root volume, root length, root diameter or root length or biomass of any other harvestable part (b) seed yield per plant, which may comprise one or more of seed biomass (weight) per plant or an individual basis, (c) seed filling rate, (d) number of filled seeds, (e) harvest index, which may be expressed as a ratio of the yield of harvestable parts such as seeds over the total biomass, (f) viability/germination efficiency, (g) number or size or weight of seeds or pods or beans or grain (h) seed volume (which may be a result of a change in the composition (i.e.
- lipid also referred to herein as oil
- protein and carbohydrate total content and composition
- i (individual or average) seed area
- j (individual or average) seed length
- k (individual or average) seed width
- I (individual or average) seed perimeter
- m growth or branching, for example inflorescences
- n fresh weight or grain fill
- o ear weight
- p thousand kernel weight (TKW), which may be taken from the number of filled seeds counted and their total weight.
- TKW thousand kernel weight
- the genetically altered organism of the invention comprising the described mutations in the BRUTUS polypeptide do not have a significant growth or yield penalty.
- the organisms are characterised by no or no significant loss or reduction in the growth of any part of the organism or the overall yield.
- it may be possible to overcome or minimise any growth or yield penalty caused by the mutation by growing the organism (e.g. plant) by vertical growing system and/or by using hydroponics.
- the method of producing a plant with an increased iron content comprises growing the plant by vertical growing system and/or by using hydroponics.
- growing the plant by using hydroponics advantageously results in a plant with leaf iron concentrations of up to 5 mg/g dry weight.
- the mutation is introduced using mutagenesis or targeted genome editing. That is, in one embodiment, the invention relates to a method and an organism that has been generated by genetic engineering methods, and where the organism is a plant, does not encompass naturally occurring varieties.
- Targeted genome modification or targeted genome editing is a genome engineering technique that uses targeted DNA double-strand breaks (DSBs) to stimulate genome editing through homologous recombination (HR)-mediated recombination events.
- DSBs DNA double-strand breaks
- HR homologous recombination
- customisable DNA binding proteins can be used: meganucleases derived from microbial mobile genetic elements, ZF nucleases based on eukaryotic transcription factors, transcription activator-like effectors (TALEs) from Xanthomonas bacteria, and the RNA-guided DNA endonuclease Cas9 from the type II bacterial adaptive immune system CRISPR (clustered regularly interspaced short palindromic repeats).
- ZF and TALE proteins all recognize specific DNA sequences through protein-DNA interactions. Although meganucleases integrate nuclease and DNA-binding domains, ZF and TALE proteins consist of individual modules targeting 3 or 1 nucleotides (nt) of DNA, respectively. ZFs and TALEs can be assembled in desired combinations and attached to the nuclease domain of Fokl to direct nucleolytic activity toward specific genomic loci.
- the genome editing method used according to the various aspects of the invention is CRISPR.
- CRISPR is a microbial nuclease system involved in defence against invading phages and plasmids.
- CRISPR loci in microbial hosts contain a combination of CRISPR- associated (Cas) genes as well as non-coding RNA elements capable of programming the specificity of the CRISPR-mediated nucleic acid cleavage (sgRNA).
- sgRNA CRISPR-associated RNA
- each CRISPR locus is the presence of an array of repetitive sequences (direct repeats) interspaced by short stretches of non-repetitive sequences (spacers).
- the non-coding CRISPR array is transcribed and cleaved within direct repeats into short crRNAs containing individual spacer sequences, which direct Cas nucleases to the target site (protospacer).
- the Type II CRISPR is one of the most well characterized systems and carries out targeted DNA double-strand break in four sequential steps. First, two non-coding RNA, the pre-crRNA array and tracrRNA, are transcribed from the CRISPR locus.
- tracrRNA hybridizes to the repeat regions of the pre-crRNA and mediates the processing of pre-crRNA into mature crRNAs containing individual spacer sequences.
- the mature crRNA:tracrRNA complex directs Cas9 to the target DNA via Watson-Crick base-pairing between the spacer on the crRNA and the protospacer on the target DNA next to the protospacer adjacent motif (PAM), an additional requirement for target recognition.
- Cas9 mediates cleavage of target DNA to create a double-stranded break within the protospacer.
- Cas12a can be used to mediate cleavage of target DNA.
- Cas9 is thus the hallmark protein of the type II CRISPR-Cas system, and is a large monomeric DNA nuclease guided to a DNA target sequence adjacent to the PAM (protospacer adjacent motif) sequence motif by a complex of two noncoding RNAs: CRISPR RNA (crRNA) and trans-activating crRNA (tracrRNA).
- the Cas9 protein contains two nuclease domains homologous to RuvC and HNH nucleases.
- the HNH nuclease domain cleaves the complementary DNA strand whereas the RuvC-like domain cleaves the non-complementary strand and, as a result, a blunt cut is introduced in the target DNA.
- Cpf 1 which is another Cas protein, can be used as the endonuclease.
- Cpf1 differs from Cas9 in several ways: Cpf1 requires a T-rich PAM sequence (TTTV) for target recognition, Cpf1 does not require a tracrRNA, (i.e.
- the CRISPR/CPf1 system consists of a Cpf1 enzyme and a crRNA.
- the nuclease may be MAD7.
- the single guide RNA is the second component of the CRISPR/Cas(Cpf or MAD7) system that forms a complex with the Cas9/Cpf1/MAD7 nuclease.
- sgRNA is a synthetic RNA chimera created by fusing crRNA with tracrRNA.
- the sgRNA guide sequence located at its 5’end confers DNA target specificity. Therefore, by modifying the guide sequence, it is possible to create sgRNAs with different target specificities.
- the canonical length of the guide sequence is 20 bp. Examples of sgRNA sequences that can be used to generate genetically altered plants of the invention are described below.
- AAACTCCGAAGAGCATCGTCATTT (SEQ ID NO: 26) CTTGCTGGGTGAGGCACGTTTGTA (SEQ ID NO: 27) AAACTACAAACGTGCCTCACCCAG (SEQ ID NO: 28) CTTGTTGTAATAAAGCAAGAAGCT (SEQ ID NO: 29) AAACAGCTTCTTGCTTTATTACAA (SEQ ID NO: 30) CTTGCGTTTGTATGGCTCCTGTGC (SEQ ID NO: 31) AAACGCACAGGAGCCATACAAACG (SEQ ID NO: 32) CTTGTTGACTCGAATATCGAGTGC (SEQ ID NO: 33) AAACGCACTCGATATTCGAGTCAA (SEQ ID NO: 34) CTTGCGTATTCCCTTGAGCACAAA (SEQ ID NO: 35) AAACTTTGTGCTCAAGGGAATACG (SEQ ID NO: 36) CTTGTATTCCCTTGAGCACAAAA (SEQ ID NO: 37) AAACTTTGTGCTCAAGGGAATACG (SEQ ID NO: 36) C
- Cas9 (or Cpf1/MAD7) expression plasmids for use in the methods of the invention can be constructed as described in the art.
- Cas9 or Cpf1 or MAD7 and the one or more sgRNA molecules may be delivered as separate or as single constructs.
- the promoters used to drive expression of the CRISPR enzyme/sgRNA molecule may be the same or different.
- RNA polymerase (Pol) Il-dependent promoters or the CaMV35S promoter can be used to drive expression of the CRISPR enzyme.
- Pol Ill-dependent promoters such as U6 or U3, can be used to drive expression of the sgRNA.
- the sgRNA molecules target a sequence selected from SEQ ID No: 20 or a variant thereof as defined herein.
- the method described herein uses the sgRNA constructs defined in detail below to introduce a targeted mutation, such as the mutations described specifically above, into a BRUTUS gene.
- aspects of the invention involve targeted mutagenesis methods, specifically genome editing, and in a preferred embodiment exclude embodiments that are solely based on generating plants by traditional breeding methods.
- the genome editing constructs may be introduced into a plant cell using any suitable method known to the skilled person (the term “introduced” can be used interchangeably with “transformation”).
- any of the nucleic acid constructs described herein may be first transcribed to form a preassembled Cas9 (or other CRISP nuclease)-sgRNA ribonucleoprotein and then delivered to at least one plant cell using any of the above described methods, such as lipofection, electroporation, holistic bombardment or microinjection.
- CRISPR constructs are well known to the skilled person.
- a suitable protocol is described in Ma & Liu (“CRISPR/Cas-based multiplex genome editing in monocot and dicot plants”) incorporated herein by reference.
- 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 may be transformed with a CRISPR construct 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.
- 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 construct 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 cell may then be used to regenerate a transformed organism.
- 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 also be selected from the calcium/polyethylene glycol method for protoplasts, electroporation of protoplasts, microinjection into plant material, DNA or RNA-coated particle bombardment, infection with (non-integrative) viruses and the like.
- Transgenic plants including transgenic crop plants, are preferably produced via Agrobacterium tumefaciens mediated transformation.
- 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.
- plant embryos are subjected to transformation and plantlets are regenerated from the transformed embryos.
- 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 is 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.
- a suitable marker can be hygromycin, bar-phosphinothricin or PPT.
- the transformed plants are screened for the presence of a selectable marker, such as, but not limited to, GFP, GUS (P-glucuronidase).
- a selectable marker such as, but not limited to, GFP, GUS (P-glucuronidase).
- GFP GFP
- GUS P-glucuronidase
- no selection is performed, and the seeds obtained in the above-described manner are planted and grown and the iron content measured.
- This alternative which avoids the introduction of transgenes, is preferable to produce transgene-free plants.
- putatively transformed plants may also be evaluated, for instance using PCR, to detect the presence of the mutation gene of interest.
- integration and expression levels of the newly introduced DNA may be monitored using Southern, 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.
- 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.
- a method of obtaining a genetically modified organism as described herein comprising a. selecting a part of the organism; b. transfecting at least one cell of the part of the organism of paragraph (a) with at least one nucleic acid construct encoding a sgRNA or at least one sgRNA molecule, using the transfection or transformation techniques described above; c. regenerating at least one organism derived from the transfected cell or cells; d. selecting one or more organisms obtained according to paragraph (c) that have an increased iron and/or zinc content.
- a method of increasing iron and/or zinc content in an organism, a part thereof or one or more cells comprising a. selecting a part of the organism; b. transfecting at least one cell of the part of the organism of paragraph (a) with at least one nucleic acid construct encoding a sgRNA or at least one sgRNA molecule, using the transfection or transformation techniques described above; c. regenerating at least one organism derived from the transfected cell or cells; d. selecting one or more organisms obtained according to paragraph (c) that have an increased iron and/or zinc content.
- the method also comprises the step of screening the genetically modified plant for SSN (preferably CRISPR)-induced mutations in the BRUTUS gene sequence.
- the method comprises obtaining a DNA sample from a transformed plant and carrying out DNA amplification to detect a mutation in at least one BRUTUS gene sequence.
- the method may further comprise producing a food composition or food product, vitamin or nutritional supplement from the selected organism or part thereof.
- the food composition is the seed.
- the food composition may be a flour of any product derivable from a seed.
- the food composition, vitamin or nutritional supplement is a vegetative part of the plant, or a composition comprising a vegetative part of the plant, or any product derivable from a vegetative part of the plant.
- a food, vitamin or nutritional supplement obtained or obtainable by the method of the invention.
- the product derivable from the plant part is a plant-based meat.
- a method of treating anaemia or iron-deficiency in an individual in need thereof comprising consuming the food, vitamin or nutritional supplement as described above, or where the organism is a plant, by consuming the seed or vegetative part of the genetically altered plant such as the leaves.
- a method for screening a population of plants and identifying and/or selecting an organism that will have an increased iron and/or zinc content comprising detecting in the organism germplasm at least one polymorphism in a BRUTUS gene, where the polymorphism is one of the abovedescribed mutations.
- Suitable tests for assessing the presence of a polymorphism would be well known to the skilled person, and include but are not limited to, Isozyme Electrophoresis, Restriction Fragment Length Polymorphisms (RFLPs), Randomly Amplified Polymorphic DNAs (RAPDs), Arbitrarily Primed Polymerase Chain Reaction (AP-PCR), DNA Amplification Fingerprinting (DAF), Sequence Characterized Amplified Regions (SCARs), Amplified Fragment Length polymorphisms (AFLPs), Simple Sequence Repeats (SSRs-which are also referred to as Microsatellites), and Single Nucleotide Polymorphisms (SNPs).
- RFLPs Restriction Fragment Length Polymorphisms
- RAPDs Randomly Amplified Polymorphic DNAs
- AP-PCR Arbitrarily Primed Polymerase Chain Reaction
- DAF Sequence Characterized Amplified Regions
- AFLPs Am
- the method comprises a) obtaining a nucleic acid sample from the organism; and b) carrying out nucleic acid amplification of one or more of BRUTUS genes using one or more primer pairs.
- the method may further comprise introgressing the chromosomal region comprising at least one of said BRUTUS polymorphisms or the chromosomal region containing the mutated residue as described above into a second organism germplasm to produce an introgressed germplasm, wherein said second organism will also display an increased iron and/or zinc content.
- the organism is a plant or an alga.
- a plant according to all aspects of the invention described herein may be a monocot or a dicot plant.
- a dicot plant may be selected from the families including, but not limited to Apiaceae, Asteraceae, Brassicaceae (eg Brassica napus, Brassica oleracea), Chenopodiaceae, Cucurbitaceae, Leguminosae (Caesalpiniaceae, Aesalpiniaceae Mimosaceae, Papilionaceae or Fabaceae), Malvaceae, Rosaceae or Solanaceae.
- the plant may be selected from carrot, parsnip, beetroot, cassava, tomato, soybean, lettuce, sunflower, Arabidopsis, broccoli, spinach, water melon, squash, cabbage, potato, yam, capsicum, tobacco, cotton, okra, apple, rose, strawberry, alfalfa, bean, field (fava) bean, pea, Medicago, lentil, peanut, chickpea, apricots, pears, peach, grape vine or citrus species.
- a monocot plant may, for example, be selected from the families Arecaceae, Amaryllidaceae or Poaceae.
- the plant may be a cereal crop.
- Examples of a crop plant include wheat, rice, barley, maize, oat, sorghum, rye, millet, buckwheat, turf grass, Italian rye grass, sugarcane or Festuca species, or a crop such as onion, leek, yam or banana.
- the plant is a legume or an edible legume.
- the plant is a plant that produces edible seeds. Examples include pea, chickpea, lentil, legume pea or member of the bean family (optionally kidney, navy, pinto, black, cannellini), lupin, soybean, or the like.
- the plant is a pea, but is not the dgl line from Pisum sativum, and in particular not from the Dippes Gelbe Viktoria cultivar or the Sparkle cultivar.
- the plant is a crop plant.
- crop plant is meant any plant which is grown on a commercial scale for human or animal consumption. Examples of crop plant include rice, wheat, maize, barley, Brassicas, soybean, potato and tomato.
- the plant is a plant that can be grown in a vertical growing system.
- Examples of such plants that can be grown in these systems include bean sprouts, lettuce, kale, chard and collard greens, chives, mint and basil.
- plant as used herein encompasses whole plants and progeny of the plants and plant parts, including seeds, fruit, shoots, stems, leaves, roots (including tubers), flowers, tissues and organs.
- 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 nucleic acid constructs or mutations as described herein.
- the invention also extends to harvestable parts of a plant of the invention as described herein, but not limited to seeds, grain, leaves, fruits, flowers, stems, roots, rhizomes, tubers and bulbs.
- the plant part is a legume seed.
- a “seed” and “bean” may be used interchangeably.
- the plant part or harvestable product is a seed or grain. Therefore, in a further aspect of the invention, there is provided a seed or grain produced from a genetically altered plant as described herein. Accordingly, in one aspect of the invention there is provided a seed, wherein the seed has an increased iron content as described herein (e.g. the seed contains one or more of the genetic alterations in BRUTUS as described herein). In another aspect of the invention there is provided a seed or grain (such terms are used interchangeably herein), wherein the seed or grain has an increased zinc content as described herein (e.g. the seed contains one or more of the genetic alterations in BRUTUS as described herein).
- a seed or grain wherein the seed or grain has an increased iron and zinc content as described herein (e.g. the seed contains one or more of the genetic alterations in BRUTUS as described herein). Also provided is a progeny plant obtained from the seed as well as seed obtained from that progeny.
- the plant part or harvestable product is the leaf or leaves. Accordingly, in one aspect of the invention there is provided a leaf, wherein the leaf has an increased iron and/or zinc content as described herein (e.g. the seed contains one or more of the genetic alterations described herein).
- the aspects of the invention also extend to products derived, preferably directly derived, from a harvestable part of such a plant, such as dry pellets or powders, or proteins.
- the aspects of the invention also relate to food products, vitamins and food supplements comprising or derived from the plant of the invention or the harvestable product.
- the food product may be an animal feed.
- the food product is plant-based product, such as plant-based meat for human consumption.
- a product derived from a plant as described herein or from a part thereof is provided.
- composition comprising the plant part thereof, such as a leaf or part thereof or extract from the plant of the invention and at least one vitamin.
- the vitamin may be Vitamin C.
- the composition may be considered to be a nutraceutical.
- the plant is a legume or edible legume.
- an organism comprising a mutation in at least one nucleic acid encoding the BRUTUS polypeptide as described herein in agromining.
- a method of agromining comprising growing an organism (e.g. plant) of the invention and extracting the iron and/or zinc.
- Agromining refers to the extraction of metals from soil.
- organisms comprising at least one mutation in the BRUTUS polypeptide can be used to extract iron and/or zinc from soil.
- the plant part is pollen, a propagule or progeny of the genetically altered plant described herein. Accordingly, in a further aspect of the invention there is provided pollen, a propagule or progeny produced from a genetically altered plant as described herein.
- control plant as used herein is a plant which has not been modified according to the methods of the invention.
- the plant has not been genetically modified, as described above.
- the control plant is a wild type plant.
- the control plant is typically of the same plant species, preferably having the same genetic background as the modified plant.
- the organism is an alga.
- the algae is selected from Chlorella (such as Auxenochlorella protothecoides), Porphyra, Dulse, Laminaria, Alaria, Nostoc, Monostroma, Ulva, Enteromorpha, Caulerpa racemose and Durvillaea antarctica.
- control or wild-type alga is one that has not been modified according to the methods of the invention (e.g. does not contain one of the described mutations in a BRUTUS polypeptide).
- RNA-Seq on leaf tissue from the dgl and Sparkle lines, with the aim of determining both the transcriptional changes underpinning the high iron phenotype and identifying the causal mutation.
- Initial GO-term analysis of the genes differentially expressed between the wild type and dgl genotypes demonstrated a strong correlation between the dgl phenotype and changes in iron homoeostasis (Table 1).
- a gene involved in zinc detoxification (PCR2) was also upregulated, whereas various sugar metabolism genes were downregulated.
- Table 1 GO terms over-represented in genes differentially expressed between dgl and Sparkle leaf tissue.
- RNA sequencing reads we searched for any sequence polymorphisms within the expressed genes, which could account for the dgl phenotype. Identification of the mutation was not straight-forward because of a dense SNP region on chromosome 6, which suggested that the mutation was present there. Nonetheless, only one small, but high-quality deletion was eventually identified, located on Chromosome 1 in Psat1g036240 (Fig 2A). The 15-bp deletion, located in exon 2, causes an in-frame deletion of five amino acids. PCR marker analysis demonstrated that this deletion segregated consistently with the high iron phenotype in two separate F2 populations (44 and 48 individuals, respectively).
- BRUTUS is an E3 ubiquitin ligase, which negatively regulates the response to iron deficiency by promoting the degradation of iron-responsive transcription factors.
- the dgl deletion identified in the pea ortholog of BRUTUS is located within the first hemerythrin domain, near to the second iron-binding HxxxE motif. Lack of the amino acids is predicted to alter the position of the nearby His and Glu residues that provide 2 of the 7 amino acid ligands to the diiron centre. This in turn is predicted to rotate this HxxxE motif away from the other two iron ligands, diminishing effective iron binding (Fig 2B).
- the BRUTUS protein is highly conserved in the green lineage, from algae to higher plants.
- lower transcript levels of the homologue OsHRZI led to miss-regulation of iron homeostasis genes, but also a 33% reduction in plant height and a drop in panicle weight per plant of around 90%.
- the identified dgl mutation in PsBRUTUS leads to only a 28% decrease in seed number and 24% in seed weight while showing a 25-fold increase in shoot iron (Fig 1 B) and a four-fold increase in seed iron. This suggests that targeted deletions within the hemerythrin domains of BRUTUS and its orthologs are a useful approach for improving iron levels in crops without excessive effects on plant yields.
- pea BTS1 is a functional orthologue of Arabidopsis BTS and that the 15 nucleotide deletion is deleterious for BTS function. Ultimately, this provides evidence that BTS is highly conserved and performs the same function between different species.
- the identification of the causal mutation in BRUTUS raises questions regarding the shoot-to-root iron responsive signal, first identified in grafting experiments using the dgl mutant lines.
- the in-frame deletion in BRUTUS is sufficient to cause constitutive activation of shoot-to-root signalling, inducing ferric reductase activity and root iron uptake despite iron accumulation in the shoot tissue.
- Perhaps the predicted changes to the iron binding site of the first hemerythin domain reduces or eliminates the responsiveness of BRUTUS protein to cellular iron levels. This would suppress the ubiquitination activity of BRUTUS, with lower turnover rates of transcription factors orchestrating iron uptake in the cell, thus promoting the shoot-to-root signal.
- RNAs were designed to generate an in frame 66 nucleotide deletion in Hr1 of the wheat HRZ1 gene (wheat BRUTUS homologue) that results in the deletion of 22 amino acids from the protein.
- Hr1 of the wheat HRZ1 gene wheat BRUTUS homologue
- Fig.9A 3D modelling showed that this 22 amino acid deletion would cause one of the histidine ligands to flip outwards, likely destabilising the di-iron site (Fig.9B).
- Pea seeds were grown on Levington’s F2 compost in a temperature-controlled greenhouse and watered as required.
- Leaf iron staining and quantification Leaf samples were stained for iron using Peris’ reagent as previously described (Roschzttardtz et al., 2009). For measuring the iron concentrations, dried leaf samples were digested in 0.25 ml nitric acid (69%) and 0.25 ml hydrogen peroxide at 90°C. After neutralization with 15% (w/v) ammonium acetate, samples were reduced with ascorbic acid. Fe2+ was quantified using the colorimetric iron chelator ferene (3-(2-pyridyl)-5,6- bis-[2-(5-furyl-sulfonic acid)]-1 ,2,4-triazine and absorbance measurement at 593 nm.
- Vegetative leaf tissue was sampled from three plants of each genotype (Sparkle and dgl) and snap frozen in liquid N2. The snap-frozen tissue was then ground to a fine powder before RNA extraction using TRIzol® Reagent (ThermoFisher) and DNase treatment with TURBO DNase (ThermoFisher). The quality and quantity of RNA was verified with the Agilent Bioanalyzer RNA 6000 Nano assay before cDNA library preparation (250- 300 bp insert) and Illumina Sequencing (PE 150, Novogene).
- Illumina reads were pseudo-aligned against the P. sativum reference transcriptome ( Kreplak et al., 2019) using Kallisto (Bray et al., 2016). Gene expression levels were determined using the R package Sleuth ( Pimentel et al ., 2017)) using the Wald test, where we considered genes to be differentially expressed between genotypes with q ⁇ 0.05. Expression levels of the FERRITIN genes were visualised using ggplot2 ( Wickham et al., 2016). Putative Arabidopsis orthologs were identified using NCBI blastp ( Altschul et al., 1990) of the P. sativum gene coding sequences against the Arabidopsis proteome. Enrichment of GO terms was calculated using the R package goseq (Young et al ., 2010).
- Illumina reads were aligned against the P. sativum reference genome (Krepalk et al., 2019) using the software BWA-mem (Li. ,2013).
- PCR primers were designed to amplify across the region of Psat1g036240 which contains the identified five amino-acid deletion.
- DNA was extracted from individual F2 plants as previously (Pallotta et al., 2003). Amplified fragments were run on a 2% (w/v) agarose gel for 2 h at 70 V, allowing separation of the wild-type Sparkle band (334 bp) and the dgl band (319 bp) and thus identification of homozygous and heterozygous individuals.
- the first hemerythrin domain of Psat1g036240.1 was modelled against the mammalian FBXL5 hemerythrin domain (PDB 3V5Y) using Phyre 2 with default settings (Thompson et al., 2012 and Kelley et al., 2015).
- the protein model was visualised using Jmol (26).
- Heterozygous bts-3 plants were transformed with plasmid plCSL869550OD (SynBio) carrying either the Arabidopsis BRUTUS coding sequence (BTS, AT3G18290); the pea BRUTUS1 coding sequence (Psat1g036240); or the pea dgl variant of BRUTUS1 (lacking nucleotides 487-510).
- the coding sequences were placed downstream of the Arabidopsis BRUTUS promoter, nucleotides -1904 to -1 , and upstream of the ocs terminator, using Golden Gate assembly. All constructs were verified by Sanger sequencing and the presence of the bts-3 allele and transgenes were confirmed by genotyping.
- a M2 population of EMS-mutagenized Medicago truncatula was screened for genetic polymorphisms in BTS1/Psat1g036240.
- primers MtBTS1-F1 and -R spanned exons 7 - 10 to maximize the ration of exomintron sequence.
- seedlings were grown up and inspected for phenotypes and iron accumulation using Peris' staining.
- SEQ ID NO: 4 >Pisum sativum; Psat1g036240.1 (Hemerythrin domains are highlighted) MATPLTGLQQHLDAGGGGVAVLSNLVSSSSPSSTSNGGGGFNRSSLSESPILIFSFFQ KAIGNELDALHRLAMAFATGNCSDIQPLSERYHFLRSMYRHHSNAEDEVIFPALDKRV KNVAQTYSLEHKGESDLFDHLFELLNSSVDNDETFRRELASCTGALQTSLSQHMAKE QQQVFPLLIEKFSVEEQASLVWQFLCSIPVNMMAEFLPWLSTSISPDESQDLRKCLSKI
- SEQ ID NO: 10 Barley >HovulHRZ1_HG0281210.1 (Hemerythrin domains are highlighted)
- SEQ ID NO: 16 Chlamydomonas reinhardtii >cre05 . g248550 (Hemerythrin domains are highlighted)
- SEQ ID NO 18 >Z.mays RefGen_V4
- SEQ ID NO: 52 Atal HR3 ERPVATIFKFHKAISKDLEFLDVESGKLIDCDGTFIRQFIGRFHLLWGFYKAHSNAEDDI
- SEQ ID NO: 53 Brassica v1.0
- SEQ ID NO: 56 Pisum sativum; Psat1g036240.1 HR1
- EAEIFLKNIQSAAPAIDS SEQ ID NO: 58 Pisum sativum; Psat1g036240.1 HR3
- SEQ ID NO: 60 Pisum sativum >Psat7gO10880.1 HR2
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| WO2014017394A1 (en) * | 2012-07-26 | 2014-01-30 | 独立行政法人科学技術振興機構 | Novel iron-zinc binding control factor, and technique for improving iron deficiency tolerance of plant and enhancing iron and zinc accumulation in edible part thereof by controlling expression of novel iron-zinc binding control factor |
| US8697359B1 (en) | 2012-12-12 | 2014-04-15 | The Broad Institute, Inc. | CRISPR-Cas systems and methods for altering expression of gene products |
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| WO2014017394A1 (en) * | 2012-07-26 | 2014-01-30 | 独立行政法人科学技術振興機構 | Novel iron-zinc binding control factor, and technique for improving iron deficiency tolerance of plant and enhancing iron and zinc accumulation in edible part thereof by controlling expression of novel iron-zinc binding control factor |
| US8697359B1 (en) | 2012-12-12 | 2014-04-15 | The Broad Institute, Inc. | CRISPR-Cas systems and methods for altering expression of gene products |
Non-Patent Citations (3)
| Title |
|---|
| HINDT MARIA N. ET AL: "BRUTUS and its paralogs, BTS LIKE1 and BTS LIKE2, encode important negative regulators of the iron deficiency response in Arabidopsis thaliana", METALLOMICS, vol. 9, no. 7, 1 January 2017 (2017-01-01), GB, pages 876 - 890, XP093018144, ISSN: 1756-5901, DOI: 10.1039/C7MT00152E * |
| KNEEN2 BARBARA E ET AL: "A Mutation in Pisum sativum (L.) cv 'Sparkle' Conditioning Decreased Nodulation and Increased Iron Uptake and Leaf Necrosis", PLANT PHYSIOL, 1 January 1990 (1990-01-01), pages 717 - 722, XP093018152, Retrieved from the Internet <URL:https://www.jstor.org> [retrieved on 20230126] * |
| SAMBROOK ET AL.: "Molecular Cloning: A Library Manual", 1989, COLD SPRING HARBOR LABORATORY PRESS |
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