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WO2025026473A1 - Procédé pour augmenter la résistance de plantes à un stress, et plantes résistantes au stress - Google Patents

Procédé pour augmenter la résistance de plantes à un stress, et plantes résistantes au stress Download PDF

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WO2025026473A1
WO2025026473A1 PCT/CZ2024/050048 CZ2024050048W WO2025026473A1 WO 2025026473 A1 WO2025026473 A1 WO 2025026473A1 CZ 2024050048 W CZ2024050048 W CZ 2024050048W WO 2025026473 A1 WO2025026473 A1 WO 2025026473A1
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dir13
plant
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expression
homolog
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Alesia MELNIKAVA
Dominique ARNAUD
Maria PANIAGUE CORREAS CANDELAS
Jan Hejatko
Gregory MOUILLE
Francois PERREAU
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Masarykova Univerzita
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    • C—CHEMISTRY; METALLURGY
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    • 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
    • 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
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
    • A01H1/00—Processes for modifying genotypes ; Plants characterised by associated natural traits
    • 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
    • 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
    • C12N15/67—General methods for enhancing the expression
    • 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
    • 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
    • C12N15/8271—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
    • C12N15/8273—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for drought, cold, salt resistance
    • 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
    • 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
    • C12N15/8291—Hormone-influenced development
    • C12N15/8295—Cytokinins

Definitions

  • Soil salinity is another stressor type with a major impact on plant production. Soil salinization has two fundamental mechanisms of its effect on plant growth and production. First, there is an increase in the osmotic potential of the environment, which makes it difficult for the plant to absorb water. Thus, salinity causes very similar effects to drought, and often this type of stress is used in model situations to simulate drought. Second, damage to leaf cells occurs after the uptake of increased amounts of salts by the transpiration stream.
  • Drought mitigation measures can be divided into three groups, i) increasing water supply, ii) reducing water consumption, and Hi) minimizing the effects of drought. To achieve the maximum effect, a combination of all three types of measures is ideal. In the case of protecting agricultural production, one of the very effective options is the breeding of plants with increased resistance to drought, which will enable both a reduction in the water demand of agricultural production (measure type ii) and a reduction in the effects of drought (measure type Hi).
  • the DIR13 gene (also called A d)IR13.
  • AGI code AT4G11190) is found in the Thale cress (Arabidopsis thcdiand).
  • a homolog is a gene in another plant species that is derived from a gene common (ancestral) to this homologous gene (homolog) and to the DIR13 gene from the Thale cress.
  • An ortholog means a gene in another plant species that is derived from a gene common (ancestral) to this homologous gene and to the DIR13 gene from the Thale cress.
  • An orthologous gene is evolved by speciation and usually retains the same function in different species throughout evolution.
  • Gene expression can generally be increased by inserting additional copies of the gene, preferably under the control of promoters increasing the level of expression as needed, and/or by applying to the plant expression activators, especially transcription activators, of the given gene.
  • the expression of the DIR13 gene or its ortholog or its homolog is increased in the plant, and simultaneously or subsequently, at least one exogenous cytokinin is applied on the growing plant.
  • An aspect of the present invention is also a plant with increased resistance to abiotic stress, in particular to drought and soil salinity, which contains inserted additional copies of the DIR13 gene or its ortholog or its homolog to increase the production of the protein encoded by this gene.
  • additional refers to copies of the genes which are inserted and thus present in the plant genome in addition to the naturally present copies of the genes.
  • DIR and DIR-like proteins have been identified throughout the plant kingdom except for algae and cyanobacteria, suggesting that DIRs are found in almost all vascular plant species including lichens, fems, gymnosperms, and angiosperms (Ralph, S. , et al. (2006). Plant Molecular Biology 68, 1975-1991 19, 347- 352; Li, Q dominant et al. (2014). BMC Genomics 15, 388).
  • DIR protein family in Arabidopsis includes 26 members with mostly unknown biochemical functions.
  • DIR13 is the closest paralog of DIR5, DIR6, and DIR12, but lacks conserved residues necessary for (-)-pinoresinol formation (Paniagua, C., et al. (2017). J Exp Bot 68, 3287-3301; Kim, K. Wminister et al. (2012). J Biol Chem 287, 33957-33972).
  • DIR13 and its homologs and orthologs in various plants increase the formation of lignans and neolignans. Furthermore, it was found within the framework of the present invention that DIR13 and its homologs and ortho logs increase reactive oxygen species (ROS) production in response to abiotic stress.
  • ROS reactive oxygen species
  • Lignins and lignans are products of phenylpropanoid metabolism. This metabolic pathway leads to the production of monolignols (coniferyl, sinapyl, and p-coumaryl alcohols), which are precursors of both lignan and lignin biosynthesis (Buchanan, B.B., et al. (2000). Biochemistry & Molecular Biology of Plants. Rockville, Md.: American Society of Plant Physiologists).
  • the term “lignan” includes a class of dimeric phenylpropanoids (CeC ) linked by an 8-8' linkage, while alternatively linked dimers are known as neolignans (Buchanan, B.B., et al. (2000).
  • Lignans and neolignans play an important role in plant defense where they act as biological weapons against pathogens (Davin, L. B., et al. (2008). Nat Prod Rep 25, 1015-1090; Davin, L. B., et al. (2005). Current Opinion in Biotechnology 16, 398-406). Lignans are able to inhibit the extracellular fungal enzymes cellulase, polygalacturonase, glucosidase, and laccase (MacRae, W.D., et al. (1984). Phytochemistry 23, 1207-1220).
  • lignans could prevent plant damage by disrupting the endocrine system of herbivorous insect larvae (Harmatha, J., et al. (2003). Phytochemistry Reviews 2, 321— 330). Lignans could also be used as drugs and chemopreventive agents in conventional medicine. For example, podophyllotoxin (derived from Podophyllum peltatum) has antiviral properties and its derivative (etopophos) has found application in cancer chemotherapy (Davin, L.B., et al. (2008). Nat Prod Rep 25, 1015-1090). In addition, lignans could serve as a reservoir of monolignols for lignification.
  • the present invention makes it possible to obtain economically important crops with resistance to salinity, drought and/or other types of stress.
  • FIG. 1 The DIR13 promoter is active early after germination and dominantly in the root.
  • a - C AtDIRl 3 promoter activity detected by GFP fluorescence (bright signal in cell nuclei, examples highlighted by white arrowheads in A and C) in 3-day-old Arabidopsis seedlings carrying the pDIR13::NLS-3xGFP construct.
  • pDIR13 activity is detectable mainly in the root (A).
  • a fluorescent signal was also detected in the shoot apical meristem (B) and in root hairs (C).
  • the plasma membrane signal due to propidium iodide (PI) staining is shown in magenta. Scale bar represents 50 pm.
  • FIG. 1 The DIR13 promoter is active in all root tissues and lateral root primordia; DIR13 expression is regulated by cytokinins.
  • A Representative images of 7-day-old (7 DAG] seedlings and transverse optical sections of root cells expressing pDIR13::NLS-3xGFP. Fluorescent GFP signal (bright signal in cell nuclei, examples highlighted by white arrowheads in A, B and E) was detected in all Arabidopsis root cell types (1-3, pictured right). Scale bar 50 pm. ep, epidermis; en, endodermis; co, cortex; pe, pericycle.
  • DIR13 expression is regulated by B-type ARR transcription factors. The expression level of DIR13 was examined by RT- qPCR in cirri, 10, arrl,12, and arr!0,12 double mutants after treatment with 5 pM BAP and in control (0.1% DMSO) for 1 hour.
  • Plasma membrane signal from PI staining is shown in magenta and GFP in green. Scale bar represents 50 pm.
  • F Number of fluorescent nuclei per root in the root apical meristem (RAM) of 5-day- old seedlings expressing pDIRl 3 : :NLS-3xGFP after 4 and 24 h of BAP treatment and in the control (0.1% DMSO). Data are presented as mean +/- SE (n > 10). Asterisks indicate statistically significant differences between BAP and control based on mixed Poisson model analysis (**P ⁇ 0.01, ***P ⁇ 0.001).
  • G Fluorescence intensity of individual nuclei after 4 h and 24 h of BAP and control (DMSO) treatment was quantified in RAM. Results are means +/- SE (n > 10). Asterisks indicate statistically significant differences between BAP and control treatments based on one-way ANOVA followed by Dunnett's HSD test (**P ⁇ 0.01, ***P ⁇ 0.001).
  • DIR13 localizes to Arabidopsis root endodermis and peripheral cells of lateral root primordia.
  • A- C DIR13 protein localizes to the endodermal cells of the root differentiation zone. Representative images of 7-day-old seedlings expressing pDIR13:DIR13::mCherry.
  • A - single layer,
  • B projection (Z-stack) of confocal sections and
  • C transverse optical section of the root from Fig. (B).
  • D, E Treatment with 5 pM BAP increases the amount of DIR13 and shifts its localization closer to the root apical meristem (indicated by arrows).
  • G-H; J-O Propidium iodide (PI, light grey) penetration of 5-day-old WT Col-0 (G, J, M), dir!3-5 (H, L), 35S:DIR13 #8 (K) esbl-1 (N) and caspl-l;3-l (O).
  • Asterisks indicate the 15 th (in G, H) and 19th (in J - O) endodermal cell from the beginning of the early differentiation zone of the root. The beginning of the early differentiation zone is defined as the zone where an endodermal of cell length greater than twice its width was observed. Scale bar represents 50 pm in (A - 0) and 20 pm in (1 - 6).
  • FIG. 1 Scheme of the gene construct used for the preparation of DIR13 overexpressing lines.
  • the coding sequence of DIR13 (green rectangle) was placed under the control of a strong constitutive promoter of tobacco mosaic 35S RNA (CaMV 35S, white arrow).
  • the annealing sites of the primers used to amplify the coding sequence of DIR13 are depicted by gray arrows under the DIR13 sequence.
  • D Semiquantitative RT- PCR gel electrophoresis shows the absence of DIR13 transcripts in dir 13-4 and dir 13-5 mutant lines. EF- la was used as a control.
  • E Expression levels of the closest DIR13 homologues are not affected by DIR13 overexpression or the dir 13-5 knock-out mutation. Expression levels of DIR6, DIR10 (ESB1), DIR! 3.
  • FIG. 8 Overexpression of DIR13 increases plant salinity tolerance.
  • A, B Seed germination rates of 35S.DIR13 #6, 35S.DIR13 #8 (A), and dirl3-5 (B) transgenic plants after salt stress. The germination rate was recorded for 7 days after stratification in the presence of 150 mM NaCl. Data shown are means of three independent experiments, error bars indicate +/- SE, (n > 100). Asterisks indicate statistically significant differences at p ⁇ 0.05 between WT Col-0 and 35S.DIR13 (A) and between WT Col-0 and dirl3-5 (B) by two-way ANOVA and Dunnetfs HSD test (*p ⁇ 0 .05, **p ⁇ .01).
  • Asterisks indicate statistically significant differences at p ⁇ 0.05 between WT Col-0 and dirl3-5 based on mixed-model ANOVA followed by Sidak's HSD test (*p ⁇ 0.05, **p ⁇ 0.01). Numbers in rectangles indicate the relative difference to WT Col-0 in percent.
  • G, H Phenotypes of 8- week-old WT Col-0 and 35S.DIR13 #8 plants growing under short-day conditions after 4 weeks of progressive salt treatment (application of increasing concentrations of NaCl each week - 100, 150, 200, and 300 mM, in that order). Scale bar corresponds to 1 cm.
  • FIG. 10 Overexpression of DIR13 increases the accumulation of reactive oxygen species in root cells in response to salinity stress.
  • A Reactive oxygen species (ROS) production analyzed using the fluorescent dye H2DCFDA in 7-day-old Col-0 WT, 35S.DIR13 #8 and dir 13-5 seedlings under control conditions (0 mM NaCl, 0.1% DMSO), after 30 min treatment with 150 mM NaCl, after 5 pM BAP treatment for 2 h and BAP treatment for 2 h followed by 30 min application of 150 mM NaCl.
  • Figure shows representative confocal images, signal specific for H2DCFDA is shown in light grey (highlighted by white arrowheads). Scale bar represents 20 pm.
  • Example 1 AtDIR13 is expressed in all root cell types and is induced by cytokinins.
  • DIR13 To determine the spatiotemporal localization of DIR13 expression, we created a gene construct containing a transcriptional fusion of the gene promoter (pl)IRI3) with the sequence encoding the nuclear localization signal and three copies of green fluorescent protein (GFP; pDIRl 3-NLS-3xGFP).
  • pl gene promoter
  • GFP green fluorescent protein
  • pDIRl 3-NLS-3xGFP green fluorescent protein
  • Example 2 DIR13 localizes to the endodermis cell wall but is not essential for the formation of Casparian strips.
  • CDS coding sequence of the DIR13 gene was amplified by PCR from gDNA with primers containing adaptor sites to introduce the desired fragment into the pPLV26 LIC vector containing an expression cassette with the cauliflower mosaic virus 35S rRNA promoter, allowing strong constitutive gene expression (Fig. 5).
  • Prl-Fw 5-3 (5'-TAGTTGGAATAGGTTCATGGCAAACCAAATCTACATAATCTCC TTGATC-3', SEQ ID NO: 1) and Pr2-Rw 5-3: (AGTATGGAGTTGGGTTCCTAATAGTAA CATTCATAGAGTTTAATATCCATTTGACACG, SEQ ID NO: 2) were used to amplify the coding sequence of DIR13.
  • the resulting plasmids were transformed using standard protocols into Escherichia coli DH5a cells and further into electrocompetent Agrobacterium tumefaciens GV3101 containing the helper plasmid pGreen pSOUP (Hellens, R., et al. (2000).
  • T3 homozygous lines 35S.DIR13 #6 and 35S.DIR13 #8 with high expression levels (33- and 85-fold increase in DIR13 expression compared to WT Col-0, Fig. 6A) were selected for further research.
  • Three independent T-DNA insertion mutants in DIR13, dirl 3-1 , dir!3-2 and dirl3-3 have insertional mutations located in the 3'UTR and promoter regions, respectively (Fig. 6B top).
  • a residual level of DIR13 expression was still detectable in the dir 13-1, dir 13-2 and dirl 3-3 mutants, indicating that they are knock-down (not knock-out) mutants (Fig. 6C).
  • Example 4 Increased expression of DIR13 leads to increased endogenous levels of lignans and neolignans.
  • Example 5 Plants with increased expression of DIR13 show increased tolerance to salinity and drought Since dirigent genes are associated with (a)biotic stress responses [see chapter Current state of the art and (Paniagua, C., et al. (2017). J Exp Bot 68, 3287-3301)], we decided to test the possible change in sensitivity of plants with increased expression of DIR13 (35S.DIR ! 3) and mutants deficient in DIR13 expression (dir 13-5) to abiotic stresses compared to plants of the standard type (WT Col-0).
  • Germination rates of WT Col-0, 35S.DIR13 #6 and 35S.DIR13 #8 were measured daily for 1 week in the presence of 0 - 150 mM NaCl. Under control conditions (0 mM NaCl), germination of transgenic seeds was not significantly different from WT Col-0 (data not shown). With increasing salt concentrations, germination was inhibited in all tested lines. However, germination rates of lines 35S.DIR13 #6 and 35S.DIR13 #8 were significantly higher than WT Col-0, with the most significant difference observed at 150 mM NaCl (Fig. 8A).
  • WT Col-0, 35S:DIR13 #6 and 35S:DIR13 #8 and dir 13-5 seeds were grown under normal conditions for 5 days. Then, the seed plants were transferred to Petri dishes containing medium with 0 or 150 mM NaCl and cultured for another 7 days. Compared to the control, the presence of 150 mM NaCl significantly reduced the length of the primary root as well as the number of lateral roots in all tested lines.
  • the primary root in lines 35S:DIR13 #6 and 35S:DIR13 #8 was 27% and 13% longer, whereas the dirl3-5 line had a root on NaCl medium 18% shorter than WT Col-0 (data not shown).
  • the 35S.DIR13 #6 and 35S.DIR13 #8 lines had a higher number and length of lateral roots compared to WT Col-0 under salt stress conditions (Fig. 8C, D).
  • the dir 13-5 mutant line showed a reduced number of lateral roots that were shorter (Fig. 8E,F).
  • the visual phenotype of leaf yellowing was quantified by measuring the ratio of variable (Fv) to maximum (F M ) fluorescence (F V /F M ) of photosystem II and thus photosynthetic efficiency (Garcia, A., et al. (2023). New Phytol 237, 60-77 ). This parameter was significantly higher under salt stress conditions in 35S.DIR13 #8 compared to wild-type plants (Fig. 81). After salt stress treatment, almost all 35S.DIR13 #8 plants survived, whereas only 44% of WT Col-0 survived (data not shown), dir 13-5 plants did not show a statistically significant difference in salt tolerance compared to WT Col-0 (data not shown).
  • 35S.DIR13 #8 plants showed a higher level of stress tolerance as indicated by a larger rosette area during the drought stress phase compared to Col-0 WT plants. This difference was even more striking during the recovery phase when 35S.DIR13 #8 plants showed a higher shoot growth rate (Fig. 9E). Moreover, a higher efficiency (maximum quantum yield) of photosystem II was found in 35S.DIR13 #8 plants during the recovery phase, indicating more productive photosynthesis (Fig. 9F).
  • Example 6 Increased expression of DIR13 increases the ability of plants to respond to drought.
  • ROS reactive oxygen species

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Abstract

La présente invention concerne un procédé d'augmentation de la résistance de plantes à un stress abiotique, en particulier à la sécheresse et à la salinité du sol, l'expression du gène DIR13 ou de son orthologue ou de son homologue dans la plante étant augmentée. Elle concerne également des plantes présentant une telle expression accrue du gène DIR13 ou de son orthologue ou de son homologue.
PCT/CZ2024/050048 2023-07-28 2024-07-21 Procédé pour augmenter la résistance de plantes à un stress, et plantes résistantes au stress Pending WO2025026473A1 (fr)

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CN119876261A (zh) * 2025-02-21 2025-04-25 上海市农业科学院 ZmDIR4基因在玉米对干旱敏感性的调控中的应用
CN120005904A (zh) * 2025-02-28 2025-05-16 上海市农业科学院 一种与植物非生物胁迫相关的抗性基因ZmDIR5及应用

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