WO2010058428A2 - Identification de gènes associés à une tolérance aux stress abiotiques chez jatropha curcas - Google Patents

Identification de gènes associés à une tolérance aux stress abiotiques chez jatropha curcas Download PDF

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WO2010058428A2
WO2010058428A2 PCT/IN2009/000673 IN2009000673W WO2010058428A2 WO 2010058428 A2 WO2010058428 A2 WO 2010058428A2 IN 2009000673 W IN2009000673 W IN 2009000673W WO 2010058428 A2 WO2010058428 A2 WO 2010058428A2
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stress
plant
abiotic
jatropha curcas
yeast
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WO2010058428A3 (fr
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Paramerswaran Sriram
Eswaran Nalini
Sathram Balaji
Anatharaman Bhagyam
Sudhakar Johnson Tangirala
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Reliance Life Sciences Pvt. Ltd.
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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
    • 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
    • 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

Definitions

  • the present invention relates to methods for identification of genes in Jatropha, including those conferring tolerance to abiotic stress such as salinity, drought and/or ion stresses.
  • the present invention also provides novel genes conferring abiotic stress tolerance in Jatropha curcas.
  • the seed and kernel oil from Jatropha curcas Linn has been proposed as an ideal source for commercial biodiesel. This is due to its high content of extractable seed oil (30-40%, of seed weight), the similarity of its lipid fractions to diesel, the ability of the plant to grow with minimal agricultural inputs and on marginal soils; and its tolerance to drought, salinity and even heavy metals.
  • Extractable seed oil (30-40%, of seed weight
  • Similarity of its lipid fractions to diesel the ability of the plant to grow with minimal agricultural inputs and on marginal soils
  • drought, salinity and even heavy metals echmans and Hirata, 2007; Francis et al., 2005; G ⁇ bitz et al., 1999; Kumar et al., 2007; Heller, 1996; Modi et al., 2007; Srivastava, 2006; Heller, 1996).
  • Juwarkar et al., 2007; Kumar et al., 2007 The seed and kernel oil from Jatropha curcas Linn, has been proposed as
  • Changes in gene expression in response to saline and drought stress have been identified in other plant species, and include: a) cellular adaptation to high Na+ levels in shoots, via vacuolar sequestration, mediated by vacuolar sodium pumps; b) tolerance to osmotic shock mediated by the synthesis and accumulation of small molecular osmoprotectants such as glycinebetain or polyols; c) the ability to tolerate high intracellular concentrations of Na+ ions, by expression and modulation of ribosomal protein synthesis, and d) the control of stress induced damage.
  • glycinebetain or polyols small molecular osmoprotectants
  • Salinity and drought tolerance is thought to be a quantitative trait locus (QTL)-associated complex trait, making selective breeding difficult.
  • QTL quantitative trait locus
  • Current approaches focus on identification of genes associated with resistance to salinity, drought and other abiotic stress.
  • QTL-associated markers for salinity tolerance have been identified in cereal crops using recombinant inbred lines (Flowers, 2004; Sahi et al., 2006). Identification of abiotic stress-resistance genes permits directed breeding and/or and direct genetic modification to develop varieties with enhanced tolerance (Sahi et al., 2006; Sreenivasulu et al., 2007; Tuteja, 2000).
  • the present invention provides a method for identifying Jatropha, such as Jatropha curcas, genes associated with tolerance to abiotic stressors.
  • the invention provides methods for a molecular genetic screen using yeast (Saccharomyces cerevisae) to identify expressed genes in Jatropha curcas root tissue, which confer resistance to salinity, drought and other abiotic stresses.
  • yeast Sacharomyces cerevisae
  • the present invention has efficiently isolated specific genes from Jatropha curcas that are associated with salinity and drought tolerance. Identification of stress-tolerance genes from Jatropha curcas permits targeted breeding programs and/or transgenetic modification of plants. Such activity enables the development of Jatropha curcas plant lines capable of productive growth in poor and marginal soils, with fewer agricultural inputs, yet yielding acceptable oil yields.
  • the novel genes from Jatropha can also be applied for the genetic improvement of other agriculturally important crops.
  • the present invention provides the development of a method capable of identifying plant genes involved in salinity, drought, ions and abiotic stress.
  • the invention in particular provides methods for a molecular genetic screen that demonstrates the ability to utilize yeast (S ⁇ cch ⁇ romyces cerevis ⁇ e) to identify expressed genes from J ⁇ troph ⁇ curc ⁇ s tissue,especially root tissue, which confers tolerance to salinity, drought and other abiotic stresses.
  • the present invention also provides additional full length sequences to demonstrate the efficacy of the screen to isolate genes from J ⁇ troph ⁇ curc ⁇ s.
  • the present invention provides methods for identification of plant genes that confer tolerance to salinity, drought and abiotic stress, using a functional screen in yeast, such as Saccharomyces cerevisea.
  • yeast such as Saccharomyces cerevisea.
  • the present invention provides a method for this purpose that is able to identify both false-positive and false-negative results in yeast transformants, thereby aiding the identification of genes expressed under a given set of conditions. Accordingly, the present invention provides a method for rapid and universal screening system that is able to identify genes that can be extended to any plant genome, irrespective of the genome information available for the target plant.
  • the present invention also provides genes from Jatropha curcas that confer tolerance to abiotic stressors, such as salinity and drought, and methods for identifying such genes.
  • the invention also provides polypeptides that mediate tolerance to abiotic stressors, such as salinity and drought.
  • the present invention further provides methods for producing plants and plant cells with enhanced tolerance to abiotic stress based on the identified genes, and plants obtained by said methods.
  • the present invention provides a cDNA library comprising coding sequences. In one embodiment, the present invention provides a cDNA library taken from the Jatropha root.
  • the present invention provides methods for screening Jatropha sequences that confer tolerance to abiotic stress, such as salinity and drought.
  • the present invention relates to nucleotide and amino acid sequences referenced in Tables 4-8 and presented in the accompanying sequence listing, including any of SEQ ID NOs: 1 to 195.
  • the invention is a polypeptide encoded by a nucleotide sequence that is at least 90%, 95%, 98%, or 99% identical to a nucleotide sequence selected from any SEQ ID NO: 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73-152, 154, 156, 158, and 160-195.
  • the invention is an isolated polypeptide having an amino acid sequence at least 90%, 95%, 98%, or 99% identical to an amino acid sequence selected from any of SEQ ID NO: 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 153, 155, 157 and 159.
  • the invention is an an isolated nucleic acid comprising a nucleotide sequence that is at least 90%, 95%, 98%, or 99% identical to a nucleotide sequence selected from any of SEQ ID NO: 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73-152, 154, 156,158, 160-195.
  • polynucleic acids referenced in Tables 4-8 and presented in the accompanying sequence listing, including any of SEQ ID NOs: 1 to 195 are obtained and/or expressed by recombinant techniques.
  • the present invention relates to a method for producing a plant with enhanced tolerance to abiotic stress, such as salinity and drought.
  • abiotic stress such as salinity and drought.
  • the present invention relates to plant cells, parts or harvestable plants, or any propagation material thereof that are transformed with genes identified as above,
  • the present invention provides methods for identifying stress tolerant variants of Jatropha.
  • variants of Jatropha can be developed through either genetic transformation methodologies or via directed breeding approaches (Agarwal et al., 2006; Bhatnagar-Mathur et al., 2008; Chen et al., 2007; Jain and Jain, 2000; Qiao et al., 2007; Witcombe et al., 2008; Zhou et al., 2008).
  • the nucleic acids described herein can be used to identify plants that express higher levels of genes confering tolerance.
  • the invention is a method for identifying at least one gene that confers tolerance to an abiotic stress in Jatropha curcus, wherein the method comprises:
  • tissue may be used, whether part of a plant or separated from it.
  • the tissue is roots from 3-4 week old plantlets.
  • the abiotic-stress comprises exposing the roots of Jatropha curcus to 100-150 mM NaCl for 1.5-3 hours, at a relative humidity of 40-50%.
  • the abiotic-stress growth condition comprises exposing the transformed yeast to an abiotic stressor selected from at least 500 mM NaCl, at least 75OmM NaCl; at least 5OmM H 2 SO 4 ; and at least 25mM NaOH.
  • the abiotic stress and the abiotic-stress growth condition are selected from the group consisting of drought, salinity, osmotic pressure, heat, cold, heavy metal, pH, ultra violet light, radiation, and combinations thereof.
  • the invention is an isolated nucleic acid comprising a nucleotide sequence that is at least 85, 90, 95, 98, or 99% identical to a nucleotide sequence listed in any of Tables 4-8 and the sequence listing.
  • the nucleic acid is isolated from Jatropha curcas.
  • the invention is a vector containing such nucleic acid, or a transgenic plant containing the isolated nucleic acid.
  • the invention is an isolated nucleic acid comprising a nucleotide sequence encoding a polypeptide, wherein the polypeptide has an amino acid sequence listed in any of Tables 4-8 and the sequence listing.
  • the nucleic acid is isolated from Jatropha curcas.
  • the invention is a vector containing such nucleic acid, or a transgenic plant containing the isolated nucleic acid.
  • the invention is an isolated polypeptide encoded by a nucleotide sequence that is at least 85, 90, 95, 98, or 99% identical to a nucleotide sequence listed in any Tables 4-8 and the sequence listing.
  • the invention is an isolated polypeptide comprising an amino acid sequence listed in any of Tables 4-8 and the sequence listing.
  • the invention comprises a method of selective breeding, wherein the method comprises breeding Jatropha curcas plants, and using the isolated nucleic acid elsewhere described herein as a probe to identify which of the Jatropha curcas plants overexpress at least one gene that confers tolerance to an abiotic stress.
  • the invention is a plant obtained by such a method.
  • the invention comprises a method for preparing a transgenic Jatropha curcas plant tolerant to abiotic stress, comprising overexpressing in individual Jatropha curcas plants one or more genes or proteins identified herein, exposing the individual plants to an abiotic stress, and identifying at least one individual plant that is tolerant of the abiotic stress.
  • the invention comprises a method for identifying genes that confer tolerance to abiotic stress, the method comprising:
  • the inducible promoter is activated by galactose and repressible by glucose.
  • Figure Ia Outline of a process to identify and isolate specific genes involved in abiotic stress responses, using the yeast Saccharomyces cerevisiae.
  • Figure Ib Illustration of certain underlying principles of a functional genetic screen in yeast to identify Jatropha genes conferring abiotic stress resistance.
  • Figure 2 Identification of salt stress conditions for wild-type Saccharomyces cerevisae (BY4741). Sectors in plates marked with a dot are wild-type, while other sectors represent salt hypersensitive yeast mutants obtained through random UV-mutagenesis followed by screening. Wild-type yeast BY4741, shows salt sensitivity from 500 mM NaCl, with complete growth arrest at 2.0M NaCl. In contrast, salt hypersensitive mutants shs-6, shs-B (isolated in the BY4741 background) show growth retardation from 100-250 mM NaCl. Similar amount of inocula were used in all the plates.
  • M lkb DNA ladder (NEB, USA, Lowest band is 500 bp and highest band corresponds to 10kb).
  • Lanel ds cDNA amplified from total RNA prepared from untreated (control) roots.
  • Lane2 ds cDNA amplified from total RNA prepared from roots treated with 15OmM
  • Lane3 ds cDNA amplified from poly (A+) RNA prepared from untreated (control) roots.
  • Lane4 ds cDNA amplified from poly (A+) RNA prepared from roots treated with
  • Figure 4 Schematic outline of process and principle of the quadruplicate plate based replica-printing, to screen of yeast transformants to various abiotic stress.
  • each individual yeast transformant is placed on four selective plates. Comparison of growth of yeast between these plates allows scoring and isolation of transformants expressing genes conferring stress tolerance.
  • Figure 5 Replica plate screen used to identify and isolated yeast transformants showing the relative growth advantage during salinity and drought stress. Photographs of a representative replica plate screen (as described in Figure 4) demonstrating the ability to identify and isolated yeast transformants showing the relative growth advantage during salinity and drought stress. Yeast transformants (selected for the plasmid-borne URA3 marker), expressing genes derived from Jatropha curcas root libraries, showing tolerance to stress induced by 750 mM NaCl are marked in panel B (black circles). Identical yeast transformants (compare panel D to B) with repressed gene expression shows arrested growth.
  • Figure 6 Identification of acid and alkali sensitive conditions for wild-type yeast, and isolation of yeast mutants generated though a process of UV mutagenesis followed by forward genetic screening showing sensitivity towards acid and alkali stress.
  • stress refers to a condition that decreases growth, prevents growth, prevents a stage of growth (such as production of flowers, seed production, seed germination, production of new shoots), or tends to kill or actually kills an organism.
  • tolerance refers to the ability of a plan to resist stress, such as the ability to grow or survive despite a condition that would decrease growth, prevent growth, or kill a organism that is not tolerant. Tolerance may be observed, for example, as a longer time to death, absence of death, or growth in the presence of the condition. Tolerance also may correspond to a range of protection from a delay to complete inhibition of alteration in cellular metabolism, reduced cell growth and/or cell death caused by the environmental stress conditions defined herein before.
  • a plant identified, isolated, bred or created by methods of the present invention is tolerant of or resistant to abiotic stress in the sense that the plant is capable of growing in a substantially normal manner under environmental conditions where a corresponding wild-type plant shows reduced growth, metabolism, viability, productivity and/or male or female sterility.
  • Methods for determining plant growth or response to stress include, but are not limited to, height measurements, leaf area, plant water relations, ability to flower, ability to generate progeny and yield or any other methodology known to those skilled in the art.
  • tolerance or resistance may be used interchangeably in the present invention.
  • abiotic stress refers to stress that is induced by or associated with non-biological factors, such as salinity, dessication, drought, radiation damage (such as that caused by UV light), heat, cold, pH (low or high), heavy metal, or ion stress.
  • non-biological factors such as salinity, dessication, drought, radiation damage (such as that caused by UV light), heat, cold, pH (low or high), heavy metal, or ion stress.
  • the amount of an abiotic factor that induces stress will vary according to multiple factors including the plant species and variant, soil type, and other co-existing abiotic stressors. For example, drought stress may be exacerabated by heat and salinity, as all three abiotic stressors may reduce the availability of water to plant cells.
  • salinity refers to stress that is induced by an elevated concentration of salt.
  • salt refers to any water soluble inorganic salt such as sodium sulfate, magnesium sulfate, calcium sulfate, sodium chloride, magnesium chloride, calcium chloride, potassium chloride, etc., salts of agricultural fertilizers and salts associated with alkaline or acid soil conditions. While low salinity water has EC 5-9 dS m "1 , high salinity includes water with EC 10-28 dS m "1 , and over 28 28 dS m "1 .
  • dipal stress refers to stress that is induced by or associated with a deprivation or reduced supply of water, and is a limitation on maximal plant performance imposed by water limitation. Jatropha normally needs at least 500mm of rainfall/yr, but can grow in Cape Verde Islands on 250mm/yr because of the high ambient humidity.
  • ion stress refers to stress caused by excessive concentrations of an ion, or ions in general. Such ions include Fe2+, Ca2+, Li+, OH-, H+, SO 4 2" etc. Excessive amounts of ions may manifest as osmotic stress, drought stress, or salinity stress. Other forms of ion stress include effects on the pH, oxidative potential, or toxicity. Ionic stress includes stress due to anions, cation, or both.
  • high pH and low pH are relative terms that vary according to the plant species, soil condition etc. Jatropha curcase normally grows well on well drained soils of pH 6-8.5. Accordingly, a pH of about 6, especially less than 6, and more especially less than 5.3, would constitute “low pH.” A pH about 9.0, especially greater than 9.0, and more especially greater than 10.0 would consistite "high pH.”
  • the term "functional gene” as used herein refers to a gene that expresses a protein having substantially the same biological activity as the protein that is expressed from the gene in the natural environment from which it is derived (e.g. in the plant).
  • a "plantlet” as used herein is young or small plant used as a propagule, such as from division of a plant into several smaller units.
  • Replica plating refers to technique in which one or more Petri plates containing different solid (agar-based) selective growth media (lacking nutrients or containing chemical growth inhibitors such as antibiotics) are inoculated with the same colonies of microorganisms from a primary plate or wells, producing the same spatial pattern of colonies on each.
  • Tissue is a cellular organizational level intermediate between cells and a complete organism. A group of cells that shares a common function may be defined as an "organ.” Organs of plants include roots, leaves, stems, flowers, seeds and developmental stages. Tissue may be obtained from an organ. "Root” typically refers to the organ of a plant body that typically lies below the surface of the soil, as part of a plant body that bears no leaves.
  • Jatropha curcas refers all variants of the species, including Jatropha curcas L. "Jatropha” refers to the genus which encompasses several species. In one embodiment, it is the species Jatropha curcas.
  • “Grow” or “growth” as used herein refers to refers to an increase in some quantity over time, including height, mass, etc. “Grow” or “growth” also refers to markers of development, including developmental stage, levels of developmentally appropriate compounds, etc.
  • Promoter refers to a regulatory region of DNA generally located upstream (towards the 5' region of the sense strand) of a gene that allows transcription of the gene.
  • An "inducible promoter” is a promoter that is controlled by an inducer.
  • galactose is an inducer for the GAL promoter, such that galactose induces transcription of any gene under the transcriptional control of the GAL promoter.
  • Plant as used herein refers to any other plant and of any variety not limited to Jatropha curcas.
  • the present invention provides a method for identifying plant genes involved in abiotic stress, such as salinity, drought and/or ion stress.
  • abiotic stress such as salinity, drought and/or ion stress.
  • the invention provides methods for a molecular genetic screen that uses yeast (Saccharomyces cerevisae) to identify genes expressed in Jatropha curcas root tissue that confer resistance to salinity, drought and other abiotic stresses.
  • Jatropha curcas Unlike many agriculturally-valuable crops, there is little genetic information available for Jatropha curcas, and consequently large-scale expression analysis is not currently possible. Lack of high-density molecular markers, the time associated with breeding and the inability to perform large-scale transformation in Jatropha curcas also prevent application of many genetic techniques.
  • the present invention has devised a functional genetic screen.
  • the screen uses yeast, Saccharomyces cerevisae (Cregg et al., 1998, Guthrie and Fink, 1991; Pringle et al., 1997), as a surrogate system to identify and isolate specific genes in Jatropha curcas.
  • yeast Saccharomyces cerevisae (Cregg et al., 1998, Guthrie and Fink, 1991; Pringle et al., 1997), as a surrogate system to identify and isolate specific genes in Jatropha curcas.
  • Yeast also have been shown to respond to salt stress, which is reflected as retardation in cell growth (Hirasawa et al., 2006).
  • Yeast strains show adaptive resistance (tolerance) to salt stress by intracellular accumulation of osmolytes as well as though membrane modification (Rodriguez-Vargas et al., 2007; Shen et al., 1999). Wild-type yeast strains have been reported to show salt sensitivity from 500 mM (Andreishcheva and Zviagil'skaia, 1999; Gaxiola et al., 1992; Nakayama et al., 2004; Shen et al., 1999), depending on the growth conditions. The conditions that lead to salt stress of wild type yeast BY4741 (yeast obtained from EUROSCARF, Germany) were identified by measurement of relative growth of the yeast under a range of salinity stress. See Examples.
  • LiCl to mimic the effects of salinity stress because cells are more sensitive to LiCl as compared to NaCl.
  • 1OmM LiCl inhibits yeast growth similarly to that obtained with ⁇ 200mM NaCl.
  • cells exhibit approximately 20-fold greater sensitivity to Li+ over Na+.
  • LiCl reduces the effect of drought responses (more precisely, osmotic effects) in the screen, due to less salt concentration.
  • the present approach uses NaCl because it (a) mimics both salt and drought stressors to which Jatropha is exposed; (b) mimics the physiological effect of NaCl, since LiCl is more toxic to cell growth; and (c) is less expensive than LiCl.
  • the present invention has identified different conditions of salt stress ideal for the construction of Jatropha curcas root tissue cDNA libraries. See Examples.
  • a cDNA library was constructed from normal and salt-stressed Jatropha roots, cloned into a shuttle vector, amplified in bacteria, and then shifted into yeast.
  • the shuttle vector provided a catabolite-regulated GALl inducible promoter (Flick and Johnston 1990; Lohr et al., 1995; Stargell and Struhl 1996),. which allowed for conditional expression of Jatropha genes in the yeast cell (Silar and Thiele, 1991).
  • yeast transformants To screen yeast transformants, a replica printing based screening process was devised to identify and isolate yeast transformants expressing heterologous gene sequences derived from Jatropha curcas root cDNA libraries. To improve performance of the screen, a more exhaustive approach was devised, which is described herein. Additional controls were introduced in the screen to allow identification of both false-positive and false- negative yeast transformants, as illustrated in Figure 4. In the Examples below, the method of the invention has identified 345 candidate yeast clones from 20,000 yeast transformants. These clones will enhance the capability of wild-type yeast cells to tolerate unfavorable conditions imposed by salinity and drought stress.
  • Example 1 Design of the functional screen using yeast Saccharomyces cerevisea
  • the screen used a yeast, Saccharomyces cerevisae (Cregg et al., 1998, Guthrie and Fink, 1991; Pringle et al., 1997), as a surrogate system to identify and isolate specific genes in Jatropha curcas.
  • Saccharomyces cerevisae Saccharomyces cerevisae
  • the screen system of the present invention uses an inducible promoter, and specifically the catabolite-regulated GALl promoter (Flick and Johnston 1990; Lohr et al., 1995; Stargell and Struhl 1996), to conditionally express a Jatropha gene in the yeast cell when cloned in a shuttle yeast vector system (Silar and Thiele, 1991).
  • the assay system is based upon the ability to select individual yeast transformants harboring plasmids containing a selectable yeast marker, and the ability to select yeast transformants that survive exposure to stress (Figure Ib).
  • the ability to score the relative survival of a yeast cell exposed to salinity, drought or other abiotic stress, when compared to a yeast cells harboring the same gene in a repressed state when subject to the similar stress conditions, allows identification of tolerant transformants.
  • Example 2 Identification of salt stress condition in Saccharomyces cervisea yeast, and treatment of 3-4 week in vitro germinated seedlings of Jatropha curcas L in NaCl to induce Jatropha genes involved in salinity stress.
  • Jatropha curcas cDNA libraries To study the effect of salinity stress on Jatropha curcas, we treated roots of young 3-4 week old Jatropha curcas plants to various levels of salt stress.
  • the present invention has identified different conditions of salt stress that allow for efficient subsequent construction of Jatropha curcas cDNA libraries.
  • the present invention has identified that exposure of Jatropha roots to 100-150 mM NaCl for 1.5-3 hours, at a relative humidity of 40-50%, sufficed to observe a salt stress response. These conditions were used for the subsequent construction of Jatropha curcas cDNA libraries.
  • Jatropha curcas seeds (Reliance breed plant R-044, RLS, DALC, Rabale) were removed from the seed coats, surface sterilized with 70% ethanol, followed by 1-5% hypochloride solution, prior to being placed in MS-Agar media bottles, as described previously in Deofe and Johnson (2008) and maintaining, at 23-25 0 C at 50- 60% RH, under long day conditions as described previously (Deore and Johnson, 2007).
  • Young 3-4 week old in vitro germinated Jatropha curcas (grown as described above) were removed from the media, and randomly separated into groups of 15-20 plantlets. Groups of these plants were either placed in sterile water or into 150 mM NaCl solution for 1.5-2.0 hours at 50%-60% ambient humidity.
  • yeast strain obtained from EUROSCARF, Germany
  • YPD media containing 2% peptone, 1% yeast extract, 2% dextrose, solidified with 1.5% Agar, Hi-Media, Mumbai, India
  • salinity stress from 0.0 mM NaCl to 2.0 M NaCl.
  • Table 1 Strain details genotype of Saccharomyces cerevisea yeast used in the functional screening process.
  • Saccharomyces YOOOOO BY4741 MATa;his3 ⁇ l;leu2 ⁇ 0; cerevisea metl5 ⁇ 0; ura3 ⁇ 0
  • Example 3 Construction of Jatropha curcas cDNA libraries from untreated and salt treated root tissue into yeast expression system driven by GAL-regulated expression system
  • Jatropha curcas root samples control treated or challenged with 150 mM NaCl were used to generate pools of cDNA.
  • Total RNA for cDNA synthesis was extracted from Jatropha curcas root samples using Qiagen RNA Miniprep Kit (Qiagen, Germany). Briefly, for total RNA extraction, root tissue samples were homogenized to a fine powder in liquid nitrogen. Total RNA was then extracted as described in the Plant mini RNA prep kit (Qiagen, Germany).
  • RNAase-free DNAaseI Sigma- Aldich, St Louis, USA
  • mRNA fraction was enriched using oligo-d(T) beads (Oligotex, Qiagen, Germany).
  • First strand cDNA pools were synthesized from normalized amounts of RNA derived from either untreated root tissue or from tissue challenged with salt stress, using PowerScript reverse transcriptase (Takara, CloneTech) as described in the Super SMART cDNA synthesis Kit, 1998). Following first strand synthesis, double stranded DNA was generated though PCR amplification using the conditions described in Table 2 (as detailed in Super SMART cDNA synthesis Kit, 1998).
  • Table 2 PCR cycling conditions and primer information used for double stranded cDNA generation and colony PCR analysis, as described in SMART cDNA Library Construction Kit (1998).
  • FIG. 1 A schematic diagram elaborating a construction of Jatropha root cDNA libraries is outlined in Figure Ia.
  • the cDNA library amplicons were cloned into a yeast expression vector, pYES 2.1 TOPO TA (Invitrogen, Carlsbrad, USA).
  • the pYES 2.1 TOPO TA a E coli-Yeast shuttle vector (Silar and Thiele, 1991), can be propagated in E. coli with the bacterial selection marker for Amp r ; while the transformants in the yeast BY4741 strain background are selected for the URA3 marker.
  • the SMART cDNA synthesis system yielded a large fraction of full-length cDNAs (Chenchik et al., 1994; Chenchik et al., 1998). Transformation of Jatropha cDNA library pools cloned in pYES2.1 TOPO TA yielded -48,000 c.f.u's, in each pool, representing un-amplified libraries. Through pilot-scale sequencing, the library was found to be representative and approximately 45-50% of the library inserts were determined to contain full-length cDNA sequences (data not shown). The average insert size in the library was approximately 800bp-lkb.
  • Example 4 Amplification and transformation of wild type yeast strain BY4741 with Jatropha root cDNA expression libraries.
  • Each library pool was plated completely into LB antibiotic plates, (supplemented with 100 ⁇ g/ml ampicilin) and grown overnight at 37 0 C.
  • E. coli containing the cDNA library were recovered from the plates and transferred to LB antibiotic media (supplemented with 100 ⁇ g/ml ampicilin), grown overnight and plasmid DNA was extracted using Plasmid Midi preparation Kit (Qiagen, Germany).
  • Plasmid transformation of yeast ⁇ Saccharromyces cerevisae was accomplished using PEG-lithium acetate based transformation protocols (Becker and Lundblad, 2001; Gietz and Schiestl, 2007; Gietz and Woods, 2006), while the plasmid selection in yeast was based on the URA3 marker borne on the yeast expression plasmid pYES2.1 TOPO TA (Invitrogen, Carlsbad, USA). Amplified plasmids were incubated with wild-type yeast strain BY4741.
  • Table 3 Composition of synthetic selection media and stocks used in the functional screen
  • Example 5 Development of replica printing based screening methodology for the identification of yeast transformants expressing genes conferring resistance to salinity and drought stress.
  • the screening scheme was based on replica-printing yeast transformants picked onto 96- well microtitre plates followed by testing the growth of yeast using quadruplicate-plate screening of yeast transformants ( Figure 4).
  • each individual yeast transformant (arrayed from 96- well plates) was tested for its ability to grow under the described four conditions: (A) Describes control conditions where GAL mediated gene expression is repressed and stress is not provided to the yeast cells. Under these conditions the cells are expected to grow on synthetic selection plates with glucose as the carbon source. Experimental conditions are defined by (B), where the gene expression is activated/induced using galactose as the carbon source, and the cells are subjected to stress, (here 75OmM NaCl). In these conditions only the yeast transformants that are capable of survival under stress (acquired due to expression of heterologous cDNA) are able to grow (Figure 4).
  • yeast transformants are grown in synthetic selection plates containing galactose, but without subjecting then to stress conditions. If the expression of any heterologous gene is detrimental to cell grown, it can be identified, thus eliminating recovery of false- negative transformants in the screen.
  • the yeast transformants were subject to yet another condition.
  • Transformants in type (D) conditions are grown in synthetic selection media with glucose as the carbon (i.e., without galactose) source, but treated under stress conditions. In these plates all transformants are expected to show retarded growth, due to the stress conditions. By comparing relative growth of marker array of transformants between above conditions it will be possible to screen against a diverse array of abiotic stresses in S. cerevisae.
  • a schematic illustration of the output expected from the replica print based screen is presented in Figure 4.
  • S. cerevisae (BY4741) transformants containing Jatropha curcas root cDNA library clones in GALl regulated yeast expression system were screened for salinity and drought resistance.
  • 20,000 individual yeast transformants were picked and inoculated into sterile 96 well U-bottom microtitre plates (Nunc, USA) containing synthetic selection media, after which the individual yeast transformants were replica printed on to quadriplicate selection plates containing either 0 mM NaCl or 750 mM NaCl (as described in Table 3) using a 96-pin replicator (Nunc, USA) ( Figure 4).
  • Example 6 Isolation of gene sequences from salinity and drought tolerant yeast transformants though plasmid rescue and plasmid amplification for determination of gene sequence
  • Isolated yeast transformants displaying the ability to tolerate salinity and drought stress imposed at 750 mM NaCl were grown on synthetic selection media containing 2% dextrose without salt (Table 3) for 36-72 hours, after which the yeast were lysed with 10 U/ ⁇ l lyticase (Sigma-Aldich, St Louis, USA) and 2%-4% SDS (final concentration). Because high concentration of NaCl used here also poses osmotic (drought) stress to cells, the yeast transformants are expected to to be useful in isolating genes that provide a response to salt and/or drought stressors.
  • the nucleic acid fraction recovered from yeast was purified with two sequential rounds of phenol: chloroform :isoamyl alcohol (25:24:1) extraction, followed by ethanol precipitation of nucleic acids.
  • the nucleic acid preparations recovered from individual yeast transformants were back-transformed into E . coli TOPlO cells via electroporation (GenePulser II, BioRad, USA)(Lundblad and Zhou, 2001; Marcil and Higgins, 1992), and then revived and plated onto LB antibiotic plates (supplemented with lOO ⁇ g/ml ampicillin).
  • E. coli backtransformants containing yeast expression plasmids were analyzed for the presence of inserts using PCR analysis with the GALl and V5/6XHIS primers as described in the pYES2.1 TOPO TA kit (Invitrogen, Carlsbad, USA). Conditions for colony PCR analysis are provide in Table 2. Subsequently, these E. coli transformants were grown and the plasmid DNA extracted as described in Qiagen plasmid miniprep kit (Qiagen, Germany).
  • Example 7 Sequence annotation for identifying novel salinity and drought tolerant genes from Jatropha curcas L.
  • BLASTX at NCBI was used to search for hits to non-redundant protein sequences, utilizing a standard genetic coding.
  • Search parameters included (i) automatic adjustment of parameters for short input sequences (ii) an expectation threshold of 10 (expected number of chances in a random model); (iii) word size of 3 (the length of the seed that initiates an alignment); (iv) BLOSUM 62 matrix; (v) Match/Mismatch Scores of +1 and -2, respectively; (vi) Gap Costs of 11 for existence, 1 for extension; (vii) no compositional adjustments; (viii) filters and masking filter on for regions of low complexity; (ix) no discontiguous word options template length;and (x) template type set to "coding.”
  • Search parameters were (i) BLOSUM62 matrix; (ii) default filter mask; (iii) expectation threshold of 10; (iv) default cutoff for reporting (v) default on analysis of top or bottom strand (vi) default limit of 20 short descriptions (vii) default word length for blastn (viii) and echofilter off (ix) ignore hypotheticals off.
  • Tables 4 and 5 indicate possible gene/protein function for isolated inserts as predicted based on nucleotide sequence homology to non-Jatropha genes. Searches of sequences against database information indicate the presence of homology hits corresponding to sequences from other plant species that have functional implications in tolerance to salinity, drought and related stresses. This indicates a possible conservation in some of the genetic pathways as well as the genes regulating salinity and drought stress in plants (Seki et al., 2003; Sreenivasulu et al., 2007; Tuteja, 2007; Vashisht and Tuteja, 2006). Several genes isolated using this screening process, however, correspond to previously uncharacterized but hypothetical proteins, or unknown or novel genes Accordingly, these genes are entirely novel determinants of tolerance to salinity and drough abiotic stress.
  • Sequencing of the inserts, followed by sequence annotation, suggests similarity of some of the inserts to other plant gene members, of which a few have been implied previously to be involved in salinity or drought stress.
  • Tables 4 & 5 presents insert clone names, as well as grouping of clones based on "hits" in the databases.
  • "Sequence annotation” refers to "hits” corresponding to genes present in non-Jatropha, plants or yeast. For clones receiving "hits” corresponding to genes in other plants or yeast that have been shown previously to confer resistance to salt, drought or related stress.
  • Jatropha homologs of previously identified non-Jatropha genes involved in confering tolerance to salt and drought stress indicates that the methods disclosed herein work unexpectedly well to identify genes related to abiotic stress in Jatropha curcas.
  • Table 4 Full length sequences of 33 genes derived from Jatropha curcas root cDNA, cloned in yeast expression vector pYES2.1 TOPO TA (Invitrogen, Calrlsbad, USA) recovered from yeast transformants showing enhanced tolerance to salinity and drought stress.
  • Column 1 lists the Reliance Life Science clone identification number.
  • Column 2 lists the accession number of the sequence deposited in GenBank.
  • Columns 3 and 4 list the sequence identifiers of the nucleotide and amino acid sequences, respectively.
  • Column 5 lists the number of amino acids in the predicted protein.
  • Columns 6-9 describe the results of a BLASTX search of GenBank data base: the best match of each sequence (col. 6); references for the best match (col. 7); the significance of the match, as an E value (col. 8); and the % identity over the region of alignment (col. 9).
  • Table 5 List of 79 partial gene sequences conferring salinity and drought tolerance obtained from the functional genetic screen
  • Column 1 lists the Reliance Life Science clone identification number.
  • Column 2 lists the accession number of the sequence deposited in GenBank.
  • Columns 3 lists the sequence identifiers of the nucleotide sequences, and column 5 lists the best match of each sequence, obtained from a BLASTX search of GenBank.
  • Jatropha clones comprised sequences that shared similarity to non-Jatropha plant gene families or other organisms. Reported functions for some of the non-Jatrophic plant families imply involvement of the herein identified Jatropha genes in conferring dominant salt stress tolerance.
  • one example is a sequence ortholog corresponding to allene oxidase cyclase.
  • Sequences of allene cyclase oxidase, isolated from mangrove have been shown in another previous investigation to confer salinity stress tolerance in multiple organisms (Yamada et al., 2002).
  • a summary of DNA sequence annotation isolated in the screen and their implications to confer salinity and drought stress resistance has been compiled in Tables 4 and 5 Approximately 59% of the sequences identified do not have a yet assigned function based on their best match (other than tolerance to salinity and/or drought), but encode hypothetical proteins conserved across plants, or sequences that do not show significant matches to existing sequences.
  • the disclosed classes of sequences represent a set of novel genes that could provide leads to yet undiscovered stress tolerance biochemical or signaling pathways operational in Jatropha curcas, through further characterization of gene function.
  • the disclosed clones are likely to be relevant to abiotic stress in other plants and/or organisms, particulary regarding the disclosed Jatropha clones with no known homology to previously identified genes.
  • Genes sequences of the present invention are useful to perform directed or selection breeding to generate elite plant cultivars in Jatropha and other species, using the methods disclosed in Sreenivasalu et al.(2007).
  • Functional genes of the present invention are also useful to genetically engineer Jatropha and other economically important plants with these sequences or their homologs for salt and drought tolerance.
  • the overexpressed candidate genes recovered in this screen are optimized in existing plant expression systems to generate and evaluate transgenic plants (generated via Agrobacterium tumefaciens mediated or biolistic transformation) to ensure optimal levels of expression and regulation, such as by switching promoters.
  • the resulting genes are then used to genetically engineer the target plant.
  • Example 8 Identification of genes conferring resistance to other abiotic stressors.
  • the plant-life cycle is not limiting to the screen.
  • Variations in the ability to tolerate salinity differ among plants that can often be ascribed to variation in their gentotype variations. Across diverse taxonomical groups, plants show distinct differences in their ability to tolerate and grow in saline ecosystems. Halophytes, for example, survive in saline environments by accumulating salt to levels in leaf vacuoles that are lethal to glycophytes.
  • the present invention helps to gain insights in the genetic difference as well as uncover novel genes by comparing the genetic basis this variation.
  • the described functional genetic screen may be used to prospect for novel genes, which are capable of providing enhanced resistance to abiotic stress by screening genomes of wild-plants occurring in naturally saline or drought prone ecosystems. Such populations of wild plants would be expected to have different expression patterns, or different genotypes, that confer resistance to the stresssor.
  • minor modification to the above-discussed functional screening methodology may be used to isolate plant genes that confer tolerance to a diverse array of possible abiotic stresses.
  • Some possible stress condition that may be screen with this assay include: a) pH stress (due to acidic or basic conditions), b) oxidative stresses, (simulated by use of media containing H 2 O 2 ), c) unfavorable temperature (by incubating media in heat or cold condition), d) heavy metal, as well as e) DNA damage/radiation (by exposure to UV, chemicals that induce DNA breakage).
  • ion stress conditions were determined for wild-type yeast BY4741 under acidic and alkaline conditions. Yeast was sensitive to acid from 5OmM H 2 SO 4 , and 50-75mM alkali NaOH (Figure 6). To improve the signal-to-noise ratio of the screen.
  • BY4741 was mutated to be hypersensitive to the stressor being screened
  • the yeast strain BY4741 was grown on YPD medium. A little inoculum of the strain was diluted in sterile distilled water and 300 ⁇ l was plated on plates containing YPD medium. These plates were exposed to UV radiation. The UV dosage was determined using Stratagene crosslinker (From 50 ⁇ joules X 100 Energy to 500 ⁇ joules X 100 Energy). These plates were stored in the dark for two days at room temperature. Colonies which grew after two days were picked and replica printed on plates containing YPD and YPD + 50OmM NaCl and kept at room temperature.
  • yeast mutant strains derived from BY4741 with salt hypersensitive (shs) ( Figure 2), acid sensitive (has) and alkali-salt hypersensitive (alks) phenotypes, isolated in with the process of random mutagenesis- selection, are shown in Figure 6. Transformation of Jatropha root cDNA libraries into these isolated yeast mutant backgrounds, and screening as described, enables isolation of additional genes involved in complementing these mutations as well as identification of more genes involved in and/or regulating these processes.
  • An acid hypersensitive mutant S. cerevisiae (has 1) was generated as a derivative of the wild type S. cerevisiae (BY4741) after UV mutagenesis. This was then transformed with the Jatropha curcas root cDNA library clones and screened for tolerance to acid stress.
  • alkali hypersensitive mutant (alks 1) of S. cerevisiae (BY4741) was generated by UV mutagenesis, and then transformed with the Jatropha curcas root cDNA library clones as before (Flick and Johnston 1990)
  • KanM NaOH or 25mM NaOH a synthetic selection media
  • yeast transformants were replica printed on to quadruplicate selection plates containing either OmM NaOH or 25mM NaOH, with glucose or galactose(as described for salinity in figure 4) using a 96-pin replicator (Nunc, USA).
  • Upon comparison of relative growth of yeast transformants we isolated yeast transformants that show consistent tolerance to stress imposed by alkali. Results
  • Table 6 List of 4 full length genes obtained from functional genetic screen showing enhanced tolerance to Acid and /or alkali stress.
  • Column 1 lists the Reliance Life Science clone identification number.
  • Column 2 lists the accession number of the sequence deposited in GenBank.
  • Columns 3 and 4 list the sequence identifiers of the nucleotide and amino acid sequences, respectively.
  • Column 5 lists the number of base pairs in the clone.
  • Columns 6-8 describe the results of a BLASTX search of GenBank data base: the best match of each sequence (col. 6); the E value, measuring the significance of the match (col. 7); and the % identity over the region of alignment (col. 8).
  • GQ 906362 and GQ 906363 refer to genes conferring acid tolerance and GQ906364 & GQ906365 refer to genes conferring alkali tolerance.
  • Table 7 List of 17 partial gene sequences conferring acid tolerance obtained from the functional genetic screen
  • the wheat cDNA LCTl generates hypersensitivity to sodium in a salt-sensitive yeast strain. Plant Physiol 126, 1061-1071.
  • GmDREB2 a soybean DRE-binding transcription factor, conferred drought and high- salt tolerance in transgenic plants. Biochem Biophys Res Commun 353, 299-305.
  • Arabidopsis thaliana AtHAL3 a flavoprotein related to salt and osmotic tolerance and plant growth. Plant J 20, 529-539.
  • FOX Full-length cDNA Over-eXpressor
  • yeast HALl gene improves salt tolerance of transgenic tomato. Plant Physiol 123, 393-402.
  • Zinc finger protein STOPl is critical for proton tolerance in Arabidopsis and coregulates a key gene in aluminum tolerance.
  • a metallothionein-like protein of rice (rgMT) functions in E. coli and its gene expression is induced by abiotic stresses. Biotechnol Lett 28, 1749- 1753.
  • STRESS RESPONSE SUPPRESSORl and STRESS RESPONSE SUPPRESSOR2 two DEAD-box RNA helicases that attenuate Arabidopsis responses to multiple abiotic stresses. Plant Physiol 145, 814-830. Ko, J. H., and Han, K. H. (2004). Arabidopsis whole-transcriptome profiling defines the features of coordinated regulations that occur during secondary growth. Plant MoI Biol 55, 433- 453.
  • the Arabidopsis thaliana SOS2 gene encodes a protein kinase that is required for salt tolerance.
  • Salt tolerance-related protein STO binds to a Myb transcription factor homologue and confers salt tolerance in Arabidopsis. J Exp Bot 54, 2231 -
  • Yeast plasma membrane Enalp ATPase alters alkali-cation homeostasis and confers increased salt tolerance in tobacco cultured cells.
  • a rice HAL2- ⁇ ike gene encodes a Ca(2+)-sensitive 3'(2'),5'- diphosphonucleoside 3'(2')-phosphohydrolase and complements yeast met22 and Escherichia coli cysQ mutations. J Biol Chem 270, 29105-291 10.
  • Thioredoxin is an essential protein induced by multiple stresses in Bacillus subtilis. J Bacteriol 180, 1869-1877.
  • RIKEN Arabidopsis full-length (RAFL) cDNA and its applications for expression profiling under abiotic stress conditions J. Exp. Bot. 55, 213-223.
  • Plant gene networks in osmotic stress response from genes to regulatory networks. Methods Enzymol 428, 109-128.

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Abstract

La présente invention concerne un nouveau procédé pour identifier des gènes dans des plantes Jatropha, telles que Jatropha curcas L., qui confèrent une tolérance aux stress abiotiques tels que la salinité, la sécheresse, et les stress ioniques. De tels gènes permettent le développement de cultivars de Jatropha curcas qui présentent une tolérance améliorée à la salinité et au stress, qui peut être réalisé par des approches de modification génétique, sélection dirigée ou sélection de mutations souhaitables dans les gènes identifiés pour la salinité, la sécheresse et le stress ionique. La présente invention concerne en outre des procédés pour générer des mutants aléatoires dans une levure sensible au stress de salinité, acide ou alcalin qui facilitent l’identification de nouveaux gènes additionnels de Jatropha curcas. La présente invention concerne en outre de nouveaux gènes de Jatropha curcas qui confèrent une tolérance à la salinité, la sécheresse et les stress abiotiques. Dans un mode de réalisation associé, l’invention concerne en outre des polypeptides qui véhiculent la tolérance à la salinité, la sécheresse et les stress abiotiques.
PCT/IN2009/000673 2008-11-21 2009-11-20 Identification de gènes associés à une tolérance aux stress abiotiques chez jatropha curcas WO2010058428A2 (fr)

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CN103421829A (zh) * 2013-08-22 2013-12-04 山东大学 小麦耐盐基因TaAOC1及其应用
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CN113151273A (zh) * 2021-04-14 2021-07-23 新疆农业大学 非生物逆境诱导型启动子及其应用
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