EP0819174A1 - Genes de resistance aux pathogenes pour les plantes et leur utilisation - Google Patents

Genes de resistance aux pathogenes pour les plantes et leur utilisation

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Publication number
EP0819174A1
EP0819174A1 EP96909256A EP96909256A EP0819174A1 EP 0819174 A1 EP0819174 A1 EP 0819174A1 EP 96909256 A EP96909256 A EP 96909256A EP 96909256 A EP96909256 A EP 96909256A EP 0819174 A1 EP0819174 A1 EP 0819174A1
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EP
European Patent Office
Prior art keywords
nucleic acid
sequence
plant
encoding
gene
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Application number
EP96909256A
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German (de)
English (en)
Inventor
Jonathan Dallas George Jones
Jane Parker
Mark Coleman
Michael John Daniels
Véronique University of California SZABO
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Plant Bioscience Ltd
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INNES JOHN CENTRE INNOV Ltd
JOHN INNES CENTRE INNOVATIONS Ltd
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Publication of EP0819174A1 publication Critical patent/EP0819174A1/fr
Withdrawn legal-status Critical Current

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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
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/37—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from fungi
    • 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
    • C12N15/8279—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 biotic stress resistance, pathogen resistance, disease resistance
    • C12N15/8281—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 biotic stress resistance, pathogen resistance, disease resistance for bacterial 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
    • C12N15/8271—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
    • C12N15/8279—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 biotic stress resistance, pathogen resistance, disease resistance
    • C12N15/8282—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 biotic stress resistance, pathogen resistance, disease resistance for fungal resistance

Definitions

  • the present invention relates to pathogen resistance in plants and more particularly to the identification and use of pathogen resistance genes. It is based on cloning of the Arabidopsis RPP5 gene. Plants are constantly challenged by potentially pathogenic microorganisms. Crop plants are particularly vulnerable, because they are usually grown as genetically uniform monocultures; when disease strikes, losses can be severe. However, most plants are resistant to most plant pathogens. To defend themselves, plants have evolved an array of both preexisting and inducible defences. Pathogens must specialize to circumvent the defence mechanisms of the host, especially those biotrophic pathogens that derive their nutrition from an intimate association with living plant cells.
  • Race specific resistance is strongly correlated with the hypersensitive response (HR) , an induced response by which (it is hypothesized) the plant deprives the pathogen of living host cells by localized cell death at sites of attempted pathogen ingress.
  • HR hypersensitive response
  • He toxin Helminthosporium carbonum races that express a toxin
  • Hml resistance gene Mutations to loss of He toxin expression are recessive, and correlated with loss of virulence, in contrast to gene-for-gene interactions in which mutations to virulence are recessive.
  • a major accomplishment was reported in 1992, with the isolation by tagging of the Hml gene- (Johal and Briggs, 1992) . Plausible arguments have been made for how gene-for-gene interactions could evolve from toxin-dependent virulence.
  • hrp genes Additional bacterial genes
  • pathogenicity Kelman, 1992; Long and Staskawicz, 1993
  • pathogens make products that enable the plant to detect them.
  • certain easily discarded Avr genes contribute to but are not required for pathogenicity, whereas other Avr genes are less dispensable (Keen, 1992; Long, et al, 1993) .
  • the characterization of two fungal avirulence genes has also been reported.
  • the Avr9 gene of Cladosporium fulvu which confers avirulence on C.
  • fulvum races that attempt to attack tomato varieties that carry the Cf-9 gene, encodes a secreted cysteine-rich peptide with a final processed size of 28 amino acids but its role in compatible interactions is not clear (De Wit, 1992) .
  • the Avr4 gene of C. fulvum encodes a secreted peptide that is processed to a final size of amino acids 106 (Joosten et al , 1994)
  • the Pto gene appears to code for little more than the kinase catalytic domain and a potential N-terminal myristoylation site that could promote association with membranes. It would be surprising if such a gene product could act alone to accomplish the specific recognition required to initiate the defence response only when the AvrPto gene is detected in invading microorganisms.
  • the race-specific elicitor molecule made by Pst strains that carry AvrPto is still unknown and needs to he characterized before possible recognition of this molecule by the Pto gene product can be investigated.
  • the isolation of the Pto gene a number of other resistance genes have been isolated.
  • the isolation of the tobacco mosaic resistance gene N from tobacco was reported by hitham et al (1994) .
  • the isolation of the flax rust resistance gene L6 from flax was reported by Lawrence et al (1995) .
  • the isolation of two Arabidopsis thaliana genes for resistance to Pseudomonas syringae has been reported.
  • the isolation of RPS2 was reported by Bent et al (1994) and by Mindrinos et al (1994) and the isolation of RPM1 was reported by Grant et al (1995) .
  • the predicted protein product of this gene exhibits an N-terminal, presumably extracellular, domain composed principally of leucine rich repeats similar to those of Cf-9 and Cf-2, a predicted transmembrane domain, and a presumably cytoplasmic domain with strong similarities to serine-threonine protein kinases, particularly that encoded by Pto.
  • a pathogen resistance gene enables a plant to detect the presence of a pathogen expressing a corresponding avirulence gene (Avr) .
  • a defence response such as the hypersensitive response (HR) is activated.
  • HR hypersensitive response
  • a plant may deprive the pathogen of living cells by localised cell death at sites of attempted pathogen ingress.
  • Other genes including the PGIP gene of W093/11241 (for example) , are induced in the plant defence response resulting from detection of a pathogen by an R gene.
  • a pathogen resistance gene may be envisaged as encoding a receptor to a pathogen-derived and Avr dependent molecule. In this way it may be likened to the RADAR of a plant for detection of a pathogen. Genes involved in the defence the plant mounts to the pathogen once detected are not pathogen resistance genes. Expression of a pathogen resistance gene in a plant causes activation of a defence response in the plant. This may be upon contact of the plant with a pathogen or a corresponding elicitor molecule, though the possibility of causing activation by over- expression of the resistance gene in the absence of elicitor has been reported. The defence response may be activated locally, e.g.
  • Activation of a defence response in a plant expressing a pathogen resistance gene may be caused upon contact of the plant with an appropriate, corresponding elicitor molecule.
  • the elicitor may be contained in an extract of a pathogen such as Peronospora parasi tica, or may be wholly or partially purified and may be wholly or partially synthetic.
  • An elicitor molecule may be said to "correspond" if it is a suitable ligand for the R gene product to elicit activation of a defence response.
  • the Arabidopsis RPP5 gene was isolated by map-based cloning.
  • the locus that confers resistance is mapped at high resolution relative to restriction fragment length polymorphism (RFLP) markers that are linked to the resistance gene.
  • RFLP restriction fragment length polymorphism
  • DNA sequence analysis of the cloned DNA identified a gene with leucine-rich repeats.
  • a subclone of 29L17, designated pRPP5-l, containing 6304 bp of DNA including 1298 bp 5' to the probable initiation codon ( Figure 1) and 458 bp 3' to the probable termination codon was constructed in a binary vector.
  • the subclone was used to transform Arabidopsis ecotype Columbia and shown to confer disease resistance.
  • Analysis of a fast neutron induced mutation of Landsberg that had become disease sensitive revealed rearrangement of the DNA structure of this gene. Taken together these data provide the necessary evidence that the sequences as shown in Figures 1 and 2 correspond to the RPP5 gene.
  • the present invention provides a nucleic acid isolate encoding a pathogen resistance gene, the gene being characterized in that it encodes the amino acid sequence shown in SEQ ID NO 2, or a fragment thereof, or an amino acid sequence showing a significant degree of homology thereto. N and L6 may be excluded.
  • nucleic acid according to the invention may be distinguished from other pathogen resistance genes such as N, L6 by optionally having any one or more of the following features: the encoded polypeptide has less than 30% homology with the amino acid sequence of the tobacco N protein, shown in Figure 3 and less than 25% homology with the amino acid sequence of the flax L6 protein, shown in Figure 3; its expression does not activate said defence response upon contact of the plant with a molecule that is an elicitor of the tobacco N protein; its expression does not activate said defence response upon contact of the plant with a molecule that is an elicitor of the flax L6 protein; its expression does not when in a tobacco plant activate said defence response upon contact of the tobacco plant with Tobacco Mosaic Virus; its expression does not when in a flax plant activate said defence response upon contact of the
  • the encoded polypeptide comprises a putative nucleotide binding site; the encoded polypeptide is a cytoplasmic protein; the encoded polypeptide comprises a region having homology to the cytoplasmic domain of the Drosophila Toll protein.
  • nucleic acid according to the present invention may be for the encoded polypeptide to comprise an N-terminal domain that has greater than 60% homology with the amino acid sequence of the N-terminal domain of RPP5 shown in Figure 2 (encoded by exon 1 of Figure 1) , and/or comprise a nucleotide binding site domain that has greater than 40% homology with the amino acid sequence of the domain of RPP5 shown in Figure 2 encoded by exon 2 of Figure 1, and/or comprise a domain that has greater than 30% homology with the amino acid sequence of the domain of RPP5 shown in Figure 2 encoded by exon 3 of Figure 1, and/or comprise a domain that has greater than 30% homology with the amino acid sequence of the leucine-rich repeat (LRR) domain of RPP5 shown in Figure 2 encoded by exons 4, 5 and 6 of Figure 1.
  • LRR leucine-rich repeat
  • Table 2 shows % amino acid identity between putative domains of RPP5 and N, and RPP5 and L6, as encoded by exons of the genomic sequences.
  • the nucleic acid may comprise a sequence of nucleotides encoding an amino acid sequence showing at least about 60% homology, preferably at least about 70% homology, at least about 80% homology, or more preferably at least about 90% or greater homology to the amino acid sequence shown in SEQ ID NO 2.
  • % amino acid homology is used to refer to % amino acid identity. High homology may be indicated by ability of complementary nucleic acid to hybridise under appropriate conditions, for instance conditions stringent enough to exclude hybridisation to sequences not encoding a pathogen resistance gene.
  • the words allele, derivative or mutant may in context be used in respect of any sequence of nucleotides capable of hybridising with any of the nucleotide sequences encoding a polypeptide comprising the relevant sequence of amino acids.
  • the nucleic acid encodes the amino acid sequence shown in SEQ ID No 2 in which case the nucleic acid may comprise DNA with an encoding sequence shown in SEQ ID NO 1 or sufficient part to encode the desired polypeptide (eg from the initiating methionine codon to the first in frame downstream stop codon of the mRNA) .
  • DNA comprises a sequence of nucleotides which are the nucleotides 1966 to 6511 of SEQ ID NO 1, or a mutant, derivative or allele thereof, for instance lacking introns.
  • Figure 4 provides a contiguous sequence encoding the amino acid sequence of Figure 2.
  • a further aspect of the invention provides a nucleic acid isolate encoding a pathogen resistance gene, or a fragment thereof, obtainable by screening a nucleic acid library with a probe comprising nucleotides 1966 to 6511 of SEQ ID NO 1, nucleotides complementary thereto, or a fragment, derivative, mutant or allele thereof, and isolating nucleic acid which encodes a polypeptide able to confer pathogen resistance to a plant. Suitable techniques are well known in the art.
  • the present invention also provides a method of identifying and/or isolating nucleic acid encoding a pathogen resistance gene comprising probing candidate (or "target") nucleic acid with nucleic acid which has a sequence of nucleotides which encodes the amino acid sequence shown in Figure 2, which is complementary to an encoding sequence or which encodes a fragment of either an encoding sequence or a sequence complementary to an encoding sequence.
  • the candidate nucleic acid (which may be, for instance, cDNA or genomic DNA) may be derived from any cell or organism which may contain or is suspected of containing nucleic acid encoding a pathogen resistance gene.
  • a preferred nucleotide sequence appears in Figure 1. Sequences complementary to the sequence shown, and fragments thereof, may be used.
  • Preferred conditions for probing are those which are stringent enough for there to be a simple pattern with a small number of hybridisations identified as positive which can be investigated further. It is well known in the art to increase stringency of hybridisation gradually until only a few positive clones remain.
  • Nucleic acid according to the present invention may encode the amino acid sequence shown in SEQ ID NO 2 or a mutant, derivative or allele of the sequence provided.
  • Preferred mutants, derivatives and alleles are those which retain a functional characteristic of the protein encoded by the wild-type gene, especially the ability to confer pathogen resistance.
  • Changes to a sequence, to produce a mutant or derivative may be by one or more of insertion, deletion or substitution of one or more nucleotides in the nucleic acid, leading to the insertion, deletion or substitution of one or more amino acids. Of course, changes to the nucleic acid which make no difference to the encoded amino acid sequence are included.
  • the nucleic acid may be DNA or RNA and may be synthetic, eg with optimised codon usage for expression in a host organism of choice.
  • Nucleic acid molecules and vectors according to the present invention may be provided isolated and/or purified from their natural environment, in substantially pure or homogeneous form, or free or substantially free of nucleic acid or genes of the species of interest or origin other than the sequence encoding a polypeptide with the required function.
  • Nucleic acid according to the present invention may comprise cDNA, RNA, genomic DNA and may be wholly or partially synthetic. The term "isolate" encompasses all these possibilities.
  • nucleic acid comprising a sequence of nucleotides complementary to a nucleotide sequence hybridisable with any encoding sequence provided herein. Another way of looking at this would be for nucleic acid according to this aspect to be hybridisable with a nucleotide sequence complementary to any encoding sequence provided herein.
  • DNA is generally double-stranded and blotting techniques such as Southern hybridisation are often performed following separation of the strands without a distinction being drawn between which of the strands is hybridising.
  • the hybridisable nucleic acid or its complement encode a polypeptide able to confer pathogen resistance on a host, i.e. includes a pathogen resistance gene.
  • the nucleic acid may be in the form of a recombinant vector, for example a phage or cosmid vector.
  • the nucleic acid may be under the control of an appropriate promoter and regulatory elements for expression in a host cell, for example a plant cell. In the case of genomic DNA, this may contain its own promoter and regulatory elements and in the case of cDNA this may be under the control of an appropriate promoter and regulatory elements for expression in the host cell.
  • Suitable vectors can be chosen or constructed, containing appropriate regulatory sequences, including promoter sequences, terminator fragments, polyadenylation sequences, enhancer sequences, marker genes and other sequences as appropriate.
  • appropriate regulatory sequences including promoter sequences, terminator fragments, polyadenylation sequences, enhancer sequences, marker genes and other sequences as appropriate.
  • Many known techniques and protocols for manipulation of nucleic acid for example in preparation of nucleic acid constructs, mutagenesis, sequencing, introduction of DNA into cells and gene expression, and analysis of proteins, are described in detail in Short Protocols in Molecular Biology, Second Edition, Ausubel et al. eds., John Wiley & Sons, 1992. The disclosures of Sambrook et al. and Ausubel et al. are incorporated herein by reference.
  • the nucleic acid to be inserted may be assembled within a construct which contains effective regulatory elements which will drive transcription. There must be available a method of transporting the construct into the cell. Once the construct is within the cell membrane, integration into the endogenous chromosomal material may or may not occur according to different embodiments of the invention. Finally, as far as plants are concerned the target cell type must be such that cells can be regenerated into whole plants.
  • Plants transformed with a DNA segment containing pre-sequence may be produced by standard techniques which are already known for the genetic manipulation of plants.
  • DNA can be transformed into plant cells using any suitable technology, such as a disarmed
  • Ti-plasmid vector carried by Agrobacterium exploiting its natural gene transfer ability (EP-A-270355, EP-A-0116718, NAR 12(22) 8711 - 87215 1984), particle or microprojectile bombardment (US 5100792, EP-A-444882, EP-A-434616). microinjection (WO 92/09696, WO 94/00583, EP 331083, EP 175966), electroporation (EP 290395, WO 8706614) or other forms of direct DNA uptake (DE 4005152, WO 9012096, US 4684611) .
  • Agrobacterium transformation is widely used by those skilled in the art to transform dicotyledonous species.
  • Agrobacterium has been reported to be able to transform foreign DNA into some monocotyledonous species (WO 92/14828) , microprojectile bombardment, electroporation and direct DNA uptake are preferred where Agrobacterium is inefficient or ineffective.
  • a combination of different techniques may be employed to enhance the efficiency of the transformation process, eg. bombardment with Agrobacterium coated microparticles (EP-A-486234) or microprojectile bombardment to induce wounding followed by co-cultivation with Agrobacterium (EP-A-486233) .
  • the particular choice of a transformation technology will be determined by its efficiency to transform certain plant species as well as the experience and preference of the person practising the invention with a particular methodology of choice. It will be apparent to the skilled person that the particular choice of a transformation system to introduce nucleic acid into plant cells is not essential to or a limitation of the invention.
  • the RPP5 gene modified versions thereof and related genes encoding a protein showing a significant degree of homology to the protein product of the RPP5 gene, alleles, mutants and derivatives thereof, may be used to confer pathogen resistance, e.g. to downy mildews, in plants.
  • nucleic acid as described above may be used for the production of a transgenic plant. Such a plant may possess pathogen resistance conferred by the RPP5 gene.
  • the invention thus further encompasses a host cell transformed with a vector as disclosed, especially a plant or a microbial cell.
  • a host cell such as a plant cell, comprising nucleic acid according to the present invention is provided.
  • the nucleic acid may be incorporated within the chromosome.
  • a vector comprising nucleic acid according to the present invention need not include a promoter, particularly if the vector is to be used to introduce the nucleic acid into cells for recombination into the genome.
  • a plant cell having incorporated into its genome a sequence of nucleotides as provided by the present invention, under operative control of a promoter for control of expression of the encoded polypeptide.
  • a further aspect of the present invention provides a method of making such a plant cell involving introduction of a vector comprising the sequence of nucleotides into a plant cell. Such introduction may be followed by recombination between the vector and the plant cell genome to introduce the sequence of nucleotides into the genome. The polypeptide encoded by the introduced nucleic acid may then be expressed.
  • a plant which comprises a plant cell according to the invention is also provided, along with any clone of such a plant, seed, selfed or hybrid progeny and descendants, and any part of any of these, such as cuttings, seed.
  • the invention provides any plant propagule, that is any part which may be used in reproduction or propagation, sexual or asexual, including cuttings, seed and so on.
  • the invention further provides a method comprising expression from nucleic acid encoding the amino acid sequence SEQ ID NO 2, or a mutant, allele or derivative thereof, or a significantly homologous amino acid sequence, within cells of a plant (thereby producing the encoded polypeptide) , following an earlier step of introduction of the nucleic acid into a cell of the plant or an ancestor thereof.
  • Such a method may confer pathogen resistance on the plant.
  • a gene stably incorporated into the genome of a plant is passed from generation to generation to descendants of the plant, cells of which descendants may express the encoded polypeptide and so may have enhanced pathogen resistance.
  • Pathogen resistance may be determined by assessing compatibility of a pathogen such as Peronospora parasi tica or Bremia lactucae .
  • the presence of LRRs may be characteristic of many pathogen resistance genes and the presence of LRRs can thus be used in a method of identifying further pathogen resistance genes.
  • the present invention provides a method of identifying a plant pathogen resistance gene comprising use of an oligonucleotide(s) which comprise(s) a sequence or sequences that are conserved between pathogen resistance genes such as RPP5, N and L6 to search for new resistance genes.
  • nucleic acid comprising a pathogen resistance gene (encoding a polypeptide able to confer pathogen resistance)
  • a method of obtaining nucleic acid comprising a pathogen resistance gene comprising hybridisation of an oligonucleotide (details of which are discussed herein) or a nucleic acid molecule comprising such an oligonucleotide to target/candidate nucleic acid.
  • Target or candidate nucleic acid may, for example, comprise a genomic or cDNA library obtainable from an organism known to encode a pathogen resistance gene. Successful hybridisation may be identified and target/candidate nucleic acid isolated for further investigation and/or use.
  • Hybridisation may involve probing nucleic acid and identifying positive hybridisation under suitably stringent conditions (in accordance with known techniques) and/or use of oligonucleotides as primers in a method of nucleic acid amplification, such as PCR.
  • stringent conditions in accordance with known techniques
  • oligonucleotides as primers in a method of nucleic acid amplification, such as PCR.
  • preferred conditions are those which are stringent enough for there to be a simple pattern with a small number of hybridisations identified as positive which can be investigated further. It is well known in the art to increase stringency of hybridisation gradually until only a few positive clones remain.
  • oligonucleotides designed to amplify DNA sequences may be used in PCR reactions or other methods involving amplification of nucleic acid, using routine procedures. See for instance "PCR protocols; A Guide to Methods and Applications", Eds. Innis et al , 1990, Academic Press, New York.
  • Preferred amino acid sequences suitable for use in the design of probes or PCR primers are sequences conserved (completely, substantially or partly) between at least two polypeptides able to confer pathogen resistance such as those encoded by RPP5 and N and/or L6.
  • oligonucleotide probes or primers may be designed, taking into account the degeneracy of the genetic code, and, where appropriate, codon usage of the organism from the candidate nucleic acid is derived.
  • Preferred nucleotide sequences may include those comprising or having a sequence encoding amino acids
  • oligonucleotide TTC/T TAC/T GAC/T GTX GAT/C CC can be derived from the amino acid sequence F Y D V D P.
  • Such an oligonucleotide primer could be used in PCR in combination with the primer A A G/A AA G/A CA XGC T/G/A AT (SEQ ID NO 11) , derived from the bottom strand of the sequence that encodes I A C F F. (All sequences given 5' to 3' ; see Figure 3) .
  • X indicates A, G, C or T.
  • an oligonucleotide in accordance with the invention e.g. for use in nucleic acid amplification, has about 10 or fewer codons (e.g. 6, 7 or 8) , i.e. is about 30 or fewer nucleotides in length (e.g. 18, 21 or 24) .
  • Assessment of whether or not such a PCR product corresponds to resistance genes may be conducted in various ways. A PCR band from such a reaction might contain a complex mix of products. Individual products may be cloned and each one individually screened for linkage to known disease resistance genes that are segregating in progeny that showed a polymorphism for this probe.
  • the PCR product may be treated in a way that enables one to display the polymorphism on a denaturing polyacrylamide gel and specific bands that are linked to the resistance gene may be preselected prior to cloning.
  • a candidate PCR band Once a candidate PCR band has been cloned and shown to be linked to a known resistance gene, it may then be used to isolate cDNA clones which may be inspected for other features and homologies to either RPP5, N or L6. It may subsequently be analysed by transformation to assess its function on introduction into a disease sensitive variety of the plant of interest.
  • the PCR band or sequences derived by analysing it may be used to assist plant breeders in monitoring the segregation of a useful resistance gene.
  • a further method of using the RPP5 sequence to identify other resistance genes is to use computer searches of expressed sequence tag (EST) and other DNA sequence databases to identify genes in other species that encode proteins with significant RPP5 homology. For example, a homology score of at least 60 using one of the BLAST algorithms (Altschul et al , 1990) would indicate a candidate resistance gene.
  • EST expressed sequence tag
  • nucleic acid molecule comprising ..all or part of the sequence of the obtained nucleic acid may be used in the production of a transgenic plant, for example in order to confer pathogen resistance on the plant.
  • Figure 1 shows the genomic DNA sequence of the RPP5 gene (SEQ ID NO. 1) . Introns are shown in this Figure in non-capitalised letters. Features: Nucleic acid sequence - Translation start at nucleotide 1966; translation stop at nucleotide 6512.
  • Figure 2 shows predicted RPP5 protein amino acid sequence (SEQ ID NO 2) .
  • Figure 3 shows a comparison of the predicted amino acid sequence of the RPP5 (SEQ ID NO 2), N (SEQ ID NO 3) and L6 (SEQ ID NO 4) genes.
  • the protein sequences are aligned according to predicted protein domains.
  • Figure 3 was produced using the PRETTYBOX and PileUp programs of the University of Wisconsin Genetics Computer Group Sequence Analysis Software Package Version 7.2.
  • Figure 4 shows a contiguous nucleotide sequence (SEQ ID NO 5) encoding the amino acid sequence-.shown in Figure 2 (SEQ ID NO 2) , and made by joining together the sequences of the exons of the sequence of Figure 1 (SEQ ID NO 1) .
  • the RPP5 gene was cloned using a map-based cloning strategy similar in principle to that used for the isolation of the tomato Pto gene, described briefly earlier.
  • the Arabidopsis genome project has as an objective the establishment of a physical map of
  • Chromosome 4 Chromosome 4, and ultimately of the entire Arabidopsis genome.
  • the C18 probe was used to identify hybridising yeast artificial chromosome (YAC) clones. This facilitated the establishment of a physical contig between 4539 and 226 incorporating other linked markers, such as gl3683.
  • the C18 RAPD band was cloned and used as a probe on Columbia and Landsberg genomic DNA. Hybridisation of this probe revealed a very polymorphic small multi-gene family in these two genotypes. Hybridisation to recombinant inbred lines (Lister and Dean, 1993) showed that all members of this multi-gene family were absolutely linked to the resistance gene locus. Using the CAPS procedure
  • a transformant was identified derived from transformation with cosmid 29L17, and self-progeny of this transformant segregated for resistance to P. parasi tica NoCO-2. This demonstrated that the clone 29L17, which carries a band that hybridises to the C18 RAPD probe, carries a functional Peronospora parasi tica resistance gene.
  • One criterion for establishing whether or not a characterised region of plant DNA corresponds to the gene of interest is to inspect whether mutations in the corresponding gene, caused by ionizing radiation, are associated with DNA rearrangements in the region of interest.
  • Fast neutron mutagenised Landsberg seed were screened with Peronospora parasi tica for mutants to disease sensitivity.
  • Three mutations were found and analysed by Southern blots for perturbations or rearrangements in DNA corresponding to the gene, carrying leucine rich repeats.
  • One mutant line, FNB387 showed an altered pattern of Southern blot hybridisation. More detailed analysis showed that the perturbation consists of an insertion of 270 bp of DNA in the C-terminus of the reading frame that carries leucine-rich repeats.
  • pRPP5-l contained a 6304 bp DNA fragment defined by a Bglll restriction enzyme site 5' to the gene (nucleotide 668 in SEQ ID NO. 1) and a PstI restriction enzyme site 3' to the gene (nucleotide
  • pRPP5-l was used to transform Arabidopsis ecotype Columbia and shown to confer disease resistance.
  • First strand cDNA was prepared from seedling leaf messenger RNA and PCR amplification from this cDNA was performed using intron flanking primers.
  • the primers were: for intron 1, 5' -GAGTTCGCTCTATCATCTCC and 5 ⁇ -TTATTGCATTCGAAACATCATTG; for introns 2 and 3,
  • primers could alone, or in combination with other primers encoding conserved and non-conserved regions of the identified resistance genes, be used to isolate other homologous gene sequences which could include previously uncharacterized resistance genes.

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Abstract

Le gène Arabidopsis RPP5 a été cloné et sa séquence a été décrite ainsi que la séquence d'aminoacides codée. L'ADN codant le polypeptide, et ses allèles, mutants et dérivés, peuvent être introduits dans les cellules des plantes et le polypeptide codé peut être exprimé, conférant ainsi aux plantes une résistance aux pathogènes comprenant de telles cellules ainsi que leur descendances. La séquence RPP5 comporte des répétitions riches en leucine et la présence de ces répétitions permet l'identification d'autres gènes de résistance aux pathogènes chez les plantes. Les homologies entre le RPP5 et d'autres gènes de résistance aux pathogènes révèlent des motifs utilisés dans l'identification d'autres gènes de résistance aux pathogènes.
EP96909256A 1995-04-07 1996-04-09 Genes de resistance aux pathogenes pour les plantes et leur utilisation Withdrawn EP0819174A1 (fr)

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GB9507232 1995-04-07
GBGB9507232.8A GB9507232D0 (en) 1995-04-07 1995-04-07 Plant pathogen resistance genes and uses thereof
PCT/GB1996/000849 WO1996031608A1 (fr) 1995-04-07 1996-04-09 Genes de resistance aux pathogenes pour les plantes et leur utilisation

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CN (1) CN1190439A (fr)
AU (1) AU703525B2 (fr)
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GB (1) GB9507232D0 (fr)
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GB9710044D0 (en) * 1997-05-16 1997-07-09 Innes John Centre Innov Ltd A plant disease resistance signalling gene: materials and methods relating thereto
GB9817278D0 (en) * 1998-08-07 1998-10-07 Plant Bioscience Ltd Plant resistance genes
AU774577B2 (en) * 1999-07-05 2004-07-01 Cropdesign N.V. Plant proteins
AU2003231768C1 (en) 2002-04-24 2010-08-19 Agrinomics, Llc Generation of plants with improved pathogen resistance
US20040216182A1 (en) 2003-04-24 2004-10-28 Federspiel Nancy Anne Generation of plants with improved pathogen resistance and drought tolerance

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DE69133552C5 (de) * 1990-08-25 2008-01-10 F. Hoffmann-La Roche Ltd. Nicht-A, nicht-B Hepatitis Virus Antigen, und diagnostische Verfahren.
AU645915B2 (en) * 1991-07-23 1994-01-27 F. Hoffmann-La Roche Ag Improvements in the in situ PCR
US5654187A (en) * 1993-02-25 1997-08-05 The United States Of America As Represented By The Department Of Health And Human Services MDR1 retroviral plasmid
US5851760A (en) * 1993-06-15 1998-12-22 The Salk Institute For Biological Studies Method for generation of sequence sampled maps of complex genomes
WO1995005731A1 (fr) * 1993-08-24 1995-03-02 Cornell Research Foundation, Inc. Gene conferant aux plantes une resistance aux maladies
US5981730A (en) * 1994-04-13 1999-11-09 The General Hospital Corporation RPS gene family, primers, probes, and detection methods
WO1995031564A2 (fr) * 1994-05-11 1995-11-23 John Innes Centre Innovations Limited Procede d'introduction d'une resistance aux agents pathogenes chez les vegetaux

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See references of WO9631608A1 *

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JPH11503319A (ja) 1999-03-26
AU5282396A (en) 1996-10-23
CA2216406A1 (fr) 1996-10-10
NZ304937A (en) 2000-01-28
AU703525B2 (en) 1999-03-25
WO1996031608A1 (fr) 1996-10-10
CN1190439A (zh) 1998-08-12
GB9507232D0 (en) 1995-05-31

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