Abstract
Disease resistance genes in plants are often found in complex multigene families. The largest known cluster of disease resistance specificities in lettuce contains the RGC2 family of genes. We compared the sequences of nine full-length genomic copies of RGC2 representing the diversity in the cluster to determine the structure of genes within this family and to examine the evolution of its members. The transcribed regions range from at least 7.0 to 13.1 kb, and the cDNAs contain deduced open reading frames of approximately 5. 5 kb. The predicted RGC2 proteins contain a nucleotide binding site and irregular leucine-rich repeats (LRRs) that are characteristic of resistance genes cloned from other species. Unique features of the RGC2 gene products include a bipartite LRR region with >40 repeats. At least eight members of this family are transcribed. The level of sequence diversity between family members varied in different regions of the gene. The ratio of nonsynonymous (Ka) to synonymous (Ks) nucleotide substitutions was lowest in the region encoding the nucleotide binding site, which is the presumed effector domain of the protein. The LRR-encoding region showed an alternating pattern of conservation and hypervariability. This alternating pattern of variation was also found in all comparisons within families of resistance genes cloned from other species. The Ka /Ks ratios indicate that diversifying selection has resulted in increased variation at these codons. The patterns of variation support the predicted structure of LRR regions with solvent-exposed hypervariable residues that are potentially involved in binding pathogen-derived ligands.
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- Anderson P. A., Lawrence G. J., Morrish B. C., Ayliffe M. A., Finnegan E. J., Ellis J. G. Inactivation of the flax rust resistance gene M associated with loss of a repeated unit within the leucine-rich repeat coding region. Plant Cell. 1997 Apr;9(4):641–651. doi: 10.1105/tpc.9.4.641. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Anderson P. A., Okubara P. A., Arroyo-Garcia R., Meyers B. C., Michelmore R. W. Molecular analysis of irradiation-induced and spontaneous deletion mutants at a disease resistance locus in Lactuca sativa. Mol Gen Genet. 1996 Jun 12;251(3):316–325. doi: 10.1007/BF02172522. [DOI] [PubMed] [Google Scholar]
- Baker B., Zambryski P., Staskawicz B., Dinesh-Kumar S. P. Signaling in plant-microbe interactions. Science. 1997 May 2;276(5313):726–733. doi: 10.1126/science.276.5313.726. [DOI] [PubMed] [Google Scholar]
- Bennetzen J. L. The contributions of retroelements to plant genome organization, function and evolution. Trends Microbiol. 1996 Sep;4(9):347–353. doi: 10.1016/0966-842x(96)10042-1. [DOI] [PubMed] [Google Scholar]
- Bent A. F., Kunkel B. N., Dahlbeck D., Brown K. L., Schmidt R., Giraudat J., Leung J., Staskawicz B. J. RPS2 of Arabidopsis thaliana: a leucine-rich repeat class of plant disease resistance genes. Science. 1994 Sep 23;265(5180):1856–1860. doi: 10.1126/science.8091210. [DOI] [PubMed] [Google Scholar]
- Bent A. F. Plant Disease Resistance Genes: Function Meets Structure. Plant Cell. 1996 Oct;8(10):1757–1771. doi: 10.1105/tpc.8.10.1757. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bevan M., Bancroft I., Bent E., Love K., Goodman H., Dean C., Bergkamp R., Dirkse W., Van Staveren M., Stiekema W. Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana. Nature. 1998 Jan 29;391(6666):485–488. doi: 10.1038/35140. [DOI] [PubMed] [Google Scholar]
- Brook J. D., McCurrach M. E., Harley H. G., Buckler A. J., Church D., Aburatani H., Hunter K., Stanton V. P., Thirion J. P., Hudson T. Molecular basis of myotonic dystrophy: expansion of a trinucleotide (CTG) repeat at the 3' end of a transcript encoding a protein kinase family member. Cell. 1992 Feb 21;68(4):799–808. doi: 10.1016/0092-8674(92)90154-5. [DOI] [PubMed] [Google Scholar]
- Crute I. R., Pink DAC. Genetics and Utilization of Pathogen Resistance in Plants. Plant Cell. 1996 Oct;8(10):1747–1755. doi: 10.1105/tpc.8.10.1747. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Dixon M. S., Jones D. A., Keddie J. S., Thomas C. M., Harrison K., Jones J. D. The tomato Cf-2 disease resistance locus comprises two functional genes encoding leucine-rich repeat proteins. Cell. 1996 Feb 9;84(3):451–459. doi: 10.1016/s0092-8674(00)81290-8. [DOI] [PubMed] [Google Scholar]
- Edwards A., Civitello A., Hammond H. A., Caskey C. T. DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Am J Hum Genet. 1991 Oct;49(4):746–756. [PMC free article] [PubMed] [Google Scholar]
- Ellis J. G., Lawrence G. J., Finnegan E. J., Anderson P. A. Contrasting complexity of two rust resistance loci in flax. Proc Natl Acad Sci U S A. 1995 May 9;92(10):4185–4188. doi: 10.1073/pnas.92.10.4185. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ellis J., Lawrence G., Ayliffe M., Anderson P., Collins N., Finnegan J., Frost D., Luck J., Pryor T. Advances in the molecular genetic analysis of the flax-flax rust interaction. Annu Rev Phytopathol. 1997;35:271–291. doi: 10.1146/annurev.phyto.35.1.271. [DOI] [PubMed] [Google Scholar]
- Endo T., Ikeo K., Gojobori T. Large-scale search for genes on which positive selection may operate. Mol Biol Evol. 1996 May;13(5):685–690. doi: 10.1093/oxfordjournals.molbev.a025629. [DOI] [PubMed] [Google Scholar]
- Frohman M. A., Dush M. K., Martin G. R. Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer. Proc Natl Acad Sci U S A. 1988 Dec;85(23):8998–9002. doi: 10.1073/pnas.85.23.8998. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Fu Y. H., Kuhl D. P., Pizzuti A., Pieretti M., Sutcliffe J. S., Richards S., Verkerk A. J., Holden J. J., Fenwick R. G., Jr, Warren S. T. Variation of the CGG repeat at the fragile X site results in genetic instability: resolution of the Sherman paradox. Cell. 1991 Dec 20;67(6):1047–1058. doi: 10.1016/0092-8674(91)90283-5. [DOI] [PubMed] [Google Scholar]
- Grant M. R., Godiard L., Straube E., Ashfield T., Lewald J., Sattler A., Innes R. W., Dangl J. L. Structure of the Arabidopsis RPM1 gene enabling dual specificity disease resistance. Science. 1995 Aug 11;269(5225):843–846. doi: 10.1126/science.7638602. [DOI] [PubMed] [Google Scholar]
- Hagiwara K., Harris C. C. 'Long distance sequencer' method; a novel strategy for large DNA sequencing projects. Nucleic Acids Res. 1996 Jun 15;24(12):2460–2461. doi: 10.1093/nar/24.12.2460. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hammond-Kosack Kim E., Jones Jonathan D. G. PLANT DISEASE RESISTANCE GENES. Annu Rev Plant Physiol Plant Mol Biol. 1997 Jun;48(NaN):575–607. doi: 10.1146/annurev.arplant.48.1.575. [DOI] [PubMed] [Google Scholar]
- Hebsgaard S. M., Korning P. G., Tolstrup N., Engelbrecht J., Rouzé P., Brunak S. Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. Nucleic Acids Res. 1996 Sep 1;24(17):3439–3452. doi: 10.1093/nar/24.17.3439. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hughes A. L., Nei M. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature. 1988 Sep 8;335(6186):167–170. doi: 10.1038/335167a0. [DOI] [PubMed] [Google Scholar]
- Hulbert S. H. Structure and evolution of the rp1 complex conferring rust resistance in maize. Annu Rev Phytopathol. 1997;35:293–310. doi: 10.1146/annurev.phyto.35.1.293. [DOI] [PubMed] [Google Scholar]
- Jones A., Davies H. M., Voelker T. A. Palmitoyl-acyl carrier protein (ACP) thioesterase and the evolutionary origin of plant acyl-ACP thioesterases. Plant Cell. 1995 Mar;7(3):359–371. doi: 10.1105/tpc.7.3.359. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kajava A. V., Vassart G., Wodak S. J. Modeling of the three-dimensional structure of proteins with the typical leucine-rich repeats. Structure. 1995 Sep 15;3(9):867–877. doi: 10.1016/S0969-2126(01)00222-2. [DOI] [PubMed] [Google Scholar]
- Kobe B., Deisenhofer J. A structural basis of the interactions between leucine-rich repeats and protein ligands. Nature. 1995 Mar 9;374(6518):183–186. doi: 10.1038/374183a0. [DOI] [PubMed] [Google Scholar]
- Kobe B., Deisenhofer J. The leucine-rich repeat: a versatile binding motif. Trends Biochem Sci. 1994 Oct;19(10):415–421. doi: 10.1016/0968-0004(94)90090-6. [DOI] [PubMed] [Google Scholar]
- Lawrence G. J., Finnegan E. J., Ayliffe M. A., Ellis J. G. The L6 gene for flax rust resistance is related to the Arabidopsis bacterial resistance gene RPS2 and the tobacco viral resistance gene N. Plant Cell. 1995 Aug;7(8):1195–1206. doi: 10.1105/tpc.7.8.1195. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Li W. H. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol. 1993 Jan;36(1):96–99. doi: 10.1007/BF02407308. [DOI] [PubMed] [Google Scholar]
- Meyers B. C., Chin D. B., Shen K. A., Sivaramakrishnan S., Lavelle D. O., Zhang Z., Michelmore R. W. The major resistance gene cluster in lettuce is highly duplicated and spans several megabases. Plant Cell. 1998 Nov;10(11):1817–1832. doi: 10.1105/tpc.10.11.1817. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Milligan S. B., Bodeau J., Yaghoobi J., Kaloshian I., Zabel P., Williamson V. M. The root knot nematode resistance gene Mi from tomato is a member of the leucine zipper, nucleotide binding, leucine-rich repeat family of plant genes. Plant Cell. 1998 Aug;10(8):1307–1319. doi: 10.1105/tpc.10.8.1307. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Mindrinos M., Katagiri F., Yu G. L., Ausubel F. M. The A. thaliana disease resistance gene RPS2 encodes a protein containing a nucleotide-binding site and leucine-rich repeats. Cell. 1994 Sep 23;78(6):1089–1099. doi: 10.1016/0092-8674(94)90282-8. [DOI] [PubMed] [Google Scholar]
- Nei M., Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol. 1986 Sep;3(5):418–426. doi: 10.1093/oxfordjournals.molbev.a040410. [DOI] [PubMed] [Google Scholar]
- Nei M., Gu X., Sitnikova T. Evolution by the birth-and-death process in multigene families of the vertebrate immune system. Proc Natl Acad Sci U S A. 1997 Jul 22;94(15):7799–7806. doi: 10.1073/pnas.94.15.7799. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Okubara P. A., Arroyo-Garcia R., Shen K. A., Mazier M., Meyers B. C., Ochoa O. E., Kim S., Yang C. H., Michelmore R. W. A transgenic mutant of Lactuca sativa (lettuce) with a T-DNA tightly linked to loss of downy mildew resistance. Mol Plant Microbe Interact. 1997 Nov;10(8):970–977. doi: 10.1094/MPMI.1997.10.8.970. [DOI] [PubMed] [Google Scholar]
- Ori N., Eshed Y., Paran I., Presting G., Aviv D., Tanksley S., Zamir D., Fluhr R. The I2C family from the wilt disease resistance locus I2 belongs to the nucleotide binding, leucine-rich repeat superfamily of plant resistance genes. Plant Cell. 1997 Apr;9(4):521–532. doi: 10.1105/tpc.9.4.521. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Parker J. E., Coleman M. J., Szabò V., Frost L. N., Schmidt R., van der Biezen E. A., Moores T., Dean C., Daniels M. J., Jones J. D. The Arabidopsis downy mildew resistance gene RPP5 shares similarity to the toll and interleukin-1 receptors with N and L6. Plant Cell. 1997 Jun;9(6):879–894. doi: 10.1105/tpc.9.6.879. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Parniske M., Hammond-Kosack K. E., Golstein C., Thomas C. M., Jones D. A., Harrison K., Wulff B. B., Jones J. D. Novel disease resistance specificities result from sequence exchange between tandemly repeated genes at the Cf-4/9 locus of tomato. Cell. 1997 Dec 12;91(6):821–832. doi: 10.1016/s0092-8674(00)80470-5. [DOI] [PubMed] [Google Scholar]
- Richter T. E., Pryor T. J., Bennetzen J. L., Hulbert S. H. New rust resistance specificities associated with recombination in the Rp1 complex in maize. Genetics. 1995 Sep;141(1):373–381. doi: 10.1093/genetics/141.1.373. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Salmeron J. M., Oldroyd G. E., Rommens C. M., Scofield S. R., Kim H. S., Lavelle D. T., Dahlbeck D., Staskawicz B. J. Tomato Prf is a member of the leucine-rich repeat class of plant disease resistance genes and lies embedded within the Pto kinase gene cluster. Cell. 1996 Jul 12;86(1):123–133. doi: 10.1016/s0092-8674(00)80083-5. [DOI] [PubMed] [Google Scholar]
- SanMiguel P., Tikhonov A., Jin Y. K., Motchoulskaia N., Zakharov D., Melake-Berhan A., Springer P. S., Edwards K. J., Lee M., Avramova Z. Nested retrotransposons in the intergenic regions of the maize genome. Science. 1996 Nov 1;274(5288):765–768. doi: 10.1126/science.274.5288.765. [DOI] [PubMed] [Google Scholar]
- Shen K. A., Meyers B. C., Islam-Faridi M. N., Chin D. B., Stelly D. M., Michelmore R. W. Resistance gene candidates identified by PCR with degenerate oligonucleotide primers map to clusters of resistance genes in lettuce. Mol Plant Microbe Interact. 1998 Aug;11(8):815–823. doi: 10.1094/MPMI.1998.11.8.815. [DOI] [PubMed] [Google Scholar]
- Shepherd K. W., Mayo G. M. Genes conferring specific plant disease resistance. Science. 1972 Jan 28;175(4020):375–380. doi: 10.1126/science.175.4020.375. [DOI] [PubMed] [Google Scholar]
- Song W. Y., Pi L. Y., Wang G. L., Gardner J., Holsten T., Ronald P. C. Evolution of the rice Xa21 disease resistance gene family. Plant Cell. 1997 Aug;9(8):1279–1287. doi: 10.1105/tpc.9.8.1279. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Staskawicz B. J., Ausubel F. M., Baker B. J., Ellis J. G., Jones J. D. Molecular genetics of plant disease resistance. Science. 1995 May 5;268(5211):661–667. doi: 10.1126/science.7732374. [DOI] [PubMed] [Google Scholar]
- Sudupak M. A., Bennetzen J. L., Hulbert S. H. Unequal exchange and meiotic instability of disease-resistance genes in the Rp1 region of maize. Genetics. 1993 Jan;133(1):119–125. doi: 10.1093/genetics/133.1.119. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tanaka T., Nei M. Positive darwinian selection observed at the variable-region genes of immunoglobulins. Mol Biol Evol. 1989 Sep;6(5):447–459. doi: 10.1093/oxfordjournals.molbev.a040569. [DOI] [PubMed] [Google Scholar]
- Thomas C. M., Jones D. A., Parniske M., Harrison K., Balint-Kurti P. J., Hatzixanthis K., Jones J. D. Characterization of the tomato Cf-4 gene for resistance to Cladosporium fulvum identifies sequences that determine recognitional specificity in Cf-4 and Cf-9. Plant Cell. 1997 Dec;9(12):2209–2224. doi: 10.1105/tpc.9.12.2209. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Traut T. W. The functions and consensus motifs of nine types of peptide segments that form different types of nucleotide-binding sites. Eur J Biochem. 1994 May 15;222(1):9–19. doi: 10.1111/j.1432-1033.1994.tb18835.x. [DOI] [PubMed] [Google Scholar]
- Wang G. L., Ruan D. L., Song W. Y., Sideris S., Chen L., Pi L. Y., Zhang S., Zhang Z., Fauquet C., Gaut B. S. Xa21D encodes a receptor-like molecule with a leucine-rich repeat domain that determines race-specific recognition and is subject to adaptive evolution. Plant Cell. 1998 May;10(5):765–779. doi: 10.1105/tpc.10.5.765. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wessler S. R., Bureau T. E., White S. E. LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. Curr Opin Genet Dev. 1995 Dec;5(6):814–821. doi: 10.1016/0959-437x(95)80016-x. [DOI] [PubMed] [Google Scholar]
- Yoshimura S., Yamanouchi U., Katayose Y., Toki S., Wang Z. X., Kono I., Kurata N., Yano M., Iwata N., Sasaki T. Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation. Proc Natl Acad Sci U S A. 1998 Feb 17;95(4):1663–1668. doi: 10.1073/pnas.95.4.1663. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zhang J., Kumar S., Nei M. Small-sample tests of episodic adaptive evolution: a case study of primate lysozymes. Mol Biol Evol. 1997 Dec;14(12):1335–1338. doi: 10.1093/oxfordjournals.molbev.a025743. [DOI] [PubMed] [Google Scholar]