The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice

Nucleic Acids Research

Volumn 33, Issue 2, 2005, Pages 577-586

  Lee, Byoung Moo ^d   Park, Young Jin ^d   Park, Dong Suk ^d   Kang, Hee Wan ^a   Kim, Jeong Gu ^d   Song, Eun Sung ^d   Park, In Cheol ^d   Yoon, Ung Han ^d   Hahn, Jang Ho ^d   Koo, Bon Sung ^d   Lee, Gil Bok ^d   Kim, Hyungtae ^b   Park, Hyun Seok ^b   Yoon, Kyong Oh ^b   Kim, Jeong Hyun ^b   Jung, Chol Hee ^b   Koh, Nea Hyung ^b   Seo, Jeong Sun ^b,c   Go, Seung Joo ^d  

^a Hankyong National University   (South Korea)

^b Macrogen Inc   (South Korea)

^c Seoul National University   (South Korea)

^d National Institute of Animal Science   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; BACTERIAL PROTEIN; CYTOSINE; EXOPOLYSACCHARIDE; GUANINE; NUCLEOTIDE; BACTERIAL POLYSACCHARIDE; VIRULENCE FACTOR;

ARTICLE; BACTERIAL BLIGHT; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIAL VIRULENCE; CELL WALL; CHROMOSOME; CONTROLLED STUDY; ENZYME DEGRADATION; GENE FUNCTION; GENE IDENTIFICATION; GENETIC CODE; HOST PATHOGEN INTERACTION; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; ORTHOLOGY; PATHOGENESIS; PATHOTYPE; PLANT CELL; PREDICTION; PRIORITY JOURNAL; RICE; SEQUENCE ANALYSIS; XANTHOMONAS; XANTHOMONAS CAMPESTRIS; XANTHOMONAS ORYZAE; BIOSYNTHESIS; GENETICS; GENOMICS; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; PATHOGENICITY; PLANT DISEASE; TRANSPOSON;

BACTERIA (MICROORGANISMS); ORYZA SATIVA; XANTHOMONAS; XANTHOMONAS ORYZAE;

BASE SEQUENCE; DNA TRANSPOSABLE ELEMENTS; GENOME, BACTERIAL; GENOMICS; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; PLANT DISEASES; POLYSACCHARIDES, BACTERIAL; VIRULENCE FACTORS; XANTHOMONAS;

EID: 13744253238     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gki206     Document Type: Article

References (82)

1. Ezuka,A. and Kaku,H. (2000) A historical review of bacterial blight of rice. Bull. Natl. Inst. Agrobiol. Resour. (Japan), 15 53-54.
2. Lindgren,P.B. (1997) The role of hrp genes during plant-bacterial interactions. Annu. Rev. Phytopathol., 35, 129-152.
3. Rossier,O., Van den Ackerveken,G. and Bonas,U. (2000) HrpB2 and HrpF from Xanthomonas are type III-secreted proteins and essential for pathogenicity and recognition by the host plant. Mol. Microbiology, 38, 828-838.
4. Xu,G.W. and Gonzalez,C.F. (1989) Evaluation of TN4431-induced protease mutants of Xanthomonas campestris pv. oryzae for growth in plants and pathogenicity. Phytopathology, 79, 1210-1215.
5. Ray,S.K., Rajeshwari,R. and Sonti,R.V. (2000) Mutants of Xanthomonas oryzae deficient in general secretory pathway are virulent deficient and unable to secrete xylase. Mol. Plant Microbe Interact. 13, 394-401.
6. Dharmapuri,S. and Sonti,R.V. (1999) A transposon insertion in gumG homologue of Xanthomonas oryzae pv. oryzae causes loss of extracellular polysaccharide production and virulence. FEMS. Microbiol. Lett., 179, 53-59.
7. Keen,N.T. (1990) Gene-for-gene complementarity in plant-pathogen interactions. Annu. Rev. Genet., 24, 447-463.
8. Leach,J.E. and White,F.F. (1996) Bacterial avirulence genes. Annu. Rev. Phytopathol., 34, 153-179.
9. Hopkins,C.M., White,F.F., Choi,S.-H., Guo,A. and Leach,J.E. (1992) Identification of a family of avirulence genes from Xanthomonas oryzae pv. oryzae. Mol. Plant Microbe Interact., 5, 451-459.
10. Leach,J.E., Vera Cruz,C.M., Bai,J. and Leung,H. (2001) Pathogen fitness penalty as a predictor of durability of disease resistance genes. Annu. Rev. Phytopathol., 39, 187-224.
11. Blair,M.W., Garris,A.J., Iyer,A.S., Chapman,B., Kresovich,S. and McCouch,S.R. (2003) High resolution genetic mapping and candidate gene identification at the Xa5 locus for bacterial blight resistance in rice (Oryza sativa L.). Theor. Appl. Genet., 107, 62-73.
12. Yoshimura,S., Umehara,Y., Kurata,N., Nagamura,Y., Sasaki,T., Minobe,Y. and Iwata,N. (1996) Characterization of candidate clones of Xa-1, the bacterial blight resistance gene in rice, isolated by map-based cloning. Theor. Appl. Genet., 93, 117-122.
13. Wang,G.L., Song,W.Y., Ruan,D.L., Sideris,S. and Ronald,P.C. (1996) The cloned gene, Xa21, confers resistance to multiple Xanthomonas oryzae pv. oryzae isolates in transgenic plants. Mol. Plant Microbe Interact., 9, 850-855.
14. Simpson,A.J., Reinach,F.C., Arruda,P., Abreu,F.A., Acencio,M., Alvarenga,R., Alves,L.M., Araya,J.E., Baia,G.S., Baptista,C.S., Barros,M.H. et al. (2000) The genome sequence of the plant pathogen Xylella fastidiosa. Nature, 406, 151-157.
15. Buell,C.R., Joardar,V., Lindeberg,M., Selengut,J., Paulsen,I.T., Gwinn,M.L., Dodson,R.J. et al. (2003) The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc. Natl Acad. Sci. 100, 10181-10186.
16. da Silva,A.C.R., Ferro,J.A., Reinach,F.C., Farah,C.S., Furlan,L.R., Quaggio,R.B., Monteiro-Vitorello,C.B., Van Sluys,M.A., Almeida,N.F., Jr, Alves,L.M.C. et al. (2002) Comparison of genomes of two Xanthomonas pathogens with differing host specificities. Nature, 417, 459-463.
17. Salanoubat,M., Genin,S., Artiguenave,F., Gouzy,J., Mangenot,S., Arlat,M., Billault,A., Brottier,P., Camus,J.C., Cattolico,L. et al. (2002) Genome sequence of the plant pathogen Ralstonia solanacearum. Nature, 415, 497-502.
18. Wood,D.W., Setubal,J.C., Kaul,R., Monks,D.E., Kitajima,J.P., Okura,V.K., Zhou,Y., Chen,L., Wood,G.E., Almeida,N.F., Jr et al. (2001) The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science, 294, 2317-2323.
19. Lee,S.W., Choi,S.H., Han,S.S., Lee,D.G. and Lee,B.Y. (1999) Distribution of Xanthomonas oryzae pv. oryzae strains virulent to Xa21 in Korea. Phytopathology, 89, 928-933.
20. Wilson,R.K. and Mardis,E. (1997) Shotgun sequencing. In Birren,B., Green,E.D., Klapholz,S., Myers,R.M. and Roskams,J. (eds), Genome Anlysis: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, Vol. I, pp. 397-454.
21. Delcher,A.L., Harmon,D., Kasif,S., White,O. and Salzberg,S.L. (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res., 27, 4636-4641.
22. Borodovsky,M. and McIninch,J. (1993) GeneMark: parallel gene recognition for both DNA strands. Computers Chemistry, 17, 123-133.
23. Lowe,T.M. and Eddy,S.R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964.
24. Ogata,H., Goto,S., Sato,K., Fujibuchi,W., Bono,H. and Kanehisa,M. (1999) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res., 27, 29-34.
25. da Silva,F.G., Shen,Y., Dardick,C., Burdman,S., Yadav,R.C., de Leon,A.L. and Ronald,P.C. (2004) Bacterial genes involved in type I secretion and sulfation are required to elicit the rice Xa21 mediated innate immune response. Mol. Plant Microbe Interact., 17, 593-601.
26. Neson,R.J., Baraoidan,M.R., Vera Cruz,C.M., Yap,I.V., Leach,J.E., Mew,T.W. and Leung,H. (1994) Relationship between phylogeny and pathotype for the bacterial blight pathogen of rice. Appl. Environ. Microbiol., 60, 3275-3283.
27. Zhu,W., Magbanua,M.M. and White,F.F. (2000) Identification of two novel hrp-associated genes in the hrp gene cluster of Xanthomonas oryzae pv. oryzae. J. Bacteriol., 182, 1844-1853.
28. Goel,A.K., Rajagopal,L., Nagesh,N. and Sonti,R.V. (2002) Genetic locus encoding functions involved in biosynthesis and outer membrane localization of xanthomonadin in Xanthomonas oryzae pv. oryzae. J. Bacteriol., 184, 3539-3548.
29. Rajeshwari,R. and Sonti,R.V. (2000) Stationary-phase variation due to transposition of novel insertion elements in Xanthomonas oryzae pv. oryzae. J. Bacteriol., 182, 4797-4802.
30. Leach,J.E., White,F.F., Rhoads,M.L. and Leung,H. (1990) A repetitive DNA sequence differentiates Xanthomonas campestris pv. oryzae from other pathovars of X.campestris. Mol. Plant Microbe Interact., 3, 238-246.
31. Birkenbihl,R.P. and Vielmetter,W. (1989) Complete maps of IS1, IS2, IS3, IS4, IS5, IS30 and IS150 locations in Escherichia coli K12. Mol. Gen. Genet., 220, 147-153.
32. Matsutani,S., Ohtsubo,H., Maeda,Y. and Ohtsubo,E. (1987) Isolation and characterization of IS elements repeated in the bacterial chromosome. J. Mol. Biol., 196, 445-455.
33. Chen,J.H., Hsieh,Y.Y., Hsiau,S.L., Lo,T.C. and Shau,C.C. (1999) Characterization of insertion of IS476 and tow newly identified insertion sequences, IS1478 and IS 1479, in Xanthomonas campestris pathovar. campestris. J. Bacteriol., 181, 1220-1228.
34. Kim,J.F., Charkowski,A.O., Alfano,J.R., Collmer,A. and Beer,S.V. (1998) Sequences related to transposable elements and bacteriophages flank avirulence genes of Pseudomonas syringae. Mol. Plant Microbe Interact., 11, 1247-1251.
35. Krylov,V.N. (2003) Role of horizontal gene transfer by bacteriophages in the origin of pathogenic bacteria. Genetika, 39, 595-620.
36. Ezuka,A. and Kaku,H. (2000) A historical review of bacterial blight of rice. Bull. Natl. Inst. Agrobiol. Resour., Japan, 15 61-74.
37. Von Bodman,S.B., Bauer,W.D. and Coplin,D. (2003) Quorum sensing in plant pathogenic bacteria. Annu. Rev. Phytopathol., 41, 455-482.
38. Fuqua,C. and Eberhard,A. (1999) Signal generation in autoinduction systems: synthesis of acyllated homoserine lactones by LuxI-type proteins. In Dunny,G.M. and Winans,S.C. (eds), Cell-Cell Signaling in Bacteria. ASM Press, Washinton, DC, pp. 211-230.
39. Whitehead,N.A., Barnard,A.M.L., Slater,H., Simpson,N.J.L. and Salmond,G.P.C. (2001) Quorum-sensing in gram-negative bacteria. FEMS Microbiol. Rev., 25, 365-404.
40. Cha,C., Gao,P., Chen,Y.C., Shaw,P.D. and Farrand,S.K. (1988) Production of acyl-homoserine lactone quorum sensing signals by gram-negative plant-associated bacteria. Mol. Plant Microbe Interact. 11, 1119-1129.
41. Elasri,M., Delome,S., Lemanceau,P., Stewart,G., Laue,B., Glickmann,E., Oger,P.M and Dessaux,Y. (2001) Acyl-homoserine lactone production is more common among plant-associated Pseudomonas spp. than among soil borne Pseudomonas spp. Appl. Environ. Microbiol. 67, 1198-1209.
42. Choi,S.H. and Leach,J.E. (1994) Identification of the XorII methyltransferase gene and a vsr-homolog from Xanthomonas oryzae pv. oryzae. Mol. Gen. Genet., 244, 383-390.
43. Wang,R.Y.H., Shedlarski,J.G., Farber,M.B., Kuebbing,D. and Ehrlich,M. (1980) Two sequence specific endonucleases from Xanthomonas oryzae. Characterization and unusual properties. Biochim. Biophys. Acta, 606, 371-385.
44. Choi,S.H., Vera Cruz,C.M. and Leach,J.E. (1998) Distribution of Xanthomonas oryzae pv. oryzae DNA modification systems in Asia. Appl. Environ. Microbiol., 64, 1663-1668.
45. Katzen,F., Becker,A., Zorreguieta,A., Puhler,A. and Ielpi,L. (1996) Promoter analysis of the Xanthomonas campestris pv. campestris gum operon directing biosynthesis of the xanthan polysaccharide. J. Bacteriol., 178, 4313-4318.
46. Coplin,D.L. and Cook,D. (1990) Molecular genetics of extracelluar polysaccharide biosynthesis in vascular phytopathogenic bacteria. Mol. Plant Microbe Interact., 3, 271-279.
47. Vojnov,A.A. Zorreguieta,A., Dow,J.M., Daniels,M.J. and Dankert,M.A. (1998) Evidence for a role for the gumB and gumC gene products in the formation of xanthan from its pentasaccharide repeating unit by Xanthomonas campestris. Microbiology, 144, 1487-1493.
48. Vorhölter,F.J., Niehaus,K. and Puhler,A. (2001) Lipopolysaccharide biosynthesis in Xanthomonas campestris pv. campestris: a cluster of 15 genes is involved in the biosynthesis of the LPS O-antigen and the LPS core. Mol. Genet. Genomics., 266 79-95.
49. Koplin,R., Wang,G., Hotte,B., Priefer,U.B. and Puhler,A. (1993) A 3.9-kb DNA region of Xanthomonas campestris pv. campestris that is necessary for lipopolysaccharide production encodes a set of enzymes involved in the synthesis of dTDP-rhamnose. J. Bacteriol., 175, 7786-7792.
50. Dow,J.M., Osbourn,A.E., Wilson,T.J. and Daniels,M.J. (1995) A locus determining pathogenicity of Xanthomonas campestris is involved in lipopolysaccharide biosynthesis. Mol. Plant Microbe Interact., 8, 768-777.
51. Whitfield,C. (1995) Biosynthesis of lipopolysaccharide O antigens. Trends Microbiol., 3, 178-185.
52. Cao,H., Baldini,R.L. and Rahme,L.G. (2001) Common mechanisms for pathogens of plants and animals. Annu. Rev. Phytopathol., 39 259-284.
53. Noel,L., Thieme,F., Nennstiel,D. and Bonas,U. (2001) cDNA-AFLP analysis unravels a genome-wide hrpG-regulon in the plant pathogen Xanthomonas campestris pv. vesicatoria. Mol. Microbiol. 41, 1271-1281.
54. Welch,R., Forestier,A., Lobo,C., Pellett,A., Thomas,S.W. and Rowe,G. (1992) The synthesis and function of the Escherichia coli hemolysins and related RTX exotoxins. FEMS Microbiol. Immunol., 105, 29-36.
55. Oresnik,I.J., Twelker,S. and Hynes,M.F. (1999) Cloning and characterization of a Rhizobium leguminosarum gene encoding a bacteriocin with similarities to RTX toxins. Appl. Environ. Microbiol. 65, 2833-2840.
56. Kuhnert,P., Heyberger-Meyer,B., Burnens,A.P., Nicolet,J. and Frey,J. (1997) Detection of RTX toxin genes in gram-negative bacteria with a set of specific probes. Appl. Environ. Microbiol., 63, 2258-2265.
57. Noda,T., Saito,Z., Iwasaki,S. and Ohuchi,A. (1989) Isolation and structural elucidation of phytotoxic substances produced by Xanthomonas campestris pv. oryzae. Bull. Hokuriku Natl Agric. Exp.Stn., 30, 105-129.
58. Rudolf,K. (1993) Xanthomonas. Chapman & Hall, London, UK.
59. Stathopoulos,C., Hendrixson,D.R., Thanassi,D.G., Hultgren,S.J., St Geme,J.W.,III and Curtiss,R.,III (2000) Secretion of virulence determinants by the general secretory pathway in gram-negative pathogens: an evolving story. Microbes Infect., 2, 1061-1072.
60. Kamoun,S. and Kado,C.I. (1990) A plant-inducible gene of Xanthomonas campestris pv. campestris encodes an exocellular component required for growth in the host and hypersensitivity on nonhosts. J. Bacteriol., 172, 5165-5172.
61. Dow,J.M., Davies,H.A. and Daniels,M.J. (1998) A metalloprotease from Xanthomonas campestris that specifically degrades proline/hydroxyproline-rich glycoproteins of the plant extracellular matrix. Mol. Plant Microbe Interact., 11, 1085-1093.
62. Dow,J.M., Clarke,B.R., Milligan,D.E., Tang,J.L. and Daniels,M.J. (1990) Extracellular proteases from Xanthomonas campestris pv. campestris, the black rot pathogen. Appl. Environ. Microbiol., 56, 2994-2998.
63. Ezuka,A. and Kaku,H. (2000) A historical review of bacterial blight of rice. Bull. Natl. Inst. Agrobiol. Resour. Japan, 15 148-149.
64. Dums,F., Dow,J.M. and Daniels,M.J. (1991) Structural characterization of the bacterial phytopathogen Xanthomonas campestris pathovar campestris: relatedness to secretion systems of other gram negative bacteria. Mol. Gen. Genet., 229, 357-364.
65. Hu,N.T., Hung,M.N., Chiou,S.J., Tang,F., Chiang,D.C., Huang,H.Y. and Wu,C.Y. (1992) Cloning and characterization of a gene required for the secretion of extracellular enzymes cross the outer membrane by Xanthomonas campestris pv. campestris. J. Bacteriol. 174, 2679-2687.
66. Dow,J.M., Feng,J.X., Barber,C.E., Tang,J.L. and Daniels,M.J. (2000) Novel genes involved in the regulation of pathogenicity factor production within the rpf gene cluster of Xanthomonas campestris. Microbiology, 146, 885-891.
67. Barber,C.E., Tang,J.L., Feng,J.X., Pan,M.Q., Wilson,T.J., Slater,H., Dow,J.M., Williams,P. and Daniels,M.J. (1997) A novel regulatory system required for pathogenicity of Xanthomonas campestris is mediated by a small diffusible signal molecule. Mol. Microbiol. 24, 555-566.
68. Tang,J.L., Feng,J.X., Li,Q.Q., Wen,H.X., Zhou,D.L., Wilson,T.J., Dow,J.M., Ma,Q.S. and Daniels,M.J. (1996) Cloning and characterization of the rpfC gene of Xanthomonas oryzae pv. oryzae: involvement in exopolysaccharide production and virulence to rice. Mol. Plant Microbe Interact., 9, 664-666.
69. Slater,H., Alvarez-Morales,A., Barber,C.E., Daniels,M.J. and Dow,J.M. (2000) A two-component system involving an HD-GYP domain protein links cell-cell signaling to pathogenicity gene expression in Xanthomonas campestris. Mol. Microbiol., 38, 986-1003.
70. Pugsley,A.P. (1993) The complete general secretory pathway in gram-negative bacteria. Microbiol. Rev., 57, 50-108.
71. Lindgren,P.B. (1997) The role of hrp genes during plant-bacterial interactions. Annu. Rev. Phytopathol., 35, 129-152.
72. He,S.Y. (1998) Type β protein secretion systems in plant and animal pathogenic bacteria. Annu. Rev. Phytopathol., 36, 363-392.
73. Dow,J.M. and Daniels,M.J. (1994) Pathogenicity determinants and global regulation of pathogenicity of Xanthomonas campestris pv. campestris. Curr. Top. Microbiol. Immunol., 192, 29-41.
74. Wengelnik,K., Van den Acerveken,G. and Bona,U. (1996) HrpG a key hrp regulatory protein of Xanthomonas campestris pv. vesicatoria is homologous to two-component response regulators. Mol. Plant Microbe Interact., 9, 704-712.
75. Fenselau,S. and Bonas,U. (1995) Sequence and expression analysis of the hrpB pathogenicity operon of Xanthomonas campestris pv. vesicatoria which encodes eight proteins with similarity to components of the Hrp, Ysc, Spa, and Fli secretion systems. Mol. Plant Microbe interact., 8, 845-854.
76. Bai,J., Choi,S.H., Ponciano,G., Leung,H. and Leach,J.E. (2000) Xanthomonas oryzae pv. oryzae avirulence genes contribute differently and specifically to pathogen aggressiveness. Mol. Plant Microbe Interact., 13, 1322-1329.
77. Mazzola,M., Leach,J.E., Nelson,R. and White,F.F. (1994) Analysis of the interaction between Xanthomonas oryzae pv. oryzae and the rice cultivars IR24 and IRBB21. Phytopathology, 84, 392-397.
78. Swords,K.M., Dahlbeck,D., Kearney,B., Roy,M. and Staskawicz,B.J. (1996) Spontaneous and induced mutations in a single open reading frame alter both virulence and avirulence in Xanthomonas campestris pv. vesicatoria avrBs2. J. Bacteriol., 178, 4661-4669.
79. Mudgett,M.B., Chesnokova,O., Dahlbeck,D., Clark,E.T., Rossier,O., Bonas,U. and Staskawicz,B.J. (2000) Molecular signals required for type III secretion and translocation of the Xanthomonas campestris AvrBs2 protein to pepper plants. Proc. Natl Acad. Sci. USA, 97, 13324-13329.
80. Young,N.D. (2000) The genetic architecture of resistance. Curr. Opin. Plant Biol., 3, 285-290.
81. Gueneron,M., Timmers,A.C., Boucher,C. and Arlat,M. (2000) Two novel proteins, PopB, which has functional nuclear localization signals, and PopC, which has a large leucine-rich repeat domain, are secreted through the hrp-secretion apparatus of Ralstonia solanacearum. Mol. Microbiol., 36, 261-277.
82. Lahaye,T. and Bonas,U. (2001) Molecular secrets of bacterial type III effector proteins. Trends Plant Sci., 6, 479-485.