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Comparative Analysis of argK-tox Clusters and Their Flanking Regions in Phaseolotoxin-Producing Pseudomonas syringae Pathovars

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Abstract

DNA fragments containing argK-tox clusters and their flanking regions were cloned from the chromosomes of Pseudomonas syringae pathovar (pv.) actinidiae strain KW-11 (ACT) and P. syringae pv. phaseolicola strain MAFF 302282 (PHA), and then their sequences were determined. Comparative analysis of these sequences and the sequences of P. syringae pv. tomato DC3000 (TOM) (Buell et al., Proc Natl Acad Sci USA 100:10181–10186, 2003) and pv. syringae B728a (SYR) (Feil et al., Proc Natl Acad Sci USA 102:11064–11069, 2005) revealed that the chromosomal backbone regions of ACT and TOM shared a high similarity to each other but presented a low similarity to those of PHA and SYR. Nevertheless, almost-identical DNA regions of about 38 kb were confirmed to be present on the chromosomes of both ACT and PHA, which we named “tox islands.” The facts that the GC content of such tox islands was 6% lower than that of the chromosomal backbone regions of P. syringae, and that argK-tox clusters, which are considered to be of exogenous origin based on our previous studies (Sawada et al., J Mol Evol 54:437–457, 2002), were confirmed to be contained within the tox islands, suggested that the tox islands were an exogenous, mobile genetic element inserted into the chromosomes of P. syringae strains. It was also predicted that the tox islands integrated site-specifically into the homologous sites of the chromosomes of ACT and PHA in the same direction, respectively, wherein 34 common gene coding sequences (CDSs) existed. Furthermore, at the left end of the tox islands were three CDSs, which encoded polypeptides and had similarities to the members of the tyrosine recombinase family, suggesting that these putative site-specific recombinases were involved in the recent horizontal transfer of tox islands.

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References

  • Arnord DL, Jackson RW, Vivian A (2000) Evidence for the mobility of an avirulence gene, avrPpiA1, between the chromosome and plasmids of races Pseudomonas syringae pv. pisi. Mol Plant Pathol 1:195–199

    Article  Google Scholar 

  • Arnold DL, Jackson RW, Fillingham AJ, Goss SC, Taylor JD, Mansfield JW, Vivian A (2001) Highly conserved sequences flank avirulence genes: isolation of novel avirulence genes from Pseudomonas syringae pv. pisi. Microbiology 147:1171–1182

    PubMed  CAS  Google Scholar 

  • Arnold DL, Pitman A, Jackson RW (2003) Pathogenicity and other genomic islands in plant pathogenic bacteria. Mol Plant Pathol 4:407–420

    Article  CAS  Google Scholar 

  • Ausubel FM, Brent R, Kingston ER, Moore DD, Seidman GJ, Smith AJ, Struhl K (1991) Current protocols in molecular biology. John Wiley & Sons, New York

    Google Scholar 

  • Bell KS, Sebaihia M, Pritchard L, Holden MT, Hyman LJ, Holeva MC, Thomson NR, Bentley SD, Churcher LJ, Mungall K, Atkin R, Bason N, Brooks K, Chillingworth T, Clark K, Doggett J, Fraser A, Hance Z, Hauser H, Jagels K, Moule S, Norbertczak H, Ormond D, Price C, Quail MA, Sanders M, Walker D, Whitehead S, Salmond GP, Birch PR, Parkhill J, Toth IK (2004) Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors. Proc Natl Acad Sci USA 101:11105–11110

    Article  PubMed  CAS  Google Scholar 

  • Bender CL, Alarcón-Chaidez F, Gross DC (1999) Pseudomonas syringae phytotoxins: mode of action, regulation, and biosynthesis by peptide and polyketide synthetases. Microbiol Mol Biol Rev 63:266–292

    PubMed  CAS  Google Scholar 

  • Bradbury JF (1986) Guide to plant pathogenic bacteria. CAB International Mycological Institute, Kew, UK

    Google Scholar 

  • Buell CR, Joardar V, Lindeberg M, Selengut J, Paulsen IT, Gwinn ML, Dodson RJ, Deboy RT, Durkin AS, Kolonay JF, Madupu R, Daugherty S, Brinkac L, Beanan MJ, Haft DH, Nelson WC, Davidsen T, Zafar N, Zhou L, Liu J, Yuan Q, Khouri H, Fedorova N, Tran B, Russell D, Berry K, Utterback T, Van Aken SE, Feldblyum TV, D’Ascenzo M, Deng WL, Ramos AR, Alfano JR, Cartinhour S, Chatterjee AK, Delaney TP, Lazarowitz SG, Martin GB, Schneider DJ, Tang X, Bender CL, White O, Fraser CM, Collmer A (2003) The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc Natl Acad Sci USA 100:10181–10186

    Article  PubMed  CAS  Google Scholar 

  • Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27:4636–4641

    Article  PubMed  CAS  Google Scholar 

  • Deng WL, Rehm AH, Charkowski AO, Rojas CM, Collmer A (2003) Pseudomonas syringae exchangeable effector loci: sequence diversity in representative pathovars and virulence function in P. syringae pv. syringae B728a. J Bacteriol 185:2592–2602

    Article  PubMed  CAS  Google Scholar 

  • Doublet B, Boyd D, Mulvey MR, Cloeckaert A (2005) The Salmonella genomic island 1 is an integrative mobilizable element. Mol Microbiol 55:1911–1924

    Article  PubMed  CAS  Google Scholar 

  • Feil H, Feil WS, Chain P, Larimer F, Dibartolo G, Copeland A, Lykidis A, Trong S, Nolan M, Goltsman E, Thiel J, Malfatti S, Loper JE, Lapidus A, Detter JC, Land M, Richardson PM, Kyrpides NC, Ivanova N, Lindow SE (2005) Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. Proc Natl Acad Sci USA 102:11064–11069

    Article  PubMed  CAS  Google Scholar 

  • Grant SG, Jessee J, Bloom FR, Hanahan D (1990) Differential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants. Proc Natl Acad Sci USA 87:4645–4649

    Article  PubMed  CAS  Google Scholar 

  • Harr R, Hagblom P, Gustafsson P (1982) Two-dimensional graphic analysis of DNA sequence homologies. Nucleic Acids Res 10:365–374

    PubMed  CAS  Google Scholar 

  • Hatziloukas E, Panopoulos NJ (1992) Origin, structure, and regulation of argK, encoding the phaseolotoxin-resistant ornithine carbamoyltransferase in Pseudomonas syringae pv. phaseolicola, and functional expression of argK in transgenic tobacco. J Bacteriol 174:5895–5909

    PubMed  CAS  Google Scholar 

  • Hernández-Flores JL, López-López K, Garcidueñas-Piña R, Jofre-Garfias AE, Alvarez-Morales A (2004) The global arginine regulator ArgR controls expression of argF in Pseudomonas syringae pv. phaseolicola but is not required for the synthesis of phaseolotoxin or for the regulated expression of argK. J Bacteriol 186:3653–3655

    Article  PubMed  Google Scholar 

  • Holden MT, Titball RW, Peacock SJ, Cerdeño-Tárraga AM, Atkins T, Crossman LC, Pitt T, Churcher C, Mungall K, Bentley SD, Sebaihia M, Thomson NR, Bason N, Beacham IR, Brooks K, Brown KA, Brown NF, Challis GL, Cherevach I, Chillingworth T, Cronin A, Crossett B, Davis P, DeShazer D, Feltwell T, Fraser A, Hance Z, Hauser H, Holroyd S, Jagels K, Keith KE, Maddison M, Moule S, Price C, Quail MA, Rabbinowitsch E, Rutherford K, Sanders M, Simmonds M, Songsivilai S, Stevens K, Tumapa S, Vesaratchavest M, Whitehead S, Yeats C, Barrell BG, Oyston PC, Parkhill J (2004) Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei. Proc Natl Acad Sci USA 101:14240–14245

    Article  PubMed  CAS  Google Scholar 

  • Jackson RW, Mansfield JW, Arnold DL, Sesma A, Paynter CD, Murillo J, Taylor JD, Vivian A (2000) Excision from tRNA genes of a large chromosomal region, carrying avrPphB, associated with race change in the bean pathogen, Pseudomonas syringae pv. phaseolicola. Mol Microbiol 38:186–197

    Article  PubMed  CAS  Google Scholar 

  • Joardar V, Lindeberg M, Jackson RW, Selengut J, Dodson R, Brinkac LM, Daugherty SC, Deboy R, Durkin AS, Giglio MG, Madupu R, Nelson WC, Rosovitz MJ, Sullivan S, Crabtree J, Creasy T, Davidsen T, Haft DH, Zafar N, Zhou L, Halpin R, Holley T, Khouri H, Feldblyum T, White O, Fraser CM, Chatterjee AK, Cartinhour S, Schneider DJ, Mansfield J, Collmer A, Buell CR (2005) Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition. J Bacteriol 187:6488–6498

    Article  PubMed  CAS  Google Scholar 

  • Lindow SE, Brandl MT (2003) Microbiology of the phyllosphere. Appl Environ Microbiol 69:1875–1883

    Article  PubMed  CAS  Google Scholar 

  • Nunes-Düby SE, Kwon HJ, Tirumalai RS, Ellenberger T, Landy A (1998) Similarities and differences among 105 members of the Int family of site-specific recombinases. Nucleic Acids Res 26:391–406

    Article  PubMed  Google Scholar 

  • Ochiai H, Inoue Y, Hasebe A, Kaku H (2001) Construction and characterization of a Xanthomonas oryzae pv. oryzae bacterial artificial chromosome library. FEMS Microbiol Lett 200:59–65

    Article  PubMed  CAS  Google Scholar 

  • Oguiza JA, Rico A, Rivas LA, Sutra L, Vivian A, Murillo J (2004) Pseudomonas syringae pv. phaseolicola can be separated into two genetic lineages distinguished by the possession of the phaseolotoxin biosynthetic cluster. Microbiology 150:473–482

    Article  PubMed  CAS  Google Scholar 

  • Rakin A, Noelting C, Schropp P, Heesemann J (2001) Integrative module of the high-pathogenicity island of Yersinia. Mol Microbiol 39:407–415

    Article  PubMed  CAS  Google Scholar 

  • Rudolph KWE (1995) Pseudomonas syringae pathovars. In: Singh US, Singh RP, Kohmoto K (eds) Pathogenesis and host specificity in plant diseases: histopathological, biochemical, genetic and molecular bases, Vol. 1. Prokaryotes. Elsevier Science, Oxford, pp 47–138

    Google Scholar 

  • Sambroook J, Russell D (2001) Molecular cloning: a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY

    Google Scholar 

  • Sato M (1988) In planta transfer of the genes for virulence between isolates of Pseudomonas syringae pv. atropurpurea. Ann Phytopathol Soc Jpn 54:20–24

    Google Scholar 

  • Sawada H, Takeuchi T, Matsuda I (1997) Comparative analysis of Pseudomonas syringae pv. actinidiae and pv. phaseolicola based on phaseolotoxin-resistant ornithine carbamoyltransferase gene (argK) and 16S-23S rRNA intergenic spacer sequences. Appl Environ Microbiol 63:282–288

    PubMed  CAS  Google Scholar 

  • Sawada H, Suzuki F, Matsuda I, Saitou N (1999) Phylogenetic analysis of Pseudomonas syringae pathovars suggests the horizontal gene transfer of argK and the evolutionary stability of hrp gene cluster. J Mol Evol 49:627–644

    Article  PubMed  CAS  Google Scholar 

  • Sawada H, Kanaya S, Tsuda M, Suzuki F, Azegami K, Saitou N (2002) A phylogenomic study of the OCTase genes in Pseudomonas syringae pathovars: the horizontal transfer of the argK-tox cluster and the evolutionary history of OCTase genes on their genomes. J Mol Evol 54:437–457

    Article  PubMed  CAS  Google Scholar 

  • Simon R, Priefer U, Pühler A (1983) A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in gram negative bacteria. Bio/Technology 1:784–791

    Article  CAS  Google Scholar 

  • Smith MC, Thorpe HM (2002) Diversity in the serine recombinases. Mol Microbiol 44:299–307

    Article  PubMed  CAS  Google Scholar 

  • Tamura K, Imamura M, Yoneyama K, Takikawa Y, Yamaguchi I, Takahashi H (2002) Role of phaseolotoxin production by Pseudomonas syringae pv. actinidiae in the formation of halo lesions of kiwifruit canker disease. Physiol Mol Plant Pathol 60:207–214

    Article  CAS  Google Scholar 

  • Tauschek M, Strugnell RA, Robins-Browne RM (2002) Characterization and evidence of mobilization of the LEE pathogenicity island of rabbit-specific strains of enteropathogenic Escherichia coli. Mol Microbiol 44:1533–1550

    Article  PubMed  CAS  Google Scholar 

  • Taylor LA, Rose RE (1988) A correction in the nucleotide sequence of the Tn903 kanamycin resistance determinant in pUC4K. Nucleic Acids Res 16:358

    PubMed  CAS  Google Scholar 

  • Tsuda M (1998) Use of a transposon-encoded site-specific resolution system for construction of large and defined deletion mutations in bacterial chromosome. Gene 207:33–41

    Article  PubMed  CAS  Google Scholar 

  • Tsuda M, Miyazaki H, Nakazawa T (1995) Genetic and physical mapping of genes involved in pyoverdin production in Pseudomonas aeruginosa PAO. J Bacteriol 177:423–431

    Article  PubMed  CAS  Google Scholar 

  • Vivian A, Murillo J, Jackson RW (2001) The roles of plasmids in phytopathogenic bacteria: mobile arsenals? Microbiology 147:763–780

    PubMed  CAS  Google Scholar 

  • Williams KP (2002) Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies. Nucleic Acids Res 30:866–875

    Article  PubMed  CAS  Google Scholar 

  • Yada T, Hirosawa M (1996) Detection of short protein coding regions within the cyanobacterium genome: application of the hidden Markov model. DNA Res 3:355–361

    Article  PubMed  CAS  Google Scholar 

  • Yanisch-Perron C, Vieira J, Messing J (1985) Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33:103–119

    Article  PubMed  CAS  Google Scholar 

  • Zhang YX, Patil SS (1997) The phtE locus in the phaseolotoxin gene cluster has ORFs with homologies to genes encoding amino acid transferases, the AraC family of transcriptional factors, and fatty acid desaturases. Mol Plant Microbe Interact 10:947–960

    PubMed  CAS  Google Scholar 

  • Zhang Y, Rowley KB, Patil SS (1993) Genetic organization of a cluster of genes involved in the production of phaseolotoxin, a toxin produced by Pseudomonas syringae pv. phaseolicola. J Bacteriol 175:6451–6458

    PubMed  CAS  Google Scholar 

  • Zhao Y, Ma Z, Sundin GW (2005) Comparative genomic analysis of the pPT23A plasmid family of Pseudomonas syringae. J Bacteriol 187:2113–2126

    Article  PubMed  CAS  Google Scholar 

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  1. Hiroyuki Sawada

    Present address: National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan

Authors and Affiliations

  1. Graduate School of Life Sciences, Tohoku University, Sendai, Japan

    Hiroyuki Genka & Masataka Tsuda

  2. Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan

    Tomoya Baba

  3. Nara Institute of Science and Technology, Ikoma, Nara, Japan

    Shigehiko Kanaya & Hirotada Mori

  4. National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan

    Takanobu Yoshida, Masako Tsujimoto Noguchi & Hiroyuki Sawada

  5. National Agriculture Research Center for Western Region, Zentsuji, Kagawa, Japan

    Kenichi Tsuchiya

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Genka, H., Baba, T., Tsuda, M. et al. Comparative Analysis of argK-tox Clusters and Their Flanking Regions in Phaseolotoxin-Producing Pseudomonas syringae Pathovars. J Mol Evol 63, 401–414 (2006). https://doi.org/10.1007/s00239-005-0271-4

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