Analysis of a genomic island housing genes for DNA S-modification system in Streptomyces lividans 66 and its counterparts in other distantly related bacteria

Molecular Microbiology

Volumn 65, Issue 4, 2007, Pages 1034-1048

  He, Xinyi ^a   Ou, Hong Yu ^a   Yu, Qing ^a   Zhou, Xiufen ^a   Wu, Jun ^a   Liang, Jingdan ^a   Zhang, Wei ^b   Rajakumar, Kumar ^c,d   Deng, Zixin ^a  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

^b ILLINOIS INSTITUTE OF TECHNOLOGY   (United States)

^c UNIVERSITY OF LEICESTER   (United Kingdom)

^d UNIVERSITY HOSPITALS OF LEICESTER NHS TRUST   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACTINOBACTERIA; ARTICLE; BACTERIAL STRAIN; CHROMOSOME 10; DNA DETERMINATION; GENE MAPPING; GENE SEQUENCE; GENETIC ANALYSIS; GENOMIC ISLAND; NONHUMAN; PLASMID; PRIORITY JOURNAL; STREPTOMYCES LIVIDANS;

BASE COMPOSITION; CHROMOSOMES, BACTERIAL; CLUSTER ANALYSIS; DNA RESTRICTION-MODIFICATION ENZYMES; DNA TRANSPOSABLE ELEMENTS; GENES, BACTERIAL; GENOMIC ISLANDS; INTEGRASES; PHYLOGENY; RECOMBINATION, GENETIC; SEQUENCE ANALYSIS, DNA; STREPTOMYCES LIVIDANS; SUBSTRATE SPECIFICITY;

ACTINOBACTERIA (CLASS); BACTERIA (MICROORGANISMS); PSEUDOALTEROMONAS HALOPLANKTIS; STREPTOMYCES; STREPTOMYCES LIVIDANS;

EID: 34547660622     PISSN: 0950382X     EISSN: 13652958     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2007.05846.x     Document Type: Article

References (69)

1. Alfano, J.R., Charkowski, A.O., Deng, W.L., Badel, J.L., Petnicki-Ocwieja, T., van Dijk, K. Collmer, A. (2000) The Pseudomonas syringae Hrp pathogenicity island has a tripartite mosaic structure composed of a cluster of type III secretion genes bounded by exchangeable effector and conserved effector loci that contribute to parasitic fitness and pathogenicity in plants. Proc Natl Acad Sci USA 97 : 4856 4861.
2. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25 : 3389 3402.
3. Bair, C.L. Black, L.W. (2006) A type IV modification dependent restriction nuclease that targets glucosylated hydroxymethyl cytosine modified DNAs. J Mol Biol 366 : 768 788.
4. Bao, K., Hu, Z., Zhou, X., Zhou, Q. Deng, Z. (1997) A bifunctional cosmid vector for the mobilized conjugal transfer of DNA from E. coli to Streptomyces sp. Prog Nat Sci 7 : 568 572.
5. Bentley, S.D., Chater, K.F., Cerdeno-Tarraga, A.M., Challis, G.L., Thomson, N.R., James, K.D., et al. (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417 : 141 147.
6. Bierman, M., Logan, R., O'Brien, K., Seno, E.T., Rao, R.N. Schoner, B.E. (1992) Plasmid cloning vectors for the conjugal transfer of DNA from Escherichia coli to Streptomyces spp. Gene 116 : 43 49.
7. Bolden, A., Ward, C., Siedlecki, J.A. Weissbach, A. (1984) DNA methylation. Inhibition of de novo and maintenance methylation in vitro by RNA and synthetic polynucleotides. J Biol Chem 259 : 12437 12443.
8. Brezellec, P., Hoebeke, M., Hiet, M.S., Pasek, S. Ferat, J.L. (2006) DomainSieve: a protein domain-based screen that led to the identification of dam-associated genes with potential link to DNA maintenance. Bioinformatics 22 : 1935 1941.
9. Choulet, F., Aigle, B., Gallois, A., Mangenot, S., Gerbaud, C., Truong, C., et al. (2006) Evolution of the terminal regions of the Streptomyces linear chromosome. Mol Biol Evol 23 : 2361 2369.
10. Dobrindt, U., Hochhut, B., Hentschel, U. Hacker, J. (2004) Genomic islands in pathogenic and environmental microorganisms. Nat Rev Microbiol 2 : 414 424.
11. Doublet, B., Boyd, D., Mulvey, M.R. Cloeckaert, A. (2005) The Salmonella genomic island 1 is an integrative mobilizable element. Mol Microbiol 55 : 1911 1924.
12. Dyson, P. Evans, M. (1998) Novel post-replicative DNA modification in Streptomyces: analysis of the preferred modification site of plasmid pIJ101. Nucleic Acids Res 26 : 1248 1253.
13. Feitelson, J.S. Hopwood, D.A. (1983) Cloning of a Streptomyces gene for an O-methyltransferase involved in antibiotic biosynthesis. Mol Gen Genet 190 : 394 398.
14. Finn, R.D., Mistry, J., Schuster-Bockler, B., Griffiths-Jones, S., Hollich, V., Lassmann, T., et al. (2006) Pfam: clans, web tools and services. Nucleic Acids Res 34 : D247 D251.
15. Fitzgerald, J.R., Monday, S.R., Foster, T.J., Bohach, G.A., Hartigan, P.J., Meaney, W.J. Smyth, C.J. (2001) Characterization of a putative pathogenicity island from bovine Staphylococcus aureus encoding multiple superantigens. J Bacteriol 183 : 63 70.
16. Flett, F., Mersinias, V. Smith, C.P. (1997) High efficiency intergeneric conjugal transfer of plasmid DNA from Escherichia coli to methyl DNA-restricting Streptomycetes. FEMS Microbiol Lett 155 : 223 229.
17. Gunes, G., Smith, B. Dyson, P. (1999) Genetic instability associated with insertion of IS6100 into one end of the Streptomyces lividans chromosome. Microbiology 145 (Part 9 2203 2208.
18. Hanahan, D. (1983) Studies on transformation of Escherichia coli with plasmids. J Mol Biol 166 : 557 580.
19. Hochhut, B. Waldor, M.K. (1999) Site-specific integration of the conjugal Vibrio cholerae SXT element into prfc. Mol Microbiol 32 : 99 110.
20. Hochhut, B., Wilde, C., Balling, G., Middendorf, B., Dobrindt, U., Brzuszkiewicz, E., et al. (2006) Role of pathogenicity island-associated integrases in the genome plasticity of uropathogenic Escherichia coli strain 536. Mol Microbiol 61 : 584 595.
21. Hopwood, D.A. (2007) Streptomyces in Nature and Medicine: The Antibiotic Makers. New York : Oxford University Press.
22. Hsiao, W., Wan, I., Jones, S.J. Brinkman, F.S. (2003) IslandPath: aiding detection of genomic islands in prokaryotes. Bioinformatics 19 : 418 420.
23. Ikeda, H., Ishikawa, J., Hanamoto, A., Shinose, M., Kikuchi, H., Shiba, T., et al. (2003) Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nat Biotechnol 21 : 526 531.
24. Ishikawa, J. Hotta, K. (1999) FramePlot: a new implementation of the frame analysis for predicting protein-coding regions in bacterial DNA with a high G+C content. FEMS Microbiol Lett 174 : 251 253.
25. Jeong, H., Yim, J.H., Lee, C., Choi, S.H., Park, Y.K., Yoon, S.H., et al. (2005) Genomic blueprint of Hahella chejuensis, a marine microbe producing an algicidal agent. Nucleic Acids Res 33 : 7066 7073.
26. Karlin, S. (2001) Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes. Trends Microbiol 9 : 335 343.
27. Kers, J.A., Cameron, K.D., Joshi, M.V., Bukhalid, R.A., Morello, J.E., Wach, M.J., et al. (2005) A large, mobile pathogenicity island confers plant pathogenicity on Streptomyces species. Mol Microbiol 55 : 1025 1033.
28. Kieser, T., Hopwood, D.A., Wright, H.M. Thompson, C.J. (1982) pIJ101, a multi-copy broad host-range Streptomyces plasmid: functional analysis and development of DNA cloning vectors. Mol Gen Genet 185 : 223 228.
29. Kieser, T., Bibb, M.J., Chater, K.F., Butter, M.J. Hopwood, D.A. (2000) Practical Streptomyces Genetics. A Laboratory Manual. Norwich : John Innes Foundation.
30. Kieser, H.M., Kieser, T. Hopwood, D.A. (1992) A combined genetic and physical map of the Streptomyces coelicolor A3(2) chromosome. J Bacteriol 174 : 5496 5507.
31. Krogh, A., Larsson, B., von Heijne, G. Sonnhammer, E.L. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305 : 567 580.
32. Kulasekara, B.R., Kulasekara, H.D., Wolfgang, M.C., Stevens, L., Frank, D.W. Lory, S. (2006) Acquisition and evolution of the exoU locus in Pseudomonas aeruginosa. J Bacteriol 188 : 4037 4050.
33. Leblond, P., Redenbach, M. Cullum, J. (1993) Physical map of the Streptomyces lividans 66 genome and comparison with that of the related strain Streptomyces coelicolor A3(2). J Bacteriol 175 : 3422 3429.
34. Li, W., Wu, J., Tao, W., Zhao, C., Wang, Y., He, X., et al. (2006) A genetic and bioinformatic analysis of Streptomyces coelicolor genes containing TTA codons, possible targets for regulation by a developmentally significant tRNA. FEMS Microbiol Lett 266 : 20 28.
35. Liang, J., Wang, Z., He, X., Li, J., Zhou, X. Deng, Z. (2007) DNA modification by sulfur: analysis of the sequence recognition specificity surrounding the modification sites. Nucleic Acids Res 35 : 2944 2954.
36. Maas, R.M., Gotz, J., Wohlleben, W. Muth, G. (1998) The conjugative plasmid pSG5 from Streptomyces ghanaensis DSM 2932 differs in its transfer functions from other Streptomyces rolling-circle-type plasmids. Microbiology 144 (Part 10 2809 2817.
37. Mantri, Y. Williams, K.P. (2004) Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities. Nucleic Acids Res 32 : D55 D58.
38. Medigue, C., Krin, E., Pascal, G., Barbe, V., Bernsel, A., Bertin, P.N., et al. (2005) Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. Genome Res 15 : 1325 1335.
39. Murase, T., Nagato, M., Shirota, K., Katoh, H. Otsuki, K. (2004) Pulsed-field gel electrophoresis-based subtyping of DNA degradation-sensitive Salmonella enterica subsp. enterica serovar Livingstone and serovar Cerro isolates obtained from a chicken layer farm. Vet Microbiol 99 : 139 143.
40. O'Shea, Y.A. Boyd, E.F. (2002) Mobilization of the Vibrio pathogenicity island between Vibrio cholerae isolates mediated by CP-T1 generalized transduction. FEMS Microbiol Lett 214 : 153 157.
41. Ou, H.Y., Smith, R., Lucchini, S., Hinton, J., Chaudhuri, R.R., Pallen, M., et al. (2005) ArrayOme: a program for estimating the sizes of microarray-visualized bacterial genomes. Nucleic Acids Res 33 : e3.
42. Ou, H.Y., Chen, L.L., Lonnen, J., Chaudhuri, R.R., Thani, A.B., Smith, R., et al. (2006) A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria. Nucleic Acids Res 34 : e3.
43. Ou, H.Y., He, X., Harrison, E.M., Kulasekara, B.R., Thani, A.B., Kadioglu, A., et al. (2007) MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands. Nucleic Acids Res (in press). doi: 10.1093/nar/gkm/380.
44. van Passel, M.W., Luyf, A.C., van Kampen, A.H., Bart, A. van der Ende, A. (2005) Deltarho-web, an online tool to assess composition similarity of individual nucleic acid sequences. Bioinformatics 21 : 3053 3055.
45. Piel, J., Hofer, I. Hui, D. (2004) Evidence for a symbiosis island involved in horizontal acquisition of pederin biosynthetic capabilities by the bacterial symbiont of Paederus fuscipes beetles. J Bacteriol 186 : 1280 1286.
46. Ramsay, J.P., Sullivan, J.T., Stuart, G.S., Lamont, I.L. Ronson, C.W. (2006) Excision and transfer of the Mesorhizobium loti R7A symbiosis island requires an integrase IntS, a novel recombination directionality factor RdfS, and a putative relaxase RlxS. Mol Microbiol 62 : 723 734.
47. Romling, U. Tummler, B. (2000) Achieving 100% typeability of Pseudomonas aeruginosa by pulsed-field gel electrophoresis. J Clin Microbiol 38 : 464 465.
48. Ruzin, A., Lindsay, J. Novick, R.P. (2001) Molecular genetics of SaPI1 - a mobile pathogenicity island in Staphylococcus aureus. Mol Microbiol 41 : 365 377.
49. Sambrook, J., Fritsch, E.F. Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor, NY : Cold Spring Harbor.
50. Schaffer, A.A., Aravind, L., Madden, T.L., Shavirin, S., Spouge, J.L., Wolf, Y.I., et al. (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res 29 : 2994 3005.
51. Schmidt, M., Wolf, S.F. Migeon, B.R. (1985) Evidence for a relationship between DNA methylation and DNA replication from studies of the 5-azacytidine-reactivated allocyclic X chromosome. Exp Cell Res 158 : 301 310.
52. Schubert, S., Dufke, S., Sorsa, J. Heesemann, J. (2004) A novel integrative and conjugative element (ICE) of Escherichia coli: the putative progenitor of the Yersinia high-pathogenicity island. Mol Microbiol 51 : 837 848.
53. Schwartz, C.J., Djaman, O., Imlay, J.A. Kiley, P.J. (2000) The cysteine desulfurase, IscS, has a major role in in vivo Fe-S cluster formation in Escherichia coli. Proc Natl Acad Sci USA 97 : 9009 9014.
54. Sentchilo, V., Ravatn, R., Werlen, C., Zehnder, A.J. van der Meer, J.R. (2003a) Unusual integrase gene expression on the clc genomic island in Pseudomonas sp. strain B13. J Bacteriol 185 : 4530 4538.
55. Sentchilo, V., Zehnder, A.J. van der Meer, J.R. (2003b) Characterization of two alternative promoters for integrase expression in the clc genomic island of Pseudomonas sp. strain B13. Mol Microbiol 49 : 93 104.
56. Sullivan, J.T. Ronson, C.W. (1998) Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. Proc Natl Acad Sci USA 95 : 5145 5149.
57. Sun, Y., Zhou, X., Liu, J., Bao, K., Zhang, G., Tu, G., et al. (2002) 'Streptomyces nanchangensis', a producer of the insecticidal polyether antibiotic nanchangmycin and the antiparasitic macrolide meilingmycin, contains multiple polyketide gene clusters. Microbiology 148 : 361 371.
58. Tomizawa, J. Ogawa, T. (1967) Effect of ultraviolet irradiation on bacteriophage lambda immunity. J Mol Biol 23 : 247 263.
59. Tsai, J.F. Chen, C.W. (1987) Isolation and characterization of Streptomyces lividans mutants deficient in intraplasmid recombination. Mol Gen Genet 208 : 211 218.
60. Ubeda, C., Tormo, M.A., Cucarella, C., Trotonda, P., Foster, T.J., Lasa, I. Penades, J.R. (2003) Sip, an integrase protein with excision, circularization and integration activities, defines a new family of mobile Staphylococcus aureus pathogenicity islands. Mol Microbiol 49 : 193 210.
61. Volff, J.N. Altenbuchner, J. (1998) Genetic instability of the Streptomyces chromosome. Mol Microbiol 27 : 239 246.
62. Williams, K.P. (2002) Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies. Nucleic Acids Res 30 : 866 875.
63. You, D., Wang, L., Yao, F., Zhou, X. Deng, Z. (2007) A novel DNA modification by sulfur: DndA is a NifS-like cysteine desulfurase capable of assembling DndC as an iron-sulfur cluster protein in Streptomyces lividans. Biochemistry 46 : 6126 6133.
64. Zhang, J., Voss, K.O., Shaw, D.F., Roos, K.P., Lewis, D.F., Yan, J., et al. (1999) A multiple-capillary electrophoresis system for small-scale DNA sequencing and analysis. Nucleic Acids Res 27 : e36.
65. Zhou, X., Deng, Z., Firmin, J.L., Hopwood, D.A. Kieser, T. (1988) Site-specific degradation of Streptomyces lividans DNA during electrophoresis in buffers contaminated with ferrous iron. Nucleic Acids Res 16 : 4341 4352.
66. Zhou, X., Deng, Z., Hopwood, D.A. Kieser, T. (1994a) Streptomyces lividans 66 contains a gene for phage resistance which is similar to the phage lambda ea59 endonuclease gene. Mol Microbiol 12 : 789 797.
67. Zhou, X., Deng, Z., Hopwood, D.A. Kieser, T. (1994b) Characterization of φHAU3, a broad-host-range temperate Streptomyces phage, and development of phasmids. J Bacteriol 176 : 2096 2099.
68. Zhou, X., He, X., Li, A., Lei, F., Kieser, T. Deng, Z. (2004) Streptomyces coelicolor A3(2) lacks a genomic island present in the chromosome of Streptomyces lividans 66. Appl Environ Microbiol 70 : 7110 7118.
69. Zhou, X., He, X., Liang, J., Li, A., Xu, T., Kieser, T., et al. (2005) A novel DNA modification by sulphur. Mol Microbiol 57 : 1428 1438.