Complete nucleotide sequence of plasmid pND6-2 from Pseudomonas putida ND6 and characterization of conjugative genes

Gene

Volumn 512, Issue 1, 2013, Pages 148-156

  Li, Shanshan ^a,b   Zhao, Huabing ^a   Li, Yaxiao ^a   Niu, Shumin ^c   Cai, Baoli ^c  

^a MEDICAL COLLEGE OF CHINESE PEOPLE'S ARMED POLICE FORCES   (China)

^b XI'AN JIAOTONG UNIVERSITY   (China)

^c NANKAI UNIVERSITY   (China)

Author keywords

Conjugative genes; Helper plasmid; Nucleotide sequence; PND6 2; Pseudomonas putida ND6

Indexed keywords

DNA; NAPHTHALENE;

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; CONTROLLED STUDY; GENE REPLICATION; GENE SEQUENCE; GENE TRANSFER; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; PREDICTION; PRIORITY JOURNAL; PSEUDOMONAS PUTIDA;

CONJUGATION, GENETIC; DNA REPAIR; DNA REPLICATION; GENE ORDER; GENES, BACTERIAL; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PLASMIDS; PSEUDOMONAS PUTIDA; RECOMBINATION, GENETIC;

ESCHERICHIA COLI; PSEUDOMONAS PUTIDA;

EID: 84868621860     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2012.09.065     Document Type: Article

References (58)

1. Akahane K., Sakai D., Furuya N., Komano T. Analysis of the pilU gene for the prepilin peptidase involved in the biogenesis of type IV pili encoded by plasmid R64. Mol. Genet. Genomics 2005, 273:350-359.
2. Altschul S.F., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
3. Apweiler R., et al. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 2001, 29:37-40.
4. Bradley D.E. Derepressed plasmids of incompatibility group I1 determine two different morphological forms of pilus. Plasmid 1983, 9:331-334.
5. Bradley D.E. Characteristics and function of thick and thin conjugative pili determined by transfer-derepressed plasmids of incompatibility groups I1, I2, I5, B K and Z. J. Gen. Microbiol. 1984, 130:1489-1502.
6. Buscher B.A., et al. The DotL protein, a member of the TraG-coupling protein family, is essential for viability of Legionella pneumophila strain Lp02. J. Bacteriol. 2005, 187:2927-2938.
7. Delcher A.L., Harmon D., Kasif S., White O., Salzberg S.L. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 1999, 27:4636-4641.
8. Dennis J.J., Zylstra G.J. Complete sequence and genetic organization of pDTG1, the 83 kilobase naphthalene degradation plasmid from Pseudomonas putida strain NCIB 9816-4. J. Mol. Biol. 2004, 341:753-768.
9. Ensley B.D., Ratzkin B.J., Osslund T.D., Simon M.J., Wackett L.P., Gibson D.T. Expression of naphthalene oxidation genes in Escherichia coli results in the biosynthesis of indigo. Science 1983, 222:167-169.
10. Fuchs R.P., Fujii S., Wagner J. Properties and functions of Escherichia coli: Pol IV and Pol V. Adv. Protein Chem. 2004, 69:229-264.
11. Fulcher N.B., Holliday P.M., Klem E., Cann M.J., Wolfgang M.C. The Pseudomonas aeruginosa Chp chemosensory system regulates intracellular cAMP levels by modulating adenylate cyclase activity. Mol. Microbiol. 2010, 76:889-904.
12. Genschel J., Litz L., Thole H., Roemling U., Urbanke C. Isolation, sequencing and overproduction of the single-stranded DNA binding protein from Pseudomonas aeruginosa PAO. Gene 1996, 182:137-143.
13. Gerdes K., Christensen S.K., Lobner-Olesen A. Prokaryotic toxin-antitoxin stress response loci. Nat. Rev. Microbiol. 2005, 3:371-382.
14. Ghai J., Das A. The virD operon of Agrobacterium tumefaciens Ti plasmid encodes a DNA-relaxing enzyme. Proc. Natl. Acad. Sci. USA 1989, 86:3109-3313.
15. Greated A., Lambertsen L., Williams P.A., Thomas C.M. Complete sequence of the IncP-9 TOL plasmid pWW0 from Pseudomonas putida. Environ. Microbiol. 2002, 4:856-871.
16. Kang C., Sun N., Honzatko R.B., Fromm H.J. Replacement of Asp333 with Asn by site-directed mutagenesis changes the substrate specificity of Escherichia coli adenylosuccinate synthetase from guanosine 5'-triphosphate to xanthosine 5'-triphosphate. J. Biol. Chem. 1994, 269:24046-24049.
17. Kim S.R., Komano T. The plasmid R64 thin pilus identified as a type IV pilus. J. Bacteriol. 1997, 179:3594-3603.
18. Kim S.R., Funayama N., Komano T. Nucleotide sequence and characterization of the traABCD region of IncI1 plasmid R64. J. Bacteriol. 1993, 175:5035-5042.
19. Komano T., Funayama N., Kim S.R., Nisioka T. Transfer region of IncI1 plasmid R64 and role of shufflon in R64 transfer. J. Bacteriol. 1990, 172:2230-2235.
20. Komano T., Kim S.R., Yoshida T. Mating variation by DNA inversions of shufflon in plasmid R64. Adv. Biophys. 1995, 31:181-193.
21. Kumar S., et al. The DNA (cytosine-5) methyltransferases. Nucleic Acids Res. 1994, 22:1-10.
22. Lang S., et al. Molecular recognition determinants for type IV secretion of diverse families of conjugative relaxases. Mol. Microbiol. 2010, 78:1539-1555.
23. Lee D.G., et al. Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatorial. Genome Biol. 2006, 7:R90.
24. Li W., et al. Complete nucleotide sequence and organization of the naphthalene catabolic plasmid pND6-1 from Pseudomonas sp. strain ND6. Gene 2004, 336:231-240.
25. Li R., et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 2010, 20:265-272.
26. Li S., Li X., Zhao H., Cai B. Physiological role of the novel salicylaldehyde dehydrogenase NahV in mineralization of naphthalene by Pseudomonas putida ND6. Microbiol. Res. 2011, 166:643-653.
27. Margulies M., et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437:376-380.
28. Martinez B., Tomkins J., Wackett L.P., Wing R., Sadowsky M.J. Complete nucleotide sequence and organization of the atrazine catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP. J. Bacteriol. 2001, 183:5684-5697.
29. McClelland M., Nelson M., Raschke E. Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases. Nucleic Acids Res. 1994, 22:3640-3659.
30. Mehr I.J., Long C.D., Serkin C.D., Seifert H.S. A homologue of the recombination-dependent growth gene, rdgC, is involved in gonococcal pilin antigenic variation. Genetics 2000, 154:523-532.
31. Monchy S., et al. Plasmids pMOL28 and pMOL30 of Cupriavidus metallidurans are specialized in the maximal viable response to heavy metals. J. Bacteriol. 2007, 189:7417-7425.
32. Moscoso M., Eritja R., Espinosa M. Initiation of replication of plasmid pMV158: mechanisms of DNA strand-transfer reactions mediated by the initiator RepB protein. J. Mol. Biol. 1997, 268:840-856.
33. Muller J., et al. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Res. 2010, 38:D190-D195.
34. Nagai H., Kubori T. Type IVB secretion systems of Legionella and other gram-negative bacteria. Front. Microbiol. 2011, 2:136.
35. Neilson L., Blakely G., Sherratt D.J. Site-specific recombination at dif by Haemophilus influenzae XerC. Mol. Microbiol. 1999, 31:915-926.
36. Norman A., Hansen L.H., Sorensen S.J. Conjugative plasmids: vessels of the communal gene pool. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2009, 364:2275-2289.
37. Novick R.P. Plasmid incompatibility. Microbiol. Rev. 1987, 51:381-395.
38. Planet P.J., Kachlany S.C., DeSalle R., Figurski D.H. Phylogeny of genes for secretion NTPases: identification of the widespread tadA subfamily and development of a diagnostic key for gene classification. Proc. Natl. Acad. Sci. U. S. A. 2001, 98:2503-2508.
39. Ramirez-Diaz M.I., Diaz-Magana A., Meza-Carmen V., Johnstone L., Cervantes C., Rensing C. Nucleotide sequence of Pseudomonas aeruginosa conjugative plasmid pUM505 containing virulence and heavy-metal resistance genes. Plasmid 2011, 66:7-18.
40. Rice P., Longden I., Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000, 16:276-277.
41. Ryder L., Sharples G.J., Lloyd R.G. Recombination-dependent growth in exonuclease-depleted recBC sbcBC strains of Escherichia coli K-12. Genetics 1996, 143:1101-1114.
42. Sakai D., Komano T. The pilL and pilN genes of IncI1 plasmids R64 and ColIb-P9 encode outer membrane lipoproteins responsible for thin pilus biogenesis. Plasmid 2000, 43:149-152.
43. Sakai D., Komano T. Genes required for plasmid R64 thin-pilus biogenesis: identification and localization of products of the pilK, pilM, pilO, pilP, pilR, and pilT genes. J. Bacteriol. 2002, 184:444-451.
44. Sakai D., Horiuchi T., Komano T. Atpase activity and multimer formation of Pilq protein are required for thin pilus biogenesis in plasmid R64. J. Biol. Chem. 2001, 276:17968-17975.
45. Schell M.A. Cloning and expression in Escherichia coli of the naphthalene degradation genes from plasmid NAH7. J. Bacteriol. 1983, 153:822-829.
46. Schumacher M.A., et al. Segrosome structure revealed by a complex of ParR with centromere DNA. Nature 2007, 450:1268-1271.
47. Segal G., Shuman H.A. Intracellular multiplication and human macrophage killing by Legionella pneumophila are inhibited by conjugal components of IncQ plasmid RSF1010. Mol. Microbiol. 1998, 30:197-208.
48. Sexton J.A., Yeo H.J., Vogel J.P. Genetic analysis of the Legionella pneumophila DotB ATPase reveals a role in type IV secretion system protein export. Mol. Microbiol. 2005, 57:70-84.
49. Shimoda E., Muto T., Horiuchi T., Furuya N., Komano T. Novel class of mutations of pilS mutants, encoding plasmid R64 type IV prepilin: interface of PilS-PilV interactions. J. Bacteriol. 2008, 190:1202-1208.
50. Shintani M., et al. Characterization of the replication, maintenance, and transfer features of the IncP-7 plasmid pCAR1, which carries genes involved in carbazole and dioxin degradation. Appl. Environ. Microbiol. 2006, 72:3206-3216.
51. Shintani M., Takahashi Y., Yamane H., Nojiri H. The behavior and significance of degradative plasmids belonging to Inc groups in Pseudomonas within natural environments and microcosms. Microbes Environ. 2010, 25:253-265.
52. Takahashi H., Shao M., Furuya N., Komano T. The genome sequence of the incompatibility group Igamma plasmid R621a: evolution of IncI plasmids. Plasmid 2011, 66:112-121.
53. Thieme F., et al. Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence. J. Bacteriol. 2005, 187:7254-7266.
54. Tian G., Kober F.X., Lewandrowski U., Sickmann A., Lennarz W.J., Schindelin H. The catalytic activity of protein-disulfide isomerase requires a conformationally flexible molecule. J. Biol. Chem. 2008, 283:33630-33640.
55. Vincent C.D., Friedman J.R., Jeong K.C., Buford E.C., Miller J.L., Vogel J.P. Identification of the core transmembrane complex of the Legionella Dot/Icm type IV secretion system. Mol. Microbiol. 2006, 62:1278-1291.
56. Vogel J.P., Andrews H.L., Wong S.K., Isberg R.R. Conjugative transfer by the virulence system of Legionella pneumophila. Science 1998, 279:873-876.
57. Wallden K., Rivera-Calzada A., Waksman G. Type IV secretion systems: versatility and diversity in function. Cell. Microbiol. 2010, 12:1203-1212.
58. Zhang X., Yue X., Huang J., Niu S., Cai B. Isolation and identification of naphthalene-degrading plasmid pND6. Chin. J. Appl. Environ. Biol. 2000, 6:187-190.