Conjugative type 4 secretion system of a novel large plasmid from the chemoautotroph Tetrathiobacter kashmirensis and construction of shuttle vectors for Alcaligenaceae

Applied and Environmental Microbiology

Volumn 75, Issue 13, 2009, Pages 4362-4373

  Dam, Bomba ^a,b   Ghosh, Wriddhiman ^a   Das Gupta, Sujoy K ^a  

^a BOSE INSTITUTE   (India)

^b VISVA BHARATI UNIVERSITY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

CLOSE PROXIMITY; CONJUGATIVE TRANSFER; COPY NUMBER; GENE CLUSTERS; GENOMIC ORGANIZATION; INSERTIONAL INACTIVATION; LARGE PLASMIDS; PHYLOGENETIC AFFINITY; REPLICATION PROTEIN A; SECRETION SYSTEMS; SHUTTLE VECTOR; UNIQUE FEATURES; UV DAMAGE;

GENE ENCODING; NUCLEIC ACIDS; SULFUR;

TRANSFER FUNCTIONS;

NUCLEOPROTEIN; REPLICATION FACTOR A; SULFUR;

BACTERIUM; CHEMOAUTOTROPHY; CHROMOSOME; GENE EXPRESSION; PHYLOGENETICS; PLASMID; PROTEIN; SECRETION; SULFUR; ULTRAVIOLET RADIATION;

ALCALIGENACEAE; ARTICLE; BACTERIAL GENE; CHEMOLITHOAUTOTROPH; EVOLUTION; GENE CLUSTER; GENE INACTIVATION; GENE LOCUS; GENE REPLICATION; GENETIC ORGANIZATION; NONHUMAN; NUCLEOTIDE SEQUENCE; ORIV GENE; PHYLOGENY; PLASMID; PROTEIN TRANSPORT; RADIATION INJURY REPAIR; REPA GENE; REPLICON; SHUTTLE VECTOR; TAGB GENE; TETRATHIOBACTER KASHMIRENSIS; TRAL GENE;

ALCALIGENACEAE; BASE SEQUENCE; CONJUGATION, GENETIC; DNA REPAIR ENZYMES; DNA, BACTERIAL; EVOLUTION, MOLECULAR; GENE ORDER; GENE TRANSFER, HORIZONTAL; GENES, BACTERIAL; GENETIC VECTORS; MOLECULAR SEQUENCE DATA; MUTAGENESIS, INSERTIONAL; PHYLOGENY; PLASMIDS; REPLICATION ORIGIN; REPLICATION PROTEIN A; REPLICON; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY;

ALCALIGENACEAE; TETRATHIOBACTER; TETRATHIOBACTER KASHMIRENSIS;

EID: 67649618951     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.02521-08     Document Type: Article

References (45)

1. Abeles, A. L., K. M. Snyder, and D. K. Chattoraj. 1984. P1 plasmid replication: replicon structure. J. Mol. Biol. 173:307-324.
2. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402. (Pubitemid 27359211)
3. An, F. Y., and D. B. Clewell. 1997. The origin of transfer (oriT) of the enterococcal, pheromone-responding, cytolysin plasmid pAD1 is located within the repA determinant. Plasmid 37:87-94. (Pubitemid 27142891)
4. Atmakuri, K., E. Cascales, and P. J. Christie. 2004. Energetic components VirD4, VirB11 and VirB4 mediate early DNA transfer reactions required for bacterial type IV secretion. Mol. Microbiol. 54:1199-1211.
5. Burns, D. L. 1999. Biochemistry of type IV secretion. Curr. Opin. Microbiol. 2:25-29.
6. Cao, T. B., and M. H. Saier, Jr. 2001. Conjugal type IV macromolecular transfer systems of Gram-negative bacteria: organismal distribution, structural constraints and evolutionary conclusions. Microbiology 147:3201-3214.
7. Cascales, E., and P. J. Christie. 2003. The versatile bacterial type IV secretion systems. Nat. Rev. Microbiol. 1:137-149.
8. Chattoraj, D. K., K. M. Snyder, and A. L. Abeles. 1985. P1 plasmid replication: multiple functions of RepA protein at the origin. Proc. Natl. Acad. Sci. USA 82:2588-2592.
9. Christie, P. J. 2001. Type IV secretion: intercellular transfer of macromolecules by systems ancestrally related to conjugation machines. Mol. Microbiol. 40:294-305.
10. Covacci, A., J. L. Telford, G. Del Giudice, J. Parsonnet, and R. Rappuoli. 1999. Helicobacter pylori virulence and genetic geography. Science 284:1328-1333.
11. Dam, B., S. Mandal, W. Ghosh, S. K. Das Gupta, and P. Roy. 2007. The S4-intermediate pathway for the oxidation of thiosulfate by the chemolithoautotroph Tetrathiobacter kashmirensis and inhibition of tetrathionate oxidation by sulfite. Res. Microbiol. 158:330-338.
12. de Paz, H. D., F. J. Sangari, S. Bolland, J. M. Garcia-Lobo, C. Dehio, F. de la Cruz, and M. Llosa. 2005. Functional interactions between type IV secretion systems involved in DNA transfer and virulence. Microbiology 151:3505-3516. (Pubitemid 41632064)
13. Fürste, J. P., W. Pansegrau, G. Ziegelin, M. Kroger, and E. Lanka. 1989. Conjugative transfer of promiscuous IncP plasmids: interaction of plasmid-encoded products with the transfer origin. Proc. Natl. Acad. Sci. USA 86:1771-1775.
14. Ghosal, D., I. S. You, D. K. Chatterjee, and A. M. Chakrabarty. 1985. Genes specifying degradation of 3-chlorobenzoic acid in plasmids pAC27 and pJP4. Proc. Natl. Acad. Sci. USA 82:1638-1642.
15. Ghosh, W., A. Bagchi, S. Mandal, B. Dam, and P. Roy. 2005. Tetrathiobacter kashmirensis gen. nov., sp. nov., a novel mesophilic, neutrophilic, tetrathionate-oxidizing, facultatively chemolithotrophic betaproteobacterium isolated from soil from a temperate orchard in Jammu and Kashmir, India. Int. J. Syst. Evol. Microbiol. 55:1779-1787.
16. Hayes, F. 1998. A family of stability determinants in pathogenic bacteria. J. Bacteriol. 180:6415-6418. (Pubitemid 28544280)
17. Hayes, F. 2000. The partition system of multidrug resistance plasmid TP228 includes a novel protein that epitomizes an evolutionarily distinct subgroup of the ParA superfamily. Mol. Microbiol. 37:528-541.
18. Hunter, W. J., and D. K. Manter. 2008. Bio-reduction of selenite to elemental red selenium by Tetrathiobacter kashmirensis. Curr. Microbiol. 57:83-88.
19. Jain, S., D. Kaushal, S. K. DasGupta, and A. K. Tyagi. 1997. Construction of shuttle vectors for genetic manipulation and molecular analysis of mycobacteria. Gene 190:37-44. (Pubitemid 27214268)
20. Jakubowski, S. J., V. Krishnamoorthy, E. Cascales, and P. J. Christie. 2004. Agrobacterium tumefaciens VirB6 domains direct the ordered export of a DNA substrate through a type IV secretion system. J. Mol. Biol. 341:961-977.
21. Kamachi, K., M. Sota, Y. Tamai, N. Nagata, T. Konda, T. Inoue, E. M. Top, and Y. Arakawa. 2006. Plasmid pBP136 from Bordetella pertussis represents an ancestral form of IncP-1β plasmids without accessory mobile elements. Microbiology 152:3477-3484.
22. Koraimann, G. 2003. Lytic transglycosylases in macromolecular transport systems of Gram-negative bacteria. Cell. Mol. Life Sci. 60:2371-2388.
23. Krall, L., U. Wiedemann, G. Unsin, S. Weiss, N. Domke, and C. Baron. 2002. Detergent extraction identifies different VirB protein subassemblies of the type IV secretion machinery in the membranes of Agrobacterium tumefaciens. Proc. Natl. Acad. Sci. USA 99:11405-11410. (Pubitemid 34920938)
24. Lai, E. M., and C. I. Kado. 1998. Processed VirB2 is the major subunit of the promiscuous pilus of Agrobacterium tumefaciens. J. Bacteriol. 180:2711-2717.
25. Lee, C. L., D. S. Ow, and S. K. Oh. 2006. Quantitative real-time polymerase chain reaction for determination of plasmid copy number in bacteria. J. Microbiol. Methods 65:258-267.
26. Mandal, S., S. Chatterjee, B. Dam, P. Roy, and S. K. Das Gupta. 2007. The dimeric repressor SoxR binds cooperatively to the promoter(s) regulating expression of the sulfur oxidation (sox) operon of Pseudaminobacter salicylatoxidans KCT001. Microbiology 153:80-91.
27. Miller, V. L., and J. J. Mekalanos. 1988. A novel suicide vector and its use in construction of insertion mutations: osmoregulation of outer membrane proteins and virulence determinants in Vibrio cholerae requires toxR. J. Bacteriol. 170:2575-2583. (Pubitemid 18148217)
28. Motallebi-Veshareh, M., D. A. Rouch, and C. M. Thomas. 1990. A family of ATPases involved in active partitioning of diverse bacterial plasmids. Mol. Microbiol. 4:1455-1463.
29. Pansegrau, W., and E. Lanka. 1991. Common sequence motifs in DNA relaxases and nick regions from a variety of DNA transfer systems. Nucleic Acids Res. 19:3455.
30. Pansegrau, W., and E. Lanka. 1996. Enzymology of DNA transfer by conjugative mechanisms. Prog. Nucleic Acid Res. Mol. Biol. 54:197-251.
31. Pansegrau, W., E. Lanka, P. T. Barth, D. H. Figurski, D. G. Guiney, D. Haas, D. R. Helinski, H. Schwab, V. A. Stanisich, and C. M. Thomas. 1994. Complete nucleotide sequence of Birmingham IncPα plasmids: compilation and comparative analysis. J. Mol. Biol. 239:623-663.
32. VIM-1-containing integron carrying a new aminoglycoside phosphotransferase gene cassette. Antimicrob. Agents Chemother. 45:1249-1253.
33. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
34. Schmidt-Eisenlohr, H., N. Domke, and C. Baron. 1999. TraC of IncN plasmid pKM101 associates with membranes and extracellular high-molecular-weight structures in Escherichia coli. J. Bacteriol. 181:5563-5571. (Pubitemid 29437125)
35. Simon, R. 1984. High frequency mobilization of gram-negative bacterial replicons by the in vitro constructed Tn5-mob transposon. Mol. Gen. Genet. 196:413-420.
36. Skorupski, K., and R. K. Taylor. 1996. Positive selection vectors for allelic exchange. Gene 169:47-52. (Pubitemid 26075696)
37. Skulj, M., V. Okrslar, S. Jalen, S. Jevsevar, P. Slanc, B. Strukelj, and V. Menart. 2008. Improved determination of plasmid copy number using quantitative real-time PCR for monitoring fermentation processes. Microb. Cell Fact. 7:6.
38. Uraji, M., K. Suzuki, and K. Yoshida. 2002. A novel plasmid curing method using incompatibility of plant pathogenic Ti plasmids in Agrobacterium tumefaciens. Genes Genet. Syst. 77:1-9.
39. Vedler, E., M. Vahter, and A. Heinaru. 2004. The completely sequenced plasmid pEST4011 contains a novel IncP1 backbone and a catabolic transposon harboring tfd genes for 2,4-dichlorophenoxyacetic acid degradation. J. Bacteriol. 186:7161-7174.
40. Wold, M. S. 1997. Replication protein A: a heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism. Annu. Rev. Biochem. 66:61-92.
41. Woodgate, R., and S. G. Sedgwick. 1992. Mutagenesis induced by bacterial UmuDC proteins and their plasmid homologues. Mol. Microbiol. 6:2213-2218.
42. Wübbeler, J. H., T. Lutke-Eversloh, S. Van Trappen, P. Vandamme, and A. Steinbuchel. 2006. Tetrathiobacter mimigardefordensis sp. nov., isolated from compost, a betaproteobacterium capable of utilizing the organic disulfide 3,3′-dithiodipropionic acid. Int. J. Syst. Evol. Microbiol. 56:1305-1310.
43. Wyka, I. M., K. Dhar, S. K. Binz, and M. S. Wold. 2003. Replication protein A interactions with DNA: differential binding of the core domains and analysis of the DNA interaction surface. Biochemistry 42:12909-12918. (Pubitemid 37385822)
44. Wyndham, R. C., R. K. Singh, and N. A. Straus. 1988. Catabolic instability, plasmid gene deletion and recombination in Alcaligenes sp. BR60. Arch. Microbiol. 150:237-243.
45. Ziegelin, G., J. P. Fürste, and E. Lanka. 1989. TraJ protein of plasmid RP4 binds to a 19-base pair invert sequence repetition within the transfer origin. J. Biol. Chem. 264:11989-11994.