Phylogenetic analysis of the incidence of lux gene horizontal transfer in Vibrionaceae

Journal of Bacteriology

Volumn 190, Issue 10, 2008, Pages 3494-3504

  Urbanczyk, Henryk ^a,c   Ast, Jennifer C ^a,d   Kaeding, Allison J ^a,e   Oliver, James D ^b   Dunlap, Paul V ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

^b UNIVERSITY OF NORTH CAROLINA AT CHARLOTTE   (United States)

^c NATIONAL RESEARCH INSTITUTE OF BREWING   (Japan)

^d UPPSALA UNIVERSITY   (Sweden)

^e JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

21N 12 BACTERIA; ALIIVIBRIO; ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BT 6 BACTERIA; GENETIC VARIABILITY; HORIZONTAL GENE TRANSFER; HOUSEKEEPING GENE; LUMINESCENCE; LUX GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHOTOBACTERIUM; PHOTOBACTERIUM DAMSELAE; PHOTOBACTERIUM LEIOGNATHI; PHYLOGENY; PRIORITY JOURNAL; SB 52 BACTERIA; SHEWANELLA; UNINDEXED SEQUENCE; VIBRIO; VIBRIO CHAGASII; VIBRIO HARVEYI; VIBRIO SPLENDIDUS; VIBRIONACEAE; CHEMISTRY; ENZYMOLOGY; GENETICS; MULTIGENE FAMILY; OPERON; PHYSIOLOGY;

BACTERIA (MICROORGANISMS); PHOTOBACTERIUM; PHOTOBACTERIUM DAMSELAE; PHOTOBACTERIUM LEIOGNATHI; PHOTOBACTERIUM MANDAPAMENSIS; VIBRIO; VIBRIO CHAGASII; VIBRIO HARVEYI; VIBRIO SPLENDIDUS; VIBRIO VULNIFICUS; VIBRIONACEAE;

BACTERIAL DNA; BACTERIAL PROTEIN; LUXC PROTEIN, BACTERIA; LUXR AUTOINDUCER BINDING PROTEINS; OXIDOREDUCTASE; REPRESSOR PROTEIN; TRANSACTIVATOR PROTEIN;

BACTERIAL PROTEINS; DNA, BACTERIAL; GENE TRANSFER, HORIZONTAL; LUMINESCENT MEASUREMENTS; MULTIGENE FAMILY; OPERON; OXIDOREDUCTASES; PHYLOGENY; REPRESSOR PROTEINS; TRANS-ACTIVATORS; VIBRIONACEAE;

EID: 47049083819     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.00101-08     Document Type: Article

References (62)

1. Ast, J. C., and P. V. Dunlap. 2004. Phylogenetic analysis of the lux operon distinguishes two evolutionarily distinct clades of Photobacterium leiognathi. Arch. Microbiol. 181:352-361.
2. Ast, J. C., and P. V. Dunlap. 2005. Phylogenetic resolution and habitat specificity of members of the Photobacterium phosphoreum species group. Environ. Microbiol. 7:1641-1654.
3. Ast, J. C., H. Urbanczyk, and P. V. Dunlap. 2007. Natural merodiploidy of the lux-rib operon of Photobacterium leiognathi from coastal waters of Honshu. Japan. J. Bacteriol. 189:6148-6158.
4. Ast, J. C., I. Cleenwerck, K. Engelbeen, H. Urbanczyk, F. L. Thompson, P. De Vos, and P. V. Dunlap. 2007. Photobacterium kishitanii sp. nov., a luminous marine bacterium symbiotic with deep-sea fishes. Int. J. Syst. Evol. Microbiol. 57:2073-2078.
5. Avise, J. C. 2004. Molecular markers, natural history, and evolution, 2nd ed. Sinauer Associates, Sunderland, MA.
6. Bapteste, E., Y. Boucher, J. Leigh, and W. F. Doolittle. 2004. Phylogenetic reconstruction and lateral gene transfer. Trends Microbiol. 12:406-411.
7. Baumann, P., A. L. Furniss, and J. V. Lee. 1984. Genus Vibrio Pacini 1854, p. 518-538. In N.R. Kreig and J. G. Holt (ed.), Bergey's manual of systematic bacteriology, vol. 1. Williams & Wilkins, Baltimore, MD.
8. Baumann, P., L. Baumann, and J. L. Reichelt. 1973. Taxonomy of marine bacteria: Beneckea parahaemolytica and Beneckea alginolytica. J. Bacteriol. 113:1144-1155.
9. Baumann, P., L. Baumann, and M. Mandell. 1971. Taxonomy of marine bacteria: the genus Beneckea. J. Bacteriol. 107:268-294.
10. Baumann, P., L. Baumann, S. S. Bang, and M. J. Woolkalis. 1980. Reevaluation of the taxonomy of Vibrio, Beneckea, and Photobacterium: abolition of the genus Beneckea. Curr. Microbiol. 4:127-132.
11. Berg, O. G., and C. G. Kurland. 2002. Evolution of microbial genomes: sequence acquisition and loss. Mol. Biol. Evol. 19:2265-2272.
12. Boettcher, K. J., and E. G. Ruby. 1990. Depressed light emission by symbiotic Vibrio fischeri of the sepiolid squid Euprymna scolopes. J. Bacteriol. 17:3701-3706.
13. Chatzidaki-Livanis, M., M. A. Hubbard, K. Gordon, V. J. Harwood, and A. C. Wright. 2006. Genetic distinctions among clinical and environmental strains of Vibrio vulnificus. Appl. Environ. Microbiol. 72:6136-6141.
14. Chen, C. Y., K. M. Wu, Y. C. Chang, C. H. Chang, H. C. Tsai, T. L. Liao, Y. M. Liu, H. J. Chen, A. B. Shen, J. C. Li, T. L. Su, C. P. Shao, C. T. Lee, L. I. Hor, and S. F. Tsai. 2003. Comparative genome analysis of Vibrio vulnificus, a marine pathogen. Genome Res. 13:2577-2587.
15. Daubin, V., N. A. Moran, and H. Ochman. 2003. Phylogenetics and the cohesion of bacterial genomes. Science 301:829-832.
16. Desmarchieler, P. M., and J. L. Reichelt. 1981. Phenotypic characterization of clinical and environmental isolates of Vibrio cholerae from Australia. Curr. Microbiol. 5:123-127.
17. Doolittle, W. F. 1999. Phylogenetic classification and the universal tree. Science 284:2124-2128.
18. Duchaud, E., C. Rusniok, L. Frangeul, C. Buchrieser, A. Givaudan, S. Taourit, S. Bocs, C. Boursaux-Eude, M. Chandler, J. F. Charles, E. Dassa, R. Derose, S. Derzelle, G. Freyssinet, S. Gaudriault, C. Medigue, A. Lanois, K. Powell, P. Siguier, R. Vincent, V. Wingate, M. Zouine, P. Glaser, N. Boemare, A. Danchin, and F. Kunst. 2003. The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens. Nat. Biotechnol. 21:1307-1313.
19. Dunlap, P. V., and E. P. Greenberg. 1991. Role of intercellular chemical communication in the Vibrio fischeri-monocentrid fish symbiosis, p. 219-253. In M. Dworkin (ed.), Microbial cell-cell interactions. American Society for Microbiology, Washington, DC.
20. Dunlap, P. V., and K. Kita-Tsukamoto. 2006. Luminous bacteria, p. 863-892. In M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer, and E. Stackebrandt (ed.), The prokaryotes, a handbook on the biology of bacteria, 3rd ed., vol. 2. Ecophysiology and biochemistry. Springer, New York, NY.
21. Dunlap, P. V., A. Jiemjit, J. C. Ast, M. M. Pearce, R. R. Marques, and C. R. Lavilla-Pitogo. 2004. Genomic polymorphism in symbiotic populations of Photobacterium leiognathi. Environ. Microbiol. 6:145-158.
22. Egidius, E., R. Wiik, K. Andersen, K. A. Hoff, and B. Hjeltnes. 1986. Vibrio salmonicida sp. nov., a new fish pathogen. Int. J. Syst. Bacteriol. 36:518-520.
23. Eisen, J. A. 2000. Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Curr. Opin. Genet. Dev. 10:606-611.
24. Eisen, J. A., and C. M. Fraser. 2003. Phylogenomics: intersection of evolution and genomics. Science 300:1706-1707.
25. Farris, J. S., V. A. Albert, M. Källersjö, D. Lipscomb, and A. G. Kluge. 1996. Parsimony jackknifing outperforms neighbor-joining, Cladistics 12:99-124.
26. Fidopiastis, P. M., H. Sorum, and E. G. Ruby. 1999. Cryptic luminescence in the cold-water fish pathogen Vibrio salmonicida. Arch. Microbiol. 171:205-209.
27. Forst, S., B. Dowds, N. Boemare, and E. Stackebrandt. 1997. Xenorhabdus and Photorhabdus spp.: bugs that kill bugs. Annu. Rev. Microbiol. 51:47-72.
28. Gauthier, G., B. Lafay, R. Ruimy, V. Breittmayer, J. L. Nicolas, M. Gauthier, and R. Christen. 1995. Small-subunit rRNA sequences and whole DNA relatedness concur for the reassignment of Pasteurella piscicida (Snieszko et al.) Janssen and Surgalla to the genus Photobacterium as Photobacterium damsela subsp. piscicida. Int. J. Syst. Bacteriol. 45:139-144.
29. Gogarten, J. P., W. F. Doolittle, and J. G. Lawrence. 2002. Prokaryotic evolution in light of gene transfer. Mol. Biol. Evol. 19:2226-2238.
30. Goloboff, P. A., J. S. Farris, and K. C. Nixon. 10 August 2006, revision date. TNT: tree analysis using new technology, version 1.0. http://www.zmuc.dk /public/phylogeny/TNT/.
31. Gomez-Gil, B., F. L. Thompson, C. C. Thompson, and J. Swings. 2003. Vibrio rotiferianus sp. nov., isolated from cultures of the rotifer Brachionus plicatilis. Int. J. Syst. Microbiol. 53:239-243.
32. Hendrie, M. S., W. Hodgkiss, and J. M. Shewan. 1970. The identification, taxonomy and classification of luminous bacteria. J. Gen. Microbiol. 64:151-169.
33. Kaeding, A. J., J. C. Ast, M. M. Pearce, H. Urbanczyk, S. Kimura, H. Endo, M. Nakamura, and P. V. Dunlap. 2007. Phylogenetic diversity and cosymbiosis in the bioluminescent symbioses of "Photobacterium mandapamensis". Appl. Environ. Microbiol. 73:3173-3182.
34. Kasai, S., K. Okada, A. Hoshino, T. Iida, and T. Honda. 2007. Horizontal transfer of the lux gene cluster. J. Biochem. 141:231-237.
35. Kim, Y. R., S. E. Lee, C. M. Kim, S. Y. Kim, E. K. Shin, D. H. Shin, S. S. Chung, H. E. Choy, A. Progulske-Fox, J. D. Hillman, M. Handfield, and J. H. Rhee. 2003. Characterization and pathogenic significance of Vibrio vulnificus antigens preferentially expressed in septicemic patients. Infect. Immun. 71: 5461-5471.
36. Kurland, C. G. 2000. Something for everyone: horizontal gene transfer in evolution. EMBO Rep. 1:92-95.
37. Kurland, C. G. 2005. What tangled web: barriers to rampant horizontal gene transfer. Bioessays 27:741-747.
38. Kurland, C. G., B. Canback, and O. G. Berg. 2003. Horizontal gene transfer: a critical view. Proc. Natl. Acad. Sci. USA 100:9658-9662.
39. Lawrence, J. G. 2001. Catalyzing bacterial speciation: correlating lateral transfer with genetic headroom. Syst. Biol. 50:479-496.
40. Lawrence, J. G., and H. Hendrickson. 2003. Lateral gene transfer: when will adolescence end? Mol. Microbiol. 50:739-749.
41. Lerat, E., V. Daubin, H. Ochman, and N. A. Moran. 2005. Evolutionary origins of genomic repertoires in bacteria. PLoS Biol. 3:e130.
42. Lunder, T., H. Sørum, G. Holstad, A. G. Steigerwalt, P. Mowinckel, and D. J. Brenner. 2000. Phenotypic and genotypic characterization of Vibrio viscosus sp. nov. and Vibrio wodanis sp. nov. isolated from Atlantic salmon (Salmo salar) with 'winter ulcer'. Int. J. Syst. Evol. Microbiol. 50:427-450.
43. Meighen, E. A., and R. B. Szittner. 1992. Multiple repetitive elements and organization of the lux operons of luminescent terrestrial bacteria. J. Bacteriol. 174:5371-5381.
44. Nealson, K. H. 1978. Isolation, identification and manipulation of luminous bacteria. Methods Enzymol. 57:153-166.
45. Nelson, E. J., H. S. Tunsjø, P. M. Fidopiastis, H. Sørum, and E. G. Ruby. 2007. A novel lux operon in the cryptically bioluminescent fish pathogen Vibrio salmonicida is associated with virulence. Appl. Environ. Microbiol. 73:1825-1833.
46. Ochman, H., J. G. Lawrence, and E. Groisman. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299-304.
47. Ochman, H., E. Lerat, and V. Daubin. 2005. Examining bacterial species under the specter of gene transfer and exchange. Proc. Natl. Acad. Sci. USA 102:6595-6599.
48. Oliver, J. D., D. M. Roberts, V. K. White, M. A. Dry, and L. M. Simpson. 1986. Bioluminescence in a strain of the human pathogenic bacterium Vibrio vulnificus. Appl. Environ. Microbiol. 52:1209-1211.
49. Palmer, L. M., and R. R. Colwell. 1991. Detection of luciferase gene sequence in nonluminescent Vibrio cholerae by colony hybridization and polymerase chain reaction. Appl. Environ. Microbiol. 57:1286-1293.
50. Paulsen, I. T., L. Banerjei, G. S. Myers, K. E. Nelson, R. Seshadri, T. D. Read, D. E. Fouts, J. A. Eisen, S. R. Gill, J. F. Heidelberg, H. Tettelin, R. J. Dodson, L. Umayam, L. Brinkac, M. Beanan, S. Daugherty, R. T. DeBoy, S. Durkin, J. Kolonay, R. Madupu, W. Nelson, J. Vamathevan, B. Tran, J. Upton, T. Hansen, J. Shetty, H. Khouri, T. Utterback, D. Radune, K. A. Ketchum, B. A. Dougherty, and C. M. Fraser. 2003. Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science 299: 2071-2074.
51. Perna, N. T., G. Plunkett HI, V. Burland, B. Mail, J. D. Glasner, D. J. Rose, G. F. Mayhew, P. S. Evans, J. Gregor, H. A. Kirkpatrick, G. Posfai, J. Hackett, S. Klink, A. Boutin, Y. Shao, L. Miller, E. J. Grotbeck, N. W. Davis, A. Lim, E. T. Dimalanta, K. D. Potamousis, J. Apodaca, T. S. Anantharaman, J. Lin, G. Yen, D. C. Schwartz, R. A. Welch, and F. R. Blattner. 2001. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409:529-533.
52. Poole, M. D., and J. D. Oliver. 1978. Experimental pathogenicity and mortality in ligated ileal loop studies of the newly reported halophilic lactosepositive Vibrio species. Infect. Immun. 20:126-129.
53. Ramaiah, N., J. Chun, J. Ravel, W. L. Straube, R. T. Hill, and R. R. Colwell. 2000. Detection of luciferase gene sequence in nonluminescent bacteria from Chesapeake Bay. FEMS Microbiol. Ecol. 33:27-34.
54. Reichelt, J. L., P. Baumann, and L. Baumann. 1976. Study of genetic relationships among marine species of the genera Beneckea and Photobacterium by means of in vitro DNA/DNA hybridization. Arch. Microbiol. 110:101-120.
55. Rosche, T. M., Y. Yano, and J. D. Oliver. 2005. A rapid and simple PCR analysis indicates there are two subgroups of Vibrio vulnificus which correlate with clinical or environmental isolation. Microbiol. Immunol. 49:381-389.
56. Sorek, R., Y. Zhu, C. J. Creevey, M. P. Francino, P. Bork, and E. M. Rubin. 2007. Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318:1449-1452.
57. Swofford, D. L. 2003. PAUP*: phylogenetic analysis using parsimony (*and other methods), version 4.0B10. Sinauer Associates, Sunderland, MA.
58. Tettelin, H., V. Masignani, M. J. Cieslewicz, C. Donati, D. Medini, N. L. Ward, S. V. Angiuoli, J. Crabtree, A. L. Jones, A. S. Durkin, R. T. Deboy, T. M. Davidsen, M. Mora, M. Scarselli, I. Margarit y Ros, J. D. Peterson, C. R. Hauser, J. P. Sundaram, W. C. Nelson, R. Madupu, L. M. Brinkac, R. J. Dodson, M. J. Rosovitz, S. A. Sullivan, S. Daugherty, D. H. Haft, J. Selengut, M. L. Gwinn, L. Zhou, N. Zafar, H. Khouri, D. Radune, G. Dimitrov, K. Watkins, K. J. O'Connor, S. Smith, T. R. Utterback, O. White, C. E. Rubens, G. Grandi, L. C. Madoff, D. L. Kasper, J. L. Telford, M. R. Wessels, R. Rappuoli, and C. M. Fraser. 2005. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc, Natl. Acad. Sci. USA 102:13950-13955.
59. Thompson, F. L., D. Gevers, C. C. Thompson, P. Dawyndt, S. Naser, B. Hoste, C. B. Munn, and J. Swings. 2005. Phylogeny and molecular identification of vibrios on the basis of multilocus sequence analysis. Appl. Environ. Microbiol. 71:5107-5115.
60. Thompson, F. L., C. C. Thompson, Y. Li, B. Gomez-Gil, J. Vandenberghe, B. Hoste, and J. Swings. 2003. Vibrio kanaloae sp. nov., Vibrio pomeroyi sp. nov. and Vibrio chagasii sp. nov., from sea water and marine animals. Int. J. Syst. Evol. Microbiol. 53:753-759.
61. Urbanczyk, H., J. C. Ast, M. J. Higgins, J. Carson, and P. V. Dunlap. 2007. Reclassification of Vibrio fischeri, Vibrio logei, Vibrio sahnonicida and Vibrio wodanis as Atiivibrio fischeri gen. nov., comb. nov., Aliivibrio logei comb. nov., Aliivibrio sahnonicida comb. nov., and Aliivibrio wodanis comb. nov. Int. J. Syst. Evol. Microbiol. 57:2823-2829.
62. Yang, Y., L. P. Yeh, Y. Cao, L. Baumann, P. Baumann, J. S. Tang, and B. Beaman. 1983. Characterization of marine luminous bacteria isolated off the coast of China and description of Vibrio orientalis sp. nov. Curr. Microbiol. 8:95-100.