The uncultured luminous symbiont of Anomalops katoptron (Beryciformes: Anomalopidae) represents a new bacterial genus

Molecular Phylogenetics and Evolution

Volumn 61, Issue 3, 2011, Pages 834-843

  Hendry, Tory A ^a   Dunlap, Paul V ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Anomalopidae; Bioluminescent symbiosis; Lux genes; Quorum sensing; Vibrionaceae

Indexed keywords

ANIMAL; ARTICLE; BACTERIAL GENE; BACTERIUM; CELL CULTURE; CLASSIFICATION; ESSENTIAL GENE; FISH; GENE EXPRESSION REGULATION; GENETICS; LUMINESCENCE; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OPERON; PHYLOGENY; STATISTICAL MODEL; SYMBIOSIS;

ANIMALS; BACTERIA; BASE SEQUENCE; CELLS, CULTURED; FISHES; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; GENES, ESSENTIAL; LIKELIHOOD FUNCTIONS; LUMINESCENCE; MOLECULAR SEQUENCE DATA; OPERON; PHYLOGENY; SYMBIOSIS;

ANOMALOPIDAE; ANOMALOPS KATOPTRON; BACTERIA (MICROORGANISMS); BERYCIFORMES; VIBRIO HARVEYI; VIBRIONACEAE;

EID: 80055102339     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2011.08.006     Document Type: Article

References (76)

1. Abbot P., Moran N.A. Extremely low levels of genetic polymorphism in endosymbionts (Buchnera) of aphids (Pemphigus). Mol. Ecol. 2002, 11:2649-2660.
2. Achtman M. Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens. Annu. Rev. Microbiol. 2008, 62:53-70.
3. Achtman M., Morelli G., Zhu P.X., Wirth T., Diehl I., Kusecek B., Vogler A.J., Wagner D.M., Allender C.J., Easterday W.R., Chenal-Francisque V., Worsham P., Thomson N.R., Parkhill J., Lindler L.E., Carniel E., Keim P. Microevolution and history of the plague bacillus, Yersinia pestis. Proc. Natl. Acad. Sci. USA 2004, 101:17837-17842.
4. Ast J.C., Dunlap P.V. Phylogenetic analysis of the lux operon distinguishes two evolutionarily distinct clades of Photobacterium leiognathi. Arch. Microbiol. 2004, 181:352-361.
5. Ast J.C., Dunlap P.V. Phylogenetic resolution and habitat specificity of members of the Photobacterium phosphoreum species group. Environ. Microbiol. 2005, 7:1641-1654.
6. Ast J.C., Urbanczyk H., Dunlap P.V. Natural merodiploidy of the lux-fib operon of Photobacterium leiognathi from coastal waters of Honshu. Jpn. J. Bacteriol. 2007, 189:6148-6158.
7. Ast J.C., Urbanczyk H., Dunlap P.V. Multi-gene analysis reveals previously unrecognized phylogenetic diversity in Aliivibrio. Syst. Appl. Microbiol. 2009, 32:379-386.
8. Balbi K.J., Feil E.J. The rise and fall of deleterious mutation. Res. Microbiol. 2007, 158:779-786.
9. Baldwin C.C., Johnson G.D., Paxton J.R. Protoblepharon rosenblatti, a new genus and species of flashlight fish (Beryciformes: Anomalopidae) from the tropical South Pacific, with comments on anomalopid phylogeny. Proc. Biol. Soc. Wash. 1997, 110:373-383.
10. Bassot J.-M. On the comparative morphology of some luminous organs. Bioluminescence in Progress 1966, Princeton University, Princeton, NJ. F.H. Johnson, Y. Haneda (Eds.).
11. Chatterjee J., Miyamoto C.M., Meighen E.A. Autoregulation of luxR: The Vibrio harveyi lux-operon activator functions as a repressor. Mol. Microbiol. 1996, 20:415-425.
12. Chatterjee J., Miyamoto C.M., Zouzoulas A., Lang B.F., Skouris N., Meighen E.A. MetR and CRP bind to the Vibrio harveyi lux promoters and regulate luminescence. Mol. Microbiol. 2002, 46:101-111.
13. Di Meo C.A., Wilbur A.E., Holben W.E., Feldman R.A., Vrijenhoek R.C., Cary S.C. Genetic variation among endosymbionts of widely distributed vestimentiferan tubeworms. Appl. Environ. Microbiol. 2000, 66:651-658.
14. Dunlap P.V. Bioluminescence, microbial. Encyclopedia of Microbiology 2009, 45-61. Elsevier, Oxford. M. Schaechter (Ed.).
15. Dunlap P.V., Ast J.C., Kimura S., Fukui A., Yoshino T., Endo H. Phylogenetic analysis of host-symbiont specificity and codivergence in bioluminescent symbioses. Cladistics 2007, 23:507-532.
16. Fidopiastis P.M., Miyamoto C.M., Jobling M.G., Meighen E.A., Ruby E.G. LitR, a new transcriptional activator in Vibrio fischeri, regulates luminescence and symbiotic light organ colonization. Mol. Microbiol. 2002, 45:131-143.
17. Funk D.J., Wernegreen J.J., Moran N.A. Intraspecific variation in symbiont genomes: Bottlenecks and the aphid-buchnera association. Genetics 2001, 157:477-489.
18. Harmer T.L., Rotjan R.D., Nussbaumer A.D., Bright M., Ng A.W., DeChaine E.G., Cavanaugh C.M. Free-living tube worm endosymbionts found at deep-sea vents. Appl. Environ. Microbiol. 2008, 74:3895-3898.
19. Harvey E.N. The Production of Light by the Fishes Photoblepharon and Anomalops 1922, Carnegie Institute of Washington, Washington, DC.
20. Hasegawa H., Hase C.C. TetR-type transcriptional regulator VtpR functions as a global regulator in Vibrio tubiashii. Appl. Environ. Microbiol. 2009, 75:7602-7609.
21. Hastings J.W., Nealson K. The symbiotic luminous bacteria. The Prokaryotes: A Handbook on Habitats, Isolation, and Identification of Bacteria 1981, 1332-1345. Springer-Verlag, Berlin. M.P. Starr, H. Stolp, H.G. Truper, A. Balows, H.G. Schlegel (Eds.).
22. Haygood M.G. Relationships of the luminous bacterial symbiont of the Caribbean flashlight fish, Kryptophanaron alfredi (family Anomalopidae) to other luminous bacteria based on bacterial luciferase (luxA) genes. Arch. Microbiol. 1990, 154:496-503.
23. Haygood M.G. Light organ symbioses in fishes. Crit. Rev. Microbiol. 1993, 19:191-216.
24. Haygood M.G., Distel D.L. Bioluminescent symbionts of flashlight fishes and deep-sea anglerfishes form unique lineages related to the genus Vibrio. Nature 1993, 363:154-156.
25. Haygood M.G., Tebo B.M., Nealson K.H. Luminous bacteria of a monocentrid fish (Monocentris japonicus) and 2 anomalopid fishes (Photoblepharon palpebratus and Kryptophanaron alfredi) - populations sizes and growth within the light organs, and rates of release into the seawater. Mar. Biol. 1984, 78:249-254.
26. Henke J.M., Bassler B.L. Quorum sensing regulates type III secretion in Vibrio harveyi and Vibrio parahaemolyticus. J. Bacteriol. 2004, 186:3794-3805.
27. Henke J.M., Bassler B.L. Three parallel quorum-sensing systems regulate gene expression in Vibrio harveyi. J. Bacteriol. 2004, 186:6902-6914.
28. Herring P.J., Morin J.G. Bioluminescence in fishes. Bioluminescence in Action 1978, Academic Press, London. P.J. Herring (Ed.).
29. Huelsenbeck, J.P., Ronquist, F., 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755.
30. Jaques S., McCarter L.L. Three new regulators of swarming in Vibrio parahaemolyticus. J. Bacteriol. 2006, 188:2625-2635.
31. Jobling M.G., Holmes R.K. Characterization of hapR, a positive regulator of the Vibrio cholerae HA protease gene hap, and its identification as a functional homologue of the Vibrio harveyi luxR gene. Mol. Microbiol. 1997, 26:1023-1034.
32. Johnson G.D., Rosenblatt R.H. Mechanisms of light organ occlusion in flashlight fishes, family Anomalopidae (Teleostei, Beryciformes), and the evolution of the group. Zool. J. Linn. Soc. 1988, 94:65-96.
33. Johnson G.D., Seeto J., Rosenblatt R.H. Parmops echinatus, a new species of flashlight fish (Beryciformes: Anomalopidae) from Fiji. Proc. Biol. Soc. Wash. 2001, 114:497-500.
34. Kaeding A.J., Ast J.C., Pearce M.M., Urbanczyk H., Kimura S., Endo H., Nakamura M., Dunlap P.V. Phylogenetic diversity and cosymbiosis in the bioluminescent symbioses of " Photobacterium mandapamensis" Appl. Environ. Microbiol. 2007, 73:3173-3182.
35. Kasai S., Okada K., Hoshino A., Iida T., Honda T. Lateral transfer of the lux gene cluster. J. Biochem. (Tokyo) 2007, 141:231-237.
36. Kessel M. The ultrastructure of the relationship between the luminous organ of the teleost fish Photoblepharon palpebratus and its symbiotic bacteria. Cytobiologie 1977, 15:145-158.
37. Lee D.H., Jeong H.S., Jeong H.G., Kim K.M., Kim H., Choi S.H. A consensus sequence for binding of SmcR, a Vibrio vulnificus LuxR homologue, and genome-wide identification of the SmcR regulon. J. Biol. Chem. 2008, 283:23610-23618.
38. Leisman G., Cohn D.H., Nealson K.H. Bacterial origin of luminescence in marine animals. Science 1980, 208:1271-1273.
39. Lenz D.H., Mok K.C., Lilley B.N., Kulkarni R.V., Wingreen N.S., Bassler B.L. The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell 2004, 118:69-82.
40. Lin J.W., Yu K.Y., Chao Y.F., Weng S.F. The lumQ gene is linked to the lumP gene and the lux operon in Photobacterium leiognathi. Biochem. Biophys. Res. Commun. 1995, 217:684-695.
41. Lin J.W., Chao Y.F., Weng S.F. Nucleotide sequence and functional analysis of the luxE gene encoding acyl-protein synthetase of the lux operon from Photobacterium leiognathi. Biochem. Biophys. Res. Commun. 1996, 228:764-773.
42. Maddison W.P., Maddison D.R. MacClade: Analysis of Phylogeny and Character Evolution 1992, Sinauer, Sunderland, Mass.
43. McCosker J.E., Rosenblatt R.H. Notes on the biology, taxonomy, and distribution of flashlight fishes (Beryciformes, Anomalopidae). Jpn. J. Ichthyol. 1987, 34:157-164.
44. Mead P.S., Slutsker L., Dietz V., McCaig L.F., Bresee J.S., Shapiro C., Griffin P.M., Tauxe R.V. Food-related illness and death in the United States. Emerg. Infect. Dis. 1999, 5:607-625.
45. Miller M.B., Bassler B.L. Quorum sensing in bacteria. Annu. Rev. Microbiol. 2001, 55:165-199.
46. Mira A., Moran N.A. Estimating population size and transmission bottlenecks in maternally transmitted endosymbiotic bacteria. Microb. Ecol. 2002, 44:137-143.
47. Miyamoto C.M., Sun W.Q., Meighen E.A. The LuxR regulator protein controls synthesis of polyhydroxybutyrate in Vibrio harveyi. Biochim. Biophys. Acta - Protein Struct. Mol. Enzymol. 1998, 1384:356-364.
48. Miyamoto C.M., Dunlap P.V., Ruby E.G., Meighen E.A. LuxO controls luxR expression in Vibrio harveyi: evidence for a common regulatory mechanism in Vibrio. Mol. Microbiol. 2003, 48:537-548.
49. Moran N.A. Accelerated evolution and Muller's rachet in endosymbiotic bacteria. Proc. Natl. Acad. Sci. USA 1996, 93:2873-2878.
50. Morin J.G., Harrington A., Nealson K., Krieger N., Baldwin T.O., Hastings J.W. Light for all reasons - versatility in behavioral repertoire of flashlight fish. Science 1975, 190:74-76.
51. Nyholm S.V., McFall-Ngai M.J. The winnowing: establishing the squid-Vibrio symbiosis. Nat. Rev. Microbiol. 2004, 2:632-642.
52. Pagel M. Inferring evolutionary processes from phylogenies. Zool. Scripta 1997, 26:331-348.
53. Posada D., Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
54. Price T. Correlated evolution and independent contrasts. Philos. Trans. Roy. Soc. Lond. Series B - Biol. Sci. 1997, 352:519-529.
55. Reen F.J., Almagro-Moreno S., Ussery D., Boyd E.F. The genomic code: inferring Vibrionaceae niche specialization. Nat. Rev. Microbiol. 2006, 4:697-704.
56. Rosenblatt R.H., Johnson G.D. Parmops coruscans, a new genus and species of flashlight fish (Beryciformes, Anomalopidae) from the south Pacific. Proc. Biol. Soc. Wash. 1991, 104:328-334.
57. Spaulding A.W., von Dohlen C.D. Phylogenetic characterization and molecular evolution of bacterial endosymbionts in psyllids (Hemiptera: Sternorrhyncha). Mol. Biol. Evol. 1998, 15:1506-1513.
58. Sreevatsan S., Escalante P., Pan X., Gillies D.A., Siddiqui S., Khalaf C.N., Kreiswirth B.N., Bifani P., Adams L.G., Ficht T., Perumaalla V.S., Cave M.D., VanEmbden J.D.A., Musser J.M. Identification of a polymorphic nucleotide in oxyR specific for Mycobacterium bovis. J. Clin. Microbiol. 1996, 34:2007-2010.
59. Tajima F. Simple methods for testing the molecular evolutionary clock hypothesis. Genetics 1993, 135:599-607.
60. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
61. Thompson J.D., Higgins D.G., Gibson T.J. ClustalW - improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matric choice. Nucl. Acids Res. 1994, 22:4673-4680.
62. Thompson, F.L., Iida, T., Swings, J., 2004. Biodiversity of vibrios. Microbiol. Mol. Biol. Rev. 68, 403-+.
63. Thompson F.L., Gevers D., Thompson C.C., Dawyndt P., Naser S., Hoste B., Munn C.B., Swings J. Phylogeny and molecular identification of vibrios on the basis of multilocus sequence analysis. Appl. Environ. Microbiol. 2005, 71:5107-5115.
64. Tu K.C., Waters C.M., Svenningsen S.L., Bassler B.L. A small-RNA-mediated negative feedback loop controls quorum-sensing dynamics in Vibrio harveyi. Mol. Microbiol. 2008, 70:896-907.
65. Ulitzur S., Dunlap P.V. Regulatory circuitry controlling luminescence autoinduction in Vibrio fischeri. Photochem. Photobiol. 1995, 62:625-632.
66. Urbanczyk H., Ast J.C., Kaeding A.J., Oliver J.D., Dunlap P.V. Phylogenetic analysis of the incidence of lux gene horizontal transfer in Vibrionaceae. J. Bacteriol. 2008, 190:3494-3504.
67. Van Ert, M.N., Easterday, W.R., Huynh, L.Y., Okinaka, R.T., Hugh-Jones, M.E., Ravel, J., Zanecki, S.R., Pearson, T., Simonson, T.S., U'Ren, J.M., Kachur, S.M., Leadem-Dougherty, R.R., Rhoton, S.D., Zinser, G., Farlow, J., Coker, P.R., Smith, K.L., Wang, B.X., Kenefic, L.J., Fraser-Liggett, C.M., Wagner, D.M., Keim, P., 2007. Global genetic population structure of Bacillus anthracis. Plos One 2.
68. Visick K.L., Ruby E.G. Vibrio fischeri and its host: it takes two to tango. Curr. Opin. Microbiol. 2006, 9:632-638.
69. Wada M., Azuma N., Mizuno N., Kurokura H. Transfer of symbiotic luminous bacteria from parental Leiognathus nuchalis to their offspring. Mar. Biol. 1999, 135:683-687.
70. Waters C.M., Bassler B.L. Quorum sensing: cell-to-cell communication in bacteria. Annu. Rev. Cell Dev. Biol. 2005, 21:319-346.
71. Wernegreen J.J. Genome evolution in bacterial endosymbionts of insects. Nat. Rev. Genet. 2002, 3:850-861.
72. Wernegreen J.J., Moran N.A. Evidence for genetic drift in endosymbionts (Buchnera): analyses of protein-coding genes. Mol. Biol. Evol. 1999, 16:83-97.
73. Wolfe C.J., Haygood M.G. Restriction fragment length polymorphism analysis reveals high levels of genetic divergence among the light organ symbionts of flashlight fish. Biol. Bull. 1991, 181:135-143.
74. Woolfit M., Bromham L. Increased rates of sequence evolution in endosymbiotic bacteria and fungi with small effective population sizes. Mol. Biol. Evol. 2003, 20:1545-1555.
75. Zerbino D.R., Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008, 18:821-829.
76. Zwickl D.J. Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets under the Maximum Likelihood Criterion 2006, The University of Texas, Austin, Texas.