The genome sequence of the fish pathogen Aliivibrio salmonicida strain LFI1238 shows extensive evidence of gene decay

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Hjerde, Erik ^a   Lorentzen, Marit ^a   Holden, Matthew T G ^b   Seeger, Kathy ^b   Paulsen, Steinar ^a   Bason, Nathalie ^b   Churcher, Carol ^b   Harris, David ^b   Norbertczak, Halina ^b   Quail, Michael A ^b   Sanders, Suzanne ^b   Thurston, Scott ^b   Parkhill, Julian ^b   Willassen, Nils Peder ^a   Thomson, Nicholas R ^b  

^a UNIVERSITY OF TROMSØ   (Norway)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CHITIN; BACTERIAL DNA;

ARTICLE; BACTERIAL GENETICS; CHROMOSOME ANALYSIS; CHROMOSOME REARRANGEMENT; DNA FRAGMENTATION; DNA TRANSFER; FISH; GENE FUNCTION; GENE INSERTION SEQUENCE; GENE LOSS; GENE SEQUENCE; GENETIC CODE; GENETIC IDENTIFICATION; GENOME ANALYSIS; NUCLEOTIDE SEQUENCE; PLASMID; PROTEIN SECRETION; SEQUENCE ANALYSIS; VIBRIO SALMONICIDA; ANIMAL; BACTERIAL CHROMOSOME; BACTERIAL GENOME; DNA SEQUENCE; GENETICS; GENOMICS; MICROBIOLOGY; SEQUENCE ALIGNMENT; TRANSPOSON;

NEGIBACTERIA; VIBRIONACEAE;

ANIMALS; CHROMOSOMES, BACTERIAL; DNA TRANSPOSABLE ELEMENTS; DNA, BACTERIAL; FISHES; GENOME, BACTERIAL; GENOMICS; PLASMIDS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; VIBRIO SALMONICIDA;

EID: 59449093840     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-616     Document Type: Article

References (78)

1. Schrøder MB Espelid S Jørgensen TØ Two serotype of Vibrio salmonicida isolated from diseased cod (Gadus morhua L.); virulence, immunological studies and advanced experiments Fish & Shellfish Immunology 1992, 2:211-221.
2. Hjeltnes B Andersen K Egidius E Multiple antibiotic resistance in Vibrio salmonicida Bulletin of the European Association of Fish Pathologists 1987, 7:4-85.
3. Colquhoun DJ Vibrio salmonicida, the causative agent of cold-water vibriosis: Factors relating to pathogenesis and vaccine protection Oslo: The Norwegian School of Veterinary Medicine 2002.
4. Poppe TT Håstein T Salte R "Hitra Disease" (Haemorrhagic Syndrome) in Norwegian Salmon Farming: Present Status Fish & Shellfish Pathology 1985, 223-229.
5. Statistisk Sentralbyrå. Statistics Norway http://www.ssb.no/
6. Midtlyng PJ Lillehaug A Growth of Atlantic salmon Salmo salar after intraperitoneal administration of vaccines containing adjuvants Dis Aquat Organ 1998, 32(2):91-97. 9696628
7. Midtlyng PJ A field study on intraperitoneal vaccination of Atlantic salmon (Salmo salarL.) against furunculosis Fish & Shellfish Immunology 1996, 6(8):553-565.
8. Riemann L Azam F Widespread N-acetyl-D-glucosamine uptake among pelagic marine bacteria and its ecological implications Appl Environ Microbiol 2002, 68(11):5554-5562. 129920 12406749
9. Thompson FL Iida T Swings J Biodiversity of vibrios Microbiol Mol Biol Rev 2004, 68(3):403-431. 515257 15353563
10. Okada K Iida T Kita-Tsukamoto K Honda T Vibrios commonly possess two chromosomes J Bacteriol 2005, 187(2):752-757. 543535 15629946
11. Heidelberg JF Eisen JA Nelson WC Clayton RA Gwinn ML Dodson RJ Haft DH Hickey EK Peterson JD Umayam L Gill SR Nelson KE Read TD Tettelin H Richardson D Ermolaeva MD Vamathevan J Bass S Qin H Dragoi I Sellers P McDonald L Utterback T Fleishmann RD Nierman WC White O Salzberg SL Smith HO Colwell RR Mekalanos JJ Venter JC Fraser CM DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae Nature 2000, 406(6795):477-483. 10952301
12. Reen FJ Almagro-Moreno S Ussery D Boyd EF The genomic code: Inferring Vibrionaceae niche specialization Nat Rev Microbiol 2006, 4(9):697-704. 16894340
13. Thompson FL Gevers D Thompson CC Dawyndt P Naser S Hoste B Munn CB Swings J Phylogeny and molecular identification of vibrios on the basis of multilocus sequence analysis Appl Environ Microbiol 2005, 71(9):5107-5115. 1214639 16151093
14. Urbanczyk H Ast JC Higgins MJ Carson J Dunlap PV Reclassification of Vibrio fischeri, Vibrio logei, Vibrio salmonicida and Vibrio wodanis as Aliivibrio fischeri gen. nov., comb. nov., Aliivibrio logei comb. nov., Aliivibrio salmonicida comb. nov. and Aliivibrio wodanis comb. nov Int J Syst Evol Microbiol 2007, 57(Pt 12):2823-2829. 18048732
15. Sørum H Myhr E Zwicker BM Lillehaug A Comparison by plasmid profiling of Vibrio salmonicida strains isolated from diseased fish from different North European and Canadian areas of the Atlantic Ocean Canadian Journal of Fish Aquatic Science 1993, 50:247-250.
16. Sørum H Hvaal AB Heum M Daae FL Wiik R Plasmid profiling of Vibrio salmonicida for epidemiological studies of cold-water vibriosis in Atlantic salmon (Salmo salar) and cod (Gadus morhua) Appl Environ Microbiol 1990, 56(4):1033-1037. 184339 2160218
17. Chen CY Wu KM Chang YC Chang CH Tsai HC Liao TL Liu YM Chen HJ Shen AB Li JC Su TL Shao CP Lee CT Hor LI Tsai SF Comparative genome analysis of Vibrio vulnificus, a marine pathogen Genome Res 2003, 13(12):2577-2587. 403799 14656965
18. Ruby EG Urbanowski M Campbell J Dunn A Faini M Gunsalus R Lostroh P Lupp C McCann J Millikan D Schaefer A Stabb E Stevens A Visick K Whistler C Greenberg EP Complete genome sequence of Vibrio fischeri: A symbiotic bacterium with pathogenic congeners Proc Natl Acad Sci USA 2005, 102(8):3004-3009. 549501 15703294
19. Slauch JM Mahan MJ Michetti P Neutra MR Mekalanos JJ Acetylation (O-factor 5) affects the structural and immunological properties of Salmonella typhimurium lipopolysaccharide O antigen Infect Immun 1995, 63(2):437-441. 173014 7529745
20. Ahmad R Hjerde E Hansen GA Haugen P Willassen NP Prediction and Experimental Testing of Ferric Uptake Regulator Regulons in Vibrios J Mol Microbiol Biotechnol 2008. 18431050
21. Valla S Frydenlund K Coucheron DH Haugan K Johansen B Jorgensen T Knudsen G Strom A Development of a gene transfer system for curing of plasmids in the marine fish pathogen Vibrio salmonicida Appl Environ Microbiol 1992, 58(6):1980-1985. 195713 1622274
22. IS Finder database http://www-is.biotoul.fr/is.html
23. Sharp PM Li WH The codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential applications Nucleic Acids Res 1987, 15(3):1281-1295. 340524 3547335
24. Karlin S Mrazek J Campbell AM Codon usages in different gene classes of the Escherichia coli genome Mol Microbiol 1998, 29(6):1341-1355. 9781873
25. Rocha EP Danchin A Viari A Universal replication biases in bacteria Mol Microbiol 1999, 32(1):11-16. 10216855
26. Parkhill J Sebaihia M Preston A Murphy LD Thomson N Harris DE Holden MT Churcher CM Bentley SD Mungall KL Cerdeno-Tarraga AM Temple L James K Harris B Quail MA Achtman M Atkin R Baker S Basham D Bason N Cherevach I Chillingworth T Collins M Cronin A Davis P Doggett J Feltwell T Goble A Hamlin N Hauser H Holroyd S Jagels K Leather S Moule S Norberczak H O'Neil S Ormond D Price C Rabbinowitsch E Rutter S Sanders M Saunders D Seeger K Sharp S Simmonds M Skelton J Squares R Squares S Stevens K Unwin L Whitehead S Barrell BG Maskell DJ Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica Nat Genet 2003, 35(1):32-40. 12910271
27. Rocha EP Danchin A Gene essentiality determines chromosome organisation in bacteria Nucleic Acids Res 2003, 31(22):6570-6577. 275555 14602916
28. Parkhill J Wren BW Thomson NR Titball RW Holden MT Prentice MB Sebaihia M James KD Churcher C Mungall KL Baker S Basham D Bentley SD Brooks K Cerdeno-Tarraga AM Chillingworth T Cronin A Davies RM Davis P Dougan G Feltwell T Hamlin N Holroyd S Jagels K Karlyshev AV Leather S Moule S Oyston PC Quail M Rutherford K Simmonds M Skelton J Stevens K Whitehead S Barrell BG Genome sequence of Yersinia pestis, the causative agent of plague Nature 2001, 413(6855):523-527. 11586360
29. Dobrindt U Hochhut B Hentschel U Hacker J Genomic islands in pathogenic and environmental microorganisms Nat Rev Microbiol 2004, 2(5):414-424. 15100694
30. Kapfhammer D Blass J Evers S Reidl J Vibrio cholerae phage K139: complete genome sequence and comparative genomics of related phages J Bacteriol 2002, 184(23):6592-6601. 135448 12426348
31. Li Q Hobbs M Reeves PR The variation of dTDP-L-rhamnose pathway genes in Vibrio cholerae Microbiology 2003, 149(Pt 9):2463-2474. 12949172
32. Nesper J Kraiss A Schild S Blass J Klose KE Bockemuhl J Reidl J Comparative and genetic analyses of the putative Vibrio cholerae lipopolysaccharide core oligosaccharide biosynthesis (wav) gene cluster Infect Immun 2002, 70(5):2419-2433. 127954 11953379
33. Corn PG Anders J Takala AK Kayhty H Hoiseth SK Genes involved in Haemophilus influenzae type b capsule expression are frequently amplified J Infect Dis 1993, 167(2):356-364. 8421169
34. Espelid S Holm KO Hjemeland K Jørgensen T Monoclonal antibodies against Vibrio salmonicida: The causative agent of coldwater vibriosis (Hitra disease) in Atlantic salmon, Salmo salar L J Fish Dis 1988, 11:207-214.
35. Hjelmeland K Stenvåg K Jørgensen TØ Espelid S Isolation and characterization of a surface layer antigen from Vibrio salmonicida Journal of Fish Diseases 1988, 11:197-205.
36. Montgomery MT Kirchman DL Role of Chitin-Binding Proteins in the Specific Attachment of the Marine Bacterium Vibrio harveyi to Chitin Appl Environ Microbiol 1993, 59(2):373-379. 202115 16348865
37. Pruzzo C Crippa A Bertone S Pane L Carli A Attachment of Vibrio alginolyticus to chitin mediated by chitin-binding proteins Microbiology 1996, 142(Pt 8):2181-2186. 8760933
38. Garay E Arnau A Amaro C Incidence of Vibrio cholerae and related vibrios in a coastal lagoon and seawater influenced by lake discharges along an annual cycle Appl Environ Microbiol 1985, 50(2):426-430. 238637 4051487
39. Hunt DE Gevers D Vahora NM Polz MF Conservation of the chitin utilization pathway in the Vibrionaceae Appl Environ Microbiol 2008, 74(1):44-51. 2223224 17933912
40. Meibom KL Li XB Nielsen AT Wu CY Roseman S Schoolnik GK The Vibrio cholerae chitin utilization program Proc Natl Acad Sci USA 2004, 101(8):2524-2529. 356983 14983042
41. Orikoshi H Nakayama S Miyamoto K Hanato C Yasuda M Inamori Y Tsujibo H Roles of four chitinases (chia, chib, chic, and chid) in the chitin degradation system of marine bacterium Alteromonas sp. strain O-7 Appl Environ Microbiol 2005, 71(4):1811-1815. 1082530 15812005
42. Svitil AL Kirchman DL A chitin-binding domain in a marine bacterial chitinase and other microbial chitinases: Implications for the ecology and evolution of 1,4-beta-glycanases Microbiology 1998, 144(Pt 5):1299-1308. 9611805
43. Keyhani NO Li XB Roseman S Chitin catabolism in the marine bacterium Vibrio furnissii. Identification and molecular cloning of a chitoporin J Biol Chem 2000, 275(42):33068-33076. 10913115
44. Keyhani NO Roseman S The chitin catabolic cascade in the marine bacterium Vibrio furnissii. Molecular cloning, isolation, and characterization of a periplasmic chitodextrinase J Biol Chem 1996, 271(52):33414-33424. 8969204
45. Li X Roseman S The chitinolytic cascade in Vibrios is regulated by chitin oligosaccharides and a two-component chitin catabolic sensor/ kinase Proc Natl Acad Sci USA 2004, 101(2):627-631. 327198 14699052
46. Farabaugh PJ Programmed translational frameshifting Microbiol Rev 1996, 60(1):103-134. 239420 8852897
47. Torres-Cruz J Woude van der MW Slipped-strand mispairing can function as a phase variation mechanism in Escherichia coli J Bacteriol 2003, 185(23):6990-6994. 262711 14617664
48. Milton DL Quorum sensing in vibrios: Complexity for diversification Int J Med Microbiol 2006, 296(2-3):61-71. 16487746
49. Bassler BL Wright M Showalter RE Silverman MR Intercellular signalling in Vibrio harveyi: Sequence and function of genes regulating expression of luminescence Mol Microbiol 1993, 9(4):773-786. 8231809
50. Faruque SM Albert MJ Mekalanos JJ Epidemiology, genetics, and ecology of toxigenic Vibrio cholerae Microbiol Mol Biol Rev 1998, 62(4):1301-1314. 98947 9841673
51. Zhang XH Austin B Haemolysins in Vibrio species J Appl Microbiol 2005, 98(5):1011-1019. 15836469
52. Miyoshi S Narukawa H Tomochika K Shinoda S Actions of Vibrio vulnificus metalloprotease on human plasma proteinase-proteinase inhibitor systems: a comparative study of native protease with its derivative modified by polyethylene glycol Microbiol Immunol 1995, 39(12):959-966. 8789055
53. Tomich M Planet PJ Figurski DH The tad locus: Postcards from the widespread colonization island Nat Rev Microbiol 2007, 5(5):363-375. 17435791
54. Pukatzki S Ma AT Sturtevant D Krastins B Sarracino D Nelson WC Heidelberg JF Mekalanos JJ Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system Proc Natl Acad Sci USA 2006, 103(5):1528-1533. 1345711 16432199
55. Rodkhum C Hirono I Crosa JH Aoki T Four novel hemolysin genes of Vibrio anguillarum and their virulence to rainbow trout Microb Pathog 2005, 39(4):109-119. 16126365
56. Andersen C Channel-tunnels: Outer membrane components of type I secretion systems and multidrug efflux pumps of Gram-negative bacteria Rev Physiol Biochem Pharmacol 2003, 147:122-165. 12783268
57. Winkelmann G Schmid DG Nicholson G Jung G Colquhoun DJ Bisucaberin - a dihydroxamate siderophore isolated from Vibrio salmonicida, an important pathogen of farmed Atlantic salmon (Salmo salar) Biometals 2002, 15(2):153-160. 12046923
58. Mourino S Osorio CR Lemos ML Characterization of heme uptake cluster genes in the fish pathogen Vibrio anguillarum J Bacteriol 2004, 186(18):6159-6167. 515166 15342586
59. Seliger SS Mey AR Valle AM Payne SM The two TonB systems of Vibrio cholerae: Redundant and specific functions Mol Microbiol 2001, 39(3):801-812. 11169119
60. Stork M Di Lorenzo M Mourino S Osorio CR Lemos ML Crosa JH Two tonB systems function in iron transport in Vibrio anguillarum, but only one is essential for virulence Infect Immun 2004, 729(12):7326-7329. 529167 15557661
61. Schell MA Ulrich RL Ribot WJ Brueggemann EE Hines HB Chen D Lipscomb L Kim HS Mrazek J Nierman WC Deshazer D Type VI secretion is a major virulence determinant in Burkholderia mallei Mol Microbiol 2007, 64(6):1466-1485. 17555434
62. Planet PJ Kachlany SC Fine DH DeSalle R Figurski DH The Widespread Colonization Island of Actinobacillus actinomycetemcomitans Nat Genet 2003, 34(2):193-198. 12717435
63. Cole ST Eiglmeier K Parkhill J James KD Thomson NR Wheeler PR Honore N Garnier T Churcher C Harris D Mungall K Basham D Brown D Chillingworth T Connor R Davies RM Devlin K Duthoy S Feltwell T Fraser A Hamlin N Holroyd S Hornsby T Jagels K Lacroix C Maclean J Moule S Murphy L Oliver K Quail MA Rajandream MA Rutherford KM Rutter S Seeger K Simon S Simmonds M Skelton J Squares R Squares S Stevens K Taylor K Whitehead S Woodward JR Barrell BG Massive gene decay in the leprosy bacillus Nature 2001, 409(6823):1007-1011. 11234002
64. Siguier P Filee J Chandler M Insertion sequences in prokaryotic genomes Curr Opin Microbiol 2006, 9(5):526-531. 16935554
65. Parkhill J Dougan G James KD Thomson NR Pickard D Wain J Churcher C Mungall KL Bentley SD Holden MT Sebaihia M Baker S Basham D Brooks K Chillingworth T Connerton P Cronin A Davis P Davies RM Dowd L White N Farrar J Feltwell T Hamlin N Haque A Hien TT Holroyd S Jagels K Krogh A Larsen TS Leather S Moule S O'Gaora P Parry C Quail M Rutherford K Simmonds M Skelton J Stevens K Whitehead S Barrell BG Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18 Nature 2001, 413(6858):848-852. 11677608
66. Rutherford K Parkhill J Crook J Horsnell T Rice P Rajandream MA Barrell B Artemis: Sequence visualization and annotation Bioinformatics 2000, 16(10):944-945. 11120685
67. Frishman D Mironov A Mewes HW Gelfand M Combining diverse evidence for gene recognition in completely sequenced bacterial genomes Nucleic Acids Res 1998, 26(12):2941-2947. 147632 9611239
68. Delcher AL Harmon D Kasif S White O Salzberg SL Improved microbial gene identification with GLIMMER Nucleic Acids Res 1999, 27(23):4636-4641. 148753 10556321
69. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool J Mol Biol 1990, 215(3):403-410. 2231712
70. Pearson WR Lipman DJ Improved tools for biological sequence comparison Proc Natl Acad Sci USA 1988, 85(8):2444-2448. 280013 3162770
71. Bateman A Birney E Cerruti L Durbin R Etwiller L Eddy SR Griffiths-Jones S Howe KL Marshall M Sonnhammer EL The Pfam protein families database Nucleic Acids Res 2002, 30(1):276-280. 99071 11752314
72. Falquet L Pagni M Bucher P Hulo N Sigrist CJ Hofmann K Bairoch A The PROSITE database, its status in 2002 Nucleic Acids Res 2002, 30(1):235-238. 99105 11752303
73. Krogh A Larsson B von Heijne G Sonnhammer EL Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes J Mol Biol 2001, 305(3):567-580. 11152613
74. Nielsen H Engelbrecht J Brunak S von Heijne G A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites Int J Neural Syst 1997, 8(5-6):581-599. 10065837
75. Griffiths-Jones S Bateman A Marshall M Khanna A Eddy SR Rfam: An RNA family database Nucleic Acids Res 2003, 31(1):439-441. 165453 12520045
76. Vernikos GS Parkhill J Interpolated variable order motifs for identification of horizontally acquired DNA: Revisiting the Salmonella pathogenicity islands Bioinformatics 2006, 22(18):2196-2203. 16837528
77. Carver TJ Rutherford KM Berriman M Rajandream MA Barrell BG Parkhill J ACT: The Artemis Comparison Tool Bioinformatics 2005, 21(16):3422-3423. 15976072
78. MultiFun. Cellfunction assignment schema http://genprotec.mbl.edu/files/ MultiFun.html