The complete genome of Teredinibacter turnerae T7901: An intracellular endosymbiont of marine wood-boring bivalves (shipworms)

PLoS ONE

Volumn 4, Issue 7, 2009, Pages

  Yang, Joyce C ^a   Madupu, Ramana ^b   Durkin, A Scott ^b   Ekborg, Nathan A ^a,n   Pedamallu, Chandra S ^d   Hostetler, Jessica B ^b   Radune, Diana ^b   Toms, Bradley S ^b   Henrissat, Bernard ^e   Coutinho, Pedro M ^e   Schwarz, Sandra ^f   Field, Lauren ^d   Trindade Silva, Amaro E ^g   Soares, Carlos A G ^g   Elshahawi, Sherif ^h   Hanora, Amro ⁱ   Schmidt, Eric W ^j   Haygood, Margo G ^h   Posfai, Janos ^d   Benner, Jack ^d   Madinger, Catherine ^d   Nove, John ^a   Anton, Brian ^d   Chaudhary, Kshitiz ^d   Foster, Jeremy ^d   Holman, Alex ^d   Kumar, Sanjay ^d   Lessard, Philip A ^c,n   Luyten, Yvette A ^a,d   Slatko, Barton ^d   Wood, Nicole ^a   Wu, Bo ^d   Teplitski, Max ^k   Mougous, Joseph D ^f   Ward, Naomi ^l   Eisen, Jonathan A ^m   Badger, Jonathan H ^b   Distel, Daniel L ^a   more..

^a Ocean Genome Legacy   (United States)

^b J CRAIG VENTER INSTITUTE   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^d NEW ENGLAND BIOLABS   (United States)

^e AIX MARSEILLE UNIVERSITY   (France)

^f UNIVERSITY OF WASHINGTON   (United States)

^g FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^h OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

ⁱ Suez Canal University   (Egypt)

^j UNIVERSITY OF UTAH   (United States)

^k UNIVERSITY OF FLORIDA   (United States)

^l UNIVERSITY OF WYOMING   (United States)

^m UNIVERSITY OF CALIFORNIA   (United States)

ⁿ Agrivida Inc   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; CELLULASE; NITROGEN; NITROGENASE; POLYSACCHARIDE;

ALGA; ARTICLE; BACTERIAL GENOME; BIOFUEL PRODUCTION; BIVALVE; CARBOHYDRATE METABOLISM; DIGESTION; ECOLOGICAL NICHE; ENDOSYMBIONT; ENDOSYMBIOSIS; ENZYME ACTIVITY; EVOLUTIONARY ADAPTATION; FUNGUS; GENE SEQUENCE; GENETIC ANALYSIS; GILL; HOST; MARINE BACTERIUM; MARINE ENVIRONMENT; MARINE SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PLANT; PROTEIN BINDING; PROTEIN STRUCTURE; PROTEOBACTERIA; SACCHAROPHAGUS DEGRADANS; SEQUENCE ANALYSIS; SPECIES COMPARISON; TEREDINIBACTER TURNERAE; WOOD; ANIMAL; BIOLOGY; CLASSIFICATION; ELECTROSPRAY MASS SPECTROMETRY; ENZYMOLOGY; GENETICS; MARINE BIOLOGY; METABOLISM; MICROBIOLOGY; PHYLOGENY; PHYSIOLOGY; QUORUM SENSING; SYMBIOSIS; TANDEM MASS SPECTROMETRY;

ALGAE; BACTERIA (MICROORGANISMS); BIVALVIA; PROTEOBACTERIA; SACCHAROPHAGUS DEGRADANS 2-40; TEREDINIBACTER TURNERAE; TEREDINIDAE;

ANIMALS; BIVALVIA; COMPUTATIONAL BIOLOGY; GENOME, BACTERIAL; MARINE BIOLOGY; NITROGEN; PHYLOGENY; POLYSACCHARIDES; PROTEOBACTERIA; QUORUM SENSING; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; SYMBIOSIS; TANDEM MASS SPECTROMETRY; WOOD;

EID: 67749097789     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0006085     Document Type: Article

References (104)

1. Waterbury JB, Calloway CB, Turner RD (1983) A Cellulolytic nitrogen-fixing bacterium cultured from the gland of Deshayes in hipworms (Bivalvia: Teredinidae). Science 221: 1401-1403.
2. Distel DL, Morrill W, MacLaren-Toussaint N, Franks D, Waterbury J (2002) Teredinibacter turnerae gen. nov., sp. nov., a dinitrogen-fixing, cellulolytic, endosymbiotic gamma-proteobacterium isolated from the gills of wood-boring molluscs (Bivalvia: Teredinidae). Int J Syst Evol Microbiol 52: 2261-2269.
3. Distel DL, Beaudoin DJ, Morrill W (2002) Coexistence of multiple proteobacterial endosymbionts in the gills of the wood-boring Bivalve Lyrodus pedicellatus (Bivalvia: Teredinidae). Appl Environ Microbiol 68: 6292-6299.
4. Luyten YA, Thompson JR, Morrill W, Polz MF, Distel DL (2006) Extensive variation in intracellular symbiont community composition among members of a single population of the wood-boring bivalve Lyrodus pedicellatus (Bivalvia: Teredinidae). Appl Environ Microbiol 72: 412-417.
5. Gallager SM, Turner RD, Berg CJ (1981) Physiological aspects of wood consumption, growth, and reproduction in the shipworm Lyrodus pedicellatus Quatrefages. Journal of Experimental Marine Biology and Ecology 52: 63-77.
6. Lechene CP, Luyten Y, McMahon G, Distel DL (2007) Quantitative imaging of nitrogen fixation by individual bacteria within animal cells. Science 317: 1563-1566.
7. Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS (2002) Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 66: 506-577, table of contents.
8. Clarke AJ (1997) Biodegradation of cellulose: enzymology and biotechnology. Lancaster, PA: Technomic Publishing Co. 272 p.
9. Wernegreen JJ (2005) For better or worse: genomic consequences of intracellular mutualism and parasitism. Curr Opin Genet Dev 15: 572-583.
10. Weiner RM, Taylor LE 2nd, Henrissat B, Hauser L, Land M, et al. (2008) Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T. PLoS Genet 4: e1000087.
11. Haygood MG, Davidson SK (1997) Small-subunit rRNA genes and in situ hybridization with oligonucleotides specific for the bacterial symbionts in the larvae of the bryozoan Bugula neritina and proposal of " Candidatus endobugula sertula". Appl Environ Microbiol 63: 4612-4616.
12. Davidson SK, Allen SW, Lim GE, Anderson CM, Haygood MG (2001) Evidence for the biosynthesis of bryostatins by the bacterial symbiont "Candidatus Endobugula sertula" of the bryozoan Bugula neritina. Appl Environ Microbiol 67: 4531-4537.
13. Lopanik N, Gustafson KR, Lindquist N (2004) Structure of bryostatin 20: a symbiont-produced chemical defense for larvae of the host bryozoan, Bugula neritina. J Nat Prod 67: 1412-1414.
14. Lopanik N, Lindquist N, Targett N (2004) Potent cytotoxins produced by a microbial symbiont protect host larvae from predation. Oecologia 139: 131-139.
15. Sudek S, Lopanik NB, Waggoner LE, Hildebrand M, Anderson C, et al. (2007) Identification of the putative bryostatin polyketide synthase gene cluster from "Candidatus Endobugula sertula", the uncultivated microbial symbiont of the marine bryozoan Bugula neritina. J Nat Prod 70: 67-74.
16. DeBoy RT, Mongodin EF, Fouts DE, Tailford LE, Khouri H, et al. (2008) Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus. J Bacteriol 190: 5455-5463.
17. Jeong H, Yim JH, Lee C, Choi SH, Park YK, et al. (2005) Genomic blueprint of Hahella chejuensis, a marine microbe producing an algicidal agent. Nucleic Acids Res 33: 7066-7073.
18. Stewart FJ, Cavanaugh CM (2007) Intragenomic variation and evolution of the internal transcribed spacer of the rRNA operon in bacteria. J Mol Evol 65: 44-67.
19. Ekborg NA, Taylor LE, Longmire AG, Henrissat B, Weiner RM, et al. (2006) Genomic and proteomic analyses of the agarolytic system expressed by Saccharophagus degradans 2-40. Appl Environ Microbiol 72: 3396-3405.
20. Howard MB, Ekborg NA, Taylor LE, Weiner RM, Hutcheson SW (2003) Genomic analysis and initial characterization of the chitinolytic system of Microbulbifer degradans strain 2-40. J Bacteriol 185: 3352-3360.
21. Taylor LE 2nd, Henrissat B, Coutinho PM, Ekborg NA, Hutcheson SW, et al. (2006) Complete cellulase system in the marine bacterium Saccharophagus degradans strain 2-40T. J Bacteriol 188: 3849-3861.
22. Warnecke F, Luginbuhl P, Ivanova N, Ghassemian M, Richardson TH, et al. (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450: 560-565.
23. Ekborg NA, Morrill W, Burgoyne AM, Li L, Distel DL (2007) CelAB, a multifunctional cellulase encoded by Teredinibacter turnerae T7902T, a culturable symbiont isolated from the wood-boring marine bivalve Lyrodus pedicellatus. Appl Environ Microbiol 73: 7785-7788.
24. Howard MB, Ekborg NA, Taylor LE 2nd, Weiner RM, Hutcheson SW (2004) Chitinase B of "Microbulbifer degradans" 2-40 contains two catalytic domains with different chitinolytic activities. J Bacteriol 186: 1297-1303.
25. Collin M, Fischetti VA (2004) A novel secreted endoglycosidase from Enterococcus faecalis with activity on human immunoglobulin G and ribonuclease B. J Biol Chem 279: 22558-22570.
26. Dekker RFH (1985) Biodegradation of the hemicelluloses. In: Higuchi T, ed. Biosynthesis and Biodegradation of Wood Components. Orlando, FL: Academic Press, Inc. pp 505-533.
27. Kosugi A, Murashima K, Doi RH (2002) Xylanase and acetyl xylan esterase activities of XynA, a key subunit of the Clostridium cellulovorans cellulosome for xylan degradation. Appl Environ Microbiol 68: 6399-6402.
28. Xie G, Bruce DC, Challacombe JF, Chertkov O, Detter JC, et al. (2007) Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii. Appl Environ Microbiol 73: 3536-3546.
29. Qi M, Jun HS, Forsberg CW (2007) Characterization and synergistic interactions of Fibrobacter succinogenes glycoside hydrolases. Appl Environ Microbiol 73: 6098-6105.
30. Berger E, Zhang D, Zverlov VV, Schwarz WH (2007) Two noncellulosomal cellulases of Clostridium thermocellum, Cel9I and Cel48Y, hydrolyse crystalline cellulose synergistically. FEMS Microbiol Lett 268: 194-201.
31. Poulsen OM, Petersen LW (1992) Degradation of microcrystalline cellulose: Synergism between different endoglucanases of Cellulomonas sp. ATCC 21399. Biotechnol Bioeng 39: 121-123.
32. Eriksson T, Karlsson J, Tjerneld F (2002) A model explaining declining rate in hydrolysis of lignocellulose substrates with cellobiohydrolase I (Cel7A) and endoglucanase I (Cel7B) of Trichoderma reesei. Appl Biochem Biotechnol 101: 41-60.
33. Warren RA, Gerhard B, Gilkes NR, Owolabi JB, Kilburn DG, et al. (1987) A bifunctional exoglucanase-endoglucanase fusion protein. Gene 61: 421-427.
34. Fierobe HP, Bayer EA, Tardif C, Czjzek M, Mechaly A, et al. (2002) Degradation of cellulose substrates by cellulosome chimeras. Substrate targeting versus proximity of enzyme components. J Biol Chem 277: 49621-49630.
35. Fierobe HP, Mingardon F, Mechaly A, Belaich A, Rincon MT, et al. (2005) Action of designer cellulosomes on homogeneous versus complex substrates: controlled incorporation of three distinct enzymes into a defined trifunctional scaffoldin. J Biol Chem 280: 16325-16334.
36. Distel DL (2003) The biology of marine wood boring bivalves and their bacterial endosymbionts. In: Goodell B, Nicholas DD, Schultz TP, eds. Wood Deterioration and Preservation. Washington: American Chemical Society Press. pp 253-271.
37. Hall J, Hazlewood GP, Huskisson NS, Durrant AJ, Gilbert HJ (1989) Conserved serine-rich sequences in xylanase and cellulase from Pseudomonas fluorescens subspecies cellulosa: internal signal sequence and unusual protein processing. Mol Microbiol 3: 1211-1219.
38. Howard MB, Ekborg NA, Taylor LE, Hutcheson SW, Weiner RM (2004) Identification and analysis of polyserine linker domains in prokaryotic proteins with emphasis on the marine bacterium Microbulbifer degradans. Protein Sci 13: 1422-1425.
39. Lee VT, Schneewind O (2001) Protein secretion and the pathogenesis of bacterial infections. Genes Dev 15: 1725-1752.
40. Ninio S, Roy CR (2007) Effector proteins translocated by Legionella pneumophila: strength in numbers. Trends Microbiol 15: 372-380.
41. Ogawa M, Handa Y, Ashida H, Suzuki M, Sasakawa C (2008) The versatility of Shigella effectors. Nat Rev Microbiol 6: 11-16.
42. Trosky JE, Liverman AD, Orth K (2008) Yersinia outer proteins: Yops. Cell Microbiol 10: 557-565.
43. Mori H, Ito K (2001) The Sec protein-translocation pathway. Trends Microbiol 9: 494-500.
44. Berks BC, Palmer T, Sargent F (2005) Protein targeting by the bacterial twin-arginine translocation (Tat) pathway. Curr Opin Microbiol 8: 174-181.
45. Rapoport TA (2007) Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes. Nature 450: 663-669.
46. Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340: 783-795.
47. Dale C, Moran NA (2006) Molecular interactions between bacterial symbionts and their hosts. Cell 126: 453-465.
48. Dale C, Young SA, Haydon DT, Welburn SC (2001) The insect endosymbiont Sodalis glossinidius utilizes a type III secretion system for cell invasion. Proc Natl Acad Sci U S A 98: 1883-1888.
49. Hubber A, Vergunst AC, Sullivan JT, Hooykaas PJ, Ronson CW (2004) Symbiotic phenotypes and translocated effector proteins of the Mesorhizobium loti strain R7A VirB/D4 type IV secretion system. Mol Microbiol 54: 561-574.
50. Aschtgen MS, Bernard CS, De Bentzmann S, Lloubes R, Cascales E (2008) SciN is an outer membrane lipoprotein required for Type VI secretion in enteroaggregative Escherichia coli. J Bacteriol.
51. Filloux A, Hachani A, Bleves S (2008) The bacterial type VI secretion machine: yet another player for protein transport across membranes. Microbiology 154: 1570-1583.
52. Enos-Berlage JL, Guvener ZT, Keenan CE, McCarter LL (2005) Genetic determinants of biofilm development of opaque and translucent Vibrio parahaemolyticus. Mol Microbiol 55: 1160-1182.
53. Parsons DA, Heffron F (2005) sciS, an icmF homolog in Salmonella enterica serovar Typhimurium, limits intracellular replication and decreases virulence. Infect Immun 73: 4338-4345.
54. Pilatz S, Breitbach K, Hein N, Fehlhaber B, Schulze J, et al. (2006) Identification of Burkholderia pseudomallei genes required for the intracellular life cycle and in vivo virulence. Infect Immun 74: 3576-3586.
55. Zheng J, Leung KY (2007) Dissection of a type VI secretion system in Edwardsiella tarda. Mol Microbiol 66: 1192-1206.
56. Pukatzki S, Ma AT, Revel AT, Sturtevant D, Mekalanos JJ (2007) Type VI secretion system translocates a phage tail spike-like protein into target cells where it cross-links actin. Proc Natl Acad Sci U S A 104: 15508-15513.
57. Van Brussel AA, Zaat SA, Cremers HC, Wijffelman CA, Pees E, et al. (1986) Role of plant root exudate and Sym plasmid-localized nodulation genes in the synthesis by Rhizobium leguminosarum of Tsr factor, which causes thick and short roots on common vetch. J Bacteriol 165: 517-522.
58. Bladergroen MR, Badelt K, Spaink HP (2003) Infection-blocking genes of a symbiotic Rhizobium leguminosarum strain that are involved in temperature-dependent protein secretion. Mol Plant Microbe Interact 16: 53-64.
59. Das S, Chaudhuri K (2003) Identification of a unique IAHP (IcmF associated homologous proteins) cluster in Vibrio cholerae and other proteobacteria through in silico analysis. In Silico Biol 3: 287-300.
60. Dudley EG, Thomson NR, Parkhill J, Morin NP, Nataro JP (2006) Proteomic and microarray characterization of the AggR regulon identifies a pheU pathogenicity island in enteroaggregative Escherichia coli. Mol Microbiol 61: 1267-1282.
61. Mougous JD, Cuff ME, Raunser S, Shen A, Zhou M, et al. (2006) A virulence locus of Pseudomonas aeruginosa encodes a protein secretion apparatus. Science 312: 1526-1530.
62. Mougous JD, Gifford CA, Ramsdell TL, Mekalanos JJ (2007) Threonine phosphorylation post-translationally regulates protein secretion in Pseudomonas aeruginosa. Nat Cell Biol 9: 797-803.
63. Pukatzki S, Ma AT, Sturtevant D, Krastins B, Sarracino D, et al. (2006) Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system. Proc Natl Acad Sci U S A 103: 1528-1533.
64. Juncker AS, Willenbrock H, Von Heijne G, Brunak S, Nielsen H, et al. (2003) Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci 12: 1652-1662.
65. Kechris KJ, Lin JC, Bickel PJ, Glazer AN (2006) Quantitative exploration of the occurrence of lateral gene transfer by using nitrogen fixation genes as a case study. Proc Natl Acad Sci U S A 103: 9584-9589.
66. Pace HC, Brenner C (2001) The nitrilase superfamily: classification, structure and function. Genome Biol 2: REVIEWS0001.
67. Podar M, Eads JR, Richardson TH (2005) Evolution of a microbial nitrilase gene family: a comparative and environmental genomics study. BMC Evol Biol 5: 42.
68. Kobayashi M, Shimizu S (2000) Nitrile hydrolases. Curr Opin Chem Biol 4: 95-102.
69. Robertson DE, Chaplin JA, DeSantis G, Podar M, Madden M, et al. (2004) Exploring nitrilase sequence space for enantioselective catalysis. Appl Environ Microbiol 70: 2429-2436.
70. Burton EO, Read HW, Pellitteri MC, Hickey WJ (2005) Identification of acylhomoserine lactone signal molecules produced by Nitrosomonas europaea strain Schmidt. Appl Environ Microbiol 71: 4906-4909.
71. Ahmer BM (2004) Cell-to-cell signalling in Escherichia coli and Salmonella enterica. Mol Microbiol 52: 933-945.
72. Federle MJ, Bassler BL (2003) Interspecies communication in bacteria. J Clin Invest 112: 1291-1299.
73. Teplitski M, Ahmer BM (2004) The control of secondary metabolism, motility, and virulence by the two-component regulatory system BarA/SirA of Salmonella and other g-proteobacteria. In: Pruss BM, ed. Global Regulatory Networks in Enteric Bacteria. Kerala, India: Research Signpost.
74. Lapouge K, Schubert M, Allain FH, Haas D (2008) Gac/Rsm signal transduction pathway of gamma-proteobacteria: from RNA recognition to regulation of social behaviour. Mol Microbiol 67: 241-253.
75. Zuber S, Carruthers F, Keel C, Mattart A, Blumer C, et al. (2003) GacS sensor domains pertinent to the regulation of exoproduct formation and to the biocontrol potential of Pseudomonas fluorescens CHA0. Mol Plant Microbe Interact 16: 634-644.
76. Bentley SD, Chater KF, Cerdenño-Tárraga AM, Challis GL, Thomson NR, et al. (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417: 141-147.
77. Ikeda H, Ishikawa J, Hanamoto A, Shinose M, Kikuchi H, et al. (2003) Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nat Biotechnol 21: 526-531.
78. Walsh CT, Liu J, Rusnak F, Sakaitani M (1990) Molecular studies on enzymes in chorismate metabolism and the enterobactin biosynthetic pathway. Chem Rev 90: 1105-1129.
79. Chen XH, Koumoutsi A, Scholz R, Eisenreich A, Schneider K, et al. (2007) Comparative analysis of the complete genome sequence of the plant growth promoting bacterium Bacillus amyloliquefaciens FZB42. Nature biotechnology 25: 1007-1014.
80. Bolotin A, Quinquis B, Sorokin A, Ehrlich SD (2005) Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 151: 2551-2561.
81. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, et al. (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315: 1709-1712.
82. Haft DH, Selengut J, Mongodin EF, Nelson KE (2005) A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput Biol 1: e60.
83. Kunin V, Sorek R, Hugenholtz P (2007) Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol 8: R61.
84. Moran NA (2002) Microbial minimalism: genome reduction in bacterial pathogens. Cell 108: 583-586.
85. Bordenstein SR, Reznikoff WS (2005) Mobile DNA in obligate intracellular bacteria. Nat Rev Microbiol 3: 688-699.
86. Plague GR, Dunbar HE, Tran PL, Moran NA (2008) Extensive proliferation of transposable elements in heritable bacterial symbionts. J Bacteriol 190: 777-779.
87. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74: 5463-5467.
88. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
89. Goldberg SM, Johnson J, Busam D, Feldblyum T, Ferriera S, et al. (2006) A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proc Natl Acad Sci U S A 103: 11240-11245.
90. Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, et al. (2000) A whole-genome assembly of Drosophila. Science 287: 2196-2204.
91. Delcher AL, Bratke KA, Powers EC, Salzberg SL (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673-679.
92. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27: 4636-4641.
93. Bramhill D, Kornberg A (1988) Duplex opening by dnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome. Cell 52: 743-755.
94. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
95. Sammut SJ, Finn RD, Bateman A (2008) Pfam 10 years on: 10,000 families and still growing. Brief Bioinform 9: 210-219.
96. Selengut JD, Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, et al. (2007) TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res 35: D260-264.
97. Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14: 755-763.
98. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20: 3551-3567.
99. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
100. Gutell RR, Larsen N, Woese CR (1994) Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol Rev 58: 10-26.
101. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
102. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, et al. (2004) Versatile and open software for comparing large genomes. Genome Biol 5: R12.
103. Shalom G, Shaw JG, Thomas MS (2007) In vivo expression technology identifies a type VI secretion system locus in Burkholderia pseudomallei that is induced upon invasion of macrophages. Microbiology 153: 2689-2699.
104. Bingle LE, Bailey CM, Pallen MJ (2008) Type VI secretion: a beginner's guide. Curr Opin Microbiol 11: 3-8.