The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2

PLoS Biology

Volumn 4, Issue 12, 2006, Pages 2196-2212

  Scott, Kathleen M ^a   Sievert, Stefan M ^b   Abril, Fereniki N ^a   Ball, Lois A ^a   Barrett, Chantell J ^a   Blake, Rodrigo A ^a   Boller, Amanda J ^a   Chain, Patrick S G ^c,d   Clark, Justine A ^a   Davis, Carisa R ^a   Detter, Chris ^d   Do, Kimberly F ^a   Dobrinski, Kimberly P ^a   Faza, Brandon I ^a   Fitzpatrick, Kelly A ^a   Freyermuth, Sharyn K ^e   Harmer, Tara L ^f   Hauser, Loren J ^g   Hügler, Michael ^b   Kerfeld, Cheryl A ^h   Klotz, Martin G ⁱ   Kong, William W ^a   Land, Miriam ^g   Lapidus, Alla ^d   Larimer, Frank W ^g   Longo, Dana L ^a   Lucas, Susan ^d   Malfatti, Stephanie A ^c,d   Massey, Steven E ^a   Martin, Darlene D ^a   McCuddin, Zoe ^j   Meyer, Folker ^k   Moore, Jessica L ^a   Ocampo Jr , Luis H ^a   Paul, John H ^l   Paulsen, Ian T ^m   Reep, Douglas K ^a   Ren, Qinghu ^m   Ross, Rachel L ^a   Sato, Priscila Y ^a   Thomas, Phaedra ^a   Tinkham, Lance E ^a   Zeruth, Gary T ^a   more..

^a UNIVERSITY OF SOUTH FLORIDA   (United States)

^b WOODS HOLE OCEANOGRAPHIC INSTITUTION   (United States)

^c LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^d DOE JOINT GENOME INSTITUTE   (United States)

^e University of Missouri   (United States)

^f RICHARD STOCKTON COLLEGE OF NEW JERSEY   (United States)

^g OAK RIDGE NATIONAL LABORATORY   (United States)

^h UNIVERSITY OF CALIFORNIA   (United States)

ⁱ UNIVERSITY OF LOUISVILLE   (United States)

^j MONSANTO COMPANY   (United States)

^k BIELEFELD UNIVERSITY   (Germany)

^l UNIVERSITY OF SOUTH FLORIDA   (United States)

^m J CRAIG VENTER INSTITUTE   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; CARBON DIOXIDE; HEAVY METAL; NITROGEN; PHOSPHATE TRANSPORTER; PHOSPHORUS; PROTEIN XCL 2; REGULATOR PROTEIN; SIGNAL PEPTIDE; PHOSPHATE;

ARTICLE; BACTERIUM ADHERENCE; CARBON DIOXIDE FIXATION; CARBON METABOLISM; CHEMOLITHOAUTOTROPH; CHEMOTAXIS; CONTROLLED STUDY; DEEP SEA SPECIES; ELECTRON TRANSPORT; GENE EXPRESSION; GENE SEQUENCE; GENE STRUCTURE; GENOME; MICROBIAL DIVERSITY; NONHUMAN; NUCLEOTIDE SEQUENCE; NUTRIENT UPTAKE; OPERON; OXIDATION REDUCTION REACTION; PROPHAGE; SULFUR OXIDIZING BACTERIUM; THIOMICROSPIRA; THIOMICROSPIRA CRUNOGENA; BACTERIAL GENOME; GENETICS; METABOLISM; MOLECULAR GENETICS; PISCIRICKETTSIACEAE; SEQUENCE ALIGNMENT; SIGNAL TRANSDUCTION;

THIOMICROSPIRA CRUNOGENA XCL-2;

BACTERIAL ADHESION; CARBON DIOXIDE; CHEMOTAXIS; GENOME, BACTERIAL; MOLECULAR SEQUENCE DATA; PHOSPHATES; PISCIRICKETTSIACEAE; PROPHAGES; SEQUENCE ALIGNMENT; SIGNAL TRANSDUCTION;

EID: 33845505324     PISSN: 15457885     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.0040383     Document Type: Article

References (114)

1. Karl DM, Wirsen CO, Jannasch HW (1980) Deep-sea primary production at the Galápagos hydrothermal vents. Science 207: 1345-1346.
2. Edwards KJ, Rogers DR, Wirsen CO, McCollom TM (2003) Isolation and characterization of novel psychrophilic, neutrophilic, Fe-oxidizing, chemolithoautotrophic alpha- and, gamma-Proteobacteria from the deep sea. Appl Environ Microbiol 69: 2906-2913.
3. Kelley DS, Karson JA, Fruh-Green GL, Yoerger DR, Shank TM, et al. (2005) A serpentinite-hosted ecosystem: The lost city hydrothermal field. Science 307: 1428-1434.
4. Johnson KS, Childress JJ, Beehler CL (1988) Short term temperature variability in the Rose Garden hydrothermal vent field. Deep-Sea Res 35: 1711-1722.
5. Goffredi SK, Childress JJ, Desaulniers NT, Lee RW, Lallier FH, et al. (1997) Inorganic carbon acquisition by the hydrothermal vent tubeworm Riftia pachyptila depends upon high external P-CO2 and upon protonequivalent ion transport by the worm. J Exp Biol 200: 883-896.
6. Jannasch H, Wirsen C, Nelson D, Robertson L (1985) Thiomicrospira crunogena sp. nov., a colorless, sulfur-oxidizing bacterium from a deep-sea hydrothermal vent. Int J Syst Bacteriol 35: 422-424.
7. Wirsen CO, Brinkhoff T, Kuever J, Muyzer G, Molyneaux S, et al. (1998) Comparison of a new Thiomicrospira strain from the Mid-Atlantic Ridge with known hydrothermal vent isolates. Appl Environ Microbiol 64: 4057-4059.
8. Muyzer G, A., Teske C.O., Wirsen , Jannasch H.W. (1995) Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch Microbiol 164: 165-172.
9. Brinkhoff T, Sievert SM, Kuever J, Muyzer G (1999) Distribution and diversity of sulfur-oxidizing Thiomicrospira spp. at a shallow-water hydrothermal vent in the Aegean Sea (Milos, Greece). Appl Environ Microbiol 65: 3843-3849.
10. Ruby EG, Wirsen CO, Jannasch HW (1981) Chemolithotrophic sulfur-oxidizing bacteria from the Galapagos Rift hydrothermal vents. Appl Environ Microbiol 42: 317-324.
11. Ruby EG, Jannasch HW (1982) Physiological characteristics of Thiomicrospira sp. strain L-12 isolated from deep-sea hydrothermal vents. J Bacteriol 149: 161-165.
12. Wirsen CO, Brinkhoff T, Kuever J, Muyzer G, Jannasch HW, et al. (1998) Comparison of a new Thiomicrospira strain from the Mid-Atlantic Ridge with known hydrothermal vent isolates. Appl Environ Microbiol 64: 4057-4059.
13. Scott KM, Bright M, Fisher CR (1998) The burden of independence: Inorganic carbon utilization strategies of the sulphur chemoautotrophic hydrothermal vent isolate Thiomicrospira crunogena and the symbionts of hydrothermal vent and cold seep vestimentiferans. Cah Biol Mar 39: 379-381.
14. Dobrinski KP, Longo DL, Scott KM (2005) A hydrothermal vent chemolithoautotroph with a carbon concentrating mechanism. J Bacteriol 187: 5761-5766.
15. Ahmad A, Barry JP, Nelson DC (1999) Phylogenetic affinity of a wide, vacuolate, nitrate-accumulating Beggiatoa sp. from Monterey Canyon, California, with Thioploca spp. Appl Environ Microbiol 65: 270-277.
16. Dufresne A, Salanoubat M, Partensky F, Artiguenave F, Axmann I, et al. (2003) Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc Natl Acad Sci U S A 100: 10020-10025.
17. Palenik B, Brahamsha B, Larimer FW, Land M, Hauser L, et al. (2003) The genome of a motile marine Synechococcus. Nature 424: 1037-1042.
18. Chain P, Lamerdin J, Larimer F, Regala W, Lao V, et al. (2003) Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. J Bacteriol 185: 2759-2773.
19. Larimer F, Chain P, Hauser L, Lamerdin J, Malfatti S, et al. (2004) Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nature Biotechnol 22: 55-61.
20. Eisen JA, Nelson KE, Paulsen IT, Heidelberg JF, Wu M, et al. (2002) The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proc Natl Acad Sci U S A 99: 9509-9514.
21. Beller HR, Chain PSG, Letain TE, Chakicherla A, Larimer FW, et al. (2006) The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans. J Bacteriol 188: 1473-1488.
22. Deckert G, Warren PV, Gaasterland T, Young WG, Lenox AL, et al. (1998) The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature 392: 353-358.
23. Lowe TM, Eddy SR (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964.
24. Casjens S (2003) Prophages and bacterial genomics: What have we learned so far? Mol Microbiol 49: 277-300.
25. Lucchini S, Desiere F, Brussow H (1999) Similarly organized lysogeny modules in temperate Siphoviridae from low GC content gram positive bacteria. Virology 263: 427-435.
26. Weigele PR, Sampson L, Winn-Stapley D, Casjens SR (2005) Molecular genetics of bacteriophage P22 scaffolding protein's functional domains. J Mol Biol 348: 831-844.
27. Sanger F, Coulson AR, Hong GF, Hill DF, Petersen GB (1982) Nucleotide sequence of bacteriophage lambda DNA. J Mol Biol 162: 729-773.
28. Rohwer F, Segall A, Steward G, Seguritan V, Breitbart M, et al. (2000) The complete genomic sequence of the marine phage Roseophage SIO1 shares homology with non-marine phages. Limnol Oceanogr 42: 408-418.
29. Sternberg N, Weisberg R (1977) Packaging of coliphage lambda DNA. II. The role of gene D protein. J Mol Biol 117: 733-759.
30. Paul JH, Sullivan MB (2005) Marine phage genomics: What have we learned? Curr Opin Biotech 16: 299-307.
31. Canchaya C, Proux C, Fournous G, Bruttin A, Brussow H (2003) Prophage genomics. Microbiol Mol Biol Rev 67: 238-276.
32. Friedrich CG, Quentmeier A, Bardischewsky F, Rother D, Kraft R, et al. (2000) Novel genes coding for lithotrophic sulfur oxidation of Paracoccus pantotrophus GB17. J Bacteriol 182: 4677-4687.
33. Rother D, Henrich HJ, Quentmeier A, Bardischewsky F, Friedrich CG (2001) Novel genes of the sox gene cluster, mutagenesis of the flavoprotein SoxF, and evidence for a general sulfur-oxidizing system in Paracoccus pantotrophus GB17. J Bacteriol 183: 4499-4508.
34. Friedrich CG, Bardischewsky F, Rother D, Quentmeier A, Fischer J (2005) Prokaryotic sulfur oxidation. Curr Opin Microbiol 8: 253-259.
35. Schutz M, Maldener I, Griesbeck C, Hauska G (1999) Sulfide-quinone reductase from Rhodobacter capsulatus: Requirement for growth, periplasmic localization, and extension of gene sequence analysis. J Bacteriol 181: 6516-6523.
36. Javor BJ, Wilmot DB, Vetter RD (1990) pH-Dependent metabolism of thiosulfate and sulfur globules in the chemolithotrophic marine bacterium Thiomicrospira crunogena. Arch Microbiol 154: 231-238.
37. Friedrich CG, Rother D, Bardischewsky F, Quentmeier A, Fischer J (2001) Oxidation of reduced inorganic sulfur compounds by bacteria: Emergence of a common mechanism? Appl Environ Microbiol 67: 2873-2882.
38. Fani R, Brilli M, Lio P (2005) The origin and evolution of operons: The piecewise building of the proteobacterial histidine operon. J Mol Evol 60: 378-390.
39. Price MN, Huang KH, Arkin AP, Alm EJ (2005) Operon formation is driven by co-regulation and not by horizontal gene transfer. Genome Res 15: 809-819.
40. Petri R, Podgorsek L, Imhoff JF (2001) Phylogeny and distribution of the soxB gene among thiosulfate-oxidizing bacteria. Fems Microbiol Lett 197: 171-178.
41. Kelly DP, Shergill JK, Lu WP, Wood AP (1997) Oxidative metabolism of inorganic sulfur compounds by bacteria. Antonie Van Leeuwenhoek Intl J Gen Mol Microbiol 71: 95-107.
42. Nelson DC, Hagen KD (1995) Physiology and biochemistry of symbiotic and free-living chemoautotrophic sulfur bacteria. Am Zool 35: 91-101.
43. Schwartz E, Friedrich B (2005) The H2-metabolizing prokaryotes. In: Dworkin M, editor. The prokaryotes: An evolving electronic resource for the microbiological community, release 3.14. New York: Springer-Verlag. Available: http://141.150.157.117:8080/prokPUB/index.htm. Accessed 28 September 2006.
44. Nishihara H, Yaguchi T, Chung SY, Suzuki K, Yanagi M, et al. (1998) Phylogenetic position of an obligately chemoautotrophic, marine hydrogen-oxidizing bacterium, Hydrogenovibrio marinus, on the basis of 16S rRNA gene sequences and two form I RubisCO gene sequences. Arch Microbiol 169: 364-368.
45. Nishihara H, Miyata Y, Miyashita Y, Bernhard M, Pohlmann A, et al. (2001) Analysis of the molecular species of hydrogenase in the cells of an obligately chemolithoautotrophic, marine hydrogen-oxidizing bacterium, Hydrogenovibrio marinus. Biosci Biotechnol Biochem 65: 2780-2784.
46. Nishihara H, Igarashi Y, Kodama T (1991) Hydrogenovibrio marinus gen. nov., sp. nov., a marine obligately chemolithoautotrophic hydrogenoxidizing bacterium. Int J Syst Bacteriol 41: 130-133.
47. Dross F, Geisler V, Lenger R, Theis F, Krafft T, et al. (1992) The quinonereactive Ni/Fe-hydrogenase of Wollinella succinogenes. Eur J Biochem 206: 93-102.
48. Friedrich T, Scheide D (2000) The respiratory complex I of bacteria, archaea and eukarya and its module common with membrane-bound multisubunit hydrogenases. FEBS Letters 479: 1-5.
49. Smith M, Finel M, Korolik V, Mendz G (2000) Characteristics of the aerobic respiratory chains of the microaerophiles Campylobacter jejuni and Helicobacter pylori. Arch Microbiol 174: 1-10.
50. Steuber J (2001) Na+ translocation by bacterial NADH:quinone oxidoreductases: An extension to the complex-I family of primary redox pumps. Biochim Biophys Acta 1505: 45-56.
51. Kumagai H, Fujiwara T, Matsubara H, Saeki K (1997) Membrane localization, topology, and mutual stabilization of the rnfABC gene products in Rhodobacter capsulatus and implications for a new family of energy-coupling NADH oxidoreductases. Biochemistry 36: 5509-5521.
52. Lange BM, Rujan T, Martin W, Croteau R (2000) Isoprenoid biosynthesis: The evolution of two ancient and distinct pathways across genomes. Proc Natl Acad Sci U S A 97: 13172-13177.
53. Hedl M, Sutherlin A, Wilding E, Mazzulla M, McDevitt D, et al. (2002) Enterococcus faecalis acetoacetyl-coenzyme A thiolase/3-hydroxy-3- methylglutaryl-coenzyme A reductase, a dual-function protein of isopentenyl diphosphate biosynthesis. J Bacteriol 184: 2116.
54. Wilding EI, Brown JR, Bryant AP, Chalker AF, Holmes DJ, et al. (2000) Identification, evolution, and essentiality of the mevalonate pathway for isopentenyl diphosphate biosynthesis in Gram-positive cocci. J Bacteriol 182: 4319-4327.
55. Humbelin M, Thomas A, Lin J, Li J, Jore J, et al. (2002) Genetics of isoprenoid biosynthesis in Paracoccus zeaxanthinifaciens. Gene 297: 129-139.
56. Preisig O, Zufferey R, Thony-Meyer L, Appleby C, Hennecke H (1996) A high-affinity cbb3-type cytochrome oxidase terminates the symbiosis-specific respiratory chain of Bradyrhizobium japonicum. J Bacteriol 178: 1532-1538.
57. Hooper AB, Arciero DM, Bergmann D, Hendrich MP (2004) The oxidation of ammonia as an energy source in bacteria. In: Zannoni D, editor. Respiration in Archaea and Bacteria. Volume 2. Dordrecht (the Netherlands): Springer. pp. 121-147.
58. Jackson JB (2003) Proton translocation by transhydrogenase. FEBS Letts 545: 18-24.
59. Boonstra B, French CE, Wainwright I, Bruce NC (1999) The udhA gene of Escherichia coli encodes a soluble pyridine nucleotide transhydrogenase. J Bacteriol 181: 1030-1034.
60. Mori S, Kawai S, Shi F, Mikami B, Murata K (2005) Molecular conversion of NAD kinase to NADH kinase through single amino acid residue substitution. J Biol Chem 280: 24104-24112.
61. Paulsen IT, Nguyen L, Sliwinski MK, Rabus R, Saier MH (2000) Microbial genome analyses: Comparative transport capabilities in eighteen prokaryotes. J Mol Biol 301: 75-100.
62. Ren Q, Paulsen IT (2005) Comparative analyses of fundamental differences in membrane transport capabilities in prokaryotes and eukaryotes. PLoS Comput Biol 1: e27. DOI: 10.1371/journal.pcbi.0010027
63. Badger MR, Price GD, Long BM, Woodger FJ (2006) The environmental plasticity and ecological genomics of the cyanobacterial CO2 concentrating mechanism. J Exp Bot 57: 249-265.
64. Smith KS, Ferry JG (2000) Prokaryotic carbonic anhydrases. FEMS Microbiol Rev 24: 335-366.
65. So AK, Espie GS, Williams EB, Shively JM, Heinhorst S, et al. (2004) A novel evolutionary lineage of carbonic anhydrase (epsilon class) is a component of the carboxysome shell. J Bacteriol 186: 623-630.
66. Sawaya MR, Cannon GC, Heinhorst S, Tanaka S, Williams EB, et al. (2006) The structure of beta-carbonic anhydrase from the carboxysomal shell reveals a distinct subclass with one active site for the price of two. J Biol Chem 281: 7546-7555.
67. Felce J, Saier MH (2004) Carbonic anhydrase fused to anion transporters of the SulP family: Evidence for a novel type of bicarbonate transporter. J Mol Microbiol Biotechnol 8: 169-176.
68. Yoshizawa Y, Toyoda K, Arai H, Ishii M, Igarashi Y (2004) CO2-responsive expression and gene organization of three ribulose-1,5-bisphosphate carboxylase/oxygenase enzymes and carboxysomes in Hydrogenovibrio marinus strain MH-110. J Bacteriol 186: 5685-5691.
69. Hayashi NR, Arai H, Kodama T, Igarashi Y (1997) The novel genes, cbbQ and cbbO, located downstream from the RubisCO genes of Pseudomonas hydrogenothermophila, affect the conformational states and activity of RubisCO. Biochem Biophys Res Commun 241: 565-569.
70. Hayashi NR, Arai H, Kodama T, Igarashi Y (1999) The cbbQ genes located downstream of the form I and form II RubisCO genes, affect the activity of both RubisCOs. Biochem Biophys Res Commun 266: 177-183.
71. Badger M, Hanson D, Price GD (2002) Evolution and diversity of CO2 concentrating mechanisms in cyanobacteria. Funct Plant Biol 29: 161-173.
72. Gibson JL, Tabita FR (1996) The molecular regulation of the reductive pentose phosphate pathway in Proteobacteria and Cyanobacteria. Arch Microbiol 166: 141-150.
73. Kusian B, Bowien B (1997) Organization and regulation of cbb CO2 assimilationgenesinautotrophic bacteria. FEMS Microbiol Rev 21:135-155.
74. Shively JM, Van Keulen G, Meijer WG (1998) Something from almost nothing: Carbon dioxide fixation in chemoautotrophs. Ann Rev Microbiol 52: 191-230.
75. Falcone DL, Tabita FR (1993) Complementation analysis and regulation of CO2 fixation gene expression in a ribulose 1,5-bisphosphate carboxylase- oxygenase deletion strain of Rhodospirillum rubrum. J Bacteriol 175: 5066-5077.
76. Ding YR, Ronimus RS, Morgan HW (2000) Sequencing, cloning, and high-level expression of the pfp gene, encoding a ppi-dependent phospho-fructokinase from the extremely thermophilic eubacterium Dictyoglomus thermophilum. J Bacteriol 182.:
77. Ronimus RS, Morgan HW (2001) The biochemical properties and phylogenies of phosphofructokinases from extremophiles. Extremophiles 5: 357-373.
78. Wood AP, Aurikko JP, Kelly DP (2004) A challenge for 21st century molecular biology and biochemistry: What are the causes of obligate autotrophy and methanotrophy? FEMS Microbiol Rev 28: 335-352.
79. Hughes NJ, Clayton C, Chalk P, Kelly D (1998) Helicobacter pylori porCDAB and oorDABC genes encode distinct pyruvate:flavodoxin and 2-oxoglutarate: acceptor oxidoreductases which mediate electron transport to NADP. J Bacteriol 180: 1119-1128.
80. Kather B, Stingl K, Van der Rest M, Altendorf K, Molenaar D (2000) Another unusual type of citric acid cycle enzyme in Helicobacter pylori: The malate:quinone oxidoreductase. J Bacteriol 182: 3204-3209.
81. Gehring U, Arnon DI (1972) Purification and properties of alpha-ketoglutarate synthase from a photosynthetic bacterium. J Biol Chem 247: 6963-6969.
82. Breese K, Boll M, Alt-Morbe J, Schagger H, Fuchs G (1998) Genes coding for the benzoyl-CoA pathway of anaerobic aromatic metabolism in the bacterium Thauera aromatica. Eur J Biochem 256: 148-154.
83. Jahn D, Verkamp E, Soll D (1992) Glutamyl-transfer RNA: A precursor of heme and chlorophyll biosynthesis. Trends Biochem Sci 17: 215-218.
84. van Veen HW (1997) Phosphate transport in prokaryotes: Molecules, mediators and mechanisms. Antonie Van Leeuwenhoek Intl J Gen Molec Microbiol 72: 299-315.
85. Prere MF, Chandler M, Fayet O (1990) Transposition in Shigella dysenteriae: isolation and analysis of IS911, a new member of the IS3 group of insertion sequences. J Bacteriol 172: 4090-4099.
86. Dyhrman ST, Chappell PD, Haley ST, Moffett JW, Orchard ED, et al. (2006) Phosphonate utilization by the globally important marine diazotroph Trichodesmium. Nature 439: 68-71.
87. Kolowith LC, Ingall ED, Benner R (2001) Composition and cycling of marine organic phosphorus. Limnol Oceanogr 46: 309-320.
88. Klotz MG, Arp DJ, Chain PSG, El-Sheikh AF, Hauser LJ, et al. (2006) The complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC19707. Appl Environ Microbiol. 72: 6299-6315.
89. Watson SW (1965) Characteristics of a marine nitrifying bacterium, Nitrosocystis oceanus Sp. N. Limnol Oceanogr 10: 274-289.
90. Romling U, Gomelsky M, Galperin MY (2005) C-di-GMP: The dawning of a novel bacterial signalling system. Molec Microbiol 57: 629-639.
91. Zhulin I, Taylor B, Dixon R (1997) PAS domain S-boxes in Archaea, Bacteria and sensors for oxygen and redox. Trends Biochem Sci 22: 331-333.
92. McCarter LL (2001) Polar flagellar motility of the Vibrionaceae. Microbiol Mol Biol Rev 65: 445-462.
93. Wadhams GH, Armitage JP (2004) Making sense of it all: Bacterial chemotaxis. Nature Rev Molec Cell Biol 5: 1024-1037.
94. Kachlany SC, Planet PJ, DeSalle R, Fine DH, Figurski DH (2001) Genes for tight adherence of Actinobacillus actinomycetemcomitans: From plaque to plague to pond scum. Trends Microbiol 9: 429-437.
95. Jannasch HW, Mottl MJ (1985) Geomicrobiology of deep-sea hydrothermal vents. Science 229: 717-725.
96. McCollom TM, Shock EL (1997) Geochemical constraints on chemolithoautotrophic metabolism by microorganisms in seafloor hydrothermal systems. Geochim Cosmochim Acta 61: 4375-4391.
97. Nies DH (2003) Efflux-mediated heavy metal resistance in prokaryotes. FEMS Microbiol Rev 27: 313-339.
98. Hou S, Saw JH, Lee KS, Freitas TA, Belisle C, et al. (2004) Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy. Proc Natl Acad Sci U S A 101: 18036-18041.
99. Nies DH (1999) Microbial heavy-metal resistance. Appl Microbiol Biotechnol 51: 730-750.
100. Edgcomb VP, Molyneaux SJ, Saito MA, Lloyd K, Boer S, et al. (2004) Sulfide ameliorates metal toxicity for deep-sea hydrothermal vent archaea. Appl Environ Microbiol 70: 2551-2555.
101. Ewing BL, Hillier M, Wendl P, Green P (1998) Basecalling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8: 175-185.
102. Ewing B, Green P (1998) Basecalling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186-194.
103. Gordon D, Abajian C, Green P (1998) Consed: A graphical tool for sequence finishing. Genome Res 8: 195-202
104. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27: 4636-4641.
105. Badger JH, Olsen GJ (1999) CRITICA: Coding region identification tool invoking comparative analysis. Molec Biol Evol 16: 512-524.
106. Kanehisa M, Goto S (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 28: 27-30.
107. McHardy AC, Goesmann A, Puhler A, Meyer F (2004) Development of joint application strategies for two microbial gene finders. Bioinformatics 20: 1622-1631.
108. Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, et al. (2003) GenDB - An open source genome annotation system for prokaryotic genomes. Nucleic Acids Res 31: 2187-2195.
109. Krogh A, Larsson B, von Heijne G, Sonnhammer ELL (2001) Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J Molec Biol 305: 567-580.
110. Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Molec Biol 340: 783-795.
111. Ren Q, Kang KH, Paulsen IT (2004) TransportDB: A relational database of cellular membrane transport systems. Nucleic Acids Res 32: D284-D288.
112. Markowitz VM, Korzeniewski F, Palaniappan K, Szeto E, Werner G, et al. (2006) The integrated microbial genomes (IMG) system. Nucl Acids Res 34: D344-348.
113. Swofford DL (2002) PAUP*. Phylogenetic analysis using parsimony (*and other methods), version 4. [computer program]. Sunderland (Massachusetts): Sinauer Associates.
114. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 25: 4876-4882.