Encapsulated in silica: Genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1

Genome Biology

Volumn 9, Issue 11, 2008, Pages

  Saw, Jimmy H ^a,j   Mountain, Bruce W ^b   Feng, Lu ^c,d,e   Omelchenko, Marina V ^f   Hou, Shaobin ^g   Saito, Jennifer A ^a   Stott, Matthew B ^b   Li, Dan ^c,d,e   Zhao, Guang ^c,d,e   Wu, Junli ^c,d,e   Galperin, Michael Y ^f   Koonin, Eugene V ^f   Makarova, Kira S ^f   Wolf, Yuri I ^f   Rigden, Daniel J ^h   Dunfield, Peter F ⁱ   Wang, Lei ^c,d,e   Alam, Maqsudul ^a,g  

^a UNIVERSITY OF HAWAII   (United States)

^b GNS SCIENCE   (New Zealand)

^c NANKAI UNIVERSITY   (China)

^d Tianjin Research Center for Functional Genomics and Biochip   (China)

^e BEIJING UNIVERSITY OF POSTS AND TELECOMMUNICATIONS   (China)

^f NATIONAL INSTITUTES OF HEALTH   (United States)

^g University of Liverpool ^*  (United States)

^h UNIVERSITY OF LIVERPOOL   (United Kingdom)

ⁱ UNIVERSITY OF CALGARY   (Canada)

^j LOS ALAMOS NATIONAL LABORATORY   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ACETATE KINASE; COPPER ZINC SUPEROXIDE DISMUTASE; CYTOCHROME C OXIDASE; FLAVOPROTEIN; GLUTATHIONE PEROXIDASE; LACTATE DEHYDROGENASE; NANOSPHERE; PHOSPHATE ACETYLTRANSFERASE; POLYAMINE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE; SILICON DIOXIDE; SUCCINATE DEHYDROGENASE; BACTERIAL PROTEIN;

AMINO ACID SYNTHESIS; ANOXYBACILLUS FLAVITHERMUS; ARTICLE; BACILLUS SUBTILIS; BACTERIAL CHROMOSOME; BACTERIAL GENETICS; BACTERIAL METABOLISM; BACTERIAL STRAIN; BACTERIUM ISOLATION; BIOFILM; CHROMOSOME PAIRING; COMPUTER MODEL; ENCAPSULATION; FOSSIL; GENE LOSS; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC CONSERVATION; GENOMICS; GEOBACILLUS; GEOTHERMAL ENERGY; GRAM POSITIVE BACTERIUM; IN VITRO STUDY; NEW ZEALAND; NONHUMAN; PREDICTION; PROTEIN FUNCTION; PROTEOMICS; SPECIES DIFFERENCE; THERMOPHILIC BACTERIUM; TISSUE PRESERVATION; WASTE WATER; BACILLACEAE; BACTERIAL GENOME; CHEMISTRY; GENETICS; HEAT; MICROBIOLOGY; PHYSIOLOGY;

ANOXYBACILLUS; ANOXYBACILLUS FLAVITHERMUS; BACILLI (CLASS); BACTERIA (MICROORGANISMS); POSIBACTERIA;

BACILLACEAE; BACTERIAL PROTEINS; FOSSILS; GENOME, BACTERIAL; HOT TEMPERATURE; NEW ZEALAND; SILICON DIOXIDE; WATER MICROBIOLOGY;

EID: 57449094163     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2008-9-11-r161     Document Type: Article

References (78)

1. Nakano MM Dailly YP Zuber P Clark DP Characterization of anaerobic fermentative growth of Bacillus subtilis: Identification of fermentation end products and genes required for growth. J Bacteriol 1997, 179:6749-6755. 179605 9352926
2. Nakano MM Zuber P Anaerobic growth of a "strict aerobe" (Bacillus subtilis). Annu Rev Microbiol 1998, 52:165-190. 9891797
3. Cruz Ramos H Hoffmann T Marino M Nedjari H Presecan-Siedel E Dreesen O Glaser P Jahn D Fermentative metabolism of Bacillus subtilis: Physiology and regulation of gene expression. J Bacteriol 2000, 182:3072-3080. 94491 10809684
4. Pikuta E Lysenko A Chuvilskaya N Mendrock U Hippe H Suzina N Nikitin D Osipov G Laurinavichius K Anoxybacillus pushchinensis gen. nov., sp. nov., a novel anaerobic, alkaliphilic, moderately thermophilic bacterium from manure, and description of Anoxybacillus flavitherms comb. nov. Int J Syst Evol Microbiol 2000, 50:2109-2117. 11155986
5. Pikuta E Cleland D Tang J Aerobic growth of Anoxybacillus pushchinoensis K1T: Emended descriptions of A. pushchinoensis and the genus Anoxybacillus. Int J Syst Evol Microbiol 2003, 53:1561-1562. 13130048
6. Heinen W Lauwers AM Mulders JW Bacillus flavothermus, a newly isolated facultative thermophile. Antonie van Leeuwenhoek 1982, 48:265-272. 7125637
7. De Clerck E Vanhoutte T Hebb T Geerinck J Devos J De Vos P Isolation, characterization, and identification of bacterial contaminants in semifinal gelatin extracts. Appl Environ Microbiol 2004, 70:3664-3672. 427776 15184171
8. Rueckert A Ronimus RS Morgan HW Development of a rapid detection and enumeration method for thermophilic bacilli in milk powders. J Microbiol Methods 2005, 60:155-167. 15590090
9. Mountain BW Benning LG Boerema JA Experimental studies on New Zealand hot spring sinters: Rates of growth and textural development. Can J Earth Sci 2003, 40:1643-1667.
10. Rainey FA Fritze D Stackebrandt E The phylogenetic diversity of thermophilic members of the genus Bacillus as revealed by 16S rDNA analysis. FEMS Microbiol Lett 1994 115 205 211 8138135
11. Lauwers AM Heinen W Thermal properties of enzymes from Bacillus flavothermus, grown between 34 and 70°C. Antonie van Leeuwenhoek 1983, 49:191-201. 6311096
12. Pancost RD Pressley S Coleman JM Benning LG Mountain BW Lipid biomolecules in silica sinters: Indicators of microbial biodiversity. Environ Microbiol 2005, 7:66-77. 15643937
13. Konhauser KO Jones B Reysenbach AL Renaut RW Hot spring sinters: Keys to understanding Earth's earliest life forms. Can J Earth Sci 2003, 40:1713-1724.
14. Konhauser KO Jones B Phoenix VR Ferris G Renaut RW The microbial role in hot spring silicification. Ambio 2004, 33:552-558. 15666688
15. Belduz AO Dulger S Demirbag Z Anoxybacillus gonensis sp. nov., a moderately thermophilic, xylose-utilizing, endospore-forming bacterium. Int J Syst Evol Microbiol 2003, 53:1315-1320. 13130012
16. Hoffmann T Troup B Szabo A Hungerer C Jahn D The anaerobic life of Bacillus subtilis: Cloning of the genes encoding the respiratory nitrate reductase system. FEMS Microbiol Lett 1995, 131:219-225. 7557333
17. Ogawa K Akagawa E Yamane K Sun ZW LaCelle M Zuber P Nakano MM The nasB operon and nasA gene are required for nitrate/nitrite assimilation in Bacillus subtilis. J Bacteriol 1995, 177:1409-1413. 176753 7868621
18. Richardson DJ Berks BC Russell DA Spiro S Taylor CJ Functional, biochemical and genetic diversity of prokaryotic nitrate reductases. Cell Mol Life Sci 2001, 58:165-178. 11289299
19. Médigue C Krin E Pascal G Barbe V Bernsel A Bertin PN Cheung F Cruveiller S D'Amico S Duilio A Fang G Feller G Ho C Mangenot S Marino G Nilsson J Parrilli E Rocha EP Rouy Z Sekowska A Tutino ML Vallenet D von Heijne G Danchin A Coping with cold: The genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. Genome Res 2005, 15:1325-1335. 1240074 16169927
20. Burnett PG Heinrich H Peak D Bremer PJ McQuillan AJ Daughney CJ The effect of pH and ionic strength on proton adsorption by the thermophilic bacterium Anoxybacillus flavithermus. Geochim Cosmochim Acta 2006, 70:1914-1927.
21. Siezen RJ Kuipers OP de Vos WM Comparison of lantibiotic gene clusters and encoded proteins. Antonie van Leeuwenhoek 1996, 69:171-184. 8775977
22. Mirkin BG Fenner TI Galperin MY Koonin EV Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol Biol 2003, 3:2. 149225 12515582
23. Makarova KS Grishin NV Shabalina SA Wolf YI Koonin EV A putative RNA-interference-based immune system in prokaryotes: Computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct 2006, 1:7. 1462988 16545108
24. Barrangou R Fremaux C Deveau H Richards M Boyaval P Moineau S Romero DA Horvath P CRISPR provides acquired resistance against viruses in prokaryotes. Science 2007, 315:1709-1712. 17379808
25. Römling U Gomelsky M Galperin MY C-di-GMP: The dawning of a novel bacterial signalling system. Mol Microbiol 2005, 57:629-639. 16045609
26. Galperin MY A census of membrane-bound and intracellular signal transduction proteins in bacteria: Bacterial IQ, extroverts and introverts. BMC Microbiol 2005, 5:35. 1183210 15955239
27. Amikam D Galperin MY PilZ domain is part of the bacterial c-di-GMP binding protein. Bioinformatics 2006, 22:3-6. 16249258
28. Ryjenkov DA Simm R Römling U Gomelsky M The PilZ domain is a receptor for the second messenger c-di-GMP: The PilZ domain protein YcgR controls motility in enterobacteria. J Biol Chem 2006, 281:30310-30314. 16920715
29. Pratt JT Tamayo R Tischler AD Camilli A PilZ domain proteins bind cyclic diguanylate and regulate diverse processes in Vibrio cholerae. J Biol Chem 2007, 282:12860-12870. 17307739
30. Ulrich LE Zhulin IB MiST: A microbial signal transduction database. Nucleic Acids Res 2007, 35:D386-D390. 1747179 17135192
31. Branda SS Gonzalez-Pastor JE Dervyn E Ehrlich SD Losick R Kolter R Genes involved in formation of structured multicellular communities by Bacillus subtilis. J Bacteriol 2004, 186:3970-3979. 419949 15175311
32. Hamon MA Stanley NR Britton RA Grossman AD Lazazzera BA Identification of AbrB-regulated genes involved in biofilm formation by Bacillus subtilis. Mol Microbiol 2004, 52:847-860. 1409746 15101989
33. Chu F Kearns DB Branda SS Kolter R Losick R Targets of the master regulator of biofilm formation in Bacillus subtilis. Mol Microbiol 2006, 59:1216-1228. 16430695
34. Branda SS Chu F Kearns DB Losick R Kolter R A major protein component of the Bacillus subtilis biofilm matrix. Mol Microbiol 2006, 59:1229-1238. 16430696
35. Benning LG Phoenix VR Yee N Tobin MJ Molecular characterization of cyanobacterial silicification using synchrotron infrared micro-spectroscopy. Geochim Cosmochim Acta 2004, 68:729-741.
36. Hecker M Volker U General stress response of Bacillus subtilis and other bacteria. Adv Microb Physiol 2001, 44:35-91. 11407115
37. Sekowska A Bertin P Danchin A Characterization of polyamine synthesis pathway in Bacillus subtilis 168. Mol Microbiol 1998, 29:851-858. 9723923
38. Knott JM Romer P Sumper M Putative spermine synthases from Thalassiosira pseudonana and Arabidopsis thaliana synthesize thermospermine rather than spermine. FEBS Lett 2007, 581:3081-3086. 17560575
39. Kröger N Deutzmann R Sumper M Polycationic peptides from diatom biosilica that direct silica nanosphere formation. Science 1999, 286:1129-1132. 10550045
40. Kröger N Deutzmann R Bergsdorf C Sumper M Species-specific polyamines from diatoms control silica morphology. Proc Natl Acad Sci USA 2000, 97:14133-14138. 18883 11106386
41. Lenoci L Camp PJ Self-assembly of peptide scaffolds in biosilica formation: Computer simulations of a coarse-grained model. J Am Chem Soc 2006, 128:10111-10117. 16881640
42. Lutz K Gröger C Sumper M Brunner E Biomimetic silica formation: Analysis of phosphate-induced self-assembly of polyamines. Phys Chem Chem Phys 2005, 7:2812-2815. 16189597
43. Sumper M Kröger N Silica formation in diatoms: The function of long-chain polyamines and silaffins. J Mater Chem 2004, 14:2059-2065.
44. Oliver S Kuperman A Coombs N Lough A Ozin GA Lamellar aluminophosphates with surface patterns that mimic diatom and radiolarian microskeletons. Nature 1995, 378:47-50.
45. Mann S Ozin GA Synthesis of inorganic materials with complex form. Nature 1996, 382:313-318.
46. Kröger N Lorenz S Brunner E Sumper M Self-assembly of highly phosphorylated silaffins and their function in biosilica morphogenesis. Science 2002, 298:584-586. 12386330
47. Brunner E Lutz K Sumper M Biomimetic synthesis of silica nanospheres depends on the aggregation and phase separation of polyamines in aqueous solution. Phys Chem Chem Phys 2004, 6:854-857.
48. Gordon R Drum RW The chemical basis for diatom morphogenesis. Int Rev Cytol 1994, 150:243-372.
49. Simpson TL Volcani BE Silicon and Siliceous Structures in Biological Systems New York: Springer 1981.
50. Iler RK The Chemistry of Silica Chichester: Wiley-Interscience 1979.
51. Mizutani T Nagase H Fujiwara N Ogoshi H Silicic acid polymerization catalyzed by amines and polyamines. Bull Chem Soc Jpn 1998, 71:2017-2022.
52. Patel CN Wortham BW Lines JL Fetherston JD Perry RD Oliveira MA Polyamines are essential for the formation of plague biofilm. J Bacteriol 2006, 188:2355-2363. 1428407 16547021
53. Karatan E Duncan TR Watnick PI NspS, a predicted polyamine sensor, mediates activation of Vibrio cholerae biofilm formation by norspermidine. J Bacteriol 2005, 187:7434-7443. 1273002 16237027
54. Urrutia Mera M Beveridge TJ Mechanism of silicate binding to the bacterial cell wall in Bacillus subtilis. J Bacteriol 1993, 175:1936-1945. 204267 8458835
55. Urrutia MM Beveridge TJ Formation of fine-grained metal and silicate precipitates on a bacterial surface (Bacillus subtilis). Chem Geol 1994, 116:261-280.
56. Armbrust EV Berges JA Bowler C Green BR Martinez D Putnam NH Zhou S Allen AE Apt KE Bechner M Brzezinski MA Chaal BK Chiovitti A Davis AK Demarest MS Detter JC Glavina T Goodstein D Hadi MZ Hellsten U Hildebrand M Jenkins BD Jurka J Kapitonov VV Kröger N Lau WW Lane TW Larimer FW Lippmeier JC Lucas S et al. The genome of the diatom Thalassiosira pseudonana: Ecology, evolution, and metabolism. Science 2004, 306:79-86. 15459382
57. Bachrach U Naturally occurring polyamines: Interaction with macromolecules. Curr Protein Pept Sci 2005, 6:559-566. 16381604
58. Kusano T Yamaguchi K Berberich T Takahashi Y Advances in polyamine research in 2007. J Plant Res 2007, 120:345-350. 17351711
59. Phoenix VR Adams DG Konhauser KO Cyanobacterial viability during hydrothermal biomineralisation. Chem Geol 2000, 169:329-338.
60. Hou S Saw JH Lee KS Freitas TA Belisle C Kawarabayasi Y Donachie SP Pikina A Galperin MY Koonin EV Makarova KS Omelchenko MV Sorokin A Wolf YI Li QX Keum YS Campbell S Denery J Aizawa S Shibata S Malahoff A Alam M 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 USA 2004, 101:18036-18041. 539801 15596722
61. Gordon D Abajian C Green P Consed: A graphical tool for sequence finishing. Genome Res 1998, 8:195-202. 9521923
62. Huang X Madan A CAP3: A DNA sequence assembly program. Genome Res 1999, 9:868-877. 310812 10508846
63. Delcher AL Harmon D Kasif S White O Salzberg SL Improved microbial gene identification with GLIMMER. Nucleic Acids Res 1999, 27: 4636-4641. 148753 10556321
64. Altschul SF Madden TL Schaffer AA Zhang J Zheng Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST - A new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 146917 9254694
65. Lowe TM Eddy SR tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25:955-964. 146525 9023104
66. Koonin EV Galperin MY Sequence - Evolution - Function. Computational Approaches in Comparative Genomics Boston: Kluwer Academic Publishers 2002.
67. Wolf YI Rogozin IB Grishin NV Tatusov RL Koonin EV Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol Biol 2001, 1:8. 60490 11734060
68. Guerreiro N Redmond JW Rolfe BG Djordjevic MA New Rhizobium leguminosarum flavonoid-induced proteins revealed by proteome analysis of differentially displayed proteins. Mol Plant Microbe Interact 1997, 10:506-516. 9150598
69. Büttner K Bernhardt J Scharf C Schmid R Mäder U Eymann C Antelmann H Völker A Völker U Hecker M A comprehensive two-dimensional map of cytosolic proteins of Bacillus subtilis. Electrophoresis 2001, 22:2908-2935. 11565787
70. Candiano G Bruschi M Musante L Santucci L Ghiggeri GM Carnemolla B Orecchia P Zardi L Righetti PG Blue silver: A very sensitive colloidal Coomassie G-250 staining for proteome analysis. Electrophoresis 2004, 25:1327-1333. 15174055
71. Shimotohno KW Iida J Takizawa N Endo T Purification and characterization of arginine amidinohydrolase from Bacillus brevis TT02-8. Biosci Biotechnol Biochem 1994, 58:1045-1049. 7765033
72. Yamamoto S Nakao H Yamasaki K Takashina K Suemoto Y Shinoda S Activities and properties of putrescine-biosynthetic enzymes in Vibrio parahaemolyticus. Microbiol Immunol 1988, 32:675-687. 3193911
73. Iyer RK Kim HK Tsoa RW Grody WW Cederbaum SD Cloning and characterization of human agmatinase. Mol Genet Metab 2002, 75:209-218. 11914032
74. Lee MJ Huang CY Sun YJ Huang H Cloning and characterization of spermidine synthase and its implication in polyamine biosynthesis in Helicobacter pylori strain 26695. Protein Expr Purif 2005, 43:140-148. 16009566
75. Zolg W Ottow JC Improved thin-layer technique for detection of arginine dihydrolase among the Pseudomonas species. Appl Microbiol 1973, 26:1001-1003. 379945 4767290
76. Redmond JW Tseng A High-pressure liquid chromatographic determination of putrescine, cadaverine, spermidine and spermine. J Chromatogr 1979, 170:479-481.
77. Morgan DM Determination of polyamines as their benzoylated derivatives by HPLC. Methods Mol Biol 1998, 79:111-118. 9463825
78. Makarova KS Sorokin AV Novichkov PS Wolf YI Koonin EV Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. Biol Direct 2007, 2:33. 2222616 18042280