메뉴 건너뛰기




Volumn 8, Issue 3, 2015, Pages 1039-1045

Complete Genome Sequence of Geobacillus strain Y4.1MC1, a Novel CO-Utilizing Geobacillus thermoglucosidasius Strain Isolated from Bath Hot Spring in Yellowstone National Park

Author keywords

Carbon fixation; Carbon monoxide; Geobacillus thermoglucosidasius; Wood Ljungdahl pathway; Yellowstone National Park

Indexed keywords

AMINO ACIDS; CARBON; CARBON CAPTURE; CARBON DIOXIDE; CARBON MONOXIDE; HOT SPRINGS; METABOLISM;

EID: 84940954017     PISSN: 19391234     EISSN: 19391242     Source Type: Journal    
DOI: 10.1007/s12155-015-9585-2     Document Type: Article
Times cited : (19)

References (37)
  • 2
    • 65349113034 scopus 로고    scopus 로고
    • ‘That which does not kill us only makes us stronger’: the role of carbon monoxide in thermophilic microbial consortia
    • COI: 1:CAS:528:DC%2BD1MXmsVeqtrw%3D, PID: 19239487
    • Techtmann SM, Colman AS, Robb FT (2009) ‘That which does not kill us only makes us stronger’: the role of carbon monoxide in thermophilic microbial consortia. Environ Microbiol 11:1027–1037
    • (2009) Environ Microbiol , vol.11 , pp. 1027-1037
    • Techtmann, S.M.1    Colman, A.S.2    Robb, F.T.3
  • 3
    • 33846476676 scopus 로고    scopus 로고
    • Distribution, diversity and ecology of aerobic CO-oxidizing bacteria
    • COI: 1:CAS:528:DC%2BD2sXkslCgtw%3D%3D, PID: 17224920
    • King GM, Weber CF (2007) Distribution, diversity and ecology of aerobic CO-oxidizing bacteria. Nat Rev Microbiol 5:107–118
    • (2007) Nat Rev Microbiol , vol.5 , pp. 107-118
    • King, G.M.1    Weber, C.F.2
  • 4
    • 84862819224 scopus 로고    scopus 로고
    • Microbiology and genetics of CO utilization in mycobacteria
    • COI: 1:CAS:528:DC%2BC38XmtVenu7k%3D, PID: 22277984
    • Kim YM, Park SW (2012) Microbiology and genetics of CO utilization in mycobacteria. Antonie Van Leeuwenhoek 101:685–700
    • (2012) Antonie Van Leeuwenhoek , vol.101 , pp. 685-700
    • Kim, Y.M.1    Park, S.W.2
  • 5
    • 54949153045 scopus 로고    scopus 로고
    • Acetogenesis and the Wood-Ljungdahl pathway of CO(2) fixation
    • COI: 1:CAS:528:DC%2BD1cXhtlaqtb7O, PID: 18801467
    • Ragsdale SW, Pierce E (2008) Acetogenesis and the Wood-Ljungdahl pathway of CO(2) fixation. Biochim Biophys Acta 1784:1873–1898
    • (2008) Biochim Biophys Acta , vol.1784 , pp. 1873-1898
    • Ragsdale, S.W.1    Pierce, E.2
  • 6
    • 51649124894 scopus 로고    scopus 로고
    • The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum)
    • COI: 1:CAS:528:DC%2BD1cXht1CmurbP, PID: 18631365
    • Pierce E, Xie G, Barabote RD, Saunders E, Han CS et al (2008) The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum). Environ Microbiol 10:2550–2573
    • (2008) Environ Microbiol , vol.10 , pp. 2550-2573
    • Pierce, E.1    Xie, G.2    Barabote, R.D.3    Saunders, E.4    Han, C.S.5
  • 7
    • 9744277455 scopus 로고    scopus 로고
    • Thermosinus carboxydivorans gen. nov., sp. nov., a new anaerobic, thermophilic, carbon-monoxide-oxidizing, hydrogenogenic bacterium from a hot pool of Yellowstone National Park
    • COI: 1:CAS:528:DC%2BD2cXhtFGjsL3F, PID: 15545483
    • Sokolova TG, Gonzalez JM, Kostrikina NA, Chernyh NA, Slepova TV et al (2004) Thermosinus carboxydivorans gen. nov., sp. nov., a new anaerobic, thermophilic, carbon-monoxide-oxidizing, hydrogenogenic bacterium from a hot pool of Yellowstone National Park. Int J Syst Evol Microbiol 54:2353–2359
    • (2004) Int J Syst Evol Microbiol , vol.54 , pp. 2353-2359
    • Sokolova, T.G.1    Gonzalez, J.M.2    Kostrikina, N.A.3    Chernyh, N.A.4    Slepova, T.V.5
  • 8
    • 33846177613 scopus 로고    scopus 로고
    • Novel chemolithotrophic, thermophilic, anaerobic bacteria Thermolithobacter ferrireducens gen. nov., sp. nov. and Thermolithobacter carboxydivorans sp. nov
    • COI: 1:CAS:528:DC%2BD2sXjsFOisg%3D%3D, PID: 17021657
    • Sokolova T, Hanel J, Onyenwoke RU, Reysenbach AL, Banta A et al (2007) Novel chemolithotrophic, thermophilic, anaerobic bacteria Thermolithobacter ferrireducens gen. nov., sp. nov. and Thermolithobacter carboxydivorans sp. nov. Extremophiles 11:145–157
    • (2007) Extremophiles , vol.11 , pp. 145-157
    • Sokolova, T.1    Hanel, J.2    Onyenwoke, R.U.3    Reysenbach, A.L.4    Banta, A.5
  • 9
    • 0035064602 scopus 로고    scopus 로고
    • Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. th
    • COI: 1:CAS:528:DC%2BD3MXivVOrtbs%3D, PID: 11321089
    • Nazina TN, Tourova TP, Poltaraus AB, Novikova EV, Grigoryan AA et al (2001) Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. th. Int J Syst Evol Microbiol 51:433–446
    • (2001) Int J Syst Evol Microbiol , vol.51 , pp. 433-446
    • Nazina, T.N.1    Tourova, T.P.2    Poltaraus, A.B.3    Novikova, E.V.4    Grigoryan, A.A.5
  • 10
    • 2342572933 scopus 로고    scopus 로고
    • Habitat, applications and genomics of the aerobic, thermophilic genus Geobacillus
    • COI: 1:CAS:528:DC%2BD2cXjtVSgtLs%3D, PID: 15046574
    • McMullan G, Christie JM, Rahman TJ, Banat IM, Ternan NG et al (2004) Habitat, applications and genomics of the aerobic, thermophilic genus Geobacillus. Biochem Soc Trans 32:214–217
    • (2004) Biochem Soc Trans , vol.32 , pp. 214-217
    • McMullan, G.1    Christie, J.M.2    Rahman, T.J.3    Banat, I.M.4    Ternan, N.G.5
  • 11
    • 2342507723 scopus 로고    scopus 로고
    • Distribution and molecular investigation of highly thermophilic bacteria associated with cool soil environments
    • COI: 1:CAS:528:DC%2BD2cXjtVSgtLo%3D, PID: 15046573
    • Rahman TJ, Marchant R, Banat IM (2004) Distribution and molecular investigation of highly thermophilic bacteria associated with cool soil environments. Biochem Soc Trans 32:209–213
    • (2004) Biochem Soc Trans , vol.32 , pp. 209-213
    • Rahman, T.J.1    Marchant, R.2    Banat, I.M.3
  • 12
    • 8744284492 scopus 로고    scopus 로고
    • Genomic characterization of thermophilic Geobacillus species isolated from the deepest sea mud of the Mariana Trench
    • COI: 1:CAS:528:DC%2BD2cXot1yltrc%3D, PID: 15168170
    • Takami H, Nishi S, Lu J, Shimamura S, Takaki Y (2004) Genomic characterization of thermophilic Geobacillus species isolated from the deepest sea mud of the Mariana Trench. Extremophiles 8:351–356
    • (2004) Extremophiles , vol.8 , pp. 351-356
    • Takami, H.1    Nishi, S.2    Lu, J.3    Shimamura, S.4    Takaki, Y.5
  • 13
    • 84865244830 scopus 로고    scopus 로고
    • Complete genome sequence of Paenibacillus strain Y4.12MC10, a novel Paenibacillus lautus strain isolated from Obsidian hot spring in Yellowstone National Park
    • PID: 23408395
    • Mead DA, Lucas S, Copeland A, Lapidus A, Cheng JF et al (2012) Complete genome sequence of Paenibacillus strain Y4.12MC10, a novel Paenibacillus lautus strain isolated from Obsidian hot spring in Yellowstone National Park. Stand Genomic Sci 6:381–400
    • (2012) Stand Genomic Sci , vol.6 , pp. 381-400
    • Mead, D.A.1    Lucas, S.2    Copeland, A.3    Lapidus, A.4    Cheng, J.F.5
  • 14
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    • COI: 1:CAS:528:DC%2BD1cXlslChsLg%3D, PID: 18349386
    • Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 15
    • 77953023066 scopus 로고    scopus 로고
    • GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes
    • COI: 1:CAS:528:DC%2BC3cXlsVyit7Y%3D, PID: 20436475
    • Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD et al (2010) GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 7:455–457
    • (2010) Nat Methods , vol.7 , pp. 455-457
    • Pati, A.1    Ivanova, N.N.2    Mikhailova, N.3    Ovchinnikova, G.4    Hooper, S.D.5
  • 16
    • 0031955518 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. I. Accuracy assessment
    • COI: 1:CAS:528:DyaK1cXitlWlu78%3D, PID: 9521921
    • Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175–185
    • (1998) Genome Res , vol.8 , pp. 175-185
    • Ewing, B.1    Hillier, L.2    Wendl, M.C.3    Green, P.4
  • 17
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. II. Error probabilities
    • COI: 1:CAS:528:DyaK1cXitlWlu7g%3D, PID: 9521922
    • Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186–194
    • (1998) Genome Res , vol.8 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 18
    • 0031955116 scopus 로고    scopus 로고
    • Consed: a graphical tool for sequence finishing
    • COI: 1:CAS:528:DyaK1cXitlWksr0%3D, PID: 9521923
    • Gordon D, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res 8:195–202
    • (1998) Genome Res , vol.8 , pp. 195-202
    • Gordon, D.1    Abajian, C.2    Green, P.3
  • 21
    • 0030854739 scopus 로고    scopus 로고
    • tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
    • COI: 1:CAS:528:DyaK2sXhvVahtrk%3D, PID: 9023104
    • 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
    • (1997) Nucleic Acids Res , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 22
    • 34250665888 scopus 로고    scopus 로고
    • RNAmmer: consistent and rapid annotation of ribosomal RNA genes
    • COI: 1:CAS:528:DC%2BD2sXmvF2ntLg%3D, PID: 17452365
    • Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T et al (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108
    • (2007) Nucleic Acids Res , vol.35 , pp. 3100-3108
    • Lagesen, K.1    Hallin, P.2    Rodland, E.A.3    Staerfeldt, H.H.4    Rognes, T.5
  • 24
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
    • COI: 1:CAS:528:DC%2BD3MXisFCguw%3D%3D, PID: 11152613
    • Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305:567–580
    • (2001) J Mol Biol , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    von Heijne, G.3    Sonnhammer, E.L.4
  • 25
    • 0025845723 scopus 로고
    • Analysis of the gluconate (gnt) operon of Bacillus subtilis
    • COI: 1:CAS:528:DyaK3MXkvVKgsb8%3D, PID: 1659648
    • Reizer A, Deutscher J, Saier MH Jr, Reizer J (1991) Analysis of the gluconate (gnt) operon of Bacillus subtilis. Mol Microbiol 5:1081–1089
    • (1991) Mol Microbiol , vol.5 , pp. 1081-1089
    • Reizer, A.1    Deutscher, J.2    Saier, M.H.3    Reizer, J.4
  • 26
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • COI: 1:CAS:528:DC%2BD2cXisF2ks7w%3D, PID: 15034147
    • Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 27
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • COI: 1:CAS:528:DC%2BC3MXht1eiu73K, PID: 21546353
    • Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739
    • (2011) Mol Biol Evol , vol.28 , pp. 2731-2739
    • Tamura, K.1    Peterson, D.2    Peterson, N.3    Stecher, G.4    Nei, M.5
  • 28
    • 0027157960 scopus 로고
    • Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
    • COI: 1:CAS:528:DyaK3sXks1CksL4%3D, PID: 8336541
    • Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–526
    • (1993) Mol Biol Evol , vol.10 , pp. 512-526
    • Tamura, K.1    Nei, M.2
  • 29
    • 33846555715 scopus 로고    scopus 로고
    • DNA-DNA hybridization values and their relationship to whole-genome sequence similarities
    • COI: 1:CAS:528:DC%2BD2sXitFGgs78%3D, PID: 17220447
    • Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91
    • (2007) Int J Syst Evol Microbiol , vol.57 , pp. 81-91
    • Goris, J.1    Konstantinidis, K.T.2    Klappenbach, J.A.3    Coenye, T.4    Vandamme, P.5
  • 30
    • 73149098333 scopus 로고    scopus 로고
    • Shifting the genomic gold standard for the prokaryotic species definition
    • COI: 1:CAS:528:DC%2BD1MXhsFGlsbbK, PID: 19855009
    • Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 106:19126–19131
    • (2009) Proc Natl Acad Sci , vol.106 , pp. 19126-19131
    • Richter, M.1    Rosselló-Móra, R.2
  • 31
    • 84893511241 scopus 로고    scopus 로고
    • Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
    • COI: 1:CAS:528:DC%2BC2cXhtlClsr7I, PID: 24505072
    • Kim M, Oh HS, Park SC, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351
    • (2014) Int J Syst Evol Microbiol , vol.64 , pp. 346-351
    • Kim, M.1    Oh, H.S.2    Park, S.C.3    Chun, J.4
  • 32
    • 0032980767 scopus 로고    scopus 로고
    • The glucuronic acid utilization gene cluster from Bacillus stearothermophilus T-6
    • COI: 1:CAS:528:DyaK1MXjvFylsL8%3D, PID: 10368143
    • Shulami S, Gat O, Sonenshein AL, Shoham Y (1999) The glucuronic acid utilization gene cluster from Bacillus stearothermophilus T-6. J Bacteriol 181:3695–3704
    • (1999) J Bacteriol , vol.181 , pp. 3695-3704
    • Shulami, S.1    Gat, O.2    Sonenshein, A.L.3    Shoham, Y.4
  • 33
    • 79958097056 scopus 로고    scopus 로고
    • The L-Arabinan utilization system of Geobacillus stearothermophilus
    • COI: 1:CAS:528:DC%2BC3MXmvFeksL8%3D, PID: 21460081
    • Shulami S, Raz-Pasteur A, Tabachnikov O, Gilead-Gropper S, Shner I et al (2011) The L-Arabinan utilization system of Geobacillus stearothermophilus. J Bacteriol 193:2838–2850
    • (2011) J Bacteriol , vol.193 , pp. 2838-2850
    • Shulami, S.1    Raz-Pasteur, A.2    Tabachnikov, O.3    Gilead-Gropper, S.4    Shner, I.5
  • 34
    • 0029895214 scopus 로고    scopus 로고
    • Cloning and molecular genetic characterization of the Escherichia coli gntR, gntK, and gntU genes of GntI, the main system for gluconate metabolism
    • COI: 1:CAS:528:DyaK28Xjt1Klsr8%3D, PID: 8655507
    • Tong S, Porco A, Isturiz T, Conway T (1996) Cloning and molecular genetic characterization of the Escherichia coli gntR, gntK, and gntU genes of GntI, the main system for gluconate metabolism. J Bacteriol 178:3260–3269
    • (1996) J Bacteriol , vol.178 , pp. 3260-3269
    • Tong, S.1    Porco, A.2    Isturiz, T.3    Conway, T.4
  • 35
    • 84865618176 scopus 로고    scopus 로고
    • Three inositol dehydrogenases involved in utilization and interconversion of inositol stereoisomers in a thermophile, Geobacillus kaustophilus HTA426
    • COI: 1:CAS:528:DC%2BC38XhtlWnsL3I, PID: 22609753
    • Yoshida K, Sanbongi A, Murakami A, Suzuki H, Takenaka S et al (2012) Three inositol dehydrogenases involved in utilization and interconversion of inositol stereoisomers in a thermophile, Geobacillus kaustophilus HTA426. Microbiology 158:1942–1952
    • (2012) Microbiology , vol.158 , pp. 1942-1952
    • Yoshida, K.1    Sanbongi, A.2    Murakami, A.3    Suzuki, H.4    Takenaka, S.5
  • 36
    • 49649111573 scopus 로고    scopus 로고
    • Protein-based organelles in bacteria: carboxysomes and related microcompartments
    • COI: 1:CAS:528:DC%2BD1cXpvVWjsbw%3D, PID: 18679172
    • Yeates TO, Kerfeld CA, Heinhorst S, Cannon GC, Shively JM (2008) Protein-based organelles in bacteria: carboxysomes and related microcompartments. Nat Rev Microbiol 6:681–691
    • (2008) Nat Rev Microbiol , vol.6 , pp. 681-691
    • Yeates, T.O.1    Kerfeld, C.A.2    Heinhorst, S.3    Cannon, G.C.4    Shively, J.M.5
  • 37
    • 14044264258 scopus 로고    scopus 로고
    • Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem
    • COI: 1:CAS:528:DC%2BD2MXhvFKiurk%3D, PID: 15671178
    • Spear JR, Walker JJ, McCollom TM, Pace NR (2005) Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem. Proc Natl Acad Sci U S A 102:2555–2560
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 2555-2560
    • Spear, J.R.1    Walker, J.J.2    McCollom, T.M.3    Pace, N.R.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.