메뉴 건너뛰기




Volumn 6, Issue 1, 2012, Pages 104-115

Complete genome sequence of Clostridium clariflavum DSM 19732

Author keywords

Anaerobic; Bioenergy; Biotechnology; Cel lulolytic; Cellulosome; Lignocellulose utilization; Thermophilic

Indexed keywords

BACTERIAL DNA; CELLULOSOME; HEMICELLULOSE; LIGNOCELLULOSE; PYRUVIC ACID;

EID: 84859139303     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.2535732     Document Type: Article
Times cited : (46)

References (43)
  • 1
    • 0036714783 scopus 로고    scopus 로고
    • Microbial cellulose utilization: Fundamentals and biotechnology
    • PubMed
    • Lynd LR, Weimer P, Van Zyl W, Pretorius I. Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 2002; 66:506-577.PubMed http://dx.doi.org/10.1128/MMBR.66.3.506-577.2002
    • (2002) Microbiol Mol Biol Rev , vol.66 , pp. 506-577
    • Lynd, L.R.1    Weimer, P.2    van Zyl, W.3    Pretorius, I.4
  • 2
    • 69449100606 scopus 로고    scopus 로고
    • Clostrid-ium clariflavum sp. nov. and Clostridium caenicola sp. nov., moderately thermophilic, cellulose-/cellobiose-digesting bacteria isolated from methanogenic sludge
    • PubMed
    • Shiratori H, Sasaya K, Ohiwa H, Ikeno H, Ayame S, Kataoka N, Miya A, Beppu T, Ueda K. Clostrid-ium clariflavum sp. nov. and Clostridium caenicola sp. nov., moderately thermophilic, cellulose-/cellobiose-digesting bacteria isolated from methanogenic sludge. Int J Syst Evol Microbiol 2009; 59:1764-1770.PubMed http://dx.doi.org/10.1099/ijs.0.003483-0
    • (2009) Int J Syst Evol Microbiol , vol.59 , pp. 1764-1770
    • Shiratori, H.1    Sasaya, K.2    Ohiwa, H.3    Ikeno, H.4    Ayame, S.5    Kataoka, N.6    Miya, A.7    Beppu, T.8    Ueda, K.9
  • 3
    • 77953109724 scopus 로고    scopus 로고
    • Diversity of bacteria and glycosyl hydrolase family 48 Genes in cellulolytic consortia enriched from thermophilic biocompost
    • PubMed
    • Izquierdo JA, Sizova MV, Lynd LR. Diversity of bacteria and glycosyl hydrolase family 48 Genes in cellulolytic consortia enriched from thermophilic biocompost. Appl Environ Microbiol 2010; 76:3545-3553.PubMed http://dx.doi.org/10.1128/AEM.02689-09
    • (2010) Appl Environ Microbiol , vol.76 , pp. 3545-3553
    • Izquierdo, J.A.1    Sizova, M.V.2    Lynd, L.R.3
  • 4
    • 79953285101 scopus 로고    scopus 로고
    • Cellulose- and xylan-degrading thermophilic anaerobic bacteria from biocompost
    • PubMed
    • Sizova MV, Izquierdo JA, Panikov NS, Lynd LR. Cellulose- and xylan-degrading thermophilic anaerobic bacteria from biocompost. Appl Environ Microbiol 2011; 77:2282-2291.PubMed http://dx.doi.org/10.1128/AEM.01219-10
    • (2011) Appl Environ Microbiol , vol.77 , pp. 2282-2291
    • Sizova, M.V.1    Izquierdo, J.A.2    Panikov, N.S.3    Lynd, L.R.4
  • 5
    • 0027185401 scopus 로고
    • Theoretical foundation of the minimum-evolution method of phylogenetic inference
    • PubMed
    • Rzhetsky A, Nei M. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 1993; 10:1073-1095.PubMed
    • (1993) Mol Biol Evol , vol.10 , pp. 1073-1095
    • Rzhetsky, A.1    Nei, M.2
  • 7
    • 33646560608 scopus 로고    scopus 로고
    • Isolation and characterization of a new Clostridium sp. that performs effective cellulosic waste digestion in a thermophilic methanogenic bioreactor
    • PubMed
    • Shiratori H, Ikeno H, Ayame S, Kataoka N, Miya A, Hosono K, Beppu T, Ueda K. Isolation and characterization of a new Clostridium sp. that performs effective cellulosic waste digestion in a thermophilic methanogenic bioreactor. Appl Environ Microbiol 2006; 72:3702-3709.PubMed http://dx.doi.org/10.1128/AEM.72.5.3702-3709.2006
    • (2006) Appl Environ Microbiol , vol.72 , pp. 3702-3709
    • Shiratori, H.1    Ikeno, H.2    Ayame, S.3    Kataoka, N.4    Miya, A.5    Hosono, K.6    Beppu, T.7    Ueda, K.8
  • 9
    • 0025300402 scopus 로고
    • Towards a natural system of organisms: Proposal for the do-mains Archaea, Bacteria, and Eucarya
    • PubMed
    • Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the do-mains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576-4579.PubMed http://dx.doi.org/10.1073/pnas.87.12.4576
    • (1990) Proc Natl Acad Sci USA , vol.87 , pp. 4576-4579
    • Woese, C.R.1    Kandler, O.2    Wheelis, M.L.3
  • 10
    • 0017843547 scopus 로고
    • Proposals concerning the higher taxa of bacteria
    • Gibbons N, Murray R. Proposals concerning the higher taxa of bacteria. Int J Syst Bacteriol 1978; 28:1-6. http://dx.doi.org/10.1099/00207713-28-1-1
    • (1978) Int J Syst Bacteriol , vol.28 , pp. 1-6
    • Gibbons, N.1    Murray, R.2
  • 11
    • 0000685441 scopus 로고    scopus 로고
    • The road map to the manu-al
    • Garrity GM, Boone DR, Castenholz RW, Second Edition, Springer, New York
    • Garrity GM, Holt JG. The road map to the manu-al. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 119-169.
    • (2001) Bergey's Manual of Systematic Bacteriology , vol.1 , pp. 119-169
    • Garrity, G.M.1    Holt, J.G.2
  • 12
    • 0344278514 scopus 로고
    • The higher taxa, or, a place for everything...
    • Holt JG, First Edition, The Williams and Wilkins Co., Baltimore
    • Murray RGE. The higher taxa, or, a place for everything...? In: Holt JG (ed), Bergey's Manual of Systematic Bacteriology, First Edition, Volume 1, The Williams and Wilkins Co., Baltimore, 1984, p. 31-34.
    • (1984) Bergey's Manual of Systematic Bacteriology , vol.1 , pp. 31-34
    • Murray, R.G.E.1
  • 13
    • 80053366426 scopus 로고    scopus 로고
    • Class II. Clostridia class nov
    • P. De Vos, G.M. Garrity, D. Jones, N.R. Krieg, W. Ludwig, F.A. Rainey, K.H. Schleifer, and W.B. Whitman, second edition, The Firmicutes), Springer, Dordrecht, Heidelberg, London, New York
    • Rainey FA. "Class II. Clostridia class nov." In: P. De Vos, G.M. Garrity, D. Jones, N.R. Krieg, W. Ludwig, F.A. Rainey, K.H. Schleifer, and W.B. Whitman (eds): Bergey's Manual of Systematic Bacteriology, second edition, vol. 3 (The Firmicutes), Springer, Dordrecht, Heidelberg, London, New York (2009) p. 736.
    • (2009) Bergey's Manual of Systematic Bacteriology , vol.3 , pp. 736
    • Rainey, F.A.1
  • 14
    • 80053365349 scopus 로고    scopus 로고
    • List of new names and new combinations previously effectively, but not valid-ly, published
    • Validation List 132
    • Validation List 132. List of new names and new combinations previously effectively, but not valid-ly, published. Int J Syst Evol Microbiol 2010; 60:469-472. http://dx.doi.org/10.1099/ijs.0.022855-0
    • (2010) Int J Syst Evol Microbiol , vol.60 , pp. 469-472
  • 15
    • 84865212442 scopus 로고
    • Hauderoy P, Ehringer G, Guillot G, Magrou. J., Prévot AR, Rosset D, Urbain A (eds), Second Edition, Masson et Cie, Paris
    • Prévot AR. In: Hauderoy P, Ehringer G, Guillot G, Magrou. J., Prévot AR, Rosset D, Urbain A (eds), Dictionnaire des Bactéries Pathogènes, Second Edition, Masson et Cie, Paris, 1953, p. 1-692.
    • (1953) Dictionnaire Des Bactéries Pathogènes , pp. 1-692
    • Prévot, A.R.1
  • 17
    • 0011082784 scopus 로고
    • Klassification der Schizomyceten
    • Pribram E. Klassification der Schizomyceten. F. Deuticke, Leipzig, (1933) pp. 1-143.
    • (1933) F. Deuticke, Leipzig , pp. 1-143
    • Pribram, E.1
  • 19
    • 0000760971 scopus 로고
    • Genus III. Clostridium Prazmowski 1880, 23
    • Buchanan RE, Gibbons NE, Eighth Edition, The Williams and Wilkins Co., Baltimore
    • Smith LDS, Hobbs G. Genus III. Clostridium Prazmowski 1880, 23. In: Buchanan RE, Gibbons NE (eds), Bergey's Manual of Determinative Bacteriology, Eighth Edition, The Williams and Wilkins Co., Baltimore, 1974, p. 551-572.
    • (1974) Bergey's Manual of Determinative Bacteriology , pp. 551-572
    • Smith, L.D.S.1    Hobbs, G.2
  • 21
    • 75549086416 scopus 로고    scopus 로고
    • The Genomes On Line Database (GOLD) in 2009: Status of genomic and metagenomic projects and their associated metadata
    • PubMed
    • Liolios K, Chen IMA, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010; 38:D346-D354.PubMed http://dx.doi.org/10.1093/nar/gkp848
    • (2010) Nucleic Acids Res , vol.38
    • Liolios, K.1    Chen, I.M.A.2    Mavromatis, K.3    Tavernarakis, N.4    Hugenholtz, P.5    Markowitz, V.M.6    Kyrpides, N.C.7
  • 22
    • 84859148447 scopus 로고    scopus 로고
    • JGI standard operating procedure
    • JGI standard operating procedure. http://my.jgi.doe.gov/general/protocols
  • 25
    • 84859153399 scopus 로고    scopus 로고
    • DOE Joint Genome Institute
    • DOE Joint Genome Institute. http://www.jgi.doe.gov
  • 26
    • 43149115851 scopus 로고    scopus 로고
    • Algorithms for de novo short read assembly using de Bruijn graphs
    • PubMed
    • Zerbino DR, Birney E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821-829.PubMed http://dx.doi.org/10.1101/gr.074492.107
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Velvet, B.E.2
  • 27
    • 0031955518 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. I. Accuracy assessment
    • PubMed
    • Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998; 8:175-185.PubMed
    • (1998) Genome Res , vol.8 , pp. 175-185
    • Ewing, B.1    Hillier, L.2    Wendl, M.C.3    Green, P.4
  • 28
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated se-quencer traces using phred. II. Error probabilities
    • PubMed
    • Ewing B, Green P. Base-calling of automated se-quencer traces using phred. II. Error probabilities. Genome Res 1998; 8:186-194.PubMed
    • (1998) Genome Res , vol.8 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 29
    • 0031955116 scopus 로고    scopus 로고
    • Consed: A graphical tool for sequence finishing
    • PubMed
    • Gordon D, Abajian C, Green P. Consed: a graphical tool for sequence finishing. Genome Res 1998; 8:195-202.PubMed
    • (1998) Genome Res , vol.8 , pp. 195-202
    • Gordon, D.1    Abajian, C.2    Green, P.3
  • 30
    • 33751109989 scopus 로고    scopus 로고
    • Arabnia HR, Valafar J, editors, Proceedings of the 2006 inter-national Conference on Bioinformatics and Computational Biology: CSREA Press
    • Han C, Chain P. Finishing repeat regions automatically with Dupfinisher. In: Arabnia HR, Valafar J, editors. Proceedings of the 2006 inter-national Conference on Bioinformatics and Computational Biology: CSREA Press; 2006. p 141-146
    • (2006) Finishing Repeat Regions Automatically With Dupfinisher , pp. 141-146
    • Han, C.1    Chain, P.2
  • 31
    • 77952299957 scopus 로고    scopus 로고
    • Prodigal: Prokaryotic gene recognition and translation initiation site identification
    • Pub-Med
    • Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119. Pub-Med http://dx.doi.org/10.1186/1471-2105-11-119
    • (2010) BMC Bioinformatics , vol.11 , pp. 119
    • Hyatt, D.1    Chen, G.L.2    Locascio, P.F.3    Land, M.L.4    Larimer, F.W.5    Hauser, L.J.6
  • 34
    • 79954572190 scopus 로고    scopus 로고
    • Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725
    • PubMed
    • Dam P, Kataeva I, Yang SJ, Zhou F, Yin Y, Chou W, Poole FL, Westpheling J, Hettich R, Giannone R, et al. Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725. Nucleic Acids Res 2011; 39:3240-3254.PubMed http://dx.doi.org/10.1093/nar/gkq1281
    • (2011) Nucleic Acids Res , vol.39 , pp. 3240-3254
    • Dam, P.1    Kataeva, I.2    Yang, S.J.3    Zhou, F.4    Yin, Y.5    Chou, W.6    Poole, F.L.7    Westpheling, J.8    Hettich, R.9    Giannone, R.10
  • 35
    • 79956112464 scopus 로고    scopus 로고
    • Glycoside hydrolase inventory drives plant polysaccharide deconstruction by the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus
    • PubMed
    • VanFossen AL, Ozdemir I, Zelin SL, Kelly RM. Glycoside hydrolase inventory drives plant polysaccharide deconstruction by the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus. Biotechnol Bioeng 2011; 108:1559-1569.PubMed http://dx.doi.org/10.1002/bit.23093
    • (2011) Biotechnol Bioeng , vol.108 , pp. 1559-1569
    • Vanfossen, A.L.1    Ozdemir, I.2    Zelin, S.L.3    Kelly, R.M.4
  • 36
    • 33846957156 scopus 로고    scopus 로고
    • Two noncellulosomal cellulases of Clostridium thermocellum, Cel9I and Cel48Y, hydrolyse crystalline cellulose synergistically
    • PubMed
    • Berger E, Zhang D, Zverlov VV, Schwarz WH. Two noncellulosomal cellulases of Clostridium thermocellum, Cel9I and Cel48Y, hydrolyse crystalline cellulose synergistically. FEMS Microbiol Lett 2007; 268:194-201.PubMed http://dx.doi.org/10.1111/j.1574-6968.2006.00583.x
    • (2007) FEMS Microbiol Lett , vol.268 , pp. 194-201
    • Berger, E.1    Zhang, D.2    Zverlov, V.V.3    Schwarz, W.H.4
  • 37
    • 67649214495 scopus 로고    scopus 로고
    • Impact of pretreated Switchgrass and biomass carbohydrates on Clostridium thermocellum ATCC 27405 cellulosome composition: A quantitative proteomic analysis
    • PubMed
    • Raman B, Pan C, Hurst G, Rodriguez M, Jr., McKeown C, Lankford P, Samatova N, Mielenz J. Impact of pretreated Switchgrass and biomass carbohydrates on Clostridium thermocellum ATCC 27405 cellulosome composition: a quantitative proteomic analysis. PLoS ONE 2009; 4:e5271.PubMed http://dx.doi.org/10.1371/journal.pone.0005271
    • (2009) PLoS ONE , vol.4
    • Raman, B.1    Pan, C.2    Hurst, G.3    Rodriguez Jr., M.4    McKeown, C.5    Lankford, P.6    Samatova, N.7    Mielenz, J.8
  • 38
    • 34948817185 scopus 로고    scopus 로고
    • Global view of the Clostridium thermocellum cellulosome revealed by quantitative proteomic analysis
    • PubMed
    • Gold ND, Martin VJJ. Global view of the Clostridium thermocellum cellulosome revealed by quantitative proteomic analysis. J Bacteriol 2007; 189:6787-6795.PubMed http://dx.doi.org/10.1128/JB.00882-07
    • (2007) J Bacteriol , vol.189 , pp. 6787-6795
    • Gold, N.D.1    Martin, V.J.J.2
  • 39
    • 77953143732 scopus 로고    scopus 로고
    • The unique set of putative membrane-associated antisigma factors in Clostridium thermocellum suggests a novel extracellular carbohydrate-sensing mechanism involved in gene regulation
    • PubMed
    • Kahel-Raifer H, Jindou S, Bahari L, Nataf Y, Shoham Y, Bayer EA, Borovok I, Lamed R. The unique set of putative membrane-associated antisigma factors in Clostridium thermocellum suggests a novel extracellular carbohydrate-sensing mechanism involved in gene regulation. FEMS Microbiol Lett 2010; 308:84-93.PubMed http://dx.doi.org/10.1111/j.1574-6968.2010.01997.x
    • (2010) FEMS Microbiol Lett , vol.308 , pp. 84-93
    • Kahel-Raifer, H.1    Jindou, S.2    Bahari, L.3    Nataf, Y.4    Shoham, Y.5    Bayer, E.A.6    Borovok, I.7    Lamed, R.8
  • 40
    • 0033167973 scopus 로고    scopus 로고
    • The cellulosome concept as an efficient microbial strategy for the degradation of insoluble polysaccharides
    • PubMed
    • Shoham Y, Lamed R, Bayer E. The cellulosome concept as an efficient microbial strategy for the degradation of insoluble polysaccharides. Trends Microbiol 1999; 7:275-281.PubMed http://dx.doi.org/10.1016/S0966-842X(99)01533-4
    • (1999) Trends Microbiol , vol.7 , pp. 275-281
    • Shoham, Y.1    Lamed, R.2    Bayer, E.3
  • 41
    • 3142757398 scopus 로고    scopus 로고
    • Cellulosomes: Plant-cell-wall-degrading enzyme complexes
    • PubMed
    • Doi RH, Kosugi A. Cellulosomes: plant-cell-wall-degrading enzyme complexes. Nat Rev Microbiol 2004; 2:541-551.PubMed http://dx.doi.org/10.1038/nrmicro925
    • (2004) Nat Rev Microbiol , vol.2 , pp. 541-551
    • Doi, R.H.1    Kosugi, A.2
  • 42
    • 4344636766 scopus 로고    scopus 로고
    • A novel Acetivibrio cellulolyticus anchoring scaffoldin that bears divergent cohesins
    • PubMed
    • Xu Q, Barak Y, Kenig R, Shoham Y, Bayer E, La-med R. A novel Acetivibrio cellulolyticus anchoring scaffoldin that bears divergent cohesins. J Bacteriol 2004; 186:5782-5789.PubMed http://dx.doi.org/10.1128/JB.186.17.5782-5789.2004
    • (2004) J Bacteriol , vol.186 , pp. 5782-5789
    • Xu, Q.1    Barak, Y.2    Kenig, R.3    Shoham, Y.4    Bayer, E.5    La-Med, R.6
  • 43
    • 0038443570 scopus 로고    scopus 로고
    • The cellulosome system of Acetivibrio cellulolytiscus includes a novel type of adaptor protein and a cell surface anchoring protein
    • PubMed
    • Xu Q, Gao W, Ding S, Kenig R, Shoham Y, Bayer E, Lamed R. The cellulosome system of Acetivibrio cellulolytiscus includes a novel type of adaptor protein and a cell surface anchoring protein. J Bacteriol 2003; 185:4548-4557.PubMed http://dx.doi.org/10.1128/JB.185.15.4548-4557.2003
    • (2003) J Bacteriol , vol.185 , pp. 4548-4557
    • Xu, Q.1    Gao, W.2    Ding, S.3    Kenig, R.4    Shoham, Y.5    Bayer, E.6    Lamed, R.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.