Literature DB >> 21216991

Complete genome sequences for the anaerobic, extremely thermophilic plant biomass-degrading bacteria Caldicellulosiruptor hydrothermalis, Caldicellulosiruptor kristjanssonii, Caldicellulosiruptor kronotskyensis, Caldicellulosiruptor owensensis, and Caldicellulosiruptor lactoaceticus.

Sara E Blumer-Schuette1, Inci Ozdemir, Dhaval Mistry, Susan Lucas, Alla Lapidus, Jan-Fang Cheng, Lynne A Goodwin, Samuel Pitluck, Miriam L Land, Loren J Hauser, Tanja Woyke, Natalia Mikhailova, Amrita Pati, Nikos C Kyrpides, Natalia Ivanova, John C Detter, Karen Walston-Davenport, Shunsheng Han, Michael W W Adams, Robert M Kelly.   

Abstract

The genus Caldicellulosiruptor contains the most thermophilic, plant biomass-degrading bacteria isolated to date. Previously, genome sequences from three cellulolytic members of this genus were reported (C. saccharolyticus, C. bescii, and C. obsidiansis). To further explore the physiological and biochemical basis for polysaccharide degradation within this genus, five additional genomes were sequenced: C. hydrothermalis, C. kristjanssonii, C. kronotskyensis, C. lactoaceticus, and C. owensensis. Taken together, the seven completed and one draft-phase Caldicellulosiruptor genomes suggest that, while central metabolism is highly conserved, significant differences in glycoside hydrolase inventories and numbers of carbohydrate transporters exist, a finding which likely relates to variability observed in plant biomass degradation capacity.

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Year:  2011        PMID: 21216991      PMCID: PMC3067630          DOI: 10.1128/JB.01515-10

Source DB:  PubMed          Journal:  J Bacteriol        ISSN: 0021-9193            Impact factor:   3.490


  17 in total

1.  Phylogenetic, microbiological, and glycoside hydrolase diversities within the extremely thermophilic, plant biomass-degrading genus Caldicellulosiruptor.

Authors:  Sara E Blumer-Schuette; Derrick L Lewis; Robert M Kelly
Journal:  Appl Environ Microbiol       Date:  2010-10-22       Impact factor: 4.792

2.  Solexa Ltd.

Authors:  Simon Bennett
Journal:  Pharmacogenomics       Date:  2004-06       Impact factor: 2.533

3.  Genome sequencing in microfabricated high-density picolitre reactors.

Authors:  Marcel Margulies; Michael Egholm; William E Altman; Said Attiya; Joel S Bader; Lisa A Bemben; Jan Berka; Michael S Braverman; Yi-Ju Chen; Zhoutao Chen; Scott B Dewell; Lei Du; Joseph M Fierro; Xavier V Gomes; Brian C Godwin; Wen He; Scott Helgesen; Chun Heen Ho; Chun He Ho; Gerard P Irzyk; Szilveszter C Jando; Maria L I Alenquer; Thomas P Jarvie; Kshama B Jirage; Jong-Bum Kim; James R Knight; Janna R Lanza; John H Leamon; Steven M Lefkowitz; Ming Lei; Jing Li; Kenton L Lohman; Hong Lu; Vinod B Makhijani; Keith E McDade; Michael P McKenna; Eugene W Myers; Elizabeth Nickerson; John R Nobile; Ramona Plant; Bernard P Puc; Michael T Ronan; George T Roth; Gary J Sarkis; Jan Fredrik Simons; John W Simpson; Maithreyan Srinivasan; Karrie R Tartaro; Alexander Tomasz; Kari A Vogt; Greg A Volkmer; Shally H Wang; Yong Wang; Michael P Weiner; Pengguang Yu; Richard F Begley; Jonathan M Rothberg
Journal:  Nature       Date:  2005-07-31       Impact factor: 49.962

4.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

Authors:  Daniel R Zerbino; Ewan Birney
Journal:  Genome Res       Date:  2008-03-18       Impact factor: 9.043

5.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment.

Authors:  B Ewing; L Hillier; M C Wendl; P Green
Journal:  Genome Res       Date:  1998-03       Impact factor: 9.043

6.  Base-calling of automated sequencer traces using phred. II. Error probabilities.

Authors:  B Ewing; P Green
Journal:  Genome Res       Date:  1998-03       Impact factor: 9.043

7.  Consed: a graphical tool for sequence finishing.

Authors:  D Gordon; C Abajian; P Green
Journal:  Genome Res       Date:  1998-03       Impact factor: 9.043

8.  Caldicellulosiruptor kristjanssonii sp. nov., a cellulolytic, extremely thermophilic, anaerobic bacterium.

Authors:  S Bredholt; J Sonne-Hansen; P Nielsen; I M Mathrani; B K Ahring
Journal:  Int J Syst Bacteriol       Date:  1999-07

9.  Caldicellulosiruptor owensensis sp. nov., an anaerobic, extremely thermophilic, xylanolytic bacterium.

Authors:  C Y Huang; B K Patel; R A Mah; L Baresi
Journal:  Int J Syst Bacteriol       Date:  1998-01

10.  Description of Caldicellulosiruptor saccharolyticus gen. nov., sp. nov: an obligately anaerobic, extremely thermophilic, cellulolytic bacterium.

Authors:  F A Rainey; A M Donnison; P H Janssen; D Saul; A Rodrigo; P L Bergquist; R M Daniel; E Stackebrandt; H W Morgan
Journal:  FEMS Microbiol Lett       Date:  1994-07-15       Impact factor: 2.742

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  25 in total

1.  Caldicellulosiruptor core and pangenomes reveal determinants for noncellulosomal thermophilic deconstruction of plant biomass.

Authors:  Sara E Blumer-Schuette; Richard J Giannone; Jeffrey V Zurawski; Inci Ozdemir; Qin Ma; Yanbin Yin; Ying Xu; Irina Kataeva; Farris L Poole; Michael W W Adams; Scott D Hamilton-Brehm; James G Elkins; Frank W Larimer; Miriam L Land; Loren J Hauser; Robert W Cottingham; Robert L Hettich; Robert M Kelly
Journal:  J Bacteriol       Date:  2012-05-25       Impact factor: 3.490

2.  Genome Diversity of Spore-Forming Firmicutes.

Authors:  Michael Y Galperin
Journal:  Microbiol Spectr       Date:  2013-12

3.  Improved growth media and culture techniques for genetic analysis and assessment of biomass utilization by Caldicellulosiruptor bescii.

Authors:  Joel Farkas; Daehwan Chung; Minseok Cha; Jennifer Copeland; Philip Grayeski; Janet Westpheling
Journal:  J Ind Microbiol Biotechnol       Date:  2012-11-13       Impact factor: 3.346

4.  Genomic and physiological analyses reveal that extremely thermophilic Caldicellulosiruptor changbaiensis deploys uncommon cellulose attachment mechanisms.

Authors:  Asma M A M Khan; Carl Mendoza; Valerie J Hauk; Sara E Blumer-Schuette
Journal:  J Ind Microbiol Biotechnol       Date:  2019-08-07       Impact factor: 3.346

5.  Comparative Analysis of Extremely Thermophilic Caldicellulosiruptor Species Reveals Common and Unique Cellular Strategies for Plant Biomass Utilization.

Authors:  Jeffrey V Zurawski; Jonathan M Conway; Laura L Lee; Hunter J Simpson; Javier A Izquierdo; Sara Blumer-Schuette; Intawat Nookaew; Michael W W Adams; Robert M Kelly
Journal:  Appl Environ Microbiol       Date:  2015-08-07       Impact factor: 4.792

6.  Detection of a novel active transposable element in Caldicellulosiruptor hydrothermalis and a new search for elements in this genus.

Authors:  Daehwan Chung; Joel Farkas; Janet Westpheling
Journal:  J Ind Microbiol Biotechnol       Date:  2013-03-10       Impact factor: 3.346

7.  A genomic signature and the identification of new sporulation genes.

Authors:  Ana B Abecasis; Mónica Serrano; Renato Alves; Leonor Quintais; José B Pereira-Leal; Adriano O Henriques
Journal:  J Bacteriol       Date:  2013-02-08       Impact factor: 3.490

8.  Multidomain, Surface Layer-associated Glycoside Hydrolases Contribute to Plant Polysaccharide Degradation by Caldicellulosiruptor Species.

Authors:  Jonathan M Conway; William S Pierce; Jaycee H Le; George W Harper; John H Wright; Allyson L Tucker; Jeffrey V Zurawski; Laura L Lee; Sara E Blumer-Schuette; Robert M Kelly
Journal:  J Biol Chem       Date:  2016-01-26       Impact factor: 5.157

9.  Genus-Wide Assessment of Lignocellulose Utilization in the Extremely Thermophilic Genus Caldicellulosiruptor by Genomic, Pangenomic, and Metagenomic Analyses.

Authors:  Laura L Lee; Sara E Blumer-Schuette; Javier A Izquierdo; Jeffrey V Zurawski; Andrew J Loder; Jonathan M Conway; James G Elkins; Mircea Podar; Alicia Clum; Piet C Jones; Marek J Piatek; Deborah A Weighill; Daniel A Jacobson; Michael W W Adams; Robert M Kelly
Journal:  Appl Environ Microbiol       Date:  2018-04-16       Impact factor: 4.792

10.  Methylation by a unique α-class N4-cytosine methyltransferase is required for DNA transformation of Caldicellulosiruptor bescii DSM6725.

Authors:  Daehwan Chung; Joel Farkas; Jennifer R Huddleston; Estefania Olivar; Janet Westpheling
Journal:  PLoS One       Date:  2012-08-22       Impact factor: 3.240

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