Literature DB >> 22843576

Complete genome sequence of the hyperthermophilic archaeon Pyrococcus sp. strain ST04, isolated from a deep-sea hydrothermal sulfide chimney on the Juan de Fuca Ridge.

Jong-Hyun Jung1, Ju-Hoon Lee, James F Holden, Dong-Ho Seo, Hakdong Shin, Hae-Yeong Kim, Wooki Kim, Sangryeol Ryu, Cheon-Seok Park.   

Abstract

Pyrococcus sp. strain ST04 is a hyperthermophilic, anaerobic, and heterotrophic archaeon isolated from a deep-sea hydrothermal sulfide chimney on the Endeavour Segment of the Juan de Fuca Ridge in the northeastern Pacific Ocean. To further understand the distinct characteristics of this archaeon at the genome level (polysaccharide utilization at high temperature and ATP generation by a Na(+) gradient), the genome of strain ST04 was completely sequenced and analyzed. Here, we present the complete genome sequence analysis results of Pyrococcus sp. ST04 and report the major findings from the genome annotation, with a focus on its saccharolytic and metabolite production potential.

Entities:  

Mesh:

Substances:

Year:  2012        PMID: 22843576      PMCID: PMC3416228          DOI: 10.1128/JB.00824-12

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


  12 in total

1.  GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.

Authors:  J Besemer; A Lomsadze; M Borodovsky
Journal:  Nucleic Acids Res       Date:  2001-06-15       Impact factor: 16.971

Review 2.  The unique features of glycolytic pathways in Archaea.

Authors:  Corné H Verhees; Servé W M Kengen; Judith E Tuininga; Gerrit J Schut; Michael W W Adams; Willem M De Vos; John Van Der Oost
Journal:  Biochem J       Date:  2003-10-15       Impact factor: 3.857

3.  Basic local alignment search tool.

Authors:  S F Altschul; W Gish; W Miller; E W Myers; D J Lipman
Journal:  J Mol Biol       Date:  1990-10-05       Impact factor: 5.469

4.  Identifying bacterial genes and endosymbiont DNA with Glimmer.

Authors:  Arthur L Delcher; Kirsten A Bratke; Edwin C Powers; Steven L Salzberg
Journal:  Bioinformatics       Date:  2007-01-19       Impact factor: 6.937

5.  Abundances of hyperthermophilic autotrophic Fe(III) oxide reducers and heterotrophs in hydrothermal sulfide chimneys of the northeastern Pacific Ocean.

Authors:  Helene C Ver Eecke; Deborah S Kelley; James F Holden
Journal:  Appl Environ Microbiol       Date:  2008-10-31       Impact factor: 4.792

6.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.

Authors:  T M Lowe; S R Eddy
Journal:  Nucleic Acids Res       Date:  1997-03-01       Impact factor: 16.971

7.  Production of hydrogen from α-1,4- and β-1,4-linked saccharides by marine hyperthermophilic Archaea.

Authors:  Daniel M Oslowski; Jong-Hyun Jung; Dong-Ho Seo; Cheon-Seok Park; James F Holden
Journal:  Appl Environ Microbiol       Date:  2011-03-18       Impact factor: 4.792

8.  A simple energy-conserving system: proton reduction coupled to proton translocation.

Authors:  Rajat Sapra; Karine Bagramyan; Michael W W Adams
Journal:  Proc Natl Acad Sci U S A       Date:  2003-06-05       Impact factor: 11.205

9.  RNAmmer: consistent and rapid annotation of ribosomal RNA genes.

Authors:  Karin Lagesen; Peter Hallin; Einar Andreas Rødland; Hans-Henrik Staerfeldt; Torbjørn Rognes; David W Ussery
Journal:  Nucleic Acids Res       Date:  2007-04-22       Impact factor: 16.971

10.  Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth.

Authors:  Ju-Hoon Lee; V N Karamychev; S A Kozyavkin; D Mills; A R Pavlov; N V Pavlova; N N Polouchine; P M Richardson; V V Shakhova; A I Slesarev; B Weimer; D J O'Sullivan
Journal:  BMC Genomics       Date:  2008-05-27       Impact factor: 3.969

View more
  6 in total

Review 1.  Diversity of CRISPR systems in the euryarchaeal Pyrococcales.

Authors:  Cédric Norais; Annick Moisan; Christine Gaspin; Béatrice Clouet-d'Orval
Journal:  RNA Biol       Date:  2013-02-19       Impact factor: 4.652

2.  Analysis of the complete genome sequence of the archaeon Pyrococcus chitonophagus DSM 10152 (formerly Thermococcus chitonophagus).

Authors:  Konstantinos Papadimitriou; Panagiotis K Baharidis; Anastasios Georgoulis; Marion Engel; Maria Louka; Georgia Karamolegkou; Aggeliki Tsoka; Jochen Blom; Bruno Pot; Piotr Malecki; Wojciech Rypniewski; Harald Huber; Michael Schloter; Constantinos Vorgias
Journal:  Extremophiles       Date:  2016-03-25       Impact factor: 2.395

3.  Identification and characterization of an archaeal kojibiose catabolic pathway in the hyperthermophilic Pyrococcus sp. strain ST04.

Authors:  Jong-Hyun Jung; Dong-Ho Seo; James F Holden; Cheon-Seok Park
Journal:  J Bacteriol       Date:  2014-01-03       Impact factor: 3.490

4.  Comparative genomics reveals conserved positioning of essential genomic clusters in highly rearranged Thermococcales chromosomes.

Authors:  Matteo Cossu; Violette Da Cunha; Claire Toffano-Nioche; Patrick Forterre; Jacques Oberto
Journal:  Biochimie       Date:  2015-07-10       Impact factor: 4.079

5.  Structural basis of substrate selectivity of E. coli prolidase.

Authors:  Jeremy Weaver; Tylan Watts; Pingwei Li; Hays S Rye
Journal:  PLoS One       Date:  2014-10-29       Impact factor: 3.240

6.  Complete Genome Sequence of the Hyperthermophilic Piezophilic Archaeon Pyrococcus kukulkanii NCB100 Isolated from the Rebecca's Roost Hydrothermal Vent in the Guaymas Basin.

Authors:  Philippe M Oger; Nolwenn Callac; Christine Oger-Desfeux; Sandrine Hughes; Benjamin Gillet; Mohamed Jebbar; Anne Godfroy
Journal:  Genome Announc       Date:  2017-02-16
  6 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.