Literature DB >> 22207743

Complete genome sequence of Sphingobium sp. strain SYK-6, a degrader of lignin-derived biaryls and monoaryls.

Eiji Masai1, Naofumi Kamimura, Daisuke Kasai, Akio Oguchi, Akiho Ankai, Shigehiro Fukui, Mikio Takahashi, Isao Yashiro, Hiroki Sasaki, Takeshi Harada, Sanae Nakamura, Yoko Katano, Sachiko Narita-Yamada, Hidekazu Nakazawa, Hirofumi Hara, Yoshihiro Katayama, Masao Fukuda, Shuji Yamazaki, Nobuyuki Fujita.   

Abstract

Sphingobium sp. strain SYK-6 is able to grow on an extensive variety of lignin-derived biaryls and monoaryls, and the catabolic genes for these compounds are useful for the production of industrially valuable metabolites from lignin. Here we report the complete nucleotide sequence of the SYK-6 genome which consists of the 4,199,332-bp-long chromosome and the 148,801-bp-long plasmid.

Entities:  

Mesh：

Substances：

Year:  2012        PMID： 22207743      PMCID： PMC3256637          DOI： 10.1128/JB.06254-11

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


  12 in total

1.  ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences.

Authors:  Dean Laslett; Bjorn Canback
Journal:  Nucleic Acids Res       Date:  2004-01-02       Impact factor: 16.971

2.  The emerging role for bacteria in lignin degradation and bio-product formation.

Authors:  Timothy D H Bugg; Mark Ahmad; Elizabeth M Hardiman; Rahul Singh
Journal:  Curr Opin Biotechnol       Date:  2010-11-09       Impact factor: 9.740

3.  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

4.  Efficient production of 2-pyrone 4,6-dicarboxylic acid as a novel polymer-based material from protocatechuate by microbial function.

Authors:  Yuichiro Otsuka; Masaya Nakamura; Kiyotaka Shigehara; Kosuke Sugimura; Eiji Masai; Seiji Ohara; Yoshihiro Katayama
Journal:  Appl Microbiol Biotechnol       Date:  2005-12-02       Impact factor: 4.813

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.  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

Review 9.  Genetic and biochemical investigations on bacterial catabolic pathways for lignin-derived aromatic compounds.

Authors:  Eiji Masai; Yoshihiro Katayama; Masao Fukuda
Journal:  Biosci Biotechnol Biochem       Date:  2007-01-07       Impact factor: 2.043

10.  Characterization of the gallate dioxygenase gene: three distinct ring cleavage dioxygenases are involved in syringate degradation by Sphingomonas paucimobilis SYK-6.

Authors:  Daisuke Kasai; Eiji Masai; Keisuke Miyauchi; Yoshihiro Katayama; Masao Fukuda
Journal:  J Bacteriol       Date:  2005-08       Impact factor: 3.490
View more
  15 in total

1.  Decoding how a soil bacterium extracts building blocks and metabolic energy from ligninolysis provides road map for lignin valorization.

Authors:  Arul M Varman; Lian He; Rhiannon Follenfant; Weihua Wu; Sarah Wemmer; Steven A Wrobel; Yinjie J Tang; Seema Singh
Journal:  Proc Natl Acad Sci U S A       Date:  2016-09-15       Impact factor: 11.205

2.  Overcoming a hemihedral twinning problem in tetrahydrofolate-dependent O-demethylase crystals by the microseeding method.

Authors:  Ayaka Harada; Yukari Sato; Naofumi Kamimura; Nagarajan Venugopalan; Eiji Masai; Toshiya Senda
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2016-11-30       Impact factor: 1.056

3.  Genomics analysis and degradation characteristics of lignin by Streptomyces thermocarboxydus strain DF3-3.

Authors:  Fangyun Tan; Jun Cheng; Yu Zhang; Xingfu Jiang; Yueqiu Liu
Journal:  Biotechnol Biofuels Bioprod       Date:  2022-07-12

4.  Three-Component O-Demethylase System Essential for Catabolism of a Lignin-Derived Biphenyl Compound in Sphingobium sp. Strain SYK-6.

Authors:  Taichi Yoshikata; Kazuya Suzuki; Naofumi Kamimura; Masahiro Namiki; Shojiro Hishiyama; Takuma Araki; Daisuke Kasai; Yuichiro Otsuka; Masaya Nakamura; Masao Fukuda; Yoshihiro Katayama; Eiji Masai
Journal:  Appl Environ Microbiol       Date:  2014-09-12       Impact factor: 4.792

5.  Comparison of 26 sphingomonad genomes reveals diverse environmental adaptations and biodegradative capabilities.

Authors:  Frank O Aylward; Bradon R McDonald; Sandra M Adams; Alejandra Valenzuela; Rebeccah A Schmidt; Lynne A Goodwin; Tanja Woyke; Cameron R Currie; Garret Suen; Michael Poulsen
Journal:  Appl Environ Microbiol       Date:  2013-04-05       Impact factor: 4.792

6.  Insights into Ongoing Evolution of the Hexachlorocyclohexane Catabolic Pathway from Comparative Genomics of Ten Sphingomonadaceae Strains.

Authors:  Stephen L Pearce; John G Oakeshott; Gunjan Pandey
Journal:  G3 (Bethesda)       Date:  2015-04-07       Impact factor: 3.154

7.  Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways.

Authors:  Helianthous Verma; Roshan Kumar; Phoebe Oldach; Naseer Sangwan; Jitendra P Khurana; Jack A Gilbert; Rup Lal
Journal:  BMC Genomics       Date:  2014-11-23       Impact factor: 3.969

8.  A group of sequence-related sphingomonad enzymes catalyzes cleavage of β-aryl ether linkages in lignin β-guaiacyl and β-syringyl ether dimers.

Authors:  Daniel L Gall; John Ralph; Timothy J Donohue; Daniel R Noguera
Journal:  Environ Sci Technol       Date:  2014-10-01       Impact factor: 9.028

9.  Reconstructing an ancestral genotype of two hexachlorocyclohexane-degrading Sphingobium species using metagenomic sequence data.

Authors:  Naseer Sangwan; Helianthous Verma; Roshan Kumar; Vivek Negi; Simon Lax; Paramjit Khurana; Jitendra P Khurana; Jack A Gilbert; Rup Lal
Journal:  ISME J       Date:  2013-09-12       Impact factor: 10.302

10.  Genomic and secretomic insight into lignocellulolytic system of an endophytic bacterium Pantoea ananatis Sd-1.

Authors:  Jiangshan Ma; Keke Zhang; Hongdong Liao; Stanton B Hector; Xiaowei Shi; Jianglin Li; Bin Liu; Ting Xu; Chunyi Tong; Xuanming Liu; Yonghua Zhu
Journal:  Biotechnol Biofuels       Date:  2016-02-02       Impact factor: 6.040
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.