Complete genome sequence of "Enterobacter lignolyticus" SCF1

被引：61

作者：

DeAngelis, Kristen M. ^{[1
,2
]}

D'Haeseleer, Patrik ^{[1
,3
]}

Chivian, Dylan ^{[4
,5
]}

Fortney, Julian L. ^{[1
]}

Khudyakov, Jane ^{[2
,3
]}

Simmons, Blake ^{[2
,6
]}

Woo, Hannah ^{[1
,2
]}

Arkin, Adam P. ^{[4
,5
]}

Davenport, Karen Walston ^{[7
]}

Goodwin, Lynne ^{[7
]}

Chen, Amy ^{[8
]}

Ivanova, Natalia ^{[8
]}

Kyrpides, Nikos C. ^{[8
]}

Mavromatis, Konstantinos ^{[8
]}

Woyke, Tanja ^{[8
]}

Hazen, Terry C. ^{[1
,2
]}

机构：

[1] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Dept Ecol, Berkeley, CA 94720 USA

[2] Joint BioEnergy Inst, Deconstruct Div, Microbial Communities Grp, Emeryville, CA USA

[3] Lawrence Livermore Natl Lab, Livermore, CA USA

[4] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA

[5] Joint BioEnergy Inst, Technol Div, Emeryville, CA USA

[6] Sandia Natl Labs, Livermore, CA USA

[7] Los Alamos Natl Lab, Los Alamos, NM USA

[8] US DOE, Joint Genome Inst, Walnut Creek, CA USA

来源：

STANDARDS IN GENOMIC SCIENCES | 2011年 / 5卷 / 01期

关键词：

Anaerobic lignin degradation; tropical forest soil isolate; facultative anaerobe; ANNOTATION; ACCURACY; BACTERIA; LIGNIN; SYSTEM; TOOL;

D O I：

10.4056/sigs.2104875

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated "Enterobacter lignolyticus" SCF1 on minimal media with alkali lignin as the sole source of carbon. This organism was isolated anaerobically from tropical forest soils collected from the Short Cloud Forest site in the El Yunque National Forest in Puerto Rico, USA, part of the Luquillo Long-Term Ecological Research Station. At this site, the soils experience strong fluctuations in redox potential and are net methane producers. Because of its ability to grow on lignin anaerobically, we sequenced the genome. The genome of "E. lignolyticus" SCF1 is 4.81 Mbp with no detected plasmids, and includes a relatively small arsenal of lignocellulolytic carbohydrate active enzymes. Lignin degradation was observed in culture, and the genome revealed two putative laccases, a putative peroxidase, and a complete 4-hydroxyphenylacetate degradation pathway encoded in a single gene cluster.

引用

页码：69 / 85

页数：17

共 49 条

[1]

[Anonymous], 1958, INT B BACT NOMENCL T, V8, P73

[2]

[Anonymous], P 2006 INT C BIOINF

[3] Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[4] Solexa Ltd [J].

Bennett, S .

PHARMACOGENOMICS, 2004, 5 (04) :433-438

[5] The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics [J].

Cantarel, Brandi L. ;

Coutinho, Pedro M. ;

Rancurel, Corinne ;

Bernard, Thomas ;

Lombard, Vincent ;

Henrissat, Bernard .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D233-D238

[6] Toward automatic reconstruction of a highly resolved tree of life [J].

Ciccarelli, FD ;

Doerks, T ;

von Mering, C ;

Creevey, CJ ;

Snel, B ;

Bork, P .

SCIENCE, 2006, 311 (5765) :1283-1287

[7] Controls on long-term root and leaf litter decomposition in neotropical forests [J].

Cusack, Daniela F. ;

Chou, Wendy W. ;

Yang, Wendy H. ;

Harmon, Mark E. ;

Silver, Whendee L. .

GLOBAL CHANGE BIOLOGY, 2009, 15 (05) :1339-1355

[8] Microbial communities acclimate to recurring changes in soil redox potential status [J].

DeAngelis, Kristen M. ;

Silver, Whendee L. ;

Thompson, Andrew W. ;

Firestone, Mary K. .

ENVIRONMENTAL MICROBIOLOGY, 2010, 12 (12) :3137-3149

[9] MicrobesOnline: an integrated portal for comparative and functional genomics [J].

Dehal, Paramvir S. ;

Joachimiak, Marcin P. ;

Price, Morgan N. ;

Bates, John T. ;

Baumohl, Jason K. ;

Chivian, Dylan ;

Friedland, Greg D. ;

Huang, Katherine H. ;

Keller, Keith ;

Novichkov, Pavel S. ;

Dubchak, Inna L. ;

Alm, Eric J. ;

Arkin, Adam P. .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D396-D400

[10]

*ED BOARD, 1963, INT B BACT NOMENCL T, V13, P38, DOI DOI 10.1099/0096266X-13-1-38

← 1 2 3 4 5 →