RASTA-Bacteria: a web-based tool for identifying toxin-antitoxin loci in prokaryotes

被引：183

作者：

Sevin, Emeric W. ^{[1
]}

Barloy-Hubler, Frederique ^{[1
,2
]}

机构：

[1] Univ Rennes 1, CNRS, UMR Genet & Dev 6061, IFR 140, F-35043 Rennes, France

[2] Univ Rennes 1, Grp DUALS, CNRS, UMR Interact Cellulaires & Mol 6026,IFR 140, F-35042 Rennes, France

来源：

GENOME BIOLOGY | 2007年 / 8卷 / 08期

关键词：

D O I：

10.1186/gb-2007-8-8-r155

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Toxin/antitoxin (TA) systems, viewed as essential regulators of growth arrest and programmed cell death, are widespread among prokaryotes, but remain sparsely annotated. We present RASTA-Bacteria, an automated method allowing quick and reliable identification of TA loci in sequenced prokaryotic genomes, whether they are annotated open reading frames or not. The tool successfully confirmed all reported TA systems, and spotted new putative loci upon screening of sequenced genomes. RASTA-Bacteria is publicly available at http://genoweb.univ-rennes1.fr/duals/ RASTA-Bacteria.

引用

页数：14

共 65 条

[31] Functional genomics of genes with small open reading frames (sORFs) in S-cerevisiae [J].

Kastenmayer, JP ;

Ni, L ;

Chu, A ;

Kitchen, LE ;

Au, WC ;

Yang, H ;

Carter, CD ;

Wheeler, D ;

Davis, RW ;

Boeke, JD ;

Snyder, MA ;

Basrai, MA .

GENOME RESEARCH, 2006, 16 (03) :365-373

[32] Induction of Escherichia coli chromosomal mazEF by stressful conditions causes an irreversible loss of viability [J].

Kolodkin-Gal, I ;

Engelberg-Kulka, H .

JOURNAL OF BACTERIOLOGY, 2006, 188 (09) :3420-3423

[33] Ectopic overexpression of wild-type and mutant hipA genes in Escherichia coli:: Effects on macromolecular synthesis and persister formation [J].

Korch, Shaleen B. ;

Hill, Thomas M. .

JOURNAL OF BACTERIOLOGY, 2006, 188 (11) :3826-3836

[34] The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide [J].

Liolios, Konstantinos ;

Tavernarakis, Nektarios ;

Hugenholtz, Philip ;

Kyrpides, Nikos C. .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D332-D334

[35] The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria [J].

Makarova, Kira S. ;

Grishin, Nick V. ;

Koonin, Eugene V. .

BIOINFORMATICS, 2006, 22 (21) :2581-2584

[36] Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities [J].

Mantri, Y ;

Williams, KP .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D55-D58

[37] CHPA AND CHPB, ESCHERICHIA-COLI CHROMOSOMAL HOMOLOGS OF THE PEM LOCUS RESPONSIBLE FOR STABLE MAINTENANCE OF PLASMID R100 [J].

MASUDA, YJ ;

MIYAKAWA, K ;

NISHIMURA, Y ;

OHTSUBO, E .

JOURNAL OF BACTERIOLOGY, 1993, 175 (21) :6850-6856

[38]

METZGER S, 1988, J BIOL CHEM, V263, P15699

[39] TRANSCRIPTION OF THE STABILITY OPERON OF INCFII PLASMID NR1 [J].

MIN, YN ;

TABUCHI, A ;

WOMBLE, DD ;

ROWND, RH .

JOURNAL OF BACTERIOLOGY, 1991, 173 (07) :2378-2384

[40]

Mittenhuber Gerhard, 1999, Journal of Molecular Microbiology and Biotechnology, V1, P295

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