TADB: A web-based resource for Type 2 toxin-antitoxin loci in bacteria and archaea

Nucleic Acids Research

Volumn 39, Issue SUPPL. 1, 2011, Pages

  Shao, Yucheng ^a   Harrison, Ewan M ^b   Bi, Dexi ^a   Tai, Cui ^a   He, Xinyi ^a   Ou, Hong Yu ^a   Rajakumar, Kumar ^b,c   Deng, Zixin ^a  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

^b UNIVERSITY OF LEICESTER   (United Kingdom)

^c UNIVERSITY HOSPITALS OF LEICESTER NHS TRUST   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEBACTERIUM; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; GENE IDENTIFICATION; GENE LOCUS; GENE SEQUENCE; GENETIC DATABASE; INTERNET; MICROBIAL ACTIVITY; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROKARYOTE; SEQUENCE ALIGNMENT; TYPE 2 TOXIN ANTITOXIN DATABASE; TYPE 2 TOXIN ANTITOXIN GENE;

ARCHAEA; ARCHAEAL PROTEINS; BACTERIA; BACTERIAL PROTEINS; BACTERIAL TOXINS; DATABASES, GENETIC; GENETIC LOCI; GENOME, ARCHAEAL; GENOME, BACTERIAL; INTERNET; TOXINS, BIOLOGICAL;

ARCHAEA; BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 78651266381     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq908     Document Type: Article

References (30)

1. Gerdes, K., Christensen, S.K. and Lobner-Olesen, A. (2005) Prokaryotic toxin-antitoxin stress response loci. Nat. Rev. Microbiol., 3, 371-382.
2. Van Melderen, L. and Saavedra De Bast, M. (2009) Bacterial toxin-antitoxin systems: More than selfish entities? PLoS Genetics, 5, e1000437.
3. Pandey, D.P. and Gerdes, K. (2005) Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Res., 33, 966-976.
4. Makarova, K.S., Wolf, Y.I. and Koonin, E.V. (2009) Comprehensive comparative-genomic analysis of Type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes. Biol. Direct, 4, 19.
5. Guglielmini, J., Szpirer, C. and Milinkovitch, M.C. (2008) Automated discovery and phylogenetic analysis of new toxin-antitoxin systems. BMC Microbiol., 8, 104.
6. Sevin, E.W. and Barloy-Hubler, F. (2007) RASTA-Bacteria: A web-based tool for identifying toxin-antitoxin loci in prokaryotes. Genome Biol., 8, R155.
7. Jorgensen, M.G., Pandey, D.P., Jaskolska, M. and Gerdes, K. (2009) HicA of Escherichia coli defines a novel family of translation-independent mRNA interferases in bacteria and archaea. J. Bacteriol., 191, 1191-1199.
8. Wozniak, R.A. and Waldor, M.K. (2009) A toxin-antitoxin system promotes the maintenance of an integrative conjugative element. PLoS Genetics, 5, e1000439.
9. Cooper, T.F., Paixao, T. and Heinemann, J.A. (2010) Within-host competition selects for plasmid-encoded toxin-antitoxin systems. Proc. Biol. Sci., 277, 3149-3155.
10. Szekeres, S., Dauti, M., Wilde, C., Mazel, D. and Rowe-Magnus, D.A. (2007) Chromosomal toxin-antitoxin loci can diminish large-scale genome reductions in the absence of selection. Mol. Microbiol., 63, 1588-1605.
11. Saavedra De Bast, M., Mine, N. and Van Melderen, L. (2008) Chromosomal toxin-antitoxin systems may act as antiaddiction modules. J. Bacteriol., 190, 4603-4609.
12. Ramage, H.R., Connolly, L.E. and Cox, J.S. (2009) Comprehensive functional analysis of Mycobacterium tuberculosis toxin-antitoxin systems: Implications for pathogenesis, stress responses, and evolution. PLoS Genetics, 5, e1000767.
13. Moyed, H.S. and Bertrand, K.P. (1983) hipA, a newly recognized gene of Escherichia coli K-12 that affects frequency of persistence after inhibition of murein synthesis. J. Bacteriol., 155, 768-775.
14. Rotem, E., Loinger, A., Ronin, I., Levin-Reisman, I., Gabay, C., Shoresh, N., Biham, O. and Balaban, N.Q. (2010) Regulation of phenotypic variability by a threshold-based mechanism underlies bacterial persistence. Proc. Natl Acad. Sci. USA, 107, 12541-12546.
15. Mungall, C.J. and Emmert, D.B. (2007) A Chado case study: An ontology-based modular schema for representing genome-associated biological information. Bioinformatics, 23, i337-i346.
16. Sayers, E.W., Barrett, T., Benson, D.A., Bolton, E., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., Dicuccio, M., Federhen, S. et al. (2010) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 38, D5-D16.
17. Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A. et al. (2002) The generic genome browser: A building block for a model organism system database. Genome Res., 12, 1599-1610.
18. Stothard, P. and Wishart, D.S. (2005) Circular genome visualization and exploration using CGView. Bioinformatics, 21, 537-539.
19. Edgar, R.C. (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
20. Waterhouse, A.M., Procter, J.B., Martin, D.M., Clamp, M. and Barton, G.J. (2009) Jalview version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics, 25, 1189-1191.
21. Untergasser, A., Nijveen, H., Rao, X., Bisseling, T., Geurts, R. and Leunissen, J.A. (2007) Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res., 35, W71-W74.
22. Langille, M.G. and Brinkman, F.S. (2009) IslandViewer: An integrated interface for computational identification and visualization of genomic islands. Bioinformatics, 25, 664-665.
23. Ou, H.Y., He, X., Shao, Y., Tai, C., Rajakumar, K. and Deng, Z. (2009) dndDB: A database focused on phosphorothioation of the DNA backbone. PLoS ONE, 4, e5132.
24. Leplae, R., Lima-Mendez, G. and Toussaint, A. (2010) ACLAME: A CLAssification of mobile genetic elements, update 2010. Nucleic Acids Res., 38, D57-D61.
25. Liolios, K., Chen, I.M., Mavromatis, K., Tavernarakis, N., Hugenholtz, P., Markowitz, V.M. and Kyrpides, N.C. (2010) The Genomes On Line Database (GOLD) in 2009: Status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res., 38, D346-D354.
26. Suzuki, Y., Kelly, S.D., Kemner, K.M. and Banfield, J.F. (2003) Microbial populations stimulated for hexavalent uranium reduction in uranium mine sediment. Appl. Environ. Microbiol., 69, 1337-1346.
27. He, X., Ou, H.Y., Yu, Q., Zhou, X., Wu, J., Liang, J., Zhang, W., Rajakumar, K. and Deng, Z. (2007) Analysis of a genomic island housing genes for DNA S-modification system in Streptomyces lividans 66 and its counterparts in other distantly related bacteria. Mol. Microbiol., 65, 1034-1048.
28. Chen, L.H., Kenyon, G.L., Curtin, F., Harayama, S., Bembenek, M.E., Hajipour, G. and Whitman, C.P. (1992) 4-Oxalocrotonate tautomerase, an enzyme composed of 62 amino acid residues per monomer. J. Biol. Chem., 267, 17716-17721.
29. Lovley, D.R., Holmes, D.E. and Nevin, K.P. (2004) Dissimilatory Fe(III) and Mn(IV) reduction. Adv. Microb. Physiol., 49, 219-286.
30. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.