Completed genome sequence of the anaerobic iron-oxidizing bacterium Acidovorax ebreus strain TPSY

Journal of Bacteriology

Volumn 192, Issue 5, 2010, Pages 1475-1476

  Byrne Bailey, Kathryne G ^a   Weber, Karrie A ^a,c   Chair, Antinea H ^a   Bose, Saumyaditya ^a   Knox, Traci ^a   Spanbauer, Trisha L ^c   Chertkov, Olga ^b   Coates, John D ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF NEBRASKA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACIDOVORAX EBREUS; ARTICLE; BACTERIAL GENOME; BIOSYNTHESIS; GENE SEQUENCE; IRON OXIDIZING BACTERIUM; MINIMUM INHIBITORY CONCENTRATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PATHOGENICITY; PHENOTYPE; PREDICTION; PRIORITY JOURNAL;

ANAEROBIOSIS; COMAMONADACEAE; DNA, BACTERIAL; GENOME, BACTERIAL; IRON; MOLECULAR SEQUENCE DATA; NITRATES; OXIDATION-REDUCTION; SEQUENCE ANALYSIS, DNA;

ACIDOVORAX; BACTERIA (MICROORGANISMS);

EID: 77749254840     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.01449-09     Document Type: Article

References (22)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. Badger, J. H., and G. J. Olsen. 1999. CRITICA: coding region identification tool invoking comparative analysis. Mol. Biol. Evol. 16:512-524.
3. Barrangou, R., C. Fremaux, H. Deveau, M. Richards, P. Boyaval, S. Moineau, D. A. Romero, and P. Horvath. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709-1712.
4. Chaudhuri, S. K., J. G. Lack, and J. D. Coates. 2001. Biogenic magnetite formation through anaerobic biooxidation of Fe(II). Appl. Environ. Microbiol. 67:2844-2848.
5. Delcher, A. L., D. Harmon, S. Kasif, O. White, and S. L. Salzberg. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27:4636-4641.
6. Ewing, B., and P. Green. 1998. Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res. 8:186-194.
7. Ewing, B., L. Hillier, M. C. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res. 8:175-185.
8. Gordon, D., C. Abajian, and P. Green. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195-202.
9. Haft, D. H., J. Selengut, E. F. Mongodin, and K. E. Nelson. 2005. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput. Biol. 1:e60.
10. Han, C. S., and P. Chain. 2006. Finishing repeat regions automatically with Dupfinisher, p. 141-146. In H. R. Arabnia and H. Valafar (ed.), Proc. 2006 Int. Conf. Bioinformatics Comput. Biol. CSREA Press, Las Vegas, NV.
11. Lack, J. G., S. K. Chaudhuri, R. Chakraborty, L. A. Achenbach, and J. D. Coates. 2002. Anaerobic biooxidation of Fe(II) by Dechlorosoma suillum. Microb. Ecol. 43:424-431.
12. Markowitz, V. M., E. Szeto, K. Palaniappan, Y. Grechkin, K. Chu, I. M. Chen, I. Dubchak, I. Anderson, A. Lykidis, K. Mavromatis, N. N. Ivanova, and N. C. Kyrpides. 2008. The Integrated Microbial Genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res. 36: D528-D533.
13. Nies, D. H. 1995. The cobalt, zinc, and cadmium efflux system CzcABC from Alcaligenes eutrophus functions as a cation-proton antiporter in Escherichia coli. J. Bacteriol. 177:2707-2712.
14. Preisig, O., D. Anthamatten, and H. Hennecke. 1993. Genes for a microaerobically induced oxidase complex in Bradyrhizobium japonicum are essential for a nitrogen-fixing endosymbiosis. Proc. Natl. Acad. Sci. U. S. A. 90:3309-3313.
15. Rojas, C. M., J. H. Ham, W. L. Deng, J. J. Doyle, and A. Collmer. 2002. HecA, a member of a class of adhesins produced by diverse pathogenic bacteria, contributes to the attachment, aggregation, epidermal cell killing, and virulence phenotypes of Erwinia chrysanthemi EC16 on Nicotiana clevelandii seedlings. Proc. Natl. Acad. Sci. U. S. A. 99:13142-13147.
16. Sorek, R., V. Kunin, and P. Hugenholtz. 2008. CRISPR - a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat. Rev. Microbiol. 6:181-186.
17. Straub, K. L., M. Benz, B. Schink, and F. Widdel. 1996. Anaerobic, nitratedependent microbial oxidation of ferrous iron. Appl. Environ. Microbiol. 62:1458-1460.
18. Straub, K. L., and B. E. E. Buchholz-Cleven. 1998. Enumeration and detection of anaerobic ferrous iron-oxidizing, nitrate-reducing bacteria from diverse European sediments. Appl. Environ. Microbiol. 64:4846-4856.
19. Wang, Y., M. Moore, H. S. Levinson, S. Silver, C. Walsh, and I. Mahler. 1989. Nucleotide sequence of a chromosomal mercury resistance determinant from a Bacillus sp. with broad-spectrum mercury resistance. J. Bacteriol. 171:83-92.
20. Weber, K. A., D. B. Hedrick, A. D. Peacock, J. C. Thrash, D. C. White, L. A. Achenbach, and J. D. Coates. 2009. Physiological and taxonomic description of the novel autotrophic, metal oxidizing bacterium, Pseudogulbenkiania sp. strain 2002. Appl. Microbiol. Biotechnol. 83:555-565.
21. Weber, K. A., J. Pollock, K. A. Cole, S. M. O'Connor, L. A. Achenbach, and J. D. Coates. 2006. Anaerobic nitrate-dependent iron(II) bio-oxidation by a novel lithoautotrophic betaproteobacterium, strain 2002. Appl. Environ. Microbiol. 72:686-694.
22. Weber, K. A., M. M. Urrutia, P. F. Churchill, R. K. Kukkadapu, and E. E. Roden. 2006. Anaerobic redox cycling of iron by freshwater sediment microorganisms. Environ. Microbiol. 8:100-113.