Affiliation:
1. Pacific Northwest National Laboratory, Richland, Washington
Abstract
ABSTRACT
Shewanella oneidensis
MR-1 is the first of 22 different
Shewanella
spp. whose genomes have been or are being sequenced and thus serves as the model organism for studying the functional repertoire of the
Shewanella
genus. The original MR-1 genome annotation revealed a large number of transposase genes and pseudogenes, indicating that many of the genome's functions may be decaying. Comparative analyses of the sequenced
Shewanella
strains suggest that 209 genes in MR-1 have in-frame stop codons, frameshifts, or interruptions and/or are truncated and that 65 of the original pseudogene predictions were erroneous. Among the decaying functions are that of one of three chemotaxis clusters, type I pilus production, starch utilization, and nitrite respiration. Many of the mutations could be attributed to members of 41 different types of insertion sequence (IS) elements and three types of miniature inverted-repeat transposable elements identified here for the first time. The high copy numbers of individual mobile elements (up to 71) are expected to promote large-scale genome recombination events, as evidenced by the displacement of the
algA
promoter. The ability of MR-1 to acquire foreign genes via reactions catalyzed by both the integron integrase and the ISSod25-encoded integrases is suggested by the presence of
attC
sites and genes whose sequences are characteristic of other species downstream of each site. This large number of mobile elements and multiple potential sites for integrase-mediated acquisition of foreign DNA indicate that the MR-1 genome is exceptionally dynamic, with many functions and regulatory control points in the process of decay or reinvention.
Publisher
American Society for Microbiology
Subject
Ecology,Applied Microbiology and Biotechnology,Food Science,Biotechnology
Reference27 articles.
1. Basic local alignment search tool
2. Baranov, P. V., O. Fayet, R. W. Hendrix, and J. F. Atkins. 2006. Recoding in bacteriophages and bacterial IS elements. Trends Genet.22:174-181.
3. Effects of ISSo
2
Insertions in Structural and Regulatory Genes of the Trimethylamine Oxide Reductase of
Shewanella oneidensis
4. Bradshaw, R. A., A. L. Burlingame, S. Carr, and R. Aebersold. 2006. Reporting protein identification data: the next generation of guidelines. Mol. Cell. Proteomics5:787-788.
5. Brettar, I., R. Christen, and M. G. Hofle. 2002. Shewanella denitrificans sp. nov., a vigorously denitrifying bacterium isolated from the oxic-anoxic interface of the Gotland Deep in the central Baltic Sea. Int. J. Syst. Evol. Microbiol.52:2211-2217.
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