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Applied and Environmental Microbiology, May 2008, p. 3257-3265, Vol. 74, No. 10
0099-2240/08/$08.00+0     doi:10.1128/AEM.02720-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Identification of Mobile Elements and Pseudogenes in the Shewanella oneidensis MR-1 Genome{triangledown} ,{dagger}

Margaret F. Romine,* Timothy S. Carlson, Angela D. Norbeck, Lee Ann McCue, and Mary S. Lipton

Pacific Northwest National Laboratory, Richland, Washington

Received 3 December 2007/ Accepted 20 March 2008

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.

* Corresponding author. Mailing address: Pacific Northwest National Laboratory, MS P7-86, P.O. Box 999, Richland, WA 99352. Phone: (509) 376-8287. Fax: (509) 372-1632. E-mail: Margie.romine{at}pnl.gov

{triangledown} Published ahead of print on 31 March 2008.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

Applied and Environmental Microbiology, May 2008, p. 3257-3265, Vol. 74, No. 10
0099-2240/08/$08.00+0     doi:10.1128/AEM.02720-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.





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