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Appl. Environ. Microbiol. doi:10.1128/AEM.02720-07
Copyright (c) 2008, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Identification of Mobile Elements and Pseudogenes in the Shewanella oneidensis MR-1 Genome

Pacific Northwest National Laboratory, Richland, Washington, USA

^* To whom correspondence should be addressed. Email: Margie.romine{at}pnl.gov.

	Abstract

Shewanella oneidensis MR-1 is the first of 22 different Shewanella spp. whose genome has been or is being sequenced and thus serves as the model organism for studying the functional repertoire of this genus. The original MR-1 genome annotation revealed a large number of transposases and pseudogenes indicating that many of its functions may be decaying. Comparative analyses of the sequenced Shewanella strains suggest that 209 genes in MR-1 have in-frame stop codons, frameshifts, interruptions, and/or are truncated and that 65 of the original pseudogene predictions were erroneous. Among the decaying functions are: 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 IS elements and three types of miniature inverted-repeat transposable elements (MITEs) identified here for the first time. The high copy number of individual mobile elements (up to 71) is expected to promote large scale genome recombination events as is evidenced by displacement of the algA promoter. The ability of MR-1 to acquire foreign genes via activity encoded by both an integron integrase and an integrase encoded by multiple copies of ISSod25 is suggested by the presence of attC sites and genes whose sequence is characteristic of other species downstream to each. 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.