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

Romine, Margaret F; Carlson, Timothy; Norbeck, Angela D; McCue, Lee Ann; Lipton, Mary S

doi:10.1128/AEM.02720-07

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

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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 attCmore »« less

Authors:: Romine, Margaret F; Carlson, Timothy; Norbeck, Angela D; McCue, Lee Ann; Lipton, Mary S

Publication Date:: Thu May 01 00:00:00 EDT 2008

Research Org.:: Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 937378

Report Number(s):: PNNL-SA-60499
Journal ID: ISSN 0099-2240; AEMIDF; KP1501021; TRN: US200819%%102

DOE Contract Number:: AC05-76RL01830

Resource Type:: Journal Article

Journal Name:: Applied and Environmental Microbiology, 74(10):3257-3265

Additional Journal Information:: Journal Volume: 74; Journal Issue: 10; Journal ID: ISSN 0099-2240

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; CODONS; DECAY; DNA; FUNCTIONALS; GENES; MUTATIONS; NITRITES; PRODUCTION; RECOMBINATION; RESPIRATION; STARCH; STRAINS

Citation Formats


                    Romine, Margaret F, Carlson, Timothy, Norbeck, Angela D, McCue, Lee Ann, and Lipton, Mary S. Identification of Mobile Elements and Pseudogenes in the Shewanella oneidensis MR-1 Genome.  United States: N. p., 2008. 
        Web.  doi:10.1128/AEM.02720-07.

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                    Romine, Margaret F, Carlson, Timothy, Norbeck, Angela D, McCue, Lee Ann, & Lipton, Mary S. Identification of Mobile Elements and Pseudogenes in the Shewanella oneidensis MR-1 Genome.  United States.  https://doi.org/10.1128/AEM.02720-07

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                    Romine, Margaret F, Carlson, Timothy, Norbeck, Angela D, McCue, Lee Ann, and Lipton, Mary S. 2008.  
        "Identification of Mobile Elements and Pseudogenes in the Shewanella oneidensis MR-1 Genome".  United States.  https://doi.org/10.1128/AEM.02720-07.

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@article{osti_937378,

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

  author       = {Romine, Margaret F and Carlson, Timothy and Norbeck, Angela D and McCue, Lee Ann and Lipton, Mary S},

  abstractNote = {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 integrasemediated 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.},

  doi          = {10.1128/AEM.02720-07},

  url          = {https://www.osti.gov/biblio/937378},
  journal      = {Applied and Environmental Microbiology, 74(10):3257-3265},

  issn         = {0099-2240},

  number       = 10,

  volume       = 74,

  place        = {United States},

  year         = {Thu May 01 00:00:00 EDT 2008},

  month        = {Thu May 01 00:00:00 EDT 2008}

}

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