ArticleApplied and environmental microbiology2008
Identification of mobile elements and pseudogenes in the Shewanella oneidensis MR-1 genome.
Article in Applied and environmental microbiology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed, 66 citations in OpenAlex.
- Influence of Different Transposon Families on Genomic Stability of Shewanella oneidensis MR1.Microbial biotechnology · 2025Article
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- Evolving Populations in Biofilms Contain More Persistent Plasmids.Molecular biology and evolution · 2020Article
- Modulation of the reactivity of multiheme cytochromes by site-directed mutagenesis: moving towards the optimization of microbial electrochemical technologies.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2017Article
- Draft Genome of Shewanella frigidimarina Ag06-30, a Marine Bacterium Isolated from Potter Peninsula, King George Island, Antarctica.Genome announcements · 2016Article
- K-shell Analysis Reveals Distinct Functional Parts in an Electron Transfer Network and Its Implications for Extracellular Electron Transfer.Frontiers in microbiology · 2016Article
- Identification and characterization of a HEPN-MNT family type II toxin-antitoxin in Shewanella oneidensis.Microbial biotechnology · 2015Article
- A dynamic periplasmic electron transfer network enables respiratory flexibility beyond a thermodynamic regulatory regime.The ISME journal · 2015Article
- A new regulatory mechanism for bacterial lipoic acid synthesis.MicrobiologyOpen · 2015Article
- Regulation of nitrite resistance of the cytochrome cbb3 oxidase by cytochrome c ScyA in Shewanella oneidensis.MicrobiologyOpen · 2015Article
- Metabolic Characteristics of a Glucose-Utilizing Shewanella oneidensis Strain Grown under Electrode-Respiring Conditions.PloS one · 2015Article
- Catabolic and regulatory systems in Shewanella oneidensis MR-1 involved in electricity generation in microbial fuel cells.Frontiers in microbiology · 2015Review
- Draft-genome sequence of Shewanella algae strain C6G3.Standards in genomic sciences · 2015Article
- Comparisons of Shewanella strains based on genome annotations, modeling, and experiments.BMC systems biology · 2014Article
- Bacterial genome instability.Microbiology and molecular biology reviews : MMBR · 2014Review
- Exploring the molecular mechanisms of electron shuttling across the microbe/metal space.Frontiers in microbiology · 2014Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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