Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis

By J. Heidelberg, Ian T. Paulsen, Karen E. Nelson, E. Gaidos, William C. Nelson, Timothy D. Read, Jonathan A. Eisen, Rekha Seshadri, N. Ward, B. Methé and 33 more. Nature Biotechnology, 2002

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Shewanella oneidensis is an important model organism for bioremediation studies because of its diverse respiratory capabilities, conferred in part by multicomponent, branched electron transport systems. Here we report the sequencing of the S. oneidensis genome, which consists of a 4,969,803–base pair circular chromosome with 4,758 predicted protein-encoding open reading frames (CDS) and a 161,613–base pair plasmid with 173 CDSs. We identified the first Shewanella lambda-like phage, providing a potential tool for further genome engineering. Genome analysis revealed 39 c-type cytochromes, including 32 previously unidentified in S. oneidensis, and a novel periplasmic [Fe] hydrogenase, which are integral members of the electron transport system. This genome sequence represents a critical step in the elucidation of the pathways for reduction (and bioremediation) of pollutants such as uranium (U) and chromium (Cr), and offers a starting point for defining this organism's complex electron transport systems and metal ion–reducing capabilities.

Subfields: Environmental Engineering, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e474c14de8b0cf448f3182ada164e1050a39fa68

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Citations in the corpus

Microbial electron transport and energy conservation – the foundation for optimizing bioelectrochemical systems (2015, methodology): “G. sulfurreducens’ genome encodes for around 110 different c-type cytochromes (Methe et al., 2003), S. oneidensis for 42 (Heidelberg et al., 2002), and P. aeruginosa for 27 (Bertini et al., 2006), while C. glutamicum genome only encodes for a single c-type cytochrome (Bertini et al., 2006).”
Predicting transmembrane beta-barrels in proteomes. (2004, background): “Those with six or more new proteins were: Vibrio vulni®cus (14 proteins), Vibrio parahaeomlyticus (67) (12 proteins), Xanthomonas campestris (68) (12 proteins), Shewanella oneidensis (69) (12 proteins), Xanthomonas axonopodis (68) (nine proteins), E.”
Secretion of Flavins by Shewanella Species and Their Role in Extracellular Electron Transfer (2007, background): “Direct electron transfer at the mineral-microbe interface is thought to involve a network of c-type cytochromes recently identified in the genome of Shewanella oneidensis MR-1 ( 8 ) and shown in several studies to be localized in the periplasm (25), in the outer membranes of Shewanella species (1, 5”
Environments that Induce Synthetic Microbial Ecosystems (2010, background): “vulgaris is known to be able to metabolize, such as pyruvate, ethanol, malate and fumarate [43,44].”
Current Production and Metal Oxide Reduction by Shewanella oneidensis MR-1 Wild Type and Mutants (2007, methodology): “This study focuses on the electron transfer mechanisms employed by Shewanella oneidensis MR-1, a strain that was chosen as a model organism based on its metabolic versatility (37), its sequenced and annotated genome ( 16 ), and its genetic accessibility with regard to both generation and complementa”
Microorganisms pumping iron: anaerobic microbial iron oxidation and reduction (2006, background): “sulfurreducens genomes revealed 39 and 111 putative c -type cytochromes, respectivel”
The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (2004, methodology): “Cloning, sequencing and assembly were as described for genomes sequenced by TIG”