Shewanella species couple the decomposition of organic matter to the reduction of various terminal electron acceptors that are present in the diverse environments that they can inhabit.
The metabolic versatility of Shewanella species makes them important mediators of carbon cycling, and allows for their potential use in the remediation of environments that are contaminated with radionuclides and other toxic metals, as well as potential sources of alternative energy through microbial fuel cells.
Systems-biology is being used to better understand the environmental sensing, signal-transduction and metabolic- and energy-generating pathways of the model organism Shewanella oneidensis MR-1.
Among other insights, this analysis has revealed the presence of novel metabolic pathways, the reorganization of regulatory pathways compared with Escherichia coli and other model organisms, and a novel mechanism for dealing with oxidative stress through autoaggregation.
Comparative genomic analysis, based on the availability of genome sequences for 23 Shewanella species, has facilitated the transfer of information gained from the study of S. oneidensis MR-1 across members of the genus.
Many of the proteins that are important for respiratory diversity in S. oneidensis MR-1 are conserved in many members of the genus.
Bacteria of the genus Shewanella are known for their versatile electron-accepting capacities, which allow them to couple the decomposition of organic matter to the reduction of the various terminal electron acceptors that they encounter in their stratified environments. Owing to their diverse metabolic capabilities, shewanellae are important for carbon cycling and have considerable potential for the remediation of contaminated environments and use in microbial fuel cells. Systems-level analysis of the model species Shewanella oneidensis MR-1 and other members of this genus has provided new insights into the signal-transduction proteins, regulators, and metabolic and respiratory subsystems that govern the remarkable versatility of the shewanellae.
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The authors thank the numerous members of the Shewanella Federation for useful discussions and concepts during the course of their systems biology investigations of Shewanella, including E.J. Crane, H. Gao, C. Giometti, K. Kostantinidis, M. Lipton, M. Marshall, L.-A. McCue, A. Obraztsova, N. Samatova, H. Scholten, E. Uberbacher, L. Ulrich, M. Ward and J. Zhou. The authors have been supported by the US Department of Energy (DOE) through the Shewanella Federation consortium and by the National Science Foundation (grant number NSFMCB0543501).
Entrez Genome Project
An enzymatic reaction in which a compound is oxidized or reduced but is not assimilated or incorporated into cells for the purposes of biosynthesis during, for example, respiration.
- Electron acceptor
An oxidant used during cellular respiration.
- One-component system
A regulatory protein that combines both sensory and regulatory capabilities that usually reside in two distinct domains. The repressor of the lactose operons (LacI) and the catabolite activator protein of Escherichia coli are classical examples.
- Two-component system
A regulatory system that is typically composed of two proteins, a sensor histidine kinase and a cognate response regulator. EnvZ and OmpR of Escherichia coli are classical examples.
- PAS domain
A ubiquitous sensory domain that is found in many one-component and two-component regulatory systems in prokaryotes, as well as in regulatory proteins in eukaryotes. The PAS domain was named after three proteins that it was found in: Per (period circadian protein), Arnt (receptor nuclear translocator protein) and Sim (single-minded protein).
- Diguanylate cyclase
An enzyme that synthesizes cyclic diguanylic acid and typically contains the canonical amino acid motif GGDEF.
A set of genes that is controlled by a common transcription factor or regulatory RNA. A regulon usually includes genes that are implicated in a common cellular subsystem or pathway.
- AMT-tag proteome database
An accurate mass and time (AMT)-tag proteome database that contains identifications for tryptic peptides based on analysis by capillary liquid chromatography followed by tandem mass spectrometry of various cellular lysates of a single organism.
- Core genome
In the context of this Review, the core genome refers to the set of proteins that have been found in each Shewanella genome analysed to date and are of high sequence similarity and are therefore predicted to encode the same function.
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Fredrickson, J., Romine, M., Beliaev, A. et al. Towards environmental systems biology of Shewanella. Nat Rev Microbiol 6, 592–603 (2008). https://doi.org/10.1038/nrmicro1947
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