Show simple item record

dc.contributor.authorKarpinets, Tatiana V.  Concept link
dc.contributor.authorObraztsova, Anna Y.  Concept link
dc.contributor.authorWang, Yanbing  Concept link
dc.contributor.authorSchmoyer, Denise D.  Concept link
dc.contributor.authorKora, Guruprasad H.  Concept link
dc.contributor.authorPark, Byung H.  Concept link
dc.contributor.authorSerres, Margrethe H.  Concept link
dc.contributor.authorRomine, Margaret F.  Concept link
dc.contributor.authorLand, Miriam L.  Concept link
dc.contributor.authorKothe, Terence B.  Concept link
dc.contributor.authorFredrickson, James K.  Concept link
dc.contributor.authorNealson, Kenneth H.  Concept link
dc.contributor.authorUberbacher, Edward C.  Concept link
dc.date.accessioned2010-03-31T13:19:26Z
dc.date.available2010-03-31T13:19:26Z
dc.date.issued2009-10-03
dc.identifier.citationFunctional & Integrative Genomics 10 (2010): 97-110en_US
dc.identifier.urihttps://hdl.handle.net/1912/3227
dc.description© The Authors 2009. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License. The definitive version was published in Functional & Integrative Genomics 10 (2010): 97-110, doi:10.1007/s10142-009-0142-y.en_US
dc.description.abstractBacteria of the genus Shewanella can thrive in different environments and demonstrate significant variability in their metabolic and ecophysiological capabilities including cold and salt tolerance. Genomic characteristics underlying this variability across species are largely unknown. In this study, we address the problem by a comparison of the physiological, metabolic, and genomic characteristics of 19 sequenced Shewanella species. We have employed two novel approaches based on association of a phenotypic trait with the number of the trait-specific protein families (Pfam domains) and on the conservation of synteny (order in the genome) of the trait-related genes. Our first approach is top-down and involves experimental evaluation and quantification of the species’ cold tolerance followed by identification of the correlated Pfam domains and genes with a conserved synteny. The second, a bottom-up approach, predicts novel phenotypes of the species by calculating profiles of each Pfam domain among their genomes and following pair-wise correlation of the profiles and their network clustering. Using the first approach, we find a link between cold and salt tolerance of the species and the presence in the genome of a Na+/H+ antiporter gene cluster. Other cold-tolerance-related genes include peptidases, chemotaxis sensory transducer proteins, a cysteine exporter, and helicases. Using the bottom-up approach, we found several novel phenotypes in the newly sequenced Shewanella species, including degradation of aromatic compounds by an aerobic hybrid pathway in Shewanella woodyi, degradation of ethanolamine by Shewanella benthica, and propanediol degradation by Shewanella putrefaciens CN32 and Shewanella sp. W3-18-1.en_US
dc.description.sponsorshipThis research was supported by the U.S. Department of Energy (DOE) Office of Biological and Environmental Research under the Genomics: GTL Program via the Shewanella Federation consortium.en_US
dc.format.mimetypeapplication/pdf
dc.format.mimetypeapplication/vnd.ms-excel
dc.language.isoen_USen_US
dc.publisherSpringeren_US
dc.relation.urihttps://doi.org/10.1007/s10142-009-0142-y
dc.rightsAttribution-NonCommercial 3.0 Unported*
dc.rights.urihttp://creativecommons.org/licenses/by-nc/3.0/*
dc.subjectPhenotypic traiten_US
dc.subjectBacteriaen_US
dc.subjectMolecular mechanisms of cold toleranceen_US
dc.subjectShewanellaen_US
dc.subjectProtein familiesen_US
dc.titleConserved synteny at the protein family level reveals genes underlying Shewanella species’ cold tolerance and predicts their novel phenotypesen_US
dc.typeArticleen_US
dc.identifier.doi10.1007/s10142-009-0142-y


Files in this item

Thumbnail
Thumbnail
Thumbnail
Thumbnail
Thumbnail
Thumbnail
Thumbnail
Thumbnail
Thumbnail
Thumbnail
Thumbnail
Thumbnail
Thumbnail
Thumbnail

This item appears in the following Collection(s)

Show simple item record

Attribution-NonCommercial 3.0 Unported
Except where otherwise noted, this item's license is described as Attribution-NonCommercial 3.0 Unported