NDLI: Conserved synteny at the protein family level reveals genes underlying Shewanella species’ cold tolerance and predicts their novel phenotypes

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Conserved synteny at the protein family level reveals genes underlying Shewanella species’ cold tolerance and predicts their novel phenotypes

Content Provider	Springer Nature Link
Author	Karpinets, Tatiana V. Obraztsova, Anna Y. Wang, Yanbing Schmoyer, Denise D. Kora, Guruprasad H. Park, Byung H. Serres, Margrethe H. Romine, Margaret F. Land, Miriam L. Kothe, Terence B. Fredrickson, Jim K. Nealson, Kenneth H. Uberbacher, Edward C.
Copyright Year	2009
Abstract	Bacteria 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.
Starting Page	97
Ending Page	110
Page Count	14
File Format	PDF
ISSN	1438793X
Journal	Functional & Integrative Genomics
Volume Number	10
Issue Number	1
e-ISSN	14387948
Language	English
Publisher	Springer-Verlag
Publisher Date	2009-10-03
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Phenotypic trait Bacteria Molecular mechanisms of cold tolerance Shewanella Protein families Animal Genetics and Genomics Bioinformatics Biochemistry Microbial Genetics and Genomics Cell Biology Plant Genetics & Genomics
Content Type	Text
Resource Type	Article
Subject	Genetics Medicine

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Conserved synteny at the protein family level reveals genes underlying Shewanella species’ cold tolerance and predicts their novel phenotypes

Conserved synteny at the protein family level reveals genes underlying Shewanella species’ cold tolerance and predicts their novel phenotypes

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Conserved synteny at the protein family level reveals genes underlying Shewanella species’ cold tolerance and predicts their novel phenotypes

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Conserved synteny at the protein family level reveals genes underlying Shewanella species’ cold tolerance and predicts their novel phenotypes