Conserved synteny at the protein family level reveals genes underlying Shewanella species’ cold tolerance and predicts their novel phenotypes
Table 2S Number of Pfam domains in the tested species and their correlations with the cold tolerance score (853.5Kb)
Table 3S Mapping cold tolerance domains (assignment to specific genes) in the S. pealeana genome (86.5Kb)
Table 6S Domain enrichments in 19 Shewanella genomes and their attribution to networks and clusters (975.5Kb)
Table 7S Conserved synteny in the identified clusters (A) and their mapping to locus tags in the organisms (136Kb)
Table 8S Predicted phenotypes of the newly sequenced Shewanella species including related domain clusters and location of the genomic clusters (25Kb)
Fig. 1S Evolutional relationship between phenotypic traits and a variety of protein domains in the genome. Changes in the environment are the driving force for changes in the genome (1) leading to changes in the number and variety of protein domains (2) and to the evolution of species with novel phenotypic traits (3) (39.83Kb)
Fig. 2S Growth scores of the tested Shewanella strains as functions of their growth temperature. Growth score for each temperature was calculated as the area under the growth profile normalized to 100 h of the growth as described in “Materials and methods” (33.11Kb)
Karpinets, Tatiana V.
Obraztsova, Anna Y.
Schmoyer, Denise D.
Kora, Guruprasad H.
Park, Byung H.
Serres, Margrethe H.
Romine, Margaret F.
Land, Miriam L.
Kothe, Terence B.
Fredrickson, James K.
Nealson, Kenneth H.
Uberbacher, Edward C.
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KeywordPhenotypic trait; Bacteria; Molecular mechanisms of cold tolerance; Shewanella; Protein families
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.
© 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.
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