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Protein evolution in deep sea bacteria: an analysis of amino acids substitution rates.

ABSTRACT: BACKGROUND: Abyssal microorganisms have evolved particular features that enable them to grow in their extreme habitat. Genes belonging to specific functional categories are known to be particularly susceptible to high-pressure; therefore, they should show some evidence of positive selection. To verify this hypothesis we computed the amino acid substitution rates between two deep-sea microorganisms, Photobacterium profundum SS9 and Shewanella benthica KT99, and their respective shallow water relatives. RESULTS: A statistical analysis of all the orthologs, led to the identification of positive selected (PS) genes, which were then used to evaluate adaptation strategies. We were able to establish "Motility" and "Transport" as two classes significantly enriched with PS genes. The prevalence of transporters led us to analyze variable amino acids (PS sites) by mapping them according to their membrane topology, the results showed a higher frequency of substitutions in the extra-cellular compartment. A similar analysis was performed on soluble proteins, mapping the PS sites on the 3D structure, revealing a prevalence of substitutions on the protein surface. Finally, the presence of some flagellar proteins in the Vibrionaceae PS list confirms the importance of bacterial motility as a SS9 specific adaptation strategy. CONCLUSION: The approach presented in this paper is suitable for identifying molecular adaptations to particular environmental conditions. The statistical method takes into account differences in the ratio between non-synonymous to synonymous substitutions, thus allowing the detection of the genes that underwent positive selection. We found that positive selection in deep-sea adapted bacteria targets a wide range of functions, for example solute transport, protein translocation, DNA synthesis and motility. From these data clearly emerges an involvement of the transport and metabolism processes in the deep-sea adaptation strategy of both bathytypes considered, whereas the adaptation of other biological processes seems to be specific to either one or the other. An important role is hypothesized for five PS genes belonging to the transport category that had been previously identified as differentially expressed in microarray experiments. Strikingly, structural mapping of PS sites performed independently on membrane and soluble proteins revealed that residues under positive selection tend to occur in specific protein regions.

SUBMITTER: Campanaro S

PROVIDER: S-EPMC2600651 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature

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Protein evolution in deep sea bacteria: an analysis of amino acids substitution rates.

Campanaro Stefano S Treu Laura L Valle Giorgio G

BMC evolutionary biology 20081113

<h4>Background</h4>Abyssal microorganisms have evolved particular features that enable them to grow in their extreme habitat. Genes belonging to specific functional categories are known to be particularly susceptible to high-pressure; therefore, they should show some evidence of positive selection. To verify this hypothesis we computed the amino acid substitution rates between two deep-sea microorganisms, Photobacterium profundum SS9 and Shewanella benthica KT99, and their respective shallow wat ...[more]

PMID: 19014525

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Project description:The number of amino acids that occupy a given protein site during evolution reflects the selective constraints operating on the site. This evolutionary variability is strongly influenced by the structural properties of the site in the native structure, and it is quantified either through sequence entropy or through substitution rates. However, while the sequence entropy only depends on the equilibrium frequencies of the amino acids, the substitution rate also depends on the exchangeability matrix that describes mutations in the mathematical model of the substitution process. Here we apply two variants of a mathematical model of protein evolution with selection for protein stability, both against unfolding and against misfolding. Exploiting the approximation of independent sites, these models allow computing site-specific substitution processes that satisfy global constraints on folding stability. We find that site-specific substitution rates do not depend only on the selective constraints acting on the site, quantified through its sequence entropy. In fact, polar sites evolve faster than hydrophobic sites even for equal sequence entropy, as a consequence of the fact that polar amino acids are characterized by higher mutational exchangeability than hydrophobic ones. Accordingly, the model predicts that more polar proteins tend to evolve faster. Nevertheless, these results change if we compare proteins that evolve under different mutation biases, such as orthologous proteins in different bacterial genomes. In this case, the substitution rates are faster in genomes that evolve under mutational bias that favor hydrophobic amino acids by preferentially incorporating the nucleotide Thymine that is more frequent in hydrophobic codons. This appearingly contradictory result arises because buried sites occupied by hydrophobic amino acids are characterized by larger selective factors that largely amplify the substitution rate between hydrophobic amino acids, while the selective factors of exposed sites have a weaker effect. Thus, changes in the mutational bias produce deep effects on the biophysical properties of the protein (hydrophobicity) and on its evolutionary properties (sequence entropy and substitution rate) at the same time. The program Prot_evol that implements the two site-specific substitution processes is freely available at https://ub.cbm.uam.es/prot_fold_evol/prot_fold_evol_soft_main.php#Prot_Evol.

Dataset Information

Protein evolution in deep sea bacteria: an analysis of amino acids substitution rates.

Publications

Protein evolution in deep sea bacteria: an analysis of amino acids substitution rates.

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