Protein evolution in deep sea bacteria: an analysis of amino acids substitution rates.
Protein evolution in deep sea bacteria: an analysis of amino acids substitution rates.
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DOI：
10.1186/1471-2148-8-313
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发表时间：
2008-11-13
影响因子：
3.4
通讯作者：
Valle G
中科院分区：
文献类型：
--
作者：
Campanaro S;Treu L;Valle G
深海微生物已经进化出特殊的特征，使它们能够在极端的生境中生长。已知属于特定功能类别的基因特别容易受到高压的影响;因此，它们应该显示出一些正选择的证据。为了验证这一假设，我们计算了两个深海微生物，发光杆菌深SS 9和希瓦氏菌benthica KT 99，和它们各自的浅水亲属之间的氨基酸取代率。所有的直系同源物的统计分析，导致确定的积极选择（PS）基因，然后用于评估适应策略。我们能够建立“运动”和“运输”作为两个类显着丰富的PS基因。转运蛋白的流行使我们分析可变氨基酸（PS位点），根据他们的膜拓扑结构映射它们，结果显示在细胞外室的置换频率较高。对可溶性蛋白质进行了类似的分析，绘制了3D结构上的PS位点，揭示了蛋白质表面置换的普遍性。最后，一些鞭毛蛋白在弧菌科PS列表中的存在证实了细菌运动作为SS 9特异性适应策略的重要性。本文提出的方法适用于识别特定环境条件下的分子适应。统计方法考虑了非同义与同义置换之间的比率差异，从而允许检测经历阳性选择的基因。我们发现，深海适应细菌中的正选择针对广泛的功能，例如溶质运输，蛋白质易位，DNA合成和运动。从这些数据中可以清楚地看出，运输和新陈代谢过程都参与了所考虑的两种深海型的深海适应战略，而其他生物过程的适应似乎只针对其中一种。一个重要的作用是假设5 PS基因属于运输类，以前已被确定为差异表达的微阵列实验。引人注目的是，独立进行膜和可溶性蛋白质的PS位点的结构映射显示，正选择下的残基往往发生在特定的蛋白质区域。
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. 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. 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.
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