Combing Transcriptomes for Secrets of Deep-Sea Survival: Environmental Diversity Drives Patterns of Protein Evolution
Combing Transcriptomes for Secrets of Deep-Sea Survival: Environmental Diversity Drives Patterns of Protein Evolution
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DOI：
10.1093/icb/icz063
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发表时间：
2019-05
影响因子：
2.6
通讯作者：
Jacob R Winnikoff;Jacob R Winnikoff;Warren R. Francis;E. V. Thuesen;S. Haddock;S. Haddock
中科院分区：
文献类型：
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作者：
Jacob R Winnikoff;Jacob R Winnikoff;Warren R. Francis;E. V. Thuesen;S. Haddock;S. Haddock
摘要栉水母，也被称为梳水母，生活在海洋中的温度和静水压力范围非常广泛。由于不同的栉水母谱系独立地适应相似的环境条件，因此栉水母门是在比较框架中研究蛋白质适应极端环境的理想系统。我们在这里提出了这样一个研究，使用遗传学上知情的方法来比较四个必需的代谢酶的序列在栖息地的深度和温度的梯度。该方法预测收敛适应这些环境参数在氨基酸水平上，提供了一个新的观点，蛋白质适应极端环境，并展示了权力和相关性的系统发育比较应用于多物种转录组数据集从早期分化后生动物。在分析的所有四种酶中，46个氨基酸位点与深度适应相关，59个与温度适应相关，56个与两者相关。预测深度和温度适应性的网站始终发生在Rossmann折叠辅因子结合基序附近，并且不成比例地在蛋白质的溶剂暴露区域。这些结果表明，疏水效应和配体结合可能介导有效的酶功能在不同的流体静压力和温度。使用预测的适应性位点图，这样的机制假设现在可以通过诱变进行测试。
Abstract Ctenophores, also known as comb jellies, live across extremely broad ranges of temperature and hydrostatic pressure in the ocean. Because various ctenophore lineages adapted independently to similar environmental conditions, Phylum Ctenophora is an ideal system for the study of protein adaptation to extreme environments in a comparative framework. We present such a study here, using a phylogenetically-informed method to compare sequences of four essential metabolic enzymes across gradients of habitat depth and temperature. This method predicts convergent adaptation to these environmental parameters at the amino acid level, providing a novel view of protein adaptation to extreme environments and demonstrating the power and relevance of phylogenetic comparison applied to multi-species transcriptomic datasets from early-diverging metazoa. Across all four enzymes analyzed, 46 amino acid sites were associated with depth-adaptation, 59 with temperature-adaptation, and 56 with both. Sites predicted to be depth- and temperature-adaptive occurred consistently near Rossmann fold cofactor binding motifs and disproportionately in solvent-exposed regions of the protein. These results suggest that the hydrophobic effect and ligand binding may mediate efficient enzyme function at different hydrostatic pressures and temperatures. Using predicted adaptive site maps, such mechanistic hypotheses can now be tested via mutagenesis.