Sciences, Museums Victoria, Melbourne, Victoria, Australia.
Centre de Bretagne, REM/EEP, Ifremer, Laboratoire Environnement Profond, Plouzané, France.
Genome Biol Evol. 2020 Nov 3;12(11):1929-1942. doi: 10.1093/gbe/evaa167.
The deep ocean is the largest biome on Earth and yet it is among the least studied environments of our planet. Life at great depths requires several specific adaptations; however, their molecular mechanisms remain understudied. We examined patterns of positive selection in 416 genes from four brittle star (Ophiuroidea) families displaying replicated events of deep-sea colonization (288 individuals from 216 species). We found consistent signatures of molecular convergence in functions related to protein biogenesis, including protein folding and translation. Five genes were recurrently positively selected, including chaperonin-containing TCP-1 subunit α (CCTα), which is essential for protein folding. Molecular convergence was detected at the functional and gene levels but not at the amino-acid level. Pressure-adapted proteins are expected to display higher stability to counteract the effects of denaturation. We thus examined in silico local protein stability of CCTα across the ophiuroid tree of life (967 individuals from 725 species) in a phylogenetically corrected context and found that deep-sea-adapted proteins display higher stability within and next to the substrate-binding region, which was confirmed by in silico global protein stability analyses. This suggests that CCTα displays not only structural but also functional adaptations to deep-water conditions. The CCT complex is involved in the folding of ∼10% of newly synthesized proteins and has previously been categorized as a "cold-shock" protein in numerous eukaryotes. We thus propose that adaptation mechanisms to cold and deep-sea environments may be linked and highlight that efficient protein biogenesis, including protein folding and translation, is a key metabolic deep-sea adaptation.
深海是地球上最大的生物群落，但它也是我们星球上研究最少的环境之一。深海生命需要几种特定的适应；然而，它们的分子机制仍未得到充分研究。我们研究了四个海星（蛇尾纲）家族的 416 个基因的正选择模式，这些家族显示出深海殖民化的重复事件（来自 216 个物种的 288 个个体）。我们发现与蛋白质生物发生相关的功能存在一致的分子趋同模式，包括蛋白质折叠和翻译。有五个基因经常受到正选择，包括热休克蛋白 10 家族细胞色素 c 氧化酶装配因子（CCTα），它是蛋白质折叠所必需的。在功能和基因水平上检测到了分子趋同，但在氨基酸水平上没有。适应压力的蛋白质预计会显示更高的稳定性，以抵消变性的影响。因此，我们在进化校正的背景下，在蛇尾纲生命之树中（来自 725 个物种的 967 个个体），对 CCTα 的局部蛋白质稳定性进行了计算机模拟，并发现深海适应蛋白在底物结合区域内和附近显示出更高的稳定性，这通过计算机模拟的全局蛋白质稳定性分析得到了证实。这表明 CCTα 不仅显示出结构适应，还显示出对深水条件的功能适应。CCT 复合物参与大约 10%新合成蛋白质的折叠，并且在许多真核生物中已被归类为“冷休克”蛋白。因此，我们提出适应寒冷和深海环境的机制可能是相关的，并强调有效的蛋白质生物发生，包括蛋白质折叠和翻译，是一种关键的深海代谢适应。
