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 CCTα (Chaperonin Containing TCP-1 subunit α), 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 not only displays 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 ‘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, are key metabolic deep-sea adaptations.

中文翻译：

---

蛋白质折叠伴侣蛋白CCTα中对深海的趋同进化和结构适应。

深海是地球上最大的生物群落，但却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，但它们的分子机制仍未得到充分研究。我们检查了来自四个脆性星 (Ophiuroidea) 家族的 416 个基因的正选择模式，这些基因显示了深海殖民化的重复事件（来自 216 个物种的 288 个个体）。我们在与蛋白质生物发生相关的功能中发现了分子收敛的一致特征，包括蛋白质折叠和翻译。五个基因被反复阳性选择，包括 CCTα（包含 TCP-1 亚基 α 的伴侣蛋白），这是蛋白质折叠必不可少的。在功能和基因水平上检测到分子收敛，但在氨基酸水平上没有检测到。预计适应压力的蛋白质将显示出更高的稳定性以抵消变性的影响。我们因此检查了在系统发育校正的背景下，在整个阿片类生命树（来自 725 个物种的 967 个个体）中的计算机模拟本地蛋白质稳定性，发现深海适应蛋白质在底物结合区域内和附近显示出更高的稳定性，这一点得到证实通过计算机全球蛋白质稳定性分析。这表明 CCTα 不仅表现出对深水条件的结构适应，而且还表现出功能适应。CCT 复合物参与了约 10% 的新合成蛋白质的折叠，之前在许多真核生物中被归类为“冷休克”蛋白质。因此，我们提出对寒冷和深海环境的适应机制可能相互关联，并强调有效的蛋白质生物发生，包括蛋白质折叠和翻译，是关键的代谢深海适应。