Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.
Department of Biological Sciences, University of Toronto Scarborough, Scarborough, ON, Canada.
Mol Biol Evol. 2021 May 4;38(5):2076-2087. doi: 10.1093/molbev/msab008.
Rhodopsin, the light-sensitive visual pigment expressed in rod photoreceptors, is specialized for vision in dim-light environments. Aquatic environments are particularly challenging for vision due to the spectrally dependent attenuation of light, which can differ greatly in marine and freshwater systems. Among fish lineages that have successfully colonized freshwater habitats from ancestrally marine environments, croakers are known as highly visual benthic predators. In this study, we isolate rhodopsins from a diversity of freshwater and marine croakers and find that strong positive selection in rhodopsin is associated with a marine to freshwater transition in South American croakers. In order to determine if this is accompanied by significant shifts in visual abilities, we resurrected ancestral rhodopsin sequences and tested the experimental properties of ancestral pigments bracketing this transition using in vitro spectroscopic assays. We found the ancestral freshwater croaker rhodopsin is redshifted relative to its marine ancestor, with mutations that recapitulate ancestral amino acid changes along this transitional branch resulting in faster kinetics that are likely to be associated with more rapid dark adaptation. This could be advantageous in freshwater due to the redshifted spectrum and relatively narrow interface and frequent transitions between bright and dim-light environments. This study is the first to experimentally demonstrate that positively selected substitutions in ancestral visual pigments alter protein function to freshwater visual environments following a transition from an ancestrally marine state and provides insight into the molecular mechanisms underlying some of the physiological changes associated with this major habitat transition.
视蛋白是一种存在于视杆细胞中的感光视觉色素，专门用于在暗光环境下进行视觉感知。水生环境对视觉感知具有挑战性，因为光的光谱依赖性衰减会有所不同，这种衰减在海洋和淡水系统中差异很大。在成功从原始海洋环境向淡水栖息地殖民的鱼类谱系中，石首鱼科鱼类是众所周知的高度视觉化的底栖捕食者。在这项研究中，我们从多种淡水和海水石首鱼科鱼类中分离出视蛋白，发现视蛋白中的强烈正选择与南美白对虾从海洋到淡水的过渡有关。为了确定这是否伴随着视觉能力的显著变化，我们复活了祖先的视蛋白序列，并使用体外光谱测定法测试了跨越这一转变的祖先色素的实验特性。我们发现，与祖先的海洋鱼类相比，祖先的淡水石首鱼科鱼类的视蛋白发生了红移，沿着这个过渡分支， recapitulate 了祖先的氨基酸变化，导致更快的动力学，这可能与更快的暗适应有关。由于光谱红移、相对较窄的界面以及在明亮和暗光环境之间频繁转换，这种变化在淡水中可能是有利的。这项研究首次通过实验证明，在从原始的海洋状态向淡水环境过渡后，祖先视觉色素中的正选择取代会改变蛋白质功能，从而适应淡水视觉环境，并为与这种主要栖息地过渡相关的一些生理变化的分子机制提供了深入了解。
