The evolutionary kaleidoscope of rhodopsins

Rhodopsins are widely distributed across all domains of life where they perform a plethora of functions through conversion of electromagnetic radiation into physicochemical signals(Rozenberg et al., 2021). As a result of an extensive survey on available genomic and metagenomic sequencing data, we report the existence of novel clades and exotic sequence motifs scattered through the evolutionary radiations of both Type-1 and -3 rhodopsins that will likely enlarge the optogenetics toolbox(Gushchin and Gordeliy, 2018; Kandori, 2021). We expand the typical rhodopsin blueprint by showing that a highly conserved (and functionally important) arginine residue (i.e., Arg82) was substituted multiple times during evolution by an extensive amino acid spectrum. We propose the umbrella term Alt-rhodopsins (AltR) for all such proteins that depart Arg82 orthodoxy. The newly uncovered diversity helped us to address the larger evolutionary scenario of microbial rhodopsins and to unearth clues about the Type-3 (heliorhodopsins) radiation. Thus, we propose that the proto-heliorhodopsins were a eukaryotic innovation that was mobilized by giant viral intermediates before their subsequent diversification into the extant Type-3 rhodopsins.视紫红质（Rhodopsins）广泛分布于所有生命域中，可通过将电磁辐射转化为物理化学信号执行多样生物学功能（Rozenberg等，2021）。通过对现有基因组与宏基因组测序数据开展全面系统调研，我们发现了分布于1型和3型视紫红质演化辐射过程中的全新演化支与独特序列基序，此类发现或将扩充光遗传学（optogenetics）工具库（Gushchin与Gordeliy，2018；Kandori，2021）。我们拓展了典型视紫红质的功能范式：研究表明，一个高度保守且功能关键的精氨酸残基（即Arg82位点）在演化过程中多次被多样的氨基酸谱系所替换。我们将所有不符合Arg82保守范式的这类蛋白统一命名为Alt-视紫红质（Alt-rhodopsins，简称AltR）。此次新发现的视紫红质多样性，帮助我们阐释了微生物视紫红质更宏观的演化图景，并为3型日光视紫红质（Heliorhodopsins）的演化辐射提供了关键线索。据此我们提出假说：原始日光视紫红质（proto-heliorhodopsins）是真核生物起源的创新性状，在后续分化为现存3型视紫红质之前，曾通过大型病毒中间体完成了跨界传播与转移。