Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan.
Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8563, Japan.
Sci Rep. 2020 Oct 7;10(1):16752. doi: 10.1038/s41598-020-73606-y.
Microbial rhodopsin is a photoreceptor protein found in various bacteria and archaea, and it is considered to be a light-utilization device unique to heterotrophs. Recent studies have shown that several cyanobacterial genomes also include genes that encode rhodopsins, indicating that these auxiliary light-utilizing proteins may have evolved within photoautotroph lineages. To explore this possibility, we performed a large-scale genomic survey to clarify the distribution of rhodopsin and its phylogeny. Our surveys revealed a novel rhodopsin clade, cyanorhodopsin (CyR), that is unique to cyanobacteria. Genomic analysis revealed that rhodopsin genes show a habitat-biased distribution in cyanobacterial taxa, and that the CyR clade is composed exclusively of non-marine cyanobacterial strains. Functional analysis using a heterologous expression system revealed that CyRs function as light-driven outward H pumps. Examination of the photochemical properties and crystal structure (2.65 Å resolution) of a representative CyR protein, N2098R from Calothrix sp. NIES-2098, revealed that the structure of the protein is very similar to that of other rhodopsins such as bacteriorhodopsin, but that its retinal configuration and spectroscopic characteristics (absorption maximum and photocycle) are distinct from those of bacteriorhodopsin. These results suggest that the CyR clade proteins evolved together with chlorophyll-based photosynthesis systems and may have been optimized for the cyanobacterial environment.
微生物视紫红质是一种在各种细菌和古菌中发现的光受体蛋白，它被认为是异养生物特有的光利用装置。最近的研究表明，几种蓝藻基因组也包含编码视紫红质的基因，这表明这些辅助光利用蛋白可能在光合自养生物谱系中进化而来。为了探索这种可能性，我们进行了大规模的基因组调查，以阐明视紫红质的分布及其系统发育。我们的调查揭示了一个新的视紫红质分支，即蓝藻视紫红质（CyR），它是蓝藻所特有的。基因组分析表明，视紫红质基因在蓝藻分类群中表现出栖息地偏倚分布，而 CyR 分支仅由非海洋蓝藻菌株组成。使用异源表达系统进行的功能分析表明，CyRs 作为光驱动外向 H 泵起作用。对代表性的 CyR 蛋白，即来自 Calothrix sp. NIES-2098 的 N2098R 的光化学性质和晶体结构（2.65 Å分辨率）进行的检查表明，该蛋白的结构与其他视紫红质非常相似，例如菌视紫红质，但它的视黄醛构型和光谱特征（吸收最大值和光循环）与菌视紫红质不同。这些结果表明，CyR 分支蛋白与基于叶绿素的光合作用系统一起进化，并且可能已经针对蓝藻环境进行了优化。
