Nakajima Yu, Tsukamoto Takashi, Kumagai Yohei, Ogura Yoshitoshi, Hayashi Tetsuya, Song Jaeho, Kikukawa Takashi, Demura Makoto, Kogure Kazuhiro, Sudo Yuki, Yoshizawa Susumu
Atmosphere and Ocean research Institute (AORI), The University of Tokyo.
Department of Natural Environmental Studies, Graduate School of Frontier Sciences, the University of Tokyo.
Microbes Environ. 2018 Mar 29;33(1):89-97. doi: 10.1264/jsme2.ME17197. Epub 2018 Mar 16.
Light-driven ion-pumping rhodopsins are widely distributed among bacteria, archaea, and eukaryotes in the euphotic zone of the aquatic environment. H-pumping rhodopsin (proteorhodopsin: PR), Na-pumping rhodopsin (NaR), and Cl-pumping rhodopsin (ClR) have been found in marine bacteria, which suggests that these genes evolved independently in the ocean. Putative microbial rhodopsin genes were identified in the genome sequences of marine Cytophagia. In the present study, one of these genes was heterologously expressed in Escherichia coli cells and the rhodopsin protein named Rubricoccus marinus halorhodopsin (RmHR) was identified as a light-driven inward Cl pump. Spectroscopic assays showed that the estimated dissociation constant (K) of this rhodopsin was similar to that of haloarchaeal halorhodopsin (HR), while the Cl-transporting photoreaction mechanism of this rhodopsin was similar to that of HR, but different to that of the already-known marine bacterial ClR. This amino acid sequence similarity also suggested that this rhodopsin is similar to haloarchaeal HR and cyanobacterial HRs (e.g., SyHR and MrHR). Additionally, a phylogenetic analysis revealed that retinal biosynthesis pathway genes (blh and crtY) belong to a phylogenetic lineage of haloarchaea, indicating that these marine Cytophagia acquired rhodopsin-related genes from haloarchaea by lateral gene transfer. Based on these results, we concluded that inward Cl-pumping rhodopsin is present in genera of the class Cytophagia and may have the same evolutionary origins as haloarchaeal HR.
光驱动离子泵视紫红质广泛分布于水生环境真光层中的细菌、古菌和真核生物中。在海洋细菌中发现了质子泵视紫红质（视紫质：PR）、钠泵视紫红质（NaR）和氯泵视紫红质（ClR），这表明这些基因是在海洋中独立进化的。在海洋噬纤维菌属的基因组序列中鉴定出了假定的微生物视紫红质基因。在本研究中，其中一个基因在大肠杆菌细胞中进行了异源表达，名为海红球菌嗜盐视紫红质（RmHR）的视紫红质蛋白被鉴定为光驱动内向氯泵。光谱分析表明，这种视紫红质的估计解离常数（K）与嗜盐古菌嗜盐视紫红质（HR）相似，而这种视紫红质的氯转运光反应机制与HR相似，但与已知的海洋细菌ClR不同。这种氨基酸序列相似性还表明，这种视紫红质与嗜盐古菌HR和蓝细菌HR（如SyHR和MrHR）相似。此外，系统发育分析表明，视网膜生物合成途径基因（blh和crtY）属于嗜盐古菌的系统发育谱系，这表明这些海洋噬纤维菌属通过横向基因转移从嗜盐古菌获得了视紫红质相关基因。基于这些结果，我们得出结论，内向氯泵视紫红质存在于噬纤维菌纲的属中，并且可能与嗜盐古菌HR具有相同的进化起源。
