Presence of a haloarchaeal halorhodopsin-like Cl pump in marine bacteria

Yu Nakajima, Takashi Tsukamoto, Yohei Kumagai, Yoshitoshi Ogura, Tetsuya Hayashi, Jaeho Song, Takashi Kikukawa, Makoto Demura, Kazuhiro Kogure, Yuki Sudo, Susumu Yoshizawa

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2 Citations (Scopus)

Abstract

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 (Kd,int.) 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.

Original languageEnglish
Pages (from-to)89-97
Number of pages9
JournalMicrobes and Environments
Volume33
Issue number1
DOIs
Publication statusPublished - 2018

Keywords

  • Chloride ion pump
  • Family Rhodothermaceae
  • Genome analysis
  • Rhodopsin

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Soil Science
  • Plant Science

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    Nakajima, Y., Tsukamoto, T., Kumagai, Y., Ogura, Y., Hayashi, T., Song, J., Kikukawa, T., Demura, M., Kogure, K., Sudo, Y., & Yoshizawa, S. (2018). Presence of a haloarchaeal halorhodopsin-like Cl pump in marine bacteria. Microbes and Environments, 33(1), 89-97. https://doi.org/10.1264/jsme2.ME17197