Light-driven ion-translocating rhodopsins in marine bacteria

Inoue, Kazuhide; Kato, Yoshitaka; Kandori, Hideki

doi:10.1016/j.tim.2014.10.009

Cited by 101 publications

(118 citation statements)

References 82 publications

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“…Functional PR is available from the heterologous Escherichia coli system with exogenous retinal [16]. Thus, the photochemistry of PR has been examined in detail (for reviews, see refs [2,19,20]). …”

Section: Introductionmentioning

confidence: 99%

Photochemical characterization of actinorhodopsin and its functional existence in the natural host

Nakamura

Kikukawa

Tamogami

et al. 2016

Biochimica et Biophysica Acta (BBA) - Bioenergetics

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Section: Introductionmentioning

confidence: 99%

Photochemical characterization of actinorhodopsin and its functional existence in the natural host

Nakamura

Kikukawa

Tamogami

et al. 2016

Biochimica et Biophysica Acta (BBA) - Bioenergetics

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“…We only briefly allude to some important aspects of the biophysics and biochemistry of rhodopsins relevant to the physiology and ecology of Bacteria and Archaea, since excellent comprehensive presentations on the structure, biophysics, and molecular mechanism of rhodopsins are already available (8,(31)(32)(33)(34). For sensory rhodopsins, we refer to insightful reviews (2,8).…”

mentioning

confidence: 99%

Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology

Pinhassi

DeLong

Béjà

et al. 2016

Microbiol Mol Biol Rev

175

172

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SUMMARYThe recognition of a new family of rhodopsins in marine planktonic bacteria, proton-pumping proteorhodopsin, expanded the known phylogenetic range, environmental distribution, and sequence diversity of retinylidene photoproteins. At the time of this discovery, microbial ion-pumping rhodopsins were known solely in haloarchaea inhabiting extreme hypersaline environments. Shortly thereafter, proteorhodopsins and other light-activated energy-generating rhodopsins were recognized to be widespread among marine bacteria. The ubiquity of marine rhodopsin photosystems now challenges prior understanding of the nature and contributions of “heterotrophic” bacteria to biogeochemical carbon cycling and energy fluxes. Subsequent investigations have focused on the biophysics and biochemistry of these novel microbial rhodopsins, their distribution across the tree of life, evolutionary trajectories, and functional expression in nature. Later discoveries included the identification of proteorhodopsin genes in all three domains of life, the spectral tuning of rhodopsin variants to wavelengths prevailing in the sea, variable light-activated ion-pumping specificities among bacterial rhodopsin variants, and the widespread lateral gene transfer of biosynthetic genes for bacterial rhodopsins and their associated photopigments. Heterologous expression experiments with marine rhodopsin genes (and associated retinal chromophore genes) provided early evidence that light energy harvested by rhodopsins could be harnessed to provide biochemical energy. Importantly, some studies with native marine bacteria show that rhodopsin-containing bacteria use light to enhance growth or promote survival during starvation. We infer from the distribution of rhodopsin genes in diverse genomic contexts that different marine bacteria probably use rhodopsins to support light-dependent fitness strategies somewhere between these two extremes.

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“…A while after these discoveries, microbial rhodopsins were thought to be restricted to hypersaline environments. However, because of the recent developments in molecular biology techniques, three different functional rhodopsins, a light-driven H ϩ -pumping proteorhodopsin, a light-driven Na ϩ (sodium ion)-pumping rhodopsin, and a light-driven Cl Ϫ -pumping rhodopsin, were found in marine microorganisms (3)(4)(5). Now it is known that ion-translocating rhodopsins are widely distributed in a variety of microorganisms in all three domains of life (6 -8).…”

mentioning

confidence: 99%

Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3

Hosaka

Yoshizawa

Nakajima

et al. 2016

Journal of Biological Chemistry

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The light-driven inward chloride ion-pumping rhodopsin Nonlabens marinus rhodopsin-3 (NM-R3), from a marine flavobacterium, belongs to a phylogenetic lineage distinct from the halorhodopsins known as archaeal inward chloride ion-pumping rhodopsins. NM-R3 and halorhodopsin have distinct motif sequences that are important for chloride ion binding and transport. In this study, we present the crystal structure of a new type of light-driven chloride ion pump, NM-R3, at 1.58 Å resolution. The structure revealed the chloride ion translocation pathway and showed that a single chloride ion resides near the Schiff base. The overall structure, chloride ion-binding site, and translocation pathway of NM-R3 are different from those of halorhodopsin. Unexpectedly, this NM-R3 structure is similar to the crystal structure of the light-driven outward sodium ion pump, Krokinobacter eikastus rhodopsin 2. Structural and mutational analyses of NM-R3 revealed that most of the important amino acid residues for chloride ion pumping exist in the ion influx region, located on the extracellular side of NM-R3. In contrast, on the opposite side, the cytoplasmic regions of K. eikastus rhodopsin 2 were reportedly important for sodium ion pumping. These results provide new insight into ion selection mechanisms in ion pumping rhodopsins, in which the ion influx regions of both the inward and outward pumps are important for their ion selectivities.

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Light-driven ion-translocating rhodopsins in marine bacteria

Cited by 101 publications

References 82 publications

Photochemical characterization of actinorhodopsin and its functional existence in the natural host

Photochemical characterization of actinorhodopsin and its functional existence in the natural host

Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology

Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3

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