Nature’s toolkit for microbial rhodopsin ion pumps

Béjà, Oded; Lanyi, Janos Κ.

doi:10.1073/pnas.1405093111

Cited by 55 publications

(39 citation statements)

References 28 publications

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“…Proton-pump rhodopsins contain DTD (D85, T89, D96 in BR) or DTE (D97, T101, E108 in PR) motif in the 3 rd helix ( Figure S4) (29). ABL4 contains DTE motif, and ABL3 and SAMEA5.1 contain GTE motif (G89, T93, E100 in SAMEA5.1) ( Figure S4).…”

Section: Resultsmentioning

confidence: 99%

Engineered Functional Recovery of Microbial Rhodopsin Without Retinal‐Binding Lysine

Yamauchi

Konno

Yamada

et al. 2019

Photochem & Photobiology

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Definition of rhodopsin is the retinal‐binding membrane protein with the Schiff base linkage at a lysine on the 7th transmembrane helix. However, ~ 600 microbial rhodopsins lack retinal‐binding lysine at the corresponding position (Rh‐noK) among ~ 5500 known microbial rhodopsins, suggesting that Rh‐noK has each functional role without chromophore. Here, we report successful functional recovery of Rh‐noK. Two Rh‐noKs from bacteria were heterologously expressed in Escherichia coli, which exhibited no color. When retinal‐binding lysine was introduced, one of them gained visible color. Additional mutation of the Schiff base counterion further gained proton‐pumping activity. Successful engineered functional recovery such as visible color and proton‐pump activity suggests that the Rh‐noK protein forms a characteristic structure of microbial rhodopsins.

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Section: Resultsmentioning

confidence: 99%

Engineered Functional Recovery of Microbial Rhodopsin Without Retinal‐Binding Lysine

Yamauchi

Konno

Yamada

et al. 2019

Photochem & Photobiology

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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).…”

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confidence: 99%

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

Pinhassi

DeLong

Béjà

et al. 2016

Microbiol Mol Biol Rev

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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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“…During last 15 years, the discovery of many new reti nal proteins [60] -proteorhodopsins [61], xan thorhodopsins [62], channel rhodopsins [63,64], chlo ride and sodium pumps [65,66] -along with substantial progress in determining their tertiary structures [40, 50, 51, 67 69] has restored interest in studying the light dependent ion transport started over 40 years ago by D. Oesterhelt and W. Stoeckenius [3]. Studying the new rep resentatives of the family supplements our knowledge of the structural basis of such transport [66] and promotes their application in bio optoelectronics as a basis for molecular memory elements and photoactive media in dynamic holography [70 72], and in a new field -opto genetics [73] -for regulation of neuronal activity [74 76]. The sensitivity of photocycle reaction kinetics and fluorescence of the proton pumps to electrochemical potentials [77,78] revealed the possibility of using them as sensors for detection of intraprotein [79] and trans membrane changes of potentials [80].…”

Section: Extracellular Mediummentioning

confidence: 99%

ESR — A retinal protein with unusual properties from Exiguobacterium sibiricum

Petrovskaya

Balashov

Лукашев

et al. 2015

Biochemistry Moscow

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This review covers the properties of a retinal protein (ESR) from the psychrotrophic bacterium Exiguobacterium sibiricum that functions as a light-driven proton pump. The presence of a lysine residue at the position corresponding to intramolecular proton donor for the Schiff base represents a unique structural feature of ESR. We have shown that Lys96 successfully facilitates delivery of protons from the cytoplasmic surface to the Schiff base, thus acting as a proton donor in ESR. Since proton uptake during the photocycle precedes Schiff base reprotonation, we conclude that this residue is initially in the uncharged state and acquires a proton for a short time after Schiff base deprotonation and M intermediate formation. Involvement of Lys as a proton donor distinguishes ESR from the related retinal proteins - bacteriorhodopsin (BR), proteorhodopsin (PR), and xanthorhodopsin (XR), in which the donor function is performed by residues with a carboxyl side chain. Like other eubacterial proton pumps (PR and XR), ESR contains a histidine residue interacting with the proton acceptor Asp85. In contrast to PR, this interaction leads to shift of the acceptor's pKa to more acidic pH, thus providing its ability to function over a wide pH range. The presence of a strong H-bond between Asp85 and His57, the structure of the proton-conducting pathways from cytoplasmic surface to the Schiff base and to extracellular surface, and other properties of ESR were demonstrated by solving its three-dimensional structure, which revealed several differences from known structures of BR and XR. The structure of ESR, its photocycle, and proton transfer reactions are discussed in comparison with homologous retinal proteins.

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Nature’s toolkit for microbial rhodopsin ion pumps

Cited by 55 publications

References 28 publications

Engineered Functional Recovery of Microbial Rhodopsin Without Retinal‐Binding Lysine

Engineered Functional Recovery of Microbial Rhodopsin Without Retinal‐Binding Lysine

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

ESR — A retinal protein with unusual properties from Exiguobacterium sibiricum

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