Evolution of the archaeal rhodopsins: evolution rate changes by gene duplication and functional differentiation

Ihara, Kenji; Umemura, Tohru; Katagiri, Izumi; Kitajima-Ihara, Tomomi; Sugiyama, Yasuo; Kimura, Yusuke; Mukohata, Yasuo

doi:10.1006/jmbi.1998.2286

Cited by 156 publications

(160 citation statements)

References 48 publications

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“…arg-4 [11,26] and the present result from JCM9743 were found at only two positions: at the was determined to be 2.2 from this spectrum shift (Fig. 2).…”

Section: Resultssupporting

confidence: 42%

“…Of interest, from this strain, Ihara et al discovered a new retinal protein [11,12], which conserves completely the amino acid residues essential for light-driven proton pumping, but the homology with bR has as low as 53%. This protein was named deltarhodopsin (abbreviated as dR, GenBank accession no.…”

Section: Mukohata and Collaborators Isolated A Bacterium From Anmentioning

confidence: 99%

“…In addition, Mukohata and his colleagues [11] discovered another class of light-driven pumps such as archaerhodopsin (aR) and cruxrhodopsin (cR) having low homology with bR and dR.…”

Section: Ab009620)mentioning

confidence: 99%

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A light-driven proton pump from Haloterrigena turkmenica: Functional expression in Escherichia coli membrane and coupling with a H+ co-transporter

Kamo

Hashiba

Kikukawa

et al. 2006

Biochemical and Biophysical Research Communications

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A gene encoding putative retinal protein was cloned from Haloterrigena turkmenica (JCM9743). The deduced amino acid sequence was most closely related to that of deltarhodopsin, which functions as a light-driven H+ pump and was identified in a novel strain Haloterrigena sp. arg-4 (K. Ihara, T. Uemura, I. Katagiri, T. Kitajima-Ihara, Y. Sugiyama, Y. Kimura, Y. Mukohata, Evolution of the archaeal rhodopsins: Evolution rate changes by gene duplication and functional differentiation, J. Mol. Biol. 285 (1999) 163–174. GenBank Accession No. AB009620). Thus, we called the present protein H. turkmenica deltarhodopsin (HtdR) in this report. Differing from the Halobacterium salinarum bacteriorhodopsin (bR), functional expression of HtdR was achieved in Escherichia coli membrane with a high yield of 10–15 mg protein/L culture. The photocycle of purified HtdR was similar to that of bR. The photo-induced electrogenic proton pumping activity of HtdR was verified. We co-expressed both HtdR and EmrE, a proton-coupled multi-drug efflux transporter in E. coli, and the cells successfully extruded ethidium, a substrate of EmrE, on illumination

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“…arg-4 [11,26] and the present result from JCM9743 were found at only two positions: at the was determined to be 2.2 from this spectrum shift (Fig. 2).…”

Section: Resultssupporting

confidence: 42%

Section: Mukohata and Collaborators Isolated A Bacterium From Anmentioning

confidence: 99%

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A light-driven proton pump from Haloterrigena turkmenica: Functional expression in Escherichia coli membrane and coupling with a H+ co-transporter

Kamo

Hashiba

Kikukawa

et al. 2006

Biochemical and Biophysical Research Communications

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“…We therefore suggest that the specific protein environment involving Thr-17 may work as the specific reaction field of photoisomerization. Tyr-57 and Asp-212 are all conserved among archaeal rhodopsins, whereas Thr-17 and Met-20 are conserved in the proton-pumping BR family (34). Thus, there may be common features in their structure and dynamics.…”

Section: Assignment Of the O-h And O-d Stretch Bands To Threonine Sidementioning

confidence: 99%

Local and distant protein structural changes on photoisomerization of the retinal in bacteriorhodopsin

Kandori

Kinoshita

Yamazaki

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

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The photoisomerization of the retinal in bacteriorhodopsin is selective and efficient and yields perturbation of the protein structure within femtoseconds. The stored light energy in the primary intermediate is then used for the net translocation of a proton across the membrane in the microsecond to millisecond regime. This study is aimed at identifying how the protein changes on photoisomerization by using the O-H groups of threonines as internal probes. Polarized Fourier-transform IR spectroscopy of [3-18 O]threonine-labeled and unlabeled bacteriorhodopsin indicates that 3 of the threonines (of a total of 18) change their hydrogen bonding. One is exchangeable in D 2O, but two are not. A comprehensive mutation study indicates that the residues involved are Thr-89, Thr-17, and Thr-121 (or Thr-90). The perturbation of only three threonine side chains suggests that the structural alteration at this stage of the photocycle is local and specific. Furthermore, the structural change of Thr-17, which is located >11 Å from the retinal chromophore, implicates a specific perturbation channel in the protein that accompanies the retinal motion. B acteriorhodopsin (BR) is a light-driven proton pump inHalobacterium salinarum that contains all-trans retinal as chromophore (1-4). Its tertiary structure has been determined recently by cryoelectron microscopy (5-7) and x-ray crystallography (8-13). The retinal binds covalently to Lys-216 through a protonated Schiff base linkage. Absorption of light triggers a cyclic reaction that comprises a series of intermediates, designated as the J, K, KL, L, M, N, and O states (1-4). Protein structural changes in these intermediate states cause proton translocation across the protein, and their mechanism is the central question in current studies of BR (14).The all-trans to 13-cis photoisomerization leads to the formation of the primary K intermediate (15)(16)(17). It is well known that photoisomerization in BR is highly selective and efficient. In solution, the photoproduct of all-trans retinal with protonated Schiff base is mainly 11-cis [82% (vol/vol) 11-cis͞6% (vol/vol) 13-cis͞12% (vol/vol) 9-cis in methanol; ref. 18], whereas in BR, the photoproduct is 100% (vol͞vol) 13-cis. The quantum efficiency for isomerization in BR (Ϸ0.6; refs. 19 and 20) is much higher than for retinal in solution (0.13 in methanol; ref. 18). This efficiency is correlated closely with the rate constant of the isomerization, because it occurs on the femtosecond time scale. The protein environment thus certainly facilitates the specificity of the reaction of the retinal chromophore.How does the highly selective and efficient isomerization occur in BR? How does the protein respond to the chromophore motion? To address these questions, structural analysis of the primary intermediates is essential. Cryoelectron microscopy of the K intermediate reported that the structural change at this stage is not resolved with 3.5-Å resolution (21). More recent analysis of the K intermediate by x-ray crystallography identified few...

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“…TR exhibits an absorption spectrum, a photocycle with intermediates and kinetics that are characteristic of retinal proteins. Of note, compared with other proton pumping rhodopsins, including the BR-like proteins from Haloquadratum walsbyi (HwBR) (18) and from Halorubrum sodomense (AR3) (19) and a PR-like protein GR, TR shows a high stability even at high temperature (75°C). Thus, in addition to the expression system, the high stability of TR should allow the use of various methods to investigate the molecular mechanisms both of the ion transport and the protein folding.…”

mentioning

confidence: 99%

Thermal and Spectroscopic Characterization of a Proton Pumping Rhodopsin from an Extreme Thermophile

Tsukamoto

Inoue

Kandori

et al. 2013

Journal of Biological Chemistry

120

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Evolution of the archaeal rhodopsins: evolution rate changes by gene duplication and functional differentiation

Cited by 156 publications

References 48 publications

A light-driven proton pump from Haloterrigena turkmenica: Functional expression in Escherichia coli membrane and coupling with a H+ co-transporter

A light-driven proton pump from Haloterrigena turkmenica: Functional expression in Escherichia coli membrane and coupling with a H+ co-transporter

Local and distant protein structural changes on photoisomerization of the retinal in bacteriorhodopsin

Thermal and Spectroscopic Characterization of a Proton Pumping Rhodopsin from an Extreme Thermophile

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