The effects of chloride ion binding on the photochemical properties of sensory rhodopsin II from Natronomonas pharaonis

Tamogami, Jun; Iwano, Katsunori; Matsuyama, Atsushi; Kikukawa, Takashi; Demura, Makoto; Nara, Toshifumi; Kamo, Naoki

doi:10.1016/j.jphotobiol.2014.10.010

Cited by 3 publications

(3 citation statements)

References 43 publications

(83 reference statements)

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“…Rhodopsins are photoreactive proteins first discovered in Halobacterium salinarum [77] with two different functions: light-driven ion transport (H + pump bacteriorhodopsin [78], Clpump halorhodopsin [79]) and phototaxis (sensory rhodopsins I and II [80,81]). Later on, distinct rhodopsins have also been identified in other organisms of the three domains of life, such as Natronomonas pharaonis, which has been a long-term target of study as a model organism for rhodopsin analyses due to its facile expression and purification in addition to other advantageous properties [82][83][84][85][86][87].…”

Section: Rhodopsin Analysismentioning

confidence: 99%

Natronomonas salsuginis sp. nov., a New Inhabitant of a Marine Solar Saltern

2020

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A halophilic archaeon, strain F20-122T, was isolated from a marine saltern of Isla Bacuta (Huelva, Spain). Cells were Gram-stain-negative, aerobic, and coccoid in morphology. It grew at 25–50 °C (optimum 37 °C), pH 6.5–9.0 (optimum pH 8.0), and 10–30% (w/v) total salts (optimum 25% salts). The phylogenetic analyses based on the 16S rRNA and rpoB’ genes showed its affiliation with the genus Natronomonas and suggested its placement as a new species within this genus. The in silico DNA–DNA hybridization (DDH) and average nucleotide identity (ANI) analyses of this strain against closely related species supported its placement in a new taxon. The DNA G + C content of this isolate was 63.0 mol%. The polar lipids of strain F20-122T were phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol (PG), and phosphatidylglycerol sulfate (PGS). Traces of biphosphatidylglycerol (BPG) and other minor phospholipids and unidentified glycolipids were also present. Based on the phylogenetic, genomic, phenotypic, and chemotaxonomic characterization, we propose strain F20-122T (= CCM 8891T = CECT 9564T = JCM 33320T) as the type strain of a new species within the genus Natronomonas, with the name Natronomonas salsuginis sp. nov. Rhodopsin-like sequence analysis of strain F20-122T revealed the presence of haloarchaeal proton pumps, suggesting a light-mediated ATP synthesis for this strain and a maximum wavelength absorption in the green spectrum.

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Section: Rhodopsin Analysismentioning

confidence: 99%

Natronomonas salsuginis sp. nov., a New Inhabitant of a Marine Solar Saltern

2020

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“…The SRII sample was prepared as described elsewhere. 22 The sample was dissolved in a detergent buffer at pH 7.0, which consists of 10 mM citrate, 2-morpholinoethanesulfonic acid, 4-hydroxyethylpiperazineethanesulfonic acid, 3-morpholinopropanesulfonic acid, N-cyclohexyl-2-aminoethanesulfonic acid, and N-cyclohexyl-3-aminopropanesulfonic acid with 400 mM NaCl and 0.05% n-dodecyl-β-D-maltoside. The sample concentration was adjusted to ∼0.73 mM for Raman/ROA measurement and ∼0.1 mM for CD measurement.…”

Section: Methodsmentioning

confidence: 99%

Raman Optical Activity of Retinal Chromophore in Sensory Rhodopsin II

Nishikawa,

Kuroiwa,

Tamogami

et al. 2023

J. Phys. Chem. B

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Raman optical activity (ROA) spectroscopy was used to study the conformation of the retinal chromophore in sensory rhodopsin II (SRII), which is a blue−green light sensor of microbes. The ROA spectrum consisted of the negative vibrational bands of the chromophore, whose relative intensities are similar to those of the parent Raman spectrum. This spectral feature was explained by the left-handed helical twist of the retinal chromophore on the basis of quantum chemical calculations. On the other hand, we found that the chromophore conformation based on the crystal structures of SRII has a right-handed helical twist, which does not agree with the observation. This specific result suggests that the consistency with chirooptical properties can be a key criterion for the accurate prediction and/or evaluation of chromophore conformation in retinal-binding proteins.

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“…To estimate the amounts of protons transferred at varying pH values, the buffering action in the medium had to be kept constant over a wide pH range (∼5 ≤ pH ≤ ∼11). Therefore, a medium solution containing six different buffer agents (0.89 mM citrate, 0.89 mM MES, 1.07 mM TES, 0.78 mM TAPS, 1.11 mM CHES, and 0.33 mM CAPS) , and 400 mM NaCl was employed for measurements. All experiments were performed at room temperature (∼25 °C).…”

Section: Materials and Methodsmentioning

confidence: 99%

Formation of M-Like Intermediates in Proteorhodopsin in Alkali Solutions (pH ≥ ∼8.5) Where the Proton Release Occurs First in Contrast to the Sequence at Lower pH

et al. 2016

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Proteorhodopsin (PR) is an outward light-driven proton pump observed in marine eubacteria. Despite many structural and functional similarities to bacteriorhodopsin (BR) in archaea, which also acts as an outward proton pump, the mechanism of the photoinduced proton release and uptake is different between two H(+)-pumps. In this study, we investigated the pH dependence of the photocycle and proton transfer in PR reconstituted with the phospholipid membrane under alkaline conditions. Under these conditions, as the medium pH increased, a blue-shifted photoproduct (defined as Ma), which is different from M, with a pKa of ca. 9.2 was produced. The sequence of the photoinduced proton uptake and release during the photocycle was inverted with the increase in pH. A pKa value of ca. 9.5 was estimated for this inversion and was in good agreement with the pKa value of the formation of Ma (∼ 9.2). In addition, we measured the photoelectric current generated by PRs attached to a thin polymer film at varying pH. Interestingly, increases in the medium pH evoked bidirectional photocurrents, which may imply a possible reversal of the direction of the proton movement at alkaline pH. On the basis of these findings, a putative photocycle and proton transfer scheme in PR under alkaline pH conditions was proposed.

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The effects of chloride ion binding on the photochemical properties of sensory rhodopsin II from Natronomonas pharaonis

Cited by 3 publications

References 43 publications

Natronomonas salsuginis sp. nov., a New Inhabitant of a Marine Solar Saltern

Natronomonas salsuginis sp. nov., a New Inhabitant of a Marine Solar Saltern

Raman Optical Activity of Retinal Chromophore in Sensory Rhodopsin II

Formation of M-Like Intermediates in Proteorhodopsin in Alkali Solutions (pH ≥ ∼8.5) Where the Proton Release Occurs First in Contrast to the Sequence at Lower pH

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