Phototrophy by antenna-containing rhodopsin pumps in aquatic environments

Chazan, Ariel; Das, Ishita; Fujiwara, Takayoshi; Murakoshi, Shunya; Rozenberg, Andrey; Molina-Márquez, Ana; Sano, Fumiya K; Tanaka, Terumichi; Gómez‐Villegas, Patricia; Larom, Shirley; Pushkarev, Alina; Malakar, Partha; Hasegawa, Masamitsu; Tsukamoto, Yuya; Ishizuka, Tomohiro; Konno, Masae; Nagata, Takashi; Mizuno, Yosuke; Katayama, Kota; Abe-Yoshizumi, Rei; Ruhman, Sanford; Inoue, Kazuhide; Kandori, Hideki; Léon, Rosa; Shihoya, Wataru; Yoshizawa, Susumu; Sheves, Mordechai; Nureki, Osamu; Béjà, Oded

doi:10.1038/s41586-023-05774-6

Cited by 17 publications

(21 citation statements)

References 65 publications

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“…Natural systems evolved an alternative, supramolecular strategy to extend the absorption spectral range of photoswitchable molecules ( 18 , 19 ). For example, deep-sea fishes install a chlorophyll antenna next to the opsin-bound retinal ( 20 , 21 ).…”

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confidence: 99%

Disequilibrating azobenzenes by visible-light sensitization under confinement

Gemen,

Church,

Ruoko

et al. 2023

Science

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Photoisomerization of azobenzenes from their stable E isomer to the metastable Z state is the basis of numerous applications of these molecules. However, this reaction typically requires ultraviolet light, which limits applicability. In this study, we introduce disequilibration by sensitization under confinement (DESC), a supramolecular approach to induce the E -to- Z isomerization by using light of a desired color, including red. DESC relies on a combination of a macrocyclic host and a photosensitizer, which act together to selectively bind and sensitize E -azobenzenes for isomerization. The Z isomer lacks strong affinity for and is expelled from the host, which can then convert additional E- azobenzenes to the Z state. In this way, the host–photosensitizer complex converts photon energy into chemical energy in the form of out-of-equilibrium photostationary states, including ones that cannot be accessed through direct photoexcitation.

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confidence: 99%

Disequilibrating azobenzenes by visible-light sensitization under confinement

Gemen,

Church,

Ruoko

et al. 2023

Science

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“…This methodology has also been effectively utilized for determining the structures of relatively small transporters. For microbial rhodopsins, nanodisc reconstitution has been used in the cryo-EM structural analyses of the ChRmine trimer 30 and the Kin4B8 pentamer 31 . We adopted this approach for KnChR, and ultimately determined the cryo-EM structure of the nanodisc-reconstituted KnChR.…”

Section: Discussionmentioning

confidence: 99%

Cryo-EM structure of a blue-shifted channelrhodopsin fromKlebsormidium nitens

Wang,

Natsume,

Tanaka

et al. 2024

Preprint

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Channelrhodopsins (ChRs) are light-gated ion channels and invaluable tools for optogenetic applications. Recent developments in multicolor optogenetics, in which different neurons are controlled by multiple colors of light simultaneously, have increased the demand for ChR mutants with more distant absorption wavelengths. Here we report the 2.9 Angstrom-resolution cryo-electron microscopy structure of a ChR from Klebsormidium nitens (KnChR), which is one of the most blue-shifted ChRs. The structure elucidates the 6-s-cis configuration of the retinal chromophore, indicating its contribution to a distinctive blue shift in action spectra. The unique architecture of the C-terminal region reveals its role in the allosteric modulation of channel kinetics, enhancing our understanding of its functional dynamics. Based on the structure-guided design, we developed mutants with blue-shifted action spectra. Finally, we confirm that UV or deep-blue light can activate KnChR-transfected precultured neurons, expanding its utility in optogenetic applications. Our findings contribute valuable insights to advance optogenetic tools and enable refined capabilities in neuroscience experiments.

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“…Although these findings suggest that XR is not the only rhodopsin using an antenna carotenoid, most microbial rhodopsins were thought not to bind antenna carotenoids. However, functional metagenomics revealed that several XRs and proteorhodopsins (PRs) bind 3-hydroxylcarotenoid, such as lutein and zeaxanthin (ZXN), indicating that these 3-hydroxylcarotenoids, which are more prevalent than SXN, are used by XRs and PRs of diverse bacteria . All XRs and PRs that can bind carotenoid antennae have a glycine homologous to Gly156 in the fifth transmembrane helix (TM5) of XR from S. ruber (Figure ).…”

Section: Fenestrations For Retinal Uptake and Energy Transfer Between...mentioning

confidence: 99%

“…In BR, Trp138 is present at a homologous position and buries the space of the XR fenestration. Because mutation of glycine homologous to XR Gly156 to bulky phenylalanine or tryptophan eliminates carotenoid binding, , it is a good indicator of microbial rhodopsins that have the potential to bind to carotenoids. This glycine is conserved in 33.1% of PR and 18.5% of XR genes on average in ocean, and these values increase to 53.9% and 81.6% in freshwater, respectively, indicating that a substantial number of rhodopsins use carotenoid antennae.…”

Section: Fenestrations For Retinal Uptake and Energy Transfer Between...mentioning

confidence: 99%

Photochemistry of the Retinal Chromophore in Microbial Rhodopsins

Inoue

2023

J. Phys. Chem. B

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Microbial rhodopsins are photoreceptive membrane proteins of microorganisms that express diverse photobiological functions. All-trans-retinylidene Schiff base, the so-called all-trans-retinal, is a chromophore of microbial rhodopsins, which captures photons. It isomerizes into the 13-cis form upon photoexcitation. Isomerization of retinal leads to sequential conformational changes in the protein, giving rise to active states that exhibit biological functions. Despite the rapidly expanding diversity of microbial rhodopsin functions, the photochemical behaviors of retinal were considered to be common among them. However, the retinal of many recently discovered rhodopsins was found to exhibit new photochemical characteristics, such as highly red-shifted absorption, isomerization to 7-cis and 11-cis forms, and energy transfer from a secondary carotenoid chromophore to the retinal, which is markedly different from that established in canonical microbial rhodopsins. Here, I review new aspects of retinal found in novel microbial rhodopsins and highlight the emerging problems that need to be addressed to understand noncanonical retinal photochemistry.

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Phototrophy by antenna-containing rhodopsin pumps in aquatic environments

Cited by 17 publications

References 65 publications

Disequilibrating azobenzenes by visible-light sensitization under confinement

Disequilibrating azobenzenes by visible-light sensitization under confinement

Cryo-EM structure of a blue-shifted channelrhodopsin fromKlebsormidium nitens

Photochemistry of the Retinal Chromophore in Microbial Rhodopsins

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