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Carotenoids bind rhodopsins and act as photocycle-accelerating pigments in marine Bacteroidota

Nature Microbiology volume 10, pages 2603–2615 (2025)Cite this article

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Abstract

Microbial rhodopsins are photoreceptor proteins widely distributed in marine microorganisms that harness light energy and support marine ecosystems. While retinal is typically the sole chromophore in microbial rhodopsins, some proteorhodopsins, which are proton-pumping rhodopsins abundant in the ocean, use carotenoid antennae to transfer light energy to retinal. However, the mechanism by which carotenoids enhance rhodopsin functions remains unclear. Here, using the marine Bacteroidota isolate Nonlabens marinus S1-08T, we reconstituted complexes of rhodopsins with the carotenoid myxol and detected energy transfer to retinal in both proteorhodopsin and chloride ion-pumping rhodopsin. Carotenoid binding facilitated light harvesting and accelerated the photocycle, thereby improving the light utilization efficiency of proteorhodopsin. Cryogenic electron microscopy structural analysis further revealed the molecular architecture of the carotenoid–rhodopsin complexes. The ability to bind carotenoids is conserved in rhodopsins of the marine-dominant phylum Bacteroidota, which are widely transcribed in the photic zone. These findings reveal how carotenoids enhance rhodopsin functions in marine Bacteroidota.

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Fig. 1: Three types of rhodopsin from N. marinus S1-08T bind to carotenoids extracted from S1-08T cells.
Fig. 2: Identification of carotenoid pigments.
Fig. 3: Spectroscopic analyses of NM-R1 and NM-R3.
Fig. 4: Cryo-EM structure of NM-R1.
Fig. 5: Cryo-EM structure of NM-R3.
Fig. 6: Environmental conditions favouring the use of blue-PRs, green-PRs and antenna-containing PRs.

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Data availability

All data are available in the main text or the Supplementary Information. The density map and structure coordinate of the cryo-EM structures of NM-R1–myxol complex, NM-R1–zeaxanthin complex, NM-R3–myxol complex and NM-R3 have been deposited in the Electron Microscopy Data Bank and the Protein Data Bank with accession numbers EMD-61686 and 9JOV, EMD-61685 and 9JOU, EMD-61687 and 9JOW, and EMD-61688 and 9JOX, respectively. Source data are provided with this paper.

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Acknowledgements

We sincerely thank O. Béjà at Technion-Israel Institute of Technology for his comments on our experiments and paper. This work was supported by MEXT Advancement of Technologies for Utilization Big Data of Marine Life (grant JPMXD1521474594), JSPS KAKENHI Grants-in-Aid (grants 22KJ1110 to T.F., JP23H04404 to K.I. and 22H00557 to S.Y.), JST CREST (grant JPMJCR22N2 to K.I.), Research Support Project for Life Science and Drug Discovery (Basis for Supporting Innovative Drug Discovery and Life Science Research) from AMED (grant JP23ama121013 to M.S.), and MEXT Promotion of Development of a Joint Usage/Research System Project: Coalition of Universities for Research Excellence Program (grant JPMXP1323015482 to K.I.). All cryo-EM data in this study were collected at the cryo-EM facility of the RIKEN Center for Biosystems Dynamics Research (Yokohama, Japan).

Author information

Author notes

  1. These authors contributed equally: Takayoshi Fujiwara, Toshiaki Hosaka.

  2. These authors jointly supervised this work: Keiichi Inoue, Mikako Shirouzu, Susumu Yoshizawa.

Authors and Affiliations

  1. Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan

    Takayoshi Fujiwara, Kento Tominaga, Kaho Mori, Satoshi Nishino, Yuno Takahashi, Keiichi Inoue & Susumu Yoshizawa

  2. Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan

    Takayoshi Fujiwara, Kaho Mori, Satoshi Nishino, Yuno Takahashi & Susumu Yoshizawa

  3. Laboratory for Protein Functional and Structural Biology, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Japan

    Toshiaki Hosaka, Tomomi Uchikubo-Kamo, Kazuharu Hanada & Mikako Shirouzu

  4. Institute for Extra-cutting-edge Science and Technology Avant-garde Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan

    Masumi Hasegawa-Takano

  5. Advanced Institute for Marine Ecosystem Change, Japan Agency for Marine-Earth Science and Technology, Yokohama, Japan

    Masumi Hasegawa-Takano

  6. Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan

    Yosuke Nishimura

  7. Research Institute for Production Development, Kyoto, Japan

    Takashi Maoka

  8. Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo, Japan

    Shinichi Takaichi

  9. The Institute for Solid State Physics, The University of Tokyo, Chiba, Japan

    Keiichi Inoue

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  1. Takayoshi Fujiwara
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Contributions

T.F. and S.Y. designed the research; T.F., M.H.-T., Y.T. and S.Y. measured absorption and emission spectra of NM-R1 and NM-R3, culturing marine Bacteroidota. T.H., T.U.-K., K.H. and M.S. performed structural analysis. Y.N., K.T., K.M. and S.N. performed bioinformatics. K.I. performed CD spectra measurements and laser-flash photolysis. S.T. and T.M. identified carotenoid pigments. T.F. and S.Y. wrote the paper with input from all authors.

Corresponding authors

Correspondence to Keiichi Inoue, Mikako Shirouzu or Susumu Yoshizawa.

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The authors declare no competing interests.

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Peer review information

Nature Microbiology thanks Sergei Balashov, Shiqiang Gao, Thomas Mock and Pu Qian for their contribution to the peer review of this work. Peer reviewer reports are available.

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Extended data

Extended Data Table 1 1H-NMR data of myxol and zeaxanthin in CDCl3
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Supplementary information

Supplementary Information

Supplementary Figs. 1–16, Appendix 1, Results and Discussion.

Reporting Summary

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Supplementary Table 1

Cryo-EM data collection, refinement and validation statistics.

Supplementary Data

Source data for Supplementary Figs. 3–5 and 16.

Source data

Source Data Fig. 1

Rhodopsin sequences and absorption spectra of NM-R1, NM-R2 and NM-R3 with/without NmC.

Source Data Fig. 2

Chromatogram and absorption spectra of carotenoids.

Source Data Fig. 3

Differential, CD and excitation spectra of rhodopsins with/without carotenoids.

Source Data Fig. 4

PDB file of NM-R1–carotenoids complexes.

Source Data Fig. 5

PDB file of NM-R3–myxol complex.

Source Data Fig. 6

Rhodopsin amino acid sequences used for building the phylogenetic tree and rhodopsin gene transcripts at each depth.

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Fujiwara, T., Hosaka, T., Hasegawa-Takano, M. et al. Carotenoids bind rhodopsins and act as photocycle-accelerating pigments in marine Bacteroidota. Nat Microbiol 10, 2603–2615 (2025). https://doi.org/10.1038/s41564-025-02109-1

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