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TitleCarotenoids bind rhodopsins and act as photocycle-accelerating pigments in marine Bacteroidota.
Journal, issue, pagesNat Microbiol, Vol. 10, Issue 10, Page 2603-2615, Year 2025
Publish dateSep 4, 2025
AuthorsTakayoshi Fujiwara / Toshiaki Hosaka / Masumi Hasegawa-Takano / Yosuke Nishimura / Kento Tominaga / Kaho Mori / Satoshi Nishino / Yuno Takahashi / Tomomi Uchikubo-Kamo / Kazuharu Hanada / Takashi Maoka / Shinichi Takaichi / Keiichi Inoue / Mikako Shirouzu / Susumu Yoshizawa /
PubMed AbstractMicrobial 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 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 S1-08, 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.
External linksNat Microbiol / PubMed:40908369
MethodsEM (single particle)
Resolution2.27 - 2.5 Å
Structure data

61685

9jou

EMDB-61685, PDB-9jou:
Cryo-EM structure of the zeaxanthin-bound light-driven proton pumping rhodopsin, NM-R1
Method: EM (single particle) / Resolution: 2.46 Å

61686

9jov

EMDB-61686, PDB-9jov:
Cryo-EM structure of the myxol-bound light-driven proton pumping rhodopsin, NM-R1
Method: EM (single particle) / Resolution: 2.27 Å

61687

9jow

EMDB-61687, PDB-9jow:
Cryo-EM structure of the myxol-bound light-driven chloride ion-pumping rhodopsin, NM-R3
Method: EM (single particle) / Resolution: 2.48 Å

61688

9jox

EMDB-61688, PDB-9jox:
Cryo-EM structure of the light-driven chloride ion-pumping rhodopsin, NM-R3
Method: EM (single particle) / Resolution: 2.5 Å

Chemicals

ChemComp-RET:
RETINAL

ChemComp-R16:
HEXADECANE

ChemComp-D12:
DODECANE

ChemComp-K3I:
Zeaxanthin

ChemComp-HOH:
WATER

PDB-1l4o:
Unknown entry

ChemComp-CL:
Unknown entry

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

ChemComp-PLC:
DIUNDECYL PHOSPHATIDYL CHOLINE / phospholipid*YM

ChemComp-8K6:
Octadecane

ChemComp-C14:
TETRADECANE

ChemComp-D10:
DECANE

Source
  • nonlabens marinus s1-08 (bacteria)
KeywordsMEMBRANE PROTEIN / proton pump rhodopsin RETINAL CELL-FREE SYNTHESIS Bacterial type rhodopsin / zeaxanthin / chloride ion-pumping rhodopsin RETINAL CELL-FREE SYNTHESIS Bacterial type rhodopsin

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