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TitleStructural basis for aerobic anoxygenic photosynthesis in the reaction center-light-harvesting 1 (RC-LH1) supercomplex of Dinoroseobacter shibae.
Journal, issue, pagesCommun Biol, Vol. 8, Issue 1, Page 1565, Year 2025
Publish dateNov 14, 2025
AuthorsZe-Kun Liu / Jian-Xun Li / Ying-Yue Zhang / Jing-Li Lv / Kang Li / Xiu-Lan Chen / Yu-Zhong Zhang / Lu-Ning Liu / Peng Wang /
PubMed AbstractAerobic anoxygenic phototrophic (AAP) bacteria are essential for oceanic carbon cycling. However, their architecture and structural adaptations of their photosynthetic systems to ensure adequate ...Aerobic anoxygenic phototrophic (AAP) bacteria are essential for oceanic carbon cycling. However, their architecture and structural adaptations of their photosynthetic systems to ensure adequate light harvesting, electron transport, and oxidative resilience in oxygen-rich environments remain poorly understood. In this study, we present a 2.4-Å cryo-EM structure of the reaction center-light-harvesting 1 (RC-LH1) supercomplex from Dinoroseobacter shibae DFL-12, a marine AAP bacterial symbiont of benthic dinoflagellates. This RC-LH1 supercomplex features a closed LH1 ring comprising 17 αβ-subunits, each containing two spheroidenones per αβ-heterodimer-a previously unreported configuration in phototrophic bacteria. The cytochrome subunit of the RC is truncated to three hemes, in contrast to the four-heme configuration found in anaerobic relatives. The structure also reveals elongated bacteriochlorophyll (BChl) spacing, which may account for its blue-shifted absorption maximum that is optimized for low-light benthic environments. Furthermore, we identify a previously unknown subunit, protein-LRC, which is hypothesized to functionally couple photochemical and respiratory electron transport. Collectively, these specific structural features allow AAP bacteria to balance anoxygenic photosynthesis and protection against oxidative damage, providing a mechanistic framework for them to thrive in oxygenated marine environments. Our study provides insights into the structural and functional variability of bacterial photosynthesis in response to oxygenated marine environments.
External linksCommun Biol / PubMed:41238682 / PubMed Central
MethodsEM (single particle)
Resolution2.44 - 2.75 Å
Structure data

63379

9lts

EMDB-63379, PDB-9lts:
Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex
Method: EM (single particle) / Resolution: 2.49 Å

63381

9ltu

EMDB-63381, PDB-9ltu:
Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex with incomplete LH1 ring(State 1)
Method: EM (single particle) / Resolution: 2.44 Å

63382

9ltv

EMDB-63382, PDB-9ltv:
Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex with incomplete LH1 ring(State 2)
Method: EM (single particle) / Resolution: 2.75 Å

Chemicals

ChemComp-U10:
UBIQUINONE-10

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

ChemComp-SPN:
SPEROIDENONE

ChemComp-MW9:
(21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaoctacosan-21-yl (9Z)-octadec-9-enoate

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

ChemComp-BPH:
BACTERIOPHEOPHYTIN A

ChemComp-FE:
Unknown entry

Source
  • dinoroseobacter shibae dfl 12 = dsm 16493 (bacteria)
KeywordsPHOTOSYNTHESIS / reaction centre light-harvesting 1

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