In situ structure of the red algal phycobilisome–PSII–PSI–LHC megacomplex

You, Xiao‐Zeng; Zhang, Xing; Jun, Cheng; Xiao, Yanan; Ma, Jianfei; Sun, Shan; Zhang, Xinzheng; Wang, Hongwei; Sui, Sen-Fang

doi:10.1038/s41586-023-05831-0

Cited by 56 publications

(51 citation statements)

References 71 publications

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“…The C. caldarium LHCIs of LHCI-1 to LHCI-5 (red) exist at the same positions of RedCAP, Lhcr2, Lhcr5, Lhcr4, and Lhcr3, respectively, in the P. purpureum PSI-LHCI structure (blue) 8 (Fig. 3c).…”

Section: Resultsmentioning

confidence: 97%

“…d, Correlation of the names of LHCs in the structures with their genes between C. caldarium and P. purpureum . The names of LHCs and their genes are derived from You et al (2023) for P. purpureum 8 .…”

Section: Resultsmentioning

confidence: 99%

“…The structures of LHCs and their association patterns with the photosystem cores have been revealed by structural studies, especially using cryo-electron microscopy (cryo-EM) 3,5 . In the red lineage, the number, sequences, and pigment compositions of LHCIs have been found to differ greatly among the PSI-LHCI structures of red algae [6][7][8] , a diatom 9,10 , and a cryptophyte 11 .…”

mentioning

confidence: 99%

“…The red alga Cyanidioschyzon merolae belongs to the Cyanidiophyceae (Cyanidiophytina) [13][14][15][16] , and its PSI-LHCI structure contained three to five LHCI subunits 6,7 . In contrast, the red alga Porphyridium purpureum belongs to the Porphyridiophyceae 16,17 , and its PSI-LHCI structure contained seven LHCI subunits and one red lineage chlorophyll a/b-binding-like protein (RedCAP) 8 which is included in the LHC protein superfamily 18,19 . Thus, the number and binding sites of LHCIs in PSI-LHCI differ significantly between the two types of red algae.…”

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confidence: 99%

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Structure of PSI-LHCI fromCyanidium caldariumprovides evolutionary insights into conservation and diversity of red-lineage LHCs

Kato,

Hamaguchi,

Kumazawa

et al. 2023

Preprint

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Light-harvesting complexes (LHCs) are diversified among photosynthetic organisms, and their structural variety in photosystem I-LHC (PSI-LHCI) supercomplexes has been shown. However, structural and evolutionary correlations of red-lineage LHCs are unknown. Here we determined a 1.92-Angstrom resolution cryo-electron microscopic structure of a PSI-LHCI supercomplex isolated from the red alga Cyanidium caldarium RK-1 (NIES-2137) which is an important taxon in the Cyanidiophyceae, and subsequently investigated these correlations through structural comparisons and phylogenetic analysis. The PSI-LHCI structure shows five LHCI subunits together with a PSI-monomer core. The five LHCIs are composed of two Lhcr1s, two Lhcr2s, and one Lhcr3. Phylogenetic analysis of LHCs bound to PSI in red-lineage algae showed clear orthology of LHCs between C. caldarium and Cyanidioschyzon merolae, whereas no orthologous relationships were found between C. caldarium Lhcr1-3 and LHCs in other red-lineage PSI-LHCI structures. These findings provide evolutionary insights into conservation and diversity of red-lineage LHCs associated with PSI.

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Section: Resultsmentioning

confidence: 97%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Structure of PSI-LHCI fromCyanidium caldariumprovides evolutionary insights into conservation and diversity of red-lineage LHCs

Kato,

Hamaguchi,

Kumazawa

et al. 2023

Preprint

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“…To illustrate the performance of ModelAngelo in identifying protein chains in cryo-EM maps, we applied ModelAngelo to two examples of large cryo-EM structures that were recently determined from endogenous sources. The first example is a structure of the supercomplex of the phycobilisome (PBS), photosystem I and II (PSI and PSII), and the transmembrane light-harvesting complexes (LHCs) that was imaged in situ in the red alga Porphyridium purpureum ( 51 ). The second example is a structure of the ciliary central apparatus and radial spokes of the green alga Chlamydomonas reinhardtii that was obtained by single-particle analysis following purification from cilia ( 12, 13 ).…”

Section: Resultsmentioning

confidence: 99%

Automated model building and protein identification in cryo-EM maps

Jamali

Käll

Zhang

et al. 2023

Preprint

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Interpreting electron cryo-microscopy (cryo-EM) maps with atomic models requires high levels of expertise and labour-intensive manual intervention. We present ModelAngelo, a machine-learning approach for automated atomic model building in cryo-EM maps. By combining information from the cryo-EM map with information from protein sequence and structure in a single graph neural network, ModelAngelo builds atomic models for proteins that are of similar quality as those generated by human experts. For nucleotides, ModelAngelo builds backbones with similar accuracy as humans. By using its predicted amino acid probabilities for each residue in hidden Markov model sequence searches, ModelAngelo outperforms human experts in the identification of proteins with unknown sequences. ModelAngelo will thus remove bottlenecks and increase objectivity in cryo-EM structure determination.

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Recognition of histidines with a synthetic zinc amino‐oxochlorin regioisomer via synergetic coordination and hydrogen bonding

Yuasa,

Hara,

Tamiaki

2024

J of Physical Organic Chem

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Zinc 13‐(N,N‐diethylamino)methyl‐3,3,7,8,12,17,18‐heptaethyl‐2‐oxochlorin was prepared from 2,3,7,8,12,13,17,18‐octaethylporphyrin via the regioselectively acid‐catalyzed double dehydration of cis‐12,13‐diethyl‐cis‐12,13‐dihydroxy‐2‐oxobacteriochlorin to the corresponding 12‐ethyl‐13‐vinyl‐2‐oxochlorin. The synthetic zinc amino‐oxochlorin was axially ligated with the imidazolyl group of Nα‐protected histidines in chloroform, and concomitantly the amino group of the former was hydrogen‐bonded with the carboxy group of the latter. The resulting two‐point bonding supramolecules served as models for the complexes of chlorophylls with peptides in photosynthetic apparatuses including light‐harvesting antennas and charge‐separating reaction centers. A similar 1:1 complex was produced by the interaction of the zinc amino‐chlorin with the related methionine possessing thioether and carboxylic acid moieties.

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In situ structure of the red algal phycobilisome–PSII–PSI–LHC megacomplex

Cited by 56 publications

References 71 publications

Structure of PSI-LHCI fromCyanidium caldariumprovides evolutionary insights into conservation and diversity of red-lineage LHCs

Structure of PSI-LHCI fromCyanidium caldariumprovides evolutionary insights into conservation and diversity of red-lineage LHCs

Automated model building and protein identification in cryo-EM maps

Recognition of histidines with a synthetic zinc amino‐oxochlorin regioisomer via synergetic coordination and hydrogen bonding

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