Plant Biology

Structural basis for molecular assembly of fucoxanthin chlorophyll a/c-binding proteins in a diatom photosystem I supercomplex

Koji Kato
Yoshiki Nakajima
Jian Xing
Minoru Kumazawa
Haruya Ogawa
Jian-Ren Shen author has email address
Kentaro Ifuku author has email address
Ryo Nagao author has email address

Research Institute for Interdisciplinary Science and Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama, Japan
Graduate School of Agriculture, Kyoto University, Kyoto, Japan
Faculty of Agriculture, Shizuoka University, Shizuoka, Japan

https://doi.org/10.7554/eLife.99858.1

Open access
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Figures and data

Overall structure of the PSI-FCPI supercomplex from T. pseudonana.
Structures are viewed from the stromal side (left panels) and the direction perpendicular to the membrane normal (right panels). Only protein structures are shown, and cofactors are omitted for clarity. The FCPI (A) and PSI-core (B) subunits are labeled and colored differently. The five FCPI subunits are labeled as FCPI-1 to 5 (red) with their gene products indicated in parentheses (black) in panel A.

Structure and diversity of Psa29.
(A) Structure of Psa29 depicted as cartoons. Psa29 was modeled from V47 to L178. (B) Cryo-EM map of Psa29 and its surrounded environments viewed from the stromal side. The red squared areas are enlarged in panels C–G. Yellow, PsaB; cyan, PsaC; blue, PsaD; magenta, PsaL; orange, Psa29. (C–G) Protein-protein interactions of Psa29 with PsaB/PsaC (C), PsaC/PsaD (D), PsaB/PsaD (E), PsaB/PsaD/PsaL (F), and PsaD (G). Interactions are indicated by dashed lines, and the numbers are distances in Å. Amino acid residues participating in the interactions are labeled; for example, A71/C means Ala71 of PsaC. B, PsaB; C, PsaC; D, PsaD, L, PsaL; 29, Psa29. (H) Phylogenetic analysis of Psa29 in photosynthetic organisms. A maximum-likelihood tree of the Psa29 proteins was inferred by IQ-TREE v2.2.2.7 using WAG+F+G4 model and trimmed alignment of 22 sequences with 245 amino-acid residues. Numbers at nodes are ultrafast bootstrap support (%) (1000 replicates). The tree was mid-point rooted between diatoms and Bolidophyceae Parmales. Psa29 of T. pseudonana CCMP1335 is indicated by a red line.

Structural characteristics of FCPI-1 (RedCAP).
(A) Interactions of FCPI-1 with PsaB, PsaI, and PsaL viewed from the stromal (left) and lumenal (right) sides. The areas encircled by black squares are enlarged in panels B, C. Yellow, PsaB; magenta, PsaI; dark red, PsaL; red, FCPI-1. (B, C) Protein-protein interactions of FCPI-1 with PsaL (B) and PsaB/PsaI/PsaL (C), respectively. Interactions are indicated by dashed lines, and the numbers are distances in Å. Amino acid residues participating in the interactions are labeled; for example, S139/1 means Ser139 of FCPI-1. B, PsaB; I, PsaI; L, PsaL; 1, FCPI-1. (D) Characteristic loop structure from Q96 to T116 in FCPI-1 viewed from the lumenal side. Q96 and T116 are labeled with sticks and the Q96–T116 loop is colored pink. (E) Superpositions of FCPI-1 (red) with FCPI-2 (green), FCPI-3 (blue), FCPI-4 (magenta), and FCPI-5 (orange). Only proteins are depicted. The Q96–T116 loop of FCPI-1 is colored pink and Q96 and T116 are labeled with sticks.

Structural characteristics of FCPI-2.
(A) Interactions of FCPI-2 with PsaB and PsaM viewed from the stromal (left) and lumenal (right) sides. The areas encircled by black squares are enlarged in panels B, C. The PSI and FCPI subunits are colored grey and yellow, respectively. Protein-protein interactions are shown as different colors: green, FCPI-2; cyan, PsaB; pink, PsaM. (B, C) Protein-protein interactions of FCPI-2 with PsaB (B) and PsaM (C), respectively. Interactions are indicated by dashed lines, and the numbers are distances in Å. Amino acid residues participating in the interactions are labeled; for example, Y138/2 means Tyr138 of FCPI-2. B, PsaB; M, PsaM.

Structural characteristics of FCPI-3, 4, and 5.
(A) Interactions among FCPIs and between FCPIs and PsaL viewed from the stromal (left) and lumenal (right) sides. The areas encircled by black squares are enlarged in panels B–D. The PSI and FCPI subunits are colored grey and yellow, respectively. Protein-protein interactions are shown as different colors: blue, FCPI-3; magenta, FCPI-4; orange, FCPI-5; purple, PsaL. (B–D) Protein-protein interactions between FCPI-3 and PsaL (B), between FCPI-4 and FCPI-5 (C), and between FCPI-5 and PsaL (D), respectively. Interactions are indicated by dashed lines, and the numbers are distances in Å. Amino acid residues participating in the interactions are labeled; for example, L126/3 means Leu126 of FCPI-3. 4, FCPI-4; 5, FCPI-5; L, PsaL.

Comparisons of structures and sequences of FCPIs in the PSI-FCPI structures between T. pseudonana and C. gracilis.
(A) Superposition of the PSI-FCPI structures between T. pseudonana and C. gracilis (PDB: 6LY5). The T. pseudonana and C. gracilis FCPI subunits are colored red and cyan, respectively. The structures are viewed from the stromal side. The FCPI-1 to 5 sites are labeled. (B) Correlation of the names of FCPIs in the structures with their genes between T. pseudonana and C. gracilis. The genes of FCPIs are derived from Kumazawa et al. (30) and Kato et al. (14) for C. gracilis. (C) Phylogenetic analysis of FCPs and RedCAPs from T. pseudonana (Tp) and C. gracilis (Cg). In addition to the RedCAP subfamily, 44 TpFCPs and 46 CgFCPs are grouped into five Lhc subfamilies and CgLhcr9 homologs. Maroon, RedCAP subfamily; magenta, Lhcq subfamily; red, Lhcz subfamily; orange, Lhcr subfamily; brown, CgLhcr9 homologs; green, Lhcf subfamily; blue, Lhcx subfamily. The FCPs and RedCAPs located at the FCPI-1 to 5 sites are labeled. The tree was inferred by IQ-TREE 2 (58) using the Q.pfam + R4 model selected with ModelFinder (59). The light purple circular symbols on the tree represent bootstrap support (%).

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