Structure of a cyanobacterial photosystem I surrounded by octadecameric IsiA antenna proteins

Abstract

Iron-stress induced protein A (IsiA) is a chlorophyll-binding membrane-spanning protein in photosynthetic prokaryote cyanobacteria, and is associated with photosystem I (PSI) trimer cores, but its structural and functional significance in light harvesting remains unclear. Here we report a 2.7-Å resolution cryo-electron microscopic structure of a supercomplex between PSI core trimer and IsiA from a thermophilic cyanobacterium Thermosynechococcus vulcanus. The structure showed that 18 IsiA subunits form a closed ring surrounding a PSI trimer core. Detailed arrangement of pigments within the supercomplex, as well as molecular interactions between PSI and IsiA and among IsiAs, were resolved. Time-resolved fluorescence spectra of the PSI-IsiA supercomplex showed clear excitation-energy transfer from IsiA to PSI, strongly indicating that IsiA functions as an energy donor, but not an energy quencher, in the supercomplex. These structural and spectroscopic findings provide important insights into the excitation-energy-transfer and subunit assembly mechanisms in the PSI-IsiA supercomplex.

Fig. 1. Overall structure of the PSI–IsiA supercomplex.

Overall structure of the PSI–IsiA supercomplex was fitted into the cryo-EM map at 2.7 Å resolution. a Left-side: top-view of the cryo-EM map from the stromal side. One of the PSI cores is colored in green, IsiA1–6 are colored in red, orange, yellow, cyan, blue, and purple, respectively, where IsiAs were numbered clockwise. Right-side: side-view of PSI–IsiA. b Cryo-EM map for each subunit of the PSI core. Color codes used are red, PsaA; blue, PsaB; yellow, PsaC; green, PsaD; purple, PsaE; cyan, PsaF; magenta, PsaI; dark green, PsaJ; brown, PsaK; pink, PsaL; orange, PsaM; gray, PsaX. c Distribution of chlorophylls in PSI–IsiA. Left- and center-panels: top views from the stromal and lumenal sides, respectively. Chls in the PSI core are colored in green, and those in IsiA1–6 are colored in red, orange, yellow, cyan, blue, and purple, respectively. Right panels: side views of the stromal side and lumenal side layers, respectively. d Distribution of carotenoids in PSI–IsiA. Left-side is the top-view from the stromal side and right-side is the side-view. Carotenoids are colored in orange.

Fig. 2. Structure of an IsiA monomer and its pigment organization.

a Ribbon diagram of an IsiA monomer. Helices and sheets are classified by Greek number. b Arrangement of the pigments (Chls and Bcrs) within the IsiA monomer. Left-side: a side-view represented by stick and light-colored cylinder model. Helices and sheets are classified by Greek number. Chlorophylls are colored by aquamarine (Chl401), gray (Chl402), yellow (Chl403), red (Chl404), coral (Chl405), forest green (Chl406), gold (Chl407), magenta (Chl408), pink (Chl409), brown (Chl410), green (Chl411), blue (Chl412), cyan (Chl413), orange (Chl414), purple (Chl415), deep pink (Chl416), and black (Chl417), respectively. Middle: Arrangement of the Bcrs. Bcrs are colored by gray. Right-side: top-view from the stromal side. c Interactions among Chls and Bcrs.

Fig. 3. Interactions and possible EET pathways within the IsiA ring.

a Overview of interactions between adjacent IsiAs. Squared areas by green dashed and red solid lines are enlarged in panels (c) and (e), respectively. b Superimposition of the structures of the six IsiAs. The squared region by a red dashed line indicates the C-terminal region of IsiA and is enlarged in the left bottom side. The C-terminal region of IsiA4 (cyan) are more ordered than that of other IsiAs. c Interactions between IsiA1 and IsiA2. The middle panel is an overview, and the left and right panels show the protein–protein and protein–chlorophylls interactions, respectively. d Pigment–pigment interactions between IsiA1 and IsiA2. Right panel is a top-view from the stromal side. e Possible EET pathways between IsiA1 and IsiA2.

Fig. 4. Interactions and possible EET pathways between IsiAs and PSI.

a Overview of interactions between IsiAs and PSI. Squared areas are enlarged in panels (b–f). b–f Interactions between each IsiA and PSI. Interactions were indicated by dashed lines. g Overview of possible EET pathways between IsiAs and PSI. Squared areas are enlarged in panels (h–j). Possible EET pathways (dashed lines) between each IsiA and PS1.

Fig. 5. TRF analyses of the PSI–IsiA supercomplex.

a 77-K TRF spectra excited at 445 nm. The spectra of the PSI–IsiA and PSI trimer cores were normalized by the maximum intensity of each spectrum. The spectra of the PSI–IsiA and PSI trimer cores are depicted in red and black lines, respectively. b 77-K FDA spectra. The spectra of the PSI–IsiA and PSI trimer cores are depicted in red and black lines, respectively. c Normalized fluorescence decay curves at 296 K monitored at 685 nm. The curves of the PSI–IsiA and PSI trimer cores are depicted in red and black lines, respectively.

Fig. 6. Possible EET pathways within PSI–IsiA and a proposed assembly model.

a Overview of possible EET pathways in the whole PSI–IsiA supercomplex. Red arrows indicate EET pathways from IsiA to PSI core; orange arrows indicate EET pathways between adjacent IsiAs; yellow arrows indicate EET pathways between different PSI cores. b A proposed assembly model for PSI–IsiA where the assembly of IsiAs starts from the attachment of IsiA4 to the PSI core. See text for more details.