Revealing the architecture of the photosynthetic apparatus in the diatom Thalassiosira pseudonana

Abstract

Diatoms are a large group of marine algae that are responsible for about one-quarter of global carbon fixation. Light-harvesting complexes of diatoms are formed by the fucoxanthin chlorophyll a/c proteins and their overall organization around core complexes of photosystems (PSs) I and II is unique in the plant kingdom. Using cryo-electron tomography, we have elucidated the structural organization of PSII and PSI supercomplexes and their spatial segregation in the thylakoid membrane of the model diatom species Thalassiosira pseudonana. 3D sub-volume averaging revealed that the PSII supercomplex of T. pseudonana incorporates a trimeric form of light-harvesting antenna, which differs from the tetrameric antenna observed previously in another diatom, Chaetoceros gracilis. Surprisingly, the organization of the PSI supercomplex is conserved in both diatom species. These results strongly suggest that different diatom classes have various architectures of PSII as an adaptation strategy, whilst a convergent evolution occurred concerning PSI and the overall plastid structure.

Figure 1

Cryo-ET of an isolated thylakoid membrane vesicle from T. pseudonana. A–D, Tomographic slices of a representative cryo-electron tomogram. A and C, tomographic slices represent the top and bottom layers of the thylakoid membrane vesicle. B and D, picking of the sub-volumes from the tomographic slices, which contain densities of PSII (blue circles), PSI (yellow circles), and ATP synthase (red circles) particles. The scale bar is 200 nm.

Figure 2

Structural model of the PSII supercomplex from T. pseudonana revealed by cryo-ET and sub-volume averaging. A, the top-view of the isosurface of the 3D map of the PSII supercomplex represents the view from the luminal side. The oxygen-evolving complex at the membrane–lumen interface is visible in the side-view. Densities representing the PSII core complex (in green) and monomeric antenna (FCPII-1 in cyan, FCPII-2 in purple) are fitted with C. gracilis PSII structure (PDB 6jlu), the trimeric form of FCP light-harvesting antenna is fitted with pea LHCII structure (in yellow; PDB 2bhw). B, mesh representation of 3D map of PSII supercomplex. The PSII core is depicted in green, monomeric antenna FCPII-1 and FCPII-2 proteins are visualized in cyan and purple, respectively, and the FCP trimer in yellow.

Figure 3

Structural models of the PSI supercomplex and the ATP synthase from T. pseudonana revealed by cryo-ET and sub-volume averaging. A–B, the top-view of the isosurface model of PSI supercomplex represents the view from the stromal side, whereas membrane extrinsic subunits of PSI are visible in the side view. Assignment of EM densities is based on the fitting of the high-resolution structure from C. gracilis (PDB 6ly5). The PSI core complex is indicated in green and FCPI subunits are in purple. C, side-view of the isosurface model shows the membrane-extrinsic densities. At the stromal side of PSI, the density is fitted with ferredoxin (in red) and two copies of the FNR complex (in salmon; PDB 1 gaq). At the luminal side, the densities are fitted with cyt c₆ (in light blue; PDB 3 dmi). D, A hypothetical model showing the association of FNR and cyt c₆ with the main subunits of the PSI supercomplex. PsaA, PsaB, PsaC, PsaE, and PsaF are shown in sky blue, yellow, blue, orange, and gray, respectively. Fd is shown in red, FNR in salmon, and cyt c₆ in blue. E–F, Top-view, and side-view of the isosurface model of ATP synthase fitted with the high-resolution structure of chloroplast ATP synthase (PDB 6 fkh).

Figure 4

Structural models of the PSII and PSI supercomplexes from T. pseudonana revealed by EM and single-particle analysis. A and C, 2D projections of isolated and negatively stained PSII and PSI supercomplexes. B, Assignment of EM densities is based on the fitting with high-resolution structures. Densities representing PSII core complex and monomeric antenna are fitted with the PSII structure from C. gracilis (PDB 6 jlu). The trimeric form of the light-harvesting antenna is fitted with pea LHCII structure (PDB 2 bhw). A density close to the PSII core subunit PsbX (designated as FCPII-3) was fitted with P. tricornutum FCP monomer (PDB 6 a2w). PSII core complex is shown in green, FCPII-1 in cyan, FCPII-2 in purple, FCPII-3 in red, and trimeric FCP antenna (FCPII-S) is in yellow. D, the assignment of EM densities is based on the fitting with high-resolution structure from C. gracilis (Xu et al., 2020; PDB 6ly5). The PSI core complex is shown in green and FCP subunits are in purple. The scale bar is 10 nm.

Figure 5

Spatial distribution of PSII, PSI, and ATP synthase particles in the vesicle of the thylakoid membrane from T. pseudonana. A, spatial distribution of PSII, PSI, and ATP synthase particles and B, their back-projection in the reconstructed thylakoid membrane. The scale bar is 200 nm. C–E, distribution of the particles viewed from the side of the membrane vesicle. Distribution of ATP synthase is shown in (C), PSI and ATP synthase in (D), and PSII, PSI, and ATP synthase in (E). PSII is shown in blue, PSI in yellow and ATP synthase is in red.