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Distinct structural modulation of photosystem I and lipid environment stabilizes its tetrameric assembly

Nature Plants volume 6, pages 314–320 (2020)Cite this article

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Abstract

Photosystem I (PSI) is able to form different oligomeric states across various species. To reveal the structural basis for PSI dimerization and tetramerization, we structurally investigated PSI from the cyanobacterium Anabaena. This revealed a disrupted trimerization domain due to lack of the terminal residues of PsaL in the lumen, which resulted in PSI dimers with loose connections between monomers and weaker energy-coupled chlorophylls than in the trimer. At the dimer surface, specific phospholipids, cofactors and interactions in combination facilitated recruitment of another dimer to form a tetramer. Taken together, the relaxed luminal connections and lipid specificity at the dimer interface account for membrane curvature. PSI tetramer assembly appears to increase the surface area of the thylakoid membrane, which would contribute to PSI crowding.

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Fig. 1: Sample optimization and structure determination.
Fig. 2: Differences between dimeric and trimeric PSI.
Fig. 3: Chlorophylls at the intradimer interface.
Fig. 4: Interdimer interface and associated lipids.

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Data availability

All data generated or analysed during this study are included in this published article and the Extended Data figure information. The cryo-EM maps have been deposited in the Electron Microscopy Data Bank with accession code no. EMD-10461. The atomic model has been deposited in the Protein Data Bank under accession code no. 6TCL.

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Acknowledgements

We thank Y. Yin from Plant Science Facility of the Institute of Botany CAS for excellent technical assistance with 77 K low-temperature fluorescence analysis, and members of Amunts laboratory for active discussions throughout the project. Data were collected at the SciLifeLab cryo-EM facility funded by the foundations Knut and Alice Wallenberg, Family Erling Persson and Kempe. We acknowledge support from SciLifeLab proteogenomics core facility. This work was supported by the National Natural Science Foundation of China (grant nos. 21506113 and 31470229), the Swedish Foundation for Strategic Research (grant no. FFL15:0325), the Ragnar Söderberg Foundation (grant no. M44/16), the Swedish Research Council (grant no. NT_2015–04107), Cancerfonden (grant no. 2017/1041), the European Research Council (grant no. ERC-2018-StG-805230) and the Knut and Alice Wallenberg Foundation (grant no. 2018.0080). A.A. is supported by the EMBO Young Investigator Programme.

Author information

Author notes

  1. These authors contributed equally: Ming Chen, Annemarie Perez-Boerema, Laixing Zhang.

Authors and Affiliations

  1. Beijing Engineering Research Center for Biofuels, Institute of Nuclear and New, Energy Technology, Tsinghua University, Beijing, P. R. China

    Ming Chen, Yanxue Li & Shizhong Li

  2. Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden

    Annemarie Perez-Boerema & Alexey Amunts

  3. Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden

    Annemarie Perez-Boerema & Alexey Amunts

  4. Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint, Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, P. R. China

    Laixing Zhang & Maojun Yang

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Contributions

M.C. and A.A. designed the project and planned the experiments. M.C., A.P.-B. and L.Z. performed protein purification and cryo-EM. A.P.-B. built and refined the model. M.C., A.P.-B. and A.A. analysed the data. A.A. wrote the manuscript with contributions from M.C. and A.P.-B. All authors discussed and commented on the final manuscript.

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Correspondence to Shizhong Li or Alexey Amunts.

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Peer review information Nature Plants thanks Christopher Gisriel, Michael Hippler and Mei Li for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Optimization of the sample preparation.

a, Comparison of PSI extraction with digitonin and β-DDM. Both detergents were set to the final concentration of 1% (w/v) and incubated for 30 min on ice. The relative intensity of the digitonin-solubilized material have been quantified: tetramer: dimer:monomer 4.9:1.5:3.6. At least three independent experiments were repeated with the similar BN-PAGE results. MW marker units are in kDa. b, Stability assay. Concentrations of 0.5%, 1% and 1.5% (w/v) were tested for extraction of PSI. For each concentration, an incubation time of 0.5 h, 1.0 h, 2.0 h was used. The experiment suggests that using 1% digitonin results most PSI tetramer, and no difference was detected for the different time points. Three independents experiments were repeated with the similar results. c, Purification of PSI tetramer. Different amounts of sample were loaded on to three sucrose gradients, labeled 1 to 3. The PSI fractions were analyzed by BN-PAGE, prior to size exclusion chromatography, for which the 280 nm absorption is shown. The eluted peak was assessed for purity on BN-PAGE and subjected to cryo-EM. At least six independent experiments were repeated with the similar results.

Extended Data Fig. 2

Cryo-EM image processing of PSI particles.

Extended Data Fig. 3 Resolution of cryo-EM reconstruction.

a, Map colored by local resolution, viewed from the surface and cut-through. b, FSC curve, showing overall resolution of the cryo-EM map. (c) Map to model FSC.

Extended Data Fig. 4 Conservation of subunit PsaL.

a, Sideview of the superimposed subunit PsaL from Anabaena, Synechocystis and T. Elongatus. C-terminus boxed. b, Corresponding sequence alignment. Both illustrate missing C-terminal residues in the lumen in PsaL from Anabaena. C-terminus boxed.

Extended Data Fig. 5 77 K fluorescence absorption spectra.

a, Sucrose gradient showing the monomer, dimer and tetramer of PSI. At least three independent experiments were repeated with similar sucrose gradients results. b, The emission spectra between 600 and 800 nm after excitation at 435 nm. As revealed in Fig. 2, dimer. Five independent experiments were repeated with similar results. c, Zoom into the peaks, showing a slight shift of 2.8 nm from PSI monomer to PSI dimer.

Extended Data Fig. 6 Localization of lipids.

Elements in the interphases found in the tetramer, but not in the trimer structures (PDBID: 1JB0 and 5OY0) are shown as circles12,17. Lipids are represented as orange circles and digitonin molecules in locations, where no lipids are found in the trimer are shown as purple circles and carotenoid as red ovals.

Extended Data Fig. 7 Nearest protein coordinates between two dimers.

a, Overview of the inter-dimer region. b, The nearest residues are within of 4.1–4.8 Å range, and no protein-protein interaction observed.

Extended Data Fig. 8 Digitonin molecules at the dimer-dimer interface.

a, Three digitonin molecules modeled into elongated densities (mesh). Residues coordinating the binding in the membrane plane are shown as described in the text, showing interactions and experimental density (contour levels used are 0.491 and 0.477 respectively). b, Environment of the digitonin molecules from a, in schematic representation, specific elements contributing to the binding are shown. c, Density for lipids found in the dimer-dimer interphase (contour levels used are 0.528, 0.422, 0.550, 0.488 and 0.422 respectively).

Extended Data Fig. 9 Carotenoid molecule at the dimer-dimer interface.

A carotenoid molecule BCR-855 is found in the PsaB region with its benzene rings in proximity to chlorophylls a816 and a821.

Extended Data Fig. 10 Model of PSI tetramer arrangement.

PSI trimer crowding model on the left is derived from the model obtained by atomic force and confocal fluorescence microscopy (MacGregor-Chatwin et al. 2017)51. PSI tetramer crowding model is adopted on the same principle, and the additional membrane surface would appear due to the curvature between the dimers as described in the text.

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Chen, M., Perez-Boerema, A., Zhang, L. et al. Distinct structural modulation of photosystem I and lipid environment stabilizes its tetrameric assembly. Nat. Plants 6, 314–320 (2020). https://doi.org/10.1038/s41477-020-0610-x

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