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Structural insights into photosystem II assembly

Nature Plants volume 7, pages 524–538 (2021)Cite this article

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Abstract

Biogenesis of photosystem II (PSII), nature’s water-splitting catalyst, is assisted by auxiliary proteins that form transient complexes with PSII components to facilitate stepwise assembly events. Using cryo-electron microscopy, we solved the structure of such a PSII assembly intermediate from Thermosynechococcus elongatus at 2.94 Å resolution. It contains three assembly factors (Psb27, Psb28 and Psb34) and provides detailed insights into their molecular function. Binding of Psb28 induces large conformational changes at the PSII acceptor side, which distort the binding pocket of the mobile quinone (QB) and replace the bicarbonate ligand of non-haem iron with glutamate, a structural motif found in reaction centres of non-oxygenic photosynthetic bacteria. These results reveal mechanisms that protect PSII from damage during biogenesis until water splitting is activated. Our structure further demonstrates how the PSII active site is prepared for the incorporation of the Mn4CaO5 cluster, which performs the unique water-splitting reaction.

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Fig. 1: Cryo-EM map of a PSII assembly intermediate (PSII-I) from T. elongatus, segmented into subunits.
Fig. 2: Psb34 binds to RC47 during attachment of the CP43 module.
Fig. 3: The role of the CP47 C terminus in binding of Psb28.
Fig. 4: Structural changes of the D1 and D2 D-E loops induced by binding of Psb28 and Psb34.
Fig. 5: Binding of Psb28 displaces bicarbonate as a ligand of the non-haem iron and protects PSII from damage.
Fig. 6: The role of Psb27 in Mn4CaO5 cluster assembly.
Fig. 7: Conformational changes within the active site of the Mn4CaO5 cluster.

Data availability

The cryo-EM density maps are deposited in the Electron Microscopy Data Bank under accession numbers EMD-12335 (PSII-M), EMD-12336 (PSII-I) and EMD-12337 (PSII-I′). The atomic models of the cryo-EM structures are deposited in the Worldwide Protein Data Bank under accession numbers 7NHO (PSII-M), 7NHP (PSII-I) and 7NHQ (PSII-I′). The NMR backbone assignments for Psb28 bound to the C-terminal peptide of CP47 are deposited in the Biological Magnetic Resonance Bank under accession code 50747. Protein sequences with the following accession codes were downloaded from the UniProt database (P0A444, Q8DIQ1, Q8DIF8, Q8CM25, Q8DIP0, Q8DIN9, Q8DJ43, Q8DJZ6, Q9F1K9, Q8DIN8, Q8DHA7, Q8DIQ0, Q9F1R6, Q8DJI1, Q8DHJ2, Q8DG60, Q8DLJ8, Q8DMP8). Source data are provided with this paper. Additional data supporting the findings of this manuscript are available from the corresponding authors on reasonable request.

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Acknowledgements

We thank C. König, M. Völkel and R. Oworah-Nkruma for excellent technical assistance, K. Becker for cloning of the pIVEXPsb28His plasmid, B. Erjavec for preparation of the scheme in Fig. 1 and N. Cox for helpful discussion. J.M.S. is grateful to E. Conti for scientific independence and great mentorship and to J. M. Plitzko and W. Baumeister for access to the cryo-EM infrastructure and early career support. M.M.N. is grateful to his mentor M. Rögner for generous support. Financial support was provided by the Max Planck Society, the Helmholtz Zentrum München, the Deutsche Forschungsgemeinschaft (DFG) Research Unit FOR2092 (grant nos. EN 1194/1-1 to B.D.E. and 836/3-2 to M.M.N.), the DFG priority programme 2002 (grant no. 836/4-1 to M.M.N. and grant no. 3542/1-1 to J.D.L.), National Institutes of Health (NIH) grant no. NIH P41-GM104601 (to E.T.) and an Emmy-Noether fellowship (SCHU 3364/1-1 to J.M.S). A.K.-L. was supported by the LabEx Saclay Plant Sciences-SPS (grant no. ANR-10-LABX-0040-SPS) and the French Infrastructure for Integrated Structural Biology (FRISBI; grant no. ANR-10-INSB-05). R.S. gratefully acknowledges support from the DFG (grant nos. INST 213/757-1 FUGG and INST 213/843-1 FUGG).

Author information

Author notes

  1. These authors contributed equally: Jure Zabret, Stefan Bohn.

Authors and Affiliations

  1. Department of Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany

    Jure Zabret, Madeline Möller, Pasqual Liauw & Marc M. Nowaczyk

  2. Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany

    Stefan Bohn & Benjamin D. Engel

  3. Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany

    Sandra K. Schuller & Jan M. Schuller

  4. CryoEM of Molecular Machines, SYNMIKRO Research Center and Department of Chemistry, Philipps University of Marburg, Marburg, Germany

    Sandra K. Schuller & Jan M. Schuller

  5. Biomolecular Spectroscopy and RUBiospek|NMR, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany

    Oliver Arnolds & Raphael Stoll

  6. Proteomics, Max Planck Institute of Biophysics, Frankfurt, Germany

    Jakob Meier-Credo & Julian D. Langer

  7. NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA

    Aaron Chan & Emad Tajkhorshid

  8. Proteomics, Max Planck Institute for Brain Research, Frankfurt, Germany

    Julian D. Langer

  9. Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France

    Anja Krieger-Liszkay

  10. Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany

    Benjamin D. Engel

  11. Department of Chemistry, Technical University of Munich, Garching, Germany

    Benjamin D. Engel

  12. Biospectroscopy, Center for Protein Diagnostics (ProDi), Ruhr University Bochum, Bochum, Germany

    Till Rudack

  13. Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany

    Till Rudack

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  1. Jure Zabret
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Contributions

B.D.E., T.R., J.M.S. and M.M.N. conceived the research, prepared the figures and wrote the manuscript with the contribution of J.Z. and all other authors. M.M.N. coordinated the activities. Preparation of mutants, PSII isolation and biochemical analysis were performed by J.Z., M.M, P.L. and M.M.N. Mass spectrometry analysis was done by J.M.-C. and J.D.L. J.M.S., S.B. and B.D.E. performed the cryo-EM analysis. T.R. built the structural model with the help of S.K.S., A.C. and E.T. Fluorescence spectroscopy was carried out by J.Z. and M.M.N. EPR experiments were conducted by A.K.-L. NMR experiments were conducted and analysed by O.A. and R.S. All authors approved the final version of the manuscript.

Corresponding authors

Correspondence to Till Rudack, Jan M. Schuller or Marc M. Nowaczyk.

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Competing interests

The authors declare no competing interests.

Additional information

Peer review information Nature Plants thanks R. Burnap, N. Nelson, A. Rutherford and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary methods, Discussion, Figs. 1–7, Tables 1 and 2, descriptions for Videos 1–4 and references.

Reporting Summary

Supplementary Video 1

Interpolated trajectory between PSII-I and PSII-M.

Supplementary Video 2

Interpolated trajectory between PSII-I and PSII-M.

Supplementary Video 3

Interpolated trajectory between PSII-I and PSII-M.

Supplementary Video 4

Interpolated trajectory between PSII-I and mature PSII (PDB-ID 3WU2).

Source data

Source Data Fig. 2

Unprocessed two-dimensional polyacrylamide gel electrophoresis.

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Zabret, J., Bohn, S., Schuller, S.K. et al. Structural insights into photosystem II assembly. Nat. Plants 7, 524–538 (2021). https://doi.org/10.1038/s41477-021-00895-0

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