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Cryo-EM structure of a plant photosystem II supercomplex with light-harvesting protein Lhcb8 and α-tocopherol

Nature Plants volume 9, pages 1359–1369 (2023)Cite this article

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Abstract

The heart of oxygenic photosynthesis is the water-splitting photosystem II (PSII), which forms supercomplexes with a variable amount of peripheral trimeric light-harvesting complexes (LHCII). Our knowledge of the structure of green plant PSII supercomplex is based on findings obtained from several representatives of green algae and flowering plants; however, data from a non-flowering plant are currently missing. Here we report a cryo-electron microscopy structure of PSII supercomplex from spruce, a representative of non-flowering land plants, at 2.8 Å resolution. Compared with flowering plants, PSII supercomplex in spruce contains an additional Ycf12 subunit, Lhcb4 protein is replaced by Lhcb8, and trimeric LHCII is present as a homotrimer of Lhcb1. Unexpectedly, we have found α-tocopherol (α-Toc)/α-tocopherolquinone (α-TQ) at the boundary between the LHCII trimer and the inner antenna CP43. The molecule of α-Toc/α-TQ is located close to chlorophyll a614 of one of the Lhcb1 proteins and its chromanol/quinone head is exposed to the thylakoid lumen. The position of α-Toc in PSII supercomplex makes it an ideal candidate for the sensor of excessive light, as α-Toc can be oxidized to α-TQ by high-light-induced singlet oxygen at low lumenal pH. The molecule of α-TQ appears to shift slightly into the PSII supercomplex, which could trigger important structure–functional modifications in PSII supercomplex. Inspection of the previously reported cryo-electron microscopy maps of PSII supercomplexes indicates that α-Toc/α-TQ can be present at the same site also in PSII supercomplexes from flowering plants, but its identification in the previous studies has been hindered by insufficient resolution.

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Fig. 1: Separation and single-particle cryo-EM analysis of spruce PSII C2S2 supercomplex.
Fig. 2: Overall architecture of the spruce PSII C2S2 supercomplex.
Fig. 3: Structure of the Lhcb8 subunit.
Fig. 4: Localization of α-Toc in spruce PSII C2S2 supercomplex.
Fig. 5: Major energy transfer pathways within the spruce PSII C2S2 supercomplex.
Fig. 6: Position of α-Toc/α-TQ in the structure of spruce PSII supercomplex.

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Data availability

The mass spectrometry proteomic data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the identifier PXD035272. The cryo-EM map of the spruce PSII supercomplex has been deposited in the Electron Microscopy Data Bank with accession code EMD-16389. The corresponding structure model has been deposited in the PDB under PDB code 8C29.

References

  1. Shen, L. et al. Structure of a C2S2M2N2-type PSII–LHCII supercomplex from the green alga Chlamydomonas reinhardtii. Proc. Natl Acad. Sci. USA 116, 21246–21255 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Sheng, X. et al. Structural insight into light harvesting for photosystem II in green algae. Nat. Plants 5, 1320–1330 (2019).

    Article  CAS  PubMed  Google Scholar 

  3. Wei, X. et al. Structure of spinach photosystem II–LHCII supercomplex at 3.2 Å resolution. Nature 534, 69–74 (2016).

    Article  CAS  PubMed  Google Scholar 

  4. van Bezouwen, L. S. et al. Subunit and chlorophyll organization of the plant photosystem II supercomplex. Nat. Plants 3, 17080 (2017).

    Article  PubMed  Google Scholar 

  5. Su, X. et al. Structure and assembly mechanism of plant C2S2M2-type PSII–LHCII supercomplex. Science 357, 815–820 (2017).

    Article  CAS  PubMed  Google Scholar 

  6. Kamiya, N. & Shen, J.-R. Crystal structure of oxygen-evolving photosystem II from Thermosynechococcus vulcanus at 3.7-Å resolution. Proc. Natl Acad. Sci. USA 100, 98–103 (2003).

    Article  CAS  PubMed  Google Scholar 

  7. Ferreira, K. N., Iverson, T. M., Maghlaoui, K., Barber, J. & Iwata, S. Architecture of the photosynthetic oxygen-evolving center. Science 303, 1831–1838 (2004).

    Article  CAS  PubMed  Google Scholar 

  8. Loll, B., Kern, J., Saenger, W., Zouni, A. & Biesiadka, J. Towards complete cofactor arrangement in the 3.0 Å resolution structure of photosystem II. Nature 438, 1040–1044 (2005).

    Article  CAS  PubMed  Google Scholar 

  9. Minagawa, J. & Takahashi, Y. Structure, function and assembly of photosystem II and its light-harvesting proteins. Photosynth. Res. 82, 241–263 (2004).

    Article  CAS  PubMed  Google Scholar 

  10. Jansson, S. The light-harvesting chlorophyll a/b-binding proteins. Biochim. Biophys. Acta 1184, 1–19 (1994).

    Article  CAS  PubMed  Google Scholar 

  11. Kouřil, R., Nosek, L., Semchonok, D., Boekema, E. J. & Ilík, P. Organization of plant photosystem II and photosystem I supercomplexes. Subcell. Biochem. 87, 259–286 (2018).

    Article  PubMed  Google Scholar 

  12. Cao, P., Pan, X., Su, X., Liu, Z. & Li, M. Assembly of eukaryotic photosystem II with diverse light-harvesting antennas. Curr. Opin. Struct. Biol. 63, 49–57 (2020).

    Article  CAS  PubMed  Google Scholar 

  13. Croce, R. & van Amerongen, H. Light harvesting in oxygenic photosynthesis: structural biology meets spectroscopy. Science 369, eaay2058 (2020).

    Article  CAS  PubMed  Google Scholar 

  14. Kouřil, R., Nosek, L., Bartoš, J., Boekema, E. J. & Ilík, P. Evolutionary loss of light-harvesting proteins Lhcb6 and Lhcb3 in major land plant groups—break-up of current dogma. N. Phytol. 210, 808–814 (2016).

    Article  Google Scholar 

  15. Kouřil, R. et al. Unique organization of photosystem II supercomplexes and megacomplexes in Norway spruce. Plant J. 104, 215–225 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  16. Grebe, S. et al. The unique photosynthetic apparatus of Pinaceae: analysis of photosynthetic complexes in Picea abies. J. Exp. Bot. 70, 3211–3225 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Klimmek, F., Sjödin, A., Noutsos, C., Leister, D. & Jansson, S. Abundantly and rarely expressed Lhc protein genes exhibit distinct regulation patterns in plants. Plant Physiol. 140, 793–804 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Albanese, P. et al. Dynamic reorganization of photosystem II supercomplexes in response to variations in light intensities. Biochim. Biophys. Acta Bioenerg. 1857, 1651–1660 (2016).

    Article  CAS  Google Scholar 

  19. Grinzato, A. et al. High-light versus low-light: effects on paired photosystem II supercomplex structural rearrangement in pea plants. Int. J. Mol. Sci. 21, 8643 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Kashino, Y. et al. Ycf12 is a core subunit in the photosystem II complex. Biochim. Biophys. Acta 1767, 1269–1275 (2007).

    Article  CAS  PubMed  Google Scholar 

  21. Crepin, A. & Caffarri, S. Functions and evolution of Lhcb isoforms composing LHCII, the major light harvesting complex of photosystem II of green eukaryotic organisms. Curr. Protein Pept. Sci. 19, 699–713 (2018).

    Article  CAS  PubMed  Google Scholar 

  22. Guardini, Z., Gomez, R. L., Caferri, R., Dall’Osto, L. & Bassi, R. Loss of a single chlorophyll in CP29 triggers re-organization of the photosystem II supramolecular assembly. Biochim. Biophys. Acta Bioenerg. 1863, 148555 (2022).

    Article  CAS  PubMed  Google Scholar 

  23. Kruk, J. & Srzałka, K. Occurrence and function of alpha-tocopherol quinone in plants. J. Plant Physiol. 145, 405–409 (1995).

    Article  CAS  Google Scholar 

  24. Kumar, A., Prasad, A. & Pospíšil, P. Formation of α-tocopherol hydroperoxide and α-tocopheroxyl radical: relevance for photooxidative stress in Arabidopsis. Sci. Rep. 10, 19646 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Graça, A. T., Hall, M., Persson, K. & Schröder, W. P. High-resolution model of Arabidopsis photosystem II reveals the structural consequences of digitonin-extraction. Sci. Rep. 11, 15534 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  26. Triantaphylides, C. & Havaux, M. Singlet oxygen in plants: production, detoxification and signaling. Trends Plant Sci. 14, 219–228 (2009).

    Article  CAS  PubMed  Google Scholar 

  27. Krieger-Liszkay, A. & Trebst, A. Tocopherol is the scavenger of singlet oxygen produced by the triplet states of chlorophyll in the PSII reaction centre. J. Exp. Bot. 57, 1677–1684 (2006).

    Article  CAS  PubMed  Google Scholar 

  28. Shi, L. X., Lorkovic, Z. J., Oelmuller, R. & Schroder, W. P. The low molecular mass PsbW protein is involved in the stabilization of the dimeric photosystem II complex in Arabidopsis thaliana. J. Biol. Chem. 275, 37945–37950 (2000).

    Article  CAS  PubMed  Google Scholar 

  29. Granvogl, B., Zoryan, M., Plöscher, M. & Eichacker, L. A. Localization of 13 one-helix integral membrane proteins in photosystem II subcomplexes. Anal. Biochem. 383, 279–288 (2008).

    Article  CAS  PubMed  Google Scholar 

  30. Kruk, J., Schmid, G. H. & Strzałka, K. Interaction of α-tocopherol quinone, α-tocopherol and other prenyllipids with photosystem II. Plant Physiol. Biochem. 38, 271–277 (2000).

    Article  CAS  Google Scholar 

  31. Bielczynski, L. W., Xu, P. & Croce, R. PSII supercomplex disassembly is not needed for the induction of energy quenching (qE). Photosynth. Res. 152, 275–281 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Novoderezhkin, V., Marin, A. & van Grondelle, R. Intra- and inter-monomeric transfers in the light harvesting LHCII complex: the Redfield–Förster picture. Phys. Chem. Chem. Phys. 13, 17093–17103 (2011).

    Article  CAS  PubMed  Google Scholar 

  33. Papadatos, S., Charalambous, A. C. & Daskalakis, V. A pathway for protective quenching in antenna proteins of photosystem II. Sci. Rep. 7, 2523 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  34. Hakala-Yatkin, M. et al. Magnetic field protects plants against high light by slowing down production of singlet oxygen. Physiol. Plant. 42, 26–34 (2011).

    Article  Google Scholar 

  35. Niewiadomska, E. et al. Lack of tocopherols influences the PSII antenna and the functioning of photosystems under low light. J. Plant Physiol. 223, 57–64 (2018).

    Article  CAS  PubMed  Google Scholar 

  36. Dau, H. et al. Structural consequences of ammonia binding to the manganese center of the photosynthetic oxygen-evolving complex: an X-ray absorption spectroscopy study of isotropic and oriented photosystem II particles. Biochemistry 34, 5274–5287 (1995).

    Article  CAS  PubMed  Google Scholar 

  37. Lichtenthaler, H. K. Chlorophylls and carotenoids: pigments of photosynthetic biomembranes. Methods Enzymol. 148, 350–382 (1987).

    Article  CAS  Google Scholar 

  38. Caffari, S., Kouril, R., Kereiche, S., Boekema, E. J. & Croce, R. Functional architecture of higher plant photosystem II supercomplexes. EMBO J. 28, 3052–3063 (2009).

    Article  Google Scholar 

  39. Sorzano, C. O. S. et al. A new algorithm for high-resolution reconstruction of single particles by electron microscopy. J. Struct. Biol. 204, 329–337 (2018).

    Article  CAS  PubMed  Google Scholar 

  40. Zheng, A. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 4, 331–332 (2017).

    Article  Google Scholar 

  41. Zhang, K. Gctf: real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. de la Rosa Tevín, J. M. et al. Xmipp 3.0: an improved software suite for image processing in electron microscopy. J. Struct. Biol. 184, 321–328 (2013).

    Article  Google Scholar 

  43. Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).

    Article  CAS  PubMed  Google Scholar 

  44. Scheres, S. H. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

    Article  CAS  PubMed  Google Scholar 

  46. DeLano, W. L. The PyMOL Molecular Graphics System (DeLano Scientific, 2002).

  47. Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D 67, 235–242 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Krissinel, E. & Henrick, K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr. D 60, 2256–2268 (2004).

    Article  CAS  PubMed  Google Scholar 

  49. Krissinel, E. & Henrick, K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774–797 (2007).

    Article  CAS  PubMed  Google Scholar 

  50. Wiśniewski, J. R., Zougman, A., Nagaraj, N. & Mann, M. Universal sample preparation method for proteome analysis. Nat. Methods 6, 359–362 (2009).

    Article  PubMed  Google Scholar 

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Acknowledgements

This work was supported by the Grant Agency of the Czech Republic (project no. 21-05497S to M.O., P.I., P.P., I.I. and R.K.) and the European Regional Development Fund (ERDF) project ‘Plants as a tool for sustainable global development’ (no. CZ.02.1.01/0.0/0.0/16_019/0000827 to M.O., P.I., P.P., R.K., S.Ć.Z. and P.T.). We acknowledge support by the Federal Ministry for Education and Research (BMBF, ZIK programme) (grant nos. 03Z22HN23, 03Z22HI2 and 03COV04 to P.L.K.), Horizon Europe ERA Chair ‘hot4cryo’ project number 101086665 to P.L.K., the European Regional Development Funds for Saxony-Anhalt (grant no. EFRE: ZS/2016/04/78115 to P.L.K.), funding by the Deutsche Forschungsgemeinschaft (DFG) (project number 391498659 and RTG 2467 to P.L.K.), and the Martin-Luther University of Halle-Wittenberg. This work was also funded by project no. RO0423 to S.Ć.Z. and P.T. (Sustainable systems and technologies, improving crop production for higher quality of production of food, feed, and raw materials, under conditions of changing climate) funded by the Ministry of Agriculture, Czechia. CIISB, Instruct-CZ Centre of Instruct-ERIC EU consortium, funded by MEYS CR infrastructure project LM2023042 and European Regional Development Fund-Project ‘UP CIISB’ (no. CZ.02.1.01/0.0/0.0/18_046/0015974), is gratefully acknowledged for the financial support of the measurements at the CEITEC Proteomics Core Facility. We thank L. Hloušková and J. Bartoš for help with FRET rate calculation. This paper is dedicated to Professor Emeritus Jan Nauš for his outstanding contribution to the development of biophysics at Palacký University.

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Author notes

  1. These authors contributed equally: Monika Opatíková, Dmitry A. Semchonok.

Authors and Affiliations

  1. Department of Biophysics, Faculty of Science, Palacký University, Olomouc, Czech Republic

    Monika Opatíková, Petr Ilík, Pavel Pospíšil & Roman Kouřil

  2. Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany

    Dmitry A. Semchonok, Fotis L. Kyrilis, Farzad Hamdi & Panagiotis L. Kastritis

  3. Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, Czech Republic

    David Kopečný

  4. Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic

    Iva Ilíková

  5. Central European Institute of Technology, Masaryk University, Brno, Czech Republic

    Pavel Roudnický

  6. Czech Advanced Technology and Research Institute, Palacký University, Olomouc, Czech Republic

    Sanja Ćavar Zeljković & Petr Tarkowski

  7. Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, Olomouc, Czech Republic

    Sanja Ćavar Zeljković & Petr Tarkowski

  8. Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany

    Panagiotis L. Kastritis

  9. Institute of Chemical Biology, National Hallenic Research Foundation, Athens, Greece

    Panagiotis L. Kastritis

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Contributions

M.O., D.K., P.I., P.P, P.L.K. and R.K., study design. M.O., D.A.S., F.L.K. and F.H., sample preparation for cryo-EM. D.A.S., image analysis of cryo-EM data. D.K. and R.K., model building. M.O. and I.I., amino acid sequence analysis. P.R., mass spectrometry analysis. P.T. and S.Ć.Z., fatty acid composition. P.T. and S.Ć.Z., α-tocopherol(quinone) analysis. M.O., D.K., P.I., P.P. I.I. and R.K., data interpretation. M.O., D.A.S., P.I., I.I. and R.K. wrote the main body of the paper, and all authors revised and approved it.

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Correspondence to Roman Kouřil.

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Nature Plants thanks Jian-Ren Shen and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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A description of MS analysis and Supplementary Figs. 1–14, Tables 1–6 and References.

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Opatíková, M., Semchonok, D.A., Kopečný, D. et al. Cryo-EM structure of a plant photosystem II supercomplex with light-harvesting protein Lhcb8 and α-tocopherol. Nat. Plants 9, 1359–1369 (2023). https://doi.org/10.1038/s41477-023-01483-0

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