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

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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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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.

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

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

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

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

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

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

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

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

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

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

Article CAS PubMed Google Scholar

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

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

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

Article CAS PubMed Google Scholar

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

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

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

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

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

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

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

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

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

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

Article CAS Google Scholar

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

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

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

Article CAS PubMed Google Scholar

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

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

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

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

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

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

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

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

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

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

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

Article CAS Google Scholar

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

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

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

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

Article CAS PubMed PubMed Central Google Scholar

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

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

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

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

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

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

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

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

Article CAS PubMed Google Scholar

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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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.

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

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

Monika Opatíková, Petr Ilík, Pavel Pospíšil & Roman Kouřil

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

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

David Kopečný

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

Iva Ilíková

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

Pavel Roudnický

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

Sanja Ćavar Zeljković & Petr Tarkowski

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

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

Panagiotis L. Kastritis

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

Panagiotis L. Kastritis

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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.

Correspondence to Roman Kouřil.

The authors declare no competing interests.

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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Received: 06 January 2023

Accepted: 04 July 2023

Published: 07 August 2023

Issue Date: August 2023

DOI: https://doi.org/10.1038/s41477-023-01483-0

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