Article

Subunit and chlorophyll organization of the plant photosystem II supercomplex

  • Nature Plants 3, Article number: 17080 (2017)
  • doi:10.1038/nplants.2017.80
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Abstract

Photosystem II (PSII) is a light-driven protein, involved in the primary reactions of photosynthesis. In plant photosynthetic membranes PSII forms large multisubunit supercomplexes, containing a dimeric core and up to four light-harvesting complexes (LHCs), which act as antenna proteins. Here we solved a three-dimensional (3D) structure of the C2S2M2 supercomplex from Arabidopsis thaliana using cryo-transmission electron microscopy (cryo-EM) and single-particle analysis at an overall resolution of 5.3 Å. Using a combination of homology modelling and restrained refinement against the cryo-EM map, it was possible to model atomic structures for all antenna complexes and almost all core subunits. We located all 35 chlorophylls of the core region based on the cyanobacterial PSII structure, whose positioning is highly conserved, as well as all the chlorophylls of the LHCII S and M trimers. A total of 13 and 9 chlorophylls were identified in CP26 and CP24, respectively. Energy flow from LHC complexes to the PSII reaction centre is proposed to follow preferential pathways: CP26 and CP29 directly transfer to the core using several routes for efficient transfer; the S trimer is directly connected to CP43 and the M trimer can efficiently transfer energy to the core through CP29 and the S trimer.

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References

  1. 1.

    & Primary charge separation in photosystem II. Photosynth. Res. 63, 195–208 (2000).

  2. 2.

    & Structure and function of photosystems I and II. Ann. Rev. Plant Biol. 57, 521–565 (2006).

  3. 3.

    , & The structure of plant photosystem I super-complex at 2.8 Å resolution. eLife 4, 213 (2015).

  4. 4.

    , , , & Architecture of the photosynthetic oxygen-evolving center. Science 303, 1831–1838 (2004).

  5. 5.

    , , & Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å. Nature 473, 55–60 (2011).

  6. 6.

    et al. Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses. Nature 517, 99–103 (2014).

  7. 7.

    et al. Novel features of eukaryotic photosystem II revealed by its crystal structure analysis from a red alga. J. Biol. Chem. 291, 5676–5687 (2016).

  8. 8.

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

  9. 9.

    , , , & The extrinsic proteins of photosystem II. Biochim. Biophys. Acta 1817, 121–142 (2012).

  10. 10.

    Localization and functional characterization of the extrinsic subunits of photosystem II: an update. Biosc. Biotechnol. Biochem. 79, 1223–1231 (2015).

  11. 11.

    , , & A look within LHCII: differential analysis of the Lhcb1−3 complexes building the major trimeric antenna complex of higher-plant photosynthesis. Biochemistry 43, 9467–9476 (2004).

  12. 12.

    , & Supramolecular organization of photosystem II in green plants. Biochim. Biophys. Acta 1817, 2–12 (2012).

  13. 13.

    , , , & Structural variability of plant photosystem II megacomplexes in thylakoid membranes. Plant J. 89, 104–111 (2017).

  14. 14.

    et al. Crystal structure of spinach major light-harvesting complex at 2.72 Å resolution. Nature 428, 287–292 (2004).

  15. 15.

    , , & Mechanisms of photoprotection and nonphotochemical quenching in pea light-harvesting complex at 2.5 Å resolution. EMBO J. 24, 919–928 (2005).

  16. 16.

    et al. Structural insights into energy regulation of light-harvesting complex CP29 from spinach. Nat. Struct. Mol. Biol. 18, 309–315 (2011).

  17. 17.

    , , & Architecture and function of plant light-harvesting complexes II. Curr. Opin. Struct. Biol. 23, 515–525 (2013).

  18. 18.

    , , & Comparison between plant photosystem I and photosystem II architecture and functioning. Curr. Protein Pept. Sci. 15, 296–331 (2014).

  19. 19.

    & Cryo-EM: a unique tool for the visualization of macromolecular complexity. Mol. Cell 58, 677–689 (2015).

  20. 20.

    , , , & Functional architecture of higher plant photosystem II supercomplexes. EMBO J. 28, 3052–3063 (2009).

  21. 21.

    , , & PsbS-dependent enhancement of feedback de-excitation protects photosystem II from photoinhibition. Proc. Natl Acad. Sci. USA 99, 15222–15227 (2002).

  22. 22.

    , , & 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).

  23. 23.

    , , & A specific binding site for neoxanthin in the monomeric antenna proteins CP26 and CP29 of photosystem II. FEBS Lett. 581, 4704–4710 (2007).

  24. 24.

    , , & Molecular basis of light harvesting and photoprotection in CP24: unique features of the most recent antenna complex. J. Biol. Chem. 284, 29536–29546 (2009).

  25. 25.

    , & Photoprotection mutants of Arabidopsis thaliana acclimate to high light by increasing photosynthesis and specific antioxidants. Plant Cell Environ. 29, 879–887 (2006).

  26. 26.

    et al. A pigment-binding protein essential for regulation of photosynthetic light harvesting. Nature 403, 391–395 (2000).

  27. 27.

    & The role of the PsbS protein in the protection of photosystems I and II against high light in Arabidopsis thaliana. Biochim. Biophys. Acta 1817, 2158–2165 (2012).

  28. 28.

    , , & Photosystem II, a growing complex: updates on newly discovered components and low molecular mass proteins. Biochim. Biophys. Acta 1817, 13–25 (2012).

  29. 29.

    et al. The PsbW protein stabilizes the supramolecular organization of photosystem II in higher plants. Plant J. 65, 368–381 (2011).

  30. 30.

    , & Biochemical and spectroscopic characterization of highly stable photosystem II supercomplexes from Arabidopsis. J. Biol. Chem. 291, 19157–19171 (2014).

  31. 31.

    et al. Psbr, a missing link in the assembly of the oxygen-evolving complex of plant photosystem II. J. Biol. Chem. 281, 145–150 (2006).

  32. 32.

    , , & In vivo identification of photosystem II light harvesting complexes interacting with Photosystem subunit S. Plant Physiol 168, 1747–1761 (2015).

  33. 33.

    , , , & Psbs interactions involved in the activation of energy dissipation in Arabidopsis. Nat. Plants 2, 15225 (2016).

  34. 34.

    et al. Proteomic characterization and three-dimensional electron microscopy study of PSII-LHCII supercomplexes from higher plants. Biochim. Biophys. Acta 1837, 1454–1462 (2014).

  35. 35.

    et al. In silico and biochemical analysis of Physcomitrella patens photosynthetic antenna: identification of subunits which evolved upon land adaptation. PloS ONE 3, e2033 (2008).

  36. 36.

    , , , & Evolutionary loss of light-harvesting proteins Lhcb6 and Lhcb3 in major land plant groups—break-up of current dogma. New Phytol. 210, 808–814 (2016).

  37. 37.

    , , & Mutational analysis of a higher plant antenna protein provides identification of chromophores bound into multiple sites. Proc. Natl Acad. Sci. USA 96, 10056–10061 (1999).

  38. 38.

    & Efficiency of energy funneling in the photosystem II supercomplex of higher plants. Chemical Sci. 7, 4174–4183 (2016).

  39. 39.

    , & A structure-based model of energy transfer reveals the principles of light harvesting in photosystem II supercomplexes. J. Am. Chem. Soc. 135, 9164–9173 (2013).

  40. 40.

    , , & Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex. Science 348, 989–995 (2015).

  41. 41.

    & Light harvesting in photosystem II core complexes is limited by the transfer to the trap: can the core complex turn into a photoprotective mode? J. Am. Chem. Soc. 130, 4431–4446 (2008).

  42. 42.

    & Could structural similarity of specific domains between animal globins and plant antenna proteins provide hints important for the photoprotection mechanism? J. Theor. Biol. 364, 71–79 (2015).

  43. 43.

    & Light harvesting in photosystem II. Photosynth. Res. 116, 251–263 (2013).

  44. 44.

    , & A highly resolved, oxygen-evolving photosystem II preparation from spinach thylakoid membranes. FEBS Lett. 134, 231–234 (1981).

  45. 45.

    et al. Structural characterization of a plant photosystem I and NAD(P)H dehydrogenase supercomplex. Plant J. 77, 568–576 (2014).

  46. 46.

    , , & Hybrid electron microscopy normal mode analysis graphical interface and protocol. J. Struct. Biol. 188, 134–141 (2014).

  47. 47.

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

  48. 48.

    , , , & Efficient initial volume determination from electron microscopy images of single particles. Bioinformatics 30, 2891–2898 (2014).

  49. 49.

    & Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142, 334–347 (2003).

  50. 50.

    & CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).

  51. 51.

    et al. Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat. Methods 10, 584–590 (2013).

  52. 52.

    Beam-induced motion correction for sub-megadalton cryo-EM particles. eLife 3, e03665 (2014).

  53. 53.

    & Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721–745 (2003).

  54. 54.

    & Prevention of overfitting in cryo-EM structure determination. Nat. Methods 9, 853–854 (2012).

  55. 55.

    , & Quantifying the local resolution of cryo-EM density maps. Nat. Methods 11, 63–65 (2013).

  56. 56.

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

  57. 57.

    et al. UCSF chimera? A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

  58. 58.

    , , & Features and development of coot. Acta Crystallogr. D 66, 486–501 (2010).

  59. 59.

    et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D 58, 1948–1954 (2002).

  60. 60.

    et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D 68, 352–367 (2012).

  61. 61.

    , , , & The Phyre2 web portal for protein modeling, prediction and analysis. Nat. Protoc. 10, 845–858 (2015).

  62. 62.

    et al. A series of PDB-related databanks for everyday needs. Nucleic Acids Res. 43, D364–D368 (2015).

  63. 63.

    et al. Molprobity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010).

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Acknowledgements

This work was supported by the FOM program ‘The thylakoid membrane—a dynamic switch (10TM02)’. S.C. is supported by the French National Research Agency Grant ANR-12-JSV8-0001-01. R.K. is supported by a Marie Curie Career Integration Grant call FP7-PEOPLE-2012-CIG and by grant LO1204 (Sustainable development of research in the Centre of the Region Haná). We acknowledge L. Franken and J. Dekker for discussions.

Author information

Author notes

    • Laura S. van Bezouwen

    Present address: Cryo-Electron Microscopy, Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, 3584 CH Utrecht, Netherlands (L.S.v.B.).

Affiliations

  1. Electron microscopy and Protein crystallography group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands

    • Laura S. van Bezouwen
    • , Andy-Mark W. H. Thunnissen
    • , Gert T. Oostergetel
    •  & Egbert J. Boekema
  2. Aix Marseille Université, CEA, CNRS, BIAM, Laboratoire de Génétique et Biophysique des Plantes, 13009 Marseille, France

    • Stefano Caffarri
  3. Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Biophysics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic

    • Ravindra S. Kale
    •  & Roman Kouřil

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Contributions

L.S.v.B., G.T.O. and E.J.B. designed the research. S.C. isolated the supercomplex, L.S.v.B. and G.T.O. collected the data. L.S.v.B. performed the single-particle analysis. L.S.v.B., S.C., G.T.O. and A.-M.W.H.T. analysed the data. R.S.K and R.K. analysed the negative stain supercomplex data. L.S.v.B., S.C., G.T.O., A.-M.W.H.T. and E.J.B. wrote the article.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Egbert J. Boekema.

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