Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction center polypeptide and promotes the initial steps of PSII assembly, but its binding site is unclear. Here we use cryo-electron microscopy to determine the structure of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached. Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that ultimately ligate the water-oxidising Mn4CaO5 cluster, thereby preventing the premature binding of Mn2+ and Ca2+ ions and protecting the site from damage. Interactions with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall, our work provides valuable insights into the early stages of PSII assembly and the structural changes that create the binding site for the Mn4CaO5 cluster.

Faculty of Science University of South Bohemia Branišovská 31 České Budĕjovice 37005 Czech Republic

Forschungszentrum Jülich GmbH Wilhelm Johnen Straße 52428 Jülich Germany

Institute of Microbiology Academy of Sciences of the Czech Republic Opatovický mlýn Třeboň 379 81 Czech Republic

Institute of Science and Technology Austria 3400 Klosterneuburg Austria

Sir Ernst Chain Building Wolfson Laboratories Department of Life Sciences Imperial College London S Kensington Campus London SW7 2AZ UK

Zobrazit více v PubMed

Shen JR. The structure of photosystem II and the mechanism of water oxidation in photosynthesis. Annu. Rev. Plant Biol. 2015;66:23–48. PubMed

Barber J. Photosystem II: the water splitting enzyme of photosynthesis and the origin of oxygen in our atmosphere. Q. Rev. Biophys. 2016;49:e14. PubMed

Komenda J, Sobotka R, Nixon PJ. Assembling and maintaining the photosystem II complex in chloroplasts and cyanobacteria. Curr. Opin. Plant Biol. 2012;15:245–251. PubMed

Boehm M, et al. Investigating the early stages of photosystem II assembly in Synechocystis sp. PCC 6803. J. Biol. Chem. 2011;286:14812–14819. PubMed PMC

Nickelsen J, Rengstl B. Photosystem II assembly: from cyanobacteria to plants. Ann. Rev. Plant Biol. 2013;64:609–635. PubMed

Huang G, et al. Structural insights into a dimeric Psb27-photosystem II complex from a cyanobacterium Thermosynechococcus vulcanus. Proc. Natl. Acad. Sci. USA. 2021;118:1–9. PubMed PMC

Zabret J, et al. Structural insights into photosystem II assembly. Nat. Plants. 2021;7:524–538. PubMed PMC

Xiao Y, et al. Structural insights into cyanobacterial photosystem II intermediates associated with Psb28 and Tsl0063. Nat. Plants. 2021;7:1132–1142. PubMed

Komenda J, et al. The cyanobacterial homologue of HCF136/YCF48 is a component of an early photosystem II assembly complex and is important for both the efficient assembly and repair of photosystem II in Synechocystis sp. PCC 6803. J. Biol. Chem. 2008;283:22390–22399. PubMed

Meurer J, Plücken H, Kowallik KV, Westhoff P. A nuclear-encoded protein of prokaryotic origin is essential for the stability of photosystem II in Arabidopsis thaliana. EMBO J. 1998;17:5286–5297. PubMed PMC

Plücken H, Müller B, Grohmann D, Westhoff P, Eichacker LA. The HCF136 protein is essential for assembly of the photosystem II reaction center in Arabidopsis thaliana. FEBS Lett. 2002;532:85–90. PubMed

Knoppová J, et al. Assembly of D1/D2 complexes of photosystem II: binding of pigments and a network of auxiliary proteins. Plant Physiol. 2022;189:790–804. PubMed PMC

Boehm M, et al. Subunit composition of CP43-less photosystem II complexes of Synechocystis sp. PCC 6803: implications for the assembly and repair of photosystem II. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 2012;367:3444–3454. PubMed PMC

Oliver N, Avramov AP, Nürnberg DJ, Dau H, Burnap RL. From manganese oxidation to water oxidation: assembly and evolution of the water-splitting complex in photosystem II. Photosynth. Res. 2022;152:107–133. PubMed

Ifuku K, Noguchi T. Structural coupling of extrinsic proteins with the oxygen-evolving center in photosystem II. Front. Plant Sci. 2016;7:1–11. PubMed PMC

Yu J, et al. Ycf48 involved in the biogenesis of the oxygen-evolving photosystem II complex is a seven-bladed beta-propeller protein. Proc. Natl. Acad. Sci. USA. 2018;115:E7824–E7833. PubMed PMC

Kiss É, et al. A photosynthesis-specific rubredoxin-like protein is required for efficient association of the D1 and D2 proteins during the initial steps of photosystem II assembly. Plant Cell. 2019;31:2241–2258. PubMed PMC

Knoppová J, et al. Discovery of a chlorophyll-binding protein complex involved in the early steps of photosystem II assembly in Synechocystis. Plant Cell. 2014;26:1200–1212. PubMed PMC

Zivanov J, Nakane T, Scheres SHW. Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in RELION -3.1. IUCrJ. 2020;7:253–267. PubMed PMC

Bepler T, et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat. Methods. 2019;16:1153–1160. PubMed PMC

Jordan P, et al. Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution. Nature. 2001;411:909–917. PubMed

Rast A, et al. Biogenic regions of cyanobacterial thylakoids form contact sites with the plasma membrane. Nat. Plants. 2019;5:436–446. PubMed

Zhao L, et al. Native architecture and acclimation of photosynthetic membranes in a fast-growing cyanobacterium. Plant Physiol. 2022;190:1883–1895. PubMed PMC

Ferreira KN, Iverson TM, Maghlaoui K, Barber J, Iwata S. Architecture of the photosynthetic oxygen-evolving center. Science. 2004;303:1831–1838. PubMed

Gisriel CJ, et al. High-resolution cryo-electron microscopy structure of photosystem II from the mesophilic cyanobacterium Synechocystis sp. PCC 6803. Proc. Natl. Acad. Sci. USA. 2022;119:1–10. PubMed PMC

Umena Y, Kawakami K, Shen JR, Kamiya N. Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9Å. Nature. 2011;473:55–60. PubMed

Tomo T, et al. Isolation and spectral characterization of Photosystem II reaction center from Synechocystis sp. PCC 6803. Photosynth. Res. 2008;98:293–302. PubMed

Saito K, Mandal M, Ishikita H. Redox potentials along the redox-active low-barrier H-bonds in electron transfer pathways. Phys. Chem. Chem. Phys. 2020;22:25467–25473. PubMed

Gisriel CJ, et al. Cryo-EM structure of monomeric photosystem II from Synechocystis sp. PCC 6803 lacking the water-oxidation complex. Joule. 2020;4:2131–2148.

Saito K, Shen JR, Ishida T, Ishikita H. Short Hydrogen bond between redox-active tyrosine YZ and D1-His190 in the photosystem II crystal structure. Biochemistry. 2011;50:9836–9844. PubMed

Imaizumi K, Ifuku K. Binding and functions of the two chloride ions in the oxygen-evolving center of photosystem II. Photosynth. Res. 2022;153:135–156. PubMed

Wang J. Experimental charge density from electron microscopic maps. Protein Sci. 2017;26:1619–1626. PubMed PMC

Gisriel CJ, et al. Structure of a monomeric photosystem II core complex from a cyanobacterium acclimated to far-red light reveals the functions of chlorophylls d and f. J. Biol. Chem. 2022;298:101424. PubMed PMC

Chiu Y, Chu H. New structural and mechanistic insights into functional roles of cytochrome b559 in photosystem II. Front. Plant Sci. 2022;13:914922. PubMed PMC

Knoppová J, et al. The photosystem II assembly factor Ycf48 from the cyanobacterium Synechocystis sp. PCC 6803 is lipidated using an atypical lipobox sequence. Int. J. Mol. Sci. 2021;22:3733. PubMed PMC

Diner BA, Nixon PJ. The rate of reduction of oxidized redox-active tyrosine, Z+, by exogenous Mn2+ is slowed in a site-directed mutant, at aspartate 170 of polypeptide D1 of photosystem II, inactive for photosynthetic oxygen evolution. Biochim. Biophys. Acta. 1992;1101:134–138.

Campbell KA, et al. Dual-Mode EPR detects the initial intermediate in photoassembly of the photosystem II Mn Cluster: The influence of amino acid residue 170 of the D1 polypeptide on Mn coordination. J. Am. Chem. Soc. 2000;122:3754–3761.

Cohen RO, Nixon PJ, Diner BA. Participation of the C-terminal region of the D1-polypeptide in the first steps in the assembly of the Mn4Ca Cluster of photosystem II. J. Biol. Chem. 2007;282:7209–7218. PubMed

Hussein R, et al. Structural dynamics in the water and proton channels of photosystem II during the S2 to S3 transition. Nat. Commun. 2021;12:1–16. PubMed PMC

Komenda J, et al. Cleavage after residue Ala352 in the C-terminal extension is an early step in the maturation of the D1 subunit of Photosystem II in Synechocystis PCC 6803. Biochim. Biophys. Acta. 2007;1767:829–837. PubMed

Knoppová J, Yu J, Konik P, Nixon PJ, Komenda J. CyanoP is involved in the early steps of photosystem II assembly in the cyanobacterium Synechocystis sp. PCC 6803. Plant Cell Physiol. 2016;57:1921–1931. PubMed

Han H, Kursula P. The olfactomedin domain from gliomedin is a β-Propeller with unique structural properties. J. Biol. Chem. 2015;290:3612–3621. PubMed PMC

Netzer-El SY, Caspy I, Nelson N. Crystal structure of photosystem I monomer from Synechocystis PCC 6803. Front. Plant Sci. 2019;9:1865. PubMed PMC

Malavath T, Caspy I, Netzer-El S, Klaiman D, Nelson N. Structure and function of wild-type and subunit-depleted photosystem I in Synechocystis. Biochim. Biophys. Acta. 2018;1859:645–654. PubMed

Chen M, et al. Distinct structural modulation of photosystem I and lipid environment stabilizes its tetrameric assembly. Nat. Plants. 2020;6:314. PubMed

Zheng L, et al. Structural and functional insights into the tetrameric photosystem I from heterocyst-forming cyanobacteria. Nat. Plants. 2019;5:1087. PubMed

Kato K, et al. Structure of a cyanobacterial photosystem I tetramer revealed by cryo-electron microscopy. Nat. Commun. 2019;10:4929. PubMed PMC

Chernev P, et al. Light-driven formation of manganese oxide by today’s photosystem II supports evolutionarily ancient manganese-oxidizing photosynthesis. Nat. Commun. 2020;11:1–10. PubMed PMC

Pospíšil P. Production of reactive oxygen species by photosystem II as a response to light and temperature stress. Front. Plant Sci. 2016;7:1950. PubMed PMC

Semin BK, Ivanov II, Rubin AB, Parak F. High-specific binding of Fe(II) at the Mn-binding site in Mn-depleted PSII membranes from spinach. FEBS Lett. 1995;375:223–226. PubMed

Stengel A, et al. Initial steps of photosystem II de novo assembly and preloading with manganese take place in biogenesis centers in Synechocystis. Plant Cell. 2012;24:660–675. PubMed PMC

Michoux F, Takasaka K, Boehm M, Nixon PJ, Murray JW. Structure of CyanoP at 2.8 Å: implications for the evolution and function of the PsbP Subunit of photosystem II. Biochemistry. 2010;49:7411–7413. PubMed

Bondarava N, Un S, Krieger-Liszkay A. Manganese binding to the 23 kDa extrinsic protein of photosystem II. Biochim. Biophys. Acta. 2007;1767:583–588. PubMed

Cao P, et al. Crystal structure analysis of extrinsic PsbP protein of photosystem II reveals a manganese-induced conformational change. Mol. Plant. 2015;8:664–666. PubMed

Calderon RH, de Vitry C, Wollman F, Niyogi KK. Rubredoxin 1 promotes the proper folding of D1 and is not required for heme b559 assembly in Chlamydomonas photosystem II. J. Biol. Chem. 2023;299:102968. PubMed PMC

Vass I, Cser K. Janus-faced charge recombinations in photosystem II photoinhibition. Trends Plant Sci. 2009;14:200–205. PubMed

Nixon PJ, Trost JT, Diner BA. Role of the carboxy-terminus of polypeptide D1 in the assembly of a functional water-oxidizing manganese cluster in photosystem II of the cyanobacterium Synechocystis sp. PCC 6803: assembly requires a free carboxyl group at C-terminal position 344. Biochemistry. 1992;31:10859–10871. PubMed

Komenda J, et al. The Psb27 assembly factor binds to the CP43 complex of photosystem II in the cyanobacterium Synechocystis sp. PCC 6803. Plant Physiol. 2012;158:476–486. PubMed PMC

Chidgey JW, et al. A cyanobacterial chlorophyll synthase-HliD complex associates with the Ycf39 Protein and the YidC/Alb3 Insertase. Plant Cell. 2014;26:1267. PubMed PMC

Kampjut D, Steiner J, Sazanov LA. Cryo-EM grid optimization for membrane proteins. iScience. 2021;24:102139. PubMed PMC

Cheng A, et al. High resolution single particle cryo-electron microscopy using beam-image shift. J. Struct. Biol. 2018;204:270–275. PubMed PMC

Zheng SQ, et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods. 2017;14:331–332. PubMed PMC

Rohou A, Grigorieff N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 2015;192:216–221. PubMed PMC

Zhang K. Gctf: Real-time CTF determination and correction. J. Struct. Biol. 2016;193:1–12. PubMed PMC

Afonine PV, et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. 2018;D74:531–544. PubMed PMC

Davis IW, et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 2007;35:W375–W383. PubMed PMC

Pettersen EF, et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 2021;30:70–82. PubMed PMC

Landau M, et al. ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucl. Acids Res. 2005;33:W299–W302. PubMed PMC

Glaser F, et al. ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics. 2003;19:163–164. PubMed

The biogenesis and maintenance of PSII: Recent advances and current challenges