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Zhang YZ, Li K, Qin BY, Guo JP, Zhang QB, Zhao DL, Chen XL, Gao J, Liu LN, Zhao LS. Structure of cryptophyte photosystem II-light-harvesting antennae supercomplex. Nat Commun 2024; 15:4999. [PMID: 38866834 PMCID: PMC11169493 DOI: 10.1038/s41467-024-49453-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024] Open
Abstract
Cryptophytes are ancestral photosynthetic organisms evolved from red algae through secondary endosymbiosis. They have developed alloxanthin-chlorophyll a/c2-binding proteins (ACPs) as light-harvesting complexes (LHCs). The distinctive properties of cryptophytes contribute to efficient oxygenic photosynthesis and underscore the evolutionary relationships of red-lineage plastids. Here we present the cryo-electron microscopy structure of the Photosystem II (PSII)-ACPII supercomplex from the cryptophyte Chroomonas placoidea. The structure includes a PSII dimer and twelve ACPII monomers forming four linear trimers. These trimers structurally resemble red algae LHCs and cryptophyte ACPI trimers that associate with Photosystem I (PSI), suggesting their close evolutionary links. We also determine a Chl a-binding subunit, Psb-γ, essential for stabilizing PSII-ACPII association. Furthermore, computational calculation provides insights into the excitation energy transfer pathways. Our study lays a solid structural foundation for understanding the light-energy capture and transfer in cryptophyte PSII-ACPII, evolutionary variations in PSII-LHCII, and the origin of red-lineage LHCIIs.
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Affiliation(s)
- Yu-Zhong Zhang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
| | - Kang Li
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Bing-Yue Qin
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jian-Ping Guo
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Quan-Bao Zhang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Dian-Li Zhao
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Xiu-Lan Chen
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China.
| | - Lu-Ning Liu
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
| | - Long-Sheng Zhao
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
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Mehra HS, Wang X, Russell BP, Kulkarni N, Ferrari N, Larson B, Vinyard DJ. Assembly and Repair of Photosystem II in Chlamydomonas reinhardtii. PLANTS (BASEL, SWITZERLAND) 2024; 13:811. [PMID: 38592843 PMCID: PMC10975043 DOI: 10.3390/plants13060811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 04/11/2024]
Abstract
Oxygenic photosynthetic organisms use Photosystem II (PSII) to oxidize water and reduce plastoquinone. Here, we review the mechanisms by which PSII is assembled and turned over in the model green alga Chlamydomonas reinhardtii. This species has been used to make key discoveries in PSII research due to its metabolic flexibility and amenability to genetic approaches. PSII subunits originate from both nuclear and chloroplastic gene products in Chlamydomonas. Nuclear-encoded PSII subunits are transported into the chloroplast and chloroplast-encoded PSII subunits are translated by a coordinated mechanism. Active PSII dimers are built from discrete reaction center complexes in a process facilitated by assembly factors. The phosphorylation of core subunits affects supercomplex formation and localization within the thylakoid network. Proteolysis primarily targets the D1 subunit, which when replaced, allows PSII to be reactivated and completes a repair cycle. While PSII has been extensively studied using Chlamydomonas as a model species, important questions remain about its assembly and repair which are presented here.
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Affiliation(s)
| | | | | | | | | | | | - David J. Vinyard
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; (H.S.M.); (X.W.); (B.P.R.); (N.K.); (N.F.); (B.L.)
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Caspy I, Fadeeva M, Mazor Y, Nelson N. Structure of Dunaliella photosystem II reveals conformational flexibility of stacked and unstacked supercomplexes. eLife 2023; 12:e81150. [PMID: 36799903 PMCID: PMC9949808 DOI: 10.7554/elife.81150] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 02/16/2023] [Indexed: 02/18/2023] Open
Abstract
Photosystem II (PSII) generates an oxidant whose redox potential is high enough to enable water oxidation , a substrate so abundant that it assures a practically unlimited electron source for life on earth . Our knowledge on the mechanism of water photooxidation was greatly advanced by high-resolution structures of prokaryotic PSII . Here, we show high-resolution cryogenic electron microscopy (cryo-EM) structures of eukaryotic PSII from the green alga Dunaliella salina at two distinct conformations. The conformers are also present in stacked PSII, exhibiting flexibility that may be relevant to the grana formation in chloroplasts of the green lineage. CP29, one of PSII associated light-harvesting antennae, plays a major role in distinguishing the two conformations of the supercomplex. We also show that the stacked PSII dimer, a form suggested to support the organisation of thylakoid membranes , can appear in many different orientations providing a flexible stacking mechanism for the arrangement of grana stacks in thylakoids. Our findings provide a structural basis for the heterogenous nature of the eukaryotic PSII on multiple levels.
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Affiliation(s)
- Ido Caspy
- Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv UniversityTel AvivIsrael
| | - Maria Fadeeva
- Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv UniversityTel AvivIsrael
| | - Yuval Mazor
- School of Molecular Sciences, Arizona State UniversityTempeUnited States
- Biodesign Center for Applied Structural Discovery, Arizona State UniversityTempeUnited States
| | - Nathan Nelson
- Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv UniversityTel AvivIsrael
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Wang D, Groves JT. Energy Landscape for the Electrocatalytic Oxidation of Water by a Single-Site Oxomanganese(V) Porphyrin. Inorg Chem 2022; 61:13667-13672. [PMID: 35993714 DOI: 10.1021/acs.inorgchem.2c02284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A cationic manganese porphyrin, MnIII-TDMImP, is an efficient, homogeneous, single-site water oxidation electrocatalyst at neutral pH. The measured turnover frequency for oxygen production is 32 s-1. Mechanistic analyses indicate that MnV(O)(OH2), the protonated form of the corresponding trans-MnV(O)2 species, is generated from the MnIII(OH2)2 precursor in a 2-e- two-proton process and is responsible for O-O bond formation with a H2O molecule. Chloride ion is a competitive substrate with H2O for the MnV(O)(OH2) oxidant, forming hypochlorous acid with a rate constant that is 3 orders of magnitude larger than that of water oxidation. The data allow the construction of an experimental energy landscape for this water oxidation catalysis process.
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Affiliation(s)
- Dong Wang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - John T Groves
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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Wang J, Natchiar SK, Moore PB, Klaholz BP. Identification of Mg 2+ ions next to nucleotides in cryo-EM maps using electrostatic potential maps. Acta Crystallogr D Struct Biol 2021; 77:534-539. [PMID: 33825713 PMCID: PMC8025889 DOI: 10.1107/s2059798321001893] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 02/16/2021] [Indexed: 11/10/2022] Open
Abstract
Cryo electron microscopy (cryo-EM) can produce maps of macromolecules that have resolutions that are sufficiently high that structural details such as chemical modifications, water molecules and bound metal ions can be discerned. However, those accustomed to interpreting the electron-density maps of macromolecules produced by X-ray crystallography need to be careful when assigning features such as these in cryo-EM maps because cations, for example, interact far more strongly with electrons than they do with X-rays. Using simulated electrostatic potential (ESP) maps as a tool led us to re-examine a recent cryo-EM map of the human ribosome, and we realized that some of the ESP peaks originally identified as novel groups covalently bonded to the N7, O6 or O4 atoms of several guanines, adenines or uridines, respectively, in this structure are likely to instead represent Mg2+ ions coordinated to these atoms, which provide only partial charge compensation compared with Mg2+ ions located next to phosphate groups. In addition, direct evidence is provided for a variation in the level of 2'-O ribose methylation of nucleotides in the human ribosome. ESP maps can thus help in identifying ions next to nucleotide bases, i.e. at positions that can be difficult to address in cryo-EM maps due to charge effects, which are specifically encountered in cryo-EM. This work is particularly relevant to nucleoprotein complexes and shows that it is important to consider charge effects when interpreting cryo-EM maps, thus opening possibilities for localizing charges in structures that may be relevant for enzymatic mechanisms and drug interactions.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - S. Kundhavai Natchiar
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch, France
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 Rue Laurent Fries, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Peter B. Moore
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
| | - Bruno P. Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch, France
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 Rue Laurent Fries, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
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