1
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Biswas S, Khaing EP, Zhong V, Eaton-Rye JJ. Arg24 and 26 of the D2 protein are important for photosystem II assembly and plastoquinol exchange in Synechocystis sp. PCC 6803. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149150. [PMID: 38906313 DOI: 10.1016/j.bbabio.2024.149150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 05/26/2024] [Accepted: 06/13/2024] [Indexed: 06/23/2024]
Abstract
Photosystem II (PS II) assembly is a stepwise process involving preassembly complexes or modules focused around four core PS II proteins. The current model of PS II assembly in cyanobacteria is derived from studies involving the deletion of one or more of these core subunits. Such deletions may destabilize other PS II assembly intermediates, making constructing a clear picture of the intermediate events difficult. Information on plastoquinone exchange pathways operating within PS II is also unclear and relies heavily on computer-aided simulations. Deletion of PsbX in [S. Biswas, J.J. Eaton-Rye, Biochim. Biophys. Acta - Bioenerg. 1863 (2022) 148519] suggested modified QB binding in PS II lacking this subunit. This study has indicated the phenotype of the ∆PsbX mutant arose by disrupting a conserved hydrogen bond between PsbX and the D2 (PsbD) protein. We mutated two conserved arginine residues (D2:Arg24 and D2:Arg26) to further understand the observations made with the ∆PsbX mutant. Mutating Arg24 disrupted the interaction between PsbX and D2, replicating the high-light sensitivity and altered fluorescence decay kinetics observed in the ∆PsbX strain. The Arg26 residue, on the other hand, was more important for either PS II assembly or for stabilizing the fully assembled complex. The effects of mutating both arginine residues to alanine or aspartate were severe enough to render the corresponding double mutants non-photoautotrophic. Our study furthers our knowledge of the amino-acid interactions stabilizing plastoquinone-exchange pathways while providing a platform to study PS II assembly and repair without the actual deletion of any proteins.
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Affiliation(s)
- Sandeep Biswas
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| | - Ei Phyo Khaing
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| | - Victor Zhong
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| | - Julian J Eaton-Rye
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand.
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2
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Komenda J, Sobotka R, Nixon PJ. The biogenesis and maintenance of PSII: Recent advances and current challenges. THE PLANT CELL 2024; 36:3997-4013. [PMID: 38484127 PMCID: PMC11449106 DOI: 10.1093/plcell/koae082] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/27/2024] [Indexed: 10/05/2024]
Abstract
The growth of plants, algae, and cyanobacteria relies on the catalytic activity of the oxygen-evolving PSII complex, which uses solar energy to extract electrons from water to feed into the photosynthetic electron transport chain. PSII is proving to be an excellent system to study how large multi-subunit membrane-protein complexes are assembled in the thylakoid membrane and subsequently repaired in response to photooxidative damage. Here we summarize recent developments in understanding the biogenesis of PSII, with an emphasis on recent insights obtained from biochemical and structural analysis of cyanobacterial PSII assembly/repair intermediates. We also discuss how chlorophyll synthesis is synchronized with protein synthesis and suggest a possible role for PSI in PSII assembly. Special attention is paid to unresolved and controversial issues that could be addressed in future research.
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Affiliation(s)
- Josef Komenda
- Center Algatech, Institute of Microbiology of the Czech Academy of Sciences, 37901 Třeboň, Czech Republic
| | - Roman Sobotka
- Center Algatech, Institute of Microbiology of the Czech Academy of Sciences, 37901 Třeboň, Czech Republic
| | - Peter J Nixon
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
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3
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Magyar M, Akhtar P, Sipka G, Domonkos I, Han W, Li X, Han G, Shen JR, Lambrev PH, Garab G. Effects of lipids on the rate-limiting steps in the dark-to-light transition of Photosystem II core complex of Thermostichus vulcanus. FRONTIERS IN PLANT SCIENCE 2024; 15:1381040. [PMID: 38576791 PMCID: PMC10991767 DOI: 10.3389/fpls.2024.1381040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/11/2024] [Indexed: 04/06/2024]
Abstract
In our earlier works, we have shown that the rate-limiting steps, associated with the dark-to-light transition of Photosystem II (PSII), reflecting the photochemical activity and structural dynamics of the reaction center complex, depend largely on the lipidic environment of the protein matrix. Using chlorophyll-a fluorescence transients (ChlF) elicited by single-turnover saturating flashes, it was shown that the half-waiting time (Δτ 1/2) between consecutive excitations, at which 50% of the fluorescence increment was reached, was considerably larger in isolated PSII complexes of Thermostichus (T.) vulcanus than in the native thylakoid membrane (TM). Further, it was shown that the addition of a TM lipid extract shortened Δτ 1/2 of isolated PSII, indicating that at least a fraction of the 'missing' lipid molecules, replaced by detergent molecules, caused the elongation of Δτ 1/2. Here, we performed systematic experiments to obtain information on the nature of TM lipids that are capable of decreasing Δτ 1/2. Our data show that while all lipid species shorten Δτ 1/2, the negatively charged lipid phosphatidylglycerol appears to be the most efficient species - suggesting its prominent role in determining the structural dynamics of PSII reaction center.
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Affiliation(s)
- Melinda Magyar
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Parveen Akhtar
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Gábor Sipka
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Ildikó Domonkos
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Wenhui Han
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xingyue Li
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Guangye Han
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jian-Ren Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Petar H. Lambrev
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Győző Garab
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czechia
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4
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Alam B, Liu R, Gong J, Li J, Yan H, Ge Q, Xiao X, Pan J, Shang H, Shi Y, Yuan Y, Gong W. Hub Genes in Stable QTLs Orchestrate the Accumulation of Cottonseed Oil in Upland Cotton via Catalyzing Key Steps of Lipid-Related Pathways. Int J Mol Sci 2023; 24:16595. [PMID: 38068920 PMCID: PMC10706765 DOI: 10.3390/ijms242316595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/10/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
Upland cotton is the fifth-largest oil crop in the world, with an average supply of nearly 20% of vegetable oil production. Cottonseed oil is also an ideal alternative raw material to be efficiently converted into biodiesel. However, the improvement in kernel oil content (KOC) of cottonseed has not received sufficient attention from researchers for a long time, due to the fact that the main product of cotton planting is fiber. Previous studies have tagged QTLs and identified individual candidate genes that regulate KOC of cottonseed. The regulatory mechanism of oil metabolism and accumulation of cottonseed are still elusive. In the current study, two high-density genetic maps (HDGMs), which were constructed based on a recombinant inbred line (RIL) population consisting of 231 individuals, were used to identify KOC QTLs. A total of forty-three stable QTLs were detected via these two HDGM strategies. Bioinformatic analysis of all the genes harbored in the marker intervals of the stable QTLs revealed that a total of fifty-one genes were involved in the pathways related to lipid biosynthesis. Functional analysis via coexpression network and RNA-seq revealed that the hub genes in the co-expression network that also catalyze the key steps of fatty acid synthesis, lipid metabolism and oil body formation pathways (ACX4, LACS4, KCR1, and SQD1) could jointly orchestrate oil accumulation in cottonseed. This study will strengthen our understanding of oil metabolism and accumulation in cottonseed and contribute to KOC improvement in cottonseed in the future, enhancing the security and stability of worldwide food supply.
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Affiliation(s)
- Beena Alam
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China (Y.S.)
| | - Ruixian Liu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China (Y.S.)
| | - Juwu Gong
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China (Y.S.)
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Junwen Li
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China (Y.S.)
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Haoliang Yan
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China (Y.S.)
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Qun Ge
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China (Y.S.)
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Xianghui Xiao
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China (Y.S.)
| | - Jingtao Pan
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China (Y.S.)
| | - Haihong Shang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China (Y.S.)
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Yuzhen Shi
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China (Y.S.)
| | - Youlu Yuan
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China (Y.S.)
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Wankui Gong
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China (Y.S.)
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Kania K, Drożak A, Borkowski A, Działak P, Majcher K, Sawicka PD, Zienkiewicz M. Mechanisms of temperature acclimatisation in the psychrotolerant green alga Coccomyxa subellipsoidea C-169 (Trebouxiophyceae). PHYSIOLOGIA PLANTARUM 2023; 175:e14034. [PMID: 37882306 DOI: 10.1111/ppl.14034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/04/2023] [Accepted: 09/15/2023] [Indexed: 10/27/2023]
Abstract
Despite the interest in different temperature acclimatisations of higher plants, few studies have considered the mechanisms that allow psychrotolerant microalgae to live in a cold environment. Although the analysis of the genomes of some algae revealed the presence of specific genes that encode enzymes that can be involved in the response to stress, this area has not been explored deeply. This work aims to clarify the acclimatisation mechanisms that enable the psychrotolerant green alga Coccomyxa subellipsoidea C-169 to grow in a broad temperature spectrum. The contents of various biochemical compounds in cells, the lipid composition of the biological membranes of entire cells, and the thylakoid fraction as well as the electron transport rate and PSII efficiency were investigated. The results demonstrate an acclimatisation mechanism that is specific for C. subellipsoidea and that allows the maintenance of appropriate membrane fluidity, for example, in thylakoid membranes. It is achieved almost exclusively by changes within the unsaturated fatty acid pool, like changes from C18:2 into C18:3 and C16:2 into C16:3 or vice versa. This ensures, for example, an effective transport rate through PSII and in consequence a maximum quantum yield of it in cells growing at different temperatures. Furthermore, reactions characteristic for both psychrotolerant and mesophilic microalgae, involving the accumulation of lipids and soluble sugars in cells at temperatures other than optimal, were observed. These findings add substantially to our understanding of the acclimatisation of psychrotolerant organisms to a wide range of temperatures and prove that this process could be accomplished in a species-specific manner.
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Affiliation(s)
- Kinga Kania
- Department of Molecular Plant Physiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Anna Drożak
- Department of Molecular Plant Physiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Andrzej Borkowski
- Faculty of Geology, Geophysics and Environmental Protection, AGH University of Science and Technology, Krakow, Poland
| | - Paweł Działak
- Faculty of Geology, Geophysics and Environmental Protection, AGH University of Science and Technology, Krakow, Poland
| | - Katarzyna Majcher
- Department of Molecular Plant Physiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Paulina D Sawicka
- Department of Molecular Plant Physiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Maksymilian Zienkiewicz
- Department of Molecular Plant Physiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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6
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Sharma P, Lakra N, Goyal A, Ahlawat YK, Zaid A, Siddique KHM. Drought and heat stress mediated activation of lipid signaling in plants: a critical review. FRONTIERS IN PLANT SCIENCE 2023; 14:1216835. [PMID: 37636093 PMCID: PMC10450635 DOI: 10.3389/fpls.2023.1216835] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/19/2023] [Indexed: 08/29/2023]
Abstract
Lipids are a principal component of plasma membrane, acting as a protective barrier between the cell and its surroundings. Abiotic stresses such as drought and temperature induce various lipid-dependent signaling responses, and the membrane lipids respond differently to environmental challenges. Recent studies have revealed that lipids serve as signal mediators forreducing stress responses in plant cells and activating defense systems. Signaling lipids, such as phosphatidic acid, phosphoinositides, sphingolipids, lysophospholipids, oxylipins, and N-acylethanolamines, are generated in response to stress. Membrane lipids are essential for maintaining the lamellar stack of chloroplasts and stabilizing chloroplast membranes under stress. However, the effects of lipid signaling targets in plants are not fully understood. This review focuses on the synthesis of various signaling lipids and their roles in abiotic stress tolerance responses, providing an essential perspective for further investigation into the interactions between plant lipids and abiotic stress.
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Affiliation(s)
- Parul Sharma
- Department of Botany and Plant Physiology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
| | - Nita Lakra
- Department of Molecular Biology, Biotechnology and Bioinformatics, Chaudhary Charan Singh (CCS) Haryana Agricultural University, Hisar, India
| | - Alisha Goyal
- Division of Crop Improvement, Indian Council of Agricultural Research (ICAR)—Central Soil Salinity Research Institute, Karnal, India
| | - Yogesh K. Ahlawat
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, United States
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Abbu Zaid
- Plant Physiology and Biochemistry Section, Department of Botany, Aligarh Muslim University, Aligarh, India
- Department of Botany, Government Gandhi Memorial (GGM) Science College, Cluster University Jammu, Jammu, India
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7
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Kamada S, Nakajima Y, Shen JR. Structural insights into the action mechanisms of artificial electron acceptors in photosystem II. J Biol Chem 2023:104839. [PMID: 37209822 PMCID: PMC10300377 DOI: 10.1016/j.jbc.2023.104839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/07/2023] [Accepted: 05/15/2023] [Indexed: 05/22/2023] Open
Abstract
Photosystem II (PSII) utilizes light energy to split water, and the electrons extracted from water are transferred to QB, a plastoquinone (PQ) molecule bound to the D1 subunit of PSII. Many artificial electron acceptors (AEAs) with similar molecular structures to PQ can accept electrons from PSII. However, the molecular mechanism by which AEAs act on PSII is unclear. Here, we solved the crystal structure of PSII treated with three different AEAs, 2,5-dibromo-1,4-benzoquinone, 2,6-dichloro-1,4-benzoquinone, and 2-phenyl-1,4-benzoquinone, at 1.95-2.10 Å resolution. Our results show that all AEAs substitute for QB and are bound to the QB-binding site (QB site) to receive electrons, but their binding strengths are different, resulting in differences in their efficiencies to accept electrons. The acceptor 2-phenyl-1,4-benzoquinone binds most weakly to the QB site, and showed the highest oxygen-evolving activity, implying a reverse relationship between the binding strength and oxygen-evolving activity. In addition, a novel quinone binding site, designated the QD site, was discovered, which is located in the vicinity of QB site and close to QC site, a binding site reported previously. This QD site is expected to play a role as a channel or a storage site for quinones to be transported to the QB site. These results provide the structural basis for elucidating the actions of AEAs and exchange mechanism of QB in PSII, and also provide information for the design of more efficient electron acceptors.
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Affiliation(s)
- Shinji Kamada
- Faculty of Science, Okayama University, Okayama 700-8503, Japan
| | - Yoshiki Nakajima
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8503, Japan.
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8503, Japan.
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8
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Roychowdhury A, Srivastava R, Akash, Shukla G, Zehirov G, Mishev K, Kumar R. Metabolic footprints in phosphate-starved plants. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:755-767. [PMID: 37363416 PMCID: PMC10284745 DOI: 10.1007/s12298-023-01319-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/28/2023]
Abstract
Plants' requirement of Phosphorus (P) as an essential macronutrient is obligatory for their normal growth and metabolism. Besides restricting plants' primary growth, P depletion affects both primary and secondary metabolism and leads to altered levels of sugars, metabolites, amino acids, and other secondary compounds. Such metabolic shifts help plants optimize their metabolism and growth under P limited conditions. Under P deprivation, both sugar levels and their mobilization change that influences the expression of Pi starvation-inducible genes. Increased sugar repartitioning from shoot to root help root growth and organic acids secretion that in turn promotes phosphate (Pi) uptake from the soil. Other metabolic changes such as lipid remodeling or P reallocation from older to younger leaves release the P from its bound forms in the cell. In this review, we summarize the metabolic footprinting of Pi-starved plants with respect to the benefits offered by such metabolic changes to intracellular Pi homeostasis.
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Affiliation(s)
- Abhishek Roychowdhury
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana 500046 India
| | - Rajat Srivastava
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana 500046 India
| | - Akash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana 500046 India
| | - Gyanesh Shukla
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana 500046 India
| | - Grigor Zehirov
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Kiril Mishev
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Rahul Kumar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana 500046 India
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Amin M. Predicting the oxidation states of Mn ions in the oxygen-evolving complex of photosystem II using supervised and unsupervised machine learning. PHOTOSYNTHESIS RESEARCH 2023; 156:89-100. [PMID: 35896927 PMCID: PMC10070209 DOI: 10.1007/s11120-022-00941-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/13/2022] [Indexed: 05/21/2023]
Abstract
Serial Femtosecond Crystallography at the X-ray Free Electron Laser (XFEL) sources enabled the imaging of the catalytic intermediates of the oxygen evolution reaction of Photosystem II (PSII). However, due to the incoherent transition of the S-states, the resolved structures are a convolution from different catalytic states. Here, we train Decision Tree Classifier and K-means clustering models on Mn compounds obtained from the Cambridge Crystallographic Database to predict the S-state of the X-ray, XFEL, and CryoEM structures by predicting the Mn's oxidation states in the oxygen-evolving complex. The model agrees mostly with the XFEL structures in the dark S1 state. However, significant discrepancies are observed for the excited XFEL states (S2, S3, and S0) and the dark states of the X-ray and CryoEM structures. Furthermore, there is a mismatch between the predicted S-states within the two monomers of the same dimer, mainly in the excited states. We validated our model against other metalloenzymes, the valence bond model and the Mn spin densities calculated using density functional theory for two of the mismatched predictions of PSII. The model suggests designing a more optimized sample delivery and illumiation systems are crucial to precisely resolve the geometry of the advanced S-states to overcome the noncoherent S-state transition. In addition, significant radiation damage is observed in X-ray and CryoEM structures, particularly at the dangler Mn center (Mn4). Our model represents a valuable tool for investigating the electronic structure of the catalytic metal cluster of PSII to understand the water splitting mechanism.
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Affiliation(s)
- Muhamed Amin
- Department of Sciences, University College Groningen, University of Groningen, Hoendiepskade 23/24, 9718 BG, Groningen, The Netherlands.
- Rijksuniversiteit Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.
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10
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Nakajima Y, Ugai-Amo N, Tone N, Nakagawa A, Iwai M, Ikeuchi M, Sugiura M, Suga M, Shen JR. Crystal structures of photosystem II from a cyanobacterium expressing psbA 2 in comparison to psbA 3 reveal differences in the D1 subunit. J Biol Chem 2022; 298:102668. [PMID: 36334624 PMCID: PMC9709244 DOI: 10.1016/j.jbc.2022.102668] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/27/2022] [Accepted: 10/30/2022] [Indexed: 11/07/2022] Open
Abstract
Three psbA genes (psbA1, psbA2, and psbA3) encoding the D1 subunit of photosystem II (PSII) are present in the thermophilic cyanobacterium Thermosynechococcus elongatus and are expressed differently in response to changes in the growth environment. To clarify the functional differences of the D1 protein expressed from these psbA genes, PSII dimers from two strains, each expressing only one psbA gene (psbA2 or psbA3), were crystallized, and we analyzed their structures at resolutions comparable to previously studied PsbA1-PSII. Our results showed that the hydrogen bond between pheophytin/D1 (PheoD1) and D1-130 became stronger in PsbA2- and PsbA3-PSII due to change of Gln to Glu, which partially explains the increase in the redox potential of PheoD1 observed in PsbA3. In PsbA2, one hydrogen bond was lost in PheoD1 due to the change of D1-Y147F, which may explain the decrease in stability of PheoD1 in PsbA2. Two water molecules in the Cl-1 channel were lost in PsbA2 due to the change of D1-P173M, leading to the narrowing of the channel, which may explain the lower efficiency of the S-state transition beyond S2 in PsbA2-PSII. In PsbA3-PSII, a hydrogen bond between D1-Ser270 and a sulfoquinovosyl-diacylglycerol molecule near QB disappeared due to the change of D1-Ser270 in PsbA1 and PsbA2 to D1-Ala270. This may result in an easier exchange of bound QB with free plastoquinone, hence an enhancement of oxygen evolution in PsbA3-PSII due to its high QB exchange efficiency. These results provide a structural basis for further functional examination of the three PsbA variants.
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Affiliation(s)
- Yoshiki Nakajima
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, Japan
| | - Natsumi Ugai-Amo
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Naoki Tone
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Akiko Nakagawa
- Proteo-Science Research Center, Ehime University, Matsuyama, Japan
| | - Masako Iwai
- Graduate School and College of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Masahiko Ikeuchi
- Graduate School and College of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Miwa Sugiura
- Proteo-Science Research Center, Ehime University, Matsuyama, Japan
| | - Michihiro Suga
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, Japan,Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan,For correspondence: Michihiro Suga; Jian-Ren Shen
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, Japan,Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan,For correspondence: Michihiro Suga; Jian-Ren Shen
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11
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Effects of Hypoxia Stress on Growth, Root Respiration, and Metabolism of Phyllostachys praecox. Life (Basel) 2022; 12:life12060808. [PMID: 35743839 PMCID: PMC9224615 DOI: 10.3390/life12060808] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 05/24/2022] [Indexed: 11/22/2022] Open
Abstract
Hypoxia affects plant growth, hormone content, various enzyme activities, cell structure, peroxide production, and metabolic level, therefore reducing crop yield. This study assessed the physiological, biochemical, and metabolic characteristics of Phyllostachys praecox. Results revealed that hypoxia stress treatment significantly inhibited plant growth. Leaf chlorophyll contents was initially improved and then reduced with plant growth time. Under hypoxia stress, the root activity significantly was reduced, leading to the decrease in the nutrient absorption and transport. Yet, with low oxygen concentration, the contents of ethanol, acetaldehyde, and lactic acid were improved. With hypoxia stress, phospholipids and amino acids were the main metabolites of Phyllostachys praecox. Glycosphospholipid metabolism is the key pathway in responding to hypoxia stress significantly (p < 0.05), and lysophosphatidlycholine (lysoPC) and phosphatidylcholines (PC) in the metabolites of this metabolic pathway were significantly enhanced. Our study reveals the mechanism of Phyllostachys praecox cell membrane responding to hypoxia stress based on molecular level. This is conducive to finding targeted solutions to improve the productivity of Phyllostachys praecox to better optimize a mulching approach in the bamboo forest.
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12
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Alterations of Content and Composition of Individual Sulfolipids, and Change of Fatty Acids Profile of Galactolipids in Lettuce Plants (Lactuca sativa L.) Grown under Sulfur Nutrition. PLANTS 2022; 11:plants11101342. [PMID: 35631767 PMCID: PMC9145530 DOI: 10.3390/plants11101342] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 12/03/2022]
Abstract
Alterations of chloroplast membrane lipids might serve as indicators of eco-physiologically induced and plant nutrition-induced changes during plant growth. The change in the degree of fatty acid saturation in the membranes is in particular a strategy of plants to adapt to abiotic stress conditions. Green multi-leaf lettuce plants (Lactuca sativa L.) were subjected to three different sulfur (S) levels. Sulfoquinovosyl diacylglycerol derivatives (SQDG) might be affected by S nutrition. Therefore, the present study was conducted to investigate the impact of S fertilization on the content and composition of individual SQDG. In addition to a change in the SQDG composition, a general change in the total lipid composition of the chloroplast membrane was observed. A significant increase in total SQDG content and doubling of the galactolipid content and significant alterations of individual SQDG were observed at elevated levels of S fertilization. High levels of S supply demonstrated a clear trend of increasing total chloroplast lipid content and concentrations of linolenic acid, in addition to a further decline in palmitic acid. The study opens perspectives on S supply and its crucial role in the build-up of photosynthetic apparatus. Moreover, it emphasizes the role of S-containing compounds, including sulfolipids, in modulating physiological adjustment mechanisms to improve tolerance ability to various abiotic stresses in plants and, consequently, plant food quality.
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13
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Yoshihara A, Kobayashi K. Lipids in photosynthetic protein complexes in the thylakoid membrane of plants, algae, and cyanobacteria. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2735-2750. [PMID: 35560200 DOI: 10.1093/jxb/erac017] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/27/2022] [Indexed: 06/15/2023]
Abstract
In the thylakoid membrane of cyanobacteria and chloroplasts, many proteins involved in photosynthesis are associated with or integrated into the fluid bilayer matrix formed by four unique glycerolipid classes, monogalactosyldiacylglycerol, digalactosyldiacylglycerol, sulfoquinovosyldiacylglycerol, and phosphatidylglycerol. Biochemical and molecular genetic studies have revealed that these glycerolipids play essential roles not only in the formation of thylakoid lipid bilayers but also in the assembly and functions of photosynthetic complexes. Moreover, considerable advances in structural biology have identified a number of lipid molecules within the photosynthetic complexes such as PSI and PSII. These data have provided important insights into the association of lipids with protein subunits in photosynthetic complexes and the distribution of lipids in the thylakoid membrane. Here, we summarize recent high-resolution observations of lipid molecules in the structures of photosynthetic complexes from plants, algae, and cyanobacteria, and evaluate the distribution of lipids among photosynthetic protein complexes and thylakoid lipid bilayers. By integrating the structural information into the findings from biochemical and molecular genetic studies, we highlight the conserved and differentiated roles of lipids in the assembly and functions of photosynthetic complexes among plants, algae, and cyanobacteria.
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Affiliation(s)
- Akiko Yoshihara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, OsakaJapan
| | - Koichi Kobayashi
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, OsakaJapan
- Faculty of Liberal Arts and Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, OsakaJapan
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14
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Aguilera A, Berdun F, Bartoli C, Steelheart C, Alegre M, Bayir H, Tyurina YY, Kagan VE, Salerno G, Pagnussat G, Martin MV. C-ferroptosis is an iron-dependent form of regulated cell death in cyanobacteria. J Cell Biol 2022; 221:212878. [PMID: 34817556 PMCID: PMC8624678 DOI: 10.1083/jcb.201911005] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 09/29/2021] [Accepted: 11/05/2021] [Indexed: 12/30/2022] Open
Abstract
Ferroptosis is an oxidative and iron-dependent form of regulated cell death (RCD) recently described in eukaryotic organisms like animals, plants, and parasites. Here, we report that a similar process takes place in the photosynthetic prokaryote Synechocystis sp. PCC 6803 in response to heat stress. After a heat shock, Synechocystis sp. PCC 6803 cells undergo a cell death pathway that can be suppressed by the canonical ferroptosis inhibitors, CPX, vitamin E, Fer-1, liproxstatin-1, glutathione (GSH), or ascorbic acid (AsA). Moreover, as described for eukaryotic ferroptosis, this pathway is characterized by an early depletion of the antioxidants GSH and AsA, and by lipid peroxidation. These results indicate that all of the hallmarks described for eukaryotic ferroptosis are conserved in photosynthetic prokaryotes and suggest that ferroptosis might be an ancient cell death program.
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Affiliation(s)
- Anabella Aguilera
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET), Fundación para Investigaciones Biológicas Aplicadas (CIB-FIBA), Mar del Plata, Argentina
| | - Federico Berdun
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET), Fundación para Investigaciones Biológicas Aplicadas (CIB-FIBA), Mar del Plata, Argentina
| | - Carlos Bartoli
- Instituto de Fisiología Vegetal (INFIVE), Facultades de Ciencias Agrarias y Forestales y de Ciencias Naturales y Museo, Universidad Nacional de La Plata, CCT-CONICET La Plata, La Plata, Argentina
| | - Charlotte Steelheart
- Instituto de Fisiología Vegetal (INFIVE), Facultades de Ciencias Agrarias y Forestales y de Ciencias Naturales y Museo, Universidad Nacional de La Plata, CCT-CONICET La Plata, La Plata, Argentina
| | - Matías Alegre
- Instituto de Fisiología Vegetal (INFIVE), Facultades de Ciencias Agrarias y Forestales y de Ciencias Naturales y Museo, Universidad Nacional de La Plata, CCT-CONICET La Plata, La Plata, Argentina
| | - Hülya Bayir
- Department of Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA.,Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA.,Children's Neuroscience Institute, University of Pittsburgh, Pittsburgh, PA.,Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA.,Departments of Environmental and Occupational Health, Chemistry, Pharmacology and Chemical Biology, Radiation Oncology, University of Pittsburgh, Pittsburgh, PA
| | - Yulia Y Tyurina
- Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA.,Departments of Environmental and Occupational Health, Chemistry, Pharmacology and Chemical Biology, Radiation Oncology, University of Pittsburgh, Pittsburgh, PA
| | - Valerian E Kagan
- Children's Neuroscience Institute, University of Pittsburgh, Pittsburgh, PA.,Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA.,Departments of Environmental and Occupational Health, Chemistry, Pharmacology and Chemical Biology, Radiation Oncology, University of Pittsburgh, Pittsburgh, PA.,Institute for Regenerative Medicine, IM Sechenov Moscow State Medical University, Moscow, Russia
| | - Graciela Salerno
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET), Fundación para Investigaciones Biológicas Aplicadas (CIB-FIBA), Mar del Plata, Argentina
| | - Gabriela Pagnussat
- Instituto de investigaciones Biológicas IIB-CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - María Victoria Martin
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET), Fundación para Investigaciones Biológicas Aplicadas (CIB-FIBA), Mar del Plata, Argentina
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15
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Snow AJD, Burchill L, Sharma M, Davies GJ, Williams SJ. Sulfoglycolysis: catabolic pathways for metabolism of sulfoquinovose. Chem Soc Rev 2021; 50:13628-13645. [PMID: 34816844 DOI: 10.1039/d1cs00846c] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Sulfoquinovose (SQ), a derivative of glucose with a C6-sulfonate, is produced by photosynthetic organisms and is the headgroup of the sulfolipid sulfoquinovosyl diacylglycerol. The degradation of SQ allows recycling of its elemental constituents and is important in the global sulfur and carbon biogeochemical cycles. Degradation of SQ by bacteria is achieved through a range of pathways that fall into two main groups. One group involves scission of the 6-carbon skeleton of SQ into two fragments with metabolic utilization of carbons 1-3 and excretion of carbons 4-6 as dihydroxypropanesulfonate or sulfolactate that is biomineralized to sulfite/sulfate by other members of the microbial community. The other involves the complete metabolism of SQ by desulfonylation involving cleavage of the C-S bond to release sulfite and glucose, the latter of which can enter glycolysis. The discovery of sulfoglycolytic pathways has revealed a wide range of novel enzymes and SQ binding proteins. Biochemical and structural characterization of the proteins and enzymes in these pathways have illuminated how the sulfonate group is recognized by Nature's catalysts, supporting bioinformatic annotation of sulfoglycolytic enzymes, and has identified functional and structural relationships with the pathways of glycolysis.
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Affiliation(s)
- Alexander J D Snow
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, UK.
| | - Laura Burchill
- School of Chemistry, University of Melbourne, Parkville, Victoria 3010, Australia. .,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Mahima Sharma
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, UK.
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, UK.
| | - Spencer J Williams
- School of Chemistry, University of Melbourne, Parkville, Victoria 3010, Australia. .,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
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16
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Lesser MP. Eutrophication on Coral Reefs: What Is the Evidence for Phase Shifts, Nutrient Limitation and Coral Bleaching. Bioscience 2021. [DOI: 10.1093/biosci/biab101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Coral reefs continue to experience extreme environmental pressure from climate change stressors, but many coral reefs are also exposed to eutrophication. It has been proposed that changes in the stoichiometry of ambient nutrients increase the mortality of corals, whereas eutrophication may facilitate phase shifts to macroalgae-dominated coral reefs when herbivory is low or absent. But are corals ever nutrient limited, and can eutrophication destabilize the coral symbiosis making it more sensitive to environmental stress because of climate change? The effects of eutrophication are confounded not just by the effects of climate change but by the presence of chemical pollutants in industrial, urban, and agricultural wastes. Because of these confounding effects, the increases in nutrients or changes in their stoichiometry in coastal environments, although they are important at the organismal and community level, cannot currently be disentangled from each other or from the more significant effects of climate change stressors on coral reefs.
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Affiliation(s)
- Michael P Lesser
- University of New Hampshire, Durham, New Hampshire, United States
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17
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Li M, Ma J, Li X, Sui SF. In situ cryo-ET structure of phycobilisome-photosystem II supercomplex from red alga. eLife 2021; 10:e69635. [PMID: 34515634 PMCID: PMC8437437 DOI: 10.7554/elife.69635] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/19/2021] [Indexed: 11/13/2022] Open
Abstract
Phycobilisome (PBS) is the main light-harvesting antenna in cyanobacteria and red algae. How PBS transfers the light energy to photosystem II (PSII) remains to be elucidated. Here we report the in situ structure of the PBS-PSII supercomplex from Porphyridium purpureum UTEX 2757 using cryo-electron tomography and subtomogram averaging. Our work reveals the organized network of hemiellipsoidal PBS with PSII on the thylakoid membrane in the native cellular environment. In the PBS-PSII supercomplex, each PBS interacts with six PSII monomers, of which four directly bind to the PBS, and two bind indirectly. Additional three 'connector' proteins also contribute to the connections between PBS and PSIIs. Two PsbO subunits from adjacent PSII dimers bind with each other, which may promote stabilization of the PBS-PSII supercomplex. By analyzing the interaction interface between PBS and PSII, we reveal that αLCM and ApcD connect with CP43 of PSII monomer and that αLCM also interacts with CP47' of the neighboring PSII monomer, suggesting the multiple light energy delivery pathways. The in situ structures illustrate the coupling pattern of PBS and PSII and the arrangement of the PBS-PSII supercomplex on the thylakoid, providing the near-native 3D structural information of the various energy transfer from PBS to PSII.
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Affiliation(s)
- Meijing Li
- Key Laboratory for Protein Sciences of Ministry of Education, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua UniversityBeijingChina
| | - Jianfei Ma
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua UniversityBeijingChina
| | - Xueming Li
- Key Laboratory for Protein Sciences of Ministry of Education, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua UniversityBeijingChina
| | - Sen-Fang Sui
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua UniversityBeijingChina
- Department of Biology, Southern University of Science and TechnologyGuangdongChina
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18
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Graça AT, Hall M, Persson K, Schröder WP. High-resolution model of Arabidopsis Photosystem II reveals the structural consequences of digitonin-extraction. Sci Rep 2021; 11:15534. [PMID: 34330992 PMCID: PMC8324835 DOI: 10.1038/s41598-021-94914-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/19/2021] [Indexed: 11/25/2022] Open
Abstract
In higher plants, the photosynthetic process is performed and regulated by Photosystem II (PSII). Arabidopsis thaliana was the first higher plant with a fully sequenced genome, conferring it the status of a model organism; nonetheless, a high-resolution structure of its Photosystem II is missing. We present the first Cryo-EM high-resolution structure of Arabidopsis PSII supercomplex with average resolution of 2.79 Å, an important model for future PSII studies. The digitonin extracted PSII complexes demonstrate the importance of: the LHG2630-lipid-headgroup in the trimerization of the light-harvesting complex II; the stabilization of the PsbJ subunit and the CP43-loop E by DGD520-lipid; the choice of detergent for the integrity of membrane protein complexes. Furthermore, our data shows at the anticipated Mn4CaO5-site a single metal ion density as a reminiscent early stage of Photosystem II photoactivation.
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Affiliation(s)
- André T Graça
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
| | - Michael Hall
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
| | - Karina Persson
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
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19
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Yu H, Hamaguchi T, Nakajima Y, Kato K, Kawakami K, Akita F, Yonekura K, Shen JR. Cryo-EM structure of monomeric photosystem II at 2.78 Å resolution reveals factors important for the formation of dimer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148471. [PMID: 34216574 DOI: 10.1016/j.bbabio.2021.148471] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/18/2021] [Accepted: 06/26/2021] [Indexed: 11/29/2022]
Abstract
Photosystem II (PSII) functions mainly as a dimer to catalyze the light energy conversion and water oxidation reactions. However, monomeric PSII also exists and functions in vivo in some cases. The crystal structure of monomeric PSII has been solved at 3.6 Å resolution, but it is still not clear which factors contribute to the formation of the dimer. Here, we solved the structure of PSII monomer at a resolution of 2.78 Å using cryo-electron microscopy (cryo-EM). From our cryo-EM density map, we observed apparent differences in pigments and lipids in the monomer-monomer interface between the PSII monomer and dimer. One β-carotene and two sulfoquinovosyl diacylglycerol (SQDG) molecules are found in the monomer-monomer interface of the dimer structure but not in the present monomer structure, although some SQDG and other lipid molecules are found in the analogous region of the low-resolution crystal structure of the monomer, or cryo-EM structure of an apo-PSII monomer lacking the extrinsic proteins from Synechocystis sp. PCC 6803. In the current monomer structure, a large part of the PsbO subunit was also found to be disordered. These results indicate the importance of the β-carotene, SQDG and PsbO in formation of the PSII dimer.
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Affiliation(s)
- Huaxin Yu
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan; Department of Picobiology, Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Tasuku Hamaguchi
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshiki Nakajima
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan
| | - Koji Kato
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan
| | - Keisuke Kawakami
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Fusamichi Akita
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan; Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
| | - Koji Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan; Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan; Advanced Electron Microscope Development Unit, RIKEN-JEOL Collaboration Center, RIKEN Baton Zone Program, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan.
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20
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Wang J, Yu LJ, Wang W, Yan Q, Kuang T, Qin X, Shen JR. Structure of plant photosystem I-light harvesting complex I supercomplex at 2.4 Å resolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1367-1381. [PMID: 33788400 DOI: 10.1111/jipb.13095] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/14/2021] [Indexed: 05/19/2023]
Abstract
Photosystem I (PSI) is one of the two photosystems in photosynthesis, and performs a series of electron transfer reactions leading to the reduction of ferredoxin. In higher plants, PSI is surrounded by four light-harvesting complex I (LHCI) subunits, which harvest and transfer energy efficiently to the PSI core. The crystal structure of PSI-LHCI supercomplex has been analyzed up to 2.6 Å resolution, providing much information on the arrangement of proteins and cofactors in this complicated supercomplex. Here we have optimized crystallization conditions, and analyzed the crystal structure of PSI-LHCI at 2.4 Å resolution. Our structure showed some shift of the LHCI, especially the Lhca4 subunit, away from the PSI core, suggesting the indirect connection and inefficiency of energy transfer from this Lhca subunit to the PSI core. We identified five new lipids in the structure, most of them are located in the gap region between the Lhca subunits and the PSI core. These lipid molecules may play important roles in binding of the Lhca subunits to the core, as well as in the assembly of the supercomplex. The present results thus provide novel information for the elucidation of the mechanisms for the light-energy harvesting, transfer and assembly of this supercomplex.
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Affiliation(s)
- Jie Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Long-Jiang Yu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wenda Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Qiujing Yan
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tingyun Kuang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiaochun Qin
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Jian-Ren Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
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21
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Yoshihara A, Nagata N, Wada H, Kobayashi K. Plastid Anionic Lipids Are Essential for the Development of Both Photosynthetic and Non-Photosynthetic Organs in Arabidopsis thaliana. Int J Mol Sci 2021; 22:4860. [PMID: 34064353 PMCID: PMC8124801 DOI: 10.3390/ijms22094860] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/01/2021] [Accepted: 05/02/2021] [Indexed: 01/03/2023] Open
Abstract
The lipid bilayer matrix of the thylakoid membrane of cyanobacteria and chloroplasts of plants and algae is mainly composed of uncharged galactolipids, but also contains anionic lipids sulfoquinovosyldiacylglycerol (SQDG) and phosphatidylglycerol (PG) as major constituents. The necessity of PG for photosynthesis is evident in all photosynthetic organisms examined to date, whereas the requirement of SQDG varies with species. In plants, although PG and SQDG are also found in non-photosynthetic plastids, their importance for the growth and functions of non-photosynthetic organs remains unclear. In addition, plants synthesize another anionic lipid glucuronosyldiacylglycerol (GlcADG) during phosphorus starvation, but its role in plant cells is not elucidated yet. To understand the functional relationships among PG, SQDG, and GlcADG, we characterized several Arabidopsis thaliana mutants defective in biosynthesis of these lipids. The mutants completely lacking both PG and SQDG biosynthesis in plastids showed developmental defects of roots, hypocotyls, and embryos in addition to leaves, which suggests that these lipids are pleiotropically required for the development of both photosynthetic and non-photosynthetic organs. Furthermore, our analysis revealed that SQDG, but not GlcADG, is essential for complementing the role of PG, particularly in photosynthesis under PG-deficient conditions such as phosphorus starvation.
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Affiliation(s)
- Akiko Yoshihara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuencho, Naka-ku, Sakai 599-8531, Japan;
| | - Noriko Nagata
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women’s University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo 112-8681, Japan;
| | - Hajime Wada
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan;
| | - Koichi Kobayashi
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuencho, Naka-ku, Sakai 599-8531, Japan;
- Faculty of Liberal Arts and Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
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22
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Zhang X, Wu C, Hu C, Li Y, Sun X, Xu N. Lipid remodeling associated with chitooligosaccharides-induced heat tolerance of marine macroalgae Gracilariopsis lemaneiformis. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.102113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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23
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Li J, Liu LN, Meng Q, Fan H, Sui N. The roles of chloroplast membrane lipids in abiotic stress responses. PLANT SIGNALING & BEHAVIOR 2020; 15:1807152. [PMID: 32815751 PMCID: PMC7588187 DOI: 10.1080/15592324.2020.1807152] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 05/11/2023]
Abstract
Plant chloroplasts have complex membrane systems. Among these, thylakoids serve as the sites for photosynthesis and photosynthesis-related adaptation. In addition to the photosynthetic membrane complexes and associated molecules, lipids in the thylakoid membranes, are predominantly composed of MGDG (monogalactosyldiacylglycerol), DGDG (digalactosyldiacylglycerol), SQDG (sulfoquinovosyldiacylglycerol) and PG (phosphatidylglycerol), play essential roles in shaping the thylakoid architecture, electron transfer, and photoregulation. In this review, we discuss the effect of abiotic stress on chloroplast structure, the changes in membrane lipid composition, and the degree of unsaturation of fatty acids. Advanced understanding of the mechanisms regulating chloroplast membrane lipids and unsaturated fatty acids in response to abiotic stresses is indispensable for improving plant resistance and may inform the strategies of crop breeding.
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Affiliation(s)
- Jinlu Li
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Lu-Ning Liu
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Qingwei Meng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Hai Fan
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Na Sui
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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Müh F, Zouni A. Structural basis of light-harvesting in the photosystem II core complex. Protein Sci 2020; 29:1090-1119. [PMID: 32067287 PMCID: PMC7184784 DOI: 10.1002/pro.3841] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 02/06/2020] [Accepted: 02/06/2020] [Indexed: 12/20/2022]
Abstract
Photosystem II (PSII) is a membrane-spanning, multi-subunit pigment-protein complex responsible for the oxidation of water and the reduction of plastoquinone in oxygenic photosynthesis. In the present review, the recent explosive increase in available structural information about the PSII core complex based on X-ray crystallography and cryo-electron microscopy is described at a level of detail that is suitable for a future structure-based analysis of light-harvesting processes. This description includes a proposal for a consistent numbering scheme of protein-bound pigment cofactors across species. The structural survey is complemented by an overview of the state of affairs in structure-based modeling of excitation energy transfer in the PSII core complex with emphasis on electrostatic computations, optical properties of the reaction center, the assignment of long-wavelength chlorophylls, and energy trapping mechanisms.
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Affiliation(s)
- Frank Müh
- Department of Theoretical Biophysics, Institute for Theoretical Physics, Johannes Kepler University Linz, Linz, Austria
| | - Athina Zouni
- Humboldt-Universität zu Berlin, Institute for Biology, Biophysics of Photosynthesis, Berlin, Germany
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Structural insights into NDH-1 mediated cyclic electron transfer. Nat Commun 2020; 11:888. [PMID: 32060291 PMCID: PMC7021789 DOI: 10.1038/s41467-020-14732-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 01/21/2020] [Indexed: 02/08/2023] Open
Abstract
NDH-1 is a key component of the cyclic-electron-transfer around photosystem I (PSI CET) pathway, an important antioxidant mechanism for efficient photosynthesis. Here, we report a 3.2-Å-resolution cryo-EM structure of the ferredoxin (Fd)-NDH-1L complex from the cyanobacterium Thermosynechococcus elongatus. The structure reveals three β-carotene and fifteen lipid molecules in the membrane arm of NDH-1L. Regulatory oxygenic photosynthesis-specific (OPS) subunits NdhV, NdhS and NdhO are close to the Fd-binding site whilst NdhL is adjacent to the plastoquinone (PQ) cavity, and they play different roles in PSI CET under high-light stress. NdhV assists in the binding of Fd to NDH-1L and accelerates PSI CET in response to short-term high-light exposure. In contrast, prolonged high-light irradiation switches on the expression and assembly of the NDH-1MS complex, which likely contains no NdhO to further accelerate PSI CET and reduce ROS production. We propose that this hierarchical mechanism is necessary for the survival of cyanobacteria in an aerobic environment. NDH-1 is a key component of the cyclic-electron-transfer around photosystem I pathway, an antioxidant mechanism for efficient photosynthesis. Here, authors report a cryo-EM structure of the ferredoxin (Fd)-NDH-1L complex from the cyanobacterium Thermosynechococcus elongatus.
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