1
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Vinyard DJ, Govindjee G. Bicarbonate is a key regulator but not a substrate for O 2 evolution in Photosystem II. PHOTOSYNTHESIS RESEARCH 2024:10.1007/s11120-024-01111-8. [PMID: 39037690 DOI: 10.1007/s11120-024-01111-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 07/11/2024] [Indexed: 07/23/2024]
Abstract
Photosystem II (PSII) uses light energy to oxidize water and to reduce plastoquinone in the photosynthetic electron transport chain. O2 is produced as a byproduct. While most members of the PSII research community agree that O2 originates from water molecules, alternative hypotheses involving bicarbonate persist in the literature. In this perspective, we provide an overview of the important roles of bicarbonate in regulating PSII activity and assembly. Further, we emphasize that biochemistry, spectroscopy, and structural biology experiments have all failed to detect bicarbonate near the active site of O2 evolution. While thermodynamic arguments for oxygen-centered bicarbonate oxidation are valid, the claim that bicarbonate is a substrate for photosynthetic O2 evolution is challenged.
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Affiliation(s)
- David J Vinyard
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
| | - Govindjee Govindjee
- Department of Biochemistry, Department of Plant Biology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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2
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Hussein R, Graça A, Forsman J, Aydin AO, Hall M, Gaetcke J, Chernev P, Wendler P, Dobbek H, Messinger J, Zouni A, Schröder WP. Cryo-electron microscopy reveals hydrogen positions and water networks in photosystem II. Science 2024; 384:1349-1355. [PMID: 38900892 DOI: 10.1126/science.adn6541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 05/16/2024] [Indexed: 06/22/2024]
Abstract
Photosystem II starts the photosynthetic electron transport chain that converts solar energy into chemical energy and thus sustains life on Earth. It catalyzes two chemical reactions: water oxidation to molecular oxygen and plastoquinone reduction. Coupling of electron and proton transfer is crucial for efficiency; however, the molecular basis of these processes remains speculative owing to uncertain water binding sites and the lack of experimentally determined hydrogen positions. We thus collected high-resolution cryo-electron microscopy data of fully hydrated photosystem II from the thermophilic cyanobacterium Thermosynechococcus vestitus to a final resolution of 1.71 angstroms. The structure reveals several previously undetected partially occupied water binding sites and more than half of the hydrogen and proton positions. This clarifies the pathways of substrate water binding and plastoquinone B protonation.
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Affiliation(s)
- Rana Hussein
- Humboldt-Universität zu Berlin, Department of Biology, D 10099 Berlin, Germany
| | - André Graça
- Department of Chemistry, Umeå University, SE 90187 Umeå, Sweden
- Molecular Biomimetics, Department of Chemistry- Ångström Laboratory, Uppsala University, SE 75120 Uppsala, Sweden
| | - Jack Forsman
- Department of Chemistry, Umeå University, SE 90187 Umeå, Sweden
| | - A Orkun Aydin
- Molecular Biomimetics, Department of Chemistry- Ångström Laboratory, Uppsala University, SE 75120 Uppsala, Sweden
| | - Michael Hall
- Department of Chemistry, Umeå University, SE 90187 Umeå, Sweden
| | - Julia Gaetcke
- Humboldt-Universität zu Berlin, Department of Biology, D 10099 Berlin, Germany
| | - Petko Chernev
- Molecular Biomimetics, Department of Chemistry- Ångström Laboratory, Uppsala University, SE 75120 Uppsala, Sweden
| | - Petra Wendler
- Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, Karl-Liebknecht Strasse 24-25, D 14476, Potsdam-Golm, Germany
| | - Holger Dobbek
- Humboldt-Universität zu Berlin, Department of Biology, D 10099 Berlin, Germany
| | - Johannes Messinger
- Molecular Biomimetics, Department of Chemistry- Ångström Laboratory, Uppsala University, SE 75120 Uppsala, Sweden
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Sweden
| | - Athina Zouni
- Humboldt-Universität zu Berlin, Department of Biology, D 10099 Berlin, Germany
| | - Wolfgang P Schröder
- Department of Chemistry, Umeå University, SE 90187 Umeå, Sweden
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Sweden
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3
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Lilay GH, Thiébaut N, du Mee D, Assunção AGL, Schjoerring JK, Husted S, Persson DP. Linking the key physiological functions of essential micronutrients to their deficiency symptoms in plants. THE NEW PHYTOLOGIST 2024; 242:881-902. [PMID: 38433319 DOI: 10.1111/nph.19645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/12/2024] [Indexed: 03/05/2024]
Abstract
In this review, we untangle the physiological key functions of the essential micronutrients and link them to the deficiency responses in plants. Knowledge of these responses at the mechanistic level, and the resulting deficiency symptoms, have improved over the last decade and it appears timely to review recent insights for each of them. A proper understanding of the links between function and symptom is indispensable for an accurate and timely identification of nutritional disorders, thereby informing the design and development of sustainable fertilization strategies. Similarly, improved knowledge of the molecular and physiological functions of micronutrients will be important for breeding programmes aiming to develop new crop genotypes with improved nutrient-use efficiency and resilience in the face of changing soil and climate conditions.
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Affiliation(s)
- Grmay Hailu Lilay
- Plant and Soil Science Section, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Noémie Thiébaut
- Plant and Soil Science Section, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
- Earth and Life Institute, Faculty of Bioscience Engineering, Université Catholique de Louvain, Louvain-la-Neuve, 1348, Belgium
| | - Dorine du Mee
- Plant and Soil Science Section, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Ana G L Assunção
- CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Portugal
| | - Jan Kofod Schjoerring
- Plant and Soil Science Section, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Søren Husted
- Plant and Soil Science Section, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Daniel Pergament Persson
- Plant and Soil Science Section, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
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4
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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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5
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Shevela D, Kern JF, Govindjee G, Messinger J. Solar energy conversion by photosystem II: principles and structures. PHOTOSYNTHESIS RESEARCH 2023; 156:279-307. [PMID: 36826741 PMCID: PMC10203033 DOI: 10.1007/s11120-022-00991-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/01/2022] [Indexed: 05/23/2023]
Abstract
Photosynthetic water oxidation by Photosystem II (PSII) is a fascinating process because it sustains life on Earth and serves as a blue print for scalable synthetic catalysts required for renewable energy applications. The biophysical, computational, and structural description of this process, which started more than 50 years ago, has made tremendous progress over the past two decades, with its high-resolution crystal structures being available not only of the dark-stable state of PSII, but of all the semi-stable reaction intermediates and even some transient states. Here, we summarize the current knowledge on PSII with emphasis on the basic principles that govern the conversion of light energy to chemical energy in PSII, as well as on the illustration of the molecular structures that enable these reactions. The important remaining questions regarding the mechanism of biological water oxidation are highlighted, and one possible pathway for this fundamental reaction is described at a molecular level.
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Affiliation(s)
- Dmitry Shevela
- Department of Chemistry, Chemical Biological Centre, Umeå University, 90187, Umeå, Sweden.
| | - Jan F Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Govindjee Govindjee
- Department of Plant Biology, Department of Biochemistry and Center of Biophysics & Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Johannes Messinger
- Department of Chemistry, Chemical Biological Centre, Umeå University, 90187, Umeå, Sweden.
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, 75120, Uppsala, Sweden.
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6
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Lee S, Lee J, Zhai H, Tong Y, Dalzell AM, Kumar A, Helms P, Gray J, Cui ZH, Liu W, Kastoryano M, Babbush R, Preskill J, Reichman DR, Campbell ET, Valeev EF, Lin L, Chan GKL. Evaluating the evidence for exponential quantum advantage in ground-state quantum chemistry. Nat Commun 2023; 14:1952. [PMID: 37029105 PMCID: PMC10082187 DOI: 10.1038/s41467-023-37587-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/22/2023] [Indexed: 04/09/2023] Open
Abstract
Due to intense interest in the potential applications of quantum computing, it is critical to understand the basis for potential exponential quantum advantage in quantum chemistry. Here we gather the evidence for this case in the most common task in quantum chemistry, namely, ground-state energy estimation, for generic chemical problems where heuristic quantum state preparation might be assumed to be efficient. The availability of exponential quantum advantage then centers on whether features of the physical problem that enable efficient heuristic quantum state preparation also enable efficient solution by classical heuristics. Through numerical studies of quantum state preparation and empirical complexity analysis (including the error scaling) of classical heuristics, in both ab initio and model Hamiltonian settings, we conclude that evidence for such an exponential advantage across chemical space has yet to be found. While quantum computers may still prove useful for ground-state quantum chemistry through polynomial speedups, it may be prudent to assume exponential speedups are not generically available for this problem.
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Affiliation(s)
- Seunghoon Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Joonho Lee
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Huanchen Zhai
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Yu Tong
- Department of Mathematics, University of California, Berkeley, CA, 94720, USA
| | | | - Ashutosh Kumar
- Department of Chemistry, Virginia Tech, Blacksburg, VA, 24061, USA
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Phillip Helms
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Johnnie Gray
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Zhi-Hao Cui
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Wenyuan Liu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Michael Kastoryano
- AWS Center for Quantum Computing, Pasadena, CA, 91125, USA
- Amazon Quantum Solutions Lab, Seattle, WA, 98170, USA
| | - Ryan Babbush
- Google Quantum AI, 340 Main Street, Venice, CA, 90291, USA
| | - John Preskill
- AWS Center for Quantum Computing, Pasadena, CA, 91125, USA
- Institute for Quantum Information and Matter, California Institute of Technology, Pasadena, CA, 91125, USA
| | - David R Reichman
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | | | - Edward F Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Lin Lin
- Department of Mathematics, University of California, Berkeley, CA, 94720, USA
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Garnet Kin-Lic Chan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
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7
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Castell C, Díaz-Santos E, Heredia-Martínez LG, López-Maury L, Ortega JM, Navarro JA, Roncel M, Hervás M. Iron Deficiency Promotes the Lack of Photosynthetic Cytochrome c550 and Affects the Binding of the Luminal Extrinsic Subunits to Photosystem II in the Diatom Phaeodactylum tricornutum. Int J Mol Sci 2022; 23:ijms232012138. [PMID: 36292994 PMCID: PMC9603157 DOI: 10.3390/ijms232012138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/06/2022] [Accepted: 10/08/2022] [Indexed: 12/04/2022] Open
Abstract
In the diatom Phaeodactylum tricornutum, iron limitation promotes a decrease in the content of photosystem II, as determined by measurements of oxygen-evolving activity, thermoluminescence, chlorophyll fluorescence analyses and protein quantification methods. Thermoluminescence experiments also indicate that iron limitation induces subtle changes in the energetics of the recombination reaction between reduced QB and the S2/S3 states of the water-splitting machinery. However, electron transfer from QA to QB, involving non-heme iron, seems not to be significantly inhibited. Moreover, iron deficiency promotes a severe decrease in the content of the extrinsic PsbV/cytochrome c550 subunit of photosystem II, which appears in eukaryotic algae from the red photosynthetic lineage (including diatoms) but is absent in green algae and plants. The decline in the content of cytochrome c550 under iron-limiting conditions is accompanied by a decrease in the binding of this protein to photosystem II, and also of the extrinsic PsbO subunit. We propose that the lack of cytochrome c550, induced by iron deficiency, specifically affects the binding of other extrinsic subunits of photosystem II, as previously described in cyanobacterial PsbV mutants.
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8
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Yilimulati M, Zhou L, Shevela D, Zhang S. Acetylacetone Interferes with Carbon and Nitrogen Metabolism of Microcystis aeruginosa by Cutting Off the Electron Flow to Ferredoxin. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:9683-9692. [PMID: 35696645 DOI: 10.1021/acs.est.2c00776] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The regulation of photosynthetic machinery with a nonoxidative approach is a powerful but challenging strategy for the selective inhibition of bloom-forming cyanobacteria. Acetylacetone (AA) was recently found to be a target-selective cyanocide for Microcystis aeruginosa, but the cause and effect in the studied system are still unclear. By recording of the chemical fingerprints of the cells at two treatment intervals (12 and 72 h with 0.1 mM AA) with omics assays, the molecular mechanism of AA in inactivating Microcystis aeruginosa was elucidated. The results clearly reveal the effect of AA on ferredoxin and the consequent effects on the physiological and biochemical processes of Microcystis aeruginosa. In addition to its role as an electron acceptor of photosystem I, ferredoxin plays pivotal roles in the assimilation of nitrogen in cyanobacterial cells. The effect of AA on ferredoxin and on nonheme iron of photosystem II first cut off the photosynthetic electron transfer flow and then interrupted the synthesis of adenosine triphosphate (ATP) and reduced nicotinamide adenine dinucleotide phosphate (NADPH), which ultimately might affect carbon fixation and nitrogen assimilation metabolisms. The results here provide missing pieces in the current knowledge on the selective inhibition of cyanobacteria, which should shed light on the better control of harmful blooms.
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Affiliation(s)
- Mihebai Yilimulati
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, People's Republic of China
| | - Lang Zhou
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, People's Republic of China
| | - Dmitry Shevela
- Department of Chemistry, Chemical Biological Centre, Umeå University, 90187 Umeå, Sweden
| | - Shujuan Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, People's Republic of China
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9
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Kato Y, Noguchi T. Redox properties and regulatory mechanism of the iron-quinone electron acceptor in photosystem II as revealed by FTIR spectroelectrochemistry. PHOTOSYNTHESIS RESEARCH 2022; 152:135-151. [PMID: 34985636 DOI: 10.1007/s11120-021-00894-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/24/2021] [Indexed: 05/09/2023]
Abstract
Photosystem II (PSII) performs oxidation of water and reduction of plastoquinone through light-induced electron transfer. Electron transfer reactions at individual redox cofactors are controlled by their redox potentials, and the forward and backward electron flows in PSII are regulated by tuning them. It is, thus, crucial to accurately estimate the redox potentials of the cofactors and their shifts by environmental changes to understand the regulatory mechanisms in PSII. Fourier-transform infrared (FTIR) spectroelectrochemistry combined with a light-induced difference technique is a powerful method to investigate the mechanisms of the redox reactions in PSII. In this review, we introduce the methodology and the application of this method in the studies of the iron-quinone complex, which consists of two plastoquinone molecules, QA and QB, and the non-heme iron, on the electron-acceptor side of PSII. It is shown that FTIR spectroelectrochemistry is a useful method not only for estimating the redox potentials but also for detecting the reactions of nearby amino-acid residues coupled with the redox reactions.
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Affiliation(s)
- Yuki Kato
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.
| | - Takumi Noguchi
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.
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10
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Solymosi D, Shevela D, Allahverdiyeva Y. Nitric oxide represses photosystem II and NDH-1 in the cyanobacterium Synechocystis sp. PCC 6803. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148507. [PMID: 34728155 DOI: 10.1016/j.bbabio.2021.148507] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022]
Abstract
Photosynthetic electron transfer comprises a series of light-induced redox reactions catalysed by multiprotein machinery in the thylakoid. These protein complexes possess cofactors susceptible to redox modifications by reactive small molecules. The gaseous radical nitric oxide (NO), a key signalling molecule in green algae and plants, has earlier been shown to bind to Photosystem (PS) II and obstruct electron transfer in plants. The effects of NO on cyanobacterial bioenergetics however, have long remained obscure. In this study, we exposed the model cyanobacterium Synechocystis sp. PCC 6803 to NO under anoxic conditions and followed changes in whole-cell fluorescence and oxidoreduction of P700 in vivo. Our results demonstrate that NO blocks photosynthetic electron transfer in cells by repressing PSII, PSI, and likely the NDH dehydrogenase-like complex 1 (NDH-1). We propose that iron‑sulfur clusters of NDH-1 complex may be affected by NO to such an extent that ferredoxin-derived electron injection to the plastoquinone pool, and thus cyclic electron transfer, may be inhibited. These findings reveal the profound effects of NO on Synechocystis cells and demonstrate the importance of controlled NO homeostasis in cyanobacteria.
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Affiliation(s)
- Daniel Solymosi
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, FI 20014, Finland
| | - Dmitry Shevela
- Chemical Biological Centre, Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Yagut Allahverdiyeva
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, FI 20014, Finland.
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11
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Gisriel CJ, Shen G, Ho MY, Kurashov V, Flesher DA, Wang J, Armstrong WH, Golbeck JH, Gunner MR, Vinyard DJ, Debus RJ, Brudvig GW, Bryant DA. 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. [PMID: 34801554 PMCID: PMC8689208 DOI: 10.1016/j.jbc.2021.101424] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/12/2021] [Accepted: 11/13/2021] [Indexed: 11/26/2022] Open
Abstract
Far-red light (FRL) photoacclimation in cyanobacteria provides a selective growth advantage for some terrestrial cyanobacteria by expanding the range of photosynthetically active radiation to include far-red/near-infrared light (700-800 nm). During this photoacclimation process, photosystem II (PSII), the water:plastoquinone photooxidoreductase involved in oxygenic photosynthesis, is modified. The resulting FRL-PSII is comprised of FRL-specific core subunits and binds chlorophyll (Chl) d and Chl f molecules in place of several of the Chl a molecules found when cells are grown in visible light. These new Chls effectively lower the energy canonically thought to define the "red limit" for light required to drive photochemical catalysis of water oxidation. Changes to the architecture of FRL-PSII were previously unknown, and the positions of Chl d and Chl f molecules had only been proposed from indirect evidence. Here, we describe the 2.25 Å resolution cryo-EM structure of a monomeric FRL-PSII core complex from Synechococcus sp. PCC 7335 cells that were acclimated to FRL. We identify one Chl d molecule in the ChlD1 position of the electron transfer chain and four Chl f molecules in the core antenna. We also make observations that enhance our understanding of PSII biogenesis, especially on the acceptor side of the complex where a bicarbonate molecule is replaced by a glutamate side chain in the absence of the assembly factor Psb28. In conclusion, these results provide a structural basis for the lower energy limit required to drive water oxidation, which is the gateway for most solar energy utilization on earth.
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Affiliation(s)
| | - Gaozhong Shen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ming-Yang Ho
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; Intercollege Graduate Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Vasily Kurashov
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - David A Flesher
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | | | - John H Golbeck
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Marilyn R Gunner
- Department of Physics, City College of New York, New York, New York, USA
| | - David J Vinyard
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Richard J Debus
- Department of Biochemistry, University of California, Riverside, California, USA
| | - Gary W Brudvig
- Department of Chemistry, Yale University, New Haven, Connecticut, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; Intercollege Graduate Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania, USA.
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12
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Yilimulati M, Jin J, Wang X, Wang X, Shevela D, Wu B, Wang K, Zhou L, Jia Y, Pan B, Govindjee G, Zhang S. Regulation of Photosynthesis in Bloom-Forming Cyanobacteria with the Simplest β-Diketone. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:14173-14184. [PMID: 34590827 DOI: 10.1021/acs.est.1c04683] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Selective inhibition of photosynthesis is a fundamental strategy to solve the global challenge caused by harmful cyanobacterial blooms. However, there is a lack of specificity of the currently used cyanocides, because most of them act on cyanobacteria by generating nontargeted oxidative stress. Here, for the first time, we find that the simplest β-diketone, acetylacetone, is a promising specific cyanocide, which acts on Microcystis aeruginosa through targeted binding on bound iron species in the photosynthetic electron transport chain, rather than by oxidizing the components of the photosynthetic apparatus. The targeted binding approach outperforms the general oxidation mechanism in terms of specificity and eco-safety. Given the essential role of photosynthesis in both natural and artificial systems, this finding not only provides a unique solution for the selective control of cyanobacteria but also sheds new light on the ways to modulate photosynthesis.
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Affiliation(s)
- Mihebai Yilimulati
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jiyuan Jin
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, People's Republic of China
| | - Xin Wang
- School of Life Science, Nanjing University, Nanjing 210023, People's Republic of China
| | - Xiaomeng Wang
- Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Dmitry Shevela
- Department of Chemistry, Chemical Biological Centre, Umeå University, 90187 Umeå, Sweden
| | - Bing Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, People's Republic of China
| | - Kai Wang
- Hansha Scientific Instruments Limited, Tai'an 271099, People's Republic of China
| | - Lang Zhou
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, People's Republic of China
| | - Yunlu Jia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, People's Republic of China
| | - Bingcai Pan
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, People's Republic of China
| | - Govindjee Govindjee
- Department of Biochemistry, Department of Plant Biology, and the Center of Biophysics & Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shujuan Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, People's Republic of China
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13
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Photoprotection during iron deficiency is mediated by the bHLH transcription factors PYE and ILR3. Proc Natl Acad Sci U S A 2021; 118:2024918118. [PMID: 34580211 DOI: 10.1073/pnas.2024918118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 02/06/2023] Open
Abstract
Iron (Fe) is an essential micronutrient whose availability is limiting in many soils. During Fe deficiency, plants alter the expression of many genes to increase Fe uptake, distribution, and utilization. In a genetic screen for suppressors of Fe sensitivity in the E3 ligase mutant bts-3, we isolated an allele of the bHLH transcription factor (TF) ILR3, ilr3-4 We identified a striking leaf bleaching phenotype in ilr3 mutants that was suppressed by limiting light intensity, indicating that ILR3 is required for phototolerance during Fe deficiency. Among its paralogs that are thought to be partially redundant, only ILR3 was required for phototolerance as well as repression of genes under Fe deficiency. A mutation in the gene-encoding PYE, a known transcriptional repressor under Fe deficiency, also caused leaf bleaching. We identified singlet oxygen as the accumulating reactive oxygen species (ROS) in ilr3-4 and pye, suggesting photosensitivity is due to a PSII defect resulting in ROS production. During Fe deficiency, ilr3-4 and pye chloroplasts retain normal ultrastructure and, unlike wild type (WT), contain stacked grana similar to Fe-sufficient plants. Additionally, we found that the D1 subunit of PSII is destabilized in WT during Fe deficiency but not in ilr3-4 and pye, suggesting that PSII repair is accelerated during Fe deficiency in an ILR3- and PYE-dependent manner. Collectively, our results indicate that ILR3 and PYE confer photoprotection during Fe deficiency to prevent the accumulation of singlet oxygen, potentially by promoting reduction of grana stacking to limit excitation and facilitate repair of the photosynthetic machinery.
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14
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Azmani K, Besora M, Soriano-López J, Landolsi M, Teillout AL, de Oliveira P, Mbomekallé IM, Poblet JM, Galán-Mascarós JR. Understanding polyoxometalates as water oxidation catalysts through iron vs. cobalt reactivity. Chem Sci 2021; 12:8755-8766. [PMID: 34257875 PMCID: PMC8246111 DOI: 10.1039/d1sc01016f] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 05/13/2021] [Indexed: 01/08/2023] Open
Abstract
Cobalt polyoxometalates (Co-POMs) have emerged as promising water oxidation catalysts (WOCs), with the added advantage of their molecular nature despite being metal oxide fragments. In comparison with metal oxides, that do not offer well-defined active surfaces, POMs have a controlled, discrete structure that allows for precise correlations between experiment and computational analyses. Thus, beyond highly active WOCs, POMs are also model systems to gain deeper mechanistic understanding on the oxygen evolution reaction (OER). The tetracobalt Weakley sandwich [CoII 4(H2O)2(B-α-PW9O34)2]10- (Co4-WS) has been one of the most extensively studied. We have compared its activity with that of the iron analog [FeIII 4(H2O)2(B-α-PW9O34)2]6- (Fe4-WS) looking for the electronic effects determining their activity. Furthermore, the effect of POM nuclearity was also investigated by comparison with the iron- and cobalt-monosubstituted Keggin clusters. Electrocatalytic experiments employing solid state electrodes containing the POMs and the corresponding computational calculations demonstrate that CoII-POMs display better WOC activity than the FeIII derivatives. Moreover, the activity of POMs is less influenced by their nuclearity, thus Weakley sandwich moieties show slightly improved WOC characteristics than Keggin clusters. In good agreement with the experimental data, computational methods, including pK a values, confirm that the resting state for Fe-POMs in neutral media corresponds to the S1 (FeIII-OH) species. Overall, the proposed reaction mechanism for Fe4-WS is analogous to that found for Co4-WS, despite their electronic differences. The potential limiting step is a proton-coupled electron transfer event yielding the active S2 (FeIV[double bond, length as m-dash]O) species, which receives a water nucleophilic attack to form the O-O bond. The latter has activation energies slightly higher than those computed for the Co-POMs, in good agreement with experimental observations. These results provide new insights for the accurate understanding of the structure-reactivity relationships of polyoxometalates in particular, and or metal oxides in general, which are of utmost importance for the development of new bottom-up synthetic approaches to design efficient, robust and non-expensive earth-abundant water oxidation catalysts.
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Affiliation(s)
- Khalid Azmani
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology (BIST) Av. Països Catalans, 16 Tarragona E-43007 Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili Marcel·lí Domingo 1 E-43007 Tarragona Spain
| | - Maria Besora
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili Marcel·lí Domingo 1 E-43007 Tarragona Spain
| | - Joaquín Soriano-López
- School of Chemistry & AMBER Center, Trinity College, University of Dublin Dublin D02 PN40 Ireland
| | - Meriem Landolsi
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili Marcel·lí Domingo 1 E-43007 Tarragona Spain
| | - Anne-Lucie Teillout
- Equipe d'Electrochimie et de Photo-électrochimie, Institut de Chimie Physique, UMR 8000, CNRS, Université Paris Saclay Orsay F-91405 France
| | - Pedro de Oliveira
- Equipe d'Electrochimie et de Photo-électrochimie, Institut de Chimie Physique, UMR 8000, CNRS, Université Paris Saclay Orsay F-91405 France
| | - Israël-Martyr Mbomekallé
- Equipe d'Electrochimie et de Photo-électrochimie, Institut de Chimie Physique, UMR 8000, CNRS, Université Paris Saclay Orsay F-91405 France
| | - Josep M Poblet
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili Marcel·lí Domingo 1 E-43007 Tarragona Spain
| | - José-Ramón Galán-Mascarós
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology (BIST) Av. Països Catalans, 16 Tarragona E-43007 Spain
- ICREA, Pg. Lluís Companys 23 08010 Barcelona Spain
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15
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Kato Y, Watanabe H, Noguchi T. ATR-FTIR Spectroelectrochemical Study on the Mechanism of the pH Dependence of the Redox Potential of the Non-Heme Iron in Photosystem II. Biochemistry 2021; 60:2170-2178. [PMID: 34181388 DOI: 10.1021/acs.biochem.1c00341] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The non-heme iron that bridges the two plastoquinone electron acceptors, QA and QB, in photosystem II (PSII) is known to have a redox potential (Em) of ∼+400 mV with a pH dependence of ∼-60 mV/pH. However, titratable amino acid residues that are coupled to the redox reaction of the non-heme ion and responsible for its pH dependence remain unidentified. In this study, to clarify the mechanism of the pH dependent change of Em(Fe2+/Fe3+), we investigated the protonation structures of amino acid residues correlated with the pH-induced Em(Fe2+/Fe3+) changes using Fourier transform infrared (FTIR) spectroelectrochemistry combined with the attenuated total reflection (ATR) and light-induced difference techniques. Flash-induced Fe2+/Fe3+ ATR-FTIR difference spectra obtained at different electrode potentials in the pH range of 5.0-8.5 showed a linear pH dependence of Em(Fe2+/Fe3+) with a slope of -52 mV/pH close to the theoretical value at 10 °C, the measurement temperature. The spectral features revealed that D1-H215, a ligand to the non-heme iron interacting with QB, was deprotonated to an imidazolate anion at higher pH with a pKa of ∼5.6 in the Fe3+ state, while carboxylate groups from Glu/Asp residues present on the stromal side of PSII were protonated at lower pH with a pKa of ∼5.7 in the Fe2+ state. It is thus concluded that the deprotonation/protonation reactions of D1-H215 and Glu/Asp residues located near the non-heme iron cause the pH-dependent changes in Em(Fe2+/Fe3+) at higher and lower pH regions, respectively, realizing a linear pH dependence over a wide pH range.
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Affiliation(s)
- Yuki Kato
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Hiroki Watanabe
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Takumi Noguchi
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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16
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Ghosh I, Banerjee G, Reiss K, Kim CJ, Debus RJ, Batista VS, Brudvig GW. D1-S169A substitution of photosystem II reveals a novel S 2-state structure. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148301. [PMID: 32860756 DOI: 10.1016/j.bbabio.2020.148301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 08/18/2020] [Accepted: 08/22/2020] [Indexed: 10/23/2022]
Abstract
In photosystem II (PSII), photosynthetic water oxidation occurs at the O2-evolving complex (OEC), a tetramanganese-calcium cluster that cycles through light-induced redox intermediates (S0-S4) to produce oxygen from two substrate water molecules. The OEC is surrounded by a hydrogen-bonded network of amino-acid residues that plays a crucial role in proton transfer and substrate water delivery. Previously, we found that D1-S169 was crucial for water oxidation and its mutation to alanine perturbed the hydrogen-bonding network. In this study, we demonstrate that the activation energy for the S2 to S1 transition of D1-S169A PSII is higher than wild-type PSII with a ~1.7-2.7× slower rate of charge recombination with QA- relative to wild-type PSII. Arrhenius analysis of the decay kinetics shows an Ea of 5.87 ± 1.15 kcal mol-1 for decay back to the S1 state, compared to 0.80 ± 0.13 kcal mol-1 for the wild-type S2 state. In addition, we find that ammonia does not affect the S2-state EPR signal, indicating that ammonia does not bind to the Mn cluster in D1-S169A PSII. Finally, a QM/MM analysis indicates that an additional water molecule binds to the Mn4 ion in place of an oxo ligand O5 in the S2 state of D1-S169A PSII. The altered S2 state of D1-S169A PSII provides insight into the S2➔S3 state transition.
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Affiliation(s)
- Ipsita Ghosh
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
| | - Gourab Banerjee
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
| | - Krystle Reiss
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
| | - Christopher J Kim
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Richard J Debus
- Department of Biochemistry, University of California, Riverside, CA 92521, USA.
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
| | - Gary W Brudvig
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA.
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17
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Kimura M, Kato Y, Noguchi T. Protonation State of a Key Histidine Ligand in the Iron–Quinone Complex of Photosystem II as Revealed by Light-Induced ATR-FTIR Spectroscopy. Biochemistry 2020; 59:4336-4343. [DOI: 10.1021/acs.biochem.0c00810] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Masakazu Kimura
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Yuki Kato
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Takumi Noguchi
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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18
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Kumar A, Neese F, Valeev EF. Explicitly correlated coupled cluster method for accurate treatment of open-shell molecules with hundreds of atoms. J Chem Phys 2020; 153:094105. [PMID: 32891102 DOI: 10.1063/5.0012753] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a near-linear scaling formulation of the explicitly correlated coupled-cluster singles and doubles with the perturbative triples method [CCSD(T)F12¯] for high-spin states of open-shell species. The approach is based on the conventional open-shell CCSD formalism [M. Saitow et al., J. Chem. Phys. 146, 164105 (2017)] utilizing the domain local pair-natural orbitals (DLPNO) framework. The use of spin-independent set of pair-natural orbitals ensures exact agreement with the closed-shell formalism reported previously, with only marginally impact on the cost (e.g., the open-shell formalism is only 1.5 times slower than the closed-shell counterpart for the C160H322 n-alkane, with the measured size complexity of ≈1.2). Evaluation of coupled-cluster energies near the complete-basis-set (CBS) limit for open-shell systems with more than 550 atoms and 5000 basis functions is feasible on a single multi-core computer in less than 3 days. The aug-cc-pVTZ DLPNO-CCSD(T)F12¯ contribution to the heat of formation for the 50 largest molecules among the 348 core combustion species benchmark set [J. Klippenstein et al., J. Phys. Chem. A 121, 6580-6602 (2017)] had root-mean-square deviation (RMSD) from the extrapolated CBS CCSD(T) reference values of 0.3 kcal/mol. For a more challenging set of 50 reactions involving small closed- and open-shell molecules [G. Knizia et al., J. Chem. Phys. 130, 054104 (2009)], the aug-cc-pVQ(+d)Z DLPNO-CCSD(T)F12¯ yielded a RMSD of ∼0.4 kcal/mol with respect to the CBS CCSD(T) estimate.
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Affiliation(s)
- Ashutosh Kumar
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Edward F Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
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19
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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: 31] [Impact Index Per Article: 7.8] [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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20
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Banerjee G, Ghosh I, Kim CJ, Debus RJ, Brudvig GW. Bicarbonate rescues damaged proton-transfer pathway in photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:611-617. [DOI: 10.1016/j.bbabio.2019.06.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/18/2019] [Accepted: 06/21/2019] [Indexed: 01/04/2023]
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21
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Schulz CE, Dutta AK, Izsák R, Pantazis DA. Systematic High-Accuracy Prediction of Electron Affinities for Biological Quinones. J Comput Chem 2018; 39:2439-2451. [PMID: 30281169 DOI: 10.1002/jcc.25570] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 08/06/2018] [Accepted: 08/07/2018] [Indexed: 11/07/2022]
Abstract
Quinones play vital roles as electron carriers in fundamental biological processes; therefore, the ability to accurately predict their electron affinities is crucial for understanding their properties and function. The increasing availability of cost-effective implementations of correlated wave function methods for both closed-shell and open-shell systems offers an alternative to density functional theory approaches that have traditionally dominated the field despite their shortcomings. Here, we define a benchmark set of quinones with experimentally available electron affinities and evaluate a range of electronic structure methods, setting a target accuracy of 0.1 eV. Among wave function methods, we test various implementations of coupled cluster (CC) theory, including local pair natural orbital (LPNO) approaches to canonical and parameterized CCSD, the domain-based DLPNO approximation, and the equations-of-motion approach for electron affinities, EA-EOM-CCSD. In addition, several variants of canonical, spin-component-scaled, orbital-optimized, and explicitly correlated (F12) Møller-Plesset perturbation theory are benchmarked. Achieving systematically the target level of accuracy is challenging and a composite scheme that combines canonical CCSD(T) with large basis set LPNO-based extrapolation of correlation energy proves to be the most accurate approach. Methods that offer comparable performance are the parameterized LPNO-pCCSD, the DLPNO-CCSD(T0 ), and the orbital optimized OO-SCS-MP2. Among DFT methods, viable practical alternatives are only the M06 and the double hybrids, but the latter should be employed with caution because of significant basis set sensitivity. A highly accurate yet cost-effective DLPNO-based coupled cluster approach is used to investigate the methoxy conformation effect on the electron affinities of ubiquinones found in photosynthetic bacterial reaction centers. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Christine E Schulz
- Fakultät für Chemie und Biochemie, Ruhr-Universität Bochum, 44780, Bochum, Germany
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Achintya Kumar Dutta
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Róbert Izsák
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
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22
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Saitow M, Becker U, Riplinger C, Valeev EF, Neese F. A new near-linear scaling, efficient and accurate, open-shell domain-based local pair natural orbital coupled cluster singles and doubles theory. J Chem Phys 2018; 146:164105. [PMID: 28456208 DOI: 10.1063/1.4981521] [Citation(s) in RCA: 242] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The Coupled-Cluster expansion, truncated after single and double excitations (CCSD), provides accurate and reliable molecular electronic wave functions and energies for many molecular systems around their equilibrium geometries. However, the high computational cost, which is well-known to scale as O(N6) with system size N, has limited its practical application to small systems consisting of not more than approximately 20-30 atoms. To overcome these limitations, low-order scaling approximations to CCSD have been intensively investigated over the past few years. In our previous work, we have shown that by combining the pair natural orbital (PNO) approach and the concept of orbital domains it is possible to achieve fully linear scaling CC implementations (DLPNO-CCSD and DLPNO-CCSD(T)) that recover around 99.9% of the total correlation energy [C. Riplinger et al., J. Chem. Phys. 144, 024109 (2016)]. The production level implementations of the DLPNO-CCSD and DLPNO-CCSD(T) methods were shown to be applicable to realistic systems composed of a few hundred atoms in a routine, black-box fashion on relatively modest hardware. In 2011, a reduced-scaling CCSD approach for high-spin open-shell unrestricted Hartree-Fock reference wave functions was proposed (UHF-LPNO-CCSD) [A. Hansen et al., J. Chem. Phys. 135, 214102 (2011)]. After a few years of experience with this method, a few shortcomings of UHF-LPNO-CCSD were noticed that required a redesign of the method, which is the subject of this paper. To this end, we employ the high-spin open-shell variant of the N-electron valence perturbation theory formalism to define the initial guess wave function, and consequently also the open-shell PNOs. The new PNO ansatz properly converges to the closed-shell limit since all truncations and approximations have been made in strict analogy to the closed-shell case. Furthermore, given the fact that the formalism uses a single set of orbitals, only a single PNO integral transformation is necessary, which offers large computational savings. We show that, with the default PNO truncation parameters, approximately 99.9% of the total CCSD correlation energy is recovered for open-shell species, which is comparable to the performance of the method for closed-shells. UHF-DLPNO-CCSD shows a linear scaling behavior for closed-shell systems, while linear to quadratic scaling is obtained for open-shell systems. The largest systems we have considered contain more than 500 atoms and feature more than 10 000 basis functions with a triple-ζ quality basis set.
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Affiliation(s)
- Masaaki Saitow
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Ute Becker
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Christoph Riplinger
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Edward F Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Frank Neese
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
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23
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Magyar M, Sipka G, Kovács L, Ughy B, Zhu Q, Han G, Špunda V, Lambrev PH, Shen JR, Garab G. Rate-limiting steps in the dark-to-light transition of Photosystem II - revealed by chlorophyll-a fluorescence induction. Sci Rep 2018; 8:2755. [PMID: 29426901 DOI: 10.1038/s41598-41018-21195-41592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 01/31/2018] [Indexed: 05/28/2023] Open
Abstract
Photosystem II (PSII) catalyses the photoinduced oxygen evolution and, by producing reducing equivalents drives, in concert with PSI, the conversion of carbon dioxide to sugars. Our knowledge about the architecture of the reaction centre (RC) complex and the mechanisms of charge separation and stabilisation is well advanced. However, our understanding of the processes associated with the functioning of RC is incomplete: the photochemical activity of PSII is routinely monitored by chlorophyll-a fluorescence induction but the presently available data are not free of controversy. In this work, we examined the nature of gradual fluorescence rise of PSII elicited by trains of single-turnover saturating flashes (STSFs) in the presence of a PSII inhibitor, permitting only one stable charge separation. We show that a substantial part of the fluorescence rise originates from light-induced processes that occur after the stabilisation of charge separation, induced by the first STSF; the temperature-dependent relaxation characteristics suggest the involvement of conformational changes in the additional rise. In experiments using double flashes with variable waiting times (∆τ) between them, we found that no rise could be induced with zero or short ∆τ, the value of which depended on the temperature - revealing a previously unknown rate-limiting step in PSII.
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Affiliation(s)
- Melinda Magyar
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári körút 62, H-6726, Szeged, Hungary
| | - Gábor Sipka
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári körút 62, H-6726, Szeged, Hungary
| | - László Kovács
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári körút 62, H-6726, Szeged, Hungary
| | - Bettina Ughy
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári körút 62, H-6726, Szeged, Hungary
| | - Qingjun Zhu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany the Chinese Academy of Sciences, Beijing, 100093, China
| | - Guangye Han
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany the Chinese Academy of Sciences, Beijing, 100093, China
| | - Vladimír Špunda
- Department of Physics, Faculty of Science, University of Ostrava, Chittussiho 10, CZ-710 00, Ostrava, Czech Republic
- Global Change Research Institute, Czech Academy of Sciences, Bělidla 986/4a, 603 00, Brno, Czech Republic
| | - Petar H Lambrev
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári körút 62, H-6726, Szeged, Hungary
| | - Jian-Ren Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany the Chinese Academy of Sciences, Beijing, 100093, China
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 1-1, Naka 3-chome, Tsushima, Okayama, 700-8530, Japan
| | - Győző Garab
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári körút 62, H-6726, Szeged, Hungary.
- Department of Physics, Faculty of Science, University of Ostrava, Chittussiho 10, CZ-710 00, Ostrava, Czech Republic.
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Rate-limiting steps in the dark-to-light transition of Photosystem II - revealed by chlorophyll-a fluorescence induction. Sci Rep 2018; 8:2755. [PMID: 29426901 PMCID: PMC5807364 DOI: 10.1038/s41598-018-21195-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 01/31/2018] [Indexed: 12/21/2022] Open
Abstract
Photosystem II (PSII) catalyses the photoinduced oxygen evolution and, by producing reducing equivalents drives, in concert with PSI, the conversion of carbon dioxide to sugars. Our knowledge about the architecture of the reaction centre (RC) complex and the mechanisms of charge separation and stabilisation is well advanced. However, our understanding of the processes associated with the functioning of RC is incomplete: the photochemical activity of PSII is routinely monitored by chlorophyll-a fluorescence induction but the presently available data are not free of controversy. In this work, we examined the nature of gradual fluorescence rise of PSII elicited by trains of single-turnover saturating flashes (STSFs) in the presence of a PSII inhibitor, permitting only one stable charge separation. We show that a substantial part of the fluorescence rise originates from light-induced processes that occur after the stabilisation of charge separation, induced by the first STSF; the temperature-dependent relaxation characteristics suggest the involvement of conformational changes in the additional rise. In experiments using double flashes with variable waiting times (∆τ) between them, we found that no rise could be induced with zero or short ∆τ, the value of which depended on the temperature - revealing a previously unknown rate-limiting step in PSII.
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25
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Adam S, Knapp-Mohammady M, Yi J, Bondar AN. Revised CHARMM force field parameters for iron-containing cofactors of photosystem II. J Comput Chem 2017; 39:7-20. [PMID: 28850168 DOI: 10.1002/jcc.24918] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 07/05/2017] [Accepted: 08/03/2017] [Indexed: 01/25/2023]
Abstract
Photosystem II is a complex protein-cofactor machinery that splits water molecules into molecular oxygen, protons, and electrons. All-atom molecular dynamics simulations have the potential to contribute to our general understanding of how photosystem II works. To perform reliable all-atom simulations, we need accurate force field parameters for the cofactor molecules. We present here CHARMM bonded and non-bonded parameters for the iron-containing cofactors of photosystem II that include a six-coordinated heme moiety coordinated by two histidine groups, and a non-heme iron complex coordinated by bicarbonate and four histidines. The force field parameters presented here give water interaction energies and geometries in good agreement with the quantum mechanical target data. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Suliman Adam
- Theoretical Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, Berlin D-14195, Germany
| | - Michaela Knapp-Mohammady
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 580, Heidelberg D-69120, Germany
| | - Jun Yi
- Department of Biological Engineering, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu Province 210094, China
| | - Ana-Nicoleta Bondar
- Theoretical Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, Berlin D-14195, Germany
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26
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Shlyk O, Samish I, Matěnová M, Dulebo A, Poláková H, Kaftan D, Scherz A. A single residue controls electron transfer gating in photosynthetic reaction centers. Sci Rep 2017; 7:44580. [PMID: 28300167 PMCID: PMC5353731 DOI: 10.1038/srep44580] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/10/2017] [Indexed: 12/31/2022] Open
Abstract
Interquinone QA− → QB electron-transfer (ET) in isolated photosystem II reaction centers (PSII-RC) is protein-gated. The temperature-dependent gating frequency “k” is described by the Eyring equation till levelling off at T ≥ 240 °K. Although central to photosynthesis, the gating mechanism has not been resolved and due to experimental limitations, could not be explored in vivo. Here we mimic the temperature dependency of “k” by enlarging VD1-208, the volume of a single residue at the crossing point of the D1 and D2 PSII-RC subunits in Synechocystis 6803 whole cells. By controlling the interactions of the D1/D2 subunits, VD1-208 (or 1/T) determines the frequency of attaining an ET-active conformation. Decelerated ET, impaired photosynthesis, D1 repair rate and overall cell physiology upon increasing VD1-208 to above 130 Å3, rationalize the >99% conservation of small residues at D1-208 and its homologous motif in non-oxygenic bacteria. The experimental means and resolved mechanism are relevant for numerous transmembrane protein-gated reactions.
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Affiliation(s)
- Oksana Shlyk
- The Weizmann Institute of Science, Department of Plant and Environmental Sciences, 76100 Rehovot, Israel
| | - Ilan Samish
- The Weizmann Institute of Science, Department of Plant and Environmental Sciences, 76100 Rehovot, Israel
| | - Martina Matěnová
- University of South Bohemia in České Budějovice, Faculty of Science, 37005 České Budějovice, Czech Republic
| | - Alexander Dulebo
- University of South Bohemia in České Budějovice, Faculty of Science, 37005 České Budějovice, Czech Republic
| | - Helena Poláková
- University of South Bohemia in České Budějovice, Faculty of Science, 37005 České Budějovice, Czech Republic
| | - David Kaftan
- University of South Bohemia in České Budějovice, Faculty of Science, 37005 České Budějovice, Czech Republic.,Institute of Microbiology CAS, Department of Phototrophic Microorganisms, 37981 Trebon, Czech Republic
| | - Avigdor Scherz
- The Weizmann Institute of Science, Department of Plant and Environmental Sciences, 76100 Rehovot, Israel
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27
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Müh F, Plöckinger M, Renger T. Electrostatic Asymmetry in the Reaction Center of Photosystem II. J Phys Chem Lett 2017; 8:850-858. [PMID: 28151674 DOI: 10.1021/acs.jpclett.6b02823] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The exciton Hamiltonian of the chlorophyll (Chl) and pheophytin (Pheo) pigments in the reaction center (RC) of photosystem II is computed based on recent crystal structures by using the Poisson-Boltzmann/quantum-chemical method. Computed site energies largely confirm a previous model inferred from fits of optical spectra, in which ChlD1 has the lowest site energy, while that of PheoD1 is higher than that of PheoD2. The latter assignment has been challenged recently under reference to mutagenesis experiments. We argue that these data are not in contradiction to our results. We conclude that ChlD1 is the primary electron donor in both isolated RCs and intact core complexes at least at cryogenic temperatures. The main source of asymmetry in site energies is the charge distribution in the protein. Because many small contributions from various structural elements have to be taken into account, it can be assumed that this asymmetry was established in evolution by global optimization of the RC protein.
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Affiliation(s)
- Frank Müh
- Institute of Theoretical Physics, Department of Theoretical Biophysics, Johannes Kepler University Linz , Altenberger Strasse 69, AT-4040 Linz, Austria
| | - Melanie Plöckinger
- Institute of Theoretical Physics, Department of Theoretical Biophysics, Johannes Kepler University Linz , Altenberger Strasse 69, AT-4040 Linz, Austria
| | - Thomas Renger
- Institute of Theoretical Physics, Department of Theoretical Biophysics, Johannes Kepler University Linz , Altenberger Strasse 69, AT-4040 Linz, Austria
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28
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Ananyev G, Gates C, Dismukes GC. The Oxygen quantum yield in diverse algae and cyanobacteria is controlled by partitioning of flux between linear and cyclic electron flow within photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1380-1391. [PMID: 27117512 DOI: 10.1016/j.bbabio.2016.04.056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 04/20/2016] [Accepted: 04/21/2016] [Indexed: 01/07/2023]
Abstract
We have measured flash-induced oxygen quantum yields (O2-QYs) and primary charge separation (Chl variable fluorescence yield, Fv/Fm) in vivo among phylogenetically diverse microalgae and cyanobacteria. Higher O2-QYs can be attained in cells by releasing constraints on charge transfer at the Photosystem II (PSII) acceptor side by adding membrane-permeable benzoquinone (BQ) derivatives that oxidize plastosemiquinone QB(-) and QBH2. This method allows uncoupling PSII turnover from its natural regulation in living cells, without artifacts of isolating PSII complexes. This approach reveals different extents of regulation across species, controlled at the QB(-) acceptor site. Arthrospira maxima is confirmed as the most efficient PSII-WOC (water oxidizing complex) and exhibits the least regulation of flux. Thermosynechococcus elongatus exhibits an O2-QY of 30%, suggesting strong downregulation. WOC cycle simulations with the most accurate model (VZAD) show that a light-driven backward transition (net addition of an electron to the WOC, distinct from recombination) occurs in up to 25% of native PSIIs in the S2 and S3 states, while adding BQ prevents backward transitions and increases the lifetime of S2 and S3 by 10-fold. Backward transitions occur in PSIIs that have plastosemiquinone radicals in the QB site and are postulated to be physiologically regulated pathways for storing light energy as proton gradient through direct PSII-cyclic electron flow (PSII-CEF). PSII-CEF is independent of classical PSI/cyt-b6f-CEF and provides an alternative proton translocation pathway for energy conversion. PSII-CEF enables variable fluxes between linear and cyclic electron pathways, thus accommodating species-dependent needs for redox and ion-gradient energy sources powered by a single photosystem.
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Affiliation(s)
- Gennady Ananyev
- The Waksman Institute of Microbiology and the Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, United States
| | - Colin Gates
- The Waksman Institute of Microbiology and the Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, United States
| | - G Charles Dismukes
- The Waksman Institute of Microbiology and the Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, United States.
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29
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González A, Sevilla E, Bes MT, Peleato ML, Fillat MF. Pivotal Role of Iron in the Regulation of Cyanobacterial Electron Transport. Adv Microb Physiol 2016; 68:169-217. [PMID: 27134024 DOI: 10.1016/bs.ampbs.2016.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Iron-containing metalloproteins are the main cornerstones for efficient electron transport in biological systems. The abundance and diversity of iron-dependent proteins in cyanobacteria makes those organisms highly dependent of this micronutrient. To cope with iron imbalance, cyanobacteria have developed a survey of adaptation strategies that are strongly related to the regulation of photosynthesis, nitrogen metabolism and other central electron transfer pathways. Furthermore, either in its ferrous form or as a component of the haem group, iron plays a crucial role as regulatory signalling molecule that directly or indirectly modulates the composition and efficiency of cyanobacterial redox reactions. We present here the major mechanism used by cyanobacteria to couple iron homeostasis to the regulation of electron transport, making special emphasis in processes specific in those organisms.
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Affiliation(s)
| | - E Sevilla
- University of Zaragoza, Zaragoza, Spain
| | - M T Bes
- University of Zaragoza, Zaragoza, Spain
| | | | - M F Fillat
- University of Zaragoza, Zaragoza, Spain.
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30
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Kato Y, Noguchi T. Long-Range Interaction between the Mn4CaO5 Cluster and the Non-heme Iron Center in Photosystem II as Revealed by FTIR Spectroelectrochemistry. Biochemistry 2014; 53:4914-23. [DOI: 10.1021/bi500549b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Yuki Kato
- Division of Material Science,
Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Takumi Noguchi
- Division of Material Science,
Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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31
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Computer modeling of electron and proton transport in chloroplasts. Biosystems 2014; 121:1-21. [PMID: 24835748 DOI: 10.1016/j.biosystems.2014.04.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 04/27/2014] [Accepted: 04/28/2014] [Indexed: 11/21/2022]
Abstract
Photosynthesis is one of the most important biological processes in biosphere, which provides production of organic substances from atmospheric CO2 and water at expense of solar energy. In this review, we contemplate computer models of oxygenic photosynthesis in the context of feedback regulation of photosynthetic electron transport in chloroplasts, the energy-transducing organelles of the plant cell. We start with a brief overview of electron and proton transport processes in chloroplasts coupled to ATP synthesis and consider basic regulatory mechanisms of oxygenic photosynthesis. General approaches to computer simulation of photosynthetic processes are considered, including the random walk models of plastoquinone diffusion in thylakoid membranes and deterministic approach to modeling electron transport in chloroplasts based on the mass action law. Then we focus on a kinetic model of oxygenic photosynthesis that includes key stages of the linear electron transport, alternative pathways of electron transfer around photosystem I (PSI), transmembrane proton transport and ATP synthesis in chloroplasts. This model includes different regulatory processes: pH-dependent control of the intersystem electron transport, down-regulation of photosystem II (PSII) activity (non-photochemical quenching), the light-induced activation of the Bassham-Benson-Calvin (BBC) cycle. The model correctly describes pH-dependent feedback control of electron transport in chloroplasts and adequately reproduces a variety of experimental data on induction events observed under different experimental conditions in intact chloroplasts (variations of CO2 and O2 concentrations in atmosphere), including a complex kinetics of P700 (primary electron donor in PSI) photooxidation, CO2 consumption in the BBC cycle, and photorespiration. Finally, we describe diffusion-controlled photosynthetic processes in chloroplasts within the framework of the model that takes into account complex architecture of chloroplasts and lateral heterogeneity of lamellar system of thylakoids. The lateral profiles of pH in the thylakoid lumen and in the narrow gap between grana thylakoids have been calculated under different metabolic conditions. Analyzing topological aspects of diffusion-controlled stages of electron and proton transport in chloroplasts, we conclude that along with the NPQ mechanism of attenuation of PSII activity and deceleration of PQH2 oxidation by the cytochrome b6f complex caused by the lumen acidification, the intersystem electron transport may be down-regulated due to the light-induced alkalization of the narrow partition between adjacent thylakoids of grana. The computer models of electron and proton transport described in this article may be integrated as appropriate modules into a comprehensive model of oxygenic photosynthesis.
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32
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Pospíšil P. The Role of Metals in Production and Scavenging of Reactive Oxygen Species in Photosystem II. ACTA ACUST UNITED AC 2014; 55:1224-32. [DOI: 10.1093/pcp/pcu053] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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