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Eckardt NA, Allahverdiyeva Y, Alvarez CE, Büchel C, Burlacot A, Cardona T, Chaloner E, Engel BD, Grossman AR, Harris D, Herrmann N, Hodges M, Kern J, Kim TD, Maurino VG, Mullineaux CW, Mustila H, Nikkanen L, Schlau-Cohen G, Tronconi MA, Wietrzynski W, Yachandra VK, Yano J. Lighting the way: Compelling open questions in photosynthesis research. THE PLANT CELL 2024; 36:3914-3943. [PMID: 39038210 PMCID: PMC11449116 DOI: 10.1093/plcell/koae203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 05/29/2024] [Accepted: 07/15/2024] [Indexed: 07/24/2024]
Abstract
Photosynthesis-the conversion of energy from sunlight into chemical energy-is essential for life on Earth. Yet there is much we do not understand about photosynthetic energy conversion on a fundamental level: how it evolved and the extent of its diversity, its dynamics, and all the components and connections involved in its regulation. In this commentary, researchers working on fundamental aspects of photosynthesis including the light-dependent reactions, photorespiration, and C4 photosynthetic metabolism pose and discuss what they view as the most compelling open questions in their areas of research.
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Affiliation(s)
| | - Yagut Allahverdiyeva
- Molecular Plant Biology Unit, Department of Life Technologies, University of Turku, 20014 Turku, Finland
| | - Clarisa E Alvarez
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacuticas, University of Rosario, Suipacha 570, 2000 Rosario, Argentina
| | - Claudia Büchel
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Adrien Burlacot
- Division of Bioscience and Engineering, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Tanai Cardona
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Emma Chaloner
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Benjamin D Engel
- Biozentrum, University of Basel, Sptialstrasse 41, 4056 Basel, Switzerland
| | - Arthur R Grossman
- Division of Bioscience and Engineering, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Dvir Harris
- Department of Chemistry, Massachusetts Institute of Technology, Massachusetts Ave, Cambridge, MA 02139, USA
| | - Nicolas Herrmann
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Michael Hodges
- Université Paris-Saclay, CNRS, INRAE, Université d’Evry, Université de Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tom Dongmin Kim
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Veronica G Maurino
- Molecular Plant Physiology, Institute for Cellular and Molecular Botany (IZMB), University of Bonn, Kirschallee 1, 53115 Bonn, Germany
| | - Conrad W Mullineaux
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Henna Mustila
- Molecular Plant Biology Unit, Department of Life Technologies, University of Turku, 20014 Turku, Finland
| | - Lauri Nikkanen
- Molecular Plant Biology Unit, Department of Life Technologies, University of Turku, 20014 Turku, Finland
| | - Gabriela Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, Massachusetts Ave, Cambridge, MA 02139, USA
| | - Marcos A Tronconi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacuticas, University of Rosario, Suipacha 570, 2000 Rosario, Argentina
| | | | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Fedorin DN, Eprintsev AT, Igamberdiev AU. The role of promoter methylation of the genes encoding the enzymes metabolizing di- and tricarboxylic acids in the regulation of plant respiration by light. JOURNAL OF PLANT PHYSIOLOGY 2024; 294:154195. [PMID: 38377939 DOI: 10.1016/j.jplph.2024.154195] [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: 11/23/2023] [Revised: 02/04/2024] [Accepted: 02/12/2024] [Indexed: 02/22/2024]
Abstract
We discuss the role of epigenetic changes at the level of promoter methylation of the key enzymes of carbon metabolism in the regulation of respiration by light. While the direct regulation of enzymes via modulation of their activity and post-translational modifications is fast and readily reversible, the role of cytosine methylation is important for providing a prolonged response to environmental changes. In addition, adenine methylation can play a role in the regulation of transcription of genes. The mitochondrial and extramitochondrial forms of several enzymes participating in the tricarboxylic acid cycle and associated reactions are regulated via promoter methylation in opposite ways. The mitochondrial forms of citrate synthase, aconitase, fumarase, NAD-malate dehydrogenase are inhibited while the cytosolic forms of aconitase, fumarase, NAD-malate dehydrogenase, and the peroxisomal form of citrate synthase are activated. It is concluded that promoter methylation represents a universal mechanism of the regulation of activity of respiratory enzymes in plant cells by light. The role of the regulation of the mitochondrial and cytosolic forms of respiratory enzymes in the operation of malate and citrate valves and in controlling the redox state and balancing the energy level of photosynthesizing plant cells is discussed.
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Affiliation(s)
- Dmitry N Fedorin
- Department of Biochemistry and Cell Physiology, Voronezh State University, 394018, Voronezh, Russia.
| | - Alexander T Eprintsev
- Department of Biochemistry and Cell Physiology, Voronezh State University, 394018, Voronezh, Russia.
| | - Abir U Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada.
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Zhao W, Li J, Sun X, Zheng Q, Liu J, Hua W, Liu J. Integrated global analysis in spider flowers illuminates features underlying the evolution and maintenance of C 4 photosynthesis. HORTICULTURE RESEARCH 2023; 10:uhad129. [PMID: 37560018 PMCID: PMC10407600 DOI: 10.1093/hr/uhad129] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 06/11/2023] [Indexed: 08/11/2023]
Abstract
The carbon concentrating mechanism-C4 photosynthesis-represents a classic example of convergent evolution, but how this important trait originated and evolved remains largely enigmatic. The spider flower Gynandropsis gynandra is a valuable leafy vegetable crop and medicinal plant that has also been recognized as a C4 model species. Here we present a high-quality chromosome-scale annotated genome assembly of G. gynandra through a combination of Oxford Nanopore Technology (ONT), HiFi and Hi-C technology. The 17 super-scaffolds cover 98.66% of the estimated genome (997.61 Mb), with a contig N50 of 11.43 Mb and a scaffold N50 of 51.02 Mb. Repetitive elements occupy up to 71.91% of its genome, and over half are long terminal repeat retrotransposons (LTR-RTs) derived from recent bursts, contributing to genome size expansion. Strikingly, LTR-RT explosion also played a critical role in C4 evolution by altering expression features of photosynthesis-associated genes via preferential insertion in promoters. Integrated multiomics analyses of G. gynandra and the ornamental horticulture C3 relative Tarenaya hassleriana reveal that species-specific whole-genome duplication, gene family expansion, recent LTR-RT amplification, and more recent tandem duplication events have all facilitated the evolution of C4 photosynthesis, revealing uniqueness of C4 evolution in the Cleome genus. Moreover, high leaf vein density and heat stress resilience are associated with shifted gene expression patterns. The mode of C3-to-C4 transition found here yields new insights into evolutionary convergence of a complex plant trait. The availability of this reference-grade genomic resource makes G. gynandra an ideal model system facilitating efforts toward C4-aimed crop engineering.
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Affiliation(s)
- Wei Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jun Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Xingchao Sun
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Qiwei Zheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jing Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Wei Hua
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jun Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
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Igamberdiev AU, Bykova NV. Mitochondria in photosynthetic cells: Coordinating redox control and energy balance. PLANT PHYSIOLOGY 2023; 191:2104-2119. [PMID: 36440979 PMCID: PMC10069911 DOI: 10.1093/plphys/kiac541] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 05/21/2023]
Abstract
In photosynthetic tissues in the light, the function of energy production is associated primarily with chloroplasts, while mitochondrial metabolism adjusts to balance ATP supply, regulate the reduction level of pyridine nucleotides, and optimize major metabolic fluxes. The tricarboxylic acid cycle in the light transforms into a noncyclic open structure (hemicycle) maintained primarily by the influx of malate and the export of citrate to the cytosol. The exchange of malate and citrate forms the basis of feeding redox energy from the chloroplast into the cytosolic pathways. This supports the level of NADPH in different compartments, contributes to the biosynthesis of amino acids, and drives secondary metabolism via a supply of substrates for 2-oxoglutarate-dependent dioxygenase and for cytochrome P450-catalyzed monooxygenase reactions. This results in the maintenance of redox and energy balance in photosynthetic plant cells and in the formation of numerous bioactive compounds specific to any particular plant species. The noncoupled mitochondrial respiration operates in coordination with the malate and citrate valves and supports intensive fluxes of respiration and photorespiration. The metabolic system of plants has features associated with the remarkable metabolic plasticity of mitochondria that permit the use of energy accumulated during photosynthesis in a way that all anabolic and catabolic pathways become optimized and coordinated.
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Le XH, Lee CP, Monachello D, Millar AH. Metabolic evidence for distinct pyruvate pools inside plant mitochondria. NATURE PLANTS 2022; 8:694-705. [PMID: 35681019 DOI: 10.1038/s41477-022-01165-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
The majority of the pyruvate inside plant mitochondria is either transported into the matrix from the cytosol via the mitochondria pyruvate carrier (MPC) or synthesized in the matrix by alanine aminotransferase (AlaAT) or NAD-malic enzyme (NAD-ME). Pyruvate from these origins could mix into a single pool in the matrix and contribute indistinguishably to respiration via the pyruvate dehydrogenase complex (PDC), or these molecules could maintain a degree of independence in metabolic regulation. Here we demonstrate that feeding isolated mitochondria with uniformly labelled 13C-pyruvate and unlabelled malate enables the assessment of pyruvate contribution from different sources to intermediate production in the tricarboxylic acid cycle. Imported pyruvate was the preferred source for citrate production even when the synthesis of NAD-ME-derived pyruvate was optimized. Genetic or pharmacological elimination of MPC activity removed this preference and allowed an equivalent amount of citrate to be generated from the pyruvate produced by NAD-ME. Increasing the mitochondrial pyruvate pool size by exogenous addition affected only metabolites from pyruvate transported by MPC, whereas depleting the pyruvate pool size by transamination to alanine affected only metabolic products derived from NAD-ME. PDC was more membrane-associated than AlaAT and NAD-ME, suggesting that the physical organization of metabolic machinery may influence metabolic rates. Together, these data reveal that the respiratory substrate supply in plants involves distinct pyruvate pools inside the matrix that can be flexibly mixed on the basis of the rate of pyruvate transport from the cytosol. These pools are independently regulated and contribute differentially to organic acid export from plant mitochondria.
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Affiliation(s)
- Xuyen H Le
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, Australia
| | - Chun Pong Lee
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, Australia
| | - Dario Monachello
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - A Harvey Millar
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia.
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, Australia.
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