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Stirbet A, Lazár D, Guo Y, Govindjee G. Photosynthesis: basics, history and modelling. ANNALS OF BOTANY 2020; 126:511-537. [PMID: 31641747 PMCID: PMC7489092 DOI: 10.1093/aob/mcz171] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/06/2019] [Accepted: 10/21/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND With limited agricultural land and increasing human population, it is essential to enhance overall photosynthesis and thus productivity. Oxygenic photosynthesis begins with light absorption, followed by excitation energy transfer to the reaction centres, primary photochemistry, electron and proton transport, NADPH and ATP synthesis, and then CO2 fixation (Calvin-Benson cycle, as well as Hatch-Slack cycle). Here we cover some of the discoveries related to this process, such as the existence of two light reactions and two photosystems connected by an electron transport 'chain' (the Z-scheme), chemiosmotic hypothesis for ATP synthesis, water oxidation clock for oxygen evolution, steps for carbon fixation, and finally the diverse mechanisms of regulatory processes, such as 'state transitions' and 'non-photochemical quenching' of the excited state of chlorophyll a. SCOPE In this review, we emphasize that mathematical modelling is a highly valuable tool in understanding and making predictions regarding photosynthesis. Different mathematical models have been used to examine current theories on diverse photosynthetic processes; these have been validated through simulation(s) of available experimental data, such as chlorophyll a fluorescence induction, measured with fluorometers using continuous (or modulated) exciting light, and absorbance changes at 820 nm (ΔA820) related to redox changes in P700, the reaction centre of photosystem I. CONCLUSIONS We highlight here the important role of modelling in deciphering and untangling complex photosynthesis processes taking place simultaneously, as well as in predicting possible ways to obtain higher biomass and productivity in plants, algae and cyanobacteria.
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Affiliation(s)
| | - Dušan Lazár
- Department of Biophysics, Center of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Ya Guo
- Key Laboratory of Advanced Process Control for Light Industry (Ministry of Education), Jiangnan University, Wuxi, China
- University of Missouri, Columbia, MO, USA
| | - Govindjee Govindjee
- Department of Biochemistry, Department of Plant Biology, and Center of Biophysics & Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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Magni S, Succurro A, Skupin A, Ebenhöh O. Data-driven dynamical model indicates that the heat shock response in Chlamydomonas reinhardtii is tailored to handle natural temperature variation. J R Soc Interface 2019; 15:rsif.2017.0965. [PMID: 29720454 PMCID: PMC6000179 DOI: 10.1098/rsif.2017.0965] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/06/2018] [Indexed: 12/29/2022] Open
Abstract
Global warming exposes plants to severe heat stress, with consequent crop yield reduction. Organisms exposed to high temperature stresses typically protect themselves with a heat shock response (HSR), where accumulation of unfolded proteins initiates the synthesis of heat shock proteins through the heat shock transcription factor HSF1. While the molecular mechanisms are qualitatively well characterized, our quantitative understanding of the underlying dynamics is still very limited. Here, we study the dynamics of HSR in the photosynthetic model organism Chlamydomonas reinhardtii with a data-driven mathematical model of HSR. We based our dynamical model mostly on mass action kinetics, with a few nonlinear terms. The model was parametrized and validated by several independent datasets obtained from the literature. We demonstrate that HSR quantitatively and significantly differs if an increase in temperature of the same magnitude occurs abruptly, as often applied under laboratory conditions, or gradually, which would rather be expected under natural conditions. In contrast to rapid temperature increases, under gradual changes only negligible amounts of misfolded proteins accumulate, indicating that the HSR of C. reinhardtii efficiently avoids the accumulation of misfolded proteins under conditions most likely to prevail in nature. The mathematical model we developed is a flexible tool to simulate the HSR to different conditions and complements the current experimental approaches.
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Affiliation(s)
- Stefano Magni
- Institute of Quantitative and Theoretical Biology, Heinrich Heine University, Düsseldorf, Germany.,Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Antonella Succurro
- Botanical Institute, University of Cologne, Cologne, Germany.,Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.,University California San Diego, La Jolla, CA, USA
| | - Oliver Ebenhöh
- Institute of Quantitative and Theoretical Biology, Heinrich Heine University, Düsseldorf, Germany .,Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
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A four state parametric model for the kinetics of the non-photochemical quenching in Photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:854-864. [PMID: 28801049 DOI: 10.1016/j.bbabio.2017.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 07/12/2017] [Accepted: 08/05/2017] [Indexed: 11/20/2022]
Abstract
The phenomenon of non-photochemical quenching (NPQ) was studied in spinach chloroplasts using pulse amplitude modulated (PAM) fluorometry. We present a new analysis method which describes the observed fluorescence quantum yield as the sum of the product of four different states of PSII and their corresponding quantum yields. These four distinct states are PSII in the quenched or unquenched state, and with its reaction center either open or closed depending upon the reduction of the QA site. With this method we can describe the dynamics of the NPQ induction and recovery as well as quantify the percentage of photoinactivated RC throughout the measurement. We show that after one cycle of quenching followed by a period of recovery, approximately 8-9% of the RC are photoinactivated, after two cycles of illumination this number becomes 15-17%. The recovery from the quenching appeared with rates of (50s)-1 and (1h)-1. The new analysis method presented here is flexible, allowing it to be applied to any type of PAM fluorometry protocol. The method allows to quantitatively compare qualitatively different PAM curves on the basis of statistically relevant fitting parameters and to quantify quenching dynamics and photoinactivation. Moreover, the results presented here demonstrate that the analysis of a single PAM fluorometry quenching experiment can already provide information on the relative quantum yield of the four different states of PSII for the intact chloroplasts - something no other form of spectroscopy could provide in a single measurement.
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Moejes FW, Matuszynska A, Adhikari K, Bassi R, Cariti F, Cogne G, Dikaios I, Falciatore A, Finazzi G, Flori S, Goldschmidt-Clermont M, Magni S, Maguire J, Le Monnier A, Müller K, Poolman M, Singh D, Spelberg S, Stella GR, Succurro A, Taddei L, Urbain B, Villanova V, Zabke C, Ebenhöh O. A systems-wide understanding of photosynthetic acclimation in algae and higher plants. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2667-2681. [PMID: 28830099 DOI: 10.1093/jxb/erx137] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 03/28/2017] [Indexed: 05/27/2023]
Abstract
The ability of phototrophs to colonise different environments relies on robust protection against oxidative stress, a critical requirement for the successful evolutionary transition from water to land. Photosynthetic organisms have developed numerous strategies to adapt their photosynthetic apparatus to changing light conditions in order to optimise their photosynthetic yield, which is crucial for life on Earth to exist. Photosynthetic acclimation is an excellent example of the complexity of biological systems, where highly diverse processes, ranging from electron excitation over protein protonation to enzymatic processes coupling ion gradients with biosynthetic activity, interact on drastically different timescales from picoseconds to hours. Efficient functioning of the photosynthetic apparatus and its protection is paramount for efficient downstream processes, including metabolism and growth. Modern experimental techniques can be successfully integrated with theoretical and mathematical models to promote our understanding of underlying mechanisms and principles. This review aims to provide a retrospective analysis of multidisciplinary photosynthetic acclimation research carried out by members of the Marie Curie Initial Training Project, AccliPhot, placing the results in a wider context. The review also highlights the applicability of photosynthetic organisms for industry, particularly with regards to the cultivation of microalgae. It intends to demonstrate how theoretical concepts can successfully complement experimental studies broadening our knowledge of common principles in acclimation processes in photosynthetic organisms, as well as in the field of applied microalgal biotechnology.
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Affiliation(s)
- Fiona Wanjiku Moejes
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Quantitative and Theoretical Biology, Heinrich Heine University Düsseldorf, Germany
- Bantry Marine Research Station, Gearhies, Bantry, Co. Cork, Ireland P75 AX07
| | - Anna Matuszynska
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Quantitative and Theoretical Biology, Heinrich Heine University Düsseldorf, Germany
| | - Kailash Adhikari
- Department of Biological and Medical Sciences, Oxford Brookes University, United Kingdom
| | - Roberto Bassi
- University of Verona, Department of Biotechnology, Italy
| | - Federica Cariti
- Department of Botany and Plant Biology, University of Geneva, Switzerland
| | | | | | - Angela Falciatore
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 15 rue de l'Ecole de Médecine, 75006 Paris, France
| | - Giovanni Finazzi
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut National Recherche Agronomique (INRA), Institut de Biosciences et Biotechnologie de Grenoble (BIG), Université Grenoble Alpes (UGA), Grenoble 38100, France
| | - Serena Flori
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut National Recherche Agronomique (INRA), Institut de Biosciences et Biotechnologie de Grenoble (BIG), Université Grenoble Alpes (UGA), Grenoble 38100, France
| | | | - Stefano Magni
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Quantitative and Theoretical Biology, Heinrich Heine University Düsseldorf, Germany
| | - Julie Maguire
- Bantry Marine Research Station, Gearhies, Bantry, Co. Cork, Ireland P75 AX07
| | | | - Kathrin Müller
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Quantitative and Theoretical Biology, Heinrich Heine University Düsseldorf, Germany
| | - Mark Poolman
- Bantry Marine Research Station, Gearhies, Bantry, Co. Cork, Ireland P75 AX07
| | - Dipali Singh
- Bantry Marine Research Station, Gearhies, Bantry, Co. Cork, Ireland P75 AX07
| | - Stephanie Spelberg
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Quantitative and Theoretical Biology, Heinrich Heine University Düsseldorf, Germany
| | - Giulio Rocco Stella
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 15 rue de l'Ecole de Médecine, 75006 Paris, France
| | - Antonella Succurro
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Quantitative and Theoretical Biology, Heinrich Heine University Düsseldorf, Germany
| | - Lucilla Taddei
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 15 rue de l'Ecole de Médecine, 75006 Paris, France
| | - Brieuc Urbain
- LUNAM, University of Nantes, GEPEA, UMR-CNRS 6144, France
| | | | | | - Oliver Ebenhöh
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Quantitative and Theoretical Biology, Heinrich Heine University Düsseldorf, Germany
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Matuszyńska A, Heidari S, Jahns P, Ebenhöh O. A mathematical model of non-photochemical quenching to study short-term light memory in plants. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1860-1869. [PMID: 27620066 DOI: 10.1016/j.bbabio.2016.09.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 09/02/2016] [Accepted: 09/07/2016] [Indexed: 11/19/2022]
Abstract
Plants are permanently exposed to rapidly changing environments, therefore it is evident that they had to evolve mechanisms enabling them to dynamically adapt to such fluctuations. Here we study how plants can be trained to enhance their photoprotection and elaborate on the concept of the short-term illumination memory in Arabidopsis thaliana. By monitoring fluorescence emission dynamics we systematically observe the extent of non-photochemical quenching (NPQ) after previous light exposure to recognise and quantify the memory effect. We propose a simplified mathematical model of photosynthesis that includes the key components required for NPQ activation, which allows us to quantify the contribution to photoprotection by those components. Due to its reduced complexity, our model can be easily applied to study similar behavioural changes in other species, which we demonstrate by adapting it to the shadow-tolerant plant Epipremnum aureum. Our results indicate that a basic mechanism of short-term light memory is preserved. The slow component, accumulation of zeaxanthin, accounts for the amount of memory remaining after relaxation in darkness, while the fast one, antenna protonation, increases quenching efficiency. With our combined theoretical and experimental approach we provide a unifying framework describing common principles of key photoprotective mechanisms across species in general, mathematical terms.
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Affiliation(s)
- Anna Matuszyńska
- Cluster of Excellence on Plant Sciences, Institute for Quantitative and Theoretical Biology, Heinrich-Heine University, Düsseldorf 40225, Germany
| | - Somayyeh Heidari
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University Of Mashhad, 9177948974 Mashhad, Iran
| | - Peter Jahns
- Plant Biochemistry and Stress Physiology, Heinrich-Heine University, Düsseldorf 40225, Germany
| | - Oliver Ebenhöh
- Cluster of Excellence on Plant Sciences, Institute for Quantitative and Theoretical Biology, Heinrich-Heine University, Düsseldorf 40225, Germany.
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