1
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Bellasio C, Lundgren MR. The operation of PEPCK increases light harvesting plasticity in C 4 NAD-ME and NADP-ME photosynthetic subtypes: A theoretical study. PLANT, CELL & ENVIRONMENT 2024; 47:2288-2309. [PMID: 38494958 DOI: 10.1111/pce.14869] [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: 11/10/2022] [Revised: 02/15/2024] [Accepted: 02/18/2024] [Indexed: 03/19/2024]
Abstract
The repeated emergence of NADP-malic enzyme (ME), NAD-ME and phosphoenolpyruvate carboxykinase (PEPCK) subtypes of C4 photosynthesis are iconic examples of convergent evolution, which suggests that these biochemistries do not randomly assemble, but are instead specific adaptations resulting from unknown evolutionary drivers. Theoretical studies that are based on the classic biochemical understanding have repeatedly proposed light-use efficiency as a possible benefit of the PEPCK subtype. However, quantum yield measurements do not support this idea. We explore this inconsistency here via an analytical model that features explicit descriptions across a seamless gradient between C4 biochemistries to analyse light harvesting and dark photosynthetic metabolism. Our simulations show that the NADP-ME subtype, operated by the most productive crops, is the most efficient. The NAD-ME subtype has lower efficiency, but has greater light harvesting plasticity (the capacity to assimilate CO2 in the broadest combination of light intensity and spectral qualities). In both NADP-ME and NAD-ME backgrounds, increasing PEPCK activity corresponds to greater light harvesting plasticity but likely imposed a reduction in photosynthetic efficiency. We draw the first mechanistic links between light harvesting and C4 subtypes, providing the theoretical basis for future investigation.
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Affiliation(s)
- Chandra Bellasio
- Laboratory of Theoretical and Applied Crop Ecophysiology, School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Department of Chemistry, Biology ond Biotechnology, Università Degli Studi Di Perugia, Perugia, Italy
- Department of Biology, University of the Balearic Islands, Palma, Illes Balears, Spain
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
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2
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Sargent D, Amthor JS, Stinziano JR, Evans JR, Whitney SM, Bange MP, Tissue DT, Conaty WC, Sharwood RE. The importance of species-specific and temperature-sensitive parameterisation of A/C i models: A case study using cotton (Gossypium hirsutum L.) and the automated 'OptiFitACi' R-package. PLANT, CELL & ENVIRONMENT 2024; 47:1701-1715. [PMID: 38294051 DOI: 10.1111/pce.14800] [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: 10/07/2022] [Revised: 11/10/2023] [Accepted: 12/15/2023] [Indexed: 02/01/2024]
Abstract
Leaf gas exchange measurements are an important tool for inferring a plant's photosynthetic biochemistry. In most cases, the responses of photosynthetic CO2 assimilation to variable intercellular CO2 concentrations (A/Ci response curves) are used to model the maximum (potential) rate of carboxylation by ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco, Vcmax) and the rate of photosynthetic electron transport at a given incident photosynthetically active radiation flux density (PAR; JPAR). The standard Farquhar-von Caemmerer-Berry model is often used with default parameters of Rubisco kinetic values and mesophyll conductance to CO2 (gm) derived from tobacco that may be inapplicable across species. To study the significance of using such parameters for other species, here we measured the temperature responses of key in vitro Rubisco catalytic properties and gm in cotton (Gossypium hirsutum cv. Sicot 71) and derived Vcmax and J2000 (JPAR at 2000 µmol m-2 s-1 PAR) from cotton A/Ci curves incrementally measured at 15°C-40°C using cotton and other species-specific sets of input parameters with our new automated fitting R package 'OptiFitACi'. Notably, parameterisation by a set of tobacco parameters produced unrealistic J2000:Vcmax ratio of <1 at 25°C, two- to three-fold higher estimates of Vcmax above 15°C, up to 2.3-fold higher estimates of J2000 and more variable estimates of Vcmax and J2000, for our cotton data compared to model parameterisation with cotton-derived values. We determined that errors arise when using a gm,25 of 2.3 mol m-2 s-1 MPa-1 or less and Rubisco CO2-affinities in 21% O2 (KC 21%O2) at 25°C outside the range of 46-63 Pa to model A/Ci responses in cotton. We show how the A/Ci modelling capabilities of 'OptiFitACi' serves as a robust, user-friendly, and flexible extension of 'plantecophys' by providing simplified temperature-sensitivity and species-specificity parameterisation capabilities to reduce variability when modelling Vcmax and J2000.
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Affiliation(s)
- Demi Sargent
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
- CSIRO Agriculture and Food, Narrabri, New South Wales, Australia
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jeffrey S Amthor
- Department of Biological Sciences, Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
| | | | - John R Evans
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Spencer M Whitney
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Michael P Bange
- Cotton Seed Distributors Ltd, Wee Waa, New South Wales, Australia
| | - David T Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
- Global Centre for Land-Based Innovation, Hawkesbury Campus, Western Sydney University, Richmond, New South Wales, Australia
| | - Warren C Conaty
- CSIRO Agriculture and Food, Narrabri, New South Wales, Australia
| | - Robert E Sharwood
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
- Global Centre for Land-Based Innovation, Hawkesbury Campus, Western Sydney University, Richmond, New South Wales, Australia
- School of Science, Western Sydney University, Richmond, New South Wales, Australia
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3
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Capó-Bauçà S, Iñiguez C, Galmés J. The diversity and coevolution of Rubisco and CO 2 concentrating mechanisms in marine macrophytes. THE NEW PHYTOLOGIST 2024; 241:2353-2365. [PMID: 38197185 DOI: 10.1111/nph.19528] [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: 10/26/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024]
Abstract
The kinetic properties of Rubisco, the most important carbon-fixing enzyme, have been assessed in a small fraction of the estimated existing biodiversity of photosynthetic organisms. Until recently, one of the most significant gaps of knowledge in Rubisco kinetics was marine macrophytes, an ecologically relevant group including brown (Ochrophyta), red (Rhodophyta) and green (Chlorophyta) macroalgae and seagrasses (Streptophyta). These organisms express various Rubisco types and predominantly possess CO2 -concentrating mechanisms (CCMs), which facilitate the use of bicarbonate for photosynthesis. Since bicarbonate is the most abundant form of dissolved inorganic carbon in seawater, CCMs allow marine macrophytes to overcome the slow gas diffusion and low CO2 availability in this environment. The present review aims to compile and integrate recent findings on the biochemical diversity of Rubisco and CCMs in the main groups of marine macrophytes. The Rubisco kinetic data provided demonstrate a more relaxed relationship among catalytic parameters than previously reported, uncovering a variability in Rubisco catalysis that has been hidden by a bias in the literature towards terrestrial vascular plants. The compiled data indicate the existence of convergent evolution between Rubisco and biophysical CCMs across the polyphyletic groups of marine macrophytes and suggest a potential role for oxygen in shaping such relationship.
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Affiliation(s)
- Sebastià Capó-Bauçà
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, 07122, Palma, Balearic Islands, Spain
| | - Concepción Iñiguez
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, 07122, Palma, Balearic Islands, Spain
- Department of Ecology, Faculty of Sciences, University of Malaga, Boulevard Louis Pasteur s/n, 29010, Málaga, Spain
| | - Jeroni Galmés
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, 07122, Palma, Balearic Islands, Spain
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4
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Gionfriddo M, Rhodes T, Whitney SM. Perspectives on improving crop Rubisco by directed evolution. Semin Cell Dev Biol 2024; 155:37-47. [PMID: 37085353 DOI: 10.1016/j.semcdb.2023.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/14/2023] [Accepted: 04/15/2023] [Indexed: 04/23/2023]
Abstract
Rubisco catalyses the entry of almost all CO2 into the biosphere and is often the rate-limiting step in plant photosynthesis and growth. Its notoriety as the most abundant protein on Earth stems from the slow and error-prone catalytic properties that require plants, cyanobacteria, algae and photosynthetic bacteria to produce it in high amounts. Efforts to improve the CO2-fixing properties of plant Rubisco has been spurred on by the discovery of more effective isoforms in some algae with the potential to significantly improve crop productivity. Incompatibilities between the protein folding machinery of leaf and algae chloroplasts have, so far, prevented efforts to transplant these more effective Rubisco variants into plants. There is therefore increasing interest in improving Rubisco catalysis by directed (laboratory) evolution. Here we review the advances being made in, and the ongoing challenges with, improving the solubility and/or carboxylation activity of differing non-plant Rubisco lineages. We provide perspectives on new opportunities for the directed evolution of crop Rubiscos and the existing plant transformation capabilities available to evaluate the extent to which Rubisco activity improvements can benefit agricultural productivity.
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Affiliation(s)
- Matteo Gionfriddo
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia; Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Timothy Rhodes
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Spencer M Whitney
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia.
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5
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Busch FA, Ainsworth EA, Amtmann A, Cavanagh AP, Driever SM, Ferguson JN, Kromdijk J, Lawson T, Leakey ADB, Matthews JSA, Meacham-Hensold K, Vath RL, Vialet-Chabrand S, Walker BJ, Papanatsiou M. A guide to photosynthetic gas exchange measurements: Fundamental principles, best practice and potential pitfalls. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38321805 DOI: 10.1111/pce.14815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/31/2023] [Indexed: 02/08/2024]
Abstract
Gas exchange measurements enable mechanistic insights into the processes that underpin carbon and water fluxes in plant leaves which in turn inform understanding of related processes at a range of scales from individual cells to entire ecosytems. Given the importance of photosynthesis for the global climate discussion it is important to (a) foster a basic understanding of the fundamental principles underpinning the experimental methods used by the broad community, and (b) ensure best practice and correct data interpretation within the research community. In this review, we outline the biochemical and biophysical parameters of photosynthesis that can be investigated with gas exchange measurements and we provide step-by-step guidance on how to reliably measure them. We advise on best practices for using gas exchange equipment and highlight potential pitfalls in experimental design and data interpretation. The Supporting Information contains exemplary data sets, experimental protocols and data-modelling routines. This review is a community effort to equip both the experimental researcher and the data modeller with a solid understanding of the theoretical basis of gas-exchange measurements, the rationale behind different experimental protocols and the approaches to data interpretation.
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Affiliation(s)
- Florian A Busch
- School of Biosciences and Birmingham Institute of Forest Research, University of Birmingham, Birmingham, UK
- Research School of Biology, The Australian National University, Canberra, Australian Captial Territory, Australia
| | | | - Anna Amtmann
- School of Molecular Biosciences, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Amanda P Cavanagh
- School of Life Sciences, University of Essex, Colchester, UK
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
| | - Steven M Driever
- Centre for Crop Systems Analysis, Wageningen University & Research, Wageningen, The Netherlands
| | - John N Ferguson
- School of Life Sciences, University of Essex, Colchester, UK
| | - Johannes Kromdijk
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Tracy Lawson
- School of Life Sciences, University of Essex, Colchester, UK
| | - Andrew D B Leakey
- Departments of Plant Biology and Crop Sciences, University of Illinois Urbana Champaign, Urbana, Illinois, USA
| | | | | | - Richard L Vath
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
- LI-COR Environmental, Lincoln, Nebraska, USA
| | - Silvere Vialet-Chabrand
- Department of Plant Sciences, Horticulture and Product Physiology, Wageningen, The Netherlands
| | - Berkley J Walker
- Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Maria Papanatsiou
- School of Molecular Biosciences, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
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6
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Amaral J, Lobo AKM, Carmo-Silva E, Orr DJ. Purification of Rubisco from Leaves. Methods Mol Biol 2024; 2790:417-426. [PMID: 38649584 DOI: 10.1007/978-1-0716-3790-6_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Rubisco fixes CO2 through the carboxylation of ribulose 1,5-bisphosphate (RuBP) during photosynthesis, enabling the synthesis of organic compounds. The natural diversity of Rubisco properties represents an opportunity to improve its performance and there is considerable research effort focusing on better understanding the properties and regulation of the enzyme. This chapter describes a method for large-scale purification of Rubisco from leaves. After the extraction of Rubisco from plant leaves, the enzyme is separated from other proteins by fractional precipitation with polyethylene glycol followed by ion-exchange chromatography. This method enables the isolation of Rubisco in large quantities for a wide range of biochemical applications.
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Affiliation(s)
- Joana Amaral
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Ana K M Lobo
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | | | - Douglas J Orr
- Lancaster Environment Centre, Lancaster University, Lancaster, UK.
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7
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Walker BJ, Driever SM, Kromdijk J, Lawson T, Busch FA. Tools for Measuring Photosynthesis at Different Scales. Methods Mol Biol 2024; 2790:1-26. [PMID: 38649563 DOI: 10.1007/978-1-0716-3790-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Measurements of in vivo photosynthesis are powerful tools that probe the largest fluxes of carbon and energy in an illuminated leaf, but often the specific techniques used are so varied and specialized that it is difficult for researchers outside the field to select and perform the most useful assays for their research questions. The goal of this chapter is to provide a broad overview of the current tools available for the study of photosynthesis, both in vivo and in vitro, so as to provide a foundation for selecting appropriate techniques, many of which are presented in detail in subsequent chapters. This chapter will also organize current methods into a comparative framework and provide examples of how they have been applied to research questions of broad agronomical, ecological, or biological importance. This chapter closes with an argument that the future of in vivo measurements of photosynthesis lies in the ability to use multiple methods simultaneously and discusses the benefits of this approach to currently open physiological questions. This chapter, combined with the relevant methods chapters, could serve as a laboratory course in methods in photosynthesis research or as part of a more comprehensive laboratory course in general plant physiology methods.
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Affiliation(s)
- Berkley J Walker
- Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Steven M Driever
- Centre for Crop Systems Analysis, Wageningen University and Research, Wageningen, The Netherlands
| | - Johannes Kromdijk
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Tracy Lawson
- School of Life Sciences, University of Essex, Colchester, UK
| | - Florian A Busch
- School of Biosciences and The Birmingham Institute of Forest Research, University of Birmingham, Birmingham, UK.
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8
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Zhou Y, Gunn LH, Birch R, Andersson I, Whitney SM. Grafting Rhodobacter sphaeroides with red algae Rubisco to accelerate catalysis and plant growth. NATURE PLANTS 2023; 9:978-986. [PMID: 37291398 DOI: 10.1038/s41477-023-01436-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 05/10/2023] [Indexed: 06/10/2023]
Abstract
Improving the carboxylation properties of Rubisco has primarily arisen from unforeseen amino acid substitutions remote from the catalytic site. The unpredictability has frustrated rational design efforts to enhance plant Rubisco towards the prized growth-enhancing carboxylation properties of red algae Griffithsia monilis GmRubisco. To address this, we determined the crystal structure of GmRubisco to 1.7 Å. Three structurally divergent domains were identified relative to the red-type bacterial Rhodobacter sphaeroides RsRubisco that, unlike GmRubisco, are expressed in Escherichia coli and plants. Kinetic comparison of 11 RsRubisco chimaeras revealed that incorporating C329A and A332V substitutions from GmRubisco Loop 6 (corresponding to plant residues 328 and 331) into RsRubisco increased the carboxylation rate (kcatc) by 60%, the carboxylation efficiency in air by 22% and the CO2/O2 specificity (Sc/o) by 7%. Plastome transformation of this RsRubisco Loop 6 mutant into tobacco enhanced photosynthesis and growth up to twofold over tobacco producing wild-type RsRubisco. Our findings demonstrate the utility of RsRubisco for the identification and in planta testing of amino acid grafts from algal Rubisco that can enhance the enzyme's carboxylase potential.
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Affiliation(s)
- Yu Zhou
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Laura H Gunn
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Rosemary Birch
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Inger Andersson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- Norwegian College of Fisheries Sciences, UiT Arctic University of Norway, Tromsø, Norway
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Biocev, Vestec, Czech Republic
| | - Spencer M Whitney
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.
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9
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Wu A. Modelling plants across scales of biological organisation for guiding crop improvement. FUNCTIONAL PLANT BIOLOGY : FPB 2023; 50:435-454. [PMID: 37105931 DOI: 10.1071/fp23010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/06/2023] [Indexed: 06/07/2023]
Abstract
Grain yield improvement in globally important staple crops is critical in the coming decades if production is to keep pace with growing demand; so there is increasing interest in understanding and manipulating plant growth and developmental traits for better crop productivity. However, this is confounded by complex cross-scale feedback regulations and a limited ability to evaluate the consequences of manipulation on crop production. Plant/crop modelling could hold the key to deepening our understanding of dynamic trait-crop-environment interactions and predictive capabilities for supporting genetic manipulation. Using photosynthesis and crop growth as an example, this review summarises past and present experimental and modelling work, bringing about a model-guided crop improvement thrust, encompassing research into: (1) advancing cross-scale plant/crop modelling that connects across biological scales of organisation using a trait dissection-integration modelling principle; (2) improving the reliability of predicted molecular-trait-crop-environment system dynamics with experimental validation; and (3) innovative model application in synergy with cross-scale experimentation to evaluate G×M×E and predict yield outcomes of genetic intervention (or lack of it) for strategising further molecular and breeding efforts. The possible future roles of cross-scale plant/crop modelling in maximising crop improvement are discussed.
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Affiliation(s)
- Alex Wu
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Qld, Australia
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10
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Capó-Bauçà S, Galmés J, Aguiló-Nicolau P, Ramis-Pozuelo S, Iñiguez C. Carbon assimilation in upper subtidal macroalgae is determined by an inverse correlation between Rubisco carboxylation efficiency and CO 2 concentrating mechanism effectiveness. THE NEW PHYTOLOGIST 2023; 237:2027-2038. [PMID: 36385703 DOI: 10.1111/nph.18623] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
Seaweeds have a wide ecophysiological and phylogenetic diversity with species expressing different Rubisco forms that frequently coexist with biophysical CO2 concentrating mechanisms (CCMs), an adaptation that overcomes the low CO2 availability and gas diffusion in seawater. Here, we assess the possible coevolution between the Rubisco catalysis and the type and effectiveness of CCMs present in six upper subtidal macroalgal species belonging to three phylogenetic groups of seaweeds. A wide diversity in the Rubisco kinetic traits was found across the analyzed species, although the specificity factor was the only parameter explained by the expressed Rubisco form. Differences in the catalytic trade-offs were found between Rubisco forms, indicating that ID Rubiscos could be better adapted to the intracellular O2 : CO2 ratio found in marine organisms during steady-state photosynthesis. The biophysical components of the CCMs also differed among macroalgal species, resulting in different effectiveness to concentrate CO2 around Rubisco active sites. Interestingly, an inverse relationship was found between the effectiveness of CCMs and the in vitro Rubisco carboxylation efficiency, which possibly led to a similar carboxylation potential across the analyzed macroalgal species. Our results demonstrate a coevolution between Rubisco kinetics and CCMs across phylogenetically distant marine macroalgal species sharing the same environment.
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Affiliation(s)
- Sebastià Capó-Bauçà
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, 07122, Balearic Islands, Spain
| | - Jeroni Galmés
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, 07122, Balearic Islands, Spain
| | - Pere Aguiló-Nicolau
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, 07122, Balearic Islands, Spain
| | - Sonia Ramis-Pozuelo
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, 07122, Balearic Islands, Spain
| | - Concepción Iñiguez
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, 07122, Balearic Islands, Spain
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11
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Chen T, Riaz S, Davey P, Zhao Z, Sun Y, Dykes GF, Zhou F, Hartwell J, Lawson T, Nixon PJ, Lin Y, Liu LN. Producing fast and active Rubisco in tobacco to enhance photosynthesis. THE PLANT CELL 2023; 35:795-807. [PMID: 36471570 PMCID: PMC9940876 DOI: 10.1093/plcell/koac348] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/24/2022] [Accepted: 12/02/2022] [Indexed: 05/28/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) performs most of the carbon fixation on Earth. However, plant Rubisco is an intrinsically inefficient enzyme given its low carboxylation rate, representing a major limitation to photosynthesis. Replacing endogenous plant Rubisco with a faster Rubisco is anticipated to enhance crop photosynthesis and productivity. However, the requirement of chaperones for Rubisco expression and assembly has obstructed the efficient production of functional foreign Rubisco in chloroplasts. Here, we report the engineering of a Form 1A Rubisco from the proteobacterium Halothiobacillus neapolitanus in Escherichia coli and tobacco (Nicotiana tabacum) chloroplasts without any cognate chaperones. The native tobacco gene encoding Rubisco large subunit was genetically replaced with H. neapolitanus Rubisco (HnRubisco) large and small subunit genes. We show that HnRubisco subunits can form functional L8S8 hexadecamers in tobacco chloroplasts at high efficiency, accounting for ∼40% of the wild-type tobacco Rubisco content. The chloroplast-expressed HnRubisco displayed a ∼2-fold greater carboxylation rate and supported a similar autotrophic growth rate of transgenic plants to that of wild-type in air supplemented with 1% CO2. This study represents a step toward the engineering of a fast and highly active Rubisco in chloroplasts to improve crop photosynthesis and growth.
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Affiliation(s)
- Taiyu Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Saba Riaz
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Philip Davey
- School of Life Sciences, University of Essex, Colchester CO4 4SQ, UK
| | - Ziyu Zhao
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Yaqi Sun
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Gregory F Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - James Hartwell
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Tracy Lawson
- School of Life Sciences, University of Essex, Colchester CO4 4SQ, UK
| | - Peter J Nixon
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
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12
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Cavanagh AP, Slattery R, Kubien DS. Temperature-induced changes in Arabidopsis Rubisco activity and isoform expression. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:651-663. [PMID: 36124740 PMCID: PMC9833042 DOI: 10.1093/jxb/erac379] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 09/16/2022] [Indexed: 06/06/2023]
Abstract
In many plant species, expression of the nuclear encoded Rubisco small subunit (SSu) varies with environmental changes, but the functional role of any changes in expression remains unclear. In this study, we investigated the impact of differential expression of Rubisco SSu isoforms on carbon assimilation in Arabidopsis. Using plants grown at contrasting temperatures (10 °C and 30 °C), we confirm the previously reported temperature response of the four RbcS genes and extend this to protein expression, finding that warm-grown plants produce Rubisco containing ~65% SSu-B and cold-grown plants produce Rubisco with ~65% SSu-A as a proportion of the total pool of subunits. We find that these changes in isoform concentration are associated with kinetic changes to Rubisco in vitro: warm-grown plants produce a Rubisco having greater CO2 affinity (i.e. higher SC/O and lower KC) but lower kcatCO2 at warm measurement temperatures. Although warm-grown plants produce 38% less Rubisco than cold-grown plants on a leaf area basis, warm-grown plants can maintain similar rates of photosynthesis to cold-grown plants at ambient CO2 and 30 °C, indicating that the carboxylation capacity of warm-grown Rubisco is enhanced at warmer measurement temperatures, and is able to compensate for the lower Rubisco content in warm-grown plants. This association between SSu isoform expression and maintenance of Rubisco activity at high temperature suggests that SSu isoform expression could impact the temperature response of C3 photosynthesis.
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Affiliation(s)
| | - Rebecca Slattery
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - David S Kubien
- Department of Biology, University of New Brunswick, Fredericton, NB, E3B 5A3, Canada
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13
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Oh ZG, Askey B, Gunn LH. Red Rubiscos and opportunities for engineering green plants. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:520-542. [PMID: 36055563 PMCID: PMC9833100 DOI: 10.1093/jxb/erac349] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Nature's vital, but notoriously inefficient, CO2-fixing enzyme Rubisco often limits the growth of photosynthetic organisms including crop species. Form I Rubiscos comprise eight catalytic large subunits and eight auxiliary small subunits and can be classified into two distinct lineages-'red' and 'green'. While red-type Rubiscos (Form IC and ID) are found in rhodophytes, their secondary symbionts, and certain proteobacteria, green-type Rubiscos (Form IA and IB) exist in terrestrial plants, chlorophytes, cyanobacteria, and other proteobacteria. Eukaryotic red-type Rubiscos exhibit desirable kinetic properties, namely high specificity and high catalytic efficiency, with certain isoforms outperforming green-type Rubiscos. However, it is not yet possible to functionally express a high-performing red-type Rubisco in chloroplasts to boost photosynthetic carbon assimilation in green plants. Understanding the molecular and evolutionary basis for divergence between red- and green-type Rubiscos could help us to harness the superior CO2-fixing power of red-type Rubiscos. Here we review our current understanding about red-type Rubisco distribution, biogenesis, and sequence-structure, and present opportunities and challenges for utilizing red-type Rubisco kinetics towards crop improvements.
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Affiliation(s)
- Zhen Guo Oh
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Bryce Askey
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
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14
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Mao Y, Catherall E, Díaz-Ramos A, Greiff GRL, Azinas S, Gunn L, McCormick AJ. The small subunit of Rubisco and its potential as an engineering target. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:543-561. [PMID: 35849331 PMCID: PMC9833052 DOI: 10.1093/jxb/erac309] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/07/2022] [Indexed: 05/06/2023]
Abstract
Rubisco catalyses the first rate-limiting step in CO2 fixation and is responsible for the vast majority of organic carbon present in the biosphere. The function and regulation of Rubisco remain an important research topic and a longstanding engineering target to enhance the efficiency of photosynthesis for agriculture and green biotechnology. The most abundant form of Rubisco (Form I) consists of eight large and eight small subunits, and is found in all plants, algae, cyanobacteria, and most phototrophic and chemolithoautotrophic proteobacteria. Although the active sites of Rubisco are located on the large subunits, expression of the small subunit regulates the size of the Rubisco pool in plants and can influence the overall catalytic efficiency of the Rubisco complex. The small subunit is now receiving increasing attention as a potential engineering target to improve the performance of Rubisco. Here we review our current understanding of the role of the small subunit and our growing capacity to explore its potential to modulate Rubisco catalysis using engineering biology approaches.
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Affiliation(s)
| | | | - Aranzazú Díaz-Ramos
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, King’s Buildings, University of Edinburgh, Edingburgh EH9 3BF, UK
| | - George R L Greiff
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Stavros Azinas
- Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
| | - Laura Gunn
- Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
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15
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Iqbal WA, Lisitsa A, Kapralov MV. Predicting plant Rubisco kinetics from RbcL sequence data using machine learning. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:638-650. [PMID: 36094849 PMCID: PMC9833099 DOI: 10.1093/jxb/erac368] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is responsible for the conversion of atmospheric CO2 to organic carbon during photosynthesis, and often acts as a rate limiting step in the later process. Screening the natural diversity of Rubisco kinetics is the main strategy used to find better Rubisco enzymes for crop engineering efforts. Here, we demonstrate the use of Gaussian processes (GPs), a family of Bayesian models, coupled with protein encoding schemes, for predicting Rubisco kinetics from Rubisco large subunit (RbcL) sequence data. GPs trained on published experimentally obtained Rubisco kinetic datasets were applied to over 9000 sequences encoding RbcL to predict Rubisco kinetic parameters. Notably, our predicted kinetic values were in agreement with known trends, e.g. higher carboxylation turnover rates (Kcat) for Rubisco enzymes from C4 or crassulacean acid metabolism (CAM) species, compared with those found in C3 species. This is the first study demonstrating machine learning approaches as a tool for screening and predicting Rubisco kinetics, which could be applied to other enzymes.
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Affiliation(s)
- Wasim A Iqbal
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Alexei Lisitsa
- Department of Computer Science, University of Liverpool, Liverpool, L69 3BX, United Kingdom
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16
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Buck S, Rhodes T, Gionfriddo M, Skinner T, Yuan D, Birch R, Kapralov MV, Whitney SM. Escherichia coli expressing chloroplast chaperones as a proxy to test heterologous Rubisco production in leaves. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:664-676. [PMID: 36322613 DOI: 10.1093/jxb/erac435] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
Rubisco is a fundamental enzyme in photosynthesis and therefore for life. Efforts to improve plant Rubisco performance have been hindered by the enzymes' complex chloroplast biogenesis requirements. New Synbio approaches, however, now allow the production of some plant Rubisco isoforms in Escherichia coli. While this enhances opportunities for catalytic improvement, there remain limitations in the utility of the expression system. Here we generate, optimize, and test a robust Golden Gate cloning E. coli expression system incorporating the protein folding machinery of tobacco chloroplasts. By comparing the expression of different plant Rubiscos in both E. coli and plastome-transformed tobacco, we show that the E. coli expression system can accurately predict high level Rubisco production in chloroplasts but poorly forecasts the biogenesis potential of isoforms with impaired production in planta. We reveal that heterologous Rubisco production in E. coli and tobacco plastids poorly correlates with Rubisco large subunit phylogeny. Our findings highlight the need to fully understand the factors governing Rubisco biogenesis if we are to deliver an efficient, low-cost screening tool that can accurately emulate chloroplast expression.
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Affiliation(s)
- Sally Buck
- ARC Centre of Excellence in Translational Photosynthesis, Australian National University, Canberra 2000, Australia
| | - Tim Rhodes
- ARC Centre of Excellence in Translational Photosynthesis, Australian National University, Canberra 2000, Australia
| | - Matteo Gionfriddo
- ARC Centre of Excellence in Translational Photosynthesis, Australian National University, Canberra 2000, Australia
| | - Tanya Skinner
- ARC Centre of Excellence in Translational Photosynthesis, Australian National University, Canberra 2000, Australia
| | - Ding Yuan
- ARC Centre of Excellence in Translational Photosynthesis, Australian National University, Canberra 2000, Australia
| | - Rosemary Birch
- ARC Centre of Excellence in Translational Photosynthesis, Australian National University, Canberra 2000, Australia
| | - Maxim V Kapralov
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Spencer M Whitney
- ARC Centre of Excellence in Translational Photosynthesis, Australian National University, Canberra 2000, Australia
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17
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Badger MR, Sharwood RE. Rubisco, the imperfect winner: it's all about the base. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:562-580. [PMID: 36412307 DOI: 10.1093/jxb/erac458] [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: 06/28/2022] [Accepted: 11/20/2022] [Indexed: 06/16/2023]
Abstract
Rubisco catalysis is complex and includes an activation step through the formation of a carbamate at the conserved active site lysine residue and the formation of a highly reactive enediol that is the key to its catalytic reaction. The formation of this enediol is both the basis of its success and its Achilles' heel, creating imperfections to its catalytic efficiency. While Rubisco originally evolved in an atmosphere of high CO2, the earth's multiple oxidation events provided challenges to Rubisco through the fixation of O2 that competes with CO2 at the active site. Numerous catalytic screens across the Rubisco superfamily have identified significant variation in catalytic properties that have been linked to large and small subunit sequences. Despite this, we still have a rudimentary understanding of Rubisco's catalytic mechanism and how the evolution of kinetic properties has occurred. This review identifies the lysine base that functions both as an activator and a proton abstractor to create the enediol as a key to understanding how Rubisco may optimize its kinetic properties. The ways in which Rubisco and its partners have overcome catalytic and activation imperfections and thrived in a world of high O2, low CO2, and variable climatic regimes is remarkable.
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Affiliation(s)
- Murray R Badger
- Research School of Biology, Building 134 Linnaeus Way, Canberra ACT, 2601, Australia
| | - Robert E Sharwood
- Hawkesbury Institute for the Environment, Western Sydney University, Bourke St, Richmond, NSW, 2753, Australia
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18
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Rosado-Souza L, Yokoyama R, Sonnewald U, Fernie AR. Understanding source-sink interactions: Progress in model plants and translational research to crops. MOLECULAR PLANT 2023; 16:96-121. [PMID: 36447435 DOI: 10.1016/j.molp.2022.11.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/27/2022] [Accepted: 11/25/2022] [Indexed: 06/16/2023]
Abstract
Agriculture is facing a massive increase in demand per hectare as a result of an ever-expanding population and environmental deterioration. While we have learned much about how environmental conditions and diseases impact crop yield, until recently considerably less was known concerning endogenous factors, including within-plant nutrient allocation. In this review, we discuss studies of source-sink interactions covering both fundamental research in model systems under controlled growth conditions and how the findings are being translated to crop plants in the field. In this respect we detail efforts aimed at improving and/or combining C3, C4, and CAM modes of photosynthesis, altering the chloroplastic electron transport chain, modulating photorespiration, adopting bacterial/algal carbon-concentrating mechanisms, and enhancing nitrogen- and water-use efficiencies. Moreover, we discuss how modulating TCA cycle activities and primary metabolism can result in increased rates of photosynthesis and outline the opportunities that evaluating natural variation in photosynthesis may afford. Although source, transport, and sink functions are all covered in this review, we focus on discussing source functions because the majority of research has been conducted in this field. Nevertheless, considerable recent evidence, alongside the evidence from classical studies, demonstrates that both transport and sink functions are also incredibly important determinants of yield. We thus describe recent evidence supporting this notion and suggest that future strategies for yield improvement should focus on combining improvements in each of these steps to approach yield optimization.
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Affiliation(s)
- Laise Rosado-Souza
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
| | - Ryo Yokoyama
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Uwe Sonnewald
- Department of Biochemistry, University of Erlangen-Nuremberg, Staudtstrasse 5, 91058 Erlangen, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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19
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Wu A, Brider J, Busch FA, Chen M, Chenu K, Clarke VC, Collins B, Ermakova M, Evans JR, Farquhar GD, Forster B, Furbank RT, Groszmann M, Hernandez‐Prieto MA, Long BM, Mclean G, Potgieter A, Price GD, Sharwood RE, Stower M, van Oosterom E, von Caemmerer S, Whitney SM, Hammer GL. A cross-scale analysis to understand and quantify the effects of photosynthetic enhancement on crop growth and yield across environments. PLANT, CELL & ENVIRONMENT 2023; 46:23-44. [PMID: 36200623 PMCID: PMC10091820 DOI: 10.1111/pce.14453] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 09/27/2022] [Indexed: 05/29/2023]
Abstract
Photosynthetic manipulation provides new opportunities for enhancing crop yield. However, understanding and quantifying the importance of individual and multiple manipulations on the seasonal biomass growth and yield performance of target crops across variable production environments is limited. Using a state-of-the-art cross-scale model in the APSIM platform we predicted the impact of altering photosynthesis on the enzyme-limited (Ac ) and electron transport-limited (Aj ) rates, seasonal dynamics in canopy photosynthesis, biomass growth, and yield formation via large multiyear-by-location crop growth simulations. A broad list of promising strategies to improve photosynthesis for C3 wheat and C4 sorghum were simulated. In the top decile of seasonal outcomes, yield gains were predicted to be modest, ranging between 0% and 8%, depending on the manipulation and crop type. We report how photosynthetic enhancement can affect the timing and severity of water and nitrogen stress on the growing crop, resulting in nonintuitive seasonal crop dynamics and yield outcomes. We predicted that strategies enhancing Ac alone generate more consistent but smaller yield gains across all water and nitrogen environments, Aj enhancement alone generates larger gains but is undesirable in more marginal environments. Large increases in both Ac and Aj generate the highest gains across all environments. Yield outcomes of the tested manipulation strategies were predicted and compared for realistic Australian wheat and sorghum production. This study uniquely unpacks complex cross-scale interactions between photosynthesis and seasonal crop dynamics and improves understanding and quantification of the potential impact of photosynthesis traits (or lack of it) for crop improvement research.
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Affiliation(s)
- Alex Wu
- ARC Centre of Excellence for Translational Photosynthesis, Centre for Crop Science, Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandBrisbaneQueenslandAustralia
| | - Jason Brider
- ARC Centre of Excellence for Translational Photosynthesis, Centre for Crop Science, Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandBrisbaneQueenslandAustralia
| | - Florian A. Busch
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
- School of BiosciencesUniversity of BirminghamBirminghamUK
- Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Min Chen
- ARC Centre of Excellence for Translational Photosynthesis, School of Life and Environmental Science, Faculty of ScienceUniversity of SydneySydneyNew South WalesAustralia
| | - Karine Chenu
- ARC Centre of Excellence for Translational Photosynthesis, Centre for Crop Science, Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandBrisbaneQueenslandAustralia
| | - Victoria C. Clarke
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Brian Collins
- College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
| | - Maria Ermakova
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - John R. Evans
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Graham D. Farquhar
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Britta Forster
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Robert T. Furbank
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Michael Groszmann
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Miguel A. Hernandez‐Prieto
- ARC Centre of Excellence for Translational Photosynthesis, School of Life and Environmental Science, Faculty of ScienceUniversity of SydneySydneyNew South WalesAustralia
| | - Benedict M. Long
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Greg Mclean
- ARC Centre of Excellence for Translational Photosynthesis, Centre for Crop Science, Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandBrisbaneQueenslandAustralia
| | - Andries Potgieter
- ARC Centre of Excellence for Translational Photosynthesis, Centre for Crop Science, Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandBrisbaneQueenslandAustralia
| | - G. Dean Price
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Robert E. Sharwood
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityRichmondNew South WalesAustralia
| | - Michael Stower
- ARC Centre of Excellence for Translational Photosynthesis, Centre for Crop Science, Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandBrisbaneQueenslandAustralia
| | - Erik van Oosterom
- ARC Centre of Excellence for Translational Photosynthesis, Centre for Crop Science, Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandBrisbaneQueenslandAustralia
| | - Susanne von Caemmerer
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Spencer M. Whitney
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Graeme L. Hammer
- ARC Centre of Excellence for Translational Photosynthesis, Centre for Crop Science, Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandBrisbaneQueenslandAustralia
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20
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Pathare VS, DiMario RJ, Koteyeva N, Cousins AB. Mesophyll conductance response to short-term changes in pCO 2 is related to leaf anatomy and biochemistry in diverse C 4 grasses. THE NEW PHYTOLOGIST 2022; 236:1281-1295. [PMID: 35959528 PMCID: PMC9825963 DOI: 10.1111/nph.18427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
Mesophyll CO2 conductance (gm ) in C3 species responds to short-term (minutes) changes in environment potentially due to changes in leaf anatomical and biochemical properties and measurement artefacts. Compared with C3 species, there is less information on gm responses to short-term changes in environmental conditions such as partial pressure of CO2 (pCO2 ) across diverse C4 species and the potential determinants of these responses. Using 16 C4 grasses we investigated the response of gm to short-term changes in pCO2 and its relationship with leaf anatomy and biochemistry. In general, gm increased as pCO2 decreased (statistically significant increase in 12 species), with percentage increases in gm ranging from +13% to +250%. Greater increase in gm at low pCO2 was observed in species exhibiting relatively thinner mesophyll cell walls along with greater mesophyll surface area exposed to intercellular air spaces, leaf N, photosynthetic capacity and activities of phosphoenolpyruvate carboxylase and Rubisco. Species with greater CO2 responses of gm were also able to maintain their leaf water-use efficiencies (TEi ) under low CO2 . Our study advances understanding of CO2 response of gm in diverse C4 species, identifies the key leaf traits related to this response and has implications for improving C4 photosynthetic models and TEi through modification of gm .
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Affiliation(s)
- Varsha S. Pathare
- School of Biological SciencesWashington State UniversityPullmanWA99164‐4236USA
| | - Robert J. DiMario
- School of Biological SciencesWashington State UniversityPullmanWA99164‐4236USA
| | - Nuria Koteyeva
- School of Biological SciencesWashington State UniversityPullmanWA99164‐4236USA
- Laboratory of Anatomy and MorphologyV.L. Komarov Botanical Institute of the Russian Academy of Sciences197376St PetersburgRussia
| | - Asaph B. Cousins
- School of Biological SciencesWashington State UniversityPullmanWA99164‐4236USA
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21
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Medeiros DB, Ishihara H, Guenther M, Rosado de Souza L, Fernie AR, Stitt M, Arrivault S. 13CO2 labeling kinetics in maize reveal impaired efficiency of C4 photosynthesis under low irradiance. PLANT PHYSIOLOGY 2022; 190:280-304. [PMID: 35751609 PMCID: PMC9434203 DOI: 10.1093/plphys/kiac306] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/06/2022] [Indexed: 06/01/2023]
Abstract
C4 photosynthesis allows faster photosynthetic rates and higher water and nitrogen use efficiency than C3 photosynthesis, but at the cost of lower quantum yield due to the energy requirement of its biochemical carbon concentration mechanism. It has also been suspected that its operation may be impaired in low irradiance. To investigate fluxes under moderate and low irradiance, maize (Zea mays) was grown at 550 µmol photons m-2 s-l and 13CO2 pulse-labeling was performed at growth irradiance or several hours after transfer to 160 µmol photons m-2 s-1. Analysis by liquid chromatography/tandem mass spectrometry or gas chromatography/mass spectrometry provided information about pool size and labeling kinetics for 32 metabolites and allowed estimation of flux at many steps in C4 photosynthesis. The results highlighted several sources of inefficiency in low light. These included excess flux at phosphoenolpyruvate carboxylase, restriction of decarboxylation by NADP-malic enzyme, and a shift to increased CO2 incorporation into aspartate, less effective use of metabolite pools to drive intercellular shuttles, and higher relative and absolute rates of photorespiration. The latter provides evidence for a lower bundle sheath CO2 concentration in low irradiance, implying that operation of the CO2 concentration mechanism is impaired in this condition. The analyses also revealed rapid exchange of carbon between the Calvin-Benson cycle and the CO2-concentration shuttle, which allows rapid adjustment of the balance between CO2 concentration and assimilation, and accumulation of large amounts of photorespiratory intermediates in low light that provides a major carbon reservoir to build up C4 metabolite pools when irradiance increases.
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Affiliation(s)
| | - Hirofumi Ishihara
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Manuela Guenther
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | | | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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22
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Capó-Bauçà S, Iñiguez C, Aguiló-Nicolau P, Galmés J. Correlative adaptation between Rubisco and CO 2-concentrating mechanisms in seagrasses. NATURE PLANTS 2022; 8:706-716. [PMID: 35729266 DOI: 10.1038/s41477-022-01171-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/13/2022] [Indexed: 05/19/2023]
Abstract
Submerged angiosperms sustain some of the most productive and diverse ecosystems worldwide. However, their carbon acquisition and assimilation mechanisms remain poorly explored, missing an important step in the evolution of photosynthesis during the colonization of aquatic environments by angiosperms. Here we reveal a convergent kinetic adaptation of Rubisco in phylogenetically distant seagrass species that share catalytic efficiencies and CO2 and O2 affinities up to three times lower than those observed in phylogenetically closer angiosperms from terrestrial, freshwater and brackish-water habitats. This Rubisco kinetic convergence was found to correlate with the effectiveness of seagrass CO2-concentrating mechanisms (CCMs), which probably evolved in response to the constant CO2 limitation in marine environments. The observed Rubisco kinetic adaptation in seagrasses more closely resembles that seen in eukaryotic algae operating CCMs rather than that reported in terrestrial C4 plants. Our results thus demonstrate a general pattern of co-evolution between Rubisco function and biophysical CCM effectiveness that traverses distantly related aquatic lineages.
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Affiliation(s)
- Sebastià Capó-Bauçà
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Spain
| | - Concepción Iñiguez
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Spain.
| | - Pere Aguiló-Nicolau
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Spain
| | - Jeroni Galmés
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Spain
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23
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Sharwood RE, Quick WP, Sargent D, Estavillo GM, Silva-Perez V, Furbank RT. Mining for allelic gold: finding genetic variation in photosynthetic traits in crops and wild relatives. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3085-3108. [PMID: 35274686 DOI: 10.1093/jxb/erac081] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Improvement of photosynthetic traits in crops to increase yield potential and crop resilience has recently become a major breeding target. Synthetic biology and genetic technologies offer unparalleled opportunities to create new genetics for photosynthetic traits driven by existing fundamental knowledge. However, large 'gene bank' collections of germplasm comprising historical collections of crop species and their relatives offer a wealth of opportunities to find novel allelic variation in the key steps of photosynthesis, to identify new mechanisms and to accelerate genetic progress in crop breeding programmes. Here we explore the available genetic resources in food and fibre crops, strategies to selectively target allelic variation in genes underpinning key photosynthetic processes, and deployment of this variation via gene editing in modern elite material.
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Affiliation(s)
- Robert E Sharwood
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - W Paul Quick
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, ACT, Australia
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Demi Sargent
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | | | | | - Robert T Furbank
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, ACT, Australia
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24
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Lin MT, Salihovic H, Clark FK, Hanson MR. Improving the efficiency of Rubisco by resurrecting its ancestors in the family Solanaceae. SCIENCE ADVANCES 2022; 8:eabm6871. [PMID: 35427154 PMCID: PMC9012466 DOI: 10.1126/sciadv.abm6871] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Plants and photosynthetic organisms have a remarkably inefficient enzyme named Rubisco that fixes atmospheric CO2 into organic compounds. Understanding how Rubisco has evolved in response to past climate change is important for attempts to adjust plants to future conditions. In this study, we developed a computational workflow to assemble de novo both large and small subunits of Rubisco enzymes from transcriptomics data. Next, we predicted sequences for ancestral Rubiscos of the (nightshade) family Solanaceae and characterized their kinetics after coexpressing them in Escherichia coli. Predicted ancestors of C3 Rubiscos were identified that have superior kinetics and excellent potential to help plants adapt to anthropogenic climate change. Our findings also advance understanding of the evolution of Rubisco's catalytic traits.
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25
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Ding Y, Yang S. Surviving and thriving: How plants perceive and respond to temperature stress. Dev Cell 2022; 57:947-958. [PMID: 35417676 DOI: 10.1016/j.devcel.2022.03.010] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 02/21/2022] [Accepted: 03/17/2022] [Indexed: 12/11/2022]
Abstract
The dramatic temperature fluctuations spurred by climate change inhibit plant growth and threaten crop productivity. Unraveling how plants defend themselves against temperature-stress-induced cellular impairment is not only a crucial fundamental issue but is also of critical importance for agricultural sustainability and food security. Here, we review recent developments in elucidating the molecular mechanisms used by plants to sense and respond to cold and heat stress at multiple levels. We also describe the trade-off between plant growth and responses to high and low temperatures. Finally, we discuss possible strategies that could be used to engineer temperature-stress-tolerant, high-yielding crops.
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Affiliation(s)
- Yanglin Ding
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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26
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Israel WK, Watson-Lazowski A, Chen ZH, Ghannoum O. High intrinsic water use efficiency is underpinned by high stomatal aperture and guard cell potassium flux in C3 and C4 grasses grown at glacial CO2 and low light. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1546-1565. [PMID: 34718533 DOI: 10.1093/jxb/erab477] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/26/2021] [Indexed: 05/15/2023]
Abstract
We compared how stomatal morphology and physiology control intrinsic leaf water use efficiency (iWUE) in two C3 and six C4 grasses grown at ambient (400 µmol mol-1) or glacial CO2 (180 µmol mol-1) and high (1000 µmol m-2 s-1) or low light intensity (200 µmol m-2 s-1). C4 grasses tended to have higher iWUE and CO2 assimilation rates, and lower stomatal conductance (gs), operational stomatal aperture (aop), and guard cell K+ influx rate relative to C3 grasses, while stomatal size (SS) and stomatal density (SD) did not vary according to the photosynthetic type. Overall, iWUE and gs depended most on aop and density of open stomata. In turn, aop correlated with K+ influx, stomatal opening speed on transition to high light, and SS. Species with higher SD had smaller and faster-opening stomata. Although C4 grasses operated with lower gs and aop at ambient CO2, they showed a greater potential to open stomata relative to maximal stomatal conductance (gmax), indicating heightened stomatal sensitivity and control. We uncovered promising links between aop, gs, iWUE, and K+ influx among C4 grasses, and differential K+ influx responses of C4 guard cells to low light, revealing molecular targets for improving iWUE in C4 crops.
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Affiliation(s)
- Walter Krystler Israel
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Australia
| | - Alexander Watson-Lazowski
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Australia
| | - Zhong-Hua Chen
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Oula Ghannoum
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Australia
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27
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Iñiguez C, Niinemets Ü, Mark K, Galmés J. Analyzing the causes of method-to-method variability among Rubisco kinetic traits: from the first to the current measurements. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7846-7862. [PMID: 34329386 DOI: 10.1093/jxb/erab356] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 07/28/2021] [Indexed: 06/13/2023]
Abstract
Due to the importance of Rubisco in the biosphere, its kinetic parameters have been measured by different methodologies in a large number of studies over the last 60 years. These parameters are essential to characterize the natural diversity in the catalytic properties of the enzyme and they are also required for photosynthesis and cross-scale crop modeling. The present compilation of Rubisco kinetic parameters in model species revealed a wide intraspecific laboratory-to-laboratory variability, which was partially solved by making corrections to account for differences in the assay buffer composition and in the acidity constant of dissolved CO2, as well as for differences in the CO2 and O2 solubilities. Part of the intraspecific variability was also related to the different analytical methodologies used. For instance, significant differences were found between the two main methods for the determination of the specificity factor (Sc/o), and also between Rubisco quantification methods, Rubisco purification versus crude extracts, and single-point versus CO2 curve measurements for the carboxylation turnover rate (kcatc) determination. Causes of the intraspecific laboratory-to-laboratory variability for Rubisco catalytic traits are discussed. This study provides a normalized kinetic dataset for model species to be used by the scientific community. Corrections and recommendations are also provided to reduce measurement variability, allowing the comparison of kinetic data obtained in different laboratories using different assay conditions.
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Affiliation(s)
- Concepción Iñiguez
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
- Department of Ecology, Faculty of Sciences, University of Málaga, Málaga, Spain
| | - Ülo Niinemets
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia
- Estonian Academy of Sciences, Kohtu 6, 10130 Tallinn, Estonia
| | - Kristiina Mark
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia
| | - Jeroni Galmés
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
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28
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Tcherkez G, Farquhar GD. Rubisco catalytic adaptation is mostly driven by photosynthetic conditions - Not by phylogenetic constraints. JOURNAL OF PLANT PHYSIOLOGY 2021; 267:153554. [PMID: 34749030 DOI: 10.1016/j.jplph.2021.153554] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 10/19/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
The prevalence of phylogenetic constraints in Rubisco evolution has been emphasised recently by (Bouvier et al., 2021), who argued that phylogenetic inheritance limits Rubisco adaptation much more than the biochemical trade-off between specificity, CO2 affinity and turn-over. In this Opinion, we have critically examined how a phylogenetic signal can be computed with Rubisco kinetic properties and phylogenetic trees, and we arrive at a different conclusion. In particular, Rubisco's adaptation is partly driven by C4 vs. C3 photosynthetic conditions in Angiosperms, apparent phylogenetic signals being mostly due to either homoplasy, computation artefacts or the use of nearly identical sister species. While phylogenetic inheritance of an ancestral enzyme form probably has some role in Rubisco's adaptation landscape, it is a minor player, at least compared to microenvironmental conditions such as CO2 and O2 concentrations.
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Affiliation(s)
- Guillaume Tcherkez
- Institut de Recherche and Horticulture et Semences, INRAe Angers, Université D'Angers, 42 Rue Georges Morel, 49070, Beaucouzé, France; Research School of Biology, ANU College of Science, Australian National University, 2601, Canberra ACT, Australia.
| | - Graham D Farquhar
- Research School of Biology, ANU College of Science, Australian National University, 2601, Canberra ACT, Australia
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29
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Iqbal WA, Miller IG, Moore RL, Hope IJ, Cowan-Turner D, Kapralov MV. Rubisco substitutions predicted to enhance crop performance through carbon uptake modelling. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6066-6075. [PMID: 34115846 PMCID: PMC8411856 DOI: 10.1093/jxb/erab278] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/09/2021] [Indexed: 05/03/2023]
Abstract
Improving the performance of the CO2-fixing enzyme Rubisco is among the targets for increasing crop yields. Here, Earth system model (ESM) representations of canopy C3 and C4 photosynthesis were combined with species-specific Rubisco parameters to quantify the consequences of bioengineering foreign Rubiscos into C3 and C4 crops under field conditions. The 'two big leaf' (sunlit/shaded) model for canopy photosynthesis was used together with species-specific Rubisco kinetic parameters including maximum rate (Kcat), Michaelis-Menten constant for CO2 at ambient atmospheric O2 (Kc21%O2), specificity for CO2 to O2 (Sc/o), and associated heat activation (Ha) values. Canopy-scale consequences of replacing native Rubiscos in wheat, maize, and sugar beet with foreign enzymes from 27 species were modelled using data from Ameriflux and Fluxnet databases. Variation among the included Rubisco kinetics differentially affected modelled carbon uptake rates, and Rubiscos from several species of C4 grasses showed the greatest potential of >50% carbon uptake improvement in wheat, and >25% improvement in sugar beet and maize. This study also reaffirms the need for data on fully characterized Rubiscos from more species, and for better parameterization of 'Vcmax' and temperature response of 'Jmax' in ESMs.
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Affiliation(s)
- Wasim A Iqbal
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
- Correspondence:
| | - Isabel G Miller
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Rebecca L Moore
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Iain J Hope
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Daniel Cowan-Turner
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Maxim V Kapralov
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
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30
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Sales CRG, Wang Y, Evers JB, Kromdijk J. Improving C4 photosynthesis to increase productivity under optimal and suboptimal conditions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5942-5960. [PMID: 34268575 PMCID: PMC8411859 DOI: 10.1093/jxb/erab327] [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: 03/12/2021] [Accepted: 07/09/2021] [Indexed: 05/05/2023]
Abstract
Although improving photosynthetic efficiency is widely recognized as an underutilized strategy to increase crop yields, research in this area is strongly biased towards species with C3 photosynthesis relative to C4 species. Here, we outline potential strategies for improving C4 photosynthesis to increase yields in crops by reviewing the major bottlenecks limiting the C4 NADP-malic enzyme pathway under optimal and suboptimal conditions. Recent experimental results demonstrate that steady-state C4 photosynthesis under non-stressed conditions can be enhanced by increasing Rubisco content or electron transport capacity, both of which may also stimulate CO2 assimilation at supraoptimal temperatures. Several additional putative bottlenecks for photosynthetic performance under drought, heat, or chilling stress or during photosynthetic induction await further experimental verification. Based on source-sink interactions in maize, sugarcane, and sorghum, alleviating these photosynthetic bottlenecks during establishment and growth of the harvestable parts are likely to improve yield. The expected benefits are also shown to be augmented by the increasing trend in planting density, which increases the impact of photosynthetic source limitation on crop yields.
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Affiliation(s)
- Cristina R G Sales
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Yu Wang
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jochem B Evers
- Centre for Crops Systems Analysis (WUR), Wageningen University, Wageningen, The Netherlands
| | - Johannes Kromdijk
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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31
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Stitt M, Luca Borghi G, Arrivault S. Targeted metabolite profiling as a top-down approach to uncover interspecies diversity and identify key conserved operational features in the Calvin-Benson cycle. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5961-5986. [PMID: 34473300 PMCID: PMC8411860 DOI: 10.1093/jxb/erab291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/21/2021] [Indexed: 05/02/2023]
Abstract
Improving photosynthesis is a promising avenue to increase crop yield. This will be aided by better understanding of natural variance in photosynthesis. Profiling of Calvin-Benson cycle (CBC) metabolites provides a top-down strategy to uncover interspecies diversity in CBC operation. In a study of four C4 and five C3 species, principal components analysis separated C4 species from C3 species and also separated different C4 species. These separations were driven by metabolites that reflect known species differences in their biochemistry and pathways. Unexpectedly, there was also considerable diversity between the C3 species. Falling atmospheric CO2 and changing temperature, nitrogen, and water availability have driven evolution of C4 photosynthesis in multiple lineages. We propose that analogous selective pressures drove lineage-dependent evolution of the CBC in C3 species. Examples of species-dependent variation include differences in the balance between the CBC and the light reactions, and in the balance between regulated steps in the CBC. Metabolite profiles also reveal conserved features including inactivation of enzymes in low irradiance, and maintenance of CBC metabolites at relatively high levels in the absence of net CO2 fixation. These features may be important for photosynthetic efficiency in low light, fluctuating irradiance, and when stomata close due to low water availability.
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Affiliation(s)
- Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Gian Luca Borghi
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Stéphanie Arrivault
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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32
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von Caemmerer S. Updating the steady-state model of C4 photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6003-6017. [PMID: 34173821 PMCID: PMC8411607 DOI: 10.1093/jxb/erab266] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 06/06/2021] [Indexed: 05/22/2023]
Abstract
C4 plants play a key role in world agriculture. For example, C4 crops such as maize and sorghum are major contributors to food production in both developed and developing countries, and the C4 grasses sugarcane, miscanthus, and switchgrass are major plant sources of bioenergy. In the challenge to manipulate and enhance C4 photosynthesis, steady-state models of leaf photosynthesis provide an important tool for gas exchange analysis and thought experiments that can explore photosynthetic pathway changes. Here a previous C4 photosynthetic model developed by von Caemmerer and Furbank has been updated with new kinetic parameterization and temperature dependencies added. The parameterization was derived from experiments on the C4 monocot, Setaria viridis, which for the first time provides a cohesive parameterization. Mesophyll conductance and its temperature dependence have also been included, as this is an important step in the quantitative correlation between the initial slope of the CO2 response curve of CO2 assimilation and in vitro phosphoenolpyruvate carboxylase activity. Furthermore, the equations for chloroplast electron transport have been updated to include cyclic electron transport flow, and equations have been added to calculate the electron transport rate from measured CO2 assimilation rates.
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Affiliation(s)
- Susanne von Caemmerer
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
- Correspondence:
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33
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Yin X, Busch FA, Struik PC, Sharkey TD. Evolution of a biochemical model of steady-state photosynthesis. PLANT, CELL & ENVIRONMENT 2021; 44:2811-2837. [PMID: 33872407 PMCID: PMC8453732 DOI: 10.1111/pce.14070] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 05/29/2023]
Abstract
On the occasion of the 40th anniversary of the publication of the landmark model by Farquhar, von Caemmerer & Berry on steady-state C3 photosynthesis (known as the "FvCB model"), we review three major further developments of the model. These include: (1) limitation by triose phosphate utilization, (2) alternative electron transport pathways, and (3) photorespiration-associated nitrogen and C1 metabolisms. We discussed the relation of the third extension with the two other extensions, and some equivalent extensions to model C4 photosynthesis. In addition, the FvCB model has been coupled with CO2 -diffusion models. We review how these extensions and integration have broadened the use of the FvCB model in understanding photosynthesis, especially with regard to bioenergetic stoichiometries associated with photosynthetic quantum yields. Based on the new insights, we present caveats in applying the FvCB model. Further research needs are highlighted.
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Affiliation(s)
- Xinyou Yin
- Centre for Crop Systems AnalysisWageningen University & ResearchWageningenThe Netherlands
| | - Florian A. Busch
- School of Biosciences and Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Paul C. Struik
- Centre for Crop Systems AnalysisWageningen University & ResearchWageningenThe Netherlands
| | - Thomas D. Sharkey
- MSU‐DOE Plant Research Laboratory, Plant Resilience InstituteMichigan State UniversityEast LansingMichiganUSA
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34
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Nakazato I, Okuno M, Yamamoto H, Tamura Y, Itoh T, Shikanai T, Takanashi H, Tsutsumi N, Arimura SI. Targeted base editing in the plastid genome of Arabidopsis thaliana. NATURE PLANTS 2021; 7:906-913. [PMID: 34211131 PMCID: PMC8289735 DOI: 10.1038/s41477-021-00954-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 05/26/2021] [Indexed: 05/17/2023]
Abstract
Bacterial cytidine deaminase fused to the DNA binding domains of transcription activator-like effector nucleases was recently reported to transiently substitute a targeted C to a T in mitochondrial DNA of mammalian cultured cells1. We applied this system to targeted base editing in the Arabidopsis thaliana plastid genome. The targeted Cs were homoplasmically substituted to Ts in some plantlets of the T1 generation and the mutations were inherited by their offspring independently of their nuclear-introduced vectors.
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Affiliation(s)
- Issei Nakazato
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Miki Okuno
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Hiroshi Yamamoto
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yoshiko Tamura
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Toshiharu Shikanai
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Hideki Takanashi
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Nobuhiro Tsutsumi
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shin-Ichi Arimura
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
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35
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Lin MT, Orr DJ, Worrall D, Parry MAJ, Carmo-Silva E, Hanson MR. A procedure to introduce point mutations into the Rubisco large subunit gene in wild-type plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:876-887. [PMID: 33576096 DOI: 10.1111/tpj.15196] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 01/22/2021] [Accepted: 02/07/2021] [Indexed: 06/12/2023]
Abstract
Photosynthetic inefficiencies limit the productivity and sustainability of crop production and the resilience of agriculture to future societal and environmental challenges. Rubisco is a key target for improvement as it plays a central role in carbon fixation during photosynthesis and is remarkably inefficient. Introduction of mutations to the chloroplast-encoded Rubisco large subunit rbcL is of particular interest for improving the catalytic activity and efficiency of the enzyme. However, manipulation of rbcL is hampered by its location in the plastome, with many species recalcitrant to plastome transformation, and by the plastid's efficient repair system, which can prevent effective maintenance of mutations introduced with homologous recombination. Here we present a system where the introduction of a number of silent mutations into rbcL within the model plant Nicotiana tabacum facilitates simplified screening via additional restriction enzyme sites. This system was used to successfully generate a range of transplastomic lines from wild-type N. tabacum with stable point mutations within rbcL in 40% of the transformants, allowing assessment of the effect of these mutations on Rubisco assembly and activity. With further optimization the approach offers a viable way forward for mutagenic testing of Rubisco function in planta within tobacco and modification of rbcL in other crops where chloroplast transformation is feasible. The transformation strategy could also be applied to introduce point mutations in other chloroplast-encoded genes.
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Affiliation(s)
- Myat T Lin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Douglas J Orr
- Lancaster Environment Centre, Lancaster University, Library Avenue, Lancaster, LA1 4YQ, UK
| | - Dawn Worrall
- Lancaster Environment Centre, Lancaster University, Library Avenue, Lancaster, LA1 4YQ, UK
| | - Martin A J Parry
- Lancaster Environment Centre, Lancaster University, Library Avenue, Lancaster, LA1 4YQ, UK
| | - Elizabete Carmo-Silva
- Lancaster Environment Centre, Lancaster University, Library Avenue, Lancaster, LA1 4YQ, UK
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
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36
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Moore CE, Meacham-Hensold K, Lemonnier P, Slattery RA, Benjamin C, Bernacchi CJ, Lawson T, Cavanagh AP. The effect of increasing temperature on crop photosynthesis: from enzymes to ecosystems. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2822-2844. [PMID: 33619527 PMCID: PMC8023210 DOI: 10.1093/jxb/erab090] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 02/19/2021] [Indexed: 05/03/2023]
Abstract
As global land surface temperature continues to rise and heatwave events increase in frequency, duration, and/or intensity, our key food and fuel cropping systems will likely face increased heat-related stress. A large volume of literature exists on exploring measured and modelled impacts of rising temperature on crop photosynthesis, from enzymatic responses within the leaf up to larger ecosystem-scale responses that reflect seasonal and interannual crop responses to heat. This review discusses (i) how crop photosynthesis changes with temperature at the enzymatic scale within the leaf; (ii) how stomata and plant transport systems are affected by temperature; (iii) what features make a plant susceptible or tolerant to elevated temperature and heat stress; and (iv) how these temperature and heat effects compound at the ecosystem scale to affect crop yields. Throughout the review, we identify current advancements and future research trajectories that are needed to make our cropping systems more resilient to rising temperature and heat stress, which are both projected to occur due to current global fossil fuel emissions.
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Affiliation(s)
- Caitlin E Moore
- School of Agriculture and Environment, The University of Western Australia, Crawley, Australia
- Institute for Sustainability, Energy & Environment, University of Illinois at Urbana-Champaign, Urbana, USA
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, USA
- Correspondence: or
| | - Katherine Meacham-Hensold
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, USA
| | | | - Rebecca A Slattery
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Claire Benjamin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Carl J Bernacchi
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, USA
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture–Agricultural Research Service, Urbana, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Tracy Lawson
- School of Life Sciences, University of Essex, Colchester, UK
| | - Amanda P Cavanagh
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, USA
- School of Life Sciences, University of Essex, Colchester, UK
- Correspondence: or
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37
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Khan HA, Nakamura Y, Furbank RT, Evans JR. Effect of leaf temperature on the estimation of photosynthetic and other traits of wheat leaves from hyperspectral reflectance. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1271-1281. [PMID: 33252664 DOI: 10.1093/jxb/eraa514] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 10/30/2020] [Indexed: 05/21/2023]
Abstract
A growing number of leaf traits can be estimated from hyperspectral reflectance data. These include structural and compositional traits, such as leaf mass per area (LMA) and nitrogen and chlorophyll content, but also physiological traits such a Rubisco carboxylation activity, electron transport rate, and respiration rate. Since physiological traits vary with leaf temperature, how does this impact on predictions made from reflectance measurements? We investigated this with two wheat varieties, by repeatedly measuring each leaf through a sequence of temperatures imposed by varying the air temperature in a growth room. Leaf temperatures ranging from 20 °C to 35 °C did not alter the estimated Rubisco capacity normalized to 25 °C (Vcmax25), or chlorophyll or nitrogen contents per unit leaf area. Models estimating LMA and Vcmax25/N were both slightly influenced by leaf temperature: estimated LMA increased by 0.27% °C-1 and Vcmax25/N increased by 0.46% °C-1. A model estimating Rubisco activity closely followed variation associated with leaf temperature. Reflectance spectra change with leaf temperature and therefore contain a temperature signal.
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Affiliation(s)
- Hammad A Khan
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Canberra, ACT, Australia
- Department of Primary Industries and Regional Development (DPIRD), Northam, WA, Australia
| | - Yukiko Nakamura
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Canberra, ACT, Australia
- Graduate School of Life Sciences, Tohoku University, Japan
| | - Robert T Furbank
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Canberra, ACT, Australia
- CSIRO Agriculture & Food, Canberra, ACT, Australia
| | - John R Evans
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Canberra, ACT, Australia
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Sibret T, Verbruggen W, Peaucelle M, Verryckt LT, Bauters M, Combe M, Boeckx P, Verbeeck H. High photosynthetic capacity of Sahelian C 3 and C 4 plants. PHOTOSYNTHESIS RESEARCH 2021; 147:161-175. [PMID: 33387194 DOI: 10.1007/s11120-020-00801-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 11/17/2020] [Indexed: 06/12/2023]
Abstract
The semi-arid ecosystems of the African Sahel play an important role in the global carbon cycle and are among the most sensitive ecosystems to future environmental pressures. Still, basic data of photosynthetic characteristics of Sahelian vegetation are very limited, preventing us to properly understand these ecosystems and to project their response to future global changes. Here, we aim to study and quantify key leaf traits, including photosynthetic parameters and leaf nutrients (Nleaf and Pleaf), of common C3 and C4 Sahelian plants (trees, lianas, and grasses) at the Dahra field site (Senegal). Dahra is a reference site for grazed semi-arid Sahelian savannah ecosystems in carbon cycle studies. Within the studied species, we found that photosynthetic parameters varied considerably between functional types. We also found significant relationships between and within photosynthetic parameters and leaf traits which mostly differed in their slopes from C3 to C4 plants. In agreement with the leaf economic spectrum, strong relationships (R2 = 0.71) were found between SLA and Nleaf whereby C3 and C4 plants showed very similar relationships. By comparing our data to a global dataset of plant traits, we show that measured Sahelian plants exhibit higher photosynthetic capacity (Asat) compared to the non-Sahelian vegetation, with values that are on average a fourfold of the global average. Moreover, Sahelian C3 plants showed photosynthetic nutrient use efficiencies that were on average roughly twice as high as global averages. We interpreted these results as the potential adaptation of Sahelian plants to short growing season lengths via an efficient nutrient allocation to optimize photosynthesis during this period. Our study provides robust estimates of key functional traits, but also traits relationships that will help to calibrate and validate vegetation models over this data-poor region.
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Affiliation(s)
- Thomas Sibret
- Isotope Bioscience Laboratory-ISOFYS, Department of Green Chemistry and Technology, Ghent University, Ghent, Belgium.
- CAVElab, Computational and Applied Vegetation Ecology, Department of Environment, Ghent University, Ghent, Belgium.
| | - Wim Verbruggen
- CAVElab, Computational and Applied Vegetation Ecology, Department of Environment, Ghent University, Ghent, Belgium
| | - Marc Peaucelle
- CAVElab, Computational and Applied Vegetation Ecology, Department of Environment, Ghent University, Ghent, Belgium
| | - Lore T Verryckt
- PLECO, Department of Biology, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Marijn Bauters
- Isotope Bioscience Laboratory-ISOFYS, Department of Green Chemistry and Technology, Ghent University, Ghent, Belgium
- CAVElab, Computational and Applied Vegetation Ecology, Department of Environment, Ghent University, Ghent, Belgium
| | - Marie Combe
- CAVElab, Computational and Applied Vegetation Ecology, Department of Environment, Ghent University, Ghent, Belgium
| | - Pascal Boeckx
- Isotope Bioscience Laboratory-ISOFYS, Department of Green Chemistry and Technology, Ghent University, Ghent, Belgium
| | - Hans Verbeeck
- CAVElab, Computational and Applied Vegetation Ecology, Department of Environment, Ghent University, Ghent, Belgium
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Degen GE, Orr DJ, Carmo-Silva E. Heat-induced changes in the abundance of wheat Rubisco activase isoforms. THE NEW PHYTOLOGIST 2021; 229:1298-1311. [PMID: 32964463 DOI: 10.1111/nph.16937] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/02/2020] [Indexed: 05/24/2023]
Abstract
The Triticum aestivum (wheat) genome encodes three isoforms of Rubisco activase (Rca) differing in thermostability, which could be exploited to improve the resilience of this crop to global warming. We hypothesized that elevated temperatures would cause an increase in the relative abundance of heat-stable Rca1β. Wheat plants were grown at 25° C : 18°C (day : night) and exposed to heat stress (38° C : 22°C) for up to 5 d at pre-anthesis. Carbon (C) assimilation, Rubisco activity, CA1Pase activity, transcripts of Rca1β, Rca2β, and Rca2α, and the quantities of the corresponding protein products were measured during and after heat stress. The transcript of Rca1β increased 40-fold in 4 h at elevated temperatures and returned to the original level after 4 h upon return of plants to control temperatures. Rca1β comprised up to 2% of the total Rca protein in unstressed leaves but increased three-fold in leaves exposed to elevated temperatures for 5 d and remained high at 4 h after heat stress. These results show that elevated temperatures cause rapid changes in Rca gene expression and adaptive changes in Rca isoform abundance. The improved understanding of the regulation of C assimilation under heat stress will inform efforts to improve wheat productivity and climate resilience.
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Affiliation(s)
- Gustaf E Degen
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Douglas J Orr
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
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Whitney SM, Sharwood RE. Rubisco Engineering by Plastid Transformation and Protocols for Assessing Expression. Methods Mol Biol 2021; 2317:195-214. [PMID: 34028770 DOI: 10.1007/978-1-0716-1472-3_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The assimilation of CO2 within chloroplasts is catalyzed by the bifunctional enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase, Rubisco. Within higher plants the Rubisco large subunit gene, rbcL, is encoded in the plastid genome, while the Rubisco small subunit gene, RbcS is coded in the nucleus by a multigene family. Rubisco is considered a poor catalyst due to its slow turnover rate and its additional fixation of O2 that can result in wasteful loss of carbon through the energy requiring photorespiratory cycle. Improving the carboxylation efficiency and CO2/O2 selectivity of Rubisco within higher plants has been a long term goal which has been greatly advanced in recent times using plastid transformation techniques. Here we present experimental methodologies for efficiently engineering Rubisco in the plastids of a tobacco master line and analyzing leaf Rubisco content.
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Affiliation(s)
- Spencer M Whitney
- Plant Sciences, Research School of Biology, College of Science, The Australian National University, Acton, ACT, Australia.
| | - Robert E Sharwood
- Plant Sciences, Research School of Biology, College of Science, The Australian National University, Acton, ACT, Australia
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41
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Cummins PL. The Coevolution of RuBisCO, Photorespiration, and Carbon Concentrating Mechanisms in Higher Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:662425. [PMID: 34539685 PMCID: PMC8440988 DOI: 10.3389/fpls.2021.662425] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 07/26/2021] [Indexed: 05/20/2023]
Abstract
Ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (RuBisCO) is the carbon-fixing enzyme present in most photosynthetic organisms, converting CO2 into organic matter. Globally, photosynthetic efficiency in terrestrial plants has become increasingly challenged in recent decades due to a rapid increase in atmospheric CO2 and associated changes toward warmer and dryer environments. Well adapted for these new climatic conditions, the C4 photosynthetic pathway utilizes carbon concentrating mechanisms to increase CO2 concentrations surrounding RuBisCO, suppressing photorespiration from the oxygenase catalyzed reaction with O2. The energy efficiency of C3 photosynthesis, from which the C4 pathway evolved, is thought to rely critically on an uninterrupted supply of chloroplast CO2. Part of the homeostatic mechanism that maintains this constancy of supply involves the CO2 produced as a byproduct of photorespiration in a negative feedback loop. Analyzing the database of RuBisCO kinetic parameters, we suggest that in genera (Flaveria and Panicum) for which both C3 and C4 examples are available, the C4 pathway evolved only from C3 ancestors possessing much lower than the average carboxylase specificity relative to that of the oxygenase reaction (S C/O=S C/S O), and hence, the higher CO2 levels required for development of the photorespiratory CO2 pump (C2 photosynthesis) essential in the initial stages of C4 evolution, while in the later stage (final optimization phase in the Flaveria model) increased CO2 turnover may have occurred, which would have been supported by the higher CO2 levels. Otherwise, C4 RuBisCO kinetic traits remain little changed from the ancestral C3 species. At the opposite end of the spectrum, C3 plants (from Limonium) with higher than average S C/O, which may be associated with the ability of increased CO2, relative to O2, affinity to offset reduced photorespiration and chloroplast CO2 levels, can tolerate high stress environments. It is suggested that, instead of inherently constrained by its kinetic mechanism, RuBisCO possesses the extensive kinetic plasticity necessary for adaptation to changes in photorespiration that occur in the homeostatic regulation of CO2 supply under a broad range of abiotic environmental conditions.
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42
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Gunn LH, Martin Avila E, Birch R, Whitney SM. The dependency of red Rubisco on its cognate activase for enhancing plant photosynthesis and growth. Proc Natl Acad Sci U S A 2020; 117:25890-25896. [PMID: 32989135 PMCID: PMC7568259 DOI: 10.1073/pnas.2011641117] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Plant photosynthesis and growth are often limited by the activity of the CO2-fixing enzyme Rubisco. The broad kinetic diversity of Rubisco in nature is accompanied by differences in the composition and compatibility of the ancillary proteins needed for its folding, assembly, and metabolic regulation. Variations in the protein folding needs of catalytically efficient red algae Rubisco prevent their production in plants. Here, we show this impediment does not extend to Rubisco from Rhodobacter sphaeroides (RsRubisco)-a red-type Rubisco able to assemble in plant chloroplasts. In transplastomic tobRsLS lines expressing a codon optimized Rs-rbcLS operon, the messenger RNA (mRNA) abundance was ∼25% of rbcL transcript and RsRubisco ∼40% the Rubisco content in WT tobacco. To mitigate the low activation status of RsRubisco in tobRsLS (∼23% sites active under ambient CO2), the metabolic repair protein RsRca (Rs-activase) was introduced via nuclear transformation. RsRca production in the tobRsLS::X progeny matched endogenous tobacco Rca levels (∼1 µmol protomer·m2) and enhanced RsRubisco activation to 75% under elevated CO2 (1%, vol/vol) growth. Accordingly, the rate of photosynthesis and growth in the tobRsLS::X lines were improved >twofold relative to tobRsLS. Other tobacco lines producing RsRubisco containing alternate diatom and red algae S-subunits were nonviable as CO2-fixation rates (kcatc) were reduced >95% and CO2/O2 specificity impaired 30-50%. We show differences in hybrid and WT RsRubisco biogenesis in tobacco correlated with assembly in Escherichia coli advocating use of this bacterium to preevaluate the kinetic and chloroplast compatibility of engineered RsRubisco, an isoform amenable to directed evolution.
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Affiliation(s)
- Laura H Gunn
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Elena Martin Avila
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Rosemary Birch
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Spencer M Whitney
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
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43
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Cavanagh AP. Big progress for small subunits: new Rubisco mutants in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5721-5724. [PMID: 33027530 PMCID: PMC7541911 DOI: 10.1093/jxb/eraa360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This article comments on:
Khumsupan P, Kozlowska MA, Orr DJ, Andreou AI, Nakayama N, Patron N, Carmo-Silva E, McCormick AJ. 2020. Generating and characterizing single- and multigene mutants of the Rubisco small subunit family in Arabidopsis. Journal of Experimental Botany 71, 5963–5975.
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Affiliation(s)
- Amanda P Cavanagh
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, UK
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44
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Lin MT, Stone WD, Chaudhari V, Hanson MR. Small subunits can determine enzyme kinetics of tobacco Rubisco expressed in Escherichia coli. NATURE PLANTS 2020; 6:1289-1299. [PMID: 32929197 DOI: 10.1038/s41477-020-00761-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 07/28/2020] [Indexed: 05/19/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase-oxygenase (Rubisco) catalyses the first step in carbon fixation and is a strategic target for improving photosynthetic efficiency. In plants, Rubisco is composed of eight large and eight small subunits, and its biogenesis requires multiple chaperones. Here, we optimized a system to produce tobacco Rubisco in Escherichia coli by coexpressing chaperones in autoinduction medium. We successfully assembled tobacco Rubisco in E. coli with each small subunit that is normally encoded by the nuclear genome. Even though each enzyme carries only a single type of small subunit in E. coli, the enzymes exhibit carboxylation kinetics that are very similar to the carboxylation kinetics of the native Rubisco. Tobacco Rubisco assembled with a recently discovered trichome small subunit has a higher catalytic rate and a lower CO2 affinity compared with Rubisco complexes that are assembled with other small subunits. Our E. coli expression system will enable the analysis of features of both subunits of Rubisco that affect its kinetic properties.
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Affiliation(s)
- Myat T Lin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - William D Stone
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Applied Physics Laboratory, Johns Hopkins University, Laurel, MD, USA
| | | | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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Affiliation(s)
- Robert E Sharwood
- ARC Centre of Excellence for Translation Photosynthesis, Research School Biology, Australian National University, Canberra, Australian Capital Territory, Australia.
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia.
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46
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Sales CRG, da Silva AB, Carmo-Silva E. Measuring Rubisco activity: challenges and opportunities of NADH-linked microtiter plate-based and 14C-based assays. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5302-5312. [PMID: 32728715 PMCID: PMC7501812 DOI: 10.1093/jxb/eraa289] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/22/2020] [Indexed: 05/28/2023]
Abstract
Rubisco is central to carbon assimilation, and efforts to improve the efficiency and sustainability of crop production have spurred interest in phenotyping Rubisco activity. We tested the hypothesis that microtiter plate-based methods provide comparable results to those obtained with the radiometric assay that measures the incorporation of 14CO2 into 3-phosphoglycerate (3-PGA). Three NADH-linked assays were tested that use alternative coupling enzymes: glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and glycerolphosphate dehydrogenase (GlyPDH); phosphoenolpyruvate carboxylase (PEPC) and malate dehydrogenase (MDH); and pyruvate kinase (PK) and lactate dehydrogenase (LDH). To date there has been no thorough evaluation of their reliability by comparison with the 14C-based method. The three NADH-linked assays were used in parallel to estimate (i) the 3-PGA concentration-response curve of NADH oxidation, (ii) the Michaelis-Menten constant for ribulose-1,5-bisphosphate, (iii) fully active and inhibited Rubisco activities, and (iv) Rubisco initial and total activities in fully illuminated and shaded leaves. All three methods correlated strongly with the 14C-based method, and the PK-LDH method showed a strong correlation and was the cheapest method. PEPC-MDH would be a suitable option for situations in which ADP/ATP might interfere with the assay. GAPDH-GlyPDH proved more laborious than the other methods. Thus, we recommend the PK-LDH method as a reliable, cheaper, and higher throughput method to phenotype Rubisco activity for crop improvement efforts.
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Affiliation(s)
- Cristina R G Sales
- Lancaster Environment Centre, Lancaster University, Library Avenue, Lancaster, UK
| | - Anabela Bernardes da Silva
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
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Davidi D, Shamshoum M, Guo Z, Bar‐On YM, Prywes N, Oz A, Jablonska J, Flamholz A, Wernick DG, Antonovsky N, de Pins B, Shachar L, Hochhauser D, Peleg Y, Albeck S, Sharon I, Mueller‐Cajar O, Milo R. Highly active rubiscos discovered by systematic interrogation of natural sequence diversity. EMBO J 2020; 39:e104081. [PMID: 32500941 PMCID: PMC7507306 DOI: 10.15252/embj.2019104081] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 04/30/2020] [Accepted: 05/07/2020] [Indexed: 11/09/2022] Open
Abstract
CO2 is converted into biomass almost solely by the enzyme rubisco. The poor carboxylation properties of plant rubiscos have led to efforts that made it the most kinetically characterized enzyme, yet these studies focused on < 5% of its natural diversity. Here, we searched for fast-carboxylating variants by systematically mining genomic and metagenomic data. Approximately 33,000 unique rubisco sequences were identified and clustered into ≈ 1,000 similarity groups. We then synthesized, purified, and biochemically tested the carboxylation rates of 143 representatives, spanning all clusters of form-II and form-II/III rubiscos. Most variants (> 100) were active in vitro, with the fastest having a turnover number of 22 ± 1 s-1 -sixfold faster than the median plant rubisco and nearly twofold faster than the fastest measured rubisco to date. Unlike rubiscos from plants and cyanobacteria, the fastest variants discovered here are homodimers and exhibit a much simpler folding and activation kinetics. Our pipeline can be utilized to explore the kinetic space of other enzymes of interest, allowing us to get a better view of the biosynthetic potential of the biosphere.
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Affiliation(s)
- Dan Davidi
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
- Present address:
Department of GeneticsHarvard Medical SchoolBostonMAUSA
| | - Melina Shamshoum
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Zhijun Guo
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Yinon M Bar‐On
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Noam Prywes
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - Aia Oz
- Migal Galilee Research InstituteKiryat ShmonaIsrael
- Tel Hai CollegeUpper GalileeIsrael
| | - Jagoda Jablonska
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Avi Flamholz
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - David G Wernick
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
- Present address:
BASF Enzymes LLCSan DiegoCAUSA
| | - Niv Antonovsky
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
- Present address:
Laboratory of Genetically Encoded Small MoleculesThe Rockefeller UniversityNew YorkNYUSA
| | - Benoit de Pins
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Lior Shachar
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Dina Hochhauser
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Yoav Peleg
- Department of Life Sciences Core FacilitiesWeizmann Institute of ScienceRehovotIsrael
| | - Shira Albeck
- Department of Life Sciences Core FacilitiesWeizmann Institute of ScienceRehovotIsrael
| | - Itai Sharon
- Migal Galilee Research InstituteKiryat ShmonaIsrael
- Tel Hai CollegeUpper GalileeIsrael
| | | | - Ron Milo
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
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48
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von Caemmerer S. Rubisco carboxylase/oxygenase: From the enzyme to the globe: A gas exchange perspective. JOURNAL OF PLANT PHYSIOLOGY 2020; 252:153240. [PMID: 32707452 DOI: 10.1016/j.jplph.2020.153240] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 07/12/2020] [Indexed: 05/28/2023]
Abstract
Rubisco is the primary carboxylase of the photosynthetic process, the most abundant enzyme in the biosphere, and also one of the best-characterized enzymes. Rubisco also functions as an oxygenase, a discovery made 50 years ago by Bill Ogren. Carboxylation of ribulose bisphosphate (RuBP) is the first step of the photosynthetic carbon reduction cycle and leads to the assimilation of CO2, whereas the oxygenase activity necessitates the recycling of phosphoglycolate through the photorespiratory carbon oxidation cycle with concomitant loss of CO2. Since the discovery of Rubisco's dual function, the biochemical properties of Rubisco have underpinned the mechanistic mathematical models of photosynthetic CO2 fixation which link Rubisco kinetic properties to gas exchange of leaves. This has allowed assessments of global CO2 exchange and predictions of how Rubisco has and will shape the environmental responses of crop and global photosynthesis in future climates. Rubisco's biochemical properties, including its slow catalytic turnover and poor affinity for CO2, constrain crop growth and therefore improving its activity and regulation and minimising photorespiration are key targets for crop improvement.
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Affiliation(s)
- Susanne von Caemmerer
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, The Australian National University, Acton, Australian Capital Territory, 2601, Australia.
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49
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Deans RM, Brodribb TJ, Busch FA, Farquhar GD. Optimization can provide the fundamental link between leaf photosynthesis, gas exchange and water relations. NATURE PLANTS 2020; 6:1116-1125. [PMID: 32895529 DOI: 10.1038/s41477-020-00760-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 07/28/2020] [Indexed: 05/12/2023]
Abstract
Tight coordination in the photosynthetic, gas exchange and water supply capacities of leaves is a globally conserved trend across land plants. Strong selective constraints on leaf carbon gain create the opportunity to use quantitative optimization theory to understand the connected evolution of leaf photosynthesis and water relations. We developed an analytical optimization model that maximizes the long-term rate of leaf carbon gain, given the carbon costs in building and maintaining stomata, leaf hydraulics and osmotic pressure. Our model demonstrates that selection for optimal gain should drive coordination between key photosynthetic, gas exchange and water relations traits. It also provides predictions of adaptation to drought and the relative costs of key leaf functional traits. Our results show that optimization in terms of carbon gain, given the carbon costs of physiological traits, successfully unites leaf photosynthesis and water relations and provides a quantitative framework to consider leaf functional evolution and adaptation.
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Affiliation(s)
- Ross M Deans
- ARC Centre of Excellence in Translational Photosynthesis, Division of Plant Science, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Timothy J Brodribb
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Florian A Busch
- ARC Centre of Excellence in Translational Photosynthesis, Division of Plant Science, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Graham D Farquhar
- ARC Centre of Excellence in Translational Photosynthesis, Division of Plant Science, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.
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50
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Furbank RT, Sharwood R, Estavillo GM, Silva-Perez V, Condon AG. Photons to food: genetic improvement of cereal crop photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2226-2238. [PMID: 32083680 PMCID: PMC7135014 DOI: 10.1093/jxb/eraa077] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/17/2020] [Indexed: 05/05/2023]
Abstract
Photosynthesis has become a major trait of interest for cereal yield improvement as breeders appear to have reached the theoretical genetic limit for harvest index, the mass of grain as a proportion of crop biomass. Yield improvements afforded by the adoption of green revolution dwarfing genes to wheat and rice are becoming exhausted, and improvements in biomass and radiation use efficiency are now sought in these crops. Exploring genetic diversity in photosynthesis is now possible using high-throughput techniques, and low-cost genotyping facilitates discovery of the genetic architecture underlying this variation. Photosynthetic traits have been shown to be highly heritable, and significant variation is present for these traits in available germplasm. This offers hope that breeding for improved photosynthesis and radiation use efficiency in cereal crops is tractable and a useful shorter term adjunct to genetic and genome engineering to boost yield potential.
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Affiliation(s)
- Robert T Furbank
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Canberra, ACT, Australia
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Robert Sharwood
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Canberra, ACT, Australia
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