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Chéron N. Binding Sites of Bicarbonate in Phosphoenolpyruvate Carboxylase. J Chem Inf Model 2024; 64:3375-3385. [PMID: 38533570 DOI: 10.1021/acs.jcim.3c01830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is used in plant metabolism for fruit maturation or seed development as well as in the C4 and crassulacean acid metabolism (CAM) mechanisms in photosynthesis, where it is used for the capture of hydrated CO2 (bicarbonate). To find the yet unknown binding site of bicarbonate in this enzyme, we have first identified putative binding sites with nonequilibrium molecular dynamics simulations and then ranked these sites with alchemical free energy calculations with corrections of computational artifacts. Fourteen pockets where bicarbonate could bind were identified, with three having realistic binding free energies with differences with the experimental value below 1 kcal/mol. One of these pockets is found far from the active site at 14 Å and predicted to be an allosteric binding site. In the two other binding sites, bicarbonate is in direct interaction with the magnesium ion; neither sequence alignment nor the study of mutant K606N allowed to discriminate between these two pockets, and both are good candidates as the binding site of bicarbonate in phosphoenolpyruvate carboxylase.
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Affiliation(s)
- Nicolas Chéron
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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2
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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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3
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Saha S, Purkayastha S, K N, Ganguly S, Das S, Ganguly S, Sinha Mahapatra N, Bhattacharya K, Das D, Saha AK, Biswas T, Bhattacharyya PK, Bhattacharyya S. Rice ( Oryza sativa) alleviates photosynthesis and yield loss by limiting specific leaf weight under low light intensity. FUNCTIONAL PLANT BIOLOGY : FPB 2023; 50:267-276. [PMID: 36624487 DOI: 10.1071/fp22241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
The physiological mechanisms of shade tolerance and trait plasticity variations under shade remain poorly understood in rice (Oryza sativa L.). Twenty-five genotypes of rice were evaluated under open and shade conditions. Various parameters to identify variations in the plasticity of these traits in growth irradiance were measured. We found wide variations in specific leaf weight (SLW) and net assimilation rate measured at 400µmolm-2 s-1 photosynthetic photon flux density (PPFD; referred to as A 400 ) among the genotypes. Under shade, tolerant genotypes maintained a high rate of net photosynthesis by limiting specific leaf weight accompanied by increased intercellular CO2 concentration (C i ) compared with open-grown plants. On average, net photosynthesis was enhanced by 20% under shade, with a range of 2-30%. Increased accumulation of biomass under shade was observed, but it showed no correlation with photosynthetic plasticity. Chlorophyll a /b ratio also showed no association with photosynthetic rate and yield. Analysis of variance showed that 11%, 16%, and 37% of the total variance of A 400 , SLW, and C i were explained due to differences in growth irradiance. SLW and A 400 plasticity in growth irradiance was associated with yield loss alleviation with R 2 values of 0.37 and 0.16, respectively. Biomass accumulation was associated with yield loss alleviation under shade, but no correlation was observed between A 400 and leaf-N concentration. Thus, limiting specific leaf weight accompanied by increased C i rather than leaf nitrogen concentration might have allowed rice genotypes to maintain a high net photosynthesis rate per unit leaf area and high yield under shade.
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Affiliation(s)
- Shoumik Saha
- Department of Genetics and Plant Breeding, Crop Research Unit, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, PIN 741252, West Bengal, India
| | - Shampa Purkayastha
- Department of Genetics and Plant Breeding, Crop Research Unit, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, PIN 741252, West Bengal, India
| | - Nimitha K
- Department of Genetics and Plant Breeding, Crop Research Unit, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, PIN 741252, West Bengal, India
| | - Sebantee Ganguly
- Department of Genetics and Plant Breeding, Crop Research Unit, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, PIN 741252, West Bengal, India
| | - Subhadeep Das
- Department of Genetics and Plant Breeding, Crop Research Unit, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, PIN 741252, West Bengal, India
| | - Shamba Ganguly
- Department of Genetics and Plant Breeding, Crop Research Unit, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, PIN 741252, West Bengal, India
| | - Nilanjan Sinha Mahapatra
- Department of Genetics and Plant Breeding, Crop Research Unit, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, PIN 741252, West Bengal, India
| | - Kriti Bhattacharya
- Department of Genetics and Plant Breeding, Crop Research Unit, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, PIN 741252, West Bengal, India
| | - Dibakar Das
- Department of Genetics and Plant Breeding, Crop Research Unit, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, PIN 741252, West Bengal, India
| | - Arup K Saha
- Department of Genetics and Plant Breeding, Crop Research Unit, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, PIN 741252, West Bengal, India
| | - Tirthankar Biswas
- Department of Genetics and Plant Breeding, Crop Research Unit, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, PIN 741252, West Bengal, India
| | - Prabir K Bhattacharyya
- Department of Genetics and Plant Breeding, Crop Research Unit, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, PIN 741252, West Bengal, India
| | - Somnath Bhattacharyya
- Department of Genetics and Plant Breeding, Crop Research Unit, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, PIN 741252, West Bengal, India
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4
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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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5
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Ang WSL, How JA, How JB, Mueller-Cajar O. The stickers and spacers of Rubiscondensation: assembling the centrepiece of biophysical CO2-concentrating mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:612-626. [PMID: 35903998 DOI: 10.1093/jxb/erac321] [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: 05/12/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Aquatic autotrophs that fix carbon using ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) frequently expend metabolic energy to pump inorganic carbon towards the enzyme's active site. A central requirement of this strategy is the formation of highly concentrated Rubisco condensates (or Rubiscondensates) known as carboxysomes and pyrenoids, which have convergently evolved multiple times in prokaryotes and eukaryotes, respectively. Recent data indicate that these condensates form by the mechanism of liquid-liquid phase separation. This mechanism requires networks of weak multivalent interactions typically mediated by intrinsically disordered scaffold proteins. Here we comparatively review recent rapid developments that detail the determinants and precise interactions that underlie diverse Rubisco condensates. The burgeoning field of biomolecular condensates has few examples where liquid-liquid phase separation can be linked to clear phenotypic outcomes. When present, Rubisco condensates are essential for photosynthesis and growth, and they are thus emerging as powerful and tractable models to investigate the structure-function relationship of phase separation in biology.
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Affiliation(s)
- Warren Shou Leong Ang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Jian Ann How
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Jian Boon How
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
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6
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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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7
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Wang A, Lv J, Wang J, Shi K. CO 2 enrichment in greenhouse production: Towards a sustainable approach. FRONTIERS IN PLANT SCIENCE 2022; 13:1029901. [PMID: 36340349 PMCID: PMC9634482 DOI: 10.3389/fpls.2022.1029901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/07/2022] [Indexed: 05/03/2023]
Abstract
As the unique source of carbon in the atmosphere, carbon dioxide (CO2) exerts a strong impact on crop yield and quality. However, CO2 deficiency in greenhouses during the daytime often limits crop productivity. Crucially, climate warming, caused by increased atmospheric CO2, urges global efforts to implement carbon reduction and neutrality, which also bring challenges to current CO2 enrichment systems applied in greenhouses. Thus, there is a timely need to develop cost-effective and environmentally friendly CO2 enrichment technologies as a sustainable approach to promoting agricultural production and alleviating environmental burdens simultaneously. Here we review several common technologies of CO2 enrichment in greenhouse production, and their characteristics and limitations. Some control strategies of CO2 enrichment in distribution, period, and concentration are also discussed. We further introduce promising directions for future CO2 enrichment including 1) agro-industrial symbiosis system (AIS); 2) interdisciplinary application of carbon capture and utilization (CCU); and 3) optimization of CO2 assimilation in C3 crops via biotechnologies. This review aims to provide perspectives on efficient CO2 utilization in greenhouse production.
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Affiliation(s)
- Anran Wang
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Jianrong Lv
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Jiao Wang
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Kai Shi
- Department of Horticulture, Zhejiang University, Hangzhou, China
- Yazhou Bay Science and Technology City, Hainan Institute, Zhejiang University, Sanya, China
- *Correspondence: Kai Shi,
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8
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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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9
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Hussain S, Ulhassan Z, Brestic M, Zivcak M, Allakhverdiev SI, Yang X, Safdar ME, Yang W, Liu W. Photosynthesis research under climate change. PHOTOSYNTHESIS RESEARCH 2021; 150:5-19. [PMID: 34235625 DOI: 10.1007/s11120-021-00861-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 06/28/2021] [Indexed: 05/13/2023]
Abstract
Increasing global population and climate change uncertainties have compelled increased photosynthetic efficiency and yields to ensure food security over the coming decades. Potentially, genetic manipulation and minimization of carbon or energy losses can be ideal to boost photosynthetic efficiency or crop productivity. Despite significant efforts, limited success has been achieved. There is a need for thorough improvement in key photosynthetic limiting factors, such as stomatal conductance, mesophyll conductance, biochemical capacity combined with Rubisco, the Calvin-Benson cycle, thylakoid membrane electron transport, nonphotochemical quenching, and carbon metabolism or fixation pathways. In addition, the mechanistic basis for the enhancement in photosynthetic adaptation to environmental variables such as light intensity, temperature and elevated CO2 requires further investigation. This review sheds light on strategies to improve plant photosynthesis by targeting these intrinsic photosynthetic limitations and external environmental factors.
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Affiliation(s)
- Sajad Hussain
- College of Agronomy, Sichuan Agricultural University, 211-Huimin Road, Wenjiang District, Chengdu, 611130, People's Republic of China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China (Ministry of Agriculture), Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Zaid Ulhassan
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Laboratory of Spectroscopy Sensing, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Marian Brestic
- Department of Plant Physiology, Slovak University of Agriculture, 94976, Nitra, Slovakia
| | - Marek Zivcak
- Department of Plant Physiology, Slovak University of Agriculture, 94976, Nitra, Slovakia
| | - Suleyman I Allakhverdiev
- К.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya St. 35, Moscow, Russia, 127276
| | - Xinghong Yang
- Department of Plant Physiology, College of Life Sciences, Shandong Agricultural University, Daizong Road No. 61, 271018, Taian, People's Republic of China
| | | | - Wenyu Yang
- College of Agronomy, Sichuan Agricultural University, 211-Huimin Road, Wenjiang District, Chengdu, 611130, People's Republic of China.
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China (Ministry of Agriculture), Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, People's Republic of China.
| | - Weiguo Liu
- College of Agronomy, Sichuan Agricultural University, 211-Huimin Road, Wenjiang District, Chengdu, 611130, People's Republic of China.
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China (Ministry of Agriculture), Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, People's Republic of China.
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10
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Bouvier JW, Emms DM, Rhodes T, Bolton JS, Brasnett A, Eddershaw A, Nielsen JR, Unitt A, Whitney SM, Kelly S. Rubisco Adaptation Is More Limited by Phylogenetic Constraint Than by Catalytic Trade-off. Mol Biol Evol 2021; 38:2880-2896. [PMID: 33739416 PMCID: PMC8233502 DOI: 10.1093/molbev/msab079] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Rubisco assimilates CO2 to form the sugars that fuel life on earth. Correlations between rubisco kinetic traits across species have led to the proposition that rubisco adaptation is highly constrained by catalytic trade-offs. However, these analyses did not consider the phylogenetic context of the enzymes that were analyzed. Thus, it is possible that the correlations observed were an artefact of the presence of phylogenetic signal in rubisco kinetics and the phylogenetic relationship between the species that were sampled. Here, we conducted a phylogenetically resolved analysis of rubisco kinetics and show that there is a significant phylogenetic signal in rubisco kinetic traits. We re-evaluated the extent of catalytic trade-offs accounting for this phylogenetic signal and found that all were attenuated. Following phylogenetic correction, the largest catalytic trade-offs were observed between the Michaelis constant for CO2 and carboxylase turnover (∼21-37%), and between the Michaelis constants for CO2 and O2 (∼9-19%), respectively. All other catalytic trade-offs were substantially attenuated such that they were marginal (<9%) or non-significant. This phylogenetically resolved analysis of rubisco kinetic evolution also identified kinetic changes that occur concomitant with the evolution of C4 photosynthesis. Finally, we show that phylogenetic constraints have played a larger role than catalytic trade-offs in limiting the evolution of rubisco kinetics. Thus, although there is strong evidence for some catalytic trade-offs, rubisco adaptation has been more limited by phylogenetic constraint than by the combined action of all catalytic trade-offs.
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Affiliation(s)
- Jacques W Bouvier
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- Doctoral Training Centre, University of Oxford, Oxford, United Kingdom
| | - David M Emms
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Timothy Rhodes
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Jai S Bolton
- Doctoral Training Centre, University of Oxford, Oxford, United Kingdom
| | - Amelia Brasnett
- Doctoral Training Centre, University of Oxford, Oxford, United Kingdom
| | - Alice Eddershaw
- Doctoral Training Centre, University of Oxford, Oxford, United Kingdom
| | - Jochem R Nielsen
- Doctoral Training Centre, University of Oxford, Oxford, United Kingdom
| | - Anastasia Unitt
- Doctoral Training Centre, University of Oxford, Oxford, United Kingdom
| | - Spencer M Whitney
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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11
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Shao Y, Li S, Gao L, Sun C, Hu J, Ullah A, Gao J, Li X, Liu S, Jiang D, Cao W, Tian Z, Dai T. Magnesium Application Promotes Rubisco Activation and Contributes to High-Temperature Stress Alleviation in Wheat During the Grain Filling. FRONTIERS IN PLANT SCIENCE 2021; 12:675582. [PMID: 34177993 PMCID: PMC8231710 DOI: 10.3389/fpls.2021.675582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/21/2021] [Indexed: 06/01/2023]
Abstract
Inhibited photosynthesis caused by post-anthesis high-temperature stress (HTS) leads to decreased wheat grain yield. Magnesium (Mg) plays critical roles in photosynthesis; however, its function under HTS during wheat grain filling remains poorly understood. Therefore, in this study, we investigated the effects of Mg on the impact of HTS on photosynthesis during wheat grain filling by conducting pot experiments in controlled-climate chambers. Plants were subjected to a day/night temperature cycle of 32°C/22°C for 5 days during post-anthesis; the control temperature was set at 26°C/16°C. Mg was applied at the booting stage, with untreated plants used as a control. HTS reduced the yield and net photosynthetic rate (P n ) of wheat plants. The maximum carboxylation rate (V Cmax ), which is limited by Rubisco activity, decreased earlier than the light-saturated potential electron transport rate. This decrease in V Cmax was caused by decreased Rubisco activation state under HTS. Mg application reduced yield loss by stabilizing P n . Rubisco activation was enhanced by increasing Rubisco activase activity following Mg application, thereby stabilizing P n . We conclude that Mg maintains Rubisco activation, thereby helping to stabilize P n under HTS.
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Affiliation(s)
- Yuhang Shao
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Shiyu Li
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Lijun Gao
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Chuanjiao Sun
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Jinling Hu
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Attiq Ullah
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Jingwen Gao
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Xinxin Li
- Rural Energy and Environment Agency, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Sixi Liu
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
- Chengdu Agricultural Technology Extension Station, Chengdu, China
| | - Dong Jiang
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Weixing Cao
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Zhongwei Tian
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Tingbo Dai
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
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12
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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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Biophysical analysis of the structural evolution of substrate specificity in RuBisCO. Proc Natl Acad Sci U S A 2020; 117:30451-30457. [PMID: 33199597 DOI: 10.1073/pnas.2018939117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the most abundant enzyme on Earth. However, its catalytic rate per molecule of protein is extremely slow and the binding of the primary substrate, CO2, is competitively displaced by O2. Hence, carbon fixation by RuBisCO is highly inefficient; indeed, in higher C3 plants, about 30% of the time the enzyme mistakes CO2 for O2 Using genomic and structural analysis, we identify regions around the catalytic site that play key roles in discriminating between CO2 and O2 Our analysis identified positively charged cavities directly around the active site, which are expanded as the enzyme evolved with higher substrate specificity. The residues that extend these cavities have recently been under selective pressure, indicating that larger charged pockets are a feature of modern RuBisCOs, enabling greater specificity for CO2 This paper identifies a key structural feature that enabled the enzyme to evolve improved CO2 sequestration in an oxygen-rich atmosphere and may guide the engineering of more efficient RuBisCOs.
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Douglas-Gallardo OA, Shepherd I, Bennie SJ, Ranaghan KE, Mulholland AJ, Vöhringer-Martinez E. Electronic structure benchmark calculations of CO 2 fixing elementary chemical steps in RuBisCO using the projector-based embedding approach. J Comput Chem 2020; 41:2151-2157. [PMID: 32640497 DOI: 10.1002/jcc.26380] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/13/2020] [Indexed: 11/10/2022]
Abstract
Ribulose 1,5-bisphosphate carboxylase-oxygenase (RuBisCO) is the main enzyme involved in atmospheric carbon dioxide (CO2 ) fixation in the biosphere. This enzyme catalyzes a set of five chemical steps that take place in the same active-site within magnesium (II) coordination sphere. Here, a set of electronic structure benchmark calculations have been carried out on a reaction path proposed by Gready et al. by means of the projector-based embedding approach. Activation and reaction energies for all main steps catalyzed by RuBisCO have been calculated at the MP2, SCS-MP2, CCSD, and CCSD(T)/aug-cc-pVDZ and cc-pVDZ levels of theory. The treatment of the magnesium cation with post-HF methods is explored to determine the nature of its involvement in the mechanism. With the high-level ab initio values as a reference, we tested the performance of a set of density functional theory (DFT) exchange-correlation (xc) functionals in reproducing the reaction energetics of RuBisCO carboxylase activity on a set of model fragments. Different DFT xc-functionals show large variation in activation and reaction energies. Activation and reaction energies computed at the B3LYP level are close to the reference SCS-MP2 results for carboxylation, hydration and protonation reactions. However, for the carbon-carbon bond dissociation reaction, B3LYP and other functionals give results that differ significantly from the ab initio reference values. The results show the applicability of the projector-based embedding approach to metalloenzymes. This technique removes the uncertainty associated with the selection of different DFT xc-functionals and so can overcome some of inherent limitations of DFT calculations, complementing, and potentially adding to modeling of enzyme reaction mechanisms with DFT methods.
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Affiliation(s)
- Oscar A Douglas-Gallardo
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile
| | - Ian Shepherd
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Simon J Bennie
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Kara E Ranaghan
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile
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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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Goudet MMM, Orr DJ, Melkonian M, Müller KH, Meyer MT, Carmo-Silva E, Griffiths H. Rubisco and carbon-concentrating mechanism co-evolution across chlorophyte and streptophyte green algae. THE NEW PHYTOLOGIST 2020; 227:810-823. [PMID: 32249430 DOI: 10.1111/nph.16577] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/23/2020] [Indexed: 05/19/2023]
Abstract
Green algae expressing a carbon-concentrating mechanism (CCM) are usually associated with a Rubisco-containing micro-compartment, the pyrenoid. A link between the small subunit (SSU) of Rubisco and pyrenoid formation in Chlamydomonas reinhardtii has previously suggested that specific RbcS residues could explain pyrenoid occurrence in green algae. A phylogeny of RbcS was used to compare the protein sequence and CCM distribution across the green algae and positive selection in RbcS was estimated. For six streptophyte algae, Rubisco catalytic properties, affinity for CO2 uptake (K0.5 ), carbon isotope discrimination (δ13 C) and pyrenoid morphology were compared. The length of the βA-βB loop in RbcS provided a phylogenetic marker discriminating chlorophyte from streptophyte green algae. Rubisco kinetic properties in streptophyte algae have responded to the extent of inducible CCM activity, as indicated by changes in inorganic carbon uptake affinity, δ13 C and pyrenoid ultrastructure between high and low CO2 conditions for growth. We conclude that the Rubisco catalytic properties found in streptophyte algae have coevolved and reflect the strength of any CCM or degree of pyrenoid leakiness, and limitations to inorganic carbon in the aquatic habitat, whereas Rubisco in extant land plants reflects more recent selective pressures associated with improved diffusive supply of the terrestrial environment.
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Affiliation(s)
- Myriam M M Goudet
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Douglas J Orr
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Michael Melkonian
- Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, 50674, Cologne, Germany
- Central Collection of Algal Cultures, Faculty of Biology, University of Duisburg-Essen, 45141, Essen, Germany
| | - Karin H Müller
- Cambridge Advanced Imaging Centre, University of Cambridge, Cambridge, CB2 3DY, UK
| | - Moritz T Meyer
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | | | - Howard Griffiths
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
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Cummins PL, Gready JE. Kohn-Sham Density Functional Calculations Reveal Proton Wires in the Enolization and Carboxylase Reactions Catalyzed by Rubisco. J Phys Chem B 2020; 124:3015-3026. [PMID: 32208706 DOI: 10.1021/acs.jpcb.0c01169] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Ribulose 1,5-bisphosphate (RuBP) carboxylase-oxygenase (Rubisco) plays a fundamental role in the carbon cycle by fixing the atmospheric CO2 used in photosynthesis. Rubisco is all the more remarkable because it must catalyze some difficult multistep reaction chemistry involving proton transfers within the one active site. In the present study, we have used Kohn-Sham density functional theory at the B3LYP/6-31G* level with basis set superposition error and dispersion corrections (B3LYP-gCP-D3) to examine the possibility that the proton transfers can take place through molecular wires (including active-site water molecules) via the classical Grotthuss proton-shuttle mechanism. The results support an essential role for water molecules found in the crystal structures of Rubisco complexes as facilitators of proton transport in all the rate-limiting (catalytic) reaction steps through a network of short proton wires within the Rubisco active site. We suggest that completion of the initial product turnover (cycle) requires two excess protons produced in the initial carbamylation that is required for Rubisco activation. By use of proton wires, a large number of reaction steps may be accommodated within a single active site without necessitating the input of excessive conformational strain energy arising from the movement of residue side chains into positions where direct protonation of substrates can occur. The involvement of the identified types of proton wires in the kinetic mechanism is capable of providing a unique explanation for various experimental observations, including deuterium isotope effects and the results of site-directed mutagenesis experiments, and may thus provide a realistic solution to the problem of Rubisco's challenging chemistry.
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Affiliation(s)
- Peter L Cummins
- Department of Genome Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 0200, Australia
| | - Jill E Gready
- Department of Genome Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 0200, Australia
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18
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Mesophyll conductance: the leaf corridors for photosynthesis. Biochem Soc Trans 2020; 48:429-439. [DOI: 10.1042/bst20190312] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/25/2020] [Accepted: 01/30/2020] [Indexed: 12/15/2022]
Abstract
Besides stomata, the photosynthetic CO2 pathway also involves the transport of CO2 from the sub-stomatal air spaces inside to the carboxylation sites in the chloroplast stroma, where Rubisco is located. This pathway is far to be a simple and direct way, formed by series of consecutive barriers that the CO2 should cross to be finally assimilated in photosynthesis, known as the mesophyll conductance (gm). Therefore, the gm reflects the pathway through different air, water and biophysical barriers within the leaf tissues and cell structures. Currently, it is known that gm can impose the same level of limitation (or even higher depending of the conditions) to photosynthesis than the wider known stomata or biochemistry. In this mini-review, we are focused on each of the gm determinants to summarize the current knowledge on the mechanisms driving gm from anatomical to metabolic and biochemical perspectives. Special attention deserve the latest studies demonstrating the importance of the molecular mechanisms driving anatomical traits as cell wall and the chloroplast surface exposed to the mesophyll airspaces (Sc/S) that significantly constrain gm. However, even considering these recent discoveries, still is poorly understood the mechanisms about signaling pathways linking the environment a/biotic stressors with gm responses. Thus, considering the main role of gm as a major driver of the CO2 availability at the carboxylation sites, future studies into these aspects will help us to understand photosynthesis responses in a global change framework.
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Iñiguez C, Capó-Bauçà S, Niinemets Ü, Stoll H, Aguiló-Nicolau P, Galmés J. Evolutionary trends in RuBisCO kinetics and their co-evolution with CO 2 concentrating mechanisms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:897-918. [PMID: 31820505 DOI: 10.1111/tpj.14643] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 11/15/2019] [Accepted: 11/27/2019] [Indexed: 05/19/2023]
Abstract
RuBisCO-catalyzed CO2 fixation is the main source of organic carbon in the biosphere. This enzyme is present in all domains of life in different forms (III, II, and I) and its origin goes back to 3500 Mya, when the atmosphere was anoxygenic. However, the RuBisCO active site also catalyzes oxygenation of ribulose 1,5-bisphosphate, therefore, the development of oxygenic photosynthesis and the subsequent oxygen-rich atmosphere promoted the appearance of CO2 concentrating mechanisms (CCMs) and/or the evolution of a more CO2 -specific RuBisCO enzyme. The wide variability in RuBisCO kinetic traits of extant organisms reveals a history of adaptation to the prevailing CO2 /O2 concentrations and the thermal environment throughout evolution. Notable differences in the kinetic parameters are found among the different forms of RuBisCO, but the differences are also associated with the presence and type of CCMs within each form, indicative of co-evolution of RuBisCO and CCMs. Trade-offs between RuBisCO kinetic traits vary among the RuBisCO forms and also among phylogenetic groups within the same form. These results suggest that different biochemical and structural constraints have operated on each type of RuBisCO during evolution, probably reflecting different environmental selective pressures. In a similar way, variations in carbon isotopic fractionation of the enzyme point to significant differences in its relationship to the CO2 specificity among different RuBisCO forms. A deeper knowledge of the natural variability of RuBisCO catalytic traits and the chemical mechanism of RuBisCO carboxylation and oxygenation reactions raises the possibility of finding unrevealed landscapes in RuBisCO evolution.
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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
| | - Sebastià Capó-Bauçà
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, 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
| | - Heather Stoll
- Department of Earth Sciences, ETH Zürich, Sonnegstrasse 5, 8092, Zürich, Switzerland
| | - Pere Aguiló-Nicolau
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
| | - Jeroni Galmés
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
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Hermida-Carrera C, Fares MA, Font-Carrascosa M, Kapralov MV, Koch MA, Mir A, Molins A, Ribas-Carbó M, Rocha J, Galmés J. Exploring molecular evolution of Rubisco in C 3 and CAM Orchidaceae and Bromeliaceae. BMC Evol Biol 2020; 20:11. [PMID: 31969115 PMCID: PMC6977233 DOI: 10.1186/s12862-019-1551-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 11/29/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The CO2-concentrating mechanism associated to Crassulacean acid metabolism (CAM) alters the catalytic context for Rubisco by increasing CO2 availability and provides an advantage in particular ecological conditions. We hypothesized about the existence of molecular changes linked to these particular adaptations in CAM Rubisco. We investigated molecular evolution of the Rubisco large (L-) subunit in 78 orchids and 144 bromeliads with C3 and CAM photosynthetic pathways. The sequence analyses were complemented with measurements of Rubisco kinetics in some species with contrasting photosynthetic mechanism and differing in the L-subunit sequence. RESULTS We identified potential positively selected sites and residues with signatures of co-adaptation. The implementation of a decision tree model related Rubisco specific variable sites to the leaf carbon isotopic composition of the species. Differences in the Rubisco catalytic traits found among C3 orchids and between strong CAM and C3 bromeliads suggested Rubisco had evolved in response to differing CO2 concentration. CONCLUSIONS The results revealed that the variability in the Rubisco L-subunit sequence in orchids and bromeliads is composed of coevolving sites under potential positive adaptive signal. The sequence variability was related to δ13C in orchids and bromeliads, however it could not be linked to the variability found in the kinetic properties of the studied species.
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Affiliation(s)
- Carmen Hermida-Carrera
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Ctra. Valldemossa km. 7.5, 07122 Palma, Illes Balears Spain
| | - Mario A. Fares
- Integrative and Systems Biology Group, Department of Abiotic Stress, Instituto de Biología Molecular y Celular de Plantas (CSIC–UPV), 46022 Valencia, Spain
- Department of Genetics, Trinity College Dublin, University of Dublin, Dublin 2, Ireland
| | - Marcel Font-Carrascosa
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Ctra. Valldemossa km. 7.5, 07122 Palma, Illes Balears Spain
| | - Maxim V. Kapralov
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU United Kingdom
| | - Marcus A. Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Im Neuenheimer Feld 345, 9120 Heidelberg, Germany
| | - Arnau Mir
- Computational Biology and Bioinformatics Research Group, Department of Mathematics and Computer Science, Universitat de les Illes Balears, 07122 Palma, Illes Balears Spain
| | - Arántzazu Molins
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Ctra. Valldemossa km. 7.5, 07122 Palma, Illes Balears Spain
| | - Miquel Ribas-Carbó
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Ctra. Valldemossa km. 7.5, 07122 Palma, Illes Balears Spain
| | - Jairo Rocha
- Computational Biology and Bioinformatics Research Group, Department of Mathematics and Computer Science, Universitat de les Illes Balears, 07122 Palma, Illes Balears Spain
| | - Jeroni Galmés
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Ctra. Valldemossa km. 7.5, 07122 Palma, Illes Balears Spain
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Four amino acids define the CO 2 binding pocket of enoyl-CoA carboxylases/reductases. Proc Natl Acad Sci U S A 2019; 116:13964-13969. [PMID: 31243147 PMCID: PMC6628652 DOI: 10.1073/pnas.1901471116] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Carboxylases capture and convert CO2, which makes them key enzymes in photosynthesis and the global carbon cycle. However, the question how enzymes bind atmospheric CO2 is still unsolved. We studied enoyl-CoA carboxylases/reductases (Ecrs), the fastest CO2-fixing enzymes in nature, using structural biology, biochemistry, and advanced computational methods. Ecrs create a highly specific CO2-binding pocket with 4 amino acids at the active site. The pocket controls the fate of the gaseous molecule during catalysis and shields the catalytic center from oxygen and water. This exquisite control makes Ecrs highly efficient carboxylases outcompeting RuBisCO, the key enzyme of photosynthesis, by an order of magnitude. Our findings define the atomic framework for the future development of CO2-converting catalysts in biology and chemistry. Carboxylases are biocatalysts that capture and convert carbon dioxide (CO2) under mild conditions and atmospheric concentrations at a scale of more than 400 Gt annually. However, how these enzymes bind and control the gaseous CO2 molecule during catalysis is only poorly understood. One of the most efficient classes of carboxylating enzymes are enoyl-CoA carboxylases/reductases (Ecrs), which outcompete the plant enzyme RuBisCO in catalytic efficiency and fidelity by more than an order of magnitude. Here we investigated the interactions of CO2 within the active site of Ecr from Kitasatospora setae. Combining experimental biochemistry, protein crystallography, and advanced computer simulations we show that 4 amino acids, N81, F170, E171, and H365, are required to create a highly efficient CO2-fixing enzyme. Together, these 4 residues anchor and position the CO2 molecule for the attack by a reactive enolate created during the catalytic cycle. Notably, a highly ordered water molecule plays an important role in an active site that is otherwise carefully shielded from water, which is detrimental to CO2 fixation. Altogether, our study reveals unprecedented molecular details of selective CO2 binding and C–C-bond formation during the catalytic cycle of nature’s most efficient CO2-fixing enzyme. This knowledge provides the basis for the future development of catalytic frameworks for the capture and conversion of CO2 in biology and chemistry.
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Iñiguez C, Galmés J, Gordillo FJL. Rubisco carboxylation kinetics and inorganic carbon utilization in polar versus cold-temperate seaweeds. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1283-1297. [PMID: 30576461 PMCID: PMC6382342 DOI: 10.1093/jxb/ery443] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 12/07/2018] [Indexed: 05/07/2023]
Abstract
Despite the high productivity and ecological importance of seaweeds in polar coastal regions, little is known about their carbon utilization mechanisms, especially the kinetics of the CO2-fixing enzyme Rubisco. We analyzed Rubisco carboxylation kinetics at 4 °C and 25 °C in 12 diverse polar seaweed species (including cold-temperate populations of the same species) and the relationship with their ability to use bicarbonate, by using 13C isotope discrimination and pH drift experiments. We observed a large variation in Rubisco carboxylation kinetics among the selected species, although no correlation was found between either the Michaelis-Menten constant for CO2 (Kc) or Rubisco content per total soluble protein ([Rubisco]/[TSP]) and the ability to use bicarbonate for non-green seaweeds. This study reports intraspecific Rubisco cold adaptation by means of either higher Rubisco carboxylation turnover rate (kcatc) and carboxylase efficiency (kcatc/Kc) at 4 °C or higher [Rubisco]/[TSP] in some of the analyzed species. Our data point to a widespread ability for photosynthetic bicarbonate usage among polar seaweeds, despite the higher affinity of Rubisco for CO2 and higher dissolved CO2 concentration in cold seawater. Moreover, the reported catalytic variation within form ID Rubisco might avert the canonical trade-off previously observed between Kc and kcatc for plant Rubiscos.
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Affiliation(s)
- Concepción Iñiguez
- Department of Ecology, Faculty of Sciences, University of Malaga, Boulevard Louis Pasteur s/n, Málaga, Spain
- Research Group in Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Carretera de Valldemossa, Palma, Illes Balears, Spain
| | - Jeroni Galmés
- Research Group in Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Carretera de Valldemossa, Palma, Illes Balears, Spain
| | - Francisco J L Gordillo
- Department of Ecology, Faculty of Sciences, University of Malaga, Boulevard Louis Pasteur s/n, Málaga, Spain
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Boyd RA, Cavanagh AP, Kubien DS, Cousins AB. Temperature response of Rubisco kinetics in Arabidopsis thaliana: thermal breakpoints and implications for reaction mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:231-242. [PMID: 30403800 PMCID: PMC6305185 DOI: 10.1093/jxb/ery355] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/09/2018] [Indexed: 05/04/2023]
Abstract
Enhancement of Rubisco kinetics could improve photosynthetic efficiency, ultimately resulting in increased crop yield. However, imprecise knowledge of the reaction mechanism and the individual rate constants limits our ability to optimize the enzyme. Membrane inlet mass spectrometry (MIMS) may offer benefits over traditional methods for determining individual rate constants of the Rubisco reaction mechanism, as it can directly monitor concentration changes in CO2, O2, and their isotopologs during assays. However, a direct comparison of MIMS with the traditional radiolabel method of determining Rubisco kinetic parameters has not been made. Here, the temperature responses of Rubisco kinetic parameters from Arabidopsis thaliana were measured using radiolabel and MIMS methods. The two methods provided comparable parameters above 25 °C, but temperature responses deviated at low temperature as MIMS-derived catalytic rates of carboxylation, oxygenation, and CO2/O2 specificity showed thermal breakpoints. Here, we discuss the variability and uncertainty surrounding breakpoints in the Rubisco temperature response and the relevance of individual rate constants of the reaction mechanisms to potential breakpoints.
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Affiliation(s)
- Ryan A Boyd
- School of Biological Sciences, Molecular Plant Sciences, Washington State University, Pullman, WA, USA
| | - Amanda P Cavanagh
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - David S Kubien
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Asaph B Cousins
- School of Biological Sciences, Molecular Plant Sciences, Washington State University, Pullman, WA, USA
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Bar-Even A. Daring metabolic designs for enhanced plant carbon fixation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:71-83. [PMID: 29907311 DOI: 10.1016/j.plantsci.2017.12.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/16/2017] [Accepted: 12/16/2017] [Indexed: 05/07/2023]
Abstract
Increasing agricultural productivity is one of the major challenges our society faces. While multiple strategies to enhance plant carbon fixation have been suggested, and partially implemented, most of them are restricted to relatively simple modifications of endogenous metabolism, i.e., "low hanging fruit". Here, I portray the next generation of metabolic solutions to increase carbon fixation rate and yield. These strategies involve major rewiring of central metabolism, including dividing Rubisco's catalysis between several enzymes, replacing Rubisco with a different carboxylation reaction, substituting the Calvin Cycle with alternative carbon fixation pathways, and engineering photorespiration bypass routes that do not release carbon. While the barriers for implementing these elaborated metabolic architectures are quite significant, if we truly want to revolutionize carbon fixation, only daring engineering efforts will lead the way.
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Affiliation(s)
- Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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Cummins PL, Kannappan B, Gready JE. Revised mechanism of carboxylation of ribulose-1,5-biphosphate by rubisco from large scale quantum chemical calculations. J Comput Chem 2018; 39:1656-1665. [PMID: 29756365 DOI: 10.1002/jcc.25343] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 04/04/2018] [Accepted: 04/06/2018] [Indexed: 01/06/2023]
Abstract
Here, we describe a computational approach for studying enzymes that catalyze complex multi-step reactions and apply it to Ribulose 1,5-bisphosphate carboxylase-oxygenase (Rubisco), the enzyme that fixes atmospheric carbon dioxide within photosynthesis. In the 5-step carboxylase reaction, the substrate Ribulose-1,5-bisphosphate (RuBP) first binds Rubisco and undergoes enolization before binding the second substrate, CO2 . Hydration of the RuBP.CO2 complex is followed by CC bond scission and stereospecific protonation. However, details of the roles and protonation states of active-site residues, and sources of protons and water, remain highly speculative. Large-scale computations on active-site models provide a means to better understand this complex chemical mechanism. The computational protocol comprises a combination of hybrid semi-empirical quantum mechanics and molecular mechanics within constrained molecular dynamics simulations, together with constrained gradient minimization calculations using density functional theory. Alternative pathways for hydration of the RuBP.CO2 complex and associated active-site protonation networks and proton and water sources were investigated. The main findings from analysis of the resulting energetics advocate major revision to existing mechanisms such that: hydration takes place anti to the CO2 ; both hydration and CC bond scission require early protonation of CO2 in the RuBP.CO2 complex; CC bond scission and stereospecific protonation reactions are concerted and, effectively, there is only one stable intermediate, the C3-gemdiolate complex. Our main conclusions for interpreting enzyme kinetic results are that the gemdiolate may represent the elusive Michaelis-Menten-like complex corresponding to the empirical Km (=Kc ) with turnover to product via bond scission concerted with stereospecific protonation consistent with the observed catalytic rate. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Peter L Cummins
- John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, 0200, Australia
| | - Babu Kannappan
- John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, 0200, Australia
| | - Jill E Gready
- John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, 0200, Australia
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26
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Increasing metabolic potential: C-fixation. Essays Biochem 2018; 62:109-118. [PMID: 29653967 DOI: 10.1042/ebc20170014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 02/17/2018] [Accepted: 02/18/2018] [Indexed: 01/30/2023]
Abstract
Due to the growing world population, crop yields must increase to meet the rising demand. Crop plants also require adaptation to optimize performance in the changing environments caused by climate change. Improving photosynthetic carbon fixation is a promising, albeit technically challenging, strategy whose potential has only just begun to be considered in breeding programmes. Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), a fundamental enzyme of carbon fixation, is extremely inefficient and many strategies to improve photosynthesis focus on overcoming the limitations of this enzyme, either by improving Rubisco activity and regulation or by improving the supply of substrates. Although progress is being made, the need to tailor solutions for each crop and their respective environments has been highlighted. Even so, continuing research will be required to achieve these objectives and to grow crops more sustainably in the future.
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Bathellier C, Tcherkez G, Lorimer GH, Farquhar GD. Rubisco is not really so bad. PLANT, CELL & ENVIRONMENT 2018; 41:705-716. [PMID: 29359811 DOI: 10.1111/pce.13149] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/09/2018] [Accepted: 01/09/2018] [Indexed: 05/19/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the most widespread carboxylating enzyme in autotrophic organisms. Its kinetic and structural properties have been intensively studied for more than half a century. Yet important aspects of the catalytic mechanism remain poorly understood, especially the oxygenase reaction. Because of its relatively modest turnover rate (a few catalytic events per second) and the competitive inhibition by oxygen, Rubisco is often viewed as an inefficient catalyst for CO2 fixation. Considerable efforts have been devoted to improving its catalytic efficiency, so far without success. In this review, we re-examine Rubisco's catalytic performance by comparison with other chemically related enzymes. We find that Rubisco is not especially slow. Furthermore, considering both the nature and the complexity of the chemical reaction, its kinetic properties are unremarkable. Although not unique to Rubisco, oxygenation is not systematically observed in enolate and enamine forming enzymes and cannot be considered as an inevitable consequence of the mechanism. It is more likely the result of a compromise between chemical and metabolic imperatives. We argue that a better description of Rubisco mechanism is still required to better understand the link between CO2 and O2 reactivity and the rationale of Rubisco diversification and evolution.
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Affiliation(s)
- Camille Bathellier
- Research School of Biology, College of Science, Australian National University, Canberra, 2601, ACT, Australia
| | - Guillaume Tcherkez
- Research School of Biology, College of Science, Australian National University, Canberra, 2601, ACT, Australia
| | - George H Lorimer
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 27042, USA
| | - Graham D Farquhar
- Research School of Biology, College of Science, Australian National University, Canberra, 2601, ACT, Australia
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Tcherkez GG, Bathellier C, Farquhar GD, Lorimer GH. Commentary: Directions for Optimization of Photosynthetic Carbon Fixation: RuBisCO's Efficiency May Not Be So Constrained After All. FRONTIERS IN PLANT SCIENCE 2018; 9:929. [PMID: 29997647 PMCID: PMC6030380 DOI: 10.3389/fpls.2018.00929] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 06/11/2018] [Indexed: 05/07/2023]
Affiliation(s)
- Guillaume G. Tcherkez
- Research School of Biology, Australian National University, ANU College of Science, Canberra, ACT, Australia
- *Correspondence: Guillaume G. Tcherkez
| | - Camille Bathellier
- Research School of Biology, Australian National University, ANU College of Science, Canberra, ACT, Australia
| | - Graham D. Farquhar
- Research School of Biology, Australian National University, ANU College of Science, Canberra, ACT, Australia
| | - George H. Lorimer
- Department of Chemistry and Biochemistry, College of Computer, Mathematical and Natural Sciences, University of Maryland, College Park, MD, United States
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Cummins PL, Kannappan B, Gready JE. Directions for Optimization of Photosynthetic Carbon Fixation: RuBisCO's Efficiency May Not Be So Constrained After All. FRONTIERS IN PLANT SCIENCE 2018; 9:183. [PMID: 29545812 PMCID: PMC5838012 DOI: 10.3389/fpls.2018.00183] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 01/31/2018] [Indexed: 05/19/2023]
Abstract
The ubiquitous enzyme Ribulose 1,5-bisphosphate carboxylase-oxygenase (RuBisCO) fixes atmospheric carbon dioxide within the Calvin-Benson cycle that is utilized by most photosynthetic organisms. Despite this central role, RuBisCO's efficiency surprisingly struggles, with both a very slow turnover rate to products and also impaired substrate specificity, features that have long been an enigma as it would be assumed that its efficiency was under strong evolutionary pressure. RuBisCO's substrate specificity is compromised as it catalyzes a side-fixation reaction with atmospheric oxygen; empirical kinetic results show a trend to tradeoff between relative specificity and low catalytic turnover rate. Although the dominant hypothesis has been that the active-site chemistry constrains the enzyme's evolution, a more recent study on RuBisCO stability and adaptability has implicated competing selection pressures. Elucidating these constraints is crucial for directing future research on improving photosynthesis, as the current literature casts doubt on the potential effectiveness of site-directed mutagenesis to improve RuBisCO's efficiency. Here we use regression analysis to quantify the relationships between kinetic parameters obtained from empirical data sets spanning a wide evolutionary range of RuBisCOs. Most significantly we found that the rate constant for dissociation of CO2 from the enzyme complex was much higher than previous estimates and comparable with the corresponding catalytic rate constant. Observed trends between relative specificity and turnover rate can be expressed as the product of negative and positive correlation factors. This provides an explanation in simple kinetic terms of both the natural variation of relative specificity as well as that obtained by reported site-directed mutagenesis results. We demonstrate that the kinetic behaviour shows a lesser rather than more constrained RuBisCO, consistent with growing empirical evidence of higher variability in relative specificity. In summary our analysis supports an explanation for the origin of the tradeoff between specificity and turnover as due to competition between protein stability and activity, rather than constraints between rate constants imposed by the underlying chemistry. Our analysis suggests that simultaneous improvement in both specificity and turnover rate of RuBisCO is possible.
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30
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Abstract
RuBisCO enables net carbon fixation through the carboxylation of RuBP during photosynthesis. Its complex biochemistry and catalytic diversity found among different plants make characterization of RuBisCO properties useful for investigations aimed at improving photosynthetic performance. This chapter reports methods for rapid extraction of soluble proteins to examine RuBisCO catalytic properties, and for large-scale purification of RuBisCO from leaves to measure the specificity of the enzyme toward its gaseous substrates.
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Affiliation(s)
- Douglas J Orr
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
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31
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Orr DJ, Pereira AM, da Fonseca Pereira P, Pereira-Lima ÍA, Zsögön A, Araújo WL. Engineering photosynthesis: progress and perspectives. F1000Res 2017; 6:1891. [PMID: 29263782 PMCID: PMC5658708 DOI: 10.12688/f1000research.12181.1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/27/2017] [Indexed: 12/11/2022] Open
Abstract
Photosynthesis is the basis of primary productivity on the planet. Crop breeding has sustained steady improvements in yield to keep pace with population growth increases. Yet these advances have not resulted from improving the photosynthetic process
per se but rather of altering the way carbon is partitioned within the plant. Mounting evidence suggests that the rate at which crop yields can be boosted by traditional plant breeding approaches is wavering, and they may reach a “yield ceiling” in the foreseeable future. Further increases in yield will likely depend on the targeted manipulation of plant metabolism. Improving photosynthesis poses one such route, with simulations indicating it could have a significant transformative influence on enhancing crop productivity. Here, we summarize recent advances of alternative approaches for the manipulation and enhancement of photosynthesis and their possible application for crop improvement.
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Affiliation(s)
- Douglas J Orr
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Auderlan M Pereira
- Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.,Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Paula da Fonseca Pereira
- Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.,Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Ítalo A Pereira-Lima
- Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.,Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Agustin Zsögön
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Wagner L Araújo
- Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.,Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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Ślesak I, Ślesak H, Kruk J. RubisCO Early Oxygenase Activity: A Kinetic and Evolutionary Perspective. Bioessays 2017; 39. [PMID: 28976010 DOI: 10.1002/bies.201700071] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 08/10/2017] [Indexed: 11/09/2022]
Abstract
RubisCO (D-ribulose 1,5-bisphosphate carboxylase/oxygenase) is Earth's main enzyme responsible for CO2 fixation via carboxylation of ribulose-1,5-bisphosphate (RuBP) into organic matter. Besides the carboxylation reaction, RubisCO also catalyzes the oxygenation of RuBP by O2 , which is probably as old as its carboxylation properties. Based on molecular phylogeny, the occurrence of the reactive oxygen species (ROS)-removing system and kinetic properties of different RubisCO forms, we postulated that RubisCO oxygenase activity appeared in local microoxic areas, yet before the appearance of oxygenic photosynthesis. Here, in reviewing the literature, we present a novel hypothesis: the RubisCO early oxygenase activity hypothesis. This hypothesis may be compared with the exaptation hypothesis, according to which latent RubisCO oxygenase properties emerged later during the oxygenation of the Earth's atmosphere. The reconstruction of ancestral RubisCO forms using ancestral sequence reconstruction (ASR) techniques, as a promising way for testing of RubisCO early oxygenase activity hypothesis, is presented.
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Affiliation(s)
- Ireneusz Ślesak
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, Kraków 30-239, Poland
| | - Halina Ślesak
- Institute of Botany, Jagiellonian University, Gronostajowa 9, Kraków 30-387, Poland
| | - Jerzy Kruk
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow 30-387, Poland
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33
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Rauch M, Ruccolo S, Parkin G. Synthesis, Structure, and Reactivity of a Terminal Magnesium Hydride Compound with a Carbatrane Motif, [Tism PriBenz]MgH: A Multifunctional Catalyst for Hydrosilylation and Hydroboration. J Am Chem Soc 2017; 139:13264-13267. [PMID: 28901762 DOI: 10.1021/jacs.7b06719] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The tris[(1-isopropylbenzimidazol-2-yl)dimethylsilyl)]methyl ligand, [TismPriBenz], has been employed to form the magnesium carbatrane compound, [TismPriBenz]MgH, which possesses a terminal hydride ligand. Specifically, [TismPriBenz]MgH is obtained via the reaction of [TismPriBenz]MgMe with PhSiH3. The reactivity of [TismPriBenz]MgMe and [TismPriBenz]MgH allows access to a variety of other structurally characterized carbatrane derivatives, including [TismPriBenz]MgX [X = F, Cl, Br, I, SH, N(H)Ph, CH(Me)Ph, O2CMe, S2CMe]. In addition, [TismPriBenz]MgH is a catalyst for (i) hydrosilylation and hydroboration of styrene to afford the Markovnikov products, Ph(Me)C(H)SiH2Ph and Ph(Me)C(H)Bpin, and (ii) hydroboration of carbodiimides and pyridine to form N-boryl formamidines and N-boryl 1,4- and 1,2-dihydropyridines, respectively.
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Affiliation(s)
- Michael Rauch
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Serge Ruccolo
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Gerard Parkin
- Department of Chemistry, Columbia University , New York, New York 10027, United States
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34
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Song Q, Su R, Chai Y, Goudia BD, Chen L, Hu YG. High photosynthetic capability observed in the wheat germplasm with rye chromosomes. JOURNAL OF PLANT PHYSIOLOGY 2017; 216:202-211. [PMID: 28710914 DOI: 10.1016/j.jplph.2017.06.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/25/2017] [Accepted: 06/28/2017] [Indexed: 06/07/2023]
Abstract
Improving photosynthetic capability is one of the most important factors for increasing wheat yield potential. The photosynthetic capability of wheat germplasm with different alien chromosomes was investigated and compared with bread wheat cultivars (BC) in this study, including wheat addition lines (CA), hexaploid triticale (HT), octoploid triticale (OT), and synthetic hexaploid wheat lines (SHW). Results indicated that HT, OT, and SHW produced significantly higher biomass plant-1(BMPP), with HT displaying the highest grain yield plant-1 (GYPP). Distinct superiority of net photosynthetic rate (Pn) and carboxylation activities of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) was observed in HT and OT. Meanwhile, OT showed the highest expression of the Rubisco large subunit gene (rbcL) in the flag leaves at heading and grain-filling stages, though the coding region of rbcL was highly conserved in all investigated materials. Further analysis indicated that OT and Chinese Spring-rye disomic addition lines displayed higher expression of Rubisco small subunit gene (rbcS). Correlation analysis revealed significant and positive correlations between Pn and the expressions of rbcL (at both heading and grain-filling stages), the expression of rbcS (at heading stage), and the carboxylation activity of Rubisco (at grain-filling stage). Anatomical structure analysis of the chloroplasts showed SHW with longer chloroplasts and more chloroplast grana and grana lamella. In the present study, HT, OT, and Chinese Spring-rye disomic addition lines with rye chromosomes displayed greater photosynthetic capability than BC and SHW, and could be applied in breeding programs to improve the photosynthetic efficiency of wheat.
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Affiliation(s)
- Quanhao Song
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Rina Su
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yongmao Chai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Bachir Daoura Goudia
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Liang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yin-Gang Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China; Institute of Water Saving Agriculture in Arid Regions of China, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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35
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Heureux AMC, Young JN, Whitney SM, Eason-Hubbard MR, Lee RBY, Sharwood RE, Rickaby REM. The role of Rubisco kinetics and pyrenoid morphology in shaping the CCM of haptophyte microalgae. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3959-3969. [PMID: 28582571 PMCID: PMC5853415 DOI: 10.1093/jxb/erx179] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/15/2017] [Indexed: 05/18/2023]
Abstract
The haptophyte algae are a cosmopolitan group of primary producers that contribute significantly to the marine carbon cycle and play a major role in paleo-climate studies. Despite their global importance, little is known about carbon assimilation in haptophytes, in particular the kinetics of their Form 1D CO2-fixing enzyme, Rubisco. Here we examine Rubisco properties of three haptophytes with a range of pyrenoid morphologies (Pleurochrysis carterae, Tisochrysis lutea, and Pavlova lutheri) and the diatom Phaeodactylum tricornutum that exhibit contrasting sensitivities to the trade-offs between substrate affinity (Km) and turnover rate (kcat) for both CO2 and O2. The pyrenoid-containing T. lutea and P. carterae showed lower Rubisco content and carboxylation properties (KC and kCcat) comparable with those of Form 1D-containing non-green algae. In contrast, the pyrenoid-lacking P. lutheri produced Rubisco in 3-fold higher amounts, and displayed a Form 1B Rubisco kCcat-KC relationship and increased CO2/O2 specificity that, when modeled in the context of a C3 leaf, supported equivalent rates of photosynthesis to higher plant Rubisco. Correlation between the differing Rubisco properties and the occurrence and localization of pyrenoids with differing intracellular CO2:O2 microenvironments has probably influenced the divergent evolution of Form 1B and 1D Rubisco kinetics.
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Affiliation(s)
- Ana M C Heureux
- University of Oxford, Department of Earth Sciences, South Parks Road, Oxford, UK
| | - Jodi N Young
- University of Washington, School of Oceanography, Seattle, WA, USA
| | - Spencer M Whitney
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra ACT, Australia
| | | | - Renee B Y Lee
- University of Oxford, Department of Earth Sciences, South Parks Road, Oxford, UK
- University of Reading, School of Biological Sciences, Reading, Berkshire, UK
| | - Robert E Sharwood
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra ACT, Australia
| | - Rosalind E M Rickaby
- University of Oxford, Department of Earth Sciences, South Parks Road, Oxford, UK
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36
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Young JN, Hopkinson BM. The potential for co-evolution of CO2-concentrating mechanisms and Rubisco in diatoms. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3751-3762. [PMID: 28645158 DOI: 10.1093/jxb/erx130] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Diatoms are a diverse group of unicellular algae that contribute significantly to global photosynthetic carbon fixation and export in the modern ocean, and are an important source of microfossils for paleoclimate reconstructions. Because of their importance in the environment, diatoms have been a focus of study on the physiology and ecophysiology of carbon fixation, in particular their CO2-concentrating mechanisms (CCMs) and Rubisco characteristics. While carbon fixation in diatoms is not as well understood as in certain model aquatic photoautotrophs, a greater number of species have been examined in diatoms. Recent work has highlighted a large diversity in the function, physiology, and kinetics of both the CCM and Rubisco between different diatom species. This diversity was unexpected since it has generally been assumed that CCMs and Rubiscos were similar within major algal lineages as the result of selective events deep in evolutionary history, and suggests a more recent co-evolution between the CCM and Rubisco within diatoms. This review explores our current understanding of the diatom CCM and highlights the diversity of both the CCM and Rubisco kinetics. We will suggest possible environmental, physiological, and evolutionary drivers for the co-evolution of the CCM and Rubisco in diatoms.
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Affiliation(s)
- Jodi N Young
- University of Washington, School of Oceanography, Seattle, WA 98105, USA
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37
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Mueller-Cajar O. The Diverse AAA+ Machines that Repair Inhibited Rubisco Active Sites. Front Mol Biosci 2017; 4:31. [PMID: 28580359 PMCID: PMC5437159 DOI: 10.3389/fmolb.2017.00031] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 04/29/2017] [Indexed: 11/13/2022] Open
Abstract
Gaseous carbon dioxide enters the biosphere almost exclusively via the active site of the enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco). This highly conserved catalyst has an almost universal propensity to non-productively interact with its substrate ribulose 1,5-bisphosphate, leading to the formation of dead-end inhibited complexes. In diverse autotrophic organisms this tendency has been counteracted by the recruitment of dedicated AAA+ (ATPases associated with various cellular activities) proteins that all use the energy of ATP hydrolysis to remodel inhibited Rubisco active sites leading to release of the inhibitor. Three evolutionarily distinct classes of these Rubisco activases (Rcas) have been discovered so far. Green and red-type Rca are mostly found in photosynthetic eukaryotes of the green and red plastid lineage respectively, whereas CbbQO is associated with chemoautotrophic bacteria. Ongoing mechanistic studies are elucidating how the various motors are utilizing both similar and contrasting strategies to ultimately perform their common function of cracking the inhibited Rubisco active site. The best studied mechanism utilized by red-type Rca appears to involve transient threading of the Rubisco large subunit C-terminal peptide, reminiscent of the action performed by Clp proteases. As well as providing a fascinating example of convergent molecular evolution, Rca proteins can be considered promising crop-improvement targets. Approaches aiming to replace Rubisco in plants with improved enzymes will need to ensure the presence of a compatible Rca protein. The thermolability of the Rca protein found in crop plants provides an opportunity to fortify photosynthesis against high temperature stress. Photosynthesis also appears to be limited by Rca when light conditions are fluctuating. Synthetic biology strategies aiming to enhance the autotrophic CO2 fixation machinery will need to take into consideration the requirement for Rubisco activases as well as their properties.
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Affiliation(s)
- Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological UniversitySingapore, Singapore
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38
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Young JN, Heureux AMC, Sharwood RE, Rickaby REM, Morel FMM, Whitney SM. Large variation in the Rubisco kinetics of diatoms reveals diversity among their carbon-concentrating mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3445-56. [PMID: 27129950 PMCID: PMC4892730 DOI: 10.1093/jxb/erw163] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
While marine phytoplankton rival plants in their contribution to global primary productivity, our understanding of their photosynthesis remains rudimentary. In particular, the kinetic diversity of the CO2-fixing enzyme, Rubisco, in phytoplankton remains unknown. Here we quantify the maximum rates of carboxylation (k cat (c)), oxygenation (k cat (o)), Michaelis constants (K m) for CO2 (K C) and O2 (K O), and specificity for CO2 over O2 (SC/O) for Form I Rubisco from 11 diatom species. Diatom Rubisco shows greater variation in K C (23-68 µM), SC/O (57-116mol mol(-1)), and K O (413-2032 µM) relative to plant and algal Rubisco. The broad range of K C values mostly exceed those of C4 plant Rubisco, suggesting that the strength of the carbon-concentrating mechanism (CCM) in diatoms is more diverse, and more effective than previously predicted. The measured k cat (c) for each diatom Rubisco showed less variation (2.1-3.7s(-1)), thus averting the canonical trade-off typically observed between K C and k cat (c) for plant Form I Rubisco. Uniquely, a negative relationship between K C and cellular Rubisco content was found, suggesting variation among diatom species in how they allocate their limited cellular resources between Rubisco synthesis and their CCM. The activation status of Rubisco in each diatom was low, indicating a requirement for Rubisco activase. This work highlights the need to better understand the correlative natural diversity between the Rubisco kinetics and CCM of diatoms and the underpinning mechanistic differences in catalytic chemistry among the Form I Rubisco superfamily.
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Affiliation(s)
- Jodi N Young
- Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
| | - Ana M C Heureux
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Robert E Sharwood
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Rosalind E M Rickaby
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - François M M Morel
- Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
| | - Spencer M Whitney
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
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39
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Tcherkez G. The mechanism of Rubisco-catalysed oxygenation. PLANT, CELL & ENVIRONMENT 2016; 39:983-997. [PMID: 26286702 DOI: 10.1111/pce.12629] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/28/2015] [Accepted: 08/09/2015] [Indexed: 06/04/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the cornerstone of photosynthetic carbon assimilation because it catalyses the fixation of CO2 onto ribulose-1,5-bisphosphate (RuBP). The enzyme also catalyses RuBP oxygenation, thereby evolving phosphoglycolate which is recycled along the photorespiratory pathway. Oxygenation is quantitatively important, because under ordinary gaseous conditions, more than one third of RuBP molecules are oxygenated rather than carboxylated. However, contrary to carboxylation, the chemical mechanism of oxygenation is not well known, and little progress has been made since the early 80s. Here, I review recent experimental data that provide some new insights into the reaction mechanism, and carry out simple calculations of kinetic parameters. Isotope effects suggest that oxygenation is less likely initiated by a redox phenomenon (such as superoxide production) and more likely involves concerted chemical events that imply interactions with protons. A possible energy profile of the reaction is drawn which suggests that the generation of the oxygenated reaction intermediate (peroxide) is irreversible. Possible changes in oxygenation-associated rate constants between Rubisco forms are discussed.
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Affiliation(s)
- Guillaume Tcherkez
- Research School of Biology, ANU College of Medicine, Biology and Environment, Australian National University, Canberra, 2601, ACT, Australia
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40
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Carmo-Silva E, Scales JC, Madgwick PJ, Parry MAJ. Optimizing Rubisco and its regulation for greater resource use efficiency. PLANT, CELL & ENVIRONMENT 2015; 38:1817-32. [PMID: 25123951 DOI: 10.1111/pce.12425] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 08/01/2014] [Accepted: 08/03/2014] [Indexed: 05/19/2023]
Abstract
Rubisco catalyses the carboxylation of ribulose-1,5-bisphosphate (RuBP), enabling net CO2 assimilation in photosynthesis. The properties and regulation of Rubisco are not optimal for biomass production in current and projected future environments. Rubisco is relatively inefficient, and large amounts of the enzyme are needed to support photosynthesis, requiring large investments in nitrogen. The competing oxygenation of RuBP by Rubisco decreases photosynthetic efficiency. Additionally, Rubisco is inhibited by some sugar phosphates and depends upon interaction with Rubisco activase (Rca) to be reactivated. Rca activity is modulated by the chloroplast redox status and ADP/ATP ratios, thereby mediating Rubisco activation and photosynthetic induction in response to irradiance. The extreme thermal sensitivity of Rca compromises net CO2 assimilation at moderately high temperatures. Given its central role in carbon assimilation, the improvement of Rubisco function and regulation is tightly linked with irradiance, nitrogen and water use efficiencies. Although past attempts have had limited success, novel technologies and an expanding knowledge base make the challenge of improving Rubisco activity in crops an achievable goal. Strategies to optimize Rubisco and its regulation are addressed in relation to their potential to improve crop resource use efficiency and climate resilience of photosynthesis.
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Affiliation(s)
| | - Joanna C Scales
- Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Pippa J Madgwick
- Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Martin A J Parry
- Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
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41
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Long SP, Marshall-Colon A, Zhu XG. Meeting the global food demand of the future by engineering crop photosynthesis and yield potential. Cell 2015; 161:56-66. [PMID: 25815985 DOI: 10.1016/j.cell.2015.03.019] [Citation(s) in RCA: 473] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Indexed: 10/23/2022]
Abstract
Increase in demand for our primary foodstuffs is outstripping increase in yields, an expanding gap that indicates large potential food shortages by mid-century. This comes at a time when yield improvements are slowing or stagnating as the approaches of the Green Revolution reach their biological limits. Photosynthesis, which has been improved little in crops and falls far short of its biological limit, emerges as the key remaining route to increase the genetic yield potential of our major crops. Thus, there is a timely need to accelerate our understanding of the photosynthetic process in crops to allow informed and guided improvements via in-silico-assisted genetic engineering. Potential and emerging approaches to improving crop photosynthetic efficiency are discussed, and the new tools needed to realize these changes are presented.
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Affiliation(s)
- Stephen P Long
- Department of Plant Biology and Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA; Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA.
| | - Amy Marshall-Colon
- Department of Plant Biology and Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Xin-Guang Zhu
- CAS Key Laboratory for Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, PRC; State Key Laboratory of Hybrid Rice, Changsha, Hunan 410125, PRC
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42
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Kaiser E, Morales A, Harbinson J, Kromdijk J, Heuvelink E, Marcelis LFM. Dynamic photosynthesis in different environmental conditions. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2415-26. [PMID: 25324402 DOI: 10.1093/jxb/eru406] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Incident irradiance on plant leaves often fluctuates, causing dynamic photosynthesis. Whereas steady-state photosynthetic responses to environmental factors have been extensively studied, knowledge of dynamic modulation of photosynthesis remains scarce and scattered. This review addresses this discrepancy by summarizing available data and identifying the research questions necessary to advance our understanding of interactions between environmental factors and dynamic behaviour of photosynthesis using a mechanistic framework. Firstly, dynamic photosynthesis is separated into sub-processes related to proton and electron transport, non-photochemical quenching, control of metabolite flux through the Calvin cycle (activation states of Rubisco and RuBP regeneration, and post-illumination metabolite turnover), and control of CO₂ supply to Rubisco (stomatal and mesophyll conductance changes). Secondly, the modulation of dynamic photosynthesis and its sub-processes by environmental factors is described. Increases in ambient CO₂ concentration and temperature (up to ~35°C) enhance rates of photosynthetic induction and decrease its loss, facilitating more efficient dynamic photosynthesis. Depending on the sensitivity of stomatal conductance, dynamic photosynthesis may additionally be modulated by air humidity. Major knowledge gaps exist regarding environmental modulation of loss of photosynthetic induction, dynamic changes in mesophyll conductance, and the extent of limitations imposed by stomatal conductance for different species and environmental conditions. The study of mutants or genetic transformants for specific processes under various environmental conditions could provide significant progress in understanding the control of dynamic photosynthesis.
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Affiliation(s)
- Elias Kaiser
- Horticulture and Product Physiology Group, Department of Plant Sciences, Wageningen University, PO Box 630, 6700 AP Wageningen, The Netherlands
| | - Alejandro Morales
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University, PO Box 430, 6700 AK Wageningen, The Netherlands
| | - Jeremy Harbinson
- Horticulture and Product Physiology Group, Department of Plant Sciences, Wageningen University, PO Box 630, 6700 AP Wageningen, The Netherlands
| | - Johannes Kromdijk
- Institute for Genomic Biology, University of Illinois, 1206 West Gregory Drive Urbana, Illinois, USA
| | - Ep Heuvelink
- Horticulture and Product Physiology Group, Department of Plant Sciences, Wageningen University, PO Box 630, 6700 AP Wageningen, The Netherlands
| | - Leo F M Marcelis
- Horticulture and Product Physiology Group, Department of Plant Sciences, Wageningen University, PO Box 630, 6700 AP Wageningen, The Netherlands
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43
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Perdomo JA, Cavanagh AP, Kubien DS, Galmés J. Temperature dependence of in vitro Rubisco kinetics in species of Flaveria with different photosynthetic mechanisms. PHOTOSYNTHESIS RESEARCH 2015; 124:67-75. [PMID: 25663529 DOI: 10.1007/s11120-015-0092-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 01/22/2015] [Indexed: 05/10/2023]
Abstract
There is general consensus in the literature that plants with different photosynthetic mechanisms (i.e. C3 vs. C4) have Rubiscos characterised by different kinetic performances. However, potential differences in the temperature dependencies of Rubisco kinetic parameters between C3 and C4 plants are uncertain. Accordingly, six species of Flaveria with contrasting photosynthetic mechanisms (C3, C3/C4 and C4) were selected and their Rubisco Michaelis-Menten constants for CO2 and RuBP (K c and K RuBP), carboxylase catalytic turnover rate ([Formula: see text]) and CO2/O2 specificity factor (S c/o) were measured between 10 and 40 °C. The results confirmed different Rubisco characteristics between C3 and C4 plants. Rubisco from the C3 species had higher E a for K c and [Formula: see text] than that from C4 species, which were translated into differences in the temperature response of the carboxylase catalytic efficiency ([Formula: see text]/K c). However, E a did not differ for S c/o or K RuBP. Although a mechanism remains uncertain, it appears that the Asp/Glu-149-Ala and Met-309-Ile substitutions lead to differences in the temperature responses of catalysis between C3 and C4 Rubiscos in Flaveria. Therefore, the above observations are consistent with the fact that C3 species have a higher photosynthetic efficiency and ecological dominance in cool environments, with respect to C4 species in temperate environments.
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Affiliation(s)
- Juan Alejandro Perdomo
- Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears, Ctra. Valldemossa km. 7.5, 07122, Palma, Balearic Islands, Spain
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44
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Schneider TW, Angeles-Boza AM. Competitive 13C and 18O kinetic isotope effects on CO2 reduction catalyzed by Re(bpy)(CO)3Cl. Dalton Trans 2015; 44:8784-7. [DOI: 10.1039/c4dt03977g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Competitive 13C and 18O kinetic isotope effects (KIEs) on CO2 reduction reactions catalyzed by Re(bpy)(CO)3Cl are reported.
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45
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Galmés J, Kapralov MV, Andralojc PJ, Conesa MÀ, Keys AJ, Parry MAJ, Flexas J. Expanding knowledge of the Rubisco kinetics variability in plant species: environmental and evolutionary trends. PLANT, CELL & ENVIRONMENT 2014; 37:1989-2001. [PMID: 24689692 DOI: 10.1111/pce.12335] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 03/19/2014] [Accepted: 03/22/2014] [Indexed: 05/18/2023]
Abstract
The present study characterizes the kinetic properties of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from 28 terrestrial plant species, representing different phylogenetic lineages, environmental adaptations and photosynthetic mechanisms. Our findings confirm that past atmospheric CO(2)/O(2) ratio changes and present environmental pressures have influenced Rubisco kinetics. One evolutionary adaptation to a decreasing atmospheric CO(2)/O(2) ratio has been an increase in the affinity of Rubisco for CO(2) (Kc falling), and a consequent decrease in the velocity of carboxylation (kcat (c)), which in turn has been ameliorated by an increase in the proportion of leaf protein accounted by Rubisco. The trade-off between K(c) and k(cat)(c) was not universal among the species studied and deviations from this relationship occur in extant forms of Rubisco. In species adapted to particular environments, including carnivorous plants, crassulacean acid metabolism species and C(3) plants from aquatic and arid habitats, Rubisco has evolved towards increased efficiency, as demonstrated by a higher k(cat)(c)/K(c) ratio. This variability in kinetics was related to the amino acid sequence of the Rubisco large subunit. Phylogenetic analysis identified 13 residues under positive selection during evolution towards specific Rubisco kinetic parameters. This crucial information provides candidate amino acid replacements, which could be implemented to optimize crop photosynthesis under a range of environmental conditions.
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Affiliation(s)
- Jeroni Galmés
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears, Palma, Spain
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46
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Dittrich-Domergue F, Joubès J, Moreau P, Lessire R, Stymne S, Domergue F. The bifunctional protein TtFARAT from Tetrahymena thermophila catalyzes the formation of both precursors required to initiate ether lipid biosynthesis. J Biol Chem 2014; 289:21984-94. [PMID: 24917677 PMCID: PMC4139215 DOI: 10.1074/jbc.m114.579318] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 06/03/2014] [Indexed: 11/06/2022] Open
Abstract
The biosynthesis of ether lipids and wax esters requires as precursors fatty alcohols, which are synthesized by fatty acyl reductases (FARs). The presence of ether glycerolipids as well as branched wax esters has been reported in several free-living ciliate protozoa. In the genome of Tetrahymena thermophila, the only ORF sharing similarities with FARs is fused to an acyltransferase-like domain, whereas, in most other organisms, FARs are monofunctional proteins of similar size and domain structure. Here, we used heterologous expression in plant and yeast to functionally characterize the activities catalyzed by this protozoan protein. Transient expression in tobacco epidermis of a truncated form fused to the green fluorescence protein followed by confocal microscopy analysis suggested peroxisomal localization. In vivo approaches conducted in yeast indicated that the N-terminal FAR-like domain produced both 16:0 and 18:0 fatty alcohols, whereas the C-terminal acyltransferase-like domain was able to rescue the lethal phenotype of the yeast double mutant gat1Δ gat2Δ. Using in vitro approaches, we further demonstrated that this domain is a dihydroxyacetone phosphate acyltransferase that uses preferentially 16:0-coenzyme A as an acyl donor. Finally, coexpression in yeast with the alkyl-dihydroxyacetone phosphate synthase from T. thermophila resulted the detection of various glycerolipids with an ether bond, indicating reconstitution of the ether lipid biosynthetic pathway. Together, these results demonstrate that this FAR-like protein is peroxisomal and bifunctional, providing both substrates required by alkyl-dihydroxyacetone phosphate synthase to initiate ether lipid biosynthesis.
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Affiliation(s)
- Franziska Dittrich-Domergue
- From the Université de Bordeaux, Laboratoire de Biogenèse Membranaire, UMR 5200, 33000 Bordeaux, France, the Centre National de la Recherche Scientifique, Laboratoire de Biogenèse Membranaire, UMR 5200, 33000 Bordeaux, France, and
| | - Jérôme Joubès
- From the Université de Bordeaux, Laboratoire de Biogenèse Membranaire, UMR 5200, 33000 Bordeaux, France, the Centre National de la Recherche Scientifique, Laboratoire de Biogenèse Membranaire, UMR 5200, 33000 Bordeaux, France, and
| | - Patrick Moreau
- From the Université de Bordeaux, Laboratoire de Biogenèse Membranaire, UMR 5200, 33000 Bordeaux, France, the Centre National de la Recherche Scientifique, Laboratoire de Biogenèse Membranaire, UMR 5200, 33000 Bordeaux, France, and
| | - René Lessire
- From the Université de Bordeaux, Laboratoire de Biogenèse Membranaire, UMR 5200, 33000 Bordeaux, France, the Centre National de la Recherche Scientifique, Laboratoire de Biogenèse Membranaire, UMR 5200, 33000 Bordeaux, France, and
| | - Sten Stymne
- the Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O.B. 101, 23053 Alnarp, Sweden
| | - Frédéric Domergue
- From the Université de Bordeaux, Laboratoire de Biogenèse Membranaire, UMR 5200, 33000 Bordeaux, France, the Centre National de la Recherche Scientifique, Laboratoire de Biogenèse Membranaire, UMR 5200, 33000 Bordeaux, France, and
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47
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Galmés J, Andralojc PJ, Kapralov MV, Flexas J, Keys AJ, Molins A, Parry MAJ, Conesa MÀ. Environmentally driven evolution of Rubisco and improved photosynthesis and growth within the C3 genus Limonium (Plumbaginaceae). THE NEW PHYTOLOGIST 2014; 203:989-99. [PMID: 24861241 DOI: 10.1111/nph.12858] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 04/23/2014] [Indexed: 05/22/2023]
Abstract
Carbon assimilation by most ecosystems requires ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). Its kinetic parameters are likely to have evolved in parallel with intracellular CO2 availability, with the result that faster forms of Rubisco occur in species with CO2 -concentrating mechanisms. The Rubisco catalytic properties were determined and evaluated in relation to growth and carbon assimilation capacity in Mediterranean Limonium species, inhabiting severe stress environments. Significant kinetic differences between closely related species depended on two amino acid substitutions at functionally important residues 309 and 328 within the Rubisco large subunit. The Rubisco of species facing the largest CO2 restrictions during drought had relatively high affinity for CO2 (low Michaelis-Menten constant for CO2 Kc) but low maximum rates of carboxylation (kcatc), while the opposite was found for species that maintained higher CO2 concentrations under similar conditions. Rubisco kinetic characteristics were correlated with photosynthetic rate in both well-watered and drought-stressed plants. Moreover, the drought-mediated decrease in plant biomass accumulation was consistently lower in species with higher Rubisco carboxylase catalytic efficiency (kcatc/Kc). The present study is the first demonstration of Rubisco adaptation during species diversification within closely related C3 plants, revealing a direct relationship between Rubisco molecular evolution and the biomass accumulation of closely related species subjected to unfavourable conditions.
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Affiliation(s)
- Jeroni Galmés
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears, Balearic Islands, Spain
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48
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von Caemmerer S, Tazoe Y, Evans JR, Whitney SM. Exploiting transplastomically modified Rubisco to rapidly measure natural diversity in its carbon isotope discrimination using tuneable diode laser spectroscopy. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3759-67. [PMID: 24687980 PMCID: PMC4085952 DOI: 10.1093/jxb/eru036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Carbon isotope discrimination (Δ) during C3 photosynthesis is dominated by the fractionation occurring during CO2-fixation by the enzyme Rubisco. While knowing the fractionation by enzymes is pivotal to fully understanding plant carbon metabolism, little is known about variation in the discrimination factor of Rubisco (b) as it is difficult to measure using existing in vitro methodologies. Tuneable diode laser absorption spectroscopy has improved the ability to make rapid measurements of Δ concurrently with photosynthetic gas exchange. This study used this technique to estimate b in vivo in five tobacco (Nicotiana tabacum L. cv Petit Havana [N,N]) genotypes expressing alternative Rubisco isoforms. For transplastomic tobacco producing Rhodospirillum rubrum Rubisco b was 23.8±0.7‰, while Rubisco containing the large subunit Leu-335-Val mutation had a b-value of 13.9±0.7‰. These values were significantly less than that for Rubisco from wild-type tobacco (b=29‰), a C3 species. Transplastomic tobacco producing chimeric Rubisco comprising tobacco Rubisco small subunits and the catalytic large subunits from either the C4 species Flaveria bidentis or the C3-C4 species Flaveria floridana had b-values of 27.8±0.8 and 28.6±0.6‰, respectively. These values were not significantly different from tobacco Rubisco.
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Affiliation(s)
- Susanne von Caemmerer
- Research School of Biology, The Australian National University, Canberra ACT 0200, Australia
| | - Youshi Tazoe
- Research School of Biology, The Australian National University, Canberra ACT 0200, Australia
| | - John R Evans
- Research School of Biology, The Australian National University, Canberra ACT 0200, Australia
| | - Spencer M Whitney
- Research School of Biology, The Australian National University, Canberra ACT 0200, Australia
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49
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Boex-Fontvieille E, Daventure M, Jossier M, Hodges M, Zivy M, Tcherkez G. Phosphorylation pattern of Rubisco activase in Arabidopsis leaves. PLANT BIOLOGY (STUTTGART, GERMANY) 2014; 16:550-7. [PMID: 24119201 DOI: 10.1111/plb.12100] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 07/20/2013] [Indexed: 05/09/2023]
Abstract
Rubisco activase (RCA) is an ancillary photosynthetic protein essential for Rubisco activity. Some data suggest that post-translational modifications (such as reduction of disulphide bridges) are involved in the regulation of RCA activity. However, despite the key role of protein phosphorylation in general metabolic regulation, RCA phosphorylation has not been well characterised. We took advantage of phosphoproteomics and gas exchange analyses with instant sampling adapted to Arabidopsis rosettes to examine the occurrence and variations of phosphopeptides associated with RCA in different photosynthetic contexts (CO2 mole fraction, light and dark). We detected two phosphopeptides from RCA corresponding to residues Thr 78 and Ser 172, and show that the former is considerably more phosphorylated in the dark than in the light, while the latter show no light/dark pattern. The CO2 mole fraction did not influence phosphorylation of either residue. Phosphorylation thus appears to be a potential mechanism associated with RCA dark inactivation, when Rubisco-catalysed carboxylation is arrested. Since Thr 78 and Ser 172 are located in the N and Walker domains of the protein, respectively, the involvement of phosphorylation in protein-protein interaction and catalysis is likely.
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Affiliation(s)
- E Boex-Fontvieille
- Institut de biologie des plantes, CNRS UMR 8618, Université Paris-Sud, Orsay, France
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