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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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DiMario RJ, Kophs AN, Apalla AJA, Schnable JN, Cousins AB. Multiple highly expressed phosphoenolpyruvate carboxylase genes have divergent enzyme kinetic properties in two C4 grasses. ANNALS OF BOTANY 2023; 132:413-428. [PMID: 37675505 PMCID: PMC10667006 DOI: 10.1093/aob/mcad116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/06/2023] [Indexed: 09/08/2023]
Abstract
BACKGROUND AND AIMS Phosphoenolpyruvate (PEP) carboxylase (PEPC) catalyses the irreversible carboxylation of PEP with bicarbonate to produce oxaloacetate. This reaction powers the carbon-concentrating mechanism (CCM) in plants that perform C4 photosynthesis. This CCM is generally driven by a single PEPC gene product that is highly expressed in the cytosol of mesophyll cells. We found two C4 grasses, Panicum miliaceum and Echinochloa colona, that each have two highly expressed PEPC genes. We characterized the kinetic properties of the two most abundant PEPCs in E. colona and P. miliaceum to better understand how the enzyme's amino acid structure influences its function. METHODS Coding sequences of the two most abundant PEPC proteins in E. colona and P. miliaceum were synthesized by GenScript and were inserted into bacteria expression plasmids. Point mutations resulting in substitutions at conserved amino acid residues (e.g. N-terminal serine and residue 890) were created via site-directed PCR mutagenesis. The kinetic properties of semi-purified plant PEPCs from Escherichia coli were analysed using membrane-inlet mass spectrometry and a spectrophotometric enzyme-coupled reaction. KEY RESULTS The two most abundant P. miliaceum PEPCs (PmPPC1 and PmPPC2) have similar sequence identities (>95 %), and as a result had similar kinetic properties. The two most abundant E. colona PEPCs (EcPPC1 and EcPPC2) had identities of ~78 % and had significantly different kinetic properties. The PmPPCs and EcPPCs had different responses to allosteric inhibitors and activators, and substitutions at the conserved N-terminal serine and residue 890 resulted in significantly altered responses to allosteric regulators. CONCLUSIONS The two, significantly expressed C4Ppc genes in P. miliaceum were probably the result of genomes combining from two closely related C4Panicum species. We found natural variation in PEPC's sensitivity to allosteric inhibition that seems to bypass the conserved 890 residue, suggesting alternative evolutionary pathways for increased malate tolerance and other kinetic properties.
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Affiliation(s)
- Robert J DiMario
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Ashley N Kophs
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Anthony J A Apalla
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - James N Schnable
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
| | - Asaph B Cousins
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
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3
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Detecting macroevolutionary genotype-phenotype associations using error-corrected rates of protein convergence. Nat Ecol Evol 2023; 7:155-170. [PMID: 36604553 PMCID: PMC9834058 DOI: 10.1038/s41559-022-01932-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/12/2022] [Indexed: 01/07/2023]
Abstract
On macroevolutionary timescales, extensive mutations and phylogenetic uncertainty mask the signals of genotype-phenotype associations underlying convergent evolution. To overcome this problem, we extended the widely used framework of non-synonymous to synonymous substitution rate ratios and developed the novel metric ωC, which measures the error-corrected convergence rate of protein evolution. While ωC distinguishes natural selection from genetic noise and phylogenetic errors in simulation and real examples, its accuracy allows an exploratory genome-wide search of adaptive molecular convergence without phenotypic hypothesis or candidate genes. Using gene expression data, we explored over 20 million branch combinations in vertebrate genes and identified the joint convergence of expression patterns and protein sequences with amino acid substitutions in functionally important sites, providing hypotheses on undiscovered phenotypes. We further extended our method with a heuristic algorithm to detect highly repetitive convergence among computationally non-trivial higher-order phylogenetic combinations. Our approach allows bidirectional searches for genotype-phenotype associations, even in lineages that diverged for hundreds of millions of years.
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4
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Singh J, Garai S, Das S, Thakur JK, Tripathy BC. Role of C4 photosynthetic enzyme isoforms in C3 plants and their potential applications in improving agronomic traits in crops. PHOTOSYNTHESIS RESEARCH 2022; 154:233-258. [PMID: 36309625 DOI: 10.1007/s11120-022-00978-9] [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: 06/02/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
As compared to C3, C4 plants have higher photosynthetic rates and better tolerance to high temperature and drought. These traits are highly beneficial in the current scenario of global warming. Interestingly, all the genes of the C4 photosynthetic pathway are present in C3 plants, although they are involved in diverse non-photosynthetic functions. Non-photosynthetic isoforms of carbonic anhydrase (CA), phosphoenolpyruvate carboxylase (PEPC), malate dehydrogenase (MDH), the decarboxylating enzymes NAD/NADP-malic enzyme (NAD/NADP-ME), and phosphoenolpyruvate carboxykinase (PEPCK), and finally pyruvate orthophosphate dikinase (PPDK) catalyze reactions that are essential for major plant metabolism pathways, such as the tricarboxylic acid (TCA) cycle, maintenance of cellular pH, uptake of nutrients and their assimilation. Consistent with this view differential expression pattern of these non-photosynthetic C3 isoforms has been observed in different tissues across the plant developmental stages, such as germination, grain filling, and leaf senescence. Also abundance of these C3 isoforms is increased considerably in response to environmental fluctuations particularly during abiotic stress. Here we review the vital roles played by C3 isoforms of C4 enzymes and the probable mechanisms by which they help plants in acclimation to adverse growth conditions. Further, their potential applications to increase the agronomic trait value of C3 crops is discussed.
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Affiliation(s)
- Jitender Singh
- National Institute of Plant Genome Research, New Delhi, 110067, India.
| | - Sampurna Garai
- International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Shubhashis Das
- National Institute of Plant Genome Research, New Delhi, 110067, India
| | - Jitendra Kumar Thakur
- National Institute of Plant Genome Research, New Delhi, 110067, India.
- International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India.
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5
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Moody NR, Phansopal C, Reid JD. An in vitro Coupled Assay for PEPC with Control of Bicarbonate Concentration. Bio Protoc 2021; 11:e4264. [PMID: 35087923 DOI: 10.21769/bioprotoc.4264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 10/03/2021] [Accepted: 10/07/2021] [Indexed: 11/02/2022] Open
Abstract
Phosphoenolpyruvate carboxylase (PEPC) catalyzes a critical step in carbon metabolism in plants and bacteria, the irreversible reaction between bicarbonate and phosphoenolpyruvate to produce the C4 compound oxaloacetate. This enzyme is particularly important in the context of C4 photosynthesis, where it is the initial carbon-fixing enzyme. Many studies have used kinetic approaches to characterize the properties of PEPCs from different species, different post-translational states, and after mutagenesis. Most of these studies have worked at a fixed saturating concentration of bicarbonate. Controlling the concentration of bicarbonate is difficult at low concentrations because of equilibration with atmospheric CO2. We describe here a simple, repeatable, and gas-tight assay system for PEPC that allows bicarbonate concentrations to be controlled above ca. 50 µM.
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Affiliation(s)
- Nicholas R Moody
- Department of Chemistry, University of Sheffield, Brook Hill, Sheffield, S3 7HF, United Kingdom
| | - Chatawal Phansopal
- Department of Chemistry, University of Sheffield, Brook Hill, Sheffield, S3 7HF, United Kingdom
| | - James D Reid
- Department of Chemistry, University of Sheffield, Brook Hill, Sheffield, S3 7HF, United Kingdom
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6
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Ermakova M, Osborn H, Groszmann M, Bala S, Bowerman A, McGaughey S, Byrt C, Alonso-Cantabrana H, Tyerman S, Furbank RT, Sharwood RE, von Caemmerer S. Expression of a CO 2-permeable aquaporin enhances mesophyll conductance in the C 4 species Setaria viridis. eLife 2021; 10:70095. [PMID: 34842138 PMCID: PMC8648302 DOI: 10.7554/elife.70095] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 11/23/2021] [Indexed: 02/02/2023] Open
Abstract
A fundamental limitation of photosynthetic carbon fixation is the availability of CO2. In C4 plants, primary carboxylation occurs in mesophyll cytosol, and little is known about the role of CO2 diffusion in facilitating C4 photosynthesis. We have examined the expression, localization, and functional role of selected plasma membrane intrinsic aquaporins (PIPs) from Setaria italica (foxtail millet) and discovered that SiPIP2;7 is CO2-permeable. When ectopically expressed in mesophyll cells of Setaria viridis (green foxtail), SiPIP2;7 was localized to the plasma membrane and caused no marked changes in leaf biochemistry. Gas exchange and C18O16O discrimination measurements revealed that targeted expression of SiPIP2;7 enhanced the conductance to CO2 diffusion from the intercellular airspace to the mesophyll cytosol. Our results demonstrate that mesophyll conductance limits C4 photosynthesis at low pCO2 and that SiPIP2;7 is a functional CO2 permeable aquaporin that can improve CO2 diffusion at the airspace/mesophyll interface and enhance C4 photosynthesis.
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Affiliation(s)
- Maria Ermakova
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, Canberra, Australia
| | - Hannah Osborn
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, Canberra, Australia
| | - Michael Groszmann
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, Canberra, Australia
| | - Soumi Bala
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, Canberra, Australia
| | - Andrew Bowerman
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, Canberra, Australia
| | - Samantha McGaughey
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, Canberra, Australia
| | - Caitlin Byrt
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, Canberra, Australia
| | - Hugo Alonso-Cantabrana
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, Canberra, Australia
| | - Steve Tyerman
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture Food and Wine, University of Adelaide, Adelaide, Australia
| | - Robert T Furbank
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, Canberra, Australia
| | - Robert E Sharwood
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, Canberra, Australia.,Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia
| | - Susanne von Caemmerer
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, Canberra, Australia
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Xu ZM, Wang JF, Li WL, Wang YF, He T, Wang FP, Lu ZY, Li QS. Nitrogen fertilizer affects rhizosphere Cd re-mobilization by mediating gene AmALM2 and AmALMT7 expression in edible amaranth roots. JOURNAL OF HAZARDOUS MATERIALS 2021; 418:126310. [PMID: 34130167 DOI: 10.1016/j.jhazmat.2021.126310] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/11/2021] [Accepted: 06/01/2021] [Indexed: 06/12/2023]
Abstract
In-situ stabilization of Cd-contaminated farmland is a commonly used remediation technology. Yet, rhizosphere metabolites (e.g., organic acids) during crop cultivation may cause Cd re-mobilization and over-accumulation. Here, we identified four pivotal cytomembrane-localized genes underlying Cd accumulation difference between two contrasting edible amaranth cultivars based on root gene expression profile, studied their subcellular localization and functional characteristics, and then investigated effects of nitrogen fertilizer on their expression and rhizosphere Cd re-mobilization. Results showed that more Cd accumulated by edible amaranth was due to rhizosphere Cd mobilization by mediating high expression of AmALMT2 and AmALMT7 genes, not Cd transporters in roots. This was confirmed by heterologous expression of AmALMT2 and AmALMT7 genes in Arabidopsis thaliana, since they mediated malic, fumaric, succinic, and aspartic acids efflux. Furthermore, nitrogen influencing rhizosphere acidification might be closely associated with organic acids efflux genes. Compared with N-NO3- application, N-NH4+ was massively assimilated into glutamates and oxaloacetates through up-regulating glutamine synthetase and alanine-aspartate-glutamate metabolic pathways, thereby enhancing TCA cycle and organic acids efflux dominated by binary carboxylic acids via up-regulating AmALMT2 and AmALMT7 genes, which finally caused Cd re-mobilization. Therefore, N-NO3--dominated nitrogen retarded rhizosphere Cd re-mobilization via inhibiting organic acids efflux function of AmALMT2 and AmALMT7 proteins.
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Affiliation(s)
- Zhi-Min Xu
- Key Laboratory of Environmental Pollution and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China; Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control of Guangdong Higher Education Institutes, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Jun-Feng Wang
- Key Laboratory of Environmental Pollution and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Wan-Li Li
- Key Laboratory of Environmental Pollution and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Yi-Fan Wang
- Key Laboratory of Environmental Pollution and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China; Department of Biotechnology, The University of Tokyo, Tokyo 113-8657, Japan
| | - Tao He
- Key Laboratory of Environmental Pollution and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Fo-Peng Wang
- Key Laboratory of Environmental Pollution and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Zi-Yan Lu
- Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control of Guangdong Higher Education Institutes, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Qu-Sheng Li
- Key Laboratory of Environmental Pollution and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China.
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8
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Sales CRG, Wang Y, Evers JB, Kromdijk J. Improving C4 photosynthesis to increase productivity under optimal and suboptimal conditions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5942-5960. [PMID: 34268575 PMCID: PMC8411859 DOI: 10.1093/jxb/erab327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/09/2021] [Indexed: 05/05/2023]
Abstract
Although improving photosynthetic efficiency is widely recognized as an underutilized strategy to increase crop yields, research in this area is strongly biased towards species with C3 photosynthesis relative to C4 species. Here, we outline potential strategies for improving C4 photosynthesis to increase yields in crops by reviewing the major bottlenecks limiting the C4 NADP-malic enzyme pathway under optimal and suboptimal conditions. Recent experimental results demonstrate that steady-state C4 photosynthesis under non-stressed conditions can be enhanced by increasing Rubisco content or electron transport capacity, both of which may also stimulate CO2 assimilation at supraoptimal temperatures. Several additional putative bottlenecks for photosynthetic performance under drought, heat, or chilling stress or during photosynthetic induction await further experimental verification. Based on source-sink interactions in maize, sugarcane, and sorghum, alleviating these photosynthetic bottlenecks during establishment and growth of the harvestable parts are likely to improve yield. The expected benefits are also shown to be augmented by the increasing trend in planting density, which increases the impact of photosynthetic source limitation on crop yields.
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Affiliation(s)
- Cristina R G Sales
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Yu Wang
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jochem B Evers
- Centre for Crops Systems Analysis (WUR), Wageningen University, Wageningen, The Netherlands
| | - Johannes Kromdijk
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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9
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von Caemmerer S. Updating the steady-state model of C4 photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6003-6017. [PMID: 34173821 PMCID: PMC8411607 DOI: 10.1093/jxb/erab266] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 06/06/2021] [Indexed: 05/22/2023]
Abstract
C4 plants play a key role in world agriculture. For example, C4 crops such as maize and sorghum are major contributors to food production in both developed and developing countries, and the C4 grasses sugarcane, miscanthus, and switchgrass are major plant sources of bioenergy. In the challenge to manipulate and enhance C4 photosynthesis, steady-state models of leaf photosynthesis provide an important tool for gas exchange analysis and thought experiments that can explore photosynthetic pathway changes. Here a previous C4 photosynthetic model developed by von Caemmerer and Furbank has been updated with new kinetic parameterization and temperature dependencies added. The parameterization was derived from experiments on the C4 monocot, Setaria viridis, which for the first time provides a cohesive parameterization. Mesophyll conductance and its temperature dependence have also been included, as this is an important step in the quantitative correlation between the initial slope of the CO2 response curve of CO2 assimilation and in vitro phosphoenolpyruvate carboxylase activity. Furthermore, the equations for chloroplast electron transport have been updated to include cyclic electron transport flow, and equations have been added to calculate the electron transport rate from measured CO2 assimilation rates.
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Affiliation(s)
- Susanne von Caemmerer
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
- Correspondence:
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10
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von Caemmerer S. Updating the steady-state model of C4 photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2021. [PMID: 34173821 DOI: 10.5061/dryad.zcrjdfnc3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
C4 plants play a key role in world agriculture. For example, C4 crops such as maize and sorghum are major contributors to food production in both developed and developing countries, and the C4 grasses sugarcane, miscanthus, and switchgrass are major plant sources of bioenergy. In the challenge to manipulate and enhance C4 photosynthesis, steady-state models of leaf photosynthesis provide an important tool for gas exchange analysis and thought experiments that can explore photosynthetic pathway changes. Here a previous C4 photosynthetic model developed by von Caemmerer and Furbank has been updated with new kinetic parameterization and temperature dependencies added. The parameterization was derived from experiments on the C4 monocot, Setaria viridis, which for the first time provides a cohesive parameterization. Mesophyll conductance and its temperature dependence have also been included, as this is an important step in the quantitative correlation between the initial slope of the CO2 response curve of CO2 assimilation and in vitro phosphoenolpyruvate carboxylase activity. Furthermore, the equations for chloroplast electron transport have been updated to include cyclic electron transport flow, and equations have been added to calculate the electron transport rate from measured CO2 assimilation rates.
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Affiliation(s)
- Susanne von Caemmerer
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
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11
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Phansopa C, Dunning LT, Reid JD, Christin PA. Lateral Gene Transfer Acts As an Evolutionary Shortcut to Efficient C4 Biochemistry. Mol Biol Evol 2021; 37:3094-3104. [PMID: 32521019 PMCID: PMC7751175 DOI: 10.1093/molbev/msaa143] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The adaptation of proteins for novel functions often requires changes in their kinetics via amino acid replacement. This process can require multiple mutations, and therefore extended periods of selection. The transfer of genes among distinct species might speed up the process, by providing proteins already adapted for the novel function. However, this hypothesis remains untested in multicellular eukaryotes. The grass Alloteropsis is an ideal system to test this hypothesis due to its diversity of genes encoding phosphoenolpyruvate carboxylase, an enzyme that catalyzes one of the key reactions in the C4 pathway. Different accessions of Alloteropsis either use native isoforms relatively recently co-opted from other functions or isoforms that were laterally acquired from distantly related species that evolved the C4 trait much earlier. By comparing the enzyme kinetics, we show that native isoforms with few amino acid replacements have substrate KM values similar to the non-C4 ancestral form, but exhibit marked increases in catalytic efficiency. The co-option of native isoforms was therefore followed by rapid catalytic improvements, which appear to rely on standing genetic variation observed within one species. Native C4 isoforms with more amino acid replacements exhibit additional changes in affinities, suggesting that the initial catalytic improvements are followed by gradual modifications. Finally, laterally acquired genes show both strong increases in catalytic efficiency and important changes in substrate handling. We conclude that the transfer of genes among distant species sharing the same physiological novelty creates an evolutionary shortcut toward more efficient enzymes, effectively accelerating evolution.
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Affiliation(s)
- Chatchawal Phansopa
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom.,Department of Chemistry, University of Sheffield, Sheffield, United Kingdom
| | - Luke T Dunning
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - James D Reid
- Department of Chemistry, University of Sheffield, Sheffield, United Kingdom
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12
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Chatterjee J, Coe RA, Acebron K, Thakur V, Yennamalli RM, Danila F, Lin HC, Balahadia CP, Bagunu E, Padhma PPOS, Bala S, Yin X, Rizal G, Dionora J, Furbank RT, von Caemmerer S, Quick WP. A low CO2-responsive mutant of Setaria viridis reveals that reduced carbonic anhydrase limits C4 photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3122-3136. [PMID: 33528493 PMCID: PMC8023212 DOI: 10.1093/jxb/erab039] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/30/2021] [Indexed: 06/12/2023]
Abstract
In C4 species, β-carbonic anhydrase (CA), localized to the cytosol of the mesophyll cells, accelerates the interconversion of CO2 to HCO3-, the substrate used by phosphoenolpyruvate carboxylase (PEPC) in the first step of C4 photosynthesis. Here we describe the identification and characterization of low CO2-responsive mutant 1 (lcr1) isolated from an N-nitroso-N-methylurea- (NMU) treated Setaria viridis mutant population. Forward genetic investigation revealed that the mutated gene Sevir.5G247800 of lcr1 possessed a single nucleotide transition from cytosine to thymine in a β-CA gene causing an amino acid change from leucine to phenylalanine. This resulted in severe reduction in growth and photosynthesis in the mutant. Both the CO2 compensation point and carbon isotope discrimination values of the mutant were significantly increased. Growth of the mutants was stunted when grown under ambient pCO2 but recovered at elevated pCO2. Further bioinformatics analyses revealed that the mutation has led to functional changes in one of the conserved residues of the protein, situated near the catalytic site. CA transcript accumulation in the mutant was 80% lower, CA protein accumulation 30% lower, and CA activity ~98% lower compared with the wild type. Changes in the abundance of other primary C4 pathway enzymes were observed; accumulation of PEPC protein was significantly increased and accumulation of malate dehydrogenase and malic enzyme decreased. The reduction of CA protein activity and abundance in lcr1 restricts the supply of bicarbonate to PEPC, limiting C4 photosynthesis and growth. This study establishes Sevir.5G247800 as the major CA allele in Setaria for C4 photosynthesis and provides important insights into the function of CA in C4 photosynthesis that would be required to generate a rice plant with a functional C4 biochemical pathway.
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Affiliation(s)
- Jolly Chatterjee
- C4 Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Robert A Coe
- CSIRO Agriculture Flagship, Australian Plant Phenomics Facility, GPO Box 1500, Canberra, ACT 2601, Australia
| | - Kelvin Acebron
- C4 Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Vivek Thakur
- C4 Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines
- Department of Systems & Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad-500046, India
| | - Ragothaman M Yennamalli
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, Tamilnadu-613401, India
| | - Florence Danila
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, GPO Box 1500, Canberra, ACT 2601, Australia
| | - Hsiang-Chun Lin
- C4 Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines
| | | | - Efren Bagunu
- C4 Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Preiya P O S Padhma
- Department of Systems & Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad-500046, India
| | - Soumi Bala
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, GPO Box 1500, Canberra, ACT 2601, Australia
| | - Xiaojia Yin
- C4 Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Govinda Rizal
- C4 Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Jacqueline Dionora
- C4 Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Robert T Furbank
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, GPO Box 1500, Canberra, ACT 2601, Australia
| | - Susanne von Caemmerer
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, GPO Box 1500, Canberra, ACT 2601, Australia
| | - William Paul Quick
- C4 Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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DiMario RJ, Kophs AN, Pathare VS, Schnable JC, Cousins AB. Kinetic variation in grass phosphoenolpyruvate carboxylases provides opportunity to enhance C 4 photosynthetic efficiency. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1677-1688. [PMID: 33345397 DOI: 10.1111/tpj.15141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
The high rates of photosynthesis and the carbon-concentrating mechanism (CCM) in C4 plants are initiated by the enzyme phosphoenolpyruvate (PEP) carboxylase (PEPC). The flow of inorganic carbon into the CCM of C4 plants is driven by PEPC's affinity for bicarbonate (KHCO3 ), which can be rate limiting when atmospheric CO2 availability is restricted due to low stomatal conductance. We hypothesize that natural variation in KHCO3 across C4 plants is driven by specific amino acid substitutions to impact rates of C4 photosynthesis under environments such as drought that restrict stomatal conductance. To test this hypothesis, we measured KHCO3 from 20 C4 grasses to compare kinetic properties with specific amino acid substitutions. There was nearly a twofold range in KHCO3 across these C4 grasses (24.3 ± 1.5 to 46.3 ± 2.4 μm), which significantly impacts modeled rates of C4 photosynthesis. Additionally, molecular engineering of a low-HCO3- affinity PEPC identified key domains that confer variation in KHCO3 . This study advances our understanding of PEPC kinetics and builds the foundation for engineering increased-HCO3- affinity and C4 photosynthetic efficiency in important C4 crops.
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Affiliation(s)
- Robert J DiMario
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Ashley N Kophs
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Varsha S Pathare
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Asaph B Cousins
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
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14
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Khoshravesh R, Stata M, Adachi S, Sage TL, Sage RF. Evolutionary Convergence of C 4 Photosynthesis: A Case Study in the Nyctaginaceae. FRONTIERS IN PLANT SCIENCE 2020; 11:578739. [PMID: 33224166 PMCID: PMC7667235 DOI: 10.3389/fpls.2020.578739] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/06/2020] [Indexed: 05/27/2023]
Abstract
C4 photosynthesis evolved over 65 times, with around 24 origins in the eudicot order Caryophyllales. In the Caryophyllales family Nyctaginaceae, the C4 pathway is known in three genera of the tribe Nyctagineae: Allionia, Okenia and Boerhavia. Phylogenetically, Allionia and Boerhavia/Okenia are separated by three genera whose photosynthetic pathway is uncertain. To clarify the distribution of photosynthetic pathways in the Nyctaginaceae, we surveyed carbon isotope ratios of 159 species of the Nyctaginaceae, along with bundle sheath (BS) cell ultrastructure, leaf gas exchange, and C4 pathway biochemistry in five species from the two C4 clades and closely related C3 genera. All species in Allionia, Okenia and Boerhavia are C4, while no C4 species occur in any other genera of the family, including three that branch between Allionia and Boerhavia. This demonstrates that C4 photosynthesis evolved twice in Nyctaginaceae. Boerhavia species use the NADP-malic enzyme (NADP-ME) subtype of C4 photosynthesis, while Allionia species use the NAD-malic enzyme (NAD-ME) subtype. The BS cells of Allionia have many more mitochondria than the BS of Boerhavia. Bundle sheath mitochondria are closely associated with chloroplasts in Allionia which facilitates CO2 refixation following decarboxylation by mitochondrial NAD-ME. The close relationship between Allionia and Boerhavia could provide insights into why NADP-ME versus NAD-ME subtypes evolve, particularly when coupled to analysis of their respective genomes. As such, the group is an excellent system to dissect the organizational hierarchy of convergent versus divergent traits produced by C4 evolution, enabling us to understand when convergence is favored versus when divergent modifications can result in a common phenotype.
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Affiliation(s)
- Roxana Khoshravesh
- Department of Ecology and Evolutionary Biology, The University of Toronto, Toronto, ON, Canada
- Department of Biology, The University of New Mexico, Albuquerque, NM, United States
| | - Matt Stata
- Department of Ecology and Evolutionary Biology, The University of Toronto, Toronto, ON, Canada
| | - Shunsuke Adachi
- Department of Ecology and Evolutionary Biology, The University of Toronto, Toronto, ON, Canada
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Tammy L. Sage
- Department of Ecology and Evolutionary Biology, The University of Toronto, Toronto, ON, Canada
| | - Rowan F. Sage
- Department of Ecology and Evolutionary Biology, The University of Toronto, Toronto, ON, Canada
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Nomura K, Sakurai Y, Dozono M. Molecular Cloning of Novel-Type Phospho enolpyruvate Carboxylase Isoforms in Pitaya ( Hylocereus undatus). PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9091241. [PMID: 32967083 PMCID: PMC7569800 DOI: 10.3390/plants9091241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/17/2020] [Accepted: 09/17/2020] [Indexed: 06/11/2023]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is an important enzyme involved in the initial CO2 fixation of crassulacean acid metabolism (CAM) photosynthesis. To understand the cultivation characteristics of a CAM plant pitaya, it is necessary to clarify the characteristics of PEPC in this species. Here, we cloned three PEPC cDNAs in pitaya, HuPPC1, HuPPC2, and HuPPC3, which encode 942, 934, and 966 amino acid residues, respectively. Phylogenetic analysis indicated that these PEPC belonged to plant-type PEPC (PTPC), although HuPPC1 and HuPPC2 have no Ser-phosphorylation motif in N-terminal region, which is a crucial regulation site in PTPC and contributes to CAM periodicity. HuPPC1 and HuPPC2 phylogenetically unique to the Cactaceae family, whereas HuPPC3 was included in a CAM clade. Two isoforms were partially purified at the protein level and were assigned as HuPPC2 and HuPPC3 using MASCOT analysis. The most distinct difference in enzymatic properties between the two was sensitivity to malate and aspartate, both of which are allosteric inhibitors of PEPC. With 2 mM malate, HuPPC3 was inhibited to 10% of the initial activity, whereas HuPPC2 activity was maintained at 70%. Aspartate inhibited HuPPC3 activity by approximately 50% at 5 mM; however, such inhibition was not observed for HuPPC2 at 10 mM. These results suggest that HuPPC3 corresponds to a general CAM-related PEPC, whereas HuPPC1 and HuPPC2 are related to carbon and/or nitrogen metabolism, with a characteristic regulation mechanism similar to those of Cactaceae plants.
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Affiliation(s)
- Keiichi Nomura
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan;
| | - Yuho Sakurai
- Faculty of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan;
| | - Mayu Dozono
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan;
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Moody NR, Christin PA, Reid JD. Kinetic Modifications of C 4 PEPC Are Qualitatively Convergent, but Larger in Panicum Than in Flaveria. FRONTIERS IN PLANT SCIENCE 2020; 11:1014. [PMID: 32719709 PMCID: PMC7350407 DOI: 10.3389/fpls.2020.01014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
C4 photosynthesis results from a set of anatomical features and biochemical components that act together to concentrate CO2 within the leaf and boost productivity. This complex trait evolved independently many times, resulting in various realizations of the phenotype, but in all C4 plants the primary fixation of atmospheric carbon is catalyzed by phosphoenolpyruvate carboxylase. Comparisons of C4 and non-C4 PEPC from a few closely related species suggested that the enzyme was modified to meet the demands of the C4 cycle. However, very few C4 groups have been investigated, hampering general conclusions. To test the hypothesis that distant C4 lineages underwent convergent biochemical changes, we compare the kinetic variation between C4 and non-C4 PEPC from a previously assessed young lineage (Flaveria, Asteraceae) with those from an older lineage found within the distantly related grass family (Panicum). Despite the evolutionary distance, the kinetic changes between the non-C4 and C4 PEPC are qualitatively similar, with a decrease in sensitivity for inhibitors, an increased specificity (k cat/K m) for bicarbonate, and a decreased specificity (k cat/K m) for PEP. The differences are more pronounced in the older lineage Panicum, which might indicate that optimization of PEPC for the C4 context increases with evolutionary time.
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Affiliation(s)
- Nicholas R. Moody
- Department of Chemistry, University of Sheffield, Sheffield, United Kingdom
| | | | - James D. Reid
- Department of Chemistry, University of Sheffield, Sheffield, United Kingdom
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Serrano-Romero EA, Cousins AB. Cold acclimation of mesophyll conductance, bundle-sheath conductance and leakiness in Miscanthus × giganteus. THE NEW PHYTOLOGIST 2020; 226:1594-1606. [PMID: 32112409 DOI: 10.1111/nph.16503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 02/16/2020] [Indexed: 06/10/2023]
Abstract
The cold acclimations of mesophyll conductance (gm ), bundle-sheath conductance (gbs ) and the CO2 concentrating mechanism (CCM) of C4 plants have not been well studied. Here, we estimated the temperature response of gm , gbs and leakiness (ϕ), the amount of concentrated CO2 that escapes the bundle-sheath cells, for the chilling-tolerant C4 plant Miscanthus × giganteus grown at 14 and 25°C. To estimate these parameters, we combined the C4 -enzyme-limited photosynthesis model and the Δ13 C discrimination model. These combined models were parameterised using in vitro activities of carbonic anhydrase (CA), pyruvate, phosphate dikinase (PPDK), ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), and phosphoenolpyruvate carboxylase (PEPc). Cold-grown Miscanthus plants increased in vitro activities of RuBisCO and PPDK but decreased PEPc activity compared with warm-grown plants. Mesophyll conductance and gbs responded strongly to measurement temperatures but did not differ between plants from the two growth temperatures. Furthermore, modelling showed that ϕ increased with measurement temperatures for both cold-grown and warm-grown plants, but was only marginally larger in cold-grown compared with warm-grown plants. Our results in Miscanthus support that gm and gbs are unresponsive to growth temperature and that the CCM is able to acclimate to cold through increased activity of PPDK and RuBisCO.
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Affiliation(s)
| | - Asaph B Cousins
- Molecular Plant Sciences, Washington State University, Pullman, WA, 99164-4236, USA
- School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
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