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Saunders HA, Calzadilla PI, Schwartz JM, Johnson GN. Cytosolic fumarase acts as a metabolic fail-safe for both high and low temperature acclimation of Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2112-2124. [PMID: 34951633 DOI: 10.1093/jxb/erab560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
Plants acclimate their photosynthetic capacity (Pmax) in response to changing environmental conditions. In Arabidopsis thaliana, photosynthetic acclimation to cold requires the accumulation of the organic acid fumarate, catalysed by a cytosolically localized fumarase, FUM2. However, the role of this accumulation is currently unknown. Here, we use an integrated experimental and modelling approach to examine the role of FUM2 and fumarate across the physiological temperature range. We have studied three genotypes: Col-0; a fum2 mutant in a Col-0 background; and C24, an accession with reduced FUM2 expression. While low temperature causes an increase in Pmax in the Col-0 plants, this parameter decreases following exposure of plants to 30 °C for 7 d. Plants in which fumarate accumulation is partially (C24) or completely (fum2) abolished show a reduced acclimation of Pmax across the physiological temperature range (i.e. Pmax changes less in response to changing temperature). To understand the role of fumarate accumulation, we have adapted a reliability engineering technique, Failure Mode and Effect Analysis (FMEA), to formalize a rigorous approach for ranking metabolites according to the potential risk that they pose to the metabolic system. FMEA identifies fumarate as a low-risk metabolite, while its precursor, malate, is shown to be high risk and liable to cause system instability. We propose that the role of FUM2 is to provide a fail-safe in order to control malate concentration, maintaining system stability in a changing environment. We suggest that FMEA is a technique that is not only useful in understanding plant metabolism but can also be used to study reliability in other systems and synthetic pathways.
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Affiliation(s)
- Helena A Saunders
- Department of Earth and Environmental Sciences, Faculty of Science and Engineering, University of Manchester, Manchester M13 9PT, UK
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Pablo I Calzadilla
- Department of Earth and Environmental Sciences, Faculty of Science and Engineering, University of Manchester, Manchester M13 9PT, UK
| | - Jean-Marc Schwartz
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Giles N Johnson
- Department of Earth and Environmental Sciences, Faculty of Science and Engineering, University of Manchester, Manchester M13 9PT, UK
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2
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Herrmann HA, Schwartz JM, Johnson GN. Metabolic acclimation-a key to enhancing photosynthesis in changing environments? JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3043-3056. [PMID: 30997505 DOI: 10.1093/jxb/erz157] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/21/2019] [Indexed: 05/18/2023]
Abstract
Plants adjust their photosynthetic capacity in response to their environment in a way that optimizes their yield and fitness. There is growing evidence that this acclimation is a response to changes in the leaf metabolome, but the extent to which these are linked and how this is optimized remain poorly understood. Using as an example the metabolic perturbations occurring in response to cold, we define the different stages required for acclimation, discuss the evidence for a metabolic temperature sensor, and suggest further work towards designing climate-smart crops. In particular, we discuss how constraint-based and kinetic metabolic modelling approaches can be used to generate targeted hypotheses about relevant pathways, and argue that a stronger integration of experimental and in silico studies will help us to understand the tightly regulated interplay of carbon partitioning and resource allocation required for photosynthetic acclimation to different environmental conditions.
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Affiliation(s)
- Helena A Herrmann
- School of Earth and Environmental Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, UK
- Division of Evolution & Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Jean-Marc Schwartz
- Division of Evolution & Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Giles N Johnson
- School of Earth and Environmental Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, UK
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3
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Zubimendi JP, Martinatto A, Valacco MP, Moreno S, Andreo CS, Drincovich MF, Tronconi MA. The complex allosteric and redox regulation of the fumarate hydratase and malate dehydratase reactions of Arabidopsis thaliana Fumarase 1 and 2 gives clues for understanding the massive accumulation of fumarate. FEBS J 2018; 285:2205-2224. [PMID: 29688630 DOI: 10.1111/febs.14483] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/22/2018] [Accepted: 04/19/2018] [Indexed: 11/30/2022]
Abstract
Arabidopsis thaliana possesses two fumarase genes (FUM), AtFUM1 (At2g47510) encoding for the mitochondrial Krebs cycle-associated enzyme and AtFUM2 (At5g50950) for the cytosolic isoform required for fumarate massive accumulation. Here, the comprehensive biochemical studies of AtFUM1 and AtFUM2 shows that they are active enzymes with similar kinetic parameters but differential regulation. For both enzymes, fumarate hydratase (FH) activity is favored over the malate dehydratase (MD) activity; however, MD is the most regulated activity with several allosteric activators. Oxalacetate, glutamine, and/or asparagine are modulators causing the MD reaction to become preferred over the FH reaction. Activity profiles as a function of pH suggest a suboptimal FUM activity in Arabidopsis cells; moreover, the direction of the FUM reaction is sensitive to pH changes. Under mild oxidation conditions, AtFUMs form high mass molecular aggregates, which present both FUM activities decreased to a different extent. The biochemical properties of oxidized AtFUMs (oxAtFUMs) were completely reversed by NADPH-supplied Arabidopsis leaf extracts, suggesting that the AtFUMs redox regulation can be accomplished in vivo. Mass spectrometry analyses indicate the presence of an active site-associated intermolecular disulfide bridge in oxAtFUMs. Finally, a phylogenetic approach points out that other plant species may also possess cytosolic FUM2 enzymes mainly encoded by paralogous genes, indicating that the evolutionary history of this trait has been drawn through a process of parallel evolution. Overall, according to our results, a multilevel regulatory pattern of FUM activities emerges, supporting the role of this enzyme as a carbon flow monitoring point through the organic acid metabolism in plants.
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Affiliation(s)
- Juan P Zubimendi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Santa Fe, Argentina
| | - Andrea Martinatto
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Santa Fe, Argentina
| | - Maria P Valacco
- Departamento de Química Biológica, Facultad de Ciencias exactas y Naturales, Universidad de Buenos Aires (UBA), Argentina
| | - Silvia Moreno
- Departamento de Química Biológica, Facultad de Ciencias exactas y Naturales, Universidad de Buenos Aires (UBA), Argentina
| | - Carlos S Andreo
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Santa Fe, Argentina
| | - María F Drincovich
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Santa Fe, Argentina
| | - Marcos A Tronconi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Santa Fe, Argentina
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4
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Maddison AL, Camargo-Rodriguez A, Scott IM, Jones CM, Elias DMO, Hawkins S, Massey A, Clifton-Brown J, McNamara NP, Donnison IS, Purdy SJ. Predicting future biomass yield in Miscanthus using the carbohydrate metabolic profile as a biomarker. GLOBAL CHANGE BIOLOGY. BIOENERGY 2017; 9:1264-1278. [PMID: 28713439 PMCID: PMC5488626 DOI: 10.1111/gcbb.12418] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 11/23/2016] [Indexed: 05/08/2023]
Abstract
In perennial energy crop breeding programmes, it can take several years before a mature yield is reached when potential new varieties can be scored. Modern plant breeding technologies have focussed on molecular markers, but for many crop species, this technology is unavailable. Therefore, prematurity predictors of harvestable yield would accelerate the release of new varieties. Metabolic biomarkers are routinely used in medicine, but they have been largely overlooked as predictive tools in plant science. We aimed to identify biomarkers of productivity in the bioenergy crop, Miscanthus, that could be used prognostically to predict future yields. This study identified a metabolic profile reflecting productivity in Miscanthus by correlating the summer carbohydrate composition of multiple genotypes with final yield 6 months later. Consistent and strong, significant correlations were observed between carbohydrate metrics and biomass traits at two separate field sites over 2 years. Machine-learning feature selection was used to optimize carbohydrate metrics for support vector regression models, which were able to predict interyear biomass traits with a correlation (R) of >0.67 between predicted and actual values. To identify a causal basis for the relationships between the glycome profile and biomass, a 13C-labelling experiment compared carbohydrate partitioning between high- and low-yielding genotypes. A lower yielding and slower growing genotype partitioned a greater percentage of the 13C pulse into starch compared to a faster growing genotype where a greater percentage was located in the structural biomass. These results supported a link between plant performance and carbon flow through two rival pathways (starch vs. sucrose), with higher yielding plants exhibiting greater partitioning into structural biomass, via sucrose metabolism, rather than starch. Our results demonstrate that the plant metabolome can be used prognostically to anticipate future yields and this is a method that could be used to accelerate selection in perennial energy crop breeding programmes.
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Affiliation(s)
- Anne L Maddison
- Institute of Biological, Environmental and Rural Sciences Aberystwyth University Plas Gogerddan SY23 3EB UK
| | - Anyela Camargo-Rodriguez
- Institute of Biological, Environmental and Rural Sciences Aberystwyth University Plas Gogerddan SY23 3EB UK
| | - Ian M Scott
- Institute of Biological, Environmental and Rural Sciences Aberystwyth University Plas Gogerddan SY23 3EB UK
| | - Charlotte M Jones
- Institute of Biological, Environmental and Rural Sciences Aberystwyth University Plas Gogerddan SY23 3EB UK
| | - Dafydd M O Elias
- Centre for Ecology and Hydrology Lancaster Environment Centre Library Avenue Bailrigg Lancaster LA1 4AP UK
| | - Sarah Hawkins
- Institute of Biological, Environmental and Rural Sciences Aberystwyth University Plas Gogerddan SY23 3EB UK
| | - Alice Massey
- Institute of Biological, Environmental and Rural Sciences Aberystwyth University Plas Gogerddan SY23 3EB UK
| | - John Clifton-Brown
- Institute of Biological, Environmental and Rural Sciences Aberystwyth University Plas Gogerddan SY23 3EB UK
| | - Niall P McNamara
- Centre for Ecology and Hydrology Lancaster Environment Centre Library Avenue Bailrigg Lancaster LA1 4AP UK
| | - Iain S Donnison
- Institute of Biological, Environmental and Rural Sciences Aberystwyth University Plas Gogerddan SY23 3EB UK
| | - Sarah J Purdy
- Institute of Biological, Environmental and Rural Sciences Aberystwyth University Plas Gogerddan SY23 3EB UK
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5
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Riewe D, Jeon HJ, Lisec J, Heuermann MC, Schmeichel J, Seyfarth M, Meyer RC, Willmitzer L, Altmann T. A naturally occurring promoter polymorphism of the Arabidopsis FUM2 gene causes expression variation, and is associated with metabolic and growth traits. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:826-838. [PMID: 27520391 DOI: 10.1111/tpj.13303] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 07/13/2016] [Accepted: 08/05/2016] [Indexed: 05/05/2023]
Abstract
Fumarate and malate are known intermediates of the TCA cycle, a mitochondrial metabolic pathway generating NADH for respiration. Arabidopsis thaliana and other Brassicaceae contain an additional cytosolic fumarase (FUM2) that functions in carbon assimilation and nitrogen use. Here, we report the identification of a hitherto unknown FUM2 promoter insertion/deletion (InDel) polymorphism found between the Col-0 and C24 accessions, which also divides a large number of Arabidopsis accessions carrying either the Col-0 or the C24 allele. The polymorphism consists of two stretches of 2.1 and 3.8 kb, which are both absent from the promotor region of Col-0 FUM2. By analysing mutants as well as mapping and natural populations with contrasting FUM2 alleles, the promotor insertion was linked to reduced FUM2 mRNA expression, reduced fumarase activity and reduced fumarate/malate ratio in leaves. In a large population of 174 natural accessions, the polymorphism was also found to be associated with the fumarate/malate ratio, malate and fumarate levels, and with dry weight at 15 days after sowing (DAS). The association with biomass production was confirmed in an even larger (251) accession population for dry weight at 22 DAS. The dominant Col-0 allele that results in increased fumarate/malate ratios and enhanced biomass production is predominantly found in central/eastern European accessions, whereas the C24 type allele is prevalent on the Iberian Peninsula, west of the Rhine and in the British Isles. Our findings support the role of FUM2 in diurnal carbon storage, and point to a growth advantage of accessions carrying the FUM2 Col-0 allele.
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Affiliation(s)
- David Riewe
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Hea-Jung Jeon
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Jan Lisec
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam-Golm, Germany
| | - Marc C Heuermann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Judith Schmeichel
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Monique Seyfarth
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Rhonda C Meyer
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Lothar Willmitzer
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam-Golm, Germany
| | - Thomas Altmann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
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6
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Chitosan oligosaccharide induces resistance to Tobacco mosaic virus in Arabidopsis via the salicylic acid-mediated signalling pathway. Sci Rep 2016; 6:26144. [PMID: 27189192 PMCID: PMC4870575 DOI: 10.1038/srep26144] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 04/27/2016] [Indexed: 12/17/2022] Open
Abstract
Chitosan is one of the most abundant carbohydrate biopolymers in the world, and chitosan oligosaccharide (COS), which is prepared from chitosan, is a plant immunity regulator. The present study aimed to validate the effect of COS on inducing resistance to tobacco mosaic virus (TMV) in Arabidopsis and to investigate the potential defence-related signalling pathways involved. Optimal conditions for the induction of TMV resistance in Arabidopsis were COS pretreatment at 50 mg/L for 1 day prior to inoculation with TMV. Multilevel indices, including phenotype data, and TMV coat protein expression, revealed that COS induced TMV resistance in wild-type and jasmonic acid pathway- deficient (jar1) Arabidopsis plants, but not in salicylic acid pathway deficient (NahG) Arabidopsis plants. Quantitative-PCR and analysis of phytohormone levels confirmed that COS pretreatment enhanced the expression of the defence-related gene PR1, which is a marker of salicylic acid signalling pathway, and increased the amount of salicylic acid in WT and jar1, but not in NahG plants. Taken together, these results confirm that COS induces TMV resistance in Arabidopsis via activation of the salicylic acid signalling pathway.
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