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Weiszmann J, Walther D, Clauw P, Back G, Gunis J, Reichardt I, Koemeda S, Jez J, Nordborg M, Schwarzerova J, Pierides I, Nägele T, Weckwerth W. Metabolome plasticity in 241 Arabidopsis thaliana accessions reveals evolutionary cold adaptation processes. PLANT PHYSIOLOGY 2023; 193:980-1000. [PMID: 37220420 PMCID: PMC10517190 DOI: 10.1093/plphys/kiad298] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/28/2023] [Accepted: 05/03/2023] [Indexed: 05/25/2023]
Abstract
Acclimation and adaptation of metabolism to a changing environment are key processes for plant survival and reproductive success. In the present study, 241 natural accessions of Arabidopsis (Arabidopsis thaliana) were grown under two different temperature regimes, 16 °C and 6 °C, and growth parameters were recorded, together with metabolite profiles, to investigate the natural genome × environment effects on metabolome variation. The plasticity of metabolism, which was captured by metabolic distance measures, varied considerably between accessions. Both relative growth rates and metabolic distances were predictable by the underlying natural genetic variation of accessions. Applying machine learning methods, climatic variables of the original growth habitats were tested for their predictive power of natural metabolic variation among accessions. We found specifically habitat temperature during the first quarter of the year to be the best predictor of the plasticity of primary metabolism, indicating habitat temperature as the causal driver of evolutionary cold adaptation processes. Analyses of epigenome- and genome-wide associations revealed accession-specific differential DNA-methylation levels as potentially linked to the metabolome and identified FUMARASE2 as strongly associated with cold adaptation in Arabidopsis accessions. These findings were supported by calculations of the biochemical Jacobian matrix based on variance and covariance of metabolomics data, which revealed that growth under low temperatures most substantially affects the accession-specific plasticity of fumarate and sugar metabolism. Our findings indicate that the plasticity of metabolic regulation is predictable from the genome and epigenome and driven evolutionarily by Arabidopsis growth habitats.
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Affiliation(s)
- Jakob Weiszmann
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, 1030 Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, 1030 Vienna, Austria
| | - Dirk Walther
- Bioinformatics, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Pieter Clauw
- Austrian Academy of Sciences, Gregor Mendel Institute (GMI), 1030 Vienna, Austria
| | - Georg Back
- Bioinformatics, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Joanna Gunis
- Austrian Academy of Sciences, Gregor Mendel Institute (GMI), 1030 Vienna, Austria
| | - Ilka Reichardt
- Genome Engineering Facility, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Stefanie Koemeda
- Plant Sciences Facility, Vienna BioCenter Core Facilities GmbH (VBCF), 1030 Vienna, Austria
| | - Jakub Jez
- Plant Sciences Facility, Vienna BioCenter Core Facilities GmbH (VBCF), 1030 Vienna, Austria
| | - Magnus Nordborg
- Austrian Academy of Sciences, Gregor Mendel Institute (GMI), 1030 Vienna, Austria
| | - Jana Schwarzerova
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, 1030 Vienna, Austria
- Brno University of Technology, Faculty of Electrical Engineering and Communication, Department of Biomedical Engineering, Technická 12, 616 00 Brno, Czech Republic
| | - Iro Pierides
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, 1030 Vienna, Austria
| | - Thomas Nägele
- LMU Munich, Faculty of Biology, Plant Evolutionary Cell Biology, 82152 Planegg, Germany
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, 1030 Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, 1030 Vienna, Austria
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Photosynthetic acclimation to changing environments. Biochem Soc Trans 2023; 51:473-486. [PMID: 36892145 DOI: 10.1042/bst20211245] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/03/2023] [Accepted: 02/21/2023] [Indexed: 03/10/2023]
Abstract
Plants are exposed to environments that fluctuate of timescales varying from seconds to months. Leaves that develop in one set of conditions optimise their metabolism to the conditions experienced, in a process called developmental acclimation. However, when plants experience a sustained change in conditions, existing leaves will also acclimate dynamically to the new conditions. Typically this process takes several days. In this review, we discuss this dynamic acclimation process, focussing on the responses of the photosynthetic apparatus to light and temperature. We briefly discuss the principal changes occurring in the chloroplast, before examining what is known, and not known, about the sensing and signalling processes that underlie acclimation, identifying likely regulators of acclimation.
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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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