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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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Back G, Walther D. Identification of cis-regulatory motifs in first introns and the prediction of intron-mediated enhancement of gene expression in Arabidopsis thaliana. BMC Genomics 2021; 22:390. [PMID: 34039279 PMCID: PMC8157754 DOI: 10.1186/s12864-021-07711-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/11/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Intron mediated enhancement (IME) is the potential of introns to enhance the expression of its respective gene. This essential function of introns has been observed in a wide range of species, including fungi, plants, and animals. However, the mechanisms underlying the enhancement are as of yet poorly understood. The goal of this study was to identify potential IME-related sequence motifs and genomic features in first introns of genes in Arabidopsis thaliana. RESULTS Based on the rationale that functional sequence motifs are evolutionarily conserved, we exploited the deep sequencing information available for Arabidopsis thaliana, covering more than one thousand Arabidopsis accessions, and identified 81 candidate hexamer motifs with increased conservation across all accessions that also exhibit positional occurrence preferences. Of those, 71 were found associated with increased correlation of gene expression of genes harboring them, suggesting a cis-regulatory role. Filtering further for effect on gene expression correlation yielded a set of 16 hexamer motifs, corresponding to five consensus motifs. While all five motifs represent new motif definitions, two are similar to the two previously reported IME-motifs, whereas three are altogether novel. Both consensus and hexamer motifs were found associated with higher expression of alleles harboring them as compared to alleles containing mutated motif variants as found in naturally occurring Arabidopsis accessions. To identify additional IME-related genomic features, Random Forest models were trained for the classification of gene expression level based on an array of sequence-related features. The results indicate that introns contain information with regard to gene expression level and suggest sequence-compositional features as most informative, while position-related features, thought to be of central importance before, were found with lower than expected relevance. CONCLUSIONS Exploiting deep sequencing and broad gene expression information and on a genome-wide scale, this study confirmed the regulatory role on first-introns, characterized their intra-species conservation, and identified a set of novel sequence motifs located in first introns of genes in the genome of the plant Arabidopsis thaliana that may play a role in inducing high and correlated gene expression of the genes harboring them.
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Affiliation(s)
- Georg Back
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany.
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Yan Y, Li Z, Li Y, Wu Z, Yang R. Correlated Evolution of Large DNA Fragments in the 3D Genome of Arabidopsis thaliana. Mol Biol Evol 2021; 37:1621-1636. [PMID: 32044988 DOI: 10.1093/molbev/msaa031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In eukaryotes, the three-dimensional (3D) conformation of the genome is far from random, and this nonrandom chromatin organization is strongly correlated with gene expression and protein function, which are two critical determinants of the selective constraints and evolutionary rates of genes. However, whether genes and other elements that are located close to each other in the 3D genome evolve in a coordinated way has not been investigated in any organism. To address this question, we constructed chromatin interaction networks (CINs) in Arabidopsis thaliana based on high-throughput chromosome conformation capture data and demonstrated that adjacent large DNA fragments in the CIN indeed exhibit more similar levels of polymorphism and evolutionary rates than random fragment pairs. Using simulations that account for the linear distance between fragments, we proved that the 3D chromosomal organization plays a role in the observed correlated evolution. Spatially interacting fragments also exhibit more similar mutation rates and functional constraints in both coding and noncoding regions than the random expectations, indicating that the correlated evolution between 3D neighbors is a result of combined evolutionary forces. A collection of 39 genomic and epigenomic features can explain much of the variance in genetic diversity and evolutionary rates across the genome. Moreover, features that have a greater effect on the evolution of regional sequences tend to show higher similarity between neighboring fragments in the CIN, suggesting a pivotal role of epigenetic modifications and chromatin organization in determining the correlated evolution of large DNA fragments in the 3D genome.
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Affiliation(s)
- Yubin Yan
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhaohong Li
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Ye Li
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Zefeng Wu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Ruolin Yang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
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