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Tengölics R, Szappanos B, Mülleder M, Kalapis D, Grézal G, Sajben C, Agostini F, Mokochinski JB, Bálint B, Nagy LG, Ralser M, Papp B. The metabolic domestication syndrome of budding yeast. Proc Natl Acad Sci U S A 2024; 121:e2313354121. [PMID: 38457520 PMCID: PMC10945815 DOI: 10.1073/pnas.2313354121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/11/2023] [Indexed: 03/10/2024] Open
Abstract
Cellular metabolism evolves through changes in the structure and quantitative states of metabolic networks. Here, we explore the evolutionary dynamics of metabolic states by focusing on the collection of metabolite levels, the metabolome, which captures key aspects of cellular physiology. Using a phylogenetic framework, we profiled metabolites in 27 populations of nine budding yeast species, providing a graduated view of metabolic variation across multiple evolutionary time scales. Metabolite levels evolve more rapidly and independently of changes in the metabolic network's structure, providing complementary information to enzyme repertoire. Although metabolome variation accumulates mainly gradually over time, it is profoundly affected by domestication. We found pervasive signatures of convergent evolution in the metabolomes of independently domesticated clades of Saccharomyces cerevisiae. Such recurring metabolite differences between wild and domesticated populations affect a substantial part of the metabolome, including rewiring of the TCA cycle and several amino acids that influence aroma production, likely reflecting adaptation to human niches. Overall, our work reveals previously unrecognized diversity in central metabolism and the pervasive influence of human-driven selection on metabolite levels in yeasts.
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Affiliation(s)
- Roland Tengölics
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
- Metabolomics Lab, Core facilities, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Balázs Szappanos
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
- Department of Biotechnology, University of Szeged, Szeged6726, Hungary
| | - Michael Mülleder
- Charité Universitätsmedizin, Core Facility High-Throughput Mass Spectrometry, Berlin10117, Germany
| | - Dorottya Kalapis
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Gábor Grézal
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Csilla Sajben
- Metabolomics Lab, Core facilities, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Federica Agostini
- Department of Biochemistry, Charité Universitätsmedizin, Berlin10117, Germany
| | - João Benhur Mokochinski
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Balázs Bálint
- Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - László G. Nagy
- Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Markus Ralser
- Department of Biochemistry, Charité Universitätsmedizin, Berlin10117, Germany
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, LondonNW11AT, United Kingdom
| | - Balázs Papp
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
- National Laboratory for Health Security, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
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Liska O, Boross G, Rocabert C, Szappanos B, Tengölics R, Papp B. Principles of metabolome conservation in animals. Proc Natl Acad Sci U S A 2023; 120:e2302147120. [PMID: 37603743 PMCID: PMC10468614 DOI: 10.1073/pnas.2302147120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/16/2023] [Indexed: 08/23/2023] Open
Abstract
Metabolite levels shape cellular physiology and disease susceptibility, yet the general principles governing metabolome evolution are largely unknown. Here, we introduce a measure of conservation of individual metabolite levels among related species. By analyzing multispecies tissue metabolome datasets in phylogenetically diverse mammals and fruit flies, we show that conservation varies extensively across metabolites. Three major functional properties, metabolite abundance, essentiality, and association with human diseases predict conservation, highlighting a striking parallel between the evolutionary forces driving metabolome and protein sequence conservation. Metabolic network simulations recapitulated these general patterns and revealed that abundant metabolites are highly conserved due to their strong coupling to key metabolic fluxes in the network. Finally, we show that biomarkers of metabolic diseases can be distinguished from other metabolites simply based on evolutionary conservation, without requiring any prior clinical knowledge. Overall, this study uncovers simple rules that govern metabolic evolution in animals and implies that most tissue metabolome differences between species are permitted, rather than favored by natural selection. More broadly, our work paves the way toward using evolutionary information to identify biomarkers, as well as to detect pathogenic metabolome alterations in individual patients.
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Affiliation(s)
- Orsolya Liska
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, 6728Szeged, Hungary
- National Laboratory of Biotechnology, Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, 6726Szeged, Hungary
- Doctoral School of Biology, University of Szeged, 6726Szeged, Hungary
| | - Gábor Boross
- National Laboratory of Biotechnology, Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, 6726Szeged, Hungary
- Department of Biology, Stanford University, Stanford, City of Palo Alto, CA94305-5020
| | - Charles Rocabert
- National Laboratory of Biotechnology, Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, 6726Szeged, Hungary
- Inria, 78150Rocquencourt, 69100Villeurbanne, France
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, 00014Helsinki, Finland
- Institute for Computational Cell Biology, Heinrich-Heine Universität, 40225Düsseldorf, Germany
| | - Balázs Szappanos
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, 6728Szeged, Hungary
- National Laboratory of Biotechnology, Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, 6726Szeged, Hungary
- Department of Biotechnology, University of Szeged, 6726Szeged, Hungary
| | - Roland Tengölics
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, 6728Szeged, Hungary
- National Laboratory of Biotechnology, Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, 6726Szeged, Hungary
- Metabolomics Lab, Core facilities, Biological Research Centre, Eötvös Loránd Research Network, 6726Szeged, Hungary
| | - Balázs Papp
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, 6728Szeged, Hungary
- National Laboratory of Biotechnology, Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, 6726Szeged, Hungary
- National Laboratory for Health Security, Biological Research Centre, Eötvös Loránd Research Network, 6726Szeged, Hungary
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