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Peters JP, Assaf C, Mohamad FH, Beitz E, Tiwari S, Aden K, Hövener JB, Pravdivtsev AN. Yeast Solutions and Hyperpolarization Enable Real-Time Observation of Metabolized Substrates Even at Natural Abundance. Anal Chem 2024; 96:17135-17144. [PMID: 39405516 PMCID: PMC11525923 DOI: 10.1021/acs.analchem.4c02419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 09/26/2024] [Accepted: 10/04/2024] [Indexed: 10/30/2024]
Abstract
Metabolic changes in an organism often occur much earlier than macroscopic manifestations of disease, such as invasive tumors. Therefore, noninvasive tools to monitor metabolism are fundamental as they provide insights into in vivo biochemistry. NMR represents one of the gold standards for such insights by observing metabolites. Using nuclear spin hyperpolarization greatly increases the NMR sensitivity, enabling μmol/L sensitivity with a time resolution of about one second. However, a metabolic phantom with reproducible, rapid, and human-like metabolism is needed to progress research in this area. Using baker's yeast as a convenient metabolic factory, we demonstrated in a single study that yeast cells provide a robust and rapidly metabolizing phantom for pyruvate and fumarate, including substrates with a natural abundance of 13C: we observed the production of ethanol, carbon dioxide, bicarbonate, lactate, alanine from pyruvate, malate, and oxaloacetate from fumarate. For observation, we hyperpolarized pyruvate and fumarate via the dissolution dynamic nuclear polarization (dDNP) technique to about 30% 13C polarization that is equivalent to 360,000 signal enhancement at 1 T and 310 K. Major metabolic pathways were observed using tracers at a natural abundance of 13C, demonstrating that isotope labeling is not always essential in vitro. Enriched [1-13C]pyruvate revealed minor lactate production, presumably via the D-lactate dehydrogenase (DLD) enzyme pathway, demonstrating the sensitivity gain using a dense yeast solution. We foresee that yeast as a metabolic factory can find application as an abundant MRI phantom standard to calibrate and optimize molecular MRI protocols. Our study highlights the potential of using hyperpolarization to probe the metabolism of yeast and other microorganisms even with naturally abundant substrates, offering valuable insights into their response to various stimuli such as drugs, treatment, nourishment, and genetic modification, thereby advancing drug development and our understanding of biochemical processes.
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Affiliation(s)
- Josh P. Peters
- Section
Biomedical Imaging, Molecular Imaging North Competence Center (MOIN
CC), Department of Radiology and Neuroradiology, University Medical Center Kiel, Kiel University, Am Botanischen Garten 18, Kiel 24118, Germany
| | - Charbel Assaf
- Section
Biomedical Imaging, Molecular Imaging North Competence Center (MOIN
CC), Department of Radiology and Neuroradiology, University Medical Center Kiel, Kiel University, Am Botanischen Garten 18, Kiel 24118, Germany
| | - Farhad Haj Mohamad
- Section
Biomedical Imaging, Molecular Imaging North Competence Center (MOIN
CC), Department of Radiology and Neuroradiology, University Medical Center Kiel, Kiel University, Am Botanischen Garten 18, Kiel 24118, Germany
| | - Eric Beitz
- Pharmaceutical
Institute, CAU Kiel, Gutenbergstr. 76, Kiel 24118, Germany
| | - Sanjay Tiwari
- Section
Biomedical Imaging, Molecular Imaging North Competence Center (MOIN
CC), Department of Radiology and Neuroradiology, University Medical Center Kiel, Kiel University, Am Botanischen Garten 18, Kiel 24118, Germany
| | - Konrad Aden
- Institute
of Clinical Molecular Biology, Kiel University, Gut Rosalind-Franklin-Straße
12, Kiel 24105, Germany
- Department
of Internal Medicine I, University Medical
Center Kiel, Arnold-Heller-Straße
3, Kiel 24105, Germany
| | - Jan-Bernd Hövener
- Section
Biomedical Imaging, Molecular Imaging North Competence Center (MOIN
CC), Department of Radiology and Neuroradiology, University Medical Center Kiel, Kiel University, Am Botanischen Garten 18, Kiel 24118, Germany
| | - Andrey N. Pravdivtsev
- Section
Biomedical Imaging, Molecular Imaging North Competence Center (MOIN
CC), Department of Radiology and Neuroradiology, University Medical Center Kiel, Kiel University, Am Botanischen Garten 18, Kiel 24118, Germany
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Lu H, Li F, Sánchez BJ, Zhu Z, Li G, Domenzain I, Marcišauskas S, Anton PM, Lappa D, Lieven C, Beber ME, Sonnenschein N, Kerkhoven EJ, Nielsen J. A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nat Commun 2019; 10:3586. [PMID: 31395883 PMCID: PMC6687777 DOI: 10.1038/s41467-019-11581-3] [Citation(s) in RCA: 171] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/17/2019] [Indexed: 01/06/2023] Open
Abstract
Genome-scale metabolic models (GEMs) represent extensive knowledgebases that provide a platform for model simulations and integrative analysis of omics data. This study introduces Yeast8 and an associated ecosystem of models that represent a comprehensive computational resource for performing simulations of the metabolism of Saccharomyces cerevisiae--an important model organism and widely used cell-factory. Yeast8 tracks community development with version control, setting a standard for how GEMs can be continuously updated in a simple and reproducible way. We use Yeast8 to develop the derived models panYeast8 and coreYeast8, which in turn enable the reconstruction of GEMs for 1,011 different yeast strains. Through integration with enzyme constraints (ecYeast8) and protein 3D structures (proYeast8DB), Yeast8 further facilitates the exploration of yeast metabolism at a multi-scale level, enabling prediction of how single nucleotide variations translate to phenotypic traits.
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Affiliation(s)
- Hongzhong Lu
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden
| | - Feiran Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden
| | - Benjamín J Sánchez
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden
| | - Zhengming Zhu
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, 214122, Wuxi, Jiangsu, China
| | - Gang Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden
| | - Iván Domenzain
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden
| | - Simonas Marcišauskas
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden
| | - Petre Mihail Anton
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden
| | - Dimitra Lappa
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden
| | - Christian Lieven
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Moritz Emanuel Beber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Nikolaus Sonnenschein
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Eduard J Kerkhoven
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden.
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark.
- BioInnovation Institute, Ole Maaløes Vej 3, DK2200, Copenhagen N, Denmark.
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