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Khattri RB, Puglise J, Ryan TE, Walter GA, Merritt ME, Barton ER. Isolated murine skeletal muscles utilize pyruvate over glucose for oxidation. Metabolomics 2022; 18:105. [PMID: 36480060 PMCID: PMC9732067 DOI: 10.1007/s11306-022-01948-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/29/2022] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Fuel sources for skeletal muscle tissue include carbohydrates and fatty acids, and utilization depends upon fiber type, workload, and substrate availability. The use of isotopically labeled substrate tracers combined with nuclear magnetic resonance (NMR) enables a deeper examination of not only utilization of substrates by a given tissue, but also their contribution to tricarboxylic acid (TCA) cycle intermediates. OBJECTIVES The goal of this study was to determine the differential utilization of substrates in isolated murine skeletal muscle, and to evaluate how isopotomer anlaysis provided insight into skeletal muscle metabolism. METHODS Isolated C57BL/6 mouse hind limb muscles were incubated in oxygenated solution containing uniformly labeled 13C6 glucose, 13C3 pyruvate, or 13C2 acetate at room temperature. Isotopomer analysis of 13C labeled glutamate was performed on pooled extracts of isolated soleus and extensor digitorum longus (EDL) muscles. RESULTS Pyruvate and acetate were more avidly consumed than glucose with resultant increases in glutamate labeling in both muscle groups. Glucose incubation resulted in glutamate labeling, but with high anaplerotic flux in contrast to the labeling by pyruvate. Muscle fiber type distinctions were evident by differences in lactate enrichment and extent of substrate oxidation. CONCLUSION Isotope tracing experiments in isolated muscles reveal that pyruvate and acetate are avidly oxidized by isolated soleus and EDL muscles, whereas glucose labeling of glutamate is accompanied by high anaplerotic flux. We believe our results may set the stage for future examination of metabolic signatures of skeletal muscles from pre-clinical models of aging, type-2 diabetes and neuromuscular disease.
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Affiliation(s)
- Ram B Khattri
- Department of Applied Physiology and Kinesiology, College of Health & Human Performance, University of Florida, 124 Florida Gym, 1864 Stadium Road, Gainesville, FL, 32611, USA
| | - Jason Puglise
- Department of Applied Physiology and Kinesiology, College of Health & Human Performance, University of Florida, 124 Florida Gym, 1864 Stadium Road, Gainesville, FL, 32611, USA
| | - Terence E Ryan
- Department of Applied Physiology and Kinesiology, College of Health & Human Performance, University of Florida, 124 Florida Gym, 1864 Stadium Road, Gainesville, FL, 32611, USA
- Myology Institute, University of Florida, Gainesville, USA
- Center for Exercise Science, University of Florida, Gainesville, FL, USA
| | - Glenn A Walter
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, USA
- Myology Institute, University of Florida, Gainesville, USA
| | - Matthew E Merritt
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, USA
| | - Elisabeth R Barton
- Department of Applied Physiology and Kinesiology, College of Health & Human Performance, University of Florida, 124 Florida Gym, 1864 Stadium Road, Gainesville, FL, 32611, USA.
- Myology Institute, University of Florida, Gainesville, USA.
- Center for Exercise Science, University of Florida, Gainesville, FL, USA.
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Capela J, Lagoa D, Rodrigues R, Cunha E, Cruz F, Barbosa A, Bastos J, Lima D, Ferreira EC, Rocha M, Dias O. merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models. Nucleic Acids Res 2022; 50:6052-6066. [PMID: 35694833 PMCID: PMC9226533 DOI: 10.1093/nar/gkac459] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/10/2022] [Indexed: 01/18/2023] Open
Abstract
Genome-scale metabolic models have been recognised as useful tools for better understanding living organisms' metabolism. merlin (https://www.merlin-sysbio.org/) is an open-source and user-friendly resource that hastens the models' reconstruction process, conjugating manual and automatic procedures, while leveraging the user's expertise with a curation-oriented graphical interface. An updated and redesigned version of merlin is herein presented. Since 2015, several features have been implemented in merlin, along with deep changes in the software architecture, operational flow, and graphical interface. The current version (4.0) includes the implementation of novel algorithms and third-party tools for genome functional annotation, draft assembly, model refinement, and curation. Such updates increased the user base, resulting in multiple published works, including genome metabolic (re-)annotations and model reconstructions of multiple (lower and higher) eukaryotes and prokaryotes. merlin version 4.0 is the only tool able to perform template based and de novo draft reconstructions, while achieving competitive performance compared to state-of-the art tools both for well and less-studied organisms.
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Affiliation(s)
- João Capela
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Davide Lagoa
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Ruben Rodrigues
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Emanuel Cunha
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Fernando Cruz
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Ana Barbosa
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - José Bastos
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Diogo Lima
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Eugénio C Ferreira
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Miguel Rocha
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Oscar Dias
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
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Amino Acid Supplementations Enhance the Stress Resistance and Fermentation Performance of Lager Yeast During High Gravity Fermentation. Appl Biochem Biotechnol 2018; 187:540-555. [DOI: 10.1007/s12010-018-2840-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/03/2018] [Indexed: 12/28/2022]
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Lee S, Wen H, An YJ, Cha JW, Ko YJ, Hyberts SG, Park S. Carbon Isotopomer Analysis with Non-Unifom Sampling HSQC NMR for Cell Extract and Live Cell Metabolomics Studies. Anal Chem 2016; 89:1078-1085. [DOI: 10.1021/acs.analchem.6b02107] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Sujin Lee
- Natural
Product Research Institute, College of Pharmacy, Seoul National University, Sillim-dong, Gwanak-gu, Seoul 151-742, Korea
| | - He Wen
- Natural
Product Research Institute, College of Pharmacy, Seoul National University, Sillim-dong, Gwanak-gu, Seoul 151-742, Korea
- Department
of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Yong Jin An
- Natural
Product Research Institute, College of Pharmacy, Seoul National University, Sillim-dong, Gwanak-gu, Seoul 151-742, Korea
| | - Jin Wook Cha
- Natural
Product Research Institute, College of Pharmacy, Seoul National University, Sillim-dong, Gwanak-gu, Seoul 151-742, Korea
- Natural
Constituents Research Center, Korea Institute of Science and Technology (KIST), Gangneung 25451, Korea
| | - Yoon-Joo Ko
- National
Center for Inter-University Research Facilities (NCIRF), Seoul National University, Sillim-dong, Gwanak-gu, Seoul 151-742, Korea
| | - Sven G. Hyberts
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Sunghyouk Park
- Natural
Product Research Institute, College of Pharmacy, Seoul National University, Sillim-dong, Gwanak-gu, Seoul 151-742, Korea
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Valletta A, De Angelis G, Badiali C, Brasili E, Miccheli A, Di Cocco ME, Pasqua G. Acetic acid acts as an elicitor exerting a chitosan-like effect on xanthone biosynthesis in Hypericum perforatum L. root cultures. PLANT CELL REPORTS 2016; 35:1009-1020. [PMID: 26795145 DOI: 10.1007/s00299-016-1934-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 12/17/2015] [Accepted: 01/08/2016] [Indexed: 06/05/2023]
Abstract
Acetic acid acts as a signal molecule, strongly enhancing xanthone biosynthesis in Hypericum perforatum root cultures. This activity is specific, as demonstrated by the comparison with other short-chain monocarboxylic acids. We have recently demonstrated that Hypericum perforatum root cultures constitutively produce xanthones at higher levels than the root of the plant and that they respond to chitosan (CHIT) elicitation with a noteworthy increase in xanthone production. In the present study, CHIT was administered to H. perforatum root cultures using three different elicitation protocols, and the increase in xanthone production was evaluated. The best results (550 % xanthone increase) were obtained by subjecting the roots to a single elicitation with 200 mg l(-1) CHIT and maintaining the elicitor in the culture medium for 7 days. To discriminate the effect of CHIT from that of the solvent, control experiments were performed by administering AcOH alone at the same concentration used for CHIT solubilization. Unexpectedly, AcOH caused an increase in xanthone production comparable to that observed in response to CHIT. Feeding experiments with (13)C-labeled AcOH demonstrated that this compound was not incorporated into the xanthone skeleton. Other short-chain monocarboxylic acids (i.e., propionic and butyric acid) have little or no effect on the production of xanthones. These results indicate that AcOH acts as a specific signal molecule, able to greatly enhance xanthone biosynthesis in H. perforatum root cultures.
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Affiliation(s)
- Alessio Valletta
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy.
| | - Giulia De Angelis
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Camilla Badiali
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Elisa Brasili
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Alfredo Miccheli
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | | | - Gabriella Pasqua
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
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