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Tong W, Hannou SA, Wang Y, Astapova I, Sargsyan A, Monn R, Thiriveedi V, Li D, McCann JR, Rawls JF, Roper J, Zhang GF, Herman MA. The intestine is a major contributor to circulating succinate in mice. FASEB J 2022; 36:e22546. [PMID: 36106538 PMCID: PMC9523828 DOI: 10.1096/fj.202200135rr] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 08/24/2022] [Accepted: 08/29/2022] [Indexed: 10/03/2023]
Abstract
The tricarboxylic acid (TCA) cycle is the epicenter of cellular aerobic metabolism. TCA cycle intermediates facilitate energy production and provide anabolic precursors, but also function as intra- and extracellular metabolic signals regulating pleiotropic biological processes. Despite the importance of circulating TCA cycle metabolites as signaling molecules, the source of circulating TCA cycle intermediates remains uncertain. We observe that in mice, the concentration of TCA cycle intermediates in the portal blood exceeds that in tail blood indicating that the gut is a major contributor to circulating TCA cycle metabolites. With a focus on succinate as a representative of a TCA cycle intermediate with signaling activities and using a combination of gut microbiota depletion mouse models and isotopomer tracing, we demonstrate that intestinal microbiota is not a major contributor to circulating succinate. Moreover, we demonstrate that endogenous succinate production is markedly higher than intestinal succinate absorption in normal physiological conditions. Altogether, these results indicate that endogenous succinate production within the intestinal tissue is a major physiological source of circulating succinate. These results provide a foundation for an investigation into the role of the intestine in regulating circulating TCA cycle metabolites and their potential signaling effects on health and disease.
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Affiliation(s)
- Wenxin Tong
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, USA
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - Sarah A. Hannou
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - You Wang
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - Inna Astapova
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
- Division of Endocrinology, Metabolism, and Nutrition, Duke University, Durham, North Carolina, USA
| | - Ashot Sargsyan
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - Ruby Monn
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | | | - Diana Li
- Division of Gastroenterology, Duke University, Durham, North Carolina, USA
| | - Jessica R. McCann
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University, Durham, NC, USA
| | - John F. Rawls
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Jatin Roper
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, USA
- Division of Gastroenterology, Duke University, Durham, North Carolina, USA
| | - Guo-fang Zhang
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - Mark A. Herman
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
- Division of Endocrinology, Metabolism, and Nutrition, Duke University, Durham, North Carolina, USA
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Jindal S, Iyer MS, Jyoti P, Masakapalli SK, Venkatesh KV. Mutants lacking global regulators, fis and arcA, in Escherichia coli enhanced growth fitness under acetate metabolism by pathway reprogramming. Appl Microbiol Biotechnol 2022; 106:3231-3243. [PMID: 35416487 DOI: 10.1007/s00253-022-11890-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 03/20/2022] [Accepted: 03/21/2022] [Indexed: 11/25/2022]
Abstract
Global regulatory transcription factors play a significant role in controlling microbial metabolism under genetic and environmental perturbations. A system-level effect of carbon sources such as acetate on microbial metabolism under disrupted global regulators has not been well established. Acetate is one of the major substrates available in various nutrient niches such as the mammalian gut and a keto diet. A substantial amount of acetate gets secreted in aerobic metabolism. Therefore, investigating the study on acetate metabolism is highly significant. It is known that the global regulators fis and arcA regulate acetate uptake genes in E. coli under glucose conditions. This study deciphered the growth and flux distribution of E. coli transcription regulatory knockouts Δfis, ΔarcA and double deletion mutant, ΔarcAΔfis under acetate using 13C-metabolic flux analysis (MFA), which has not been investigated before. We observed that the mutants exhibited an expeditious growth rate (~ 1.2-1.6-fold) with a proportionate increase in acetate uptake rates compared to the wild type. 13C-MFA displayed the distinct metabolic reprogramming of intracellular fluxes via the TCA cycle, anaplerotic pathway and gluconeogenesis, which conferred an advantage of a faster growth rate with better carbon usage in all the mutants. This resulted in higher metabolic fluxes through the TCA cycle (~ 18-90%), lower gluconeogenesis (~ 15-35%) and higher CO2 and ATP production with the proportional increase in growth rate. The study reveals a novel insight by stating the sub-optimality of the wild-type strain grown under acetate substrate aerobically. These mutant strains efficiently oxidize acetate, thus acting as potential candidates for the biosynthesis of isoprenoids, biofuels, vitamins and various pharmaceutical products.Key Points• Mutants exhibited a better balance between energy and precursor synthesis than WT.• Leveraged in the unravelling of regulatory control under various nutrient shifts.• Metabolic readjustment resulted in optimal biomass requirement and faster growth.
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Affiliation(s)
- Shikha Jindal
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Mahesh S Iyer
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Poonam Jyoti
- BioX Center, School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, 175075, India
| | - Shyam Kumar Masakapalli
- BioX Center, School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, 175075, India.
| | - K V Venkatesh
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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Jyoti P, Patil N, Masakapalli SK. Insights into the Polyhydroxybutyrate Biosynthesis in Ralstonia solanacearum Using Parallel 13C Tracers and Comparative Genome Analysis. ACS Chem Biol 2021; 16:1215-1222. [PMID: 34143620 DOI: 10.1021/acschembio.1c00249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacterial accumulation of poly(3-hydroxybutyrate) [P(3HB)] is a metabolic strategy often adopted to cope with challenging surroundings. Ralstonia solanacearum, a phytopathogen, seems to be an ideal candidate with inherent ability to accumulate this biodegradable polymer of high industrial relevance. This study is focused on investigating the metabolic networks that channel glucose into P(3HB) using comparative genome analysis, 13C tracers, microscopy, gas chromatography-mass spectrometry (GC-MS), and proton nuclear magnetic resonance (1H NMR). Comparative genome annotation of 87 R. solanacearum strains confirmed the presence of a conserved P(3HB) biosynthetic pathway genes in the chromosome. Parallel 13C glucose feeding ([1-13C], [1,2-13C]) analysis mapped the glucose oxidation to 3-hydroxybutyrate (3HB), the metabolic precursor of P(3HB) via the Entner-Doudoroff pathway (ED pathway), potentially to meet the NADPH demands. Fluorescence microscopy, GC-MS, and 1H NMR analysis further confirmed the ability of R. solanacearum to accumulate P(3HB) granules. In addition, it is demonstrated that the carbon/nitrogen (C/N) ratio influences the P(3HB) yields, thereby highlighting the need to further optimize the bioprocessing parameters. This study provided key insights into the biosynthetic abilities of R. solanacearum as a promising P(3HB) producer.
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Affiliation(s)
- Poonam Jyoti
- BioX Center, School of Basic Sciences, Indian Institute of Technology Mandi, Kamand 175075, Himachal Pradesh, India
| | - Nitin Patil
- BioX Center, School of Basic Sciences, Indian Institute of Technology Mandi, Kamand 175075, Himachal Pradesh, India
| | - Shyam Kumar Masakapalli
- BioX Center, School of Basic Sciences, Indian Institute of Technology Mandi, Kamand 175075, Himachal Pradesh, India
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4
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Bhatia M, Thakur J, Suyal S, Oniel R, Chakraborty R, Pradhan S, Sharma M, Sengupta S, Laxman S, Masakapalli SK, Bachhawat AK. Allosteric inhibition of MTHFR prevents futile SAM cycling and maintains nucleotide pools in one-carbon metabolism. J Biol Chem 2020; 295:16037-16057. [PMID: 32934008 PMCID: PMC7681022 DOI: 10.1074/jbc.ra120.015129] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/12/2020] [Indexed: 01/05/2023] Open
Abstract
Methylenetetrahydrofolate reductase (MTHFR) links the folate cycle to the methionine cycle in one-carbon metabolism. The enzyme is known to be allosterically inhibited by SAM for decades, but the importance of this regulatory control to one-carbon metabolism has never been adequately understood. To shed light on this issue, we exchanged selected amino acid residues in a highly conserved stretch within the regulatory region of yeast MTHFR to create a series of feedback-insensitive, deregulated mutants. These were exploited to investigate the impact of defective allosteric regulation on one-carbon metabolism. We observed a strong growth defect in the presence of methionine. Biochemical and metabolite analysis revealed that both the folate and methionine cycles were affected in these mutants, as was the transsulfuration pathway, leading also to a disruption in redox homeostasis. The major consequences, however, appeared to be in the depletion of nucleotides. 13C isotope labeling and metabolic studies revealed that the deregulated MTHFR cells undergo continuous transmethylation of homocysteine by methyltetrahydrofolate (CH3THF) to form methionine. This reaction also drives SAM formation and further depletes ATP reserves. SAM was then cycled back to methionine, leading to futile cycles of SAM synthesis and recycling and explaining the necessity for MTHFR to be regulated by SAM. The study has yielded valuable new insights into the regulation of one-carbon metabolism, and the mutants appear as powerful new tools to further dissect out the intersection of one-carbon metabolism with various pathways both in yeasts and in humans.
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Affiliation(s)
- Muskan Bhatia
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, S.A.S. Nagar, Punjab, India
| | - Jyotika Thakur
- BioX Center, School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, India
| | - Shradha Suyal
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, S.A.S. Nagar, Punjab, India
| | - Ruchika Oniel
- Institute for Stem Cell Science and Regenerative Medicine (inStem), NCBS-TIFR Campus, Bangalore, India
| | - Rahul Chakraborty
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Shalini Pradhan
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, S.A.S. Nagar, Punjab, India
| | - Shantanu Sengupta
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem), NCBS-TIFR Campus, Bangalore, India
| | - Shyam Kumar Masakapalli
- BioX Center, School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, India
| | - Anand Kumar Bachhawat
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, S.A.S. Nagar, Punjab, India.
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The Entner-Doudoroff and Nonoxidative Pentose Phosphate Pathways Bypass Glycolysis and the Oxidative Pentose Phosphate Pathway in Ralstonia solanacearum. mSystems 2020; 5:5/2/e00091-20. [PMID: 32156794 PMCID: PMC7065512 DOI: 10.1128/msystems.00091-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Understanding the metabolic versatility of Ralstonia solanacearum is important, as it regulates the trade-off between virulence and metabolism (1, 2) in a wide range of plant hosts. Due to a lack of clear evidence until this work, several published research papers reported on the potential roles of glycolysis and the oxidative pentose phosphate pathway (OxPPP) in R. solanacearum (3, 4). This work provided evidence from 13C stable isotope feeding and genome annotation-based comparative metabolic network analysis that the Entner-Doudoroff pathway and non-OxPPP bypass glycolysis and OxPPP during the oxidation of glucose, a component of the host xylem pool that serves as a potential carbon source (5). The outcomes help better define the central carbon metabolic network of R. solanacearum that can be integrated with 13C metabolic flux analysis as well as flux balance analysis studies for defining the metabolic phenotypes. The study highlights the need to critically examine phytopathogens whose metabolism is poorly understood. In Ralstonia solanacearum, a devastating phytopathogen whose metabolism is poorly understood, we observed that the Entner-Doudoroff (ED) pathway and nonoxidative pentose phosphate pathway (non-OxPPP) bypass glycolysis and OxPPP under glucose oxidation. Evidence derived from 13C stable isotope feeding and genome annotation-based comparative metabolic network analysis supported the observations. Comparative metabolic network analysis derived from the currently available 53 annotated R. solanacearum strains, including a recently reported strain (F1C1), representing the four phylotypes, confirmed the lack of key genes coding for phosphofructokinase (pfk-1) and phosphogluconate dehydrogenase (gnd) enzymes that are relevant for glycolysis and OxPPP, respectively. R. solanacearum F1C1 cells fed with [13C]glucose (99% [1-13C]glucose or 99% [1,2-13C]glucose or 40% [13C6]glucose) followed by gas chromatography-mass spectrometry (GC-MS)-based labeling analysis of fragments from amino acids, glycerol, and ribose provided clear evidence that rather than glycolysis and the OxPPP, the ED pathway and non-OxPPP are the main routes sustaining metabolism in R. solanacearum. The 13C incorporation in the mass ions of alanine (m/z 260 and m/z 232), valine (m/z 288 and m/z 260), glycine (m/z 218), serine (m/z 390 and m/z 362), histidine (m/z 440 and m/z 412), tyrosine (m/z 466 and m/z 438), phenylalanine (m/z 336 and m/z 308), glycerol (m/z 377), and ribose (m/z 160) mapped the pathways supporting the observations. The outcomes help better define the central carbon metabolic network of R. solanacearum that can be integrated with 13C metabolic flux analysis as well as flux balance analysis studies for defining the metabolic phenotypes. IMPORTANCE Understanding the metabolic versatility of Ralstonia solanacearum is important, as it regulates the trade-off between virulence and metabolism (1, 2) in a wide range of plant hosts. Due to a lack of clear evidence until this work, several published research papers reported on the potential roles of glycolysis and the oxidative pentose phosphate pathway (OxPPP) in R. solanacearum (3, 4). This work provided evidence from 13C stable isotope feeding and genome annotation-based comparative metabolic network analysis that the Entner-Doudoroff pathway and non-OxPPP bypass glycolysis and OxPPP during the oxidation of glucose, a component of the host xylem pool that serves as a potential carbon source (5). The outcomes help better define the central carbon metabolic network of R. solanacearum that can be integrated with 13C metabolic flux analysis as well as flux balance analysis studies for defining the metabolic phenotypes. The study highlights the need to critically examine phytopathogens whose metabolism is poorly understood.
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