One‐shot 13C15N‐metabolic flux analysis for simultaneous quantification of carbon and nitrogen flux
Abstract Metabolic flux is the final output of cellular regulation and has been extensively studied for carbon but much less is known about nitrogen, which is another important building block for living organisms. For the tuberculosis pathogen, this is particularly important in informing the develop...
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| Format: | Article |
| Language: | English |
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Springer Nature
2023-01-01
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| Series: | Molecular Systems Biology |
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| Online Access: | https://doi.org/10.15252/msb.202211099 |
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| author | Khushboo Borah Slater Martin Beyß Ye Xu Jim Barber Catia Costa Jane Newcombe Axel Theorell Melanie J Bailey Dany J V Beste Johnjoe McFadden Katharina Nöh |
| author_facet | Khushboo Borah Slater Martin Beyß Ye Xu Jim Barber Catia Costa Jane Newcombe Axel Theorell Melanie J Bailey Dany J V Beste Johnjoe McFadden Katharina Nöh |
| author_sort | Khushboo Borah Slater |
| collection | DOAJ |
| description | Abstract Metabolic flux is the final output of cellular regulation and has been extensively studied for carbon but much less is known about nitrogen, which is another important building block for living organisms. For the tuberculosis pathogen, this is particularly important in informing the development of effective drugs targeting the pathogen's metabolism. Here we performed 13C15N dual isotopic labeling of Mycobacterium bovis BCG steady state cultures, quantified intracellular carbon and nitrogen fluxes and inferred reaction bidirectionalities. This was achieved by model scope extension and refinement, implemented in a multi‐atom transition model, within the statistical framework of Bayesian model averaging (BMA). Using BMA‐based 13C15N‐metabolic flux analysis, we jointly resolve carbon and nitrogen fluxes quantitatively. We provide the first nitrogen flux distributions for amino acid and nucleotide biosynthesis in mycobacteria and establish glutamate as the central node for nitrogen metabolism. We improved resolution of the notoriously elusive anaplerotic node in central carbon metabolism and revealed possible operation modes. Our study provides a powerful and statistically rigorous platform to simultaneously infer carbon and nitrogen metabolism in any biological system. |
| format | Article |
| id | doaj-art-5bb60f4298fe4261b1609c783aff848a |
| institution | DOAJ |
| issn | 1744-4292 |
| language | English |
| publishDate | 2023-01-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-5bb60f4298fe4261b1609c783aff848a2025-08-20T03:06:10ZengSpringer NatureMolecular Systems Biology1744-42922023-01-0119311810.15252/msb.202211099One‐shot 13C15N‐metabolic flux analysis for simultaneous quantification of carbon and nitrogen fluxKhushboo Borah Slater0Martin Beyß1Ye Xu2Jim Barber3Catia Costa4Jane Newcombe5Axel Theorell6Melanie J Bailey7Dany J V Beste8Johnjoe McFadden9Katharina Nöh10Faculty of Health and Medical Sciences, University of SurreyForschungszentrum Jülich GmbH, Institute of Bio‐ and Geosciences, IBG‐1: BiotechnologyFaculty of Health and Medical Sciences, University of SurreyFaculty of Health and Medical Sciences, University of SurreyFaculty of Engineering and Physical Sciences, University of SurreyFaculty of Health and Medical Sciences, University of SurreyForschungszentrum Jülich GmbH, Institute of Bio‐ and Geosciences, IBG‐1: BiotechnologyFaculty of Engineering and Physical Sciences, University of SurreyFaculty of Health and Medical Sciences, University of SurreyFaculty of Health and Medical Sciences, University of SurreyForschungszentrum Jülich GmbH, Institute of Bio‐ and Geosciences, IBG‐1: BiotechnologyAbstract Metabolic flux is the final output of cellular regulation and has been extensively studied for carbon but much less is known about nitrogen, which is another important building block for living organisms. For the tuberculosis pathogen, this is particularly important in informing the development of effective drugs targeting the pathogen's metabolism. Here we performed 13C15N dual isotopic labeling of Mycobacterium bovis BCG steady state cultures, quantified intracellular carbon and nitrogen fluxes and inferred reaction bidirectionalities. This was achieved by model scope extension and refinement, implemented in a multi‐atom transition model, within the statistical framework of Bayesian model averaging (BMA). Using BMA‐based 13C15N‐metabolic flux analysis, we jointly resolve carbon and nitrogen fluxes quantitatively. We provide the first nitrogen flux distributions for amino acid and nucleotide biosynthesis in mycobacteria and establish glutamate as the central node for nitrogen metabolism. We improved resolution of the notoriously elusive anaplerotic node in central carbon metabolism and revealed possible operation modes. Our study provides a powerful and statistically rigorous platform to simultaneously infer carbon and nitrogen metabolism in any biological system.https://doi.org/10.15252/msb.202211099Bayesian metabolic flux analysiscarbon metabolismisotope labelingMycobacterium tuberculosisnitrogen metabolism |
| spellingShingle | Khushboo Borah Slater Martin Beyß Ye Xu Jim Barber Catia Costa Jane Newcombe Axel Theorell Melanie J Bailey Dany J V Beste Johnjoe McFadden Katharina Nöh One‐shot 13C15N‐metabolic flux analysis for simultaneous quantification of carbon and nitrogen flux Molecular Systems Biology Bayesian metabolic flux analysis carbon metabolism isotope labeling Mycobacterium tuberculosis nitrogen metabolism |
| title | One‐shot 13C15N‐metabolic flux analysis for simultaneous quantification of carbon and nitrogen flux |
| title_full | One‐shot 13C15N‐metabolic flux analysis for simultaneous quantification of carbon and nitrogen flux |
| title_fullStr | One‐shot 13C15N‐metabolic flux analysis for simultaneous quantification of carbon and nitrogen flux |
| title_full_unstemmed | One‐shot 13C15N‐metabolic flux analysis for simultaneous quantification of carbon and nitrogen flux |
| title_short | One‐shot 13C15N‐metabolic flux analysis for simultaneous quantification of carbon and nitrogen flux |
| title_sort | one shot 13c15n metabolic flux analysis for simultaneous quantification of carbon and nitrogen flux |
| topic | Bayesian metabolic flux analysis carbon metabolism isotope labeling Mycobacterium tuberculosis nitrogen metabolism |
| url | https://doi.org/10.15252/msb.202211099 |
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