1
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Mitosch K, Beyß M, Phapale P, Drotleff B, Nöh K, Alexandrov T, Patil KR, Typas A. A pathogen-specific isotope tracing approach reveals metabolic activities and fluxes of intracellular Salmonella. PLoS Biol 2023; 21:e3002198. [PMID: 37594988 PMCID: PMC10468081 DOI: 10.1371/journal.pbio.3002198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/30/2023] [Accepted: 06/16/2023] [Indexed: 08/20/2023] Open
Abstract
Pathogenic bacteria proliferating inside mammalian host cells need to rapidly adapt to the intracellular environment. How they achieve this and scavenge essential nutrients from the host has been an open question due to the difficulties in distinguishing between bacterial and host metabolites in situ. Here, we capitalized on the inability of mammalian cells to metabolize mannitol to develop a stable isotopic labeling approach to track Salmonella enterica metabolites during intracellular proliferation in host macrophage and epithelial cells. By measuring label incorporation into Salmonella metabolites with liquid chromatography-mass spectrometry (LC-MS), and combining it with metabolic modeling, we identify relevant carbon sources used by Salmonella, uncover routes of their metabolization, and quantify relative reaction rates in central carbon metabolism. Our results underline the importance of the Entner-Doudoroff pathway (EDP) and the phosphoenolpyruvate carboxylase for intracellularly proliferating Salmonella. More broadly, our metabolic labeling strategy opens novel avenues for understanding the metabolism of pathogens inside host cells.
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Affiliation(s)
- Karin Mitosch
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martin Beyß
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- RWTH Aachen University, Computational Systems Biotechnology, Aachen, Germany
| | - Prasad Phapale
- Metabolomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Bernhard Drotleff
- Metabolomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Theodore Alexandrov
- Metabolomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- BioInnovation Institute, Copenhagen, Denmark
| | - Kiran R. Patil
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Athanasios Typas
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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2
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Borah Slater K, Beyß M, Xu Y, Barber J, Costa C, Newcombe J, Theorell A, Bailey MJ, Beste DJV, McFadden J, Nöh K. One-shot 13 C 15 N-metabolic flux analysis for simultaneous quantification of carbon and nitrogen flux. Mol Syst Biol 2023; 19:e11099. [PMID: 36705093 PMCID: PMC9996240 DOI: 10.15252/msb.202211099] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 01/06/2023] [Accepted: 01/13/2023] [Indexed: 01/28/2023] Open
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 13 C15 N 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 13 C15 N-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.
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Affiliation(s)
| | - Martin Beyß
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-1: Biotechnology, Jülich, Germany.,Computational Systems Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Ye Xu
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Jim Barber
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Catia Costa
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, UK
| | - Jane Newcombe
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Axel Theorell
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-1: Biotechnology, Jülich, Germany
| | - Melanie J Bailey
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, UK
| | - Dany J V Beste
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Johnjoe McFadden
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Katharina Nöh
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-1: Biotechnology, Jülich, Germany
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3
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Borah K, Beyß M, Girardi K, Mendum T, Lara F, Nöh K, Beste D, McFadden J. Probing mycobacterial metabolism in tuberculosis and leprosy to identify vulnerable metabolic nodes for drug development. Access Microbiol 2022. [DOI: 10.1099/acmi.ac2021.po0271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Metabolism of pathogens in infectious diseases is important for their survival, virulence and pathogenesis. Mycobacterial pathogens successfully scavenge multiple host nutrient sources in the intracellular niche. It is therefore important to identify the intracellular nutrient sources and their metabolic fates in these pathogens. Metabolic phenotype of an organism is defined by metabolic fluxes. We quantified in vivo fluxes of the pathogens and probed host-bacterial metabolic cross talks in tuberculosis (TB) and leprosy using systems-based strategies and techniques of isotopic labelling, metabolic modelling and metabolic flux analysis (MFA). We show that the TB pathogen metabolizes a number of carbon and nitrogen sources in human macrophages and identified vulnerable nodes such as glutamine and serine biosynthesis as potential drug targets. Mycobacterium leprae, the leprosy causing pathogen, uses host cell glucose in infected schwann cells and the enzyme, phoenolpyruvate carboxylase is a potential drug target. Our research provides an understanding of the intracellular diets and metabolism of these important human pathogens and identified vulnerable metabolic nodes that can be used for developing innovative chemotherapies in TB and leprosy.
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Affiliation(s)
| | - Martin Beyß
- Forschungszentrum Jülich,Institute of Bio- and Geosciences, IBG-1: Biotechnology, Germany
| | | | | | | | - Katharina Nöh
- Forschungszentrum Jülich,Institute of Bio- and Geosciences, IBG-1: Biotechnology, Germany
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4
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Beyß M, Parra-Peña VD, Ramirez-Malule H, Nöh K. Robustifying Experimental Tracer Design for 13C-Metabolic Flux Analysis. Front Bioeng Biotechnol 2021; 9:685323. [PMID: 34239861 PMCID: PMC8258161 DOI: 10.3389/fbioe.2021.685323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/19/2021] [Indexed: 11/25/2022] Open
Abstract
13C metabolic flux analysis (MFA) has become an indispensable tool to measure metabolic reaction rates (fluxes) in living organisms, having an increasingly diverse range of applications. Here, the choice of the13C labeled tracer composition makes the difference between an information-rich experiment and an experiment with only limited insights. To improve the chances for an informative labeling experiment, optimal experimental design approaches have been devised for13C-MFA, all relying on some a priori knowledge about the actual fluxes. If such prior knowledge is unavailable, e.g., for research organisms and producer strains, existing methods are left with a chicken-and-egg problem. In this work, we present a general computational method, termed robustified experimental design (R-ED), to guide the decision making about suitable tracer choices when prior knowledge about the fluxes is lacking. Instead of focusing on one mixture, optimal for specific flux values, we pursue a sampling based approach and introduce a new design criterion, which characterizes the extent to which mixtures are informative in view of all possible flux values. The R-ED workflow enables the exploration of suitable tracer mixtures and provides full flexibility to trade off information and cost metrics. The potential of the R-ED workflow is showcased by applying the approach to the industrially relevant antibiotic producer Streptomyces clavuligerus, where we suggest informative, yet economic labeling strategies.
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Affiliation(s)
- Martin Beyß
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, Aachen, Germany
| | | | | | - Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
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Kappelmann J, Beyß M, Nöh K, Noack S. Separation of 13C- and 15N-Isotopologues of Amino Acids with a Primary Amine without Mass Resolution by Means of O-Phthalaldehyde Derivatization and Collision Induced Dissociation. Anal Chem 2019; 91:13407-13417. [PMID: 31577133 DOI: 10.1021/acs.analchem.9b01788] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Computational and experimental advances of recent years have culminated in establishing 13C-Metabolic Flux Analysis (13C-MFA) as a routine methodology to unravel the fluxome. As the acronym suggests, 13C-MFA has relied on the relative abundance of 13C-isotopes in metabolites for flux inference, most commonly measured by mass spectrometry. In this manuscript we expand the scope of labeling measurements to the case of simultaneous 13C- and 15N-labeling of amino acids. Analytically, the separation of isotopologues of this metabolite class can only be achieved at resolving power beyond 65,000. In this manuscript we harvest an overlooked property of the collision induced dissociation of amino acid adducts to discern 13C- and 15N- isotopologues of amino acids with a primary amine without separating them in the m/z domain.
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Affiliation(s)
- Jannick Kappelmann
- Institute of Bio- and Geosciences I, IBG-1: Biotechnology , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
| | - Martin Beyß
- Institute of Bio- and Geosciences I, IBG-1: Biotechnology , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
| | - Katharina Nöh
- Institute of Bio- and Geosciences I, IBG-1: Biotechnology , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences I, IBG-1: Biotechnology , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany.,Bioeconomy Science Center (BioSC) , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
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6
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Beyß M, Azzouzi S, Weitzel M, Wiechert W, Nöh K. Corrigendum: The Design of FluxML: A Universal Modeling Language for 13C Metabolic Flux Analysis. Front Microbiol 2019; 10:1734. [PMID: 31417525 PMCID: PMC6682752 DOI: 10.3389/fmicb.2019.01734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 11/15/2022] Open
Affiliation(s)
- Martin Beyß
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Salah Azzouzi
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Michael Weitzel
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, Aachen, Germany
| | - Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- *Correspondence: Katharina Nöh
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7
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Beyß M, Azzouzi S, Weitzel M, Wiechert W, Nöh K. The Design of FluxML: A Universal Modeling Language for 13C Metabolic Flux Analysis. Front Microbiol 2019; 10:1022. [PMID: 31178829 PMCID: PMC6543931 DOI: 10.3389/fmicb.2019.01022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/24/2019] [Indexed: 12/16/2022] Open
Abstract
13C metabolic flux analysis (MFA) is the method of choice when a detailed inference of intracellular metabolic fluxes in living organisms under metabolic quasi-steady state conditions is desired. Being continuously developed since two decades, the technology made major contributions to the quantitative characterization of organisms in all fields of biotechnology and health-related research. 13C MFA, however, stands out from other "-omics sciences," in that it requires not only experimental-analytical data, but also mathematical models and a computational toolset to infer the quantities of interest, i.e., the metabolic fluxes. At present, these models cannot be conveniently exchanged between different labs. Here, we present the implementation-independent model description language FluxML for specifying 13C MFA models. The core of FluxML captures the metabolic reaction network together with atom mappings, constraints on the model parameters, and the wealth of data configurations. In particular, we describe the governing design processes that shaped the FluxML language. We demonstrate the utility of FluxML to represent many contemporary experimental-analytical requirements in the field of 13C MFA. The major aim of FluxML is to offer a sound, open, and future-proof language to unambiguously express and conserve all the necessary information for model re-use, exchange, and comparison. Along with FluxML, several powerful computational tools are supplied for easy handling, but also to maintain a maximum of flexibility. Altogether, the FluxML collection is an "all-around carefree package" for 13C MFA modelers. We believe that FluxML improves scientific productivity as well as transparency and therewith contributes to the efficiency and reproducibility of computational modeling efforts in the field of 13C MFA.
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Affiliation(s)
- Martin Beyß
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Salah Azzouzi
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Michael Weitzel
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, Aachen, Germany
| | - Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
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8
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Nöh K, Niedenführ S, Beyß M, Wiechert W. A Pareto approach to resolve the conflict between information gain and experimental costs: Multiple-criteria design of carbon labeling experiments. PLoS Comput Biol 2018; 14:e1006533. [PMID: 30379837 PMCID: PMC6209137 DOI: 10.1371/journal.pcbi.1006533] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 09/27/2018] [Indexed: 01/23/2023] Open
Abstract
Science revolves around the best way of conducting an experiment to obtain insightful results. Experiments with maximal information content can be found by computational experimental design (ED) strategies that identify optimal conditions under which to perform the experiment. Several criteria have been proposed to measure the information content, each emphasizing different aspects of the design goal, i.e., reduction of uncertainty. Where experiments are complex or expensive, second sight is at the budget governing the achievable amount of information. In this context, the design objectives cost and information gain are often incommensurable, though dependent. By casting the ED task into a multiple-criteria optimization problem, a set of trade-off designs is derived that approximates the Pareto-frontier which is instrumental for exploring preferable designs. In this work, we present a computational methodology for multiple-criteria ED of information-rich experiments that accounts for virtually any set of design criteria. The methodology is implemented for the case of 13C metabolic flux analysis (MFA), which is arguably the most expensive type among the ‘omics’ technologies, featuring dozens of design parameters (tracer composition, analytical platform, measurement selection etc.). Supported by an innovative visualization scheme, we demonstrate with two realistic showcases that the use of multiple criteria reveals deep insights into the conflicting interplay between information carriers and cost factors that are not amendable to single-objective ED. For instance, tandem mass spectrometry turns out as best-in-class with respect to information gain, while it delivers this information quality cheaper than the other, routinely applied analytical technologies. Therewith, our Pareto approach to ED offers the investigator great flexibilities in the conception phase of a study to balance costs and benefits. Designing experiments is obligatory in the biosciences to valorize their scientific outcome. When the experiments are expensive, unfortunately, in practice often the costs emerge to be showstoppers. In this situation the question arises: How to get the most out of the experiment for your invest in terms of time and money? We approach this question by formulating the design task as a multiple-criteria optimization problem. Its solution produces a set of Pareto-optimal design proposals that feature the trade-off between information gain, as measured by different metrics, and the costs. Then, exploration of the design proposals allows us to make the best decision on information-economic experiments under given circumstances. Implemented in the field of isotope-based metabolic flux analysis, practical application of the Pareto approach provides detailed insight into the tight interplay of plenty of information carriers and cost factors. Supported by an innovative tailored visual representation scheme, the investigator is enabled to explore the options before conducting the experiment. With a practical showcase at hand, our computational study highlights the benefits of incorporating multiple information criteria apart from the costs, balancing the shortcomings of conventional single-objective experimental design strategies.
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Affiliation(s)
- Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- * E-mail:
| | - Sebastian Niedenführ
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Martin Beyß
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Computational Systems Biotechnology, RWTH Aachen University, Aachen, Germany
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