1
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Chengalroyen MD, Mehaffy C, Lucas M, Bauer N, Raphela ML, Oketade N, Warner DF, Lewinsohn DA, Lewinsohn DM, Dobos KM, Mizrahi V. Modulation of riboflavin biosynthesis and utilization in mycobacteria. Microbiol Spectr 2024; 12:e0320723. [PMID: 38916330 PMCID: PMC11302143 DOI: 10.1128/spectrum.03207-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 05/17/2024] [Indexed: 06/26/2024] Open
Abstract
Riboflavin (vitamin B2) is the precursor of the flavin coenzymes, FAD and FMN, which play a central role in cellular redox metabolism. While humans must obtain riboflavin from dietary sources, certain microbes, including Mycobacterium tuberculosis (Mtb), can biosynthesize riboflavin de novo. Riboflavin precursors have also been implicated in the activation of mucosal-associated invariant T (MAIT) cells which recognize metabolites derived from the riboflavin biosynthesis pathway complexed to the MHC-I-like molecule, MR1. To investigate the biosynthesis and function of riboflavin and its pathway intermediates in mycobacterial metabolism and physiology, we constructed conditional knockdowns (hypomorphs) in riboflavin biosynthesis and utilization genes in Mycobacterium smegmatis (Msm) and Mtb by inducible CRISPR interference. Using this comprehensive panel of hypomorphs, we analyzed the impact of gene silencing on viability, on the transcription of (other) riboflavin pathway genes, on the levels of the pathway proteins, and on riboflavin itself. Our results revealed that (i) despite lacking a canonical transporter, both Msm and Mtb assimilate exogenous riboflavin when supplied at high concentration; (ii) there is functional redundancy in lumazine synthase activity in Msm; (iii) silencing of ribA2 or ribF is profoundly bactericidal in Mtb; and (iv) in Msm, ribA2 silencing results in concomitant knockdown of other pathway genes coupled with RibA2 and riboflavin depletion and is also bactericidal. In addition to their use in genetic validation of potential drug targets for tuberculosis, this collection of hypomorphs provides a useful resource for future studies investigating the role of pathway intermediates in MAIT cell recognition of mycobacteria. IMPORTANCE The pathway for biosynthesis and utilization of riboflavin, precursor of the essential coenzymes, FMN and FAD, is of particular interest in the flavin-rich pathogen, Mycobacterium tuberculosis (Mtb), for two important reasons: (i) the pathway includes potential tuberculosis (TB) drug targets and (ii) intermediates from the riboflavin biosynthesis pathway provide ligands for mucosal-associated invariant T (MAIT) cells, which have been implicated in TB pathogenesis. However, the riboflavin pathway is poorly understood in mycobacteria, which lack canonical mechanisms to transport this vitamin and to regulate flavin coenzyme homeostasis. By conditionally disrupting each step of the pathway and assessing the impact on mycobacterial viability and on the levels of the pathway proteins as well as riboflavin, our work provides genetic validation of the riboflavin pathway as a target for TB drug discovery and offers a resource for further exploring the association between riboflavin biosynthesis, MAIT cell activation, and TB infection and disease.
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Affiliation(s)
- Melissa D. Chengalroyen
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Carolina Mehaffy
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Megan Lucas
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Niel Bauer
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Mabule L. Raphela
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Nurudeen Oketade
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Digby F. Warner
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town, South Africa
| | | | - David M. Lewinsohn
- Oregon Health and Science University, Portland, Oregon, USA
- Portland VA Medical Center, Portland, Oregon, USA
| | - Karen M. Dobos
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Valerie Mizrahi
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town, South Africa
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2
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Fitzpatrick TB. B Vitamins: An Update on Their Importance for Plant Homeostasis. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:67-93. [PMID: 38424064 DOI: 10.1146/annurev-arplant-060223-025336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
B vitamins are a source of coenzymes for a vast array of enzyme reactions, particularly those of metabolism. As metabolism is the basis of decisions that drive maintenance, growth, and development, B vitamin-derived coenzymes are key components that facilitate these processes. For over a century, we have known about these essential compounds and have elucidated their pathways of biosynthesis, repair, salvage, and degradation in numerous organisms. Only now are we beginning to understand their importance for regulatory processes, which are becoming an important topic in plants. Here, I highlight and discuss emerging evidence on how B vitamins are integrated into vital processes, from energy generation and nutrition to gene expression, and thereby contribute to the coordination of growth and developmental programs, particularly those that concern maintenance of a stable state, which is the foundational tenet of plant homeostasis.
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3
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Dong T, Zhang L, Hao S, Yang J, Peng Y. Interspecies cooperation-driven photogenerated electron transfer processes and efficient multi-pathway nitrogen removal in the g-C 3N 4-anammox consortia biohybrid system. WATER RESEARCH 2024; 255:121532. [PMID: 38564893 DOI: 10.1016/j.watres.2024.121532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/18/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
Photocatalytic materials-microbial biohybrid systems pave the way for solar-driven wastewater nitrogen removal. In this study, interspecies cooperation in photogenerated electron transfer and efficient nitrogen removal mechanism in the g-C3N4-anammox consortia biohybrid system were first deciphered. The results indicated that the essential extracellular electron carriers (cytochrome c and flavin) for anammox genomes were provided by associated bacteria (BACT3 and CHLO2). This cooperation, regulated by the ArcAB system and electron transfer flavoprotein, made anammox bacteria the primary photogenerated electron sink. Furthermore, an efficient photogenerated electron harness was used to construct a reductive glycine pathway (rGlyP) in anammox bacteria inventively, which coexisted with the Wood-Ljungdahl pathway (WLP), constituting a dual-pathway carbon fixation model, rGlyP-WLP. Carbon fixation products efficiently contributed to the tricarboxylic acid cycle, while inhibiting electron diversion in anabolism. Photogenerated electrons were targeted channeled into nitrogen metabolism-available electron carriers, enhancing anammox and dissimilatory nitrate reduction to ammonium (DNRA) processes. Moreover, ammonia assimilation by the glycine cleavage system in rGlyP established an alternative ammonia removal route. Ultimately, multi-pathway nitrogen removal involving anammox, DNRA, and rGlyP achieved 100 % ammonia removal and 94.25 % total nitrogen removal efficiency. This study has expanded understanding of anammox metabolic diversity, enhancing its potential application in carbon-neutral wastewater treatment.
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Affiliation(s)
- Tingjun Dong
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing, 100124, China
| | - Li Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing, 100124, China.
| | - Shiwei Hao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing, 100124, China
| | - Jiachun Yang
- China Coal Technology & Engineering Group Co. Ltd., Tokyo, 100-0011, Japan
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing, 100124, China
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4
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Bernstein DB, Akkas B, Price MN, Arkin AP. Evaluating E. coli genome-scale metabolic model accuracy with high-throughput mutant fitness data. Mol Syst Biol 2023; 19:e11566. [PMID: 37888487 DOI: 10.15252/msb.202311566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 09/23/2023] [Accepted: 10/05/2023] [Indexed: 10/28/2023] Open
Abstract
The Escherichia coli genome-scale metabolic model (GEM) is an exemplar systems biology model for the simulation of cellular metabolism. Experimental validation of model predictions is essential to pinpoint uncertainty and ensure continued development of accurate models. Here, we quantified the accuracy of four subsequent E. coli GEMs using published mutant fitness data across thousands of genes and 25 different carbon sources. This evaluation demonstrated the utility of the area under a precision-recall curve relative to alternative accuracy metrics. An analysis of errors in the latest (iML1515) model identified several vitamins/cofactors that are likely available to mutants despite being absent from the experimental growth medium and highlighted isoenzyme gene-protein-reaction mapping as a key source of inaccurate predictions. A machine learning approach further identified metabolic fluxes through hydrogen ion exchange and specific central metabolism branch points as important determinants of model accuracy. This work outlines improved practices for the assessment of GEM accuracy with high-throughput mutant fitness data and highlights promising areas for future model refinement in E. coli and beyond.
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Affiliation(s)
- David B Bernstein
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Batu Akkas
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Morgan N Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Adam P Arkin
- Department of Bioengineering, University of California, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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5
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Chengalroyen MD, Mehaffy C, Lucas M, Bauer N, Raphela ML, Oketade N, Warner DF, Lewinsohn DA, Lewinsohn DM, Dobos KM, Mizrahi V. Modulation of riboflavin biosynthesis and utilization in mycobacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555301. [PMID: 37693561 PMCID: PMC10491194 DOI: 10.1101/2023.08.30.555301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Riboflavin (vitamin B2) is the precursor of the flavin coenzymes, FAD and FMN, which play a central role in cellular redox metabolism. While humans must obtain riboflavin from dietary sources, certain microbes, including Mycobacterium tuberculosis (Mtb), can biosynthesize riboflavin de novo. Riboflavin precursors have also been implicated in the activation of mucosal-associated invariant T (MAIT) cells which recognize metabolites derived from the riboflavin biosynthesis pathway complexed to the MHC-I-like molecule, MR1. To investigate the biosynthesis and function of riboflavin and its pathway intermediates in mycobacterial metabolism, physiology and MAIT cell recognition, we constructed conditional knockdowns (hypomorphs) in riboflavin biosynthesis and utilization genes in Mycobacterium smegmatis (Msm) and Mtb by inducible CRISPR interference. Using this comprehensive panel of hypomorphs, we analyzed the impact of gene silencing on viability, on the transcription of (other) riboflavin pathway genes, on the levels of the pathway proteins and on riboflavin itself. Our results revealed that (i) despite lacking a canonical transporter, both Msm and Mtb assimilate exogenous riboflavin when supplied at high concentration; (ii) there is functional redundancy in lumazine synthase activity in Msm; (iii) silencing of ribA2 or ribF is profoundly bactericidal in Mtb; and (iv) in Msm, ribA2 silencing results in concomitant knockdown of other pathway genes coupled with RibA2 and riboflavin depletion and is also bactericidal. In addition to their use in genetic validation of potential drug targets for tuberculosis, this collection of hypomorphs provides a useful resource for investigating the role of pathway intermediates in MAIT cell recognition of mycobacteria.
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Affiliation(s)
- Melissa D. Chengalroyen
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, South Africa
| | - Carolina Mehaffy
- Department of Microbiology, Immunology and Pathology, Colorado State University, Colorado, USA
| | - Megan Lucas
- Department of Microbiology, Immunology and Pathology, Colorado State University, Colorado, USA
| | - Niel Bauer
- Department of Microbiology, Immunology and Pathology, Colorado State University, Colorado, USA
| | - Mabule L. Raphela
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, South Africa
| | - Nurudeen Oketade
- Department of Microbiology, Immunology and Pathology, Colorado State University, Colorado, USA
| | - Digby F. Warner
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, South Africa
- Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town, South Africa
| | | | - David M. Lewinsohn
- Oregon Health and Science University, Oregon, USA
- Portland VA Medical Center, Oregon, USA
| | - Karen M. Dobos
- Department of Microbiology, Immunology and Pathology, Colorado State University, Colorado, USA
| | - Valerie Mizrahi
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, South Africa
- Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town, South Africa
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6
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Ryback B, Vorholt JA. Coenzyme biosynthesis in response to precursor availability reveals incorporation of β-alanine from pantothenate in prototrophic bacteria. J Biol Chem 2023; 299:104919. [PMID: 37315792 PMCID: PMC10393543 DOI: 10.1016/j.jbc.2023.104919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/16/2023] Open
Abstract
Coenzymes are important for all classes of enzymatic reactions and essential for cellular metabolism. Most coenzymes are synthesized from dedicated precursors, also referred to as vitamins, which prototrophic bacteria can either produce themselves from simpler substrates or take up from the environment. The extent to which prototrophs use supplied vitamins and whether externally available vitamins affect the size of intracellular coenzyme pools and control endogenous vitamin synthesis is currently largely unknown. Here, we studied coenzyme pool sizes and vitamin incorporation into coenzymes during growth on different carbon sources and vitamin supplementation regimes using metabolomics approaches. We found that the model bacterium Escherichia coli incorporated pyridoxal, niacin, and pantothenate into pyridoxal 5'-phosphate, NAD, and coenzyme A (CoA), respectively. In contrast, riboflavin was not taken up and was produced exclusively endogenously. Coenzyme pools were mostly homeostatic and not affected by externally supplied precursors. Remarkably, we found that pantothenate is not incorporated into CoA as such but is first degraded to pantoate and β-alanine and then rebuilt. This pattern was conserved in various bacterial isolates, suggesting a preference for β-alanine over pantothenate utilization in CoA synthesis. Finally, we found that the endogenous synthesis of coenzyme precursors remains active when vitamins are supplied, which is consistent with described expression data of genes for enzymes involved in coenzyme biosynthesis under these conditions. Continued production of endogenous coenzymes may ensure rapid synthesis of the mature coenzyme under changing environmental conditions, protect against coenzyme limitation, and explain vitamin availability in naturally oligotrophic environments.
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7
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Teufel M, Henkel W, Sobetzko P. The role of replication-induced chromosomal copy numbers in spatio-temporal gene regulation and evolutionary chromosome plasticity. Front Microbiol 2023; 14:1119878. [PMID: 37152747 PMCID: PMC10157177 DOI: 10.3389/fmicb.2023.1119878] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/31/2023] [Indexed: 05/09/2023] Open
Abstract
For a coherent response to environmental changes, bacterial evolution has formed a complex transcriptional regulatory system comprising classical DNA binding proteins sigma factors and modulation of DNA topology. In this study, we investigate replication-induced gene copy numbers - a regulatory concept that is unlike the others not based on modulation of promoter activity but on replication dynamics. We show that a large fraction of genes are predominantly affected by transient copy numbers and identify cellular functions and central pathways governed by this mechanism in Escherichia coli. Furthermore, we show quantitatively that the previously observed spatio-temporal expression pattern between different growth phases mainly emerges from transient chromosomal copy numbers. We extend the analysis to the plant pathogen Dickeya dadantii and the biotechnologically relevant organism Vibrio natriegens. The analysis reveals a connection between growth phase dependent gene expression and evolutionary gene migration in these species. A further extension to the bacterial kingdom indicates that chromosome evolution is governed by growth rate related transient copy numbers.
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Affiliation(s)
- Marc Teufel
- Synthetic Microbiology Center Marburg (SYNMIKRO), Philipps Universität Marburg, Marburg, Germany
| | - Werner Henkel
- Transmission Systems Group, Jacobs University Bremen, Bremen, Germany
| | - Patrick Sobetzko
- Synthetic Microbiology Center Marburg (SYNMIKRO), Philipps Universität Marburg, Marburg, Germany
- DynAMic Department, Universitè de Lorraine, INRAE, Nancy, France
- *Correspondence: Patrick Sobetzko
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8
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Ryback B, Bortfeld-Miller M, Vorholt JA. Metabolic adaptation to vitamin auxotrophy by leaf-associated bacteria. THE ISME JOURNAL 2022; 16:2712-2724. [PMID: 35987782 PMCID: PMC9666465 DOI: 10.1038/s41396-022-01303-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 07/13/2022] [Accepted: 07/25/2022] [Indexed: 12/15/2022]
Abstract
Auxotrophs are unable to synthesize all the metabolites essential for their metabolism and rely on others to provide them. They have been intensively studied in laboratory-generated and -evolved mutants, but emergent adaptation mechanisms to auxotrophy have not been systematically addressed. Here, we investigated auxotrophies in bacteria isolated from Arabidopsis thaliana leaves and found that up to half of the strains have auxotrophic requirements for biotin, niacin, pantothenate and/or thiamine. We then explored the genetic basis of auxotrophy as well as traits that co-occurred with vitamin auxotrophy. We found that auxotrophic strains generally stored coenzymes with the capacity to grow exponentially for 1-3 doublings without vitamin supplementation; however, the highest observed storage was for biotin, which allowed for 9 doublings in one strain. In co-culture experiments, we demonstrated vitamin supply to auxotrophs, and found that auxotrophic strains maintained higher species richness than prototrophs upon external supplementation with vitamins. Extension of a consumer-resource model predicted that auxotrophs can utilize carbon compounds provided by other organisms, suggesting that auxotrophic strains benefit from metabolic by-products beyond vitamins.
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Affiliation(s)
- Birgitta Ryback
- grid.5801.c0000 0001 2156 2780Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Miriam Bortfeld-Miller
- grid.5801.c0000 0001 2156 2780Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Julia A. Vorholt
- grid.5801.c0000 0001 2156 2780Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
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9
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Kleijn IT, Martínez-Segura A, Bertaux F, Saint M, Kramer H, Shahrezaei V, Marguerat S. Growth-rate-dependent and nutrient-specific gene expression resource allocation in fission yeast. Life Sci Alliance 2022; 5:e202101223. [PMID: 35228260 PMCID: PMC8886410 DOI: 10.26508/lsa.202101223] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/25/2022] [Accepted: 01/25/2022] [Indexed: 12/20/2022] Open
Abstract
Cellular resources are limited and their relative allocation to gene expression programmes determines physiological states and global properties such as the growth rate. Here, we determined the importance of the growth rate in explaining relative changes in protein and mRNA levels in the simple eukaryote Schizosaccharomyces pombe grown on non-limiting nitrogen sources. Although expression of half of fission yeast genes was significantly correlated with the growth rate, this came alongside wide-spread nutrient-specific regulation. Proteome and transcriptome often showed coordinated regulation but with notable exceptions, such as metabolic enzymes. Genes positively correlated with growth rate participated in every level of protein production apart from RNA polymerase II-dependent transcription. Negatively correlated genes belonged mainly to the environmental stress response programme. Critically, metabolic enzymes, which represent ∼55-70% of the proteome by mass, showed mostly condition-specific regulation. In summary, we provide a rich account of resource allocation to gene expression in a simple eukaryote, advancing our basic understanding of the interplay between growth-rate-dependent and nutrient-specific gene expression.
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Affiliation(s)
- Istvan T Kleijn
- Medical Research Council London Institute of Medical Sciences (MRC LMS), London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
- Department of Mathematics, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Amalia Martínez-Segura
- Medical Research Council London Institute of Medical Sciences (MRC LMS), London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - François Bertaux
- Medical Research Council London Institute of Medical Sciences (MRC LMS), London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
- Department of Mathematics, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Malika Saint
- Medical Research Council London Institute of Medical Sciences (MRC LMS), London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Holger Kramer
- Medical Research Council London Institute of Medical Sciences (MRC LMS), London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Vahid Shahrezaei
- Department of Mathematics, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Samuel Marguerat
- Medical Research Council London Institute of Medical Sciences (MRC LMS), London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
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10
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Pepi MJ, Chacko S, Marqus GM, Singh V, Wang Z, Planck K, Cullinane RT, Meka PN, Gollapalli DR, Ioerger TR, Rhee KY, Cuny GD, Boshoff HI, Hedstrom L. A d-Phenylalanine-Benzoxazole Derivative Reveals the Role of the Essential Enzyme Rv3603c in the Pantothenate Biosynthetic Pathway of Mycobacterium tuberculosis. ACS Infect Dis 2022; 8:330-342. [PMID: 35015509 DOI: 10.1021/acsinfecdis.1c00461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New drugs and new targets are urgently needed to treat tuberculosis. We discovered that d-phenylalanine-benzoxazole Q112 displays potent antibacterial activity against Mycobacterium tuberculosis (Mtb) in multiple media and in macrophage infections. A metabolomic profiling indicates that Q112 has a unique mechanism of action. Q112 perturbs the essential pantothenate/coenzyme A biosynthetic pathway, depleting pantoate while increasing ketopantoate, as would be expected if ketopantoate reductase (KPR) were inhibited. We searched for alternative KPRs, since the enzyme annotated as PanE KPR is not essential in Mtb. The ketol-acid reductoisomerase IlvC catalyzes the KPR reaction in the close Mtb relative Corynebacterium glutamicum, but Mtb IlvC does not display KPR activity. We identified the essential protein Rv3603c as an orthologue of PanG KPR and demonstrated that a purified recombinant Rv3603c has KPR activity. Q112 inhibits Rv3603c, explaining the metabolomic changes. Surprisingly, pantothenate does not rescue Q112-treated bacteria, indicating that Q112 has an additional target(s). Q112-resistant strains contain loss-of-function mutations in the twin arginine translocase TatABC, further underscoring Q112's unique mechanism of action. Loss of TatABC causes a severe fitness deficit attributed to changes in nutrient uptake, suggesting that Q112 resistance may derive from a decrease in uptake.
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Affiliation(s)
- Michael J. Pepi
- Graduate Program in Chemistry, Brandeis University, Waltham 02453, Massachusetts, United States
| | - Shibin Chacko
- Department of Biology, Brandeis University, Waltham 02453, Massachusetts, United States
| | - Gary M. Marqus
- Graduate Program in Chemistry, Brandeis University, Waltham 02453, Massachusetts, United States
| | - Vinayak Singh
- Drug Discovery and Development Centre (H3D), and South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Zhe Wang
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York 10065, New York, United States
| | - Kyle Planck
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York 10065, New York, United States
| | - Ryan T. Cullinane
- Department of Biology, Brandeis University, Waltham 02453, Massachusetts, United States
| | - Penchala N. Meka
- Department of Biology, Brandeis University, Waltham 02453, Massachusetts, United States
| | | | - Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station 77843, Texas, United States
| | - Kyu Y. Rhee
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York 10065, New York, United States
| | - Gregory D. Cuny
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston 77204, Texas, United States
| | - Helena I.M. Boshoff
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda 20892, Maryland, United States
| | - Lizbeth Hedstrom
- Department of Biology, Brandeis University, Waltham 02453, Massachusetts, United States
- Department of Chemistry, Brandeis University, Waltham 02453, Massachusetts, United States
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11
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Banh RS, Kim ES, Spillier Q, Biancur DE, Yamamoto K, Sohn ASW, Shi G, Jones DR, Kimmelman AC, Pacold ME. The polar oxy-metabolome reveals the 4-hydroxymandelate CoQ10 synthesis pathway. Nature 2021; 597:420-425. [PMID: 34471290 PMCID: PMC8538427 DOI: 10.1038/s41586-021-03865-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/29/2021] [Indexed: 12/17/2022]
Abstract
Oxygen is critical for a multitude of metabolic processes that are essential for human life. Biological processes can be identified by treating cells with 18O2 or other isotopically labelled gases and systematically identifying biomolecules incorporating labeled atoms. Here we labelled cell lines of distinct tissue origins with 18O2 to identify the polar oxy-metabolome, defined as polar metabolites labelled with 18O under different physiological O2 tensions. The most highly 18O-labelled feature was 4-hydroxymandelate (4-HMA). We demonstrate that 4-HMA is produced by hydroxyphenylpyruvate dioxygenase-like (HPDL), a protein of previously unknown function in human cells. We identify 4-HMA as an intermediate involved in the biosynthesis of the coenzyme Q10 (CoQ10) headgroup in human cells. The connection of HPDL to CoQ10 biosynthesis provides crucial insights into the mechanisms underlying recently described neurological diseases related to HPDL deficiencies1-4 and cancers with HPDL overexpression5.
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Affiliation(s)
- Robert S Banh
- Department of Radiation Oncology, New York University Langone Health, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Esther S Kim
- Department of Radiation Oncology, New York University Langone Health, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Quentin Spillier
- Department of Radiation Oncology, New York University Langone Health, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Douglas E Biancur
- Department of Radiation Oncology, New York University Langone Health, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Keisuke Yamamoto
- Department of Radiation Oncology, New York University Langone Health, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Albert S W Sohn
- Department of Radiation Oncology, New York University Langone Health, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Guangbin Shi
- Department of Radiation Oncology, New York University Langone Health, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Drew R Jones
- Metabolomics Core Resource Laboratory, New York University Langone Health, New York, NY, USA
| | - Alec C Kimmelman
- Department of Radiation Oncology, New York University Langone Health, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Michael E Pacold
- Department of Radiation Oncology, New York University Langone Health, New York, NY, USA.
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA.
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12
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Evans JC, Murugesan D, Post JM, Mendes V, Wang Z, Nahiyaan N, Lynch SL, Thompson S, Green SR, Ray PC, Hess J, Spry C, Coyne AG, Abell C, Boshoff HIM, Wyatt PG, Rhee KY, Blundell TL, Barry CE, Mizrahi V. Targeting Mycobacterium tuberculosis CoaBC through Chemical Inhibition of 4'-Phosphopantothenoyl-l-cysteine Synthetase (CoaB) Activity. ACS Infect Dis 2021; 7:1666-1679. [PMID: 33939919 PMCID: PMC8205227 DOI: 10.1021/acsinfecdis.0c00904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Indexed: 02/02/2023]
Abstract
Coenzyme A (CoA) is a ubiquitous cofactor present in all living cells and estimated to be required for up to 9% of intracellular enzymatic reactions. Mycobacterium tuberculosis (Mtb) relies on its own ability to biosynthesize CoA to meet the needs of the myriad enzymatic reactions that depend on this cofactor for activity. As such, the pathway to CoA biosynthesis is recognized as a potential source of novel tuberculosis drug targets. In prior work, we genetically validated CoaBC as a bactericidal drug target in Mtb in vitro and in vivo. Here, we describe the identification of compound 1f, a small molecule inhibitor of the 4'-phosphopantothenoyl-l-cysteine synthetase (PPCS; CoaB) domain of the bifunctional Mtb CoaBC, and show that this compound displays on-target activity in Mtb. Compound 1f was found to inhibit CoaBC uncompetitively with respect to 4'-phosphopantothenate, the substrate for the CoaB-catalyzed reaction. Furthermore, metabolomic profiling of wild-type Mtb H37Rv following exposure to compound 1f produced a signature consistent with perturbations in pantothenate and CoA biosynthesis. As the first report of a direct small molecule inhibitor of Mtb CoaBC displaying target-selective whole-cell activity, this study confirms the druggability of CoaBC and chemically validates this target.
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Affiliation(s)
- Joanna C. Evans
- MRC/NHLS/UCT
Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence
for Biomedical TB Research & Wellcome Centre for Infectious Diseases
Research in Africa, Institute of Infectious Disease and Molecular
Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, South Africa
| | - Dinakaran Murugesan
- Drug
Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, Scotland, U.K.
| | - John M. Post
- Drug
Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, Scotland, U.K.
| | - Vitor Mendes
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.
| | - Zhe Wang
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Navid Nahiyaan
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Sasha L. Lynch
- MRC/NHLS/UCT
Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence
for Biomedical TB Research & Wellcome Centre for Infectious Diseases
Research in Africa, Institute of Infectious Disease and Molecular
Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, South Africa
| | - Stephen Thompson
- Drug
Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, Scotland, U.K.
| | - Simon R. Green
- Drug
Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, Scotland, U.K.
| | - Peter C. Ray
- Drug
Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, Scotland, U.K.
| | - Jeannine Hess
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Christina Spry
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Anthony G. Coyne
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Chris Abell
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Helena I. M. Boshoff
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease,
National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Paul G. Wyatt
- Drug
Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, Scotland, U.K.
| | - Kyu Y. Rhee
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Tom L. Blundell
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.
| | - Clifton E. Barry
- MRC/NHLS/UCT
Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence
for Biomedical TB Research & Wellcome Centre for Infectious Diseases
Research in Africa, Institute of Infectious Disease and Molecular
Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, South Africa
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease,
National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Valerie Mizrahi
- MRC/NHLS/UCT
Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence
for Biomedical TB Research & Wellcome Centre for Infectious Diseases
Research in Africa, Institute of Infectious Disease and Molecular
Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, South Africa
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13
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Mendes V, Green SR, Evans JC, Hess J, Blaszczyk M, Spry C, Bryant O, Cory-Wright J, Chan DSH, Torres PHM, Wang Z, Nahiyaan N, O’Neill S, Damerow S, Post J, Bayliss T, Lynch SL, Coyne AG, Ray PC, Abell C, Rhee KY, Boshoff HIM, Barry CE, Mizrahi V, Wyatt PG, Blundell TL. Inhibiting Mycobacterium tuberculosis CoaBC by targeting an allosteric site. Nat Commun 2021; 12:143. [PMID: 33420031 PMCID: PMC7794376 DOI: 10.1038/s41467-020-20224-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 11/18/2020] [Indexed: 02/02/2023] Open
Abstract
Coenzyme A (CoA) is a fundamental co-factor for all life, involved in numerous metabolic pathways and cellular processes, and its biosynthetic pathway has raised substantial interest as a drug target against multiple pathogens including Mycobacterium tuberculosis. The biosynthesis of CoA is performed in five steps, with the second and third steps being catalysed in the vast majority of prokaryotes, including M. tuberculosis, by a single bifunctional protein, CoaBC. Depletion of CoaBC was found to be bactericidal in M. tuberculosis. Here we report the first structure of a full-length CoaBC, from the model organism Mycobacterium smegmatis, describe how it is organised as a dodecamer and regulated by CoA thioesters. A high-throughput biochemical screen focusing on CoaB identified two inhibitors with different chemical scaffolds. Hit expansion led to the discovery of potent and selective inhibitors of M. tuberculosis CoaB, which we show to bind to a cryptic allosteric site within CoaB.
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Affiliation(s)
- Vitor Mendes
- grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - Simon R. Green
- grid.8241.f0000 0004 0397 2876Drug Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH Scotland UK
| | - Joanna C. Evans
- grid.7836.a0000 0004 1937 1151MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research & Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa
| | - Jeannine Hess
- grid.5335.00000000121885934Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Michal Blaszczyk
- grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - Christina Spry
- grid.5335.00000000121885934Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Owain Bryant
- grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - James Cory-Wright
- grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - Daniel S-H. Chan
- grid.5335.00000000121885934Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Pedro H. M. Torres
- grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - Zhe Wang
- grid.5386.8000000041936877XDivision of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10065 USA
| | - Navid Nahiyaan
- grid.5386.8000000041936877XDivision of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10065 USA
| | - Sandra O’Neill
- grid.8241.f0000 0004 0397 2876Drug Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH Scotland UK
| | - Sebastian Damerow
- grid.8241.f0000 0004 0397 2876Drug Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH Scotland UK
| | - John Post
- grid.8241.f0000 0004 0397 2876Drug Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH Scotland UK
| | - Tracy Bayliss
- grid.8241.f0000 0004 0397 2876Drug Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH Scotland UK
| | - Sasha L. Lynch
- grid.7836.a0000 0004 1937 1151MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research & Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa
| | - Anthony G. Coyne
- grid.5335.00000000121885934Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Peter C. Ray
- grid.8241.f0000 0004 0397 2876Drug Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH Scotland UK
| | - Chris Abell
- grid.5335.00000000121885934Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Kyu Y. Rhee
- grid.5386.8000000041936877XDivision of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10065 USA
| | - Helena I. M. Boshoff
- grid.419681.30000 0001 2164 9667Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892 USA
| | - Clifton E. Barry
- grid.7836.a0000 0004 1937 1151MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research & Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa ,grid.419681.30000 0001 2164 9667Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892 USA
| | - Valerie Mizrahi
- grid.7836.a0000 0004 1937 1151MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research & Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa
| | - Paul G. Wyatt
- grid.8241.f0000 0004 0397 2876Drug Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH Scotland UK
| | - Tom L. Blundell
- grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
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14
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Shyp V, Dubey BN, Böhm R, Hartl J, Nesper J, Vorholt JA, Hiller S, Schirmer T, Jenal U. Reciprocal growth control by competitive binding of nucleotide second messengers to a metabolic switch in Caulobacter crescentus. Nat Microbiol 2020; 6:59-72. [PMID: 33168988 DOI: 10.1038/s41564-020-00809-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 10/02/2020] [Indexed: 12/13/2022]
Abstract
Bacteria use small signalling molecules such as (p)ppGpp or c-di-GMP to tune their physiology in response to environmental changes. It remains unclear whether these regulatory networks operate independently or whether they interact to optimize bacterial growth and survival. We report that (p)ppGpp and c-di-GMP reciprocally regulate the growth of Caulobacter crescentus by converging on a single small-molecule-binding protein, SmbA. While c-di-GMP binding inhibits SmbA, (p)ppGpp competes for the same binding site to sustain SmbA activity. We demonstrate that (p)ppGpp specifically promotes Caulobacter growth on glucose, whereas c-di-GMP inhibits glucose consumption. We find that SmbA contributes to this metabolic switch and promotes growth on glucose by quenching the associated redox stress. The identification of an effector protein that acts as a central regulatory hub for two global second messengers opens up future studies on specific crosstalk between small-molecule-based regulatory networks.
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Affiliation(s)
| | | | - Raphael Böhm
- Biozentrum, University of Basel, Basel, Switzerland
| | - Johannes Hartl
- Institute of Microbiology, ETH Zurich, Zürich, Switzerland
| | - Jutta Nesper
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | | | - Urs Jenal
- Biozentrum, University of Basel, Basel, Switzerland.
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15
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Nguyen BD, Cuenca V M, Hartl J, Gül E, Bauer R, Meile S, Rüthi J, Margot C, Heeb L, Besser F, Escriva PP, Fetz C, Furter M, Laganenka L, Keller P, Fuchs L, Christen M, Porwollik S, McClelland M, Vorholt JA, Sauer U, Sunagawa S, Christen B, Hardt WD. Import of Aspartate and Malate by DcuABC Drives H 2/Fumarate Respiration to Promote Initial Salmonella Gut-Lumen Colonization in Mice. Cell Host Microbe 2020; 27:922-936.e6. [PMID: 32416061 PMCID: PMC7292772 DOI: 10.1016/j.chom.2020.04.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 02/16/2020] [Accepted: 04/14/2020] [Indexed: 12/13/2022]
Abstract
Initial enteropathogen growth in the microbiota-colonized gut is poorly understood. Salmonella Typhimurium is metabolically adaptable and can harvest energy by anaerobic respiration using microbiota-derived hydrogen (H2) as an electron donor and fumarate as an electron acceptor. As fumarate is scarce in the gut, the source of this electron acceptor is unclear. Here, transposon sequencing analysis along the colonization trajectory of S. Typhimurium implicates the C4-dicarboxylate antiporter DcuABC in early murine gut colonization. In competitive colonization assays, DcuABC and enzymes that convert the C4-dicarboxylates aspartate and malate into fumarate (AspA, FumABC), are required for fumarate/H2-dependent initial growth. Thus, S. Typhimurium obtains fumarate by DcuABC-mediated import and conversion of L-malate and L-aspartate. Fumarate reduction yields succinate, which is exported by DcuABC in exchange for L-aspartate and L-malate. This cycle allows S. Typhimurium to harvest energy by H2/fumarate respiration in the microbiota-colonized gut. This strategy may also be relevant for commensal E. coli diminishing the S. Typhimurium infection.
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Affiliation(s)
- Bidong D Nguyen
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | | | - Johannes Hartl
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Ersin Gül
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Rebekka Bauer
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Susanne Meile
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Joel Rüthi
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Céline Margot
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Laura Heeb
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Franziska Besser
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Pau Pérez Escriva
- Institute of Molecular Systems Biology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Céline Fetz
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Markus Furter
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Leanid Laganenka
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Philipp Keller
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Lea Fuchs
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Matthias Christen
- Institute of Molecular Systems Biology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Steffen Porwollik
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697-4025, USA
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697-4025, USA
| | - Julia A Vorholt
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Shinichi Sunagawa
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland.
| | - Beat Christen
- Institute of Molecular Systems Biology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland.
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16
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Wolf N, Bussmann M, Koch-Koerfges A, Katcharava N, Schulte J, Polen T, Hartl J, Vorholt JA, Baumgart M, Bott M. Molecular Basis of Growth Inhibition by Acetate of an Adenylate Cyclase-Deficient Mutant of Corynebacterium glutamicum. Front Microbiol 2020; 11:87. [PMID: 32117117 PMCID: PMC7026483 DOI: 10.3389/fmicb.2020.00087] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/15/2020] [Indexed: 01/02/2023] Open
Abstract
In Corynebacterium glutamicum, cyclic adenosine monophosphate (cAMP) serves as an effector of the global transcriptional regulator GlxR. Synthesis of cAMP is catalyzed by the membrane-bound adenylate cyclase CyaB. In this study, we investigated the consequences of decreased intracellular cAMP levels in a ΔcyaB mutant. While no growth defect of the ΔcyaB strain was observed on glucose, fructose, sucrose, or gluconate alone, the addition of acetate to these growth media resulted in a severe growth inhibition, which could be reversed by plasmid-based cyaB expression or by supplementation of the medium with cAMP. The effect was concentration- and pH-dependent, suggesting a link to the uncoupling activity of acetate. In agreement, the ΔcyaB mutant had an increased sensitivity to the protonophore carbonyl cyanide m-chlorophenyl hydrazone (CCCP). The increased uncoupler sensitivity correlated with a lowered membrane potential of acetate-grown ΔcyaB cells compared to wild-type cells. A reduced membrane potential affects major cellular processes, such as ATP synthesis by F1F O -ATP synthase and numerous transport processes. The impaired membrane potential of the ΔcyaB mutant could be due to a decreased expression of the cytochrome bc 1-aa 3 supercomplex, which is the major contributor of proton-motive force in C. glutamicum. Expression of the supercomplex genes was previously reported to be activated by GlxR-cAMP. A suppressor mutant of the ΔcyaB strain with improved growth on acetate was isolated, which carried a single mutation in the genome leading to an Ala131Thr exchange in GlxR. Introduction of this point mutation into the original ΔcyaB mutant restored the growth defect on acetate. This supported the importance of GlxR for the phenotype of the ΔcyaB mutant and, more generally, of the cAMP-GlxR system for the control of energy metabolism in C. glutamicum.
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Affiliation(s)
- Natalie Wolf
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Michael Bussmann
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Abigail Koch-Koerfges
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Nino Katcharava
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Julia Schulte
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Tino Polen
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Johannes Hartl
- Institute of Microbiology, ETH Zürich, Zurich, Switzerland
| | | | - Meike Baumgart
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
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17
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Hartl J, Kiefer P, Kaczmarczyk A, Mittelviefhaus M, Meyer F, Vonderach T, Hattendorf B, Jenal U, Vorholt JA. Untargeted metabolomics links glutathione to bacterial cell cycle progression. Nat Metab 2020; 2:153-166. [PMID: 32090198 PMCID: PMC7035108 DOI: 10.1038/s42255-019-0166-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 12/17/2019] [Indexed: 12/21/2022]
Abstract
Cell cycle progression requires the coordination of cell growth, chromosome replication, and division. Consequently, a functional cell cycle must be coupled with metabolism. However, direct measurements of metabolome dynamics remained scarce, in particular in bacteria. Here, we describe an untargeted metabolomics approach with synchronized Caulobacter crescentus cells to monitor the relative abundance changes of ~400 putative metabolites as a function of the cell cycle. While the majority of metabolite pools remains homeostatic, ~14% respond to cell cycle progression. In particular, sulfur metabolism is redirected during the G1-S transition, and glutathione levels periodically change over the cell cycle with a peak in late S phase. A lack of glutathione perturbs cell size by uncoupling cell growth and division through dysregulation of KefB, a K+/H+ antiporter. Overall, we here describe the impact of the C. crescentus cell cycle progression on metabolism, and in turn relate glutathione and potassium homeostasis to timely cell division.
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Affiliation(s)
- Johannes Hartl
- ETH Zurich, Institute of Microbiology, Zurich, Switzerland.
| | - Patrick Kiefer
- ETH Zurich, Institute of Microbiology, Zurich, Switzerland
| | | | | | - Fabian Meyer
- ETH Zurich, Institute of Microbiology, Zurich, Switzerland
| | - Thomas Vonderach
- ETH Zurich, Laboratory of Inorganic Chemistry, Zurich, Switzerland
| | - Bodo Hattendorf
- ETH Zurich, Laboratory of Inorganic Chemistry, Zurich, Switzerland
| | - Urs Jenal
- Biozentrum of the University of Basel, Basel, Switzerland
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18
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Heat Stress-Induced Metabolic Remodeling in Saccharomyces cerevisiae. Metabolites 2019; 9:metabo9110266. [PMID: 31694329 PMCID: PMC6918159 DOI: 10.3390/metabo9110266] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 10/25/2019] [Accepted: 10/30/2019] [Indexed: 01/22/2023] Open
Abstract
Yeast cells respond to heat stress by remodeling their gene expression, resulting in the changes of the corresponding proteins and metabolites. Compared to the intensively investigated transcriptome and proteome, the metabolic response to heat stress is not sufficiently characterized. Mitochondria have been recognized to play an essential role in heat stress tolerance. Given the compartmentalization of the cell, it is not clear if the heat stress-induced metabolic response occurs in mitochondria or in the cytosol. Therefore, a compartment-specific metabolite analysis was performed to analyze the heat stress-induced metabolic response in mitochondria and the cytoplasm. In this work, the isolated mitochondria and the cytoplasm of yeast cells grown at permissive temperature and cells adapting to heat stress were subjected to mass spectrometry-based metabolomics. Over a hundred metabolites could be identified, covering amino acid metabolism, energy metabolism, arginine metabolism, purine and pyrimidine metabolism, and others. Highly accumulated citrulline and reduced arginine suggested remodeled arginine metabolism. A stable isotope-labeled experiment was performed to analyze the heat stress-induced metabolic remodeling of the arginine metabolism, identifying activated de novo ornithine biosynthesis to support arginine and spermidine synthesis. The short-term increased spermidine and trehalose suggest their important roles as heat stress markers. These data provide metabolic clues of heat stress-induced metabolic remodeling, which helps in understanding the heat stress response.
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19
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Richts B, Rosenberg J, Commichau FM. A Survey of Pyridoxal 5'-Phosphate-Dependent Proteins in the Gram-Positive Model Bacterium Bacillus subtilis. Front Mol Biosci 2019; 6:32. [PMID: 31134210 PMCID: PMC6522883 DOI: 10.3389/fmolb.2019.00032] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 04/18/2019] [Indexed: 11/13/2022] Open
Abstract
The B6 vitamer pyridoxal 5′-phosphate (PLP) is a co-factor for proteins and enzymes that are involved in diverse cellular processes. Therefore, PLP is essential for organisms from all kingdoms of life. Here we provide an overview about the PLP-dependent proteins from the Gram-positive soil bacterium Bacillus subtilis. Since B. subtilis serves as a model system in basic research and as a production host in industry, knowledge about the PLP-dependent proteins could facilitate engineering the bacteria for biotechnological applications. The survey revealed that the majority of the PLP-dependent proteins are involved in metabolic pathways like amino acid biosynthesis and degradation, biosynthesis of antibacterial compounds, utilization of nucleotides as well as in iron and carbon metabolism. Many PLP-dependent proteins participate in de novo synthesis of the co-factors biotin, folate, heme, and NAD+ as well as in cell wall metabolism, tRNA modification, regulation of gene expression, sporulation, and biofilm formation. A surprisingly large group of PLP-dependent proteins (29%) belong to the group of poorly characterized proteins. This review underpins the need to characterize the PLP-dependent proteins of unknown function to fully understand the “PLP-ome” of B. subtilis.
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Affiliation(s)
- Björn Richts
- Department of General Microbiology, University of Goettingen, Göttingen, Germany
| | - Jonathan Rosenberg
- Department of General Microbiology, University of Goettingen, Göttingen, Germany
| | - Fabian M Commichau
- Department of General Microbiology, University of Goettingen, Göttingen, Germany
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20
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Barriers to 3-Hydroxypropionate-Dependent Growth of Rhodobacter sphaeroides by Distinct Disruptions of the Ethylmalonyl Coenzyme A Pathway. J Bacteriol 2019; 201:JB.00556-18. [PMID: 30455284 DOI: 10.1128/jb.00556-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 11/05/2018] [Indexed: 11/20/2022] Open
Abstract
Rhodobacter sphaeroides is able to use 3-hydroxypropionate as the sole carbon source through the reductive conversion of 3-hydroxypropionate to propionyl coenzyme A (propionyl-CoA). The ethylmalonyl-CoA pathway is not required in this process because a crotonyl-CoA carboxylase/reductase (Ccr)-negative mutant still grew with 3-hydroxypropionate. Much to our surprise, a mutant defective for another specific enzyme of the ethylmalonyl-CoA pathway, mesaconyl-CoA hydratase (Mch), lost its ability for 3-hydroxypropionate-dependent growth. Interestingly, the Mch-deficient mutant was rescued either by introducing an additional ccr in-frame deletion that resulted in the blockage of an earlier step in the pathway or by heterologously expressing a gene encoding a thioesterase (YciA) that can act on several CoA intermediates of the ethylmalonyl-CoA pathway. The mch mutant expressing yciA metabolized only less than half of the 3-hydroxypropionate supplied, and over 50% of that carbon was recovered in the spent medium as free acids of the key intermediates mesaconyl-CoA and methylsuccinyl-CoA. A gradual increase in growth inhibition due to the blockage of consecutive steps of the ethylmalonyl-CoA pathway by gene deletions suggests that the growth defects were due to the titration of free CoA and depletion of the CoA pool in the cell rather than to detrimental effects arising from the accumulation of a specific metabolite. Recovery of carbon in mesaconate for the wild-type strain expressing yciA demonstrated that carbon flux through the ethylmalonyl-CoA pathway occurs during 3-hydroxypropionate-dependent growth. A possible role of the ethylmalonyl-CoA pathway is proposed that functions outside its known role in providing tricarboxylic acid intermediates during acetyl-CoA assimilation.IMPORTANCE Mutant analysis is an important tool utilized in metabolic studies to understand which role a particular pathway might have under certain growth conditions for a given organism. The importance of the enzyme and of the pathway in which it participates is discretely linked to the resulting phenotype observed after mutation of the corresponding gene. This work highlights the possibility of incorrectly interpreting mutant growth results that are based on studying a single unit (gene and encoded enzyme) of a metabolic pathway rather than the pathway in its entirety. This work also hints at the possibility of using an enzyme as a drug target although the enzyme may participate in a nonessential pathway and still be detrimental to the cell when inhibited.
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21
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Sander T, Farke N, Diehl C, Kuntz M, Glatter T, Link H. Allosteric Feedback Inhibition Enables Robust Amino Acid Biosynthesis in E. coli by Enforcing Enzyme Overabundance. Cell Syst 2019; 8:66-75.e8. [PMID: 30638812 PMCID: PMC6345581 DOI: 10.1016/j.cels.2018.12.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 10/08/2018] [Accepted: 12/10/2018] [Indexed: 02/06/2023]
Abstract
Microbes must ensure robust amino acid metabolism in the face of external and internal perturbations. This robustness is thought to emerge from regulatory interactions in metabolic and genetic networks. Here, we explored the consequences of removing allosteric feedback inhibition in seven amino acid biosynthesis pathways in Escherichia coli (arginine, histidine, tryptophan, leucine, isoleucine, threonine, and proline). Proteome data revealed that enzyme levels decreased in five of the seven dysregulated pathways. Despite that, flux through the dysregulated pathways was not limited, indicating that enzyme levels are higher than absolutely needed in wild-type cells. We showed that such enzyme overabundance renders the arginine, histidine, and tryptophan pathways robust against perturbations of gene expression, using a metabolic model and CRISPR interference experiments. The results suggested a sensitive interaction between allosteric feedback inhibition and enzyme-level regulation that ensures robust yet efficient biosynthesis of histidine, arginine, and tryptophan in E. coli. Amino acid biosynthesis enzymes do not normally operate at maximum capacity Allosteric feedback inhibition ensures that enzymes are overabundant Enzyme overabundance provides robustness against decreases in gene expression
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Affiliation(s)
- Timur Sander
- Max Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Niklas Farke
- Max Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Christoph Diehl
- Max Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Michelle Kuntz
- Max Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Timo Glatter
- Max Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Hannes Link
- Max Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany.
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22
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Rudroff F. Whole-cell based synthetic enzyme cascades-light and shadow of a promising technology. Curr Opin Chem Biol 2018; 49:84-90. [PMID: 30458384 DOI: 10.1016/j.cbpa.2018.10.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/05/2018] [Accepted: 10/15/2018] [Indexed: 01/16/2023]
Abstract
Mimicking Nature by biocatalytic cascade reactions in a whole-cell environment is a revolutionary development in multistep synthesis for the production of bulk and fine chemicals. In the past decade, several proof of concept success stories demonstrated the power of those synthetic cascades and paved the road for future industrial applications. Although enzymes and their promiscuity are best suited to construct such artificial pathways, the complexity and the lack of understanding of the cellular machinery slowed down this progress significantly. In this review, recent achievements in the field of whole-cell biocatalysis are described, challenges and hidden traps that have to be overcome are depicted, and strategies are illustrated how to increase overall cascade productivity.
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Affiliation(s)
- Florian Rudroff
- TU Wien, Institute of Applied Synthetic Chemistry, Getreidemarkt 9, 163-OC, 1060 Vienna, Austria.
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23
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de Crécy-Lagard V, Haas D, Hanson AD. Newly-discovered enzymes that function in metabolite damage-control. Curr Opin Chem Biol 2018; 47:101-108. [PMID: 30268903 DOI: 10.1016/j.cbpa.2018.09.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 08/19/2018] [Accepted: 09/11/2018] [Indexed: 01/26/2023]
Abstract
Enzymes of unknown function are estimated to make up around 25% of the sequenced proteome. In the past decade, over 20 conserved families have been shown to function in the metabolism of 'damaged' or abnormal metabolites that are wasteful and often toxic. These newly discovered damage-control enzymes either repair or inactivate the offending metabolites, or pre-empt their formation in the first place. Comparative genomics has been of prime importance in predicting the functions of damage-control enzymes and in guiding the biochemical and genetic tests required to validate these functions.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA; Genetics Institute, University of Florida, Gainesville, FL, USA.
| | - Drago Haas
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
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24
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Becker-Kettern J, Paczia N, Conrotte JF, Zhu C, Fiehn O, Jung PP, Steinmetz LM, Linster CL. NAD(P)HX repair deficiency causes central metabolic perturbations in yeast and human cells. FEBS J 2018; 285:3376-3401. [PMID: 30098110 DOI: 10.1111/febs.14631] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/20/2018] [Accepted: 08/08/2018] [Indexed: 12/20/2022]
Abstract
NADHX and NADPHX are hydrated and redox inactive forms of the NADH and NADPH cofactors, known to inhibit several dehydrogenases in vitro. A metabolite repair system that is conserved in all domains of life and that comprises the two enzymes NAD(P)HX dehydratase and NAD(P)HX epimerase, allows reconversion of both the S- and R-epimers of NADHX and NADPHX to the normal cofactors. An inherited deficiency in this system has recently been shown to cause severe neurometabolic disease in children. Although evidence for the presence of NAD(P)HX has been obtained in plant and human cells, little is known about the mechanism of formation of these derivatives in vivo and their potential effects on cell metabolism. Here, we show that NAD(P)HX dehydratase deficiency in yeast leads to an important, temperature-dependent NADHX accumulation in quiescent cells with a concomitant depletion of intracellular NAD+ and serine pools. We demonstrate that NADHX potently inhibits the first step of the serine synthesis pathway in yeast. Human cells deficient in the NAD(P)HX dehydratase also accumulated NADHX and showed decreased viability. In addition, those cells consumed more glucose and produced more lactate, potentially indicating impaired mitochondrial function. Our results provide first insights into how NADHX accumulation affects cellular functions and pave the way for a better understanding of the mechanism(s) underlying the rapid and severe neurodegeneration leading to early death in NADHX repair-deficient children.
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Affiliation(s)
- Julia Becker-Kettern
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Nicole Paczia
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Jean-François Conrotte
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Chenchen Zhu
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Oliver Fiehn
- NIH West Coast Metabolomics Center, University of California Davis, CA, USA
| | - Paul P Jung
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.,Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Genetics, Stanford University School of Medicine, CA, USA
| | - Carole L Linster
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
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25
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Jaiswal D, Prasannan CB, Hendry JI, Wangikar PP. SWATH Tandem Mass Spectrometry Workflow for Quantification of Mass Isotopologue Distribution of Intracellular Metabolites and Fragments Labeled with Isotopic 13C Carbon. Anal Chem 2018; 90:6486-6493. [PMID: 29712418 DOI: 10.1021/acs.analchem.7b05329] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Accurate quantification of mass isotopologue distribution (MID) of metabolites is a prerequisite for 13C-metabolic flux analysis. Currently used mass spectrometric (MS) techniques based on multiple reaction monitoring (MRM) place limitations on the number of MIDs that can be analyzed in a single run. Moreover, the deconvolution step results in amplification of error. Here, we demonstrate that SWATH MS/MS, a data independent acquisition (DIA) technique allows quantification of a large number of precursor and product MIDs in a single run. SWATH sequentially fragments all precursor ions in stacked mass isolation windows. Co-fragmentation of all precursor isotopologues in a single SWATH window yields higher sensitivity enabling quantification of MIDs of fragments with low abundance and lower systematic and random errors. We quantify the MIDs of 53 precursor and product ions corresponding to 19 intracellular metabolites from a dynamic 13C-labeling of a model cyanobacterium, Synechococcus sp. PCC 7002. The use of product MIDs resulted in an improved precision of many measured fluxes compared to when only precursor MIDs were used for flux analysis. The approach is truly untargeted and allows additional metabolites to be quantified from the same data.
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Affiliation(s)
- Damini Jaiswal
- Department of Chemical Engineering , Indian Institute of Technology Bombay , Powai , Mumbai 400076 , India
| | - Charulata B Prasannan
- Department of Chemical Engineering , Indian Institute of Technology Bombay , Powai , Mumbai 400076 , India.,DBT-Pan IIT Center for Bioenergy , Indian Institute of Technology Bombay , Powai , Mumbai 400076 , India
| | - John I Hendry
- Department of Chemical Engineering , Indian Institute of Technology Bombay , Powai , Mumbai 400076 , India
| | - Pramod P Wangikar
- Department of Chemical Engineering , Indian Institute of Technology Bombay , Powai , Mumbai 400076 , India.,DBT-Pan IIT Center for Bioenergy , Indian Institute of Technology Bombay , Powai , Mumbai 400076 , India.,Wadhwani Research Center for Bioengineering , Indian Institute of Technology Bombay , Powai , Mumbai 400076 , India
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26
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Campbell K, Herrera-Dominguez L, Correia-Melo C, Zelezniak A, Ralser M. Biochemical principles enabling metabolic cooperativity and phenotypic heterogeneity at the single cell level. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.coisb.2017.12.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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27
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Campbell K, Xia J, Nielsen J. The Impact of Systems Biology on Bioprocessing. Trends Biotechnol 2017; 35:1156-1168. [DOI: 10.1016/j.tibtech.2017.08.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 12/16/2022]
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28
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Transposon Sequencing Uncovers an Essential Regulatory Function of Phosphoribulokinase for Methylotrophy. Curr Biol 2017; 27:2579-2588.e6. [PMID: 28823675 DOI: 10.1016/j.cub.2017.07.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/04/2017] [Accepted: 07/11/2017] [Indexed: 11/21/2022]
Abstract
Methylotrophy is the ability of organisms to grow at the expense of reduced one-carbon compounds, such as methanol or methane. Here, we used transposon sequencing combining hyper-saturated transposon mutagenesis with high-throughput sequencing to define the essential methylotrophy genome of Methylobacterium extorquens PA1, a model methylotroph. To distinguish genomic regions required for growth only on methanol from general required genes, we contrasted growth on methanol with growth on succinate, a non-methylotrophic reference substrate. About 500,000 insertions were mapped for each condition, resulting in a median insertion distance of five base pairs. We identified 147 genes and 76 genes as specific for growth on methanol and succinate, respectively, and a set of 590 genes as required under both growth conditions. For the integration of metabolic functions, we reconstructed a genome-scale metabolic model and performed in silico essentiality analysis. In total, the approach uncovered 95 genes not previously described as crucial for methylotrophy, including genes involved in respiration, carbon metabolism, transport, and regulation. Strikingly, regardless of the absence of the Calvin cycle in the methylotroph, the screen led to the identification of the gene for phosphoribulokinase as essential during growth on methanol, but not during growth on succinate. Genetic experiments in addition to metabolomics and proteomics revealed that phosphoribulokinase serves a key regulatory function. Our data support a model according to which ribulose-1,5-bisphosphate is an essential metabolite that induces a transcriptional regulator driving one-carbon assimilation.
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