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Chilamakuru NB, Vn AD, G VB, Pallaprolu N, Dande A, Nair D, Pemmadi RV, Reddy Y P, Peraman R. New synergistic benzoquinone scaffolds as inhibitors of mycobacterial cytochrome bc1 complex to treat multi-drug resistant tuberculosis. Eur J Med Chem 2024; 272:116479. [PMID: 38733886 DOI: 10.1016/j.ejmech.2024.116479] [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: 03/18/2024] [Revised: 04/25/2024] [Accepted: 05/04/2024] [Indexed: 05/13/2024]
Abstract
Through a comprehensive molecular docking study, a unique series of naphthoquinones clubbed azetidinone scaffolds was arrived with promising binding affinity to Mycobacterial Cytbc1 complex, a drug target chosen to kill multi-drug resistant Mycobacterium tuberculosis (MDR-Mtb). Five compounds from series-2, 2a, 2c, 2g, 2h, and 2j, showcased significant in vitro anti-tubercular activities against Mtb H37Rv and MDR clinical isolates. Further, synergistic studies of these compounds in combination with INH and RIF revealed a potent bactericidal effect of compound 2a at concentration of 0.39 μg/mL, and remaining (2c, 2g, 2h, and 2j) at 0.78 μg/mL. Exploration into the mechanism study through chemo-stress assay and proteome profiling uncovered the down-regulation of key proteins of electron-transport chain and Cytbc1 inhibition pathway. Metabolomics corroborated these proteome findings, and heightened further understanding of the underlying mechanism. Notably, in vitro and in vivo animal toxicity studies demonstrated minimal toxicity, thus underscoring the potential of these compounds as promising anti-TB agents in combination with RIF and INH. These active compounds adhered to Lipinski's Rule of Five, indicating the suitability of these compounds for drug development. Particular significance of molecules NQ02, 2a, and 2h, which have been patented (Published 202141033473).
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Affiliation(s)
- Naresh Babu Chilamakuru
- Research Scholar, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India; RERDS-CPR, Raghavendra Institute of Pharmaceutical Education and Research Campus, Ananthapuramu, 515721, Andhra Pradesh, India
| | - Azger Dusthackeer Vn
- ICMR-National Institute for Research in Tuberculosis (NIRT), Chennai, 600031, Tamil Nadu, India
| | - Varadaraj Bhat G
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Nikhil Pallaprolu
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur 844102, Bihar, India
| | - Aishwarya Dande
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur 844102, Bihar, India
| | - Dina Nair
- ICMR-National Institute for Research in Tuberculosis (NIRT), Chennai, 600031, Tamil Nadu, India
| | - Raghuveer Varma Pemmadi
- RERDS-CPR, Raghavendra Institute of Pharmaceutical Education and Research Campus, Ananthapuramu, 515721, Andhra Pradesh, India; Department of Pharmaceutical Chemistry, A.K.R.G College of Pharmacy, Nallajerla, Andhra Pradesh 534112.
| | - Padmanabha Reddy Y
- RERDS-CPR, Raghavendra Institute of Pharmaceutical Education and Research Campus, Ananthapuramu, 515721, Andhra Pradesh, India
| | - Ramalingam Peraman
- RERDS-CPR, Raghavendra Institute of Pharmaceutical Education and Research Campus, Ananthapuramu, 515721, Andhra Pradesh, India; Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur 844102, Bihar, India.
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2
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Sao Emani C, Reiling N. The efflux pumps Rv1877 and Rv0191 play differential roles in the protection of Mycobacterium tuberculosis against chemical stress. Front Microbiol 2024; 15:1359188. [PMID: 38516013 PMCID: PMC10956863 DOI: 10.3389/fmicb.2024.1359188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/12/2024] [Indexed: 03/23/2024] Open
Abstract
Background It was previously shown that GlnA3sc enabled Streptomyces coelicolor to survive in excess polyamines. However, subsequent studies revealed that Rv1878, the corresponding Mycobacterium tuberculosis (M.tb) ortholog, was not essential for the detoxification of spermine (Spm), in M.tb. On the other hand, the multi-drug efflux pump Rv1877 was previously shown to enable export of a wide range of compounds, while Rv0191 was shown to be more specific to chloramphenicol. Rationale Therefore, we first wanted to determine if detoxification of Spm by efflux can be achieved by any efflux pump, or if that was dependent upon the function of the pump. Next, since Rv1878 was found not to be essential for the detoxification of Spm, we sought to follow-up on the investigation of the physiological role of Rv1878 along with Rv1877 and Rv0191. Approach To evaluate the specificity of efflux pumps in the mycobacterial tolerance to Spm, we generated unmarked ∆rv1877 and ∆rv0191 M.tb mutants and evaluated their susceptibility to Spm. To follow up on the investigation of any other physiological roles they may have, we characterized them along with the ∆rv1878 M.tb mutant. Results The ∆rv1877 mutant was sensitive to Spm stress, while the ∆rv0191 mutant was not. On the other hand, the ∆rv1878 mutant grew better than the wild-type during iron starvation yet was sensitive to cell wall stress. The proteins Rv1877 and Rv1878 seemed to play physiological roles during hypoxia and acidic stress. Lastly, the ∆rv0191 mutant was the only mutant that was sensitive to oxidative stress. Conclusion The multidrug MFS-type efflux pump Rv1877 is required for Spm detoxification, as opposed to Rv0191 which seems to play a more specific role. Moreover, Rv1878 seems to play a role in the regulation of iron homeostasis and the reconstitution of the cell wall of M.tb. On the other hand, the sensitivity of the ∆rv0191 mutant to oxidative stress, suggests that Rv0191 may be responsible for the transport of low molecular weight thiols.
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Affiliation(s)
- Carine Sao Emani
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Norbert Reiling
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
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3
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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: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [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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4
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Ncube P, Bagheri B, Goosen WJ, Miller MA, Sampson SL. Evidence, Challenges, and Knowledge Gaps Regarding Latent Tuberculosis in Animals. Microorganisms 2022; 10:microorganisms10091845. [PMID: 36144447 PMCID: PMC9503773 DOI: 10.3390/microorganisms10091845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 01/30/2023] Open
Abstract
Mycobacterium bovis and other Mycobacterium tuberculosis complex (MTBC) pathogens that cause domestic animal and wildlife tuberculosis have received considerably less attention than M. tuberculosis, the primary cause of human tuberculosis (TB). Human TB studies have shown that different stages of infection can exist, driven by host–pathogen interactions. This results in the emergence of heterogeneous subpopulations of mycobacteria in different phenotypic states, which range from actively replicating (AR) cells to viable but slowly or non-replicating (VBNR), viable but non-culturable (VBNC), and dormant mycobacteria. The VBNR, VBNC, and dormant subpopulations are believed to underlie latent tuberculosis (LTB) in humans; however, it is unclear if a similar phenomenon could be happening in animals. This review discusses the evidence, challenges, and knowledge gaps regarding LTB in animals, and possible host–pathogen differences in the MTBC strains M. tuberculosis and M. bovis during infection. We further consider models that might be adapted from human TB research to investigate how the different phenotypic states of bacteria could influence TB stages in animals. In addition, we explore potential host biomarkers and mycobacterial changes in the DosR regulon, transcriptional sigma factors, and resuscitation-promoting factors that may influence the development of LTB.
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5
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Krysenko S, Wohlleben W. Polyamine and Ethanolamine Metabolism in Bacteria as an Important Component of Nitrogen Assimilation for Survival and Pathogenicity. Med Sci (Basel) 2022; 10:40. [PMID: 35997332 PMCID: PMC9397018 DOI: 10.3390/medsci10030040] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
Nitrogen is an essential element required for bacterial growth. It serves as a building block for the biosynthesis of macromolecules and provides precursors for secondary metabolites. Bacteria have developed the ability to use various nitrogen sources and possess two enzyme systems for nitrogen assimilation involving glutamine synthetase/glutamate synthase and glutamate dehydrogenase. Microorganisms living in habitats with changeable availability of nutrients have developed strategies to survive under nitrogen limitation. One adaptation is the ability to acquire nitrogen from alternative sources including the polyamines putrescine, cadaverine, spermidine and spermine, as well as the monoamine ethanolamine. Bacterial polyamine and monoamine metabolism is not only important under low nitrogen availability, but it is also required to survive under high concentrations of these compounds. Such conditions can occur in diverse habitats such as soil, plant tissues and human cells. Strategies of pathogenic and non-pathogenic bacteria to survive in the presence of poly- and monoamines offer the possibility to combat pathogens by using their capability to metabolize polyamines as an antibiotic drug target. This work aims to summarize the knowledge on poly- and monoamine metabolism in bacteria and its role in nitrogen metabolism.
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Affiliation(s)
- Sergii Krysenko
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Department of Microbiology and Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany;
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, 72076 Tübingen, Germany
| | - Wolfgang Wohlleben
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Department of Microbiology and Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany;
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, 72076 Tübingen, Germany
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6
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Mycolicibacter acidiphilus sp. nov., an extremely acid-tolerant member of the genus Mycolicibacter. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005419] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A nonmotile, facultatively anaerobic and rod-shaped bacterial strain, designated M1T was isolated from a bioreactor being operated at pH ~2 at Brisbane, Australia. Colonies appeared to be convex and white. Phylogenetic analysis of its genome revealed an affiliation with the genus
Mycolicibacter
and its closest species based on 16S rRNA gene analysis were
Mycolicibacter algericus
DSM 45454T (98.8 % similarity) and
Mycolicibacter terrae
CIP 104321T (98.8 %) with which strain M1T shared average nucleotide identity of 81.2 % and digital DNA–DNA hybridization similarity of 23.8 %. Strain M1T grew optimally at 0 % NaCl, at pH 6 and at between 30–33 °C. The polar lipid profile of strain M1T consisted of diphosphatidylglycerol, aminophosphoglycolipid, phosphatidylcholine, phospholipid, aminolipid, phosphoglyolipid, phosphatidylglycerol, two unidentified glycolipids and four unidentified lipids. The dominant cellular fatty acids (>10 %) were C16 : 0 and C18 : 1
ω9c and summed feature 7 (C19 : 1
ω7c and/or C19 : 1
ω6c). The DNA G+C content of strain M1T was 69.1 mol%. Based on in silico phylogenomic analysis coupled with physiological and chemotaxonomic characterizations, we classify strain M1T as representing a novel species within the genus
Mycolicibacter
, for which the name Mycolicibacter acidiphilus nov. is proposed. The type strain is M1T (=MCCC 1H00416T=KCTC 49392T).
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7
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Chen Z, Li J, Wan Y, Bai R, Wang W, Gao X, Li D, Hu Q, Li Y, Ruan BH. Rapid High-Throughput Assay Identified Gemcitabine and Derivatives As Potent Inhibitors Against Multidrug-Resistant Staphylococcus aureus. Assay Drug Dev Technol 2022; 20:175-182. [DOI: 10.1089/adt.2022.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Zhao Chen
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, China
| | - Jinxiu Li
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, China
| | - Yue Wan
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, China
| | - Ruisong Bai
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, China
| | - Wenjuan Wang
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, China
| | - Xuan Gao
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, China
| | - Di Li
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, China
| | - Qingfeng Hu
- Clinical Diagnostic Lab, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Yong Li
- Hangzhou Simbiospharma Co. Ltd., Hangzhou, China
| | - Benfang Helen Ruan
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, China
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8
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Dawson CC, Cummings JE, Starkey JM, Slayden RA. Discovery of a novel type IIb RelBE toxin-antitoxin system in Mycobacterium tuberculosis defined by co-regulation with an antisense RNA. Mol Microbiol 2022; 117:1419-1433. [PMID: 35526138 PMCID: PMC9325379 DOI: 10.1111/mmi.14917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 04/30/2022] [Accepted: 05/05/2022] [Indexed: 11/29/2022]
Abstract
Toxin‐antitoxin loci regulate adaptive responses to stresses associated with the host environment and drug exposure. Phylogenomic studies have shown that Mycobacterium tuberculosis encodes a naturally expanded type II toxin‐antitoxin system, including ParDE/RelBE superfamily members. Type II toxins are presumably regulated exclusively through protein–protein interactions with type II antitoxins. However, experimental observations in M. tuberculosis indicated that additional control mechanisms regulate RelBE2 type II loci under host‐associated stress conditions. Herein, we describe for the first time a novel antisense RNA, termed asRelE2, that co‐regulates RelE2 production via targeted processing by the Mtb RNase III, Rnc. We find that convergent expression of this coding‐antisense hybrid TA locus, relBE2‐asrelE2, is controlled in a cAMP‐dependent manner by the essential cAMP receptor protein transcription factor, Crp, in response to the host‐associated stresses of low pH and nutrient limitation. Ex vivo survival studies with relE2 and asrelE2 knockout strains showed that RelE2 contributes to Mtb survival in activated macrophages and low pH to nutrient limitation. To our knowledge, this is the first report of a novel tripartite type IIb TA loci and antisense post‐transcriptional regulation of a type II TA loci.
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Affiliation(s)
- Clinton C Dawson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins.,Endolytix Technology, Inc. Beverly, 01915
| | - Jason E Cummings
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins
| | - Julie M Starkey
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins
| | - Richard A Slayden
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins
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9
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3D architecture and structural flexibility revealed in the subfamily of large glutamate dehydrogenases by a mycobacterial enzyme. Commun Biol 2021; 4:684. [PMID: 34083757 PMCID: PMC8175468 DOI: 10.1038/s42003-021-02222-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 05/14/2021] [Indexed: 11/16/2022] Open
Abstract
Glutamate dehydrogenases (GDHs) are widespread metabolic enzymes that play key roles in nitrogen homeostasis. Large glutamate dehydrogenases composed of 180 kDa subunits (L-GDHs180) contain long N- and C-terminal segments flanking the catalytic core. Despite the relevance of L-GDHs180 in bacterial physiology, the lack of structural data for these enzymes has limited the progress of functional studies. Here we show that the mycobacterial L-GDH180 (mL-GDH180) adopts a quaternary structure that is radically different from that of related low molecular weight enzymes. Intersubunit contacts in mL-GDH180 involve a C-terminal domain that we propose as a new fold and a flexible N-terminal segment comprising ACT-like and PAS-type domains that could act as metabolic sensors for allosteric regulation. These findings uncover unique aspects of the structure-function relationship in the subfamily of L-GDHs. Lázaro et. al. report the first 3D structure of a large glutamate dehydrogenase (L-GDH), the one corresponding to the Mycobacterium smegmatis enzyme composed of 180 kDa subunits (mL-GDH180), obtained by X-ray crystallography and cryo-electron microscopy. This structure reveals that mL-GDH180 assembles as tetramers with the N- and C-terminal domains being involved in inter-subunit contacts and unveils unique features of the subfamily of L-GDHs.
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10
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Yelamanchi SD, Surolia A. Targeting amino acid metabolism of Mycobacterium tuberculosis for developing inhibitors to curtail its survival. IUBMB Life 2021; 73:643-658. [PMID: 33624925 DOI: 10.1002/iub.2455] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 12/31/2020] [Accepted: 12/31/2020] [Indexed: 12/29/2022]
Abstract
Tuberculosis caused by the bacterium, Mycobacterium tuberculosis (Mtb), continues to remain one of the most devastating infectious diseases afflicting humans. Although there are several drugs for treating tuberculosis available currently, the emergence of the drug resistant forms of this pathogen has made its treatment and eradication a challenging task. While the replication machinery, protein synthesis and cell wall biogenesis of Mtb have been targeted often for anti-tubercular drug development a number of essential metabolic pathways crucial to its survival have received relatively less attention. In this context a number of amino acid biosynthesis pathways have recently been shown to be essential for the survival and pathogenesis of Mtb. Many of these pathways and or their key enzymes homologs are absent in humans hence they could be harnessed for anti-tubercular drug development. In this review, we describe comprehensively the amino acid metabolic pathways essential in Mtb and the key enzymes involved therein that are being investigated for developing inhibitors that compromise the survival and pathogenesis caused by this pathogen.
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Affiliation(s)
| | - Avadhesha Surolia
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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11
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Pisu D, Huang L, Grenier JK, Russell DG. Dual RNA-Seq of Mtb-Infected Macrophages In Vivo Reveals Ontologically Distinct Host-Pathogen Interactions. Cell Rep 2021; 30:335-350.e4. [PMID: 31940480 PMCID: PMC7032562 DOI: 10.1016/j.celrep.2019.12.033] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/31/2019] [Accepted: 12/10/2019] [Indexed: 12/13/2022] Open
Abstract
Dissecting the in vivo host-pathogen interplay is crucial to understanding the molecular mechanisms governing control or progression of intracellular infections. In this work, we explore the in vivo molecular dynamics of Mtb infection by performing dual RNA-seq on Mycobacterium tuberculosis-infected, ontogenetically distinct macrophage lineages isolated directly from murine lungs. We first define an in vivo signature of 180 genes specifically upregulated by Mtb in mouse lung macrophages, then we uncover a divergent transcriptional response of the bacteria between alveolar macrophages that appear to sustain Mtb growth through increased access to iron and fatty acids and interstitial macrophages that restrict Mtb growth through iron sequestration and higher levels of nitric oxide. We use an enrichment protocol for bacterial transcripts, which enables us to probe Mtb physiology at the host cell level in an in vivo environment, with broader application in understanding the infection dynamics of intracellular pathogens in general. In this study Pisu et al. performed dual RNA-seq on Mycobacterium tuberculosis-infected, ontogenetically distinct macrophage lineages isolated directly from infected murine lungs. The transcriptional response of host and bacteria diverged between alveolar macrophages that sustain Mtb growth and interstitial macrophages that restrict Mtb growth.
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Affiliation(s)
- Davide Pisu
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Lu Huang
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Jennifer K Grenier
- RNA Sequencing Core, Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - David G Russell
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
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12
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Bedaquiline reprograms central metabolism to reveal glycolytic vulnerability in Mycobacterium tuberculosis. Nat Commun 2020; 11:6092. [PMID: 33257709 PMCID: PMC7705017 DOI: 10.1038/s41467-020-19959-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/04/2020] [Indexed: 02/06/2023] Open
Abstract
The approval of bedaquiline (BDQ) for the treatment of tuberculosis has generated substantial interest in inhibiting energy metabolism as a therapeutic paradigm. However, it is not known precisely how BDQ triggers cell death in Mycobacterium tuberculosis (Mtb). Using 13C isotopomer analysis, we show that BDQ-treated Mtb redirects central carbon metabolism to induce a metabolically vulnerable state susceptible to genetic disruption of glycolysis and gluconeogenesis. Metabolic flux profiles indicate that BDQ-treated Mtb is dependent on glycolysis for ATP production, operates a bifurcated TCA cycle by increasing flux through the glyoxylate shunt, and requires enzymes of the anaplerotic node and methylcitrate cycle. Targeting oxidative phosphorylation (OXPHOS) with BDQ and simultaneously inhibiting substrate level phosphorylation via genetic disruption of glycolysis leads to rapid sterilization. Our findings provide insight into the metabolic mechanism of BDQ-induced cell death and establish a paradigm for the development of combination therapies that target OXPHOS and glycolysis.
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13
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Intracellular Mycobacterium tuberculosis Exploits Multiple Host Nitrogen Sources during Growth in Human Macrophages. Cell Rep 2020; 29:3580-3591.e4. [PMID: 31825837 PMCID: PMC6915324 DOI: 10.1016/j.celrep.2019.11.037] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 07/05/2019] [Accepted: 11/07/2019] [Indexed: 02/05/2023] Open
Abstract
Nitrogen metabolism of Mycobacterium tuberculosis (Mtb) is crucial for the survival of this important pathogen in its primary human host cell, the macrophage, but little is known about the source(s) and their assimilation within this intracellular niche. Here, we have developed 15N-flux spectral ratio analysis (15N-FSRA) to explore Mtb’s nitrogen metabolism; we demonstrate that intracellular Mtb has access to multiple amino acids in the macrophage, including glutamate, glutamine, aspartate, alanine, glycine, and valine; and we identify glutamine as the predominant nitrogen donor. Each nitrogen source is uniquely assimilated into specific amino acid pools, indicating compartmentalized metabolism during intracellular growth. We have discovered that serine is not available to intracellular Mtb, and we show that a serine auxotroph is attenuated in macrophages. This work provides a systems-based tool for exploring the nitrogen metabolism of intracellular pathogens and highlights the enzyme phosphoserine transaminase as an attractive target for the development of novel anti-tuberculosis therapies. Mycobacterium tuberculosis utilizes multiple amino acids as nitrogen sources in human macrophages 15N-FSRA tool identified the intracellular nitrogen sources Glutamine is the predominant nitrogen donor for M. tuberculosis Serine biosynthesis is essential for the survival of intracellular M. tuberculosis
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14
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Guallar-Garrido S, Campo-Pérez V, Sánchez-Chardi A, Luquin M, Julián E. Each Mycobacterium Requires a Specific Culture Medium Composition for Triggering an Optimized Immunomodulatory and Antitumoral Effect. Microorganisms 2020; 8:microorganisms8050734. [PMID: 32423030 PMCID: PMC7284523 DOI: 10.3390/microorganisms8050734] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/01/2020] [Accepted: 05/13/2020] [Indexed: 11/30/2022] Open
Abstract
Mycobacterium bovis bacillus Calmette-Guérin (BCG) remains the first treatment option for non-muscle-invasive bladder cancer (BC) patients. In research laboratories, M. bovis BCG is mainly grown in commercially available media supplemented with animal-derived agents that favor its growth, while biomass production for patient treatment is performed in Sauton medium which lacks animal-derived components. However, there is not a standardized formulation of Sauton medium, which could affect mycobacterial characteristics. Here, the impact of culture composition on the immunomodulatory and antitumor capacity of M. bovis BCG and Mycolicibacterium brumae, recently described as efficacious for BC treatment, has been addressed. Both mycobacteria grown in Middlebrook and different Sauton formulations, differing in the source of nitrogen and amount of carbon source, were studied. Our results indicate the relevance of culture medium composition on the antitumor effect triggered by mycobacteria, indicating that the most productive culture medium is not necessarily the formulation that provides the most favorable immunomodulatory profile and the highest capacity to inhibit BC cell growth. Strikingly, each mycobacterial species requires a specific culture medium composition to provide the best profile as an immunotherapeutic agent for BC treatment. Our results highlight the relevance of meticulousness in mycobacteria production, providing insight into the application of these bacteria in BC research.
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Affiliation(s)
- Sandra Guallar-Garrido
- Departament de Genètica i de Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; (S.G.-G.); (V.C.-P.); (M.L.)
| | - Víctor Campo-Pérez
- Departament de Genètica i de Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; (S.G.-G.); (V.C.-P.); (M.L.)
- Bacterial Infections and Antimicrobial Therapies group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Alejandro Sánchez-Chardi
- Servei de Microscòpia, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain;
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Marina Luquin
- Departament de Genètica i de Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; (S.G.-G.); (V.C.-P.); (M.L.)
| | - Esther Julián
- Departament de Genètica i de Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; (S.G.-G.); (V.C.-P.); (M.L.)
- Correspondence: ; Tel.: +34-93-5814870
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15
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Rizvi A, Shankar A, Chatterjee A, More TH, Bose T, Dutta A, Balakrishnan K, Madugulla L, Rapole S, Mande SS, Banerjee S, Mande SC. Rewiring of Metabolic Network in Mycobacterium tuberculosis During Adaptation to Different Stresses. Front Microbiol 2019; 10:2417. [PMID: 31736886 PMCID: PMC6828651 DOI: 10.3389/fmicb.2019.02417] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/07/2019] [Indexed: 12/15/2022] Open
Abstract
Metabolic adaptation of Mycobacterium tuberculosis (M. tuberculosis) to microbicidal intracellular environment of host macrophages is fundamental to its pathogenicity. However, an in-depth understanding of metabolic adjustments through key reaction pathways and networks is limited. To understand how such changes occur, we measured the cellular metabolome of M. tuberculosis subjected to four microbicidal stresses using liquid chromatography-mass spectrometric multiple reactions monitoring (LC-MRM/MS). Overall, 87 metabolites were identified. The metabolites best describing the separation between stresses were identified through multivariate analysis. The coupling of the metabolite measurements with existing genome-scale metabolic model, and using constraint-based simulation led to several new concepts and unreported observations in M. tuberculosis; such as (i) the high levels of released ammonia as an adaptive response to acidic stress was due to increased flux through L-asparaginase rather than urease activity; (ii) nutrient starvation-induced anaplerotic pathway for generation of TCA intermediates from phosphoenolpyruvate using phosphoenolpyruvate kinase; (iii) quenching of protons through GABA shunt pathway or sugar alcohols as possible mechanisms of early adaptation to acidic and oxidative stresses; and (iv) usage of alternate cofactors by the same enzyme as a possible mechanism of rewiring metabolic pathways to overcome stresses. Besides providing new leads and important nodes that can be used for designing intervention strategies, the study advocates the strength of applying flux balance analyses coupled with metabolomics to get a global picture of complex metabolic adjustments.
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Affiliation(s)
- Arshad Rizvi
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Arvind Shankar
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, India
| | | | | | - Tungadri Bose
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, India
| | - Anirban Dutta
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, India
| | - Kannan Balakrishnan
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Lavanya Madugulla
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | | | - Sharmila S Mande
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, India
| | - Sharmistha Banerjee
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
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16
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Ribosomal maturation factor (RimP) is essential for survival of nontuberculous mycobacteria Mycobacterium fortuitum under in vitro acidic stress conditions. 3 Biotech 2019; 9:127. [PMID: 30863706 DOI: 10.1007/s13205-019-1659-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 02/27/2019] [Indexed: 01/13/2023] Open
Abstract
Mycobacterium fortuitum is an important human pathogenic NTM, which resists stress conditions inside macrophages by exploitation of specific genes. TnphoA-based transposon mutagenesis was employed to identify membrane genes responsible for survival of M. fortuitum under such stress conditions. A library of about 450 mutants was constructed after electroporation of vector pRT291 into wild-type M. fortuitum. On the basis of blue color development and alkaline phosphatase assay, 20 mutants were shortlisted to screen for growth and survival under acidic stress at pH 6.5, 5.5, 4.5, and 3.5. Mutant MT727 showed reduced growth and survival under acidic stress. The acid susceptible mutant MT727 was subjected to other in vitro stress conditions prevalent inside macrophages including oxidative, nutrient starvation and nitrosative stress. However, the mutant showed no appreciable difference in growth behavior under oxidative, nutrient starvation and nitrosative stress conditions in comparison to the wild type. Genomic and bioinformatics analysis of MT727 led to identification of putative ribosomal maturation factor RimP of M. fortuitum to be affected by mutagenesis, showing closest homology to M. abscessus RimP. In silico functional interaction of RimP protein using STRING database showed its interaction with proteins of ribosomal assembly and maturation. Results indicate role of rimP gene in survival of M. fortuitum under acidic stress conditions which may be further explored for use as a potential drug target against M. fortuitum and other mycobacterial infections.
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17
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Lee JJ, Lim J, Gao S, Lawson CP, Odell M, Raheem S, Woo J, Kang SH, Kang SS, Jeon BY, Eoh H. Glutamate mediated metabolic neutralization mitigates propionate toxicity in intracellular Mycobacterium tuberculosis. Sci Rep 2018; 8:8506. [PMID: 29855554 PMCID: PMC5981324 DOI: 10.1038/s41598-018-26950-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 05/23/2018] [Indexed: 11/09/2022] Open
Abstract
Metabolic networks in biological systems are interconnected, such that malfunctioning parts can be corrected by other parts within the network, a process termed adaptive metabolism. Unlike Bacillus Calmette-Guérin (BCG), Mycobacterium tuberculosis (Mtb) better manages its intracellular lifestyle by executing adaptive metabolism. Here, we used metabolomics and identified glutamate synthase (GltB/D) that converts glutamine to glutamate (Q → E) as a metabolic effort used to neutralize cytoplasmic pH that is acidified while consuming host propionate carbon through the methylcitrate cycle (MCC). Methylisocitrate lyase, the last step of the MCC, is intrinsically downregulated in BCG, leading to obstruction of carbon flux toward central carbon metabolism, accumulation of MCC intermediates, and interference with GltB/D mediated neutralizing activity against propionate toxicity. Indeed, vitamin B12 mediated bypass MCC and additional supplement of glutamate led to selectively correct the phenotypic attenuation in BCG and restore the adaptive capacity of BCG to the similar level of Mtb phenotype. Collectively, a defective crosstalk between MCC and Q → E contributes to attenuation of intracellular BCG. Furthermore, GltB/D inhibition enhances the level of propionate toxicity in Mtb. Thus, these findings revealed a new adaptive metabolism and propose GltB/D as a synergistic target to improve the antimicrobial outcomes of MCC inhibition in Mtb.
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Affiliation(s)
- Jae Jin Lee
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Juhyeon Lim
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Shengjia Gao
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Christopher P Lawson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, United Kingdom
| | - Mark Odell
- School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln, LN6 7TS, United Kingdom.,Department of Life Sciences, Faculty of Science and Technology, University of Westminster, W1W 6UV, London, United Kingdom
| | - Saki Raheem
- Department of Life Sciences, Faculty of Science and Technology, University of Westminster, W1W 6UV, London, United Kingdom
| | - JeongIm Woo
- Department of Biomedical Laboratory Science, College of Health Science, Yonsei University, Wonju, 26493, Korea
| | - Sung-Ho Kang
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Shin-Seok Kang
- Chungbuk Veterinary Service Laboratory, 380-230, Chungju, Republic of Korea
| | - Bo-Young Jeon
- Department of Biomedical Laboratory Science, College of Health Science, Yonsei University, Wonju, 26493, Korea
| | - Hyungjin Eoh
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
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18
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Sao Emani C, Williams M, Van Helden P, Taylor M, Wiid I, Baker B. Gamma-glutamylcysteine protects ergothioneine-deficient Mycobacterium tuberculosis mutants against oxidative and nitrosative stress. Biochem Biophys Res Commun 2018; 495:174-178. [DOI: 10.1016/j.bbrc.2017.10.163] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 10/29/2017] [Indexed: 11/15/2022]
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19
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Abstract
Coevolution of pathogens and host has led to many metabolic strategies employed by intracellular pathogens to deal with the immune response and the scarcity of food during infection. Simply put, bacterial pathogens are just looking for food. As a consequence, the host has developed strategies to limit nutrients for the bacterium by containment of the intruder in a pathogen-containing vacuole and/or by actively depleting nutrients from the intracellular space, a process called nutritional immunity. Since metabolism is a prerequisite for virulence, such pathways could potentially be good targets for antimicrobial therapies. In this chapter, we review the current knowledge about the in vivo diet of Mycobacterium tuberculosis, with a focus on amino acid and cofactors, discuss evidence for the bacilli's nutritionally independent lifestyle in the host, and evaluate strategies for new chemotherapeutic interventions.
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20
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Silva WM, Folador EL, Soares SC, Souza GHMF, Santos AV, Sousa CS, Figueiredo H, Miyoshi A, Le Loir Y, Silva A, Azevedo V. Label-free quantitative proteomics of Corynebacterium pseudotuberculosis isolates reveals differences between Biovars ovis and equi strains. BMC Genomics 2017; 18:451. [PMID: 28595597 PMCID: PMC5463331 DOI: 10.1186/s12864-017-3835-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 05/31/2017] [Indexed: 11/24/2022] Open
Affiliation(s)
- Wanderson M Silva
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil.,INRA, UMR1253 STLO, 35042, Rennes, France.,Agrocampus Ouest, UMR1253 STLO, 35042, Rennes, France
| | - Edson L Folador
- Centro de Biotecnologia, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brasil
| | - Siomar C Soares
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil.,Departmento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brasil
| | - Gustavo H M F Souza
- Waters Corporation, Waters Technologies Brazil, MS Applications Laboratory, Alphaville, São Paulo, Brasil
| | - Agenor V Santos
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brasil
| | - Cassiana S Sousa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Henrique Figueiredo
- Escola de Veterinária, Aquavet, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Anderson Miyoshi
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Yves Le Loir
- INRA, UMR1253 STLO, 35042, Rennes, France.,Agrocampus Ouest, UMR1253 STLO, 35042, Rennes, France
| | - Artur Silva
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brasil
| | - Vasco Azevedo
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil.
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21
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PknG senses amino acid availability to control metabolism and virulence of Mycobacterium tuberculosis. PLoS Pathog 2017; 13:e1006399. [PMID: 28545104 PMCID: PMC5448819 DOI: 10.1371/journal.ppat.1006399] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 05/30/2017] [Accepted: 05/04/2017] [Indexed: 11/19/2022] Open
Abstract
Sensing and response to changes in nutrient availability are essential for the lifestyle of environmental and pathogenic bacteria. Serine/threonine protein kinase G (PknG) is required for virulence of the human pathogen Mycobacterium tuberculosis, and its putative substrate GarA regulates the tricarboxylic acid cycle in M. tuberculosis and other Actinobacteria by protein-protein binding. We sought to understand the stimuli that lead to phosphorylation of GarA, and the roles of this regulatory system in pathogenic and non-pathogenic bacteria. We discovered that M. tuberculosis lacking garA was severely attenuated in mice and macrophages and furthermore that GarA lacking phosphorylation sites failed to restore the growth of garA deficient M. tuberculosis in macrophages. Additionally we examined the impact of genetic disruption of pknG or garA upon protein phosphorylation, nutrient utilization and the intracellular metabolome. We found that phosphorylation of GarA requires PknG and depends on nutrient availability, with glutamate and aspartate being the main stimuli. Disruption of pknG or garA caused opposing effects on metabolism: a defect in glutamate catabolism or depletion of intracellular glutamate, respectively. Strikingly, disruption of the phosphorylation sites of GarA was sufficient to recapitulate defects caused by pknG deletion. The results suggest that GarA is a cellular target of PknG and the metabolomics data demonstrate that the function of this signaling system is in metabolic regulation. This function in amino acid homeostasis is conserved amongst the Actinobacteria and provides an example of the close relationship between metabolism and virulence.
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