1
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Devlin KL, Leach DT, Stratton KG, Lamichhane G, Lin VS, Beatty KE. Proteomic characterization of Mycobacterium tuberculosis subjected to carbon starvation. mSystems 2025; 10:e0153024. [PMID: 40231840 PMCID: PMC12090744 DOI: 10.1128/msystems.01530-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Accepted: 03/15/2025] [Indexed: 04/16/2025] Open
Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis (TB), the leading cause of infectious disease-related deaths worldwide. TB infections present on a spectrum from active to latent disease. In the human host, Mtb faces hostile environments, such as nutrient deprivation, hypoxia, and low pH. Under these conditions, Mtb can enter a dormant, but viable, state characterized by a lack of cell replication and increased resistance to antibiotics. Dormant Mtb poses a major challenge to curing infections and eradicating TB globally. We subjected Mtb mc26020 (ΔlysA and ΔpanCD), a double auxotrophic strain, to carbon starvation (CS), a culture condition that induces growth stasis and mimics environmental conditions associated with dormancy in vivo. We provide a detailed analysis of the proteome in CS compared to replicating samples. We observed extensive proteomic reprogramming, with 36% of identified proteins significantly altered in CS. Many enzymes involved in oxidative phosphorylation and lipid metabolism were retained or more abundant in CS. The cell wall biosynthetic machinery was present in CS, although numerous changes in the abundance of peptidoglycan, arabinogalactan, and mycolic acid biosynthetic enzymes likely result in pronounced remodeling of the cell wall. Many clinically approved anti-TB drugs target cell wall biosynthesis, and we found that these enzymes were largely retained in CS. Lastly, we compared our results to those of other dormancy models and propose that CS produces a physiologically distinct state of stasis compared to hypoxia in Mtb.IMPORTANCETuberculosis is a devastating human disease that kills over 1.2 million people a year. This disease is caused by the bacterial pathogen Mycobacterium tuberculosis (Mtb). Mtb excels at surviving in the human host by entering a non-replicating, dormant state. The current work investigated the proteomic changes that Mtb undergoes in response to carbon starvation, a culture condition that models dormancy. The authors found broad effects of carbon starvation on the proteome, with the relative abundance of 37% of proteins significantly altered. Protein changes related to cell wall biosynthesis, metabolism, and drug susceptibility are discussed. Proteins associated with a carbon starvation phenotype are identified, and results are compared to other dormancy models, including hypoxia.
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Affiliation(s)
- Kaylyn L. Devlin
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon, USA
| | - Damon T. Leach
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kelly G. Stratton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Gyanu Lamichhane
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Vivian S. Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kimberly E. Beatty
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon, USA
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2
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Biswas D, Benson S, Matunis A, Gebretsadik G, Wertz A, StPierre BJ, Schacht N, Yan Y, Gebremichael HY, Wong PK, Baughn AD, Medina SH. Lead Informed Artificial Intelligence Mining of Antitubercular Host Defense Peptides. Biomacromolecules 2025; 26:3167-3179. [PMID: 40310992 PMCID: PMC12076502 DOI: 10.1021/acs.biomac.5c00244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2025] [Revised: 04/16/2025] [Accepted: 04/18/2025] [Indexed: 05/03/2025]
Abstract
Identifying host defense peptides (HDPs) that are effective against drug-resistant infections is challenging due to their vast sequence space. Artificial intelligence (AI)-guided design can accelerate HDP discovery, but it traditionally requires large data sets to operationalize. We report an AI workflow that utilizes limited data sets (∼100 peptides) to uncover potent, selective, and safe HDPs by informing selection through lead candidate mutational scanning. This approach, referred to as Lead Informed Machine Interrogation of Therapeutic Sequences (LIMITS), is applied against the exemplary pathogen Mycobacterium tuberculosis. Experimental validation of predicted sequences shows nearly an order of magnitude improvement in potency, selectivity, and safety, relative to the initial template. Post hoc analysis suggests sequence length may be a unique and underappreciated driver of antitubercular HDP activity. These results demonstrate that, with continued development, the LIMITS approach can identify selective HDPs under data-limited conditions and elucidate structure-function-performance relationships previously hidden in biologic complexity.
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Affiliation(s)
- Diptomit Biswas
- Department
of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
- Huck
Institutes of the Life Sciences, Penn State
University, University Park, Pennsylvania 16802, United States
- Molecular,
Cellular, and Integrative Biosciences Graduate Program, Penn State University, University Park, Pennsylvania 16802, United States
| | - Sara Benson
- Department
of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
| | - Aidan Matunis
- Huck
Institutes of the Life Sciences, Penn State
University, University Park, Pennsylvania 16802, United States
- Department
of Biochemistry and Molecular Biology, Penn
State University, University Park, Pennsylvania 16802, United States
| | - Gebremichal Gebretsadik
- Department
of Microbiology and Immunology, University
of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Adam Wertz
- Department
of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
| | - Ben J. StPierre
- Department
of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
| | - Nathan Schacht
- Department
of Microbiology and Immunology, University
of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Yue Yan
- Department
of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
| | - Hanna Y. Gebremichael
- Department
of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
| | - Pak Kin Wong
- Department
of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
| | - Anthony D. Baughn
- Department
of Microbiology and Immunology, University
of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Scott H. Medina
- Department
of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
- Huck
Institutes of the Life Sciences, Penn State
University, University Park, Pennsylvania 16802, United States
- Molecular,
Cellular, and Integrative Biosciences Graduate Program, Penn State University, University Park, Pennsylvania 16802, United States
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3
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Singh DK, Ahmed M, Akter S, Shivanna V, Bucşan AN, Mishra A, Golden NA, Didier PJ, Doyle LA, Hall-Ursone S, Roy CJ, Arora G, Dick EJ, Jagannath C, Mehra S, Khader SA, Kaushal D. Prevention of tuberculosis in cynomolgus macaques by an attenuated Mycobacterium tuberculosis vaccine candidate. Nat Commun 2025; 16:1957. [PMID: 40000643 PMCID: PMC11861635 DOI: 10.1038/s41467-025-57090-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 02/11/2025] [Indexed: 02/27/2025] Open
Abstract
The need for novel vaccination strategies to control tuberculosis (TB) is underscored by the limited and variable efficacy of the currently licensed vaccine, Bacille Calmette-Guerin (BCG). SigH is critical for Mycobacterium tuberculosis (Mtb) to mitigate oxidative stress, and in its absence Mtb is unable to scavenge host oxidative/nitrosative bursts. The MtbΔsigH (ΔsigH) isogenic mutant induces signatures of the innate immunity in macrophages and protects rhesus macaques from a lethal Mtb challenge. To understand the immune mechanisms of protection via mucosal vaccination with ΔsigH, we employed the resistant cynomolgus macaque model; and our results show that ΔsigH vaccination significantly protects against lethal Mtb challenge in this species. ΔsigH-vaccinated macaques are devoid of granulomas and instead generate inducible bronchus associated lymphoid structures, and robust antigen-specific CD4+ and CD8+ T cell responses, driven by a hyper-immune, trained immunity-like phenotype in host macrophages with enhanced antigen presentation. Correlates of protection in ΔsigH-vaccinated macaques include gene signatures of T cell activation, IFNG production, including IFN-responsive, activated T cells, concomitant with IFNG production, and suppression of IDO+ Type I IFN-responsive macrophage recruitment. Thus, ΔsigH is a promising lead candidate for further development as an antitubercular vaccine.
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Affiliation(s)
- Dhiraj K Singh
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Mushtaq Ahmed
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Sadia Akter
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Vinay Shivanna
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Allison N Bucşan
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA, USA
| | - Abhishek Mishra
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, USA
| | - Nadia A Golden
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA, USA
| | - Peter J Didier
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA, USA
| | - Lara A Doyle
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA, USA
| | - Shannan Hall-Ursone
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Chad J Roy
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA, USA
| | - Garima Arora
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Edward J Dick
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Chinnaswamy Jagannath
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, USA
| | - Smriti Mehra
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA, USA
| | - Shabaana A Khader
- Department of Microbiology, University of Chicago, Chicago, IL, USA.
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA.
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4
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Devlin KL, Leach DT, Stratton KG, Lamichhane G, Lin VS, Beatty KE. Proteomic characterization of Mycobacterium tuberculosis subjected to carbon starvation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.12.623260. [PMID: 39605331 PMCID: PMC11601416 DOI: 10.1101/2024.11.12.623260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
Abstract
Mycobacterium tuberculosis ( Mtb ) is the causative agent of tuberculosis (TB), the leading cause of infectious-disease related deaths worldwide. TB infections present as a spectrum from active to latent disease. In the human host, Mtb faces hostile environments, such as nutrient deprivation, hypoxia, and low pH. Under these conditions, Mtb can enter a dormant, but viable, state characterized by a lack of cell replication and increased resistance to antibiotics. These dormant Mtb pose a major challenge to curing infections and eradicating TB globally. In the current study, we subjected Mtb to carbon starvation (CS), a culture condition that induces growth stasis and mimics nutrient-starved conditions associated with dormancy in vivo . We provide a detailed analysis of the proteome in CS compared to replicating samples. We observed extensive proteomic reprogramming, with 36% of identified proteins significantly altered in CS. Many enzymes involved in oxidative phosphorylation and lipid metabolism were retained or upregulated in CS. The cell wall biosynthetic machinery was present in CS, although numerous changes in the abundance of peptidoglycan, arabinogalactan, and mycolic acid biosynthetic enzymes likely result in pronounced remodeling of the cell wall. Many clinically approved anti-TB drugs target cell wall biosynthesis, and we found that these enzymes were largely retained in CS. Lastly, we compared our results to those of other dormancy models and propose that CS produces a physiologically-distinct state of stasis compared to hypoxia in Mtb .
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5
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Schneider RF, Hallstrom K, DeMott C, McDonough KA. Conditional protein splicing of the Mycobacterium tuberculosis RecA intein in its native host. Sci Rep 2024; 14:20664. [PMID: 39237639 PMCID: PMC11377839 DOI: 10.1038/s41598-024-71248-y] [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: 04/17/2024] [Accepted: 08/26/2024] [Indexed: 09/07/2024] Open
Abstract
The recA gene, encoding Recombinase A (RecA) is one of three Mycobacterium tuberculosis (Mtb) genes encoding an in-frame intervening protein sequence (intein) that must splice out of precursor host protein to produce functional protein. Ongoing debate about whether inteins function solely as selfish genetic elements or benefit their host cells requires understanding of interplay between inteins and their hosts. We measured environmental effects on native RecA intein splicing within Mtb using a combination of western blots and promoter reporter assays. RecA splicing was stimulated in bacteria exposed to DNA damaging agents or by treatment with copper in hypoxic, but not normoxic, conditions. Spliced RecA was processed by the Mtb proteasome, while free intein was degraded efficiently by other unknown mechanisms. Unspliced precursor protein was not observed within Mtb despite its accumulation during ectopic expression of Mtb recA within E. coli. Surprisingly, Mtb produced free N-extein in some conditions, and ectopic expression of Mtb N-extein activated LexA in E. coli. These results demonstrate that the bacterial environment greatly impacts RecA splicing in Mtb, underscoring the importance of studying intein splicing in native host environments and raising the exciting possibility of intein splicing as a novel regulatory mechanism in Mtb.
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Affiliation(s)
- Ryan F Schneider
- Biomedical Sciences Department, School of Public Health, State University of New York at Albany, Albany, USA
| | - Kelly Hallstrom
- Wadsworth Center, New York Department of Health, 120 New Scotland Avenue, Albany, NY, 12208, USA
- Albany College of Pharmacy and Health Sciences, Albany, NY, USA
| | - Christopher DeMott
- Wadsworth Center, New York Department of Health, 120 New Scotland Avenue, Albany, NY, 12208, USA
- Regeneron Pharmaceuticals Inc, Albany, NY, USA
| | - Kathleen A McDonough
- Biomedical Sciences Department, School of Public Health, State University of New York at Albany, Albany, USA.
- Wadsworth Center, New York Department of Health, 120 New Scotland Avenue, Albany, NY, 12208, USA.
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6
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Schneider RF, Hallstrom K, DeMott C, McDonough KA. Conditional protein splicing of the Mycobacterium tuberculosis RecA intein in its native host. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589443. [PMID: 38659745 PMCID: PMC11042385 DOI: 10.1101/2024.04.15.589443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The recA gene, encoding Recombinase A (RecA) is one of three Mycobacterium tuberculosis (Mtb) genes encoding an in-frame intervening protein sequence (intein) that must splice out of precursor host protein to produce functional protein. Ongoing debate about whether inteins function solely as selfish genetic elements or benefit their host cells requires understanding of interplay between inteins and their hosts. We measured environmental effects on native RecA intein splicing within Mtb using a combination of western blots and promoter reporter assays. RecA splicing was stimulated in bacteria exposed to DNA damaging agents or by treatment with copper in hypoxic, but not normoxic, conditions. Spliced RecA was processed by the Mtb proteasome, while free intein was degraded efficiently by other unknown mechanisms. Unspliced precursor protein was not observed within Mtb despite its accumulation during ectopic expression of Mtb recA within E. coli. Surprisingly, Mtb produced free N-extein in some conditions, and ectopic expression of Mtb N-extein activated LexA in E. coli. These results demonstrate that the bacterial environment greatly impacts RecA splicing in Mtb, underscoring the importance of studying intein splicing in native host environments and raising the exciting possibility of intein splicing as a novel regulatory mechanism in Mtb.
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Affiliation(s)
- Ryan F. Schneider
- Biomedical Sciences Department, School of Public Health, State University of New York at Albany
| | | | | | - Kathleen A. McDonough
- Biomedical Sciences Department, School of Public Health, State University of New York at Albany
- Wadsworth Center, New York Department of Health
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7
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Jaisinghani N, Previti ML, Andrade J, Askenazi M, Ueberheide B, Seeliger JC. Proteomics from compartment-specific APEX2 labeling in Mycobacterium tuberculosis reveals Type VII secretion substrates in the cell wall. Cell Chem Biol 2024; 31:523-533.e4. [PMID: 37967559 PMCID: PMC11106752 DOI: 10.1016/j.chembiol.2023.10.013] [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: 03/29/2023] [Revised: 07/20/2023] [Accepted: 10/13/2023] [Indexed: 11/17/2023]
Abstract
The cell wall of mycobacteria plays a key role in interactions with the environment. Its ability to act as a selective filter is crucial to bacterial survival. Proteins in the cell wall enable this function by mediating the import and export of diverse metabolites, from ions to lipids to proteins. Identifying cell wall proteins is an important step in assigning function, especially as many mycobacterial proteins lack functionally characterized homologues. Current methods for protein localization have inherent limitations that reduce accuracy. Here we showed that although chemical labeling of live cells did not exclusively label surface proteins, protein tagging by the engineered peroxidase APEX2 within live Mycobacterium tuberculosis accurately identified the cytosolic and cell wall proteomes. Our data indicate that substrates of the virulence-associated Type VII ESX secretion system are exposed to the periplasm, providing insight into the currently unknown mechanism by which these proteins cross the mycobacterial cell envelope.
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Affiliation(s)
- Neetika Jaisinghani
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Mary L Previti
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Joshua Andrade
- Proteomics Laboratory, New York University Grossman School of Medicine, New York, NY 10016, USA
| | | | - Beatrix Ueberheide
- Proteomics Laboratory, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Jessica C Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA.
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8
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Zhu C, Dong J, Duan Y, Jia H, Zhang L, Xing A, Du B, Sun Q, Huang Y, Zhang Z, Pan L, Li Z. Comparative analysis of genomic characteristics and immune response between Mycobacterium tuberculosis strains cultured continuously for 25 years and H37Rv. Pathog Dis 2024; 82:ftae014. [PMID: 38845379 PMCID: PMC11187990 DOI: 10.1093/femspd/ftae014] [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: 11/16/2023] [Revised: 05/07/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024] Open
Abstract
Tuberculosis (TB) continues to pose a significant global health challenge, emphasizing the critical need for effective preventive measures. Although many studies have tried to develop new attenuated vaccines, there is no effective TB vaccine. In this study, we report a novel attenuated Mycobacterium tuberculosis (M. tb) strain, CHVAC-25, cultured continuously for 25 years in the laboratory. CHVAC-25 exhibited significantly reduced virulence compared to both the virulent H37Rv strain in C57BL/6J and severe combined immunodeficiency disease mice. The comparative genomic analysis identified 93 potential absent genomic segments and 65 single nucleotide polymorphic sites across 47 coding genes. Notably, the deletion mutation of ppsC (Rv2933) involved in phthiocerol dimycocerosate synthesis likely contributes to CHVAC-25 virulence attenuation. Furthermore, the comparative analysis of immune responses between H37Rv- and CHVAC-25-infected macrophages showed that CHVAC-25 triggered a robust upregulation of 173 genes, particularly cytokines crucial for combating M. tb infection. Additionally, the survival of CHVAC-25 was significantly reduced compared to H37Rv in macrophages. These findings reiterate the possibility of obtaining attenuated M. tb strains through prolonged laboratory cultivation, echoing the initial conception of H37Ra nearly a century ago. Additionally, the similarity of CHVAC-25 to genotypes associated with attenuated M. tb vaccine positions it as a promising candidate for TB vaccine development.
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Affiliation(s)
- Chuanzhi Zhu
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Jing Dong
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Yuheng Duan
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Hongyan Jia
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Lanyue Zhang
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Aiying Xing
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Boping Du
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Qi Sun
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Yinxia Huang
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Zongde Zhang
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Liping Pan
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Zihui Li
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
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9
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Hegelmeyer NK, Parkin LA, Previti ML, Andrade J, Utama R, Sejour RJ, Gardin J, Muller S, Ketchum S, Yurovsky A, Futcher B, Goodwin S, Ueberheide B, Seeliger JC. Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria. mBio 2023; 14:e0084123. [PMID: 37787543 PMCID: PMC10653884 DOI: 10.1128/mbio.00841-23] [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: 04/05/2023] [Accepted: 08/16/2023] [Indexed: 10/04/2023] Open
Abstract
IMPORTANCE Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, one of the deadliest infectious diseases worldwide. Previous studies have established that synonymous recoding to introduce rare codon pairings can attenuate viral pathogens. We hypothesized that non-optimal codon pairing could be an effective strategy for attenuating gene expression to create a live vaccine for Mtb. We instead discovered that these synonymous changes enabled the transcription of functional mRNA that initiated in the middle of the open reading frame and from which many smaller protein products were expressed. To our knowledge, this is one of the first reports that synonymous recoding of a gene in any organism can create or induce intragenic transcription start sites.
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Affiliation(s)
- Nuri K. Hegelmeyer
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Lia A. Parkin
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Mary L. Previti
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Joshua Andrade
- Proteomics Laboratory, New York University Grossman School of Medicine, New York, New York, USA
| | - Raditya Utama
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Richard J. Sejour
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Justin Gardin
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Stephanie Muller
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Steven Ketchum
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Alisa Yurovsky
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Bruce Futcher
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Beatrix Ueberheide
- Proteomics Laboratory, New York University Grossman School of Medicine, New York, New York, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
| | - Jessica C. Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
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10
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Adefisayo OO, Curtis ER, Smith CM. Mycobacterial Genetic Technologies for Probing the Host-Pathogen Microenvironment. Infect Immun 2023; 91:e0043022. [PMID: 37249448 PMCID: PMC10269127 DOI: 10.1128/iai.00430-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, is one of the oldest and most successful pathogens in the world. Diverse selective pressures encountered within host cells have directed the evolution of unique phenotypic traits, resulting in the remarkable evolutionary success of this largely obligate pathogen. Despite centuries of study, the genetic repertoire utilized by Mtb to drive virulence and host immune evasion remains to be fully understood. Various genetic approaches have been and continue to be developed to tackle the challenges of functional gene annotation and validation in an intractable organism such as Mtb. In vitro and ex vivo systems remain the primary approaches to generate and confirm hypotheses that drive a general understanding of mycobacteria biology. However, it remains of great importance to characterize genetic requirements for successful infection within a host system as in vitro and ex vivo studies fail to fully replicate the complex microenvironment experienced by Mtb. In this review, we evaluate the employment of the mycobacterial genetic toolkit to probe the host-pathogen interface by surveying the current state of mycobacterial genetic studies within host systems, with a major focus on the murine model. Specifically, we discuss the different ways that these tools have been utilized to examine various aspects of infection, including bacterial survival/virulence, bacterial evasion of host immunity, and development of novel antibacterial/vaccine strategies.
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Affiliation(s)
| | - Erin R. Curtis
- Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Clare M. Smith
- Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
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11
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Jaisinghani N, Previti ML, Andrade J, Askenazi M, Ueberheide B, Seeliger JC. Cell wall proteomics in live Mycobacterium tuberculosis uncovers exposure of ESX substrates to the periplasm. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.29.534792. [PMID: 37034674 PMCID: PMC10081232 DOI: 10.1101/2023.03.29.534792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
The cell wall of mycobacteria plays a key role in interactions with the environment and its ability to act as a selective filter is crucial to bacterial survival. Proteins in the cell wall enable this function by mediating the import and export of diverse metabolites from ions to lipids to proteins. Accurately identifying cell wall proteins is an important step in assigning function, especially as many mycobacterial proteins lack functionally characterized homologues. Current methods for protein localization have inherent limitations that reduce accuracy. Here we showed that protein tagging by the engineered peroxidase APEX2 within live Mycobacterium tuberculosis enabled the accurate identification of the cytosolic and cell wall proteomes. Our data indicate that substrates of the virulence-associated Type VII ESX secretion system are exposed to the Mtb periplasm, providing insight into the currently unknown mechanism by which these proteins cross the mycobacterial cell envelope.
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Affiliation(s)
- Neetika Jaisinghani
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Mary L Previti
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Joshua Andrade
- Proteomics Laboratory, New York University Grossman School of Medicine, New York, New York, USA
| | | | - Beatrix Ueberheide
- Proteomics Laboratory, New York University Grossman School of Medicine, New York, New York, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
| | - Jessica C Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
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12
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Hegelmeyer NK, Previti ML, Andrade J, Utama R, Sejour RJ, Gardin J, Muller S, Ketchum S, Yurovsky A, Futcher B, Goodwin S, Ueberheide B, Seeliger JC. Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.532606. [PMID: 36993691 PMCID: PMC10055193 DOI: 10.1101/2023.03.17.532606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Each genome encodes some codons more frequently than their synonyms (codon usage bias), but codons are also arranged more frequently into specific pairs (codon pair bias). Recoding viral genomes and yeast or bacterial genes with non-optimal codon pairs has been shown to decrease gene expression. Gene expression is thus importantly regulated not only by the use of particular codons but by their proper juxtaposition. We therefore hypothesized that non-optimal codon pairing could likewise attenuate Mtb genes. We explored the role of codon pair bias by recoding Mtb genes ( rpoB, mmpL3, ndh ) and assessing their expression in the closely related and tractable model organism M. smegmatis . To our surprise, recoding caused the expression of multiple smaller protein isoforms from all three genes. We confirmed that these smaller proteins were not due to protein degradation, but instead issued from new transcription initiation sites positioned within the open reading frame. New transcripts gave rise to intragenic translation initiation sites, which in turn led to the expression of smaller proteins. We next identified the nucleotide changes associated with these new sites of transcription and translation. Our results demonstrated that apparently benign, synonymous changes can drastically alter gene expression in mycobacteria. More generally, our work expands our understanding of the codon-level parameters that control translation and transcription initiation. IMPORTANCE Mycobacterium tuberculosis ( Mtb ) is the causative agent of tuberculosis, one of the deadliest infectious diseases worldwide. Previous studies have established that synonymous recoding to introduce rare codon pairings can attenuate viral pathogens. We hypothesized that non-optimal codon pairing could be an effective strategy for attenuating gene expression to create a live vaccine for Mtb . We instead discovered that these synonymous changes enabled the transcription of functional mRNA that initiated in the middle of the open reading frame and from which many smaller protein products were expressed. To our knowledge, this is the first report that synonymous recoding of a gene in any organism can create or induce intragenic transcription start sites.
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Affiliation(s)
- Nuri K. Hegelmeyer
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Mary L. Previti
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Joshua Andrade
- Proteomics Laboratory, New York University Grossman School of Medicine, New York, New York, USA
| | - Raditya Utama
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Richard J. Sejour
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Justin Gardin
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Stephanie Muller
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Steven Ketchum
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Alisa Yurovsky
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Bruce Futcher
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Beatrix Ueberheide
- Proteomics Laboratory, New York University Grossman School of Medicine, New York, New York, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
| | - Jessica C. Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
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13
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Sparks IL, Derbyshire KM, Jacobs WR, Morita YS. Mycobacterium smegmatis: The Vanguard of Mycobacterial Research. J Bacteriol 2023; 205:e0033722. [PMID: 36598232 PMCID: PMC9879119 DOI: 10.1128/jb.00337-22] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The genus Mycobacterium contains several slow-growing human pathogens, including Mycobacterium tuberculosis, Mycobacterium leprae, and Mycobacterium avium. Mycobacterium smegmatis is a nonpathogenic and fast growing species within this genus. In 1990, a mutant of M. smegmatis, designated mc2155, that could be transformed with episomal plasmids was isolated, elevating M. smegmatis to model status as the ideal surrogate for mycobacterial research. Classical bacterial models, such as Escherichia coli, were inadequate for mycobacteria research because they have low genetic conservation, different physiology, and lack the novel envelope structure that distinguishes the Mycobacterium genus. By contrast, M. smegmatis encodes thousands of conserved mycobacterial gene orthologs and has the same cell architecture and physiology. Dissection and characterization of conserved genes, structures, and processes in genetically tractable M. smegmatis mc2155 have since provided previously unattainable insights on these same features in its slow-growing relatives. Notably, tuberculosis (TB) drugs, including the first-line drugs isoniazid and ethambutol, are active against M. smegmatis, but not against E. coli, allowing the identification of their physiological targets. Furthermore, Bedaquiline, the first new TB drug in 40 years, was discovered through an M. smegmatis screen. M. smegmatis has become a model bacterium, not only for M. tuberculosis, but for all other Mycobacterium species and related genera. With a repertoire of bioinformatic and physical resources, including the recently established Mycobacterial Systems Resource, M. smegmatis will continue to accelerate mycobacterial research and advance the field of microbiology.
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Affiliation(s)
- Ian L. Sparks
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Keith M. Derbyshire
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA
| | - William R. Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Yasu S. Morita
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
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14
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Saelens JW, Sweeney MI, Viswanathan G, Xet-Mull AM, Jurcic Smith KL, Sisk DM, Hu DD, Cronin RM, Hughes EJ, Brewer WJ, Coers J, Champion MM, Champion PA, Lowe CB, Smith CM, Lee S, Stout JE, Tobin DM. An ancestral mycobacterial effector promotes dissemination of infection. Cell 2022; 185:4507-4525.e18. [PMID: 36356582 PMCID: PMC9691622 DOI: 10.1016/j.cell.2022.10.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 08/27/2022] [Accepted: 10/16/2022] [Indexed: 11/11/2022]
Abstract
The human pathogen Mycobacterium tuberculosis typically causes lung disease but can also disseminate to other tissues. We identified a M. tuberculosis (Mtb) outbreak presenting with unusually high rates of extrapulmonary dissemination and bone disease. We found that the causal strain carried an ancestral full-length version of the type VII-secreted effector EsxM rather than the truncated version present in other modern Mtb lineages. The ancestral EsxM variant exacerbated dissemination through enhancement of macrophage motility, increased egress of macrophages from established granulomas, and alterations in macrophage actin dynamics. Reconstitution of the ancestral version of EsxM in an attenuated modern strain of Mtb altered the migratory mode of infected macrophages, enhancing their motility. In a zebrafish model, full-length EsxM promoted bone disease. The presence of a derived nonsense variant in EsxM throughout the major Mtb lineages 2, 3, and 4 is consistent with a role for EsxM in regulating the extent of dissemination.
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Affiliation(s)
- Joseph W Saelens
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mollie I Sweeney
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Gopinath Viswanathan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ana María Xet-Mull
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kristen L Jurcic Smith
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Dana M Sisk
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Daniel D Hu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Rachel M Cronin
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Erika J Hughes
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - W Jared Brewer
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jörn Coers
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Matthew M Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Patricia A Champion
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA; Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Craig B Lowe
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Clare M Smith
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sunhee Lee
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Jason E Stout
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Division of Infectious Diseases and International Health, Duke University School of Medicine, Durham, NC 27710, USA.
| | - David M Tobin
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.
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15
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Quigley J, Lewis K. Noise in a Metabolic Pathway Leads to Persister Formation in Mycobacterium tuberculosis. Microbiol Spectr 2022; 10:e0294822. [PMID: 36194154 PMCID: PMC9602276 DOI: 10.1128/spectrum.02948-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 09/22/2022] [Indexed: 01/04/2023] Open
Abstract
Tuberculosis is difficult to treat due to dormant cells formed in response to immune stress and stochastically formed persisters, both of which are tolerant of antibiotics. Bactericidal antibiotics kill by corrupting their energy-dependent targets. We reasoned that stochastic variation, or noise, in the expression of an energy-generating component will produce rare persister cells. In sorted M. tuberculosis cells grown on acetate, there is considerable cell-to-cell variation in the level of mRNA coding for AckA, the acetate kinase. Quenching the noise by overexpressing ackA sharply decreases persisters, showing that it acts as the main persister gene under these conditions. This demonstrates that a low energy mechanism is responsible for the formation of M. tuberculosis persisters. Entrance into a low-energy state driven by noise in expression of energy-producing enzymes is likely a general mechanism by which bacteria produce persisters. IMPORTANCE M. tuberculosis infection requires the administration of multiple antibiotics for a prolonged period of time. Treatment difficulty is generally attributed to M. tuberculosis entrance into a nonreplicative, antibiotic-tolerant state. M. tuberculosis enters this nonreplicative state in response to immune stress. However, a small population of cells enter a nonreplicative, multidrug-tolerant state under normal growth conditions, absent any stress. These cells are termed persisters. The mechanisms by which persisters enter a nonreplicative state are largely unknown. Here, we show that, as with other bacteria, M. tuberculosis persisters are low-energy cells formed stochastically during normal growth. Additionally, we identify the natural variation in the expression of energy producing genes as a source of the stochastic entrance of M. tuberculosis into the low-energy persister state. These findings have important implications for understanding the heterogeneous nature of M. tuberculosis infection and will aid in designing better treatment regimens against this important human pathogen.
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Affiliation(s)
- Jeffrey Quigley
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, USA
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16
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Ottavi S, Scarry SM, Mosior J, Ling Y, Roberts J, Singh A, Zhang D, Goullieux L, Roubert C, Bacqué E, Lagiakos HR, Vendome J, Moraca F, Li K, Perkowski AJ, Ramesh R, Bowler MM, Tracy W, Feher VA, Sacchettini JC, Gold BS, Nathan CF, Aubé J. In Vitro and In Vivo Inhibition of the Mycobacterium tuberculosis Phosphopantetheinyl Transferase PptT by Amidinoureas. J Med Chem 2022; 65:1996-2022. [PMID: 35044775 PMCID: PMC8842310 DOI: 10.1021/acs.jmedchem.1c01565] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A newly validated target for tuberculosis treatment is phosphopantetheinyl transferase, an essential enzyme that plays a critical role in the biosynthesis of cellular lipids and virulence factors in Mycobacterium tuberculosis. The structure-activity relationships of a recently disclosed inhibitor, amidinourea (AU) 8918 (1), were explored, focusing on the biochemical potency, determination of whole-cell on-target activity for active compounds, and profiling of selective active congeners. These studies show that the AU moiety in AU 8918 is largely optimized and that potency enhancements are obtained in analogues containing a para-substituted aromatic ring. Preliminary data reveal that while some analogues, including 1, have demonstrated cardiotoxicity (e.g., changes in cardiomyocyte beat rate, amplitude, and peak width) and inhibit Cav1.2 and Nav1.5 ion channels (although not hERG channels), inhibition of the ion channels is largely diminished for some of the para-substituted analogues, such as 5k (p-benzamide) and 5n (p-phenylsulfonamide).
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Affiliation(s)
- Samantha Ottavi
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Sarah M Scarry
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - John Mosior
- Departments of Biochemistry and Biophysics, Texas Agricultural and Mechanical University, College Station, Texas 77843, United States
| | - Yan Ling
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Julia Roberts
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Amrita Singh
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - David Zhang
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | | | | | - Eric Bacqué
- Evotec ID (Lyon), SAS 40 Avenue Tony Garnier, Lyon 69001, France
| | - H Rachel Lagiakos
- Schrödinger, Inc., 120 W. 45 Street, New York, New York 10036, United States
| | - Jeremie Vendome
- Schrödinger, Inc., 120 W. 45 Street, New York, New York 10036, United States
| | - Francesca Moraca
- Schrödinger, Inc., 120 W. 45 Street, New York, New York 10036, United States
| | - Kelin Li
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Andrew J Perkowski
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Remya Ramesh
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Matthew M Bowler
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - William Tracy
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Victoria A Feher
- Schrödinger, Inc., 120 W. 45 Street, New York, New York 10036, United States
| | - James C Sacchettini
- Departments of Biochemistry and Biophysics, Texas Agricultural and Mechanical University, College Station, Texas 77843, United States
| | - Ben S Gold
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Carl F Nathan
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, New York 10065, United States.,Department of Medicine, Weill Cornell Medicine, New York, New York 10065, United States
| | - Jeffrey Aubé
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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17
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Ahamed M, Jaisinghani N, Li M, Winkeler I, Silva S, Previti ML, Seeliger JC. Optimized APEX2 peroxidase-mediated proximity labeling in fast- and slow-growing mycobacteria. Methods Enzymol 2021; 664:267-289. [PMID: 35331378 PMCID: PMC11628366 DOI: 10.1016/bs.mie.2021.11.021] [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] [Indexed: 11/21/2022]
Abstract
Proximity labeling is a technology for tagging proteins and other biomolecules in living cells. These methods use enzymes that generate reactive species whose properties afford high spatial resolution for the localization of proteins to subcellular compartments and the identification of endogenous interaction partners. Here we present the adaptation of the engineered peroxidase APEX2 to proximity labeling in mycobacteria, including the human pathogen Mycobacterium tuberculosis. APEX2 is uniquely suited for general use in bacteria because unlike other proximity labeling enzymes, it does not depend on metabolites like ATP that are found in the cytoplasm, but are absent from the bacterial periplasm. Importantly, we found that in slow-growing mycobacteria like M. tuberculosis, codon usage optimization is required for APEX2 export into the periplasm via fusion to an N-terminal secretion signal. APEX2 expressed from codon-optimized genes affords robust, compartment-specific protein labeling in the cytoplasm and the periplasm of both fast- and slow-growing species. Here we detail these updated constructs and provide an optimized protocol for APEX2-mediated protein labeling in mycobacteria. We expect this approach to be broadly useful for determining the localization of specific proteins, cataloging subcellular proteomes, and identifying interaction partners of 'bait' proteins expressed as fusions to APEX2.
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Affiliation(s)
- Mukshud Ahamed
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, United States
| | - Neetika Jaisinghani
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, United States
| | - Michael Li
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, United States
| | - Ian Winkeler
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, United States
| | - Shalika Silva
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, United States
| | - Mary L Previti
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, United States
| | - Jessica C Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, United States.
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18
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Babin B, Fernandez-Cuervo G, Sheng J, Green O, Ordonez AA, Turner ML, Keller LJ, Jain SK, Shabat D, Bogyo M. Chemiluminescent Protease Probe for Rapid, Sensitive, and Inexpensive Detection of Live Mycobacterium tuberculosis. ACS CENTRAL SCIENCE 2021; 7:803-814. [PMID: 34079897 PMCID: PMC8161474 DOI: 10.1021/acscentsci.0c01345] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Indexed: 05/05/2023]
Abstract
Tuberculosis (TB) is a top-ten cause of death worldwide. Successful treatment is often limited by insufficient diagnostic capabilities, especially at the point of care in low-resource settings. The ideal diagnostic must be fast, be cheap, and require minimal clinical resources while providing high sensitivity, selectivity, and the ability to differentiate live from dead bacteria. We describe here the development of a fast, luminescent, and affordable sensor of Hip1 (FLASH) for detecting and monitoring drug susceptibility of Mycobacterium tuberculosis (Mtb). FLASH is a selective chemiluminescent substrate for the Mtb protease Hip1 that, when processed, produces visible light that can be measured with a high signal-to-noise ratio using inexpensive sensors. FLASH is sensitive to fmol of recombinant Hip1 enzyme in vitro and can detect as few as thousands of Mtb cells in culture or in human sputum samples within minutes. The probe is highly selective for Mtb compared to other nontuberculous mycobacteria and can distinguish live from dead cells. Importantly, FLASH can be used to measure antibiotic killing of Mtb in culture with greatly accelerated timelines compared to traditional protocols. Overall, FLASH has the potential to enhance both TB diagnostics and drug resistance monitoring in resource-limited settings.
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Affiliation(s)
- Brett
M. Babin
- Department
of Pathology, Stanford University School
of Medicine, Stanford, California 94305, United States
| | - Gabriela Fernandez-Cuervo
- Department
of Pathology, Stanford University School
of Medicine, Stanford, California 94305, United States
| | - Jessica Sheng
- Department
of Pathology, Stanford University School
of Medicine, Stanford, California 94305, United States
| | - Ori Green
- School
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Alvaro A. Ordonez
- Center
for Infection and Inflammation Imaging Research, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
- Center
for Tuberculosis Research, Johns Hopkins
University School of Medicine, Baltimore, Maryland 21287, United States
- Department
of Pediatrics, Johns Hopkins University
School of Medicine, Baltimore, Maryland 21205, United States
| | - Mitchell L. Turner
- Center
for Infection and Inflammation Imaging Research, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
- Center
for Tuberculosis Research, Johns Hopkins
University School of Medicine, Baltimore, Maryland 21287, United States
- Department
of Pediatrics, Johns Hopkins University
School of Medicine, Baltimore, Maryland 21205, United States
| | - Laura J. Keller
- Department
of Chemical and Systems Biology, Stanford
University School of Medicine, Stanford, California 94305, United States
| | - Sanjay K. Jain
- Center
for Infection and Inflammation Imaging Research, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
- Center
for Tuberculosis Research, Johns Hopkins
University School of Medicine, Baltimore, Maryland 21287, United States
- Department
of Pediatrics, Johns Hopkins University
School of Medicine, Baltimore, Maryland 21205, United States
| | - Doron Shabat
- School
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Matthew Bogyo
- Department
of Pathology, Stanford University School
of Medicine, Stanford, California 94305, United States
- Department
of Chemical and Systems Biology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Microbiology and Immunology, Stanford
University School of Medicine, Stanford, California 94305, United States
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19
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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: 22] [Impact Index Per Article: 5.5] [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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20
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Levine SR, Beatty KE. Investigating β-Lactam Drug Targets in Mycobacterium tuberculosis Using Chemical Probes. ACS Infect Dis 2021; 7:461-470. [PMID: 33470787 DOI: 10.1021/acsinfecdis.0c00809] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tuberculosis (TB), caused by the bacterial pathogen Mycobacterium tuberculosis (Mtb), infects 10 million people a year. An estimated 25% of humans harbor latent TB infections, an asymptomatic form of the disease. In both active and latent infections, Mtb relies on cell wall peptidoglycan for viability. In the current work, we synthesized fluorescent analogues of β-lactam antibiotics to study two classes of enzymes that maintain Mtb's peptidoglycan: penicillin-binding proteins (PBPs) and l,d-transpeptidases (LDTs). This set of activity-based probes included analogues of three classes of β-lactams: a monobactam (aztreonam-Cy5), a cephalosporin (cephalexin-Cy5), and a carbapenem (meropenem-Cy5). We used these probes to profile enzyme activity in protein gel-resolved lysates of Mtb. All three out-performed the commercial reagent Bocillin-FL, a penam. Meropenem-Cy5 was used to identify β-lactam targets by mass spectrometry, including PBPs, LDTs, and the β-lactamase BlaC. New probes were also used to compare PBP and LDT activity in two metabolic states: dormancy and active replication. We provide the first direct evidence that Mtb dynamically regulates the enzymes responsible for maintaining peptidoglycan in dormancy. Lastly, we profiled drug susceptibility in lysates and found that meropenem inhibits PBPs, LDTs, and BlaC.
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Affiliation(s)
- Samantha R. Levine
- Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, California 92617, United States
| | - Kimberly E. Beatty
- Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, California 92617, United States
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21
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Nadolinskaia NI, Karpov DS, Goncharenko AV. Vaccines Against Tuberculosis: Problems and Prospects (Review). APPL BIOCHEM MICRO+ 2020; 56:497-504. [PMID: 32981943 PMCID: PMC7508421 DOI: 10.1134/s0003683820050129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/13/2020] [Accepted: 04/22/2020] [Indexed: 12/12/2022]
Abstract
Despite the efforts of the global medical and scientific community, tuberculosis remains the leading cause of death from infectious diseases. The expectation of success associated with the development of new anti-TB drugs was not justified, and the attention of researchers was largely drawn to the creation of new mycobacterial strains for vaccination against tuberculosis. The proposed review contains current information on the existing vaccine strains and the development of new, genetically engineered strains for the prevention of tuberculosis and the prevention and treatment of other diseases. The review includes relevant information on the correlation between BCG vaccination and the frequency and severity of COVID-19 infection.
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Affiliation(s)
- N. I. Nadolinskaia
- Bach Institute of Biochemistry, Federal Research Center Fundamentals of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - D. S. Karpov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - A. V. Goncharenko
- Bach Institute of Biochemistry, Federal Research Center Fundamentals of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
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22
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Li Z, Zheng C, Terreni M, Tanzi L, Sollogoub M, Zhang Y. Novel Vaccine Candidates against Tuberculosis. Curr Med Chem 2020; 27:5095-5118. [PMID: 30474525 DOI: 10.2174/0929867326666181126112124] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/08/2018] [Accepted: 11/19/2018] [Indexed: 12/18/2022]
Abstract
Ranking above AIDS, Tuberculosis (TB) is the ninth leading cause of death affecting and
killing many individuals every year. Drugs’ efficacy is limited by a series of problems such as Multi-
Drug Resistance (MDR) and Extensively-Drug Resistance (XDR). Meanwhile, the only licensed vaccine
BCG (Bacillus Calmette-Guérin) existing for over 90 years is not effective enough. Consequently,
it is essential to develop novel vaccines for TB prevention and immunotherapy. This paper
provides an overall review of the TB prevalence, immune system response against TB and recent
progress of TB vaccine research and development. Several vaccines in clinical trials are described as
well as LAM-based candidates.
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Affiliation(s)
- Zhihao Li
- Sorbonne Universite, CNRS, Institut Parisien de Chimie Moleculaire (UMR 8232), 4 Place Jussieu, 75005 Paris, France
| | - Changping Zheng
- Sorbonne Universite, CNRS, Institut Parisien de Chimie Moleculaire (UMR 8232), 4 Place Jussieu, 75005 Paris, France
| | - Marco Terreni
- Drug Sciences Department, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - Lisa Tanzi
- Drug Sciences Department, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - Matthieu Sollogoub
- Sorbonne Universite, CNRS, Institut Parisien de Chimie Moleculaire (UMR 8232), 4 Place Jussieu, 75005 Paris, France
| | - Yongmin Zhang
- Sorbonne Universite, CNRS, Institut Parisien de Chimie Moleculaire (UMR 8232), 4 Place Jussieu, 75005 Paris, France
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23
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Meijers AS, Troost R, Ummels R, Maaskant J, Speer A, Nejentsev S, Bitter W, Kuijl CP. Efficient genome editing in pathogenic mycobacteria using Streptococcus thermophilus CRISPR1-Cas9. Tuberculosis (Edinb) 2020; 124:101983. [PMID: 32829077 PMCID: PMC7612230 DOI: 10.1016/j.tube.2020.101983] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/27/2020] [Accepted: 07/27/2020] [Indexed: 01/08/2023]
Abstract
The ability to genetically engineer pathogenic mycobacteria has increased significantly over the last decades due to the generation of new molecular tools. Recently, the application of the Streptococcus pyogenes and the Streptococcus thermophilus CRISPR-Cas9 systems in mycobacteria has enabled gene editing and efficient CRISPR interference-mediated transcriptional regulation. Here, we converted CRISPR interference into an efficient genome editing tool for mycobacteria. We demonstrate that the Streptococcus thermophilus CRISPR1-Cas9 (Sth1Cas9) is functional in Mycobacterium marinum and Mycobacterium tuberculosis, enabling highly efficient and precise DNA breaks and indel formation, without any off-target effects. In addition, with dual sgRNAs this system can be used to generate two indels simultaneously or to create specific deletions. The ability to use the power of the CRISPR-Cas9-mediated gene editing toolbox in M. tuberculosis with a single step will accelerate research into this deadly pathogen.
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Affiliation(s)
- Aniek S Meijers
- Department of Medical Microbiology and Infection Control, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, Netherlands.
| | - Ran Troost
- Department of Medical Microbiology and Infection Control, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, Netherlands.
| | - Roy Ummels
- Department of Medical Microbiology and Infection Control, Amsterdam Institute of Infection & Immunity, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, Netherlands.
| | - Janneke Maaskant
- Department of Medical Microbiology and Infection Control, Amsterdam Institute of Infection & Immunity, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, Netherlands.
| | - Alexander Speer
- Department of Medical Microbiology and Infection Control, Amsterdam Institute of Infection & Immunity, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, Netherlands.
| | - Sergey Nejentsev
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC, De Boelelaan 1117, 1081 HV, Amsterdam, Netherlands; Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, United Kingdom.
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Control, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, Netherlands; Department of Medical Microbiology and Infection Control, Amsterdam Institute of Infection & Immunity, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, Netherlands; Department of Molecular Microbiology, Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, Netherlands.
| | - Coenraad P Kuijl
- Department of Medical Microbiology and Infection Control, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, Netherlands; Department of Medical Microbiology and Infection Control, Amsterdam Institute of Infection & Immunity, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, Netherlands.
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24
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Abstract
Immune responses to infectious agents are initiated when a pathogen or its components bind to pattern recognition receptors (PRRs). PRR binding sets off a cascade of events that activates immune responses. We now show that, in addition to activating immune responses, PRR signaling also initiates an immunosuppressive response, probably to limit inflammation. The importance of the current findings is that blockade of immunomodulatory signaling, which is mediated by the upregulation of the CD47 molecule, can lead to enhanced immune responses to any pathogen that triggers PRR signaling. Since most or all pathogens trigger PRRs, CD47 blockade could be used to speed up and strengthen both innate and adaptive immune responses when medically indicated. Such immunotherapy could be done without a requirement for knowing the HLA type of the individual, the specific antigens of the pathogen, or, in the case of bacterial infections, the antimicrobial resistance profile. It is well understood that the adaptive immune response to infectious agents includes a modulating suppressive component as well as an activating component. We now show that the very early innate response also has an immunosuppressive component. Infected cells upregulate the CD47 “don’t eat me” signal, which slows the phagocytic uptake of dying and viable cells as well as downstream antigen-presenting cell (APC) functions. A CD47 mimic that acts as an essential virulence factor is encoded by all poxviruses, but CD47 expression on infected cells was found to be upregulated even by pathogens, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), that encode no mimic. CD47 upregulation was revealed to be a host response induced by the stimulation of both endosomal and cytosolic pathogen recognition receptors (PRRs). Furthermore, proinflammatory cytokines, including those found in the plasma of hepatitis C patients, upregulated CD47 on uninfected dendritic cells, thereby linking innate modulation with downstream adaptive immune responses. Indeed, results from antibody-mediated CD47 blockade experiments as well as CD47 knockout mice revealed an immunosuppressive role for CD47 during infections with lymphocytic choriomeningitis virus and Mycobacterium tuberculosis. Since CD47 blockade operates at the level of pattern recognition receptors rather than at a pathogen or antigen-specific level, these findings identify CD47 as a novel potential immunotherapeutic target for the enhancement of immune responses to a broad range of infectious agents.
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25
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Asay BC, Edwards BB, Andrews J, Ramey ME, Richard JD, Podell BK, Gutiérrez JFM, Frank CB, Magunda F, Robertson GT, Lyons M, Ben-Hur A, Lenaerts AJ. Digital Image Analysis of Heterogeneous Tuberculosis Pulmonary Pathology in Non-Clinical Animal Models using Deep Convolutional Neural Networks. Sci Rep 2020; 10:6047. [PMID: 32269234 PMCID: PMC7142129 DOI: 10.1038/s41598-020-62960-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 03/18/2020] [Indexed: 01/28/2023] Open
Abstract
Efforts to develop effective and safe drugs for treatment of tuberculosis require preclinical evaluation in animal models. Alongside efficacy testing of novel therapies, effects on pulmonary pathology and disease progression are monitored by using histopathology images from these infected animals. To compare the severity of disease across treatment cohorts, pathologists have historically assigned a semi-quantitative histopathology score that may be subjective in terms of their training, experience, and personal bias. Manual histopathology therefore has limitations regarding reproducibility between studies and pathologists, potentially masking successful treatments. This report describes a pathologist-assistive software tool that reduces these user limitations, while providing a rapid, quantitative scoring system for digital histopathology image analysis. The software, called 'Lesion Image Recognition and Analysis' (LIRA), employs convolutional neural networks to classify seven different pathology features, including three different lesion types from pulmonary tissues of the C3HeB/FeJ tuberculosis mouse model. LIRA was developed to improve the efficiency of histopathology analysis for mouse tuberculosis infection models, this approach has also broader applications to other disease models and tissues. The full source code and documentation is available from https://Github.com/TB-imaging/LIRA.
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Affiliation(s)
- Bryce C Asay
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Blake Blue Edwards
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Department of Computer Science, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jenna Andrews
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Michelle E Ramey
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jameson D Richard
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Brendan K Podell
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Juan F Muñoz Gutiérrez
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Chad B Frank
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Forgivemore Magunda
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Gregory T Robertson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Michael Lyons
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Asa Ben-Hur
- Department of Computer Science, Colorado State University, Fort Collins, Colorado, United States of America
| | - Anne J Lenaerts
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America.
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26
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Mouton JM, Heunis T, Dippenaar A, Gallant JL, Kleynhans L, Sampson SL. Comprehensive Characterization of the Attenuated Double Auxotroph Mycobacterium tuberculosisΔ leuDΔ panCD as an Alternative to H37Rv. Front Microbiol 2019; 10:1922. [PMID: 31481950 PMCID: PMC6710366 DOI: 10.3389/fmicb.2019.01922] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/05/2019] [Indexed: 01/04/2023] Open
Abstract
Although currently available model organisms such as Mycobacterium smegmatis and Mycobacterium bovis Bacillus Calmette-Guérin (BCG) have significantly contributed to our understanding of tuberculosis (TB) biology, these models have limitations such as differences in genome size, growth rates and virulence. However, attenuated Mycobacterium tuberculosis strains may provide more representative, safer models to study M. tuberculosis biology. For example, the M. tuberculosis ΔleuDΔpanCD double auxotroph, has undergone rigorous in vitro and in vivo safety testing. Like other auxotrophic strains, this has subsequently been approved for use in biosafety level (BSL) 2 facilities. Auxotrophic strains have been assessed as models for drug-resistant M. tuberculosis and for studying latent TB. These offer the potential as safe and useful models, but it is important to understand how well these recapitulate salient features of non-attenuated M. tuberculosis. We therefore performed a comprehensive comparison of M. tuberculosis H37Rv and M. tuberculosisΔleuDΔpanCD. These strains demonstrated similar in vitro and intra-macrophage replication rates, similar responses to anti-TB agents and whole genome sequence conservation. Shotgun proteomics analysis suggested that M. tuberculosisΔleuDΔpanCD has a heightened stress response that leads to reduced bacterial replication during exposure to acid stress, which has been verified using a dual-fluorescent replication reporter assay. Importantly, infection of human peripheral blood mononuclear cells with the 2 strains elicited comparable cytokine production, demonstrating the suitability of M. tuberculosisΔleuDΔpanCD for immunological assays. We provide comprehensive evidence to support the judicious use of M. tuberculosisΔleuDΔpanCD as a safe and suitable model organism for M. tuberculosis research, without the need for a BSL3 facility.
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Affiliation(s)
- Jomien M Mouton
- Department of Science and Technology/National Research Foundation (DST/NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Tiaan Heunis
- Department of Science and Technology/National Research Foundation (DST/NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Anzaan Dippenaar
- Department of Science and Technology/National Research Foundation (DST/NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - James L Gallant
- Department of Science and Technology/National Research Foundation (DST/NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Section of Molecular Microbiology, Amsterdam Institute of Molecules, Medicines, and Systems, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Léanie Kleynhans
- Department of Science and Technology/National Research Foundation (DST/NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Samantha L Sampson
- Department of Science and Technology/National Research Foundation (DST/NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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27
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Bactericidal Disruption of Magnesium Metallostasis in Mycobacterium tuberculosis Is Counteracted by Mutations in the Metal Ion Transporter CorA. mBio 2019; 10:mBio.01405-19. [PMID: 31289182 PMCID: PMC6747715 DOI: 10.1128/mbio.01405-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Antimycobacterial agents might shorten the course of treatment by reducing the number of phenotypically tolerant bacteria if they could kill M. tuberculosis in diverse metabolic states. Here we report two chemically disparate classes of agents that kill M. tuberculosis both when it is replicating and when it is not. Under replicating conditions, the tricyclic 4-hydroxyquinolines and a barbituric acid analogue deplete intrabacterial magnesium as a mechanism of action, and for both compounds, mutations in CorA, a putative Mg2+/Co2+ transporter, conferred resistance to the compounds when M. tuberculosis was under replicating conditions but not under nonreplicating conditions, illustrating that a given compound can kill M. tuberculosis in different metabolic states by disparate mechanisms. Targeting magnesium metallostasis represents a previously undescribed antimycobacterial mode of action that might cripple M. tuberculosis in a Mg2+-deficient intraphagosomal environment of macrophages. A defining characteristic of treating tuberculosis is the need for prolonged administration of multiple drugs. This may be due in part to subpopulations of slowly replicating or nonreplicating Mycobacterium tuberculosis bacilli exhibiting phenotypic tolerance to most antibiotics in the standard treatment regimen. Confounding this problem is the increasing incidence of heritable multidrug-resistant M. tuberculosis. A search for new antimycobacterial chemical scaffolds that can kill phenotypically drug-tolerant mycobacteria uncovered tricyclic 4-hydroxyquinolines and a barbituric acid derivative with mycobactericidal activity against both replicating and nonreplicating M. tuberculosis. Both families of compounds depleted M. tuberculosis of intrabacterial magnesium. Complete or partial resistance to both chemotypes arose from mutations in the putative mycobacterial Mg2+/Co2+ ion channel, CorA. Excess extracellular Mg2+, but not other divalent cations, diminished the compounds’ cidality against replicating M. tuberculosis. These findings establish depletion of intrabacterial magnesium as an antimicrobial mechanism of action and show that M. tuberculosis magnesium homeostasis is vulnerable to disruption by structurally diverse, nonchelating, drug-like compounds.
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28
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Mandal S, Njikan S, Kumar A, Early JV, Parish T. The relevance of persisters in tuberculosis drug discovery. MICROBIOLOGY-SGM 2019; 165:492-499. [PMID: 30775961 DOI: 10.1099/mic.0.000760] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Bacterial persisters are a subpopulation of cells that exhibit phenotypic resistance during exposure to a lethal dose of antibiotics. They are difficult to target and thought to contribute to the long treatment duration required for tuberculosis. Understanding the molecular and cellular biology of persisters is critical to finding new tuberculosis drugs that shorten treatment. This review focuses on mycobacterial persisters and describes the challenges they pose in tuberculosis therapy, their characteristics and formation, how persistence leads to resistance, and the current approaches being used to target persisters within mycobacterial drug discovery.
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Affiliation(s)
- Soma Mandal
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Ave. E, Suite 400, Seattle, WA 98102, USA
| | - Samuel Njikan
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Ave. E, Suite 400, Seattle, WA 98102, USA
| | - Anuradha Kumar
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Ave. E, Suite 400, Seattle, WA 98102, USA
| | - Julie V Early
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Ave. E, Suite 400, Seattle, WA 98102, USA
| | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Ave. E, Suite 400, Seattle, WA 98102, USA
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29
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Abdallah AM, Weerdenburg EM, Guan Q, Ummels R, Borggreve S, Adroub SA, Malas TB, Naeem R, Zhang H, Otto TD, Bitter W, Pain A. Integrated transcriptomic and proteomic analysis of pathogenic mycobacteria and their esx-1 mutants reveal secretion-dependent regulation of ESX-1 substrates and WhiB6 as a transcriptional regulator. PLoS One 2019; 14:e0211003. [PMID: 30673778 PMCID: PMC6343904 DOI: 10.1371/journal.pone.0211003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 01/04/2019] [Indexed: 12/14/2022] Open
Abstract
The mycobacterial type VII secretion system ESX-1 is responsible for the secretion of a number of proteins that play important roles during host infection. The regulation of the expression of secreted proteins is often essential to establish successful infection. Using transcriptome sequencing, we found that the abrogation of ESX-1 function in Mycobacterium marinum leads to a pronounced increase in gene expression levels of the espA operon during the infection of macrophages. In addition, the disruption of ESX-1-mediated protein secretion also leads to a specific down-regulation of the ESX-1 substrates, but not of the structural components of this system, during growth in culture medium. This effect is observed in both M. marinum and M. tuberculosis. We established that down-regulation of ESX-1 substrates is the result of a regulatory process that is influenced by the putative transcriptional regulator whib6, which is located adjacent to the esx-1 locus. In addition, the overexpression of the ESX-1-associated PE35/PPE68 protein pair resulted in a significantly increased secretion of the ESX-1 substrate EsxA, demonstrating a functional link between these proteins. Taken together, these data show that WhiB6 is required for the secretion-dependent regulation of ESX-1 substrates and that ESX-1 substrates are regulated independently from the structural components, both during infection and as a result of active secretion.
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Affiliation(s)
- Abdallah M. Abdallah
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal-Jeddah, Kingdom of Saudi Arabia
- * E-mail: (AMA); (WB); (AP)
| | - Eveline M. Weerdenburg
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - Qingtian Guan
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal-Jeddah, Kingdom of Saudi Arabia
| | - Roy Ummels
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - Stephanie Borggreve
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - Sabir A. Adroub
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal-Jeddah, Kingdom of Saudi Arabia
| | - Tareq B. Malas
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal-Jeddah, Kingdom of Saudi Arabia
| | - Raeece Naeem
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal-Jeddah, Kingdom of Saudi Arabia
| | - Huoming Zhang
- Bioscience Core Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal-Jeddah, Kingdom of Saudi Arabia
| | - Thomas D. Otto
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
- * E-mail: (AMA); (WB); (AP)
| | - Arnab Pain
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal-Jeddah, Kingdom of Saudi Arabia
- * E-mail: (AMA); (WB); (AP)
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30
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Soundarya JSV, Ranganathan UD, Tripathy SP. Current trends in tuberculosis vaccine. Med J Armed Forces India 2019; 75:18-24. [PMID: 30705473 DOI: 10.1016/j.mjafi.2018.12.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 12/26/2018] [Indexed: 12/21/2022] Open
Abstract
Despite the global efforts made to control tuberculosis (TB) and the large number of available new anti-TB drugs, TB still affects one-third of the world population. The conventional vaccine bacille Calmette-Guérin (BCG) shows varying efficacy in different populations, and there are safety issues in immunocompromised patients. Hence, there is an urgent requirement for a new and better TB vaccine candidate than BCG. There are several alternate vaccines available for TB such as DNA, subunit, adjuvant, and live-attenuated vaccines. Use of auxotrophic vaccine is an emerging technology. Newer vaccine technologies include vaccine delivery methods such as adenovirus- and cytomegalovirus (CMV)-based vector delivery, chimeric monoclonal antibody, single-chain fragment variable, RNA-lipoplexes, and nanoparticle-based technology. Based on its application, TB vaccines are classified as conventional, prophylactic, booster, therapeutic, and reinfection preventive vaccines. Currently, there are 12 vaccine candidates in clinical trials. In this review, we have briefly discussed about each of these vaccines in different phases of clinical trials. These vaccines should be analyzed further for developing a safe and more efficacious vaccine for TB.
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Affiliation(s)
- J S V Soundarya
- PhD Research Scholar, Department of Immunology, National Institute for Research in Tuberculosis, Chennai 600031, India
| | - Uma Devi Ranganathan
- Scientist 'D', Department of Immunology, National Institute for Research in Tuberculosis, Chennai 600031, India
| | - Srikanth P Tripathy
- Scientist 'G' & Director-in-charge, National Institute for Research in Tuberculosis, Chennai 600031, India
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31
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Nurul Islam M, Hitchings R, Kumar S, Fontes FL, Lott JS, Kruh-Garcia NA, Crick DC. Mechanism of Fluorinated Anthranilate-Induced Growth Inhibition in Mycobacterium tuberculosis. ACS Infect Dis 2019; 5:55-62. [PMID: 30406991 DOI: 10.1021/acsinfecdis.8b00092] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The biosynthesis of tryptophan in Mycobacterium tuberculosis is initiated by the transformation of chorismate to anthranilate, catalyzed by anthranilate synthase (TrpE/TrpG). Five additional enzymes are required to complete tryptophan biosynthesis. M. tuberculosis strains auxotrophic for tryptophan, an essential amino acid in the human diet, are avirulent. Thus, tryptophan synthesis in M. tuberculosis has been suggested as a potential drug target, and it has been reported that fluorinated anthranilate is lethal to the bacillus. Two mechanisms that could explain the cellular toxicity were tested: (1) the inhibition of tryptophan biosynthesis by a fluorinated intermediate or (2) formation of fluorotryptophan and its subsequent effects. Here, M. tuberculosis mc2 6230 cultures were treated with anthranilates fluorinated at positions 4, 5, and 6. These compounds inhibited bacterial growth on tryptophan-free media with 4-fluoroanthranilate being more potent than 5-fluoroanthranilate or 6-fluoroanthranilate. LC-MS based analysis of extracts from bacteria treated with these compounds did not reveal accumulation of any of the expected fluorinated intermediates in tryptophan synthesis. However, in all cases, significant levels of fluorotryptophan were readily observed, suggesting that the enzymes involved in the conversion of fluoro-anthranilate to fluorotryptophan were not being inhibited. Inclusion of tryptophan in cultures treated with the fluoro-anthranilates obviated the cellular toxicity. Bacterial growth was also inhibited in a dose-dependent manner by exposure to tryptophan substituted with fluorine at positions 5 or 6. Thus, the data suggest that fluorotryptophan rather than fluoro-anthranilate or intermediates in the synthesis of fluorotryptophan causes the inhibition of M. tuberculosis growth.
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Affiliation(s)
- M. Nurul Islam
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Reese Hitchings
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Santosh Kumar
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Fabio L. Fontes
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - J. Shaun Lott
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Nicole A. Kruh-Garcia
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Dean C. Crick
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
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De Groote MA, Jarvis TC, Wong C, Graham J, Hoang T, Young CL, Ribble W, Day J, Li W, Jackson M, Gonzalez-Juarrero M, Sun X, Ochsner UA. Optimization and Lead Selection of Benzothiazole Amide Analogs Toward a Novel Antimycobacterial Agent. Front Microbiol 2018; 9:2231. [PMID: 30294313 PMCID: PMC6158578 DOI: 10.3389/fmicb.2018.02231] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/31/2018] [Indexed: 12/14/2022] Open
Abstract
Mycobacteria remain an important problem worldwide, especially drug resistant human pathogens. Novel therapeutics are urgently needed to tackle both drug-resistant tuberculosis (TB) and difficult-to-treat infections with nontuberculous mycobacteria (NTM). Benzothiazole adamantyl amide had previously emerged as a high throughput screening hit against M. tuberculosis (Mtb) and was subsequently found to be active against NTM as well. For lead optimization, we applied an iterative process of design, synthesis and screening of several 100 analogs to improve antibacterial potency as well as physicochemical and pharmacological properties to ultimately achieve efficacy. Replacement of the adamantyl group with cyclohexyl derivatives, including bicyclic moieties, resulted in advanced lead compounds that showed excellent potency and a mycobacteria-specific spectrum of activity. MIC values ranged from 0.03 to 0.12 μg/mL against M. abscessus (Mabs) and other rapid- growing NTM, 1–2 μg/mL against M. avium complex (MAC), and 0.12–0.5 μg/mL against Mtb. No pre-existing resistance was found in a collection of n = 54 clinical isolates of rapid-growing NTM. Unlike many antibacterial agents commonly used to treat mycobacterial infections, benzothiazole amides demonstrated bactericidal effects against both Mtb and Mabs. Metabolic labeling provided evidence that the compounds affect the transfer of mycolic acids to their cell envelope acceptors in mycobacteria. Mapping of resistance mutations pointed to the trehalose monomycolate transporter (MmpL3) as the most likely target. In vivo efficacy and tolerability of a benzothiazole amide was demonstrated in a mouse model of chronic NTM lung infection with Mabs. Once daily dosing over 4 weeks by intrapulmonary microspray administration as 5% corn oil/saline emulsion achieved statistically significant CFU reductions compared to vehicle control and non-inferiority compared to azithromycin. The benzothiazole amides hold promise for development of a novel therapeutic agent with broad antimycobacterial activity, though further work is needed to develop drug formulations for direct intrapulmonary delivery via aerosol.
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Affiliation(s)
- Mary A De Groote
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | | | | | | | | | | | | | - Joshua Day
- Crestone, Inc., Boulder, CO, United States
| | - Wei Li
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Mercedes Gonzalez-Juarrero
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
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Lu P, Asseri AH, Kremer M, Maaskant J, Ummels R, Lill H, Bald D. The anti-mycobacterial activity of the cytochrome bcc inhibitor Q203 can be enhanced by small-molecule inhibition of cytochrome bd. Sci Rep 2018; 8:2625. [PMID: 29422632 PMCID: PMC5805707 DOI: 10.1038/s41598-018-20989-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 01/23/2018] [Indexed: 11/09/2022] Open
Abstract
Mycobacterial energy metabolism currently attracts strong attention as new target space for development of anti-tuberculosis drugs. The imidazopyridine Q203 targets the cytochrome bcc complex of the respiratory chain, a key component in energy metabolism. Q203 blocks growth of Mycobacterium tuberculosis at nanomolar concentrations, however, it fails to actually kill the bacteria, which may limit the clinical applicability of this candidate drug. In this report we show that inhibition of cytochrome bd, a parallel branch of the mycobacterial respiratory chain, by aurachin D invoked bactericidal activity of Q203. In biochemical assays using inverted membrane vesicles from Mycobacterium tuberculosis and Mycobacterium smegmatis we found that inhibition of respiratory chain activity by Q203 was incomplete, but could be enhanced by inactivation of cytochrome bd, either by genetic knock-out or by inhibition with aurachin D. These results indicate that simultaneously targeting the cytochrome bcc and the cytochrome bd branch of the mycobacterial respiratory chain may turn out as effective strategy for combating M. tuberculosis.
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Affiliation(s)
- Ping Lu
- Department of Molecular Cell Biology, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Earth- and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Amer H Asseri
- Department of Molecular Cell Biology, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Earth- and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.,Biochemsitry Department, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Martijn Kremer
- Department of Molecular Cell Biology, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Earth- and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Janneke Maaskant
- Department of Medical Microbiology and Infection Control, VU university Medical Center, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Roy Ummels
- Department of Medical Microbiology and Infection Control, VU university Medical Center, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Holger Lill
- Department of Molecular Cell Biology, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Earth- and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Dirk Bald
- Department of Molecular Cell Biology, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Earth- and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
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Köster S, Klevorn T, Papavinasasundaram K, Sassetti CM, Portal-Celhay C, Philips JA. Consequence of enhanced LC3-trafficking for a live, attenuated M. tuberculosis vaccine. Vaccine 2018; 36:939-944. [PMID: 29343411 DOI: 10.1016/j.vaccine.2018.01.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/15/2017] [Accepted: 01/08/2018] [Indexed: 01/01/2023]
Abstract
Development of a new vaccine against tuberculosis is urgently needed. Recent work has demonstrated that two related LC3-associated trafficking pathways, autophagy and LC3-associated phagocytosis (LAP), enhance antigen presentation and might play a role in vaccine efficacy. Mycobacterium tuberculosis inhibits both LC3-trafficking pathways. Moreover, the vaccine strain, BCG, induces even less LC3-trafficking than M. tuberculosis, which may help explain its limited efficacy. To determine whether enhanced LC3-trafficking can improve efficacy of a live, attenuated M. tuberculosis vaccine, we took advantage of our recent finding that the bacterial virulence factor CpsA inhibits LAP. When we deleted cpsA in the mc26206 vaccine strain, it dramatically increased LC3-trafficking. We compared the protective efficacy of the strain lacking cpsA to the parent strain and to BCG in mice challenged with M. tuberculosis. We found that the strain lacking cpsA generated modestly enhanced protection in the spleen, but overall did not outperform BCG.
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Affiliation(s)
- Stefan Köster
- Division of Infectious Diseases, Department of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Thais Klevorn
- Division of Infectious Diseases, Department of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Kadamba Papavinasasundaram
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Cynthia Portal-Celhay
- Division of Infectious Diseases, Department of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Jennifer A Philips
- Division of Infectious Diseases, Department of Medicine, Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Bahal RK, Mathur S, Chauhan P, Tyagi AK. An attenuated quadruple gene mutant of Mycobacterium tuberculosis imparts protection against tuberculosis in guinea pigs. Biol Open 2018; 7:bio.029546. [PMID: 29242198 PMCID: PMC5829500 DOI: 10.1242/bio.029546] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Previously we had developed a triple gene mutant of Mycobacterium tuberculosis (MtbΔmms) harboring disruption in three genes, namely mptpA, mptpB and sapM. Though vaccination with MtbΔmms strain induced protection in the lungs of guinea pigs, the mutant strain failed to control the hematogenous spread of the challenge strain to the spleen. Additionally, inoculation with MtbΔmms resulted in some pathological damage to the spleens in the early phase of infection. In order to generate a strain that overcomes the pathology caused by MtbΔmms in spleen of guinea pigs and controls dissemination of the challenge strain, MtbΔmms was genetically modified by disrupting bioA gene to generate MtbΔmmsb strain. Further, in vivo attenuation of MtbΔmmsb was evaluated and its protective efficacy was assessed against virulent M. tuberculosis challenge in guinea pigs. MtbΔmmsb mutant strain was highly attenuated for growth and virulence in guinea pigs. Vaccination with MtbΔmmsb mutant generated significant protection in comparison to sham-immunized animals at 4 and 12 weeks post-infection in lungs and spleen of infected animals. However, the protection imparted by MtbΔmmsb was significantly less in comparison to BCG immunized animals. This study indicates the importance of attenuated multiple gene deletion mutants of M. tuberculosis for generating protection against tuberculosis. Summary: In this study, a mutant of M. tuberculosis with the deletion of four important genes has been evaluated in guinea pigs for its attenuation and protective efficacy against tuberculosis.
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Affiliation(s)
- Ritika Kar Bahal
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Shubhita Mathur
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Priyanka Chauhan
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Anil K Tyagi
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India .,Guru Gobind Singh Indraprastha University, Sector 16-C, Dwarka, New Delhi 110078, India
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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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Kim BJ, Kim BR, Kook YH, Kim BJ. A temperature sensitive Mycobacterium paragordonae induces enhanced protective immune responses against mycobacterial infections in the mouse model. Sci Rep 2017; 7:15230. [PMID: 29123166 PMCID: PMC5680210 DOI: 10.1038/s41598-017-15458-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 10/25/2017] [Indexed: 01/22/2023] Open
Abstract
Recently, we introduced a temperature sensitive Mycobacterium spp., Mycobacterium paragordonae (Mpg). Here, we checked its potential as a candidate for live vaccination against Mycobacterium tuberculosis and Mycobacterium abscessus. Intravenous infections of mice with Mpg led to lower colony forming units (CFUs) compared to infection with BCG, suggesting its usefulness as a live vaccine. The analyses of immune responses indicated that the highly protective immunity elicited by Mpg was dependent on effective dendritic maturation, shift of cytokine patterns and antibody production toward a Th1 phenotype, and enhanced cytotoxic T cell response. Compared to BCG, Mpg showed a more effective protective immune response in the vaccinated mice against challenges with 2 different mycobacterial strains, M. tuberculosis H37Ra or M. abscessus Asan 50594. Our data suggest that a temperature sensitive Mpg may be a potentially powerful candidate vaccine strain to induce enhanced protective immune responses against M. tuberculosis and M. abscessus.
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Affiliation(s)
- Byoung-Jun Kim
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, College of Medicine, Seoul National University, Seoul, Korea
| | - Bo-Ram Kim
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, College of Medicine, Seoul National University, Seoul, Korea
| | - Yoon-Hoh Kook
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, College of Medicine, Seoul National University, Seoul, Korea
| | - Bum-Joon Kim
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, College of Medicine, Seoul National University, Seoul, Korea.
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Abstract
INTRODUCTION Tuberculosis (TB) is an infectious disease caused mainly by Mycobacterium tuberculosis. In 2016, the WHO estimated 10.5 million new cases and 1.8 million deaths, making this disease the leading cause of death by an infectious agent. The current and projected TB situation necessitates the development of new vaccines with improved attributes compared to the traditional BCG method. Areas covered: In this review, the authors describe the most promising candidate vaccines against TB and discuss additional key elements in vaccine development, such as animal models, new adjuvants and immunization routes and new strategies for the identification of candidate vaccines. Expert opinion: At present, around 13 candidate vaccines for TB are in the clinical phase of evaluation; however, there is still no substitute for the BCG vaccine. One major impediment to developing an effective vaccine is our lack of understanding of several of the mechanisms associated with infection and the immune response against TB. However, the recent implementation of an entirely new set of technological advances will facilitate the proposal of new candidates. Finally, development of a new vaccine will require a major coordination of effort in order to achieve its effective administration to the people most in need of it.
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Abstract
Bacille Calmette-Guérin (BCG), the only tuberculosis (TB) vaccine in clinical practice, has limitations in efficacy, immunogenicity and safety. Much current TB vaccine research focuses on engineering live mycobacteria to interfere with phagosome biology and host intracellular pathways including apoptosis and autophagy, with candidates such as BCG Δzmp1, BCG ΔureC::hly, BCG::ESX-1Mmar, Mtb ΔphoP ΔfadD26, Mtb ΔRD1 ΔpanCD and M. smegmatis Δesx-3::esx-3(Mtb) in the development pipeline. Correlates of protection in preclinical studies include increased central memory CD4+ T cells and recruitment of antigen-specific T cells to the lungs, with mucosal vaccination found to be superior to parenteral vaccination. Finally, recent studies suggest beneficial non-specific effects of BCG on immunity, which should be taken into account when considering these vaccines for BCG replacement.
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40
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Kar R, Nangpal P, Mathur S, Singh S, Tyagi AK. bioA mutant of Mycobacterium tuberculosis shows severe growth defect and imparts protection against tuberculosis in guinea pigs. PLoS One 2017; 12:e0179513. [PMID: 28658275 PMCID: PMC5489182 DOI: 10.1371/journal.pone.0179513] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/30/2017] [Indexed: 01/03/2023] Open
Abstract
Owing to the devastation caused by tuberculosis along with the unsatisfactory performance of the Bacillus Calmette–Guérin (BCG) vaccine, a more efficient vaccine than BCG is required for the global control of tuberculosis. A number of studies have demonstrated an essential role of biotin biosynthesis in the growth and survival of several microorganisms, including mycobacteria, through deletion of the genes involved in de novo biotin biosynthesis. In this study, we demonstrate that a bioA mutant of Mycobacterium tuberculosis (MtbΔbioA) is highly attenuated in the guinea pig model of tuberculosis when administered aerogenically as well as intradermally. Immunization with MtbΔbioA conferred significant protection in guinea pigs against an aerosol challenge with virulent M. tuberculosis, when compared with the unvaccinated animals. Booster immunization with MtbΔbioA offered no advantage over a single immunization. These experiments demonstrate the vaccinogenic potential of the attenuated M. tuberculosis bioA mutant against tuberculosis.
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Affiliation(s)
- Ritika Kar
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi, India
| | - Prachi Nangpal
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi, India
| | - Shubhita Mathur
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi, India
| | - Swati Singh
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi, India
| | - Anil K. Tyagi
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi, India
- Vice Chancellor, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, India
- * E-mail:
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41
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Gold B, Nathan C. Targeting Phenotypically Tolerant Mycobacterium tuberculosis. Microbiol Spectr 2017; 5:10.1128/microbiolspec.tbtb2-0031-2016. [PMID: 28233509 PMCID: PMC5367488 DOI: 10.1128/microbiolspec.tbtb2-0031-2016] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Indexed: 01/08/2023] Open
Abstract
While the immune system is credited with averting tuberculosis in billions of individuals exposed to Mycobacterium tuberculosis, the immune system is also culpable for tempering the ability of antibiotics to deliver swift and durable cure of disease. In individuals afflicted with tuberculosis, host immunity produces diverse microenvironmental niches that support suboptimal growth, or complete growth arrest, of M. tuberculosis. The physiological state of nonreplication in bacteria is associated with phenotypic drug tolerance. Many of these host microenvironments, when modeled in vitro by carbon starvation, complete nutrient starvation, stationary phase, acidic pH, reactive nitrogen intermediates, hypoxia, biofilms, and withholding streptomycin from the streptomycin-addicted strain SS18b, render M. tuberculosis profoundly tolerant to many of the antibiotics that are given to tuberculosis patients in clinical settings. Targeting nonreplicating persisters is anticipated to reduce the duration of antibiotic treatment and rate of posttreatment relapse. Some promising drugs to treat tuberculosis, such as rifampin and bedaquiline, only kill nonreplicating M. tuberculosisin vitro at concentrations far greater than their minimal inhibitory concentrations against replicating bacilli. There is an urgent demand to identify which of the currently used antibiotics, and which of the molecules in academic and corporate screening collections, have potent bactericidal action on nonreplicating M. tuberculosis. With this goal, we review methods of high-throughput screening to target nonreplicating M. tuberculosis and methods to progress candidate molecules. A classification based on structures and putative targets of molecules that have been reported to kill nonreplicating M. tuberculosis revealed a rich diversity in pharmacophores.
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Affiliation(s)
- Ben Gold
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065
| | - Carl Nathan
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065
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Tallman KR, Levine SR, Beatty KE. Small-Molecule Probes Reveal Esterases with Persistent Activity in Dormant and Reactivating Mycobacterium tuberculosis. ACS Infect Dis 2016; 2:936-944. [PMID: 27690385 DOI: 10.1021/acsinfecdis.6b00135] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is the deadliest bacterial pathogen in the world. An estimated one-third of humans harbor Mtb in a dormant state. These asymptomatic, latent infections impede tuberculosis eradication due to the long-term potential for reactivation. Dormant Mtb has reduced enzymatic activity, but hydrolases that remain active facilitate pathogen survival. We targeted Mtb esterases, a diverse set of enzymes in the serine hydrolase family, and studied their activities using both activity-based probes (ABPs) and fluorogenic esterase substrates. These small-molecule probes revealed functional esterases in active, dormant, and reactivating cultures. Using ABPs, we identified five esterases that remained active in dormant Mtb, including LipM (Rv2284), LipN (Rv2970c), CaeA (Rv2224c), Rv0183, and Rv1683. Three of these, CaeA, Rv0183, and Rv1683, were catalytically active in all three culture conditions. Fluorogenic probes additionally revealed LipH (Rv1399c), Culp1 (Rv1984c), and Rv3036c esterase activity in dormant and active cultures. Esterases with persistent activity are potential diagnostic biomarkers or therapeutic targets for Mtb-infected individuals with latent or active tuberculosis.
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Affiliation(s)
- Katie R. Tallman
- Program in Chemical Biology and Department of Biomedical Engineering, Oregon Health & Science University, Mail Code CL3B, 2730 S.W. Moody Avenue, Portland, Oregon 97201, United States
| | - Samantha R. Levine
- Program in Chemical Biology and Department of Biomedical Engineering, Oregon Health & Science University, Mail Code CL3B, 2730 S.W. Moody Avenue, Portland, Oregon 97201, United States
| | - Kimberly E. Beatty
- Program in Chemical Biology and Department of Biomedical Engineering, Oregon Health & Science University, Mail Code CL3B, 2730 S.W. Moody Avenue, Portland, Oregon 97201, United States
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43
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Tallman KR, Levine SR, Beatty KE. Profiling Esterases in Mycobacterium tuberculosis Using Far-Red Fluorogenic Substrates. ACS Chem Biol 2016; 11:1810-5. [PMID: 27177211 DOI: 10.1021/acschembio.6b00233] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Enzyme-activated, fluorogenic probes are powerful tools for studying bacterial pathogens, including Mycobacterium tuberculosis (Mtb). In prior work, we reported two 7-hydroxy-9H-(1,3-dichloro-9,9-dimethylacridin-2-one) (DDAO)-derived acetoxymethyl ether probes for esterase and lipase detection. Here, we report four-carbon (C4) and eight-carbon (C8) acyloxymethyl ether derivatives, which are longer-chain fluorogenic substrates. These new probes demonstrate greater stability and lipase reactivity than the two-carbon (C2) acetoxymethyl ether-masked substrates. We used these new C4 and C8 probes to profile esterases and lipases from Mtb. The C8-masked probes revealed a new esterase band in gel-resolved Mtb lysates that was not present in lysates from nonpathogenic M. bovis (bacillus Calmette-Guérin), a close genetic relative. We identified this Mtb-specific enzyme as the secreted esterase Culp1 (Rv1984c). Our C4- and C8-masked probes also produced distinct Mtb banding patterns in lysates from Mtb-infected macrophages, demonstrating the potential of these probes for detecting Mtb esterases that are active during infections.
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Affiliation(s)
- Katie R. Tallman
- Program in Chemical Biology and the Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon 97201, United States
| | - Samantha R. Levine
- Program in Chemical Biology and the Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon 97201, United States
| | - Kimberly E. Beatty
- Program in Chemical Biology and the Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon 97201, United States
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44
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Gold B, Smith R, Nguyen Q, Roberts J, Ling Y, Lopez Quezada L, Somersan S, Warrier T, Little D, Pingle M, Zhang D, Ballinger E, Zimmerman M, Dartois V, Hanson P, Mitscher LA, Porubsky P, Rogers S, Schoenen FJ, Nathan C, Aubé J. Novel Cephalosporins Selectively Active on Nonreplicating Mycobacterium tuberculosis. J Med Chem 2016; 59:6027-44. [PMID: 27144688 PMCID: PMC4947980 DOI: 10.1021/acs.jmedchem.5b01833] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We report two series of novel cephalosporins that are bactericidal to Mycobacterium tuberculosis alone of the pathogens tested, which only kill M. tuberculosis when its replication is halted by conditions resembling those believed to pertain in the host, and whose bactericidal activity is not dependent upon or enhanced by clavulanate, a β-lactamase inhibitor. The two classes of cephalosporins bear an ester or alternatively an oxadiazole isostere at C-2 of the cephalosporin ring system, a position that is almost exclusively a carboxylic acid in clinically used agents in the class. Representatives of the series kill M. tuberculosis within macrophages without toxicity to the macrophages or other mammalian cells.
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Affiliation(s)
| | | | - Quyen Nguyen
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | | | | | | | | | | | | | | | | | | | - Matthew Zimmerman
- Public Health Research Institute, New Jersey Medical School, Rutgers, the State University of New Jersey , Newark, New Jersey 07013, United States
| | - Véronique Dartois
- Public Health Research Institute, New Jersey Medical School, Rutgers, the State University of New Jersey , Newark, New Jersey 07013, United States
| | | | | | | | - Steven Rogers
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | | | | | - Jeffrey Aubé
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
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Scriba TJ, Kaufmann SHE, Henri Lambert P, Sanicas M, Martin C, Neyrolles O. Vaccination Against Tuberculosis With Whole-Cell Mycobacterial Vaccines. J Infect Dis 2016; 214:659-64. [PMID: 27247343 DOI: 10.1093/infdis/jiw228] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/24/2016] [Indexed: 12/20/2022] Open
Abstract
Live attenuated and killed whole-cell vaccines (WCVs) offer promising vaccination strategies against tuberculosis. A number of WCV candidates, based on recombinant bacillus Calmette-Guerin (BCG), attenuated Mycobacterium tuberculosis, or related mycobacterial species are in various stages of preclinical or clinical development. In this review, we discuss the vaccine candidates and key factors shaping the development pathway for live and killed WCVs and provide an update on progress.
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Affiliation(s)
- Thomas J Scriba
- Department of Pathology, South African Tuberculosis Vaccine Initiative Institute of Infectious Disease and Molecular Medicine Division of Immunology, University of Cape Town, South Africa
| | - Stefan H E Kaufmann
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Paul Henri Lambert
- Center of Vaccinology, University Medical Center, University of Geneva, Switzerland
| | | | - Carlos Martin
- Department of Microbiology, Faculty of Medicine, University of Zaragoza ISS Aragón Zaragoza CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Olivier Neyrolles
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale) Université de Toulouse, UPS, IPBS, France
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Torrey HL, Keren I, Via LE, Lee JS, Lewis K. High Persister Mutants in Mycobacterium tuberculosis. PLoS One 2016; 11:e0155127. [PMID: 27176494 PMCID: PMC4866775 DOI: 10.1371/journal.pone.0155127] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 04/25/2016] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium tuberculosis forms drug-tolerant persister cells that are the probable cause of its recalcitrance to antibiotic therapy. While genetically identical to the rest of the population, persisters are dormant, which protects them from killing by bactericidal antibiotics. The mechanism of persister formation in M. tuberculosis is not well understood. In this study, we selected for high persister (hip) mutants and characterized them by whole genome sequencing and transcriptome analysis. In parallel, we identified and characterized clinical isolates that naturally produce high levels of persisters. We compared the hip mutants obtained in vitro with clinical isolates to identify candidate persister genes. Genes involved in lipid biosynthesis, carbon metabolism, toxin-antitoxin systems, and transcriptional regulators were among those identified. We also found that clinical hip isolates exhibited greater ex vivo survival than the low persister isolates. Our data suggest that M. tuberculosis persister formation involves multiple pathways, and hip mutants may contribute to the recalcitrance of the infection.
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Affiliation(s)
- Heather L. Torrey
- Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Iris Keren
- Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Laura E. Via
- Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jong Seok Lee
- International Tuberculosis Research Center, Changwon, Republic of Korea
| | - Kim Lewis
- Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
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Tang J, Yam WC, Chen Z. Mycobacterium tuberculosis infection and vaccine development. Tuberculosis (Edinb) 2016; 98:30-41. [PMID: 27156616 DOI: 10.1016/j.tube.2016.02.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 02/22/2016] [Indexed: 12/17/2022]
Abstract
Following HIV/AIDS, tuberculosis (TB) continues to be the second most deadly infectious disease in humans. The global TB prevalence has become worse in recent years due to the emergence of multi-drug resistant (MDR) and extensively-drug resistant (XDR) strains, as well as co-infection with HIV. Although Bacillus Calmette-Guérin (BCG) vaccine has nearly been used for a century in many countries, it does not protect adult pulmonary tuberculosis and even causes disseminated BCG disease in HIV-positive population. It is impossible to use BCG to eliminate the Mycobacterium tuberculosis (M. tb) infection or to prevent TB onset and reactivation. Consequently, novel vaccines are urgently needed for TB prevention and immunotherapy. In this review, we discuss the TB prevalence, interaction between M. tb and host immune system, as well as recent progress of TB vaccine research and development.
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Affiliation(s)
- Jiansong Tang
- AIDS Institute and Department of Microbiology, Research Centre for Infection and Immunity, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Wing-Cheong Yam
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Zhiwei Chen
- AIDS Institute and Department of Microbiology, Research Centre for Infection and Immunity, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region; HKU-AIDS Institute Shenzhen Research Laboratory and AIDS Clinical Research Laboratory, Guangdong Key Laboratory of Emerging Infectious Diseases and Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People's Hospital, Guangdong Medical College, Shenzhen, PR China.
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Samala G, Devi PB, Saxena S, Meda N, Yogeeswari P, Sriram D. Design, synthesis and biological evaluation of imidazo[2,1-b]thiazole and benzo[d]imidazo[2,1-b]thiazole derivatives as Mycobacterium tuberculosis pantothenate synthetase inhibitors. Bioorg Med Chem 2016; 24:1298-307. [PMID: 26867485 DOI: 10.1016/j.bmc.2016.01.059] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 01/29/2016] [Accepted: 01/30/2016] [Indexed: 11/29/2022]
Abstract
In the present study, we have designed imidazo[2,1-b]thiazole and benzo[d]imidazo[2,1-b]thiazole derivatives from earlier reported imidazo[1,2-a]pyridine based Mycobacterium tuberculosis (MTB) pantothenate synthetase (PS) inhibitors. We synthesized thirty compounds and they were evaluated for MTB PS inhibition study, in vitro anti-TB activities against replicative and non-replicative MTB, in vivo activity using Mycobacterium marinum infected Zebra fish and cytotoxicity against RAW 264.7 cell line. Among them compound 2-methyl-N'-(4-phenoxybenzoyl)benzo[d]imidazo[2,1-b]thiazole-3-carbohydrazide (5bc) emerged as potent compound active against MTB PS with IC50 of 0.53±0.13 μM, MIC of 3.53 μM, 2.1 log reduction against nutrient starved MTB, with 33% cytotoxicity at 50 μM. It also showed 1.5 log reduction of M. marinum load in Zebra fish at 10mg/kg.
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Affiliation(s)
- Ganesh Samala
- Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Shameerpet, Hyderabad 500078, India
| | - Parthiban Brindha Devi
- Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Shameerpet, Hyderabad 500078, India
| | - Shalini Saxena
- Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Shameerpet, Hyderabad 500078, India
| | - Nikhila Meda
- Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Shameerpet, Hyderabad 500078, India
| | - Perumal Yogeeswari
- Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Shameerpet, Hyderabad 500078, India
| | - Dharmarajan Sriram
- Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Shameerpet, Hyderabad 500078, India.
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Abstract
Pantothenate is vitamin B5 and is the key precursor for the biosynthesis of coenzyme A (CoA), a universal and essential cofactor involved in a myriad of metabolic reactions, including the synthesis of phospholipids, the synthesis and degradation of fatty acids, and the operation of the tricarboxylic acid cycle. CoA is also the only source of the phosphopantetheine prosthetic group for enzymes that shuttle intermediates between the active sites of enzymes involved in fatty acid, nonribosomal peptide, and polyketide synthesis. Pantothenate can be synthesized de novo and/or transported into the cell through a pantothenatepermease. Pantothenate uptake is essential for those organisms that lack the genes to synthesize this vitamin. The intracellular levels of CoA are controlled by the balance between synthesis and degradation. In particular, CoA is assembled in five enzymatic steps, starting from the phosphorylation of pantothenate to phosphopantothenatecatalyzed by pantothenate kinase, the product of the coaA gene. In some bacteria, the production of phosphopantothenate by pantothenate kinase is the rate limiting and most regulated step in the biosynthetic pathway. CoA synthesis additionally networks with other vitamin-associated pathways, such as thiamine and folic acid.
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50
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Pavelka MS. One of these is not like the others. Trends Microbiol 2015; 23:668-670. [PMID: 26439291 DOI: 10.1016/j.tim.2015.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 09/21/2015] [Indexed: 02/01/2023]
Abstract
A Mycobacterium tuberculosis metA mutant that is auxotrophic for methionine is unlike other auxotrophic mutants of this important species as methionine starvation results in rapid death instead of cessation of growth. Evidence suggests that this phenotype results from starvation affecting essential pathways that utilize S-adenosylmethionine in addition to methionine.
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Affiliation(s)
- Martin S Pavelka
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA.
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