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Patel RR, Arun PP, Singh SK, Singh M. Mycobacterial biofilms: Understanding the genetic factors playing significant role in pathogenesis, resistance and diagnosis. Life Sci 2024; 351:122778. [PMID: 38879157 DOI: 10.1016/j.lfs.2024.122778] [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: 12/27/2023] [Revised: 05/25/2024] [Accepted: 06/04/2024] [Indexed: 07/03/2024]
Abstract
Even though the genus Mycobacterium is a diverse group consisting of a majority of environmental bacteria known as non-tuberculous mycobacteria (NTM), it also contains some of the deadliest pathogens (Mycobacterium tuberculosis) in history associated with chronic disease called tuberculosis (TB). Formation of biofilm is one of the unique strategies employed by mycobacteria to enhance their ability to survive in hostile conditions. Biofilm formation by Mycobacterium species is an emerging area of research with significant implications for understanding its pathogenesis and treatment of related infections, specifically TB. This review provides an overview of the biofilm-forming abilities of different species of Mycobacterium and the genetic factors influencing biofilm formation with a detailed focus on M. tuberculosis. Biofilm-mediated resistance is a significant challenge as it can limit antibiotic penetration and promote the survival of dormant mycobacterial cells. Key genetic factors promoting biofilm formation have been explored such as the mmpL genes involved in lipid transport and cell wall integrity as well as the groEL gene essential for mature biofilm formation. Additionally, biofilm-mediated antibiotic resistance and pathogenesis highlighting the specific niches, sites of infection along with the possible mechanisms of biofilm dissemination have been discussed. Furthermore, drug targets within mycobacterial biofilm and their role as potential biomarkers in the development of rapid diagnostic tools have been highlighted. The review summarises the current understanding of the complex nature of Mycobacterium biofilm and its clinical implications, paving the way for advancements in the field of disease diagnosis, management and treatment against its multi-drug resistant species.
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Affiliation(s)
- Ritu Raj Patel
- Department of Medicinal Chemistry, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Pandey Priya Arun
- Department of Medicinal Chemistry, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Sudhir Kumar Singh
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Meenakshi Singh
- Department of Medicinal Chemistry, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India.
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2
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Bhargavi G, Mallakuntla MK, Kale D, Tiwari S. Rv0687 a Putative Short-Chain Dehydrogenase Is Required for In Vitro and In Vivo Survival of Mycobacterium tuberculosis. Int J Mol Sci 2024; 25:7862. [PMID: 39063103 PMCID: PMC11277061 DOI: 10.3390/ijms25147862] [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: 06/12/2024] [Revised: 07/12/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Mycobacterium tuberculosis (Mtb), a successful human pathogen, resides in host sentinel cells and combats the stressful intracellular environment induced by reactive oxygen and nitrogen species during infection. Mtb employs several evasion mechanisms in the face of the host as a survival strategy, including detoxifying enzymes as short-chain dehydrogenases/reductases (SDRs) to withstand host-generated insults. In this study, using specialized transduction, we have generated a Rv0687 deletion mutant and its complemented strain and investigated the functional role of Rv0687, a member of SDRs family genes in Mtb pathogenesis. A wildtype (WT) and a mutant Mtb strain lacking Rv0687 (RvΔ0687) were tested for the in vitro stress response and in vivo survival in macrophages and mice models of infection. The study demonstrates that the deletion of Rv0687 elevated the sensitivity of Mtb to oxidative and nitrosative stress-inducing agents. Furthermore, the lack of Rv0687 compromised the survival of Mtb in primary bone marrow macrophages and led to an increase in the levels of the secreted proinflammatory cytokines TNF-α and MIP-1α. Interestingly, the growth of WT and RvΔ0687 was similar in the lungs of infected immunocompromised mice; however, a significant reduction in RvΔ0687 growth was observed in the spleen of immunocompromised Rag-/- mice at 4 weeks post-infection. Moreover, Rag-/- mice infected with RvΔ0687 survived longer compared to those infected with the WT Mtb strain. Additionally, we observed a significant reduction in the bacterial burden in the spleens and lungs of immunocompetent C57BL/6 mice infected with RvΔ0687 compared to those infected with complemented and WT Mtb strains. Collectively, this study reveals that Rv0687 plays a role in Mtb pathogenesis.
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Affiliation(s)
| | | | | | - Sangeeta Tiwari
- Department of Biological Sciences, Border Biomedical Research Centre, University of Texas at El Paso, El Paso, TX 79968, USA
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3
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Fu X, Wan X, Memon AA, Fan XY, Sun Q, Chen H, Yao Y, Deng Z, Ma J, Ma W. Regulatory role of Mycobacterium tuberculosis MtrA on dormancy/resuscitation revealed by a novel target gene-mining strategy. Front Microbiol 2024; 15:1415554. [PMID: 38952446 PMCID: PMC11215152 DOI: 10.3389/fmicb.2024.1415554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/28/2024] [Indexed: 07/03/2024] Open
Abstract
Introduction The unique dormancy of Mycobacterium tuberculosis plays a significant role in the major clinical treatment challenge of tuberculosis, such as its long treatment cycle, antibiotic resistance, immune escape, and high latent infection rate. Methods To determine the function of MtrA, the only essential response regulator, one strategy was developed to establish its regulatory network according to high-quality genome-wide binding sites. Results and discussion The complex modulation mechanisms were implied by the strong bias distribution of MtrA binding sites in the noncoding regions, and 32.7% of the binding sites were located inside the target genes. The functions of 288 potential MtrA target genes predicted according to 294 confirmed binding sites were highly diverse, and DNA replication and damage repair, lipid metabolism, cell wall component biosynthesis, cell wall assembly, and cell division were the predominant pathways. Among the 53 pathways shared between dormancy/resuscitation and persistence, which accounted for 81.5% and 93.0% of the total number of pathways, respectively, MtrA regulatory genes were identified not only in 73.6% of their mutual pathways, but also in 75.4% of the pathways related to dormancy/resuscitation and persistence respectively. These results suggested the pivotal roles of MtrA in regulating dormancy/resuscitation and the apparent relationship between dormancy/resuscitation and persistence. Furthermore, the finding that 32.6% of the MtrA regulons were essential in vivo and/or in vitro for M. tuberculosis provided new insight into its indispensability. The findings mentioned above indicated that MtrA is a novel promising therapeutic target for tuberculosis treatment since the crucial function of MtrA may be a point of weakness for M. tuberculosis.
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Affiliation(s)
- Xiang Fu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoyu Wan
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Shanghai, China
| | - Aadil Ahmed Memon
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao-Yong Fan
- Shanghai Public Health Clinical Center, Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai, China
| | - Qiuhong Sun
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Shanghai, China
| | - Haifeng Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yufeng Yao
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jian Ma
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Shanghai, China
| | - Wei Ma
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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4
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Sarangi A, Singh SP, Das BS, Rajput S, Fatima S, Bhattacharya D. Mycobacterial biofilms: A therapeutic target against bacterial persistence and generation of antibiotic resistance. Heliyon 2024; 10:e32003. [PMID: 38882302 PMCID: PMC11176842 DOI: 10.1016/j.heliyon.2024.e32003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/18/2024] Open
Abstract
Mycobacterium tuberculosis (M. tb) is the causative agent of Tuberculosis, one of the deadliest infectious diseases. According to the WHO Report 2023, in 2022, approximately 10.6 million people got infected with TB, and 1.6 million died. It has multiple antibiotics for treatment, but the major drawback of anti-tuberculosis therapy (ATT) is, its prolonged treatment duration. The major contributors to the lengthy treatment period are mycobacterial persistence and drug tolerance. Persistent M. tb is phenotypically drug tolerant and metabolically slow down which makes it difficult to be eliminated during ATT. These persisting bacteria are a huge reservoir of impending disease, waiting to get reactivated upon the onset of an immune compromising state. Directly Observed Treatment Short-course, although effective against replicating bacteria; fails to eliminate the drug-tolerant persisters making TB still the second-highest killer globally. There are different mechanisms for the development of drug-tolerant mycobacterial populations being investigated. Recently, the role of biofilms in the survival and host-evasion mechanism of persisters has come to light. Therefore, it is crucial to understand the mechanism of adaptation, survival and attainment of drug tolerance by persisting M. tb-populations, in order to design better immune responses and therapeutics for the effective elimination of these bacteria by reducing the duration of treatment and also circumvent the generation of drug-resistance to achieve the goal of global eradication of TB. This review summarizes the drug-tolerance mechanism and biofilms' role in providing a niche to dormant-M.tb. We also discuss methods of targeting biofilms to achieve sterile eradication of the mycobacteria and prevent its reactivation by achieving adequate immune responses.
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Affiliation(s)
- Ashirbad Sarangi
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Shashi Prakash Singh
- Vaccine and Gene Therapy Institute (VGTI) Oregon National Primate Research Centre (ONPRC) Oregon Health and Science University (OHSU) Beaverton, Oregon, USA
| | - Bhabani Shankar Das
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Sristi Rajput
- Departmental of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh, India
| | - Samreen Fatima
- UMass Chan Medical School, University of Massachusetts, Worcester, MA, USA
| | - Debapriya Bhattacharya
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
- Departmental of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh, India
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5
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Bauman AA, Sarathy JP, Kaya F, Massoudi LM, Scherman MS, Hastings C, Liu J, Xie M, Brooks EJ, Ramey ME, Jones IL, Benedict ND, Maclaughlin MR, Miller-Dawson JA, Waidyarachchi SL, Butler MM, Bowlin TL, Zimmerman MD, Lenaerts AJ, Meibohm B, Gonzalez-Juarrero M, Lyons MA, Dartois V, Lee RE, Robertson GT. Spectinamide MBX-4888A exhibits favorable lesion and tissue distribution and promotes treatment shortening in advanced murine models of tuberculosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593953. [PMID: 38798577 PMCID: PMC11118289 DOI: 10.1101/2024.05.13.593953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The spectinamides are novel, narrow-spectrum semisynthetic analogs of spectinomycin, modified to avoid intrinsic efflux by Mycobacterium tuberculosis . Spectinamides, including lead MBX-4888A (Lee-1810), exhibit promising therapeutic profiles in mice, as single drugs and as partner agents with other anti-tuberculosis antibiotics including rifampin and/or pyrazinamide. To demonstrate that this translates to more effective cure, we first confirmed the role of rifampin, with or without pyrazinamide, as essential to achieve effective bactericidal responses and sterilizing cure in the current standard of care regimen in chronically infected C3HeB/FeJ mice compared to BALB/c mice. Thus, demonstrating added value in testing clinically relevant regimens in murine models of increasing pathologic complexity. Next we show that MBX-4888A, given by injection with the front-line standard of care regimen, is treatment shortening in multiple murine tuberculosis infection models. The positive treatment responses to MBX-4888A combination therapy in multiple mouse models including mice exhibiting advanced pulmonary disease can be attributed to favorable distribution in tissues and lesions, retention in caseum, along with favorable effects with rifampin and pyrazinamide under conditions achieved in necrotic lesions. This study also provides an additional data point regarding the safety and tolerability of spectinamide MBX-4888A in long-term murine efficacy studies.
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6
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Youngblom MA, Smith TM, Murray HJ, Pepperell CS. Adaptation of the Mycobacterium tuberculosis transcriptome to biofilm growth. PLoS Pathog 2024; 20:e1012124. [PMID: 38635841 PMCID: PMC11060545 DOI: 10.1371/journal.ppat.1012124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 04/30/2024] [Accepted: 03/14/2024] [Indexed: 04/20/2024] Open
Abstract
Mycobacterium tuberculosis (M. tb), the causative agent of tuberculosis (TB), is a leading global cause of death from infectious disease. Biofilms are increasingly recognized as a relevant growth form during M. tb infection and may impede treatment by enabling bacterial drug and immune tolerance. M. tb has a complicated regulatory network that has been well-characterized for many relevant disease states, including dormancy and hypoxia. However, despite its importance, our knowledge of the genes and pathways involved in biofilm formation is limited. Here we characterize the biofilm transcriptomes of fully virulent clinical isolates and find that the regulatory systems underlying biofilm growth vary widely between strains and are also distinct from regulatory programs associated with other environmental cues. We used experimental evolution to investigate changes to the transcriptome during adaptation to biofilm growth and found that the application of a uniform selection pressure resulted in loss of strain-to-strain variation in gene expression, resulting in a more uniform biofilm transcriptome. The adaptive trajectories of transcriptomes were shaped by the genetic background of the M. tb population leading to convergence on a sub-lineage specific transcriptome. We identified widespread upregulation of non-coding RNA (ncRNA) as a common feature of the biofilm transcriptome and hypothesize that ncRNA function in genome-wide modulation of gene expression, thereby facilitating rapid regulatory responses to new environments. These results reveal a new facet of the M. tb regulatory system and provide valuable insight into how M. tb adapts to new environments.
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Affiliation(s)
- Madison A. Youngblom
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Madison-Wisconsin, Madison, Wisconsin, United States of America
| | - Tracy M. Smith
- Department of Medicine (Infectious Diseases), School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Holly J. Murray
- Department of Medicine (Infectious Diseases), School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Caitlin S. Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Madison-Wisconsin, Madison, Wisconsin, United States of America
- Department of Medicine (Infectious Diseases), School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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7
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Bhargavi G, Mallakuntla MK, Kale D, Tiwari S. Rv0687 a Putative Short-Chain Dehydrogenase is indispensable for pathogenesis of Mycobacterium tuberculosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571312. [PMID: 38168250 PMCID: PMC10760034 DOI: 10.1101/2023.12.12.571312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Mycobacterium tuberculosis (Mtb), a successful human pathogen, resides in host sentinel cells and combats the stressful intracellular environment induced by reactive oxygen and nitrogen species during infection. Mtb employs several evasion mechanisms in the face of the host as a survival strategy, including detoxifying enzymes as short-chain dehydrogenases/ reductases (SDRs) to withstand host-generated insults. In this study, using specialized transduction we have generated a Rv0687 deletion mutant and its complemented strain and investigated the functional role of Rv0687, a member of SDRs family genes in Mtb pathogenesis. Wildtype (WT) and mutant Mtb strain lacking Rv0687 (RvΔ0687) were tested for in-vitro stress response and in-vivo survival in macrophages and mice models of infection. The study demonstrates that Rv0687 is crucial for sustaining bacterial growth in nutrition-limited conditions. The deletion of Rv0687 elevated the sensitivity of Mtb to oxidative and nitrosative stress-inducing agents. Furthermore, the lack of Rv0687 compromised the survival of Mtb in primary bone marrow macrophages and led to an increase in the levels of the secreted proinflammatory cytokines TNF-α, and MIP-1α. Interestingly, the growth of WT and RvΔ0687 was similar in the lungs of infected immunocompromised mice however, a significant reduction in RvΔ0687 growth was observed in the spleen of immunocompromised Rag -/- mice at 4 weeks post-infection. Moreover Rag -/- mice infected with RvΔ0687 survived longer compared to WT Mtb strain. Additionally, we observed significant reduction in bacterial burden in spleens and lungs of immunocompetent C57BL/6 mice infected with RvΔ0687 compared to complemented and WT Mtb strains. Collectively, this study reveals that Rv0687 plays a role in Mtb pathogenesis.
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8
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Cui Y, Dang G, Wang H, Tang Y, Lv M, Liu S, Song N. DosR's multifaceted role on Mycobacterium bovis BCG revealed through multi-omics. Front Cell Infect Microbiol 2023; 13:1292864. [PMID: 38076461 PMCID: PMC10703047 DOI: 10.3389/fcimb.2023.1292864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/31/2023] [Indexed: 12/18/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is an intracellular bacterium that causes a highly contagious and potentially lethal tuberculosis (TB) in humans. It can maintain a dormant TB infection within the host. DosR (dormancy survival regulator) (Rv3133c) has been recognized as one of the key transcriptional proteins regulating bacterial dormancy and participating in various metabolic processes. In this study, we extensively investigate the still not well-comprehended role and mechanism of DosR in Mycobacterium bovis (M. bovis) Bacillus Calmette-Guérin (BCG) through a combined omics analysis. Our study finds that deleting DosR significantly affects the transcriptional levels of 104 genes and 179 proteins. Targeted metabolomics data for amino acids indicate that DosR knockout significantly upregulates L-Aspartic acid and serine synthesis, while downregulating seven other amino acids, including L-histidine and lysine. This suggests that DosR regulates amino acid synthesis and metabolism. Taken together, these findings provide molecular and metabolic bases for DosR effects, suggesting that DosR may be a novel regulatory target.
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Affiliation(s)
- Yingying Cui
- State Key Laboratory for Animal Disease Control and Prevention, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Guanghui Dang
- State Key Laboratory for Animal Disease Control and Prevention, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hui Wang
- State Key Laboratory for Animal Disease Control and Prevention, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yiyi Tang
- State Key Laboratory for Animal Disease Control and Prevention, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Mingyue Lv
- State Key Laboratory for Animal Disease Control and Prevention, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Siguo Liu
- State Key Laboratory for Animal Disease Control and Prevention, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ningning Song
- State Key Laboratory for Animal Disease Control and Prevention, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
- School of Life Science and Technology, Weifang Medical University, Weifang, China
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, Weifang, China
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9
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Ramey ME, Kaya F, Bauman AA, Massoudi LM, Sarathy JP, Zimmerman MD, Scott DWL, Job AM, Miller-Dawson JA, Podell BK, Lyons MA, Dartois V, Lenaerts AJ, Robertson GT. Drug distribution and efficacy of the DprE1 inhibitor BTZ-043 in the C3HeB/FeJ mouse tuberculosis model. Antimicrob Agents Chemother 2023; 67:e0059723. [PMID: 37791784 PMCID: PMC10648937 DOI: 10.1128/aac.00597-23] [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: 05/09/2023] [Accepted: 08/04/2023] [Indexed: 10/05/2023] Open
Abstract
BTZ-043, a suicide inhibitor of the Mycobacterium tuberculosis cell wall synthesis decaprenylphosphoryl-beta-D-ribose 2' epimerase, is under clinical development as a potential new anti-tuberculosis agent. BTZ-043 is potent and bactericidal in vitro but has limited activity against non-growing bacilli in rabbit caseum. To better understand its behavior in vivo, BTZ-043 was evaluated for efficacy and spatial drug distribution as a single agent in the C3HeB/FeJ mouse model presenting with caseous necrotic pulmonary lesions upon Mycobacterium tuberculosis infection. BTZ-043 promoted significant reductions in lung and spleen bacterial burdens in the C3HeB/FeJ mouse model after 2 months of therapy. BTZ-043 penetrates cellular and necrotic lesions and was retained at levels above the serum-shifted minimal inhibitory concentration in caseum. The calculated rate of kill was found to be highest and dose-dependent during the second month of treatment. BTZ-043 treatment was associated with improved histology scores of pulmonary lesions, especially compared to control mice, which experienced advanced fulminant neutrophilic alveolitis in the absence of treatment. These positive treatment responses to BTZ-043 monotherapy in a mouse model of advanced pulmonary disease can be attributed to favorable distribution in tissues and lesions, retention in the caseum, and its high potency and bactericidal nature at drug concentrations achieved in necrotic lesions.
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Affiliation(s)
- Michelle E. Ramey
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Firat Kaya
- Center for Discovery and Innovation, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Allison A. Bauman
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Lisa M. Massoudi
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Jansy P. Sarathy
- Center for Discovery and Innovation, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Matthew D. Zimmerman
- Center for Discovery and Innovation, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Dashick W. L. Scott
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Alyx M. Job
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Jake A. Miller-Dawson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Brendan K. Podell
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Michael A. Lyons
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Véronique Dartois
- Center for Discovery and Innovation, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Anne J. Lenaerts
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Gregory T. Robertson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
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10
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Rubinstein M, Makhon A, Losev Y, Valenci GZ, Gatt YE, Margalit H, Fass E, Kutikov I, Murik O, Zeevi DA, Savyon M, Tau L, Kaidar Shwartz H, Dveyrin Z, Rorman E, Nissan I. Prolonged survival of a patient with active MDR-TB HIV co-morbidity: insights from a Mycobacterium tuberculosis strain with a unique genomic deletion. Front Med (Lausanne) 2023; 10:1292665. [PMID: 38020140 PMCID: PMC10657812 DOI: 10.3389/fmed.2023.1292665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Coinfection of HIV and multidrug-resistant tuberculosis (MDR-TB) presents significant challenges in terms of the treatment and prognosis of tuberculosis, leading to complexities in managing the disease and impacting the overall outcome for TB patients. This study presents a remarkable case of a patient with MDR-TB and HIV coinfection who survived for over 8 years, despite poor treatment adherence and comorbidities. Whole genome sequencing (WGS) of the infecting Mycobacterium tuberculosis (Mtb) strain revealed a unique genomic deletion, spanning 18 genes, including key genes involved in hypoxia response, intracellular survival, immunodominant antigens, and dormancy. This deletion, that we have called "Del-X," potentially exerts a profound influence on the bacterial physiology and its virulence. Only few similar deletions were detected in other non-related Mtb genomes worldwide. In vivo evolution analysis identified drug resistance and metabolic adaptation mutations and their temporal dynamics during the patient's treatment course.
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Affiliation(s)
- Mor Rubinstein
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Andrei Makhon
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Yelena Losev
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Gal Zizelski Valenci
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Yair E. Gatt
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ephraim Fass
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Ina Kutikov
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Omer Murik
- Translational Genomics Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - David A. Zeevi
- Translational Genomics Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Michal Savyon
- Tel Aviv District Health Office, Ministry of Health, Tel Aviv, Israel
| | - Luba Tau
- Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hasia Kaidar Shwartz
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Zeev Dveyrin
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Efrat Rorman
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Israel Nissan
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
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11
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Youngblom MA, Smith TM, Pepperell CS. Adaptation of the Mycobacterium tuberculosis transcriptome to biofilm growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.18.549484. [PMID: 37503306 PMCID: PMC10370045 DOI: 10.1101/2023.07.18.549484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Mycobacterium tuberculosis ( M. tb ), the causative agent of tuberculosis (TB), is a leading global cause of death from infectious disease. Biofilms are increasingly recognized as a relevant growth form during M. tb infection and may impede treatment by enabling bacterial drug and immune tolerance. M. tb has a complicated regulatory network that has been well-characterized for many relevant disease states, including dormancy and hypoxia. However, despite its importance, our knowledge of the genes and pathways involved in biofilm formation is limited. Here we characterize the biofilm transcriptomes of fully virulent clinical isolates and find that the regulatory systems underlying biofilm growth vary widely between strains and are also distinct from regulatory programs associated with other environmental cues. We used experimental evolution to investigate changes to the transcriptome during adaptation to biofilm growth and found that the application of a uniform selection pressure resulted in loss of strain-to-strain variation in gene expression, resulting in a more uniform biofilm transcriptome. The adaptive trajectories of transcriptomes were shaped by the genetic background of the M. tb population leading to convergence on a sub-lineage specific transcriptome. We identified widespread upregulation of non-coding RNA (ncRNA) as a common feature of the biofilm transcriptome and hypothesize that ncRNA function in genome-wide modulation of gene expression, thereby facilitating rapid regulatory responses to new environments. These results reveal a new facet of the M. tb regulatory system and provide valuable insight into how M. tb adapts to new environments. Importance Understanding mechanisms of resistance and tolerance in Mycobacterium tuberculosis ( M. tb ) can help us develop new treatments that capitalize on M. tb 's vulnerabilities. Here we used transcriptomics to study both the regulation of biofilm formation in clinical isolates as well as how those regulatory systems adapt to new environments. We find that closely related clinical populations have diverse strategies for growth under biofilm conditions, and that genetic background plays a large role in determining the trajectory of evolution. These results have implications for future treatment strategies that may be informed by our knowledge of the evolutionary constraints on strain(s) from an individual infection. This work provides new information about the mechanisms of biofilm formation in M. tb and outlines a framework for population level approaches for studying bacterial adaptation.
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McDowell JR, Bai G, Lasek-Nesselquist E, Eisele LE, Wu Y, Hurteau G, Johnson R, Bai Y, Chen Y, Chan J, McDonough KA. Mycobacterial phosphodiesterase Rv0805 is a virulence determinant and its cyclic nucleotide hydrolytic activity is required for propionate detoxification. Mol Microbiol 2023; 119:401-422. [PMID: 36760076 PMCID: PMC10315211 DOI: 10.1111/mmi.15030] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 01/15/2023] [Accepted: 01/21/2023] [Indexed: 02/11/2023]
Abstract
Cyclic AMP (cAMP) signaling is essential to Mycobacterium tuberculosis (Mtb) pathogenesis. However, the roles of phosphodiesterases (PDEs) Rv0805, and the recently identified Rv1339, in cAMP homeostasis and Mtb biology are unclear. We found that Rv0805 modulates Mtb growth within mice, macrophages and on host-associated carbon sources. Mycobacterium bovis BCG grown on a combination of propionate and glycerol as carbon sources showed high levels of cAMP and had a strict requirement for Rv0805 cNMP hydrolytic activity. Supplementation with vitamin B12 or spontaneous genetic mutations in the pta-ackA operon restored the growth of BCGΔRv0805 and eliminated propionate-associated cAMP increases. Surprisingly, reduction of total cAMP levels by ectopic expression of Rv1339 restored only 20% of growth, while Rv0805 complementation fully restored growth despite a smaller effect on total cAMP levels. Deletion of an Rv0805 localization domain also reduced BCG growth in the presence of propionate and glycerol. We propose that localized Rv0805 cAMP hydrolysis modulates activity of a specialized pathway associated with propionate metabolism, while Rv1339 has a broader role in cAMP homeostasis. Future studies will address the biological roles of Rv0805 and Rv1339, including their impacts on metabolism, cAMP signaling and Mtb pathogenesis.
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Affiliation(s)
- James R. McDowell
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany NY 12208
| | - Guangchun Bai
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
- Department of Immunology and Microbial Disease, MC-151, Albany Medical College, Albany, NY 12208-3479
| | - Erica Lasek-Nesselquist
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany NY 12208
| | - Leslie E. Eisele
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
| | - Yan Wu
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
| | - Gregory Hurteau
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
| | - Richard Johnson
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany NY 12208
| | - Yinlan Bai
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany NY 12208
| | - Yong Chen
- Albert Einstein College of Medicine, Bronx, NY
| | - John Chan
- Albert Einstein College of Medicine, Bronx, NY
| | - Kathleen A. McDonough
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany NY 12208
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Simcox BS, Tomlinson BR, Shaw LN, Rohde KH. Mycobacterium abscessus DosRS two-component system controls a species-specific regulon required for adaptation to hypoxia. Front Cell Infect Microbiol 2023; 13:1144210. [PMID: 36968107 PMCID: PMC10034137 DOI: 10.3389/fcimb.2023.1144210] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/15/2023] [Indexed: 03/12/2023] Open
Abstract
Mycobacterium abscessus (Mab), an emerging opportunistic pathogen, predominantly infects individuals with underlying pulmonary diseases such as cystic fibrosis (CF). Current treatment outcomes for Mab infections are poor due to Mab's inherent antibiotic resistance and unique host interactions that promote phenotypic tolerance and hinder drug access. The hypoxic, mucus-laden airways in the CF lung and antimicrobial phagosome within macrophages represent hostile niches Mab must overcome via alterations in gene expression for survival. Regulatory mechanisms important for the adaptation and long-term persistence of Mab within the host are poorly understood, warranting further genetic and transcriptomics study of this emerging pathogen. DosRS Mab , a two-component signaling system (TCS), is one proposed mechanism utilized to subvert host defenses and counteract environmental stress such as hypoxia. The homologous TCS of Mycobacterium tuberculosis (Mtb), DosRS Mtb , is known to induce a ~50 gene regulon in response to hypoxia, carbon monoxide (CO) and nitric oxide (NO) in vitro and in vivo. Previously, a small DosR Mab regulon was predicted using bioinformatics based on DosR Mtb motifs however, the role and regulon of DosRS Mab in Mab pathogenesis have yet to be characterized in depth. To address this knowledge gap, our lab generated a Mab dosRS knockout strain (MabΔdosRS) to investigate differential gene expression, and phenotype in an in vitro hypoxia model of dormancy. qRT-PCR and lux reporter assays demonstrate Mab_dosR and 6 predicted downstream genes are induced in hypoxia. In addition, RNAseq revealed induction of a much larger hypoxia response comprised of >1000 genes, including 127 differentially expressed genes in a dosRS mutant strain. Deletion of DosRS Mab led to attenuated growth under low oxygen conditions, a shift in morphotype from smooth to rough, and down-regulation of 216 genes. This study provides the first look at the global transcriptomic response of Mab to low oxygen conditions encountered in the airways of CF patients and within macrophage phagosomes. Our data also demonstrate the importance of DosRS Mab for adaptation of Mab to hypoxia, highlighting a distinct regulon (compared to Mtb) that is significantly larger than previously described, including both genes conserved across mycobacteria as well as Mab-specific genes.
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Affiliation(s)
- Breven S. Simcox
- Division of Immunology and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Brooke R. Tomlinson
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, United States
| | - Lindsey N. Shaw
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, United States
| | - Kyle H. Rohde
- Division of Immunology and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
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14
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Oh Y, Lee HN, Ko EM, Jeong JA, Park SW, Oh JI. Mycobacterial Regulatory Systems Involved in the Regulation of Gene Expression Under Respiration-Inhibitory Conditions. J Microbiol 2023; 61:297-315. [PMID: 36847970 DOI: 10.1007/s12275-023-00026-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 03/01/2023]
Abstract
Mycobacterium tuberculosis is the causative agent of tuberculosis. M. tuberculosis can survive in a dormant state within the granuloma, avoiding the host-mounting immune attack. M. tuberculosis bacilli in this state show increased tolerance to antibiotics and stress conditions, and thus the transition of M. tuberculosis to the nonreplicating dormant state acts as an obstacle to tuberculosis treatment. M. tuberculosis in the granuloma encounters hostile environments such as hypoxia, nitric oxide, reactive oxygen species, low pH, and nutrient deprivation, etc., which are expected to inhibit respiration of M. tuberculosis. To adapt to and survive in respiration-inhibitory conditions, it is required for M. tuberculosis to reprogram its metabolism and physiology. In order to get clues to the mechanism underlying the entry of M. tuberculosis to the dormant state, it is important to understand the mycobacterial regulatory systems that are involved in the regulation of gene expression in response to respiration inhibition. In this review, we briefly summarize the information regarding the regulatory systems implicated in upregulation of gene expression in mycobacteria exposed to respiration-inhibitory conditions. The regulatory systems covered in this review encompass the DosSR (DevSR) two-component system, SigF partner switching system, MprBA-SigE-SigB signaling pathway, cAMP receptor protein, and stringent response.
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Affiliation(s)
- Yuna Oh
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Ha-Na Lee
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Eon-Min Ko
- Division of Bacterial Disease Research, Center for Infectious Disease Research, Korea Disease Control and Prevention Agency, National Institute of Infectious Diseases, National Institute of Health, Osong, 28159, Republic of Korea
| | - Ji-A Jeong
- Division of Bacterial Disease Research, Center for Infectious Disease Research, Korea Disease Control and Prevention Agency, National Institute of Infectious Diseases, National Institute of Health, Osong, 28159, Republic of Korea
| | - Sae Woong Park
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Jeong-Il Oh
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea. .,Microbiological Resource Research Institute, Pusan National University, Busan, 46241, Republic of Korea.
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15
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Kaur K, Laal S, Ryndak MB. Mycobacterium tuberculosis transcriptome in intraocular tuberculosis. J Med Microbiol 2023; 72. [PMID: 36762529 DOI: 10.1099/jmm.0.001649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Introduction. Intraocular tuberculosis (IOTB) is a significant cause of visual morbidity in tuberculosis (TB)-endemic countries. Although Mycobacterium tuberculosis (M. tb) has been detected in both the retinal pigment epithelial (RPE) cells and in the intraocular fluid (IOF) in some cases, IOTB is paucibacillary in the vast majority of patients. As a result, M. tb pathogenesis in the ocular compartment is poorly defined.Hypothesis. The transcriptional profile of M. tb in the ocular compartment will differ from those of M. tb in environments that represent earlier stages of infection.Aim. Our aim is to shed light on the pathogenesis of M. tb in a clinically relevant but challenging environment to study.Methodology. Whole-genome microarray analysis was performed on M. tb grown in an IOF model (artificial IOF; AIOF) over 6 days against reference log phase bacteria grown in 7H9. Results were compared to published M. tb transcriptomes in other physiologically relevant environments, e.g. RPE cell line.Results. M. tb replicates slowly in AIOF. Genes involved in active replication and aerobic respiration as well as lipid metabolism were either downregulated or not differentially expressed. Yet, M. tb in AIOF downregulated genes of the DosR regulon, indicating the suppression of dormancy, similar to M. tb in RPE cells. This transcriptional profile is distinct from the active and virulent transcriptomes of M. tb in alveolar epithelial cells and blood.Conclusion. M. tb likely acquires a non-invasive and quiescent phenotype, between active infection and dormancy, upon reaching an extrapulmonary niche, i.e. the ocular environment.
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Affiliation(s)
- Kamaljit Kaur
- Department of Ophthalmology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.,Present address: Public Health Research Institute, Rutgers University, New Jersey Medical School, The State University of New Jersey, Newark, NJ, USA
| | - Suman Laal
- Departments of Pathology and Microbiology, New York University Langone Medical Center, New York, NY, USA.,Veterans Affairs New York Harbor Healthcare System, New York, NY, NY, USA
| | - Michelle B Ryndak
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA.,Present address: Columbia University, Vagelos College of Physicians and Surgeons, Office for Research, New York, NY, USA
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Cioetto-Mazzabò L, Boldrin F, Beauvineau C, Speth M, Marina A, Namouchi A, Segafreddo G, Cimino M, Favre-Rochex S, Balasingham S, Trastoy B, Munier-Lehmann H, Griffiths G, Gicquel B, Guerin M, Manganelli R, Alonso-Rodríguez N. SigH stress response mediates killing of Mycobacterium tuberculosis by activating nitronaphthofuran prodrugs via induction of Mrx2 expression. Nucleic Acids Res 2022; 51:144-165. [PMID: 36546765 PMCID: PMC9841431 DOI: 10.1093/nar/gkac1173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/17/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
The emergence of drug-resistant Mycobacterium tuberculosis strains highlights the need to discover anti-tuberculosis drugs with novel mechanisms of action. Here we discovered a mycobactericidal strategy based on the prodrug activation of selected chemical derivatives classified as nitronaphthofurans (nNFs) mediated by the coordinated action of the sigH and mrx2 genes. The transcription factor SigH is a key regulator of an extensive transcriptional network that responds to oxidative, nitrosative, and heat stresses in M. tuberculosis. The nNF action induced the SigH stress response which in turn induced the mrx2 overexpression. The nitroreductase Mrx2 was found to activate nNF prodrugs, killing replicating, non-replicating and intracellular forms of M. tuberculosis. Analysis of SigH DNA sequences obtained from spontaneous nNF-resistant M. tuberculosis mutants suggests disruption of SigH binding to the mrx2 promoter site and/or RNA polymerase core, likely promoting the observed loss of transcriptional control over Mrx2. Mutations found in mrx2 lead to structural defects in the thioredoxin fold of the Mrx2 protein, significantly impairing the activity of the Mrx2 enzyme against nNFs. Altogether, our work brings out the SigH/Mrx2 stress response pathway as a promising target for future drug discovery programs.
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Affiliation(s)
| | | | - Claire Beauvineau
- Chemical Library Institut Curie/CNRS, CNRS UMR9187, INSERM U1196 and CNRS UMR3666, INSERM U1193, Université Paris-Saclay, Orsay 91405, France
| | - Martin Speth
- Department Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0371, Norway
| | - Alberto Marina
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio 48160 Spain
| | - Amine Namouchi
- Génétique Mycobactérienne, Institute Pasteur, Paris 75015, France,Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0371, Norway
| | - Greta Segafreddo
- Department of Molecular Medicine, University of Padova, Padova 35122, Italy
| | - Mena Cimino
- Génétique Mycobactérienne, Institute Pasteur, Paris 75015, France
| | | | | | - Beatriz Trastoy
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio 48160 Spain,Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Bizkaia 48903, Spain
| | - Hélène Munier-Lehmann
- Département de Biologie Structurale et Chimie, Institut Pasteur, CNRS UMR3523, Université de Paris, Paris 75015, France
| | - Gareth Griffiths
- Department Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0371, Norway
| | - Brigitte Gicquel
- Génétique Mycobactérienne, Institute Pasteur, Paris 75015, France,Department of Tuberculosis Control and Prevention, Shenzhen Nanshan Centre for Chronic Disease Control, Shenzhen 518054, China
| | - Marcelo E Guerin
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio 48160 Spain,Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Bizkaia 48903, Spain,IKERBASQUE, Basque Foundation for Science, Bilbao 48009, Spain
| | - Riccardo Manganelli
- Correspondence may also be addressed to Riccardo Manganelli. Tel: +39 049 827 2366; Fax: +39 049 827 2355;
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Chauhan P, Datta I, Dhiman A, Shankar U, Kumar A, Vashist A, Sharma TK, Tyagi JS. DNA Aptamer Targets Mycobacterium tuberculosis DevR/DosR Response Regulator Function by Inhibiting Its Dimerization and DNA Binding Activity. ACS Infect Dis 2022; 8:2540-2551. [PMID: 36332135 DOI: 10.1021/acsinfecdis.2c00414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Tuberculosis is recognized as one of the major public health threats worldwide. The DevR-DevS (DosR/DosS) two-component system is considered a novel drug target in Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis, owing to its central role in bacterial adaptation and long-term persistence. An increase in DevR levels and the decreased permeability of the mycobacterial cell wall during hypoxia-associated dormancy pose formidable challenges to the development of anti-DevR compounds. Using an in vitro evolution approach of Systematic Evolution of Ligands by EXponential enrichment (SELEX), we developed a panel of single-stranded DNA aptamers that interacted with Mtb DevR protein in solid-phase binding assays. The best-performing aptamer, APT-6, forms a G-quadruplex structure and inhibits DevR-dependent transcription in Mycobacterium smegmatis. Mechanistic studies indicate that APT-6 functions by inhibiting the dimerization and DNA binding activity of DevR protein. In silico studies reveal that APT-6 interacts majorly with C-terminal domain residues that participate in DNA binding and formation of active dimer species of DevR. To the best of our knowledge, this is the first report of a DNA aptamer that inhibits the function of a cytosolic bacterial response regulator. By inhibiting the dimerization of DevR, APT-6 targets an essential step in the DevR activation mechanism, and therefore, it has the potential to universally block the expression of DevR-regulated genes for intercepting dormancy pathways in mycobacteria. These findings also pave the way for exploring aptamer-based approaches to design and develop potent inhibitors against intracellular proteins of various bacterial pathogens of global concern.
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Affiliation(s)
- Priyanka Chauhan
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi110029, India
| | - Ishara Datta
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi110029, India
| | - Abhijeet Dhiman
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi110029, India
| | - Uma Shankar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore453552, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore453552, India
| | - Atul Vashist
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi110029, India
| | - Tarun Kumar Sharma
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana121001, India
| | - Jaya Sivaswami Tyagi
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi110029, India
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18
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Mycobacterium tuberculosis Dormancy: How to Fight a Hidden Danger. Microorganisms 2022; 10:microorganisms10122334. [PMID: 36557586 PMCID: PMC9784227 DOI: 10.3390/microorganisms10122334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/20/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Both latent and active TB infections are caused by a heterogeneous population of mycobacteria, which includes actively replicating and dormant bacilli in different proportions. Dormancy substantially affects M. tuberculosis drug tolerance and TB clinical management due to a significant decrease in the metabolic activity of bacilli, which leads to the complexity of both the diagnosis and the eradication of bacilli. Most diagnostic approaches to latent infection deal with a subpopulation of active M. tuberculosis, underestimating the contribution of dormant bacilli and leading to limited success in the fight against latent TB. Moreover, active TB appears not only as a primary form of infection but can also develop from latent TB, when resuscitation from dormancy is followed by bacterial multiplication, leading to disease progression. To win against latent infection, the identification of the Achilles' heel of dormant M. tuberculosis is urgently needed. Regulatory mechanisms and metabolic adaptation to growth arrest should be studied using in vitro and in vivo models that adequately imitate latent TB infection in macroorganisms. Understanding the mechanisms underlying M. tuberculosis dormancy and resuscitation may provide clues to help control latent infection, reduce disease severity in patients, and prevent pathogen transmission in the population.
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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: 7] [Impact Index Per Article: 3.5] [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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Liebenberg D, Gordhan BG, Kana BD. Drug resistant tuberculosis: Implications for transmission, diagnosis, and disease management. Front Cell Infect Microbiol 2022; 12:943545. [PMID: 36211964 PMCID: PMC9538507 DOI: 10.3389/fcimb.2022.943545] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/06/2022] [Indexed: 01/17/2023] Open
Abstract
Drug resistant tuberculosis contributes significantly to the global burden of antimicrobial resistance, often consuming a large proportion of the healthcare budget and associated resources in many endemic countries. The rapid emergence of resistance to newer tuberculosis therapies signals the need to ensure appropriate antibiotic stewardship, together with a concerted drive to develop new regimens that are active against currently circulating drug resistant strains. Herein, we highlight that the current burden of drug resistant tuberculosis is driven by a combination of ongoing transmission and the intra-patient evolution of resistance through several mechanisms. Global control of tuberculosis will require interventions that effectively address these and related aspects. Interrupting tuberculosis transmission is dependent on the availability of novel rapid diagnostics which provide accurate results, as near-patient as is possible, together with appropriate linkage to care. Contact tracing, longitudinal follow-up for symptoms and active mapping of social contacts are essential elements to curb further community-wide spread of drug resistant strains. Appropriate prophylaxis for contacts of drug resistant index cases is imperative to limit disease progression and subsequent transmission. Preventing the evolution of drug resistant strains will require the development of shorter regimens that rapidly eliminate all populations of mycobacteria, whilst concurrently limiting bacterial metabolic processes that drive drug tolerance, mutagenesis and the ultimate emergence of resistance. Drug discovery programs that specifically target bacterial genetic determinants associated with these processes will be paramount to tuberculosis eradication. In addition, the development of appropriate clinical endpoints that quantify drug tolerant organisms in sputum, such as differentially culturable/detectable tubercle bacteria is necessary to accurately assess the potential of new therapies to effectively shorten treatment duration. When combined, this holistic approach to addressing the critical problems associated with drug resistance will support delivery of quality care to patients suffering from tuberculosis and bolster efforts to eradicate this disease.
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21
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Ncube P, Bagheri B, Goosen WJ, Miller MA, Sampson SL. Evidence, Challenges, and Knowledge Gaps Regarding Latent Tuberculosis in Animals. Microorganisms 2022; 10:microorganisms10091845. [PMID: 36144447 PMCID: PMC9503773 DOI: 10.3390/microorganisms10091845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 01/30/2023] Open
Abstract
Mycobacterium bovis and other Mycobacterium tuberculosis complex (MTBC) pathogens that cause domestic animal and wildlife tuberculosis have received considerably less attention than M. tuberculosis, the primary cause of human tuberculosis (TB). Human TB studies have shown that different stages of infection can exist, driven by host–pathogen interactions. This results in the emergence of heterogeneous subpopulations of mycobacteria in different phenotypic states, which range from actively replicating (AR) cells to viable but slowly or non-replicating (VBNR), viable but non-culturable (VBNC), and dormant mycobacteria. The VBNR, VBNC, and dormant subpopulations are believed to underlie latent tuberculosis (LTB) in humans; however, it is unclear if a similar phenomenon could be happening in animals. This review discusses the evidence, challenges, and knowledge gaps regarding LTB in animals, and possible host–pathogen differences in the MTBC strains M. tuberculosis and M. bovis during infection. We further consider models that might be adapted from human TB research to investigate how the different phenotypic states of bacteria could influence TB stages in animals. In addition, we explore potential host biomarkers and mycobacterial changes in the DosR regulon, transcriptional sigma factors, and resuscitation-promoting factors that may influence the development of LTB.
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22
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Giacalone D, Yap RE, Ecker AMV, Tan S. PrrA modulates Mycobacterium tuberculosis response to multiple environmental cues and is critically regulated by serine/threonine protein kinases. PLoS Genet 2022; 18:e1010331. [PMID: 35913986 PMCID: PMC9371303 DOI: 10.1371/journal.pgen.1010331] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/11/2022] [Accepted: 07/08/2022] [Indexed: 12/04/2022] Open
Abstract
The ability of Mycobacterium tuberculosis (Mtb) to adapt to its surrounding environment is critical for the bacterium to successfully colonize its host. Transcriptional changes are a vital mechanism by which Mtb responds to key environmental signals experienced, such as pH, chloride (Cl-), nitric oxide (NO), and hypoxia. However, much remains unknown regarding how Mtb coordinates its response to the disparate signals seen during infection. Utilizing a transcription factor (TF) overexpression plasmid library in combination with a pH/Cl--responsive luciferase reporter, we identified the essential TF, PrrA, part of the PrrAB two-component system, as a TF involved in modulation of Mtb response to pH and Cl-. Further studies revealed that PrrA also affected Mtb response to NO and hypoxia, with prrA overexpression dampening induction of NO and hypoxia-responsive genes. PrrA is phosphorylated not just by its cognate sensor histidine kinase PrrB, but also by serine/threonine protein kinases (STPKs) at a second distinct site. Strikingly, a STPK-phosphoablative PrrA variant was significantly dampened in its response to NO versus wild type Mtb, disrupted in its ability to adaptively enter a non-replicative state upon extended NO exposure, and attenuated for in vivo colonization. Together, our results reveal PrrA as an important regulator of Mtb response to multiple environmental signals, and uncover a critical role of STPK regulation of PrrA in its function. Vital to successful host colonization by Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, is the bacterium’s ability to respond and adapt to changes in its local environment during infection. Here, we discover that the essential transcription factor PrrA, part of the PrrAB two-component system (TCS), modulates Mtb response to four important environmental cues encountered within the host: pH, chloride, nitric oxide, and hypoxia. PrrA acts as a rheostat, adjusting the amplitude of Mtb gene expression changes upon bacterial exposure to each of the four environmental signals. Further, we reveal a critical impact of serine/threonine protein kinases (STPKs) on PrrA function, with prevention of STPK phosphorylation of PrrA disrupting adaptive response of Mtb to growth-inhibiting cues and attenuating the bacterium’s ability to colonize its host. Our work uncovers PrrA as a regulator with broad impact across environmental signals, and highlights how two regulatory systems, TCSs and STPKs, critically interact in coordinating Mtb response to environmental cues.
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Affiliation(s)
- David Giacalone
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - Rochelle E. Yap
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Alwyn M. V. Ecker
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Shumin Tan
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- * E-mail:
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23
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Wang X, Liu Y. Offense and Defense in Granulomatous Inflammation Disease. Front Cell Infect Microbiol 2022; 12:797749. [PMID: 35846773 PMCID: PMC9277142 DOI: 10.3389/fcimb.2022.797749] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Granulomatous inflammation (GI) diseases are a group of chronic inflammation disorders characterized by focal collections of multinucleated giant cells, epithelioid cells and macrophages, with or without necrosis. GI diseases are closely related to microbes, especially virulent intracellular bacterial infections are important factors in the progression of these diseases. They employ a range of strategies to survive the stresses imposed upon them and persist in host cells, becoming the initiator of the fighting. Microbe-host communication is essential to maintain functions of a healthy host, so defense capacity of hosts is another influence factor, which is thought to combine to determine the result of the fighting. With the development of gene research technology, many human genetic loci were identified to be involved in GI diseases susceptibility, providing more insights into and knowledge about GI diseases. The current review aims to provide an update on the most recent progress in the identification and characterization of bacteria in GI diseases in a variety of organ systems and clinical conditions, and examine the invasion and escape mechanisms of pathogens that have been demonstrated in previous studies, we also review the existing data on the predictive factors of the host, mainly on genetic findings. These strategies may improve our understanding of the mechanisms underlying GI diseases, and open new avenues for the study of the associated conditions in the future.
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Affiliation(s)
- Xinwen Wang
- Shaanxi Clinical Research Center for Oral Diseases, National Clinical Research Center for Oral Diseases, State Key Laboratory of Military Stomatology, Department of Oral Medicine, School of Stomatology, The Fourth Military Medical University, Xi'an, China
| | - Yuan Liu
- Shaanxi International Joint Research Center for Oral Diseases, State Key Laboratory of Military Stomatology, Department of Histology and Pathology, School of Stomatology, The Fourth Military Medical University, Xi'an, China
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24
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The ctpF Gene Encoding a Calcium P-Type ATPase of the Plasma Membrane Contributes to Full Virulence of Mycobacterium tuberculosis. Int J Mol Sci 2022; 23:ijms23116015. [PMID: 35682696 PMCID: PMC9180918 DOI: 10.3390/ijms23116015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/22/2022] [Accepted: 05/24/2022] [Indexed: 12/04/2022] Open
Abstract
Identification of alternative attenuation targets of Mycobacterium tuberculosis (Mtb) is pivotal for designing new candidates for live attenuated anti-tuberculosis (TB) vaccines. In this context, the CtpF P-type ATPase of Mtb is an interesting target; specifically, this plasma membrane enzyme is involved in calcium transporting and response to oxidative stress. We found that a mutant of MtbH37Rv lacking ctpF expression (MtbΔctpF) displayed impaired proliferation in mouse alveolar macrophages (MH-S) during in vitro infection. Further, the levels of tumor necrosis factor and interferon-gamma in MH-S cells infected with MtbΔctpF were similar to those of cells infected with the parental strain, suggesting preservation of the immunogenic capacity. In addition, BALB/c mice infected with Mtb∆ctpF showed median survival times of 84 days, while mice infected with MtbH37Rv survived 59 days, suggesting reduced virulence of the mutant strain. Interestingly, the expression levels of ctpF in a mouse model of latent TB were significantly higher than in a mouse model of progressive TB, indicating that ctpF is involved in Mtb persistence in the dormancy state. Finally, the possibility of complementary mechanisms that counteract deficiencies in Ca2+ transport mediated by P-type ATPases is suggested. Altogether, our results demonstrate that CtpF could be a potential target for Mtb attenuation.
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25
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Shanmuga Priya VG, Bhandare V, Muddapur UM, Swaminathan P, Fandilolu PM, Sonawane KD. Molecular modeling approach to identify inhibitors of Rv2004c (rough morphology and virulent strain gene), a DosR (dormancy survival regulator) regulon protein from Mycobacterium tuberculosis. J Biomol Struct Dyn 2022; 40:3242-3257. [DOI: 10.1080/07391102.2020.1846620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- V. G. Shanmuga Priya
- Department of Biotechnology, KLE Dr.M.S.Sheshgiri College of Engineering and Technology, Belagavi, India
| | - Vishwambhar Bhandare
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai Mumbai, India
| | - Uday M. Muddapur
- Department of Biotechnology, B.V.B College of Engineering and Technology, KLE Technological University, Hubballi, India
| | - Priya Swaminathan
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Chennai, India
| | - Prayagraj M. Fandilolu
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, India
| | - Kailas D. Sonawane
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, India
- Department of Microbiology, Shivaji University, Kolhapur, India
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26
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Mycobacterium tuberculosis Transcription Factor EmbR Regulates the Expression of Key Virulence Factors That Aid in Ex Vivo and In Vivo Survival. mBio 2022; 13:e0383621. [PMID: 35471080 PMCID: PMC9239209 DOI: 10.1128/mbio.03836-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis encodes ~200 transcription factors that modulate gene expression under different microenvironments in the host. Even though high-throughput chromatin immunoprecipitation sequencing and transcriptome sequencing (RNA-seq) studies have identified the regulatory network for ~80% of transcription factors, many transcription factors remain uncharacterized. EmbR is one such transcription factor whose in vivo regulon and biological function are yet to be elucidated. Previous in vitro studies suggested that phosphorylation of EmbR by PknH upregulates the embCAB operon. Using a gene replacement mutant of embR, we investigated its role in modulating cellular morphology, antibiotic resistance, and survival in the host. Contrary to the prevailing hypothesis, under normal growth conditions, EmbR is neither phosphorylated nor impacted by ethambutol resistance through the regulation of the embCAB operon. The embR deletion mutant displayed attenuated M. tuberculosis survival in vivo. RNA-seq analysis suggested that EmbR regulates operons involved in the secretion pathway, lipid metabolism, virulence, and hypoxia, including well-known hypoxia-inducible genes devS and hspX. Lipidome analysis revealed that EmbR modulates levels of all lysophospholipids, several phospholipids, and M. tuberculosis-specific lipids, which is more pronounced under hypoxic conditions. We found that the EmbR mutant is hypersusceptible to hypoxic stress, and RNA sequencing performed under hypoxic conditions indicated that EmbR majorly regulates genes involved in response to acidic pH, hypoxia, and fatty acid metabolism. We observed condition-specific phosphorylation of EmbR, which contributes to EmbR-mediated transcription of several essential genes, ensuring enhanced survival. Collectively, the study establishes EmbR as a key modulator of hypoxic response that facilitates mycobacterial survival in the host.
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27
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Rosenberg G, Riquelme S, Prince A, Avraham R. Immunometabolic crosstalk during bacterial infection. Nat Microbiol 2022; 7:497-507. [PMID: 35365784 DOI: 10.1038/s41564-022-01080-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 02/03/2022] [Indexed: 01/22/2023]
Abstract
Following detection of bacteria, macrophages switch their metabolism from oxidative respiration through the tricarboxylic acid cycle to high-rate aerobic glycolysis. This immunometabolic shift enables pro-inflammatory and antimicrobial responses and is facilitated by the accumulation of fatty acids, tricarboxylic acid-derived metabolites and catabolism of amino acids. Recent studies have shown that these immunometabolites are co-opted by pathogens as environmental cues for expression of virulence genes. We review mechanisms by which host immunometabolites regulate bacterial pathogenicity and discuss opportunities for the development of therapeutics targeting metabolic host-pathogen crosstalk.
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Affiliation(s)
- Gili Rosenberg
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | | | - Alice Prince
- Columbia University Medical Center, New York, NY, USA.
| | - Roi Avraham
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
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28
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Chung ES, Johnson WC, Aldridge BB. Types and functions of heterogeneity in mycobacteria. Nat Rev Microbiol 2022; 20:529-541. [PMID: 35365812 DOI: 10.1038/s41579-022-00721-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2022] [Indexed: 12/24/2022]
Abstract
The remarkable ability of Mycobacterium tuberculosis to survive attacks from the host immune response and drug treatment is due to the resilience of a few bacilli rather than a result of survival of the entire population. Maintenance of mycobacterial subpopulations with distinct phenotypic characteristics is key for survival in the face of dynamic and variable stressors encountered during infection. Mycobacterial populations develop a wide range of phenotypes through an innate asymmetric growth pattern and adaptation to fluctuating microenvironments during infection that point to heterogeneity being a vital survival strategy. In this Review, we describe different types of mycobacterial heterogeneity and discuss how heterogeneity is generated and regulated in response to environmental cues. We discuss how this heterogeneity may have a key role in recording memory of their environment at both the single-cell level and the population level to give mycobacterial populations plasticity to withstand complex stressors.
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Affiliation(s)
- Eun Seon Chung
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - William C Johnson
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.,Tufts University School of Graduate Biomedical Sciences, Boston, MA, USA
| | - Bree B Aldridge
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA. .,Tufts University School of Graduate Biomedical Sciences, Boston, MA, USA. .,Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Tufts University, Boston, MA, USA. .,Department of Biomedical Engineering, Tufts University School of Engineering, Medford, MA, USA.
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29
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Kondratieva E, Majorov K, Grigorov A, Skvortsova Y, Kondratieva T, Rubakova E, Linge I, Azhikina T, Apt A. An In Vivo Model of Separate M. tuberculosis Phagocytosis by Neutrophils and Macrophages: Gene Expression Profiles in the Parasite and Disease Development in the Mouse Host. Int J Mol Sci 2022; 23:ijms23062961. [PMID: 35328388 PMCID: PMC8954342 DOI: 10.3390/ijms23062961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 11/21/2022] Open
Abstract
The role of neutrophils in tuberculosis infection remains less well studied compared to that of the CD4+ T-lymphocytes and macrophages. Thus, alterations in Mycobacterium tuberculosis transcription profile following phagocytosis by neutrophils and how these shifts differ from those caused by macrophage phagocytosis remain unknown. We developed a mouse model that allows obtaining large amounts of either neutrophils or macrophages infected in vivo with M. tuberculosis for mycobacteria isolation in quantities sufficient for the whole genome RNA sequencing and aerosol challenge of mice. Here, we present: (i) the differences in transcription profiles of mycobacteria isolated from liquid cultures, neutrophils and macrophages infected in vivo; (ii) phenotypes of infection and lung inflammation (life span, colony forming units (CFU) counts in organs, lung pathology, immune cells infiltration and cytokine production) in genetically TB-susceptible mice identically infected via respiratory tract with neutrophil-passaged (NP), macrophage-passaged (MP) and conventionally prepared (CP) mycobacteria. Two-hour residence within neutrophils caused transcriptome shifts consistent with mycobacterial transition to dormancy and diminished their capacity to attract immune cells to infected lung tissue. Mycobacterial multiplication in organs did not depend upon pre-phagocytosis, whilst survival time of infected mice was shorter in the group infected with NP bacilli. We also discuss possible reasons for these phenotypic divergences.
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Affiliation(s)
- Elena Kondratieva
- Laboratory for Immunogenetics, Central Research TB Institute, 107564 Moscow, Russia; (E.K.); (K.M.); (T.K.); (E.R.); (I.L.)
| | - Konstantin Majorov
- Laboratory for Immunogenetics, Central Research TB Institute, 107564 Moscow, Russia; (E.K.); (K.M.); (T.K.); (E.R.); (I.L.)
| | - Artem Grigorov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.G.); (Y.S.); (T.A.)
| | - Yulia Skvortsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.G.); (Y.S.); (T.A.)
| | - Tatiana Kondratieva
- Laboratory for Immunogenetics, Central Research TB Institute, 107564 Moscow, Russia; (E.K.); (K.M.); (T.K.); (E.R.); (I.L.)
| | - Elvira Rubakova
- Laboratory for Immunogenetics, Central Research TB Institute, 107564 Moscow, Russia; (E.K.); (K.M.); (T.K.); (E.R.); (I.L.)
| | - Irina Linge
- Laboratory for Immunogenetics, Central Research TB Institute, 107564 Moscow, Russia; (E.K.); (K.M.); (T.K.); (E.R.); (I.L.)
| | - Tatyana Azhikina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.G.); (Y.S.); (T.A.)
| | - Alexander Apt
- Laboratory for Immunogenetics, Central Research TB Institute, 107564 Moscow, Russia; (E.K.); (K.M.); (T.K.); (E.R.); (I.L.)
- Correspondence:
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30
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Belardinelli JM, Verma D, Li W, Avanzi C, Wiersma CJ, Williams JT, Johnson BK, Zimmerman M, Whittel N, Angala B, Wang H, Jones V, Dartois V, de Moura VCN, Gonzalez-Juarrero M, Pearce C, Schenkel AR, Malcolm KC, Nick JA, Charman SA, Wells TNC, Podell BK, Vennerstrom JL, Ordway DJ, Abramovitch RB, Jackson M. Therapeutic efficacy of antimalarial drugs targeting DosRS signaling in Mycobacterium abscessus. Sci Transl Med 2022; 14:eabj3860. [PMID: 35196022 DOI: 10.1126/scitranslmed.abj3860] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A search for alternative Mycobacterium abscessus treatments led to our interest in the two-component regulator DosRS, which, in Mycobacterium tuberculosis, is required for the bacterium to establish a state of nonreplicating, drug-tolerant persistence in response to a variety of host stresses. We show here that the genetic disruption of dosRS impairs the adaptation of M. abscessus to hypoxia, resulting in decreased bacterial survival after oxygen depletion, reduced tolerance to a number of antibiotics in vitro and in vivo, and the inhibition of biofilm formation. We determined that three antimalarial drugs or drug candidates, artemisinin, OZ277, and OZ439, can target DosS-mediated hypoxic signaling in M. abscessus and recapitulate the phenotypic effects of genetically disrupting dosS. OZ439 displayed bactericidal activity comparable to standard-of-care antibiotics in chronically infected mice, in addition to potentiating the activity of antibiotics used in combination. The identification of antimalarial drugs as potent inhibitors and adjunct inhibitors of M. abscessus in vivo offers repurposing opportunities that could have an immediate impact in the clinic.
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Affiliation(s)
- Juan Manuel Belardinelli
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Deepshikha Verma
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Wei Li
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Charlotte Avanzi
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Crystal J Wiersma
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - John T Williams
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | | | - Matthew Zimmerman
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Nicholas Whittel
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Bhanupriya Angala
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Han Wang
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Victoria Jones
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Véronique Dartois
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Vinicius C N de Moura
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Mercedes Gonzalez-Juarrero
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Camron Pearce
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Alan R Schenkel
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Kenneth C Malcolm
- Department of Medicine, National Jewish Health, Denver, CO, USA.,Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Jerry A Nick
- Department of Medicine, National Jewish Health, Denver, CO, USA.,Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Susan A Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | | | - Brendan K Podell
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | | | - Diane J Ordway
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Robert B Abramovitch
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
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31
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Abstract
Persisters represent a small subpopulation of cells that are tolerant of killing by antibiotics and are implicated in the recalcitrance of chronic infections to antibiotic therapy. One general theme has emerged regarding persisters formed by different bacterial species, namely, a state of relative dormancy characterized by diminished activity of antibiotic targets. Within this framework, a number of studies have linked persister formation to stochastic decreases in energy-generating components, leading to low ATP and target activity. In this study, we screen knockouts in the main global regulators of Escherichia coli for their effect on persisters. A knockout in integration host factor (IHF) had elevated ATP and a diminished level of persisters. This was accompanied by an overexpression of isocitrate dehydrogenase (Icd) and a downregulation of isocitrate lyase (AceA), two genes located at the bifurcation between the tricarboxylic acid (TCA) cycle and the glyoxylate bypass. Using a translational ihfA-mVenus fusion, we sort out rare bright cells, and this subpopulation is enriched in persisters. Our results suggest that noise in the expression of ihf produces rare cells with low Icd/high AceA, diverting substrates into the glyoxylate bypass, which decreases ATP, leading to antibiotic-tolerant persisters. We further examine noise in a simple model, the lac operon, and show that a knockout of the lacI repressor increases expression of the operon and decreases persister formation. Our results suggest that noise quenching by overexpression serves as a general approach to determine the nature of persister genes in a variety of bacterial species and conditions. IMPORTANCE Persisters are phenotypic variants that survive exposure to antibiotics through temporary dormancy. Mutants with increased levels of persisters have been identified in clinical isolates, and evidence suggests these cells contribute to chronic infections and antibiotic treatment failure. Understanding the underlying mechanism of persister formation and tolerance is important for developing therapeutic approaches to treat chronic infections. In this study, we examine a global regulator, IHF, that plays a role in persister formation. We find that noise in expression of IHF contributes to persister formation, likely by regulating the switch between the TCA cycle that efficiently produces energy and the glyoxylate bypass. We extend this study to a simple model lac operon and show that when grown on lactose as the sole carbon source, noise in its expression influences ATP levels and determines persister formation. This noise is quenched by overexpression of the lac operon, providing a simple approach to test the involvement of a gene in persister formation.
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32
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Birhanu AG, Gómez-Muñoz M, Kalayou S, Riaz T, Lutter T, Yimer SA, Abebe M, Tønjum T. Proteome Profiling of Mycobacterium tuberculosis Cells Exposed to Nitrosative Stress. ACS OMEGA 2022; 7:3470-3482. [PMID: 35128256 PMCID: PMC8811941 DOI: 10.1021/acsomega.1c05923] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Reactive nitrogen species (RNS) are secreted by human cells in response to infection by Mycobacterium tuberculosis (Mtb). Although RNS can kill Mtb under some circumstances, Mtb can adapt and survive in the presence of RNS by a process that involves modulation of gene expression. Previous studies focused primarily on stress-related changes in the Mtb transcriptome. This study unveils changes in the Mtb proteome in response to a sub-lethal dose of nitric oxide (NO) over several hours of exposure. Proteins were identified using liquid chromatography coupled with electrospray ionization mass spectrometry (LC-MS/MS). A total of 2911 Mtb proteins were identified, of which 581 were differentially abundant (DA) after exposure to NO in at least one of the four time points (30 min, 2 h, 6 h, and 20 h). The proteomic response to NO was marked by two phases, with few DA proteins in the early phase and a multitude of DA proteins in the later phase. The efflux pump Rv1687 stood out as being the only protein more abundant at all the time points and might play a role in the early protection of Mtb against nitrosative stress. These changes appeared to be compensatory in nature, contributing to iron homeostasis, energy metabolism, and other stress responses. This study thereby provides new insights into the response of Mtb to NO at the level of proteomics.
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Affiliation(s)
- Alemayehu Godana Birhanu
- Department
of Microbiology, University of Oslo, P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway
- Institute
of Biotechnology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Marta Gómez-Muñoz
- Department
of Microbiology, University of Oslo, P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway
| | - Shewit Kalayou
- Department
of Microbiology, Oslo University Hospital, P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway
- International
Center of Insect Physiology and Ecology (ICIPE), P.O. Box 30772-00100 Nairobi, Kenya
| | - Tahira Riaz
- Department
of Microbiology, University of Oslo, P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway
| | - Timo Lutter
- Department
of Microbiology, University of Oslo, P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway
| | - Solomon Abebe Yimer
- Department
of Microbiology, University of Oslo, P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway
- Coalition
for Epidemic Preparedness Innovations (CEPI), P.O. Box 123, Torshov, 0412 Oslo, Norway
| | - Markos Abebe
- Armauer
Hansen Research Institute, Jimma Road, P.O. Box 1005 Addis Ababa, Ethiopia
| | - Tone Tønjum
- Department
of Microbiology, University of Oslo, P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway
- Department
of Microbiology, Oslo University Hospital, P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway
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33
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Kanaparthi KJ, Afroz S, Minhas G, Moitra A, Khan RA, Medikonda J, Naz S, Cholleti SN, Banerjee S, Khan N. Immunogenic profiling of Mycobacterium tuberculosis DosR protein Rv0569 reveals its ability to switch on Th1 based immunity. Immunol Lett 2022; 242:27-36. [PMID: 35007662 DOI: 10.1016/j.imlet.2022.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 12/15/2021] [Accepted: 01/05/2022] [Indexed: 12/20/2022]
Abstract
Mycobacterium tuberculosis (M.tb) is a multifaceted bacterial pathogen known to infect more than 2 billion people globally. However, a majority of the individuals (>90%) show no overt clinical symptoms of active Tuberculosis (TB) and, it is reported that M.tb in these individuals resides in the latent form. Therefore, huge burden of latently infected population poses serious threat to human health. Inconsistent efficacy of BCG vaccine and poor understanding of latency-associated determinants contribute to the failure of combating M.tb. The discovery of DosR as the master regulator of dormancy, opened new avenues to understand the pathophysiology of the bacterium. Though the specific functions of various DosR genes are yet to be discovered, they have been reported as potent T-cell activators and could elicit strong protective immune responses. Rv0569 is a DosR-encoded conserved hypothetical protein overexpressed during dormancy. However, it is not clearly understood how this protein modulates the host immune response. In the present study, we have demonstrated that Rv0569 has a high antigenic index and induces enhanced secretion of Th1 cytokines IL-12p40 and TNF-α as compared to Th2 cytokine IL-10 in macrophages. Mechanistically, Rv0569 induced the transcription of these pro-inflammatory signatures through the activation of NF-κB pathway. Further, immunization of mice with DosR protein Rv0569 switched the immune response towards Th1-biased cytokine pattern, characterized by the enhanced production of IFN-γ, IL-12p40, and TNF-α. Rv0569 augmented the expansion of antigen-specific IFN-γ and IL-2 producing effector CD4+ and CD8+ T-cells which are hallmarks of Th1 biased protective immunity. Additionally, IgG2a/IgG1 and IgG2b/IgG1 ratio in the serum of immunized mice further confirmed the ability of Rv0569 to skew Th1 biased immune response. In conclusion, we emphasize that Rv0569 has the ability to generate signals to switch on Th1-dominated responses and further suggest that it could be a potential vaccine candidate against latent M.tb infection.
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Affiliation(s)
- Kala Jyothi Kanaparthi
- Department of Biotechnology and Bioinformatics, School of Life-Sciences, University of Hyderabad, Hyderabad-500046, Telangana, India
| | - Sumbul Afroz
- Department of Biotechnology and Bioinformatics, School of Life-Sciences, University of Hyderabad, Hyderabad-500046, Telangana, India
| | - Gillipsie Minhas
- Department of Biotechnology and Bioinformatics, School of Life-Sciences, University of Hyderabad, Hyderabad-500046, Telangana, India
| | - Anurupa Moitra
- Department of Biotechnology and Bioinformatics, School of Life-Sciences, University of Hyderabad, Hyderabad-500046, Telangana, India
| | - Rafiq Ahmad Khan
- Department of Biotechnology and Bioinformatics, School of Life-Sciences, University of Hyderabad, Hyderabad-500046, Telangana, India
| | - Jayashankar Medikonda
- Department of Biochemistry, School of Life-Sciences, University of Hyderabad, Hyderabad-500046, Telangana, India
| | - Saima Naz
- Department of Biochemistry, School of Life-Sciences, University of Hyderabad, Hyderabad-500046, Telangana, India
| | - Sai Nikhith Cholleti
- Department of Biotechnology and Bioinformatics, School of Life-Sciences, University of Hyderabad, Hyderabad-500046, Telangana, India
| | - Sharmistha Banerjee
- Department of Biochemistry, School of Life-Sciences, University of Hyderabad, Hyderabad-500046, Telangana, India
| | - Nooruddin Khan
- Department of Biotechnology and Bioinformatics, School of Life-Sciences, University of Hyderabad, Hyderabad-500046, Telangana, India.; Department of Animal Biology, School of Life-Sciences, University of Hyderabad, Hyderabad-500046, Telangana, India..
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Apiyo D, Mouton JM, Louw C, Sampson SL, Louw TM. Dynamic mathematical model development and validation of in vitro Mycobacterium smegmatis growth under nutrient- and pH-stress. J Theor Biol 2022; 532:110921. [PMID: 34582827 DOI: 10.1016/j.jtbi.2021.110921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/27/2021] [Accepted: 09/21/2021] [Indexed: 10/20/2022]
Abstract
Mycobacterium tuberculosis can exist within a host for lengthy periods, tolerating even antibiotic challenge. This non-heritable, antibiotic tolerant "persister" state, is thought to underlie latent Tuberculosis (TB) infection and a deeper understanding thereof could inform treatment strategies. In addition to experimental studies, mathematical and computational modelling approaches are widely employed to study persistence from both an in vivo and in vitro perspective. However, specialized models (partial differential equations, agent-based, multiscale, etc.) rely on several difficult to determine parameters. In this study, a dynamic mathematical model was developed to predict the response of Mycobacterium smegmatis (a model organism for M. tuberculosis) grown in batch culture and subjected to a range of in vitro environmental stresses. Lag phase dynamics, pH variations and internal nitrogen storage were mechanistically modelled. Experimental results were used to train model parameters using global optimization, with extensive subsequent model validation to ensure extensibility to more complex modelling frameworks. This included an identifiability analysis which indicated that seven of the thirteen model parameters were uniquely identifiable. Non-identifiable parameters were critically evaluated. Model predictions compared to validation data (based on experimental results not used during training) were accurate with less than 16% maximum absolute percentage error, indicating that the model is accurate even when extrapolating to new experimental conditions. The bulk growth model can be extended to spatially heterogeneous simulations such as an agent-based model to simulate in vitro granuloma models or, eventually, in vivo conditions, where distributed environmental conditions are difficult to measure.
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Affiliation(s)
- D Apiyo
- Department of Process Engineering, Faculty of Engineering, Stellenbosch University, Stellenbosch, South Africa
| | - J M Mouton
- Department of Science and Innovation/National Research Foundation (DSI/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
| | - C Louw
- Department of Process Engineering, Faculty of Engineering, Stellenbosch University, Stellenbosch, South Africa
| | - S L Sampson
- Department of Science and Innovation/National Research Foundation (DSI/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
| | - T M Louw
- Department of Process Engineering, Faculty of Engineering, Stellenbosch University, Stellenbosch, South Africa.
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Joshi H, Kandari D, Bhatnagar R. Insights into the molecular determinants involved in Mycobacterium tuberculosis persistence and their therapeutic implications. Virulence 2021; 12:2721-2749. [PMID: 34637683 PMCID: PMC8565819 DOI: 10.1080/21505594.2021.1990660] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/17/2021] [Accepted: 10/05/2021] [Indexed: 01/08/2023] Open
Abstract
The establishment of persistent infections and the reactivation of persistent bacteria to active bacilli are the two hurdles in effective tuberculosis treatment. Mycobacterium tuberculosis, an etiologic tuberculosis agent, adapts to numerous antibiotics and resists the host immune system causing a disease of public health concern. Extensive research has been employed to combat this disease due to its sheer ability to persist in the host system, undetected, waiting for the opportunity to declare itself. Persisters are a bacterial subpopulation that possesses transient tolerance to high doses of antibiotics. There are certain inherent mechanisms that facilitate the persister cell formation in Mycobacterium tuberculosis, some of those had been characterized in the past namely, stringent response, transcriptional regulators, energy production pathways, lipid metabolism, cell wall remodeling enzymes, phosphate metabolism, and proteasome protein degradation. This article reviews the recent advancements made in various in vitro persistence models that assist to unravel the mechanisms involved in the persister cell formation and to hunt for the possible preventive or treatment measures. To tackle the persister population the immunodominant proteins that express specifically at the latent phase of infection can be used for diagnosis to distinguish between the active and latent tuberculosis, as well as to select potential drug or vaccine candidates. In addition, we discuss the genes engaged in the persistence to get more insights into resuscitation and persister cell formation. The in-depth understanding of persistent cells of mycobacteria can certainly unravel novel ways to target the pathogen and tackle its persistence.
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Affiliation(s)
- Hemant Joshi
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Divya Kandari
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Rakesh Bhatnagar
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
- Amity University of Rajasthan, Jaipur, Rajasthan, India
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King A, Blackledge MS. Evaluation of small molecule kinase inhibitors as novel antimicrobial and antibiofilm agents. Chem Biol Drug Des 2021; 98:1038-1064. [PMID: 34581492 PMCID: PMC8616828 DOI: 10.1111/cbdd.13962] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/24/2021] [Accepted: 09/15/2021] [Indexed: 12/25/2022]
Abstract
Antibiotic resistance is a global and pressing concern. Our current therapeutic arsenal is increasingly limited as bacteria are developing resistance at a rate that far outpaces our ability to create new treatments. Novel approaches to treating and curing bacterial infections are urgently needed. Bacterial kinases have been increasingly explored as novel drug targets and are poised for development into novel therapeutic agents to combat bacterial infections. This review describes several general classes of bacterial kinases that play important roles in bacterial growth, antibiotic resistance, and biofilm formation. General features of these kinase classes are discussed and areas of particular interest for the development of inhibitors will be highlighted. Small molecule kinase inhibitors are described and organized by phenotypic effect, spotlighting particularly interesting inhibitors with novel functions and potential therapeutic benefit. Finally, we provide our perspective on the future of bacterial kinase inhibition as a viable strategy to combat bacterial infections and overcome the pressures of increasing antibiotic resistance.
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Affiliation(s)
- Ashley King
- Department of Chemistry, High Point University, One University Parkway, High Point, NC 27268
| | - Meghan S. Blackledge
- Department of Chemistry, High Point University, One University Parkway, High Point, NC 27268
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Davies-Bolorunduro OF, Ajayi A, Adeleye IA, Kristanti AN, Aminah NS. Bioprospecting for antituberculosis natural products – A review. OPEN CHEM 2021. [DOI: 10.1515/chem-2021-0095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Abstract
There has been an increase in the reported cases of tuberculosis, a disease caused by Mycobacterium tuberculosis, which is still currently affecting most of the world’s population, especially in resource-limited countries. The search for novel antitubercular chemotherapeutics from underexplored natural sources is therefore of paramount importance. The renewed interest in studies related to natural products, driven partly by the growing incidence of MDR-TB, has increased the prospects of discovering new antitubercular drug leads. This is because most of the currently available chemotherapeutics such as rifampicin and capreomycin used in the treatment of TB were derived from natural products, which are proven to be an abundant source of novel drugs used to treat many diseases. To meet the global need for novel antibiotics from natural sources, various strategies for high-throughput screening have been designed and implemented. This review highlights the current antitubercular drug discovery strategies from natural sources.
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Affiliation(s)
- Olabisi Flora Davies-Bolorunduro
- Centre for Tuberculosis Research, Nigerian Institute of Medical Research , Yaba , Lagos , Nigeria
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga , Surabaya , Indonesia
| | - Abraham Ajayi
- Molecular Biology and Biotechnology Department, Nigerian Institute of Medical Research , Yaba , Lagos , Nigeria
- Department of Microbiology, University of Lagos , Akoka , Lagos , Nigeria
| | | | - Alfinda Novi Kristanti
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga , Surabaya , Indonesia
- Biotechnology of Tropical Medicinal Plants Research Group, Universitas Airlangga , Surabaya , Indonesia
| | - Nanik Siti Aminah
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga , Surabaya , Indonesia
- Biotechnology of Tropical Medicinal Plants Research Group, Universitas Airlangga , Surabaya , Indonesia
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Mekonnen D, Derbie A, Mihret A, Yimer SA, Tønjum T, Gelaw B, Nibret E, Munshae A, Waddell SJ, Aseffa A. Lipid droplets and the transcriptome of Mycobacterium tuberculosis from direct sputa: a literature review. Lipids Health Dis 2021; 20:129. [PMID: 34602073 PMCID: PMC8487580 DOI: 10.1186/s12944-021-01550-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/09/2021] [Indexed: 11/21/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the main etiology of tuberculosis (TB), is predominantly an intracellular pathogen that has caused infection, disease and death in humans for centuries. Lipid droplets (LDs) are dynamic intracellular organelles that are found across the evolutionary tree of life. This review is an evaluation of the current state of knowledge regarding Mtb-LD formation and associated Mtb transcriptome directly from sputa.Based on the LD content, Mtb in sputum may be classified into three groups: LD positive, LD negative and LD borderline. However, the clinical and evolutionary importance of each state is not well elaborated. Mounting evidence supports the view that the presence of LD positive Mtb bacilli in sputum is a biomarker of slow growth, low energy state, towards lipid degradation, and drug tolerance. In Mtb, LD may serve as a source of chemical energy, scavenger of toxic compounds, prevent destruction of Mtb through autophagy, delay trafficking of lysosomes towards the phagosome, and contribute to Mtb persistence. It is suggest that LD is a key player in the induction of a spectrum of phenotypic and metabolic states of Mtb in the macrophage, granuloma and extracellular sputum microenvironment. Tuberculosis patients with high proportion of LD positive Mtb in pretreatment sputum was associated with higher rate of poor treatment outcome, indicating that LD may have a clinical application in predicting treatment outcome.The propensity for LD formation among Mtb lineages is largely unknown. The role of LD on Mtb transmission and disease phenotype (pulmonary TB vs extra-pulmonary TB) is not well understood. Thus, further studies are needed to understand the relationships between LD positivity and Mtb lineage, Mtb transmission and clinical types.
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Affiliation(s)
- Daniel Mekonnen
- Department of Medical Microbiology, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia.
- Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia.
| | - Awoke Derbie
- Department of Medical Microbiology, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia
- Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- The Centre for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), Addis Ababa University, Addis Ababa, Ethiopia
| | - Adane Mihret
- Armauer Hansen Research Institute, Jimma Road, ALERT Compound, PO Box 1005, Addis Ababa, Ethiopia
- Department of Medical Microbiology, Immunology and Parasitology, College of Medicine and Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Solomon Abebe Yimer
- Department of Microbiology, University of Oslo, PO Box 1071, Blindern, NO-0316, Oslo, Norway
- Coalition for Epidemic Preparedness Innovations, CEPI, P.O. Box 123, Torshov, 0412, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, University of Oslo, PO Box 1071, Blindern, NO-0316, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, PO Box 4950, Nydalen, NO-0424, Oslo, Norway
| | - Baye Gelaw
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Endalkachew Nibret
- Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Abaineh Munshae
- Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Simon J Waddell
- Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX, UK
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Jimma Road, ALERT Compound, PO Box 1005, Addis Ababa, Ethiopia
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Comparative Analysis of Pharmacodynamics in the C3HeB/FeJ Mouse Tuberculosis Model for DprE1 inhibitors TBA-7371, PBTZ169 and OPC-167832. Antimicrob Agents Chemother 2021; 65:e0058321. [PMID: 34370580 PMCID: PMC8522729 DOI: 10.1128/aac.00583-21] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multiple drug discovery initiatives for tuberculosis are currently ongoing to identify and develop new potent drugs with novel targets in order to shorten treatment duration. One of the drug classes with a new mode of action are DprE1 inhibitors targeting an essential process in cell wall synthesis of Mycobacterium tuberculosis. In this investigation, three DprE1 inhibitors currently in clinical trials, TBA-7371, PBTZ169 and OPC-167832, were evaluated side-by-side as single agents in the C3HeB/FeJ mouse model presenting with caseous necrotic pulmonary lesions upon tuberculosis infection. The goal was to confirm the efficacy of the DprE1 inhibitors in a mouse tuberculosis model with advanced pulmonary pathology, and perform comprehensive analysis of plasma, lung and lesion-centric drug levels to establish pharmacokinetic-pharmacodynamic (PK-PD) parameters predicting efficacy at the site of infection. Results showed significant efficacy for all three DprE1 inhibitors in the C3HeB/FeJ mouse model after two months of treatment. Superior efficacy was observed for OPC-167832 even at low dose levels, which can be attributed to its low MIC, favorable distribution and sustained retention above the MIC throughout the dosing interval in caseous necrotic lesions where the majority of bacteria reside in C3HeB/FeJ mice. These results support further progression of the three drug candidates through clinical development for tuberculosis treatment.
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Soe PT, Hanthamrongwit J, Saelee C, Kyaw SP, Khaenam P, Warit S, Satproedprai N, Mahasirimongkol S, Yanai H, Chootong P, Leepiyasakulchai C. Circulating IgA/IgG memory B cells against Mycobacterium tuberculosis dormancy-associated antigens Rv2659c and Rv3128c in active and latent tuberculosis. Int J Infect Dis 2021; 110:75-82. [PMID: 34284090 DOI: 10.1016/j.ijid.2021.07.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE To elucidate the antigenic potential of dormancy-associated antigens Rv2659c and Rv3128c of Mycobacterium tuberculosis by examining the persistence of specific IgG and IgA memory B cells (MBCs) among patients with active tuberculosis (TB), household contacts with latent tuberculosis (LTBI), and an endemic healthy control group. METHODS Fresh peripheral blood mononuclear cells from the three study groups were used to enumerate the numbers of IgG and IgA MBCs specific to recombinant protein Rv2659c and Rv3128c by ELISpot assay. The composition of MBC subsets IgA+ and IgG + was analyzed by flow cytometry. RESULTS The number of IgA MBCs specific to antigen Rv2659c was significantly higher in the LTBI group than the TB group. In contrast, no significant difference was found in IgA or IgG MBCs against antigen Rv3128c. The number of IgA+ MBCs was significantly higher than that of IgG+ MBCs in the classical MBC subset of the LTBI group. CONCLUSION The results indicated that the dormancy-associated antigen Rv2659c induced an IgA MBCs response in individuals with latent TB, and IgA+ classical MBCs formed a major portion of the MBCs subset. This new knowledge will be beneficial for the development of novel TB vaccines and their control of latent TB.
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Affiliation(s)
- Phyu Thwe Soe
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand; Department of Medical Laboratory Technology, University of Medical Technology, Mandalay, Myanmar
| | - Jariya Hanthamrongwit
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Chutiphon Saelee
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Soe Paing Kyaw
- Clinical Pathology Laboratory, (1000) Bedded General Hospital, Nay Pyi Taw, Myanmar
| | - Prasong Khaenam
- Center of Standardization and Product Validation, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Saradee Warit
- Industrial Tuberculosis Team, IMMBRG, National Center for Genetic Engineering and Biotechnology (BIOTEC), NSTDA, Pathum Thani, Thailand
| | - Nusara Satproedprai
- Genomic Medicine and Innovation Support Division, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Surakameth Mahasirimongkol
- Genomic Medicine and Innovation Support Division, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Hideki Yanai
- Department of Clinical Laboratory, Fukujuji Hospital, Japan Anti-Tuberculosis Association (JATA), Tokyo, Japan
| | - Patchanee Chootong
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Chaniya Leepiyasakulchai
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand.
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Anand K, Tripathi A, Shukla K, Malhotra N, Jamithireddy AK, Jha RK, Chaudhury SN, Rajmani RS, Ramesh A, Nagaraja V, Gopal B, Nagaraju G, Narain Seshayee AS, Singh A. Mycobacterium tuberculosis SufR responds to nitric oxide via its 4Fe-4S cluster and regulates Fe-S cluster biogenesis for persistence in mice. Redox Biol 2021; 46:102062. [PMID: 34392160 PMCID: PMC8371249 DOI: 10.1016/j.redox.2021.102062] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/21/2021] [Accepted: 06/29/2021] [Indexed: 12/13/2022] Open
Abstract
The persistence of Mycobacterium tuberculosis (Mtb) is a major problem in managing tuberculosis (TB). Host-generated nitric oxide (NO) is perceived as one of the signals by Mtb to reprogram metabolism and respiration for persistence. However, the mechanisms involved in NO sensing and reorganizing Mtb's physiology are not fully understood. Since NO damages iron-sulfur (Fe-S) clusters of essential enzymes, the mechanism(s) involved in regulating Fe-S cluster biogenesis could help Mtb persist in host tissues. Here, we show that a transcription factor SufR (Rv1460) senses NO via its 4Fe-4S cluster and promotes persistence of Mtb by mobilizing the Fe-S cluster biogenesis system; suf operon (Rv1460-Rv1466). Analysis of anaerobically purified SufR by UV-visible spectroscopy, circular dichroism, and iron-sulfide estimation confirms the presence of a 4Fe-4S cluster. Atmospheric O2 and H2O2 gradually degrade the 4Fe-4S cluster of SufR. Furthermore, electron paramagnetic resonance (EPR) analysis demonstrates that NO directly targets SufR 4Fe-4S cluster by forming a protein-bound dinitrosyl-iron-dithiol complex. DNase I footprinting, gel-shift, and in vitro transcription assays confirm that SufR directly regulates the expression of the suf operon in response to NO. Consistent with this, RNA-sequencing of MtbΔsufR demonstrates deregulation of the suf operon under NO stress. Strikingly, NO inflicted irreversible damage upon Fe-S clusters to exhaust respiratory and redox buffering capacity of MtbΔsufR. Lastly, MtbΔsufR failed to recover from a NO-induced non-growing state and displayed persistence defect inside immune-activated macrophages and murine lungs in a NO-dependent manner. Data suggest that SufR is a sensor of NO that supports persistence by reprogramming Fe-S cluster metabolism and bioenergetics.
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Affiliation(s)
- Kushi Anand
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
| | - Ashutosh Tripathi
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
| | - Kaustubh Shukla
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Nitish Malhotra
- National Centre for Biological Science, Bangalore, 560065, India
| | | | - Rajiv Kumar Jha
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | | | - Raju S Rajmani
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
| | - Arati Ramesh
- National Centre for Biological Science, Bangalore, 560065, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | | | - Ganesh Nagaraju
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | | | - Amit Singh
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India; Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India.
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Pawełczyk J, Brzostek A, Minias A, Płociński P, Rumijowska-Galewicz A, Strapagiel D, Zakrzewska-Czerwińska J, Dziadek J. Cholesterol-dependent transcriptome remodeling reveals new insight into the contribution of cholesterol to Mycobacterium tuberculosis pathogenesis. Sci Rep 2021; 11:12396. [PMID: 34117327 PMCID: PMC8196197 DOI: 10.1038/s41598-021-91812-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/01/2021] [Indexed: 02/05/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is an obligate human pathogen that can adapt to the various nutrients available during its life cycle. However, in the nutritionally stringent environment of the macrophage phagolysosome, Mtb relies mainly on cholesterol. In previous studies, we demonstrated that Mtb can accumulate and utilize cholesterol as the sole carbon source. However, a growing body of evidence suggests that a lipid-rich environment may have a much broader impact on the pathogenesis of Mtb infection than previously thought. Therefore, we applied high-resolution transcriptome profiling and the construction of various mutants to explore in detail the global effect of cholesterol on the tubercle bacillus metabolism. The results allow re-establishing the complete list of genes potentially involved in cholesterol breakdown. Moreover, we identified the modulatory effect of vitamin B12 on Mtb transcriptome and the novel function of cobalamin in cholesterol metabolite dissipation which explains the probable role of B12 in Mtb virulence. Finally, we demonstrate that a key role of cholesterol in mycobacterial metabolism is not only providing carbon and energy but involves also a transcriptome remodeling program that helps in developing tolerance to the unfavorable host cell environment far before specific stress-inducing phagosomal signals occur.
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Affiliation(s)
- Jakub Pawełczyk
- grid.413454.30000 0001 1958 0162Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Anna Brzostek
- grid.413454.30000 0001 1958 0162Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Alina Minias
- grid.413454.30000 0001 1958 0162Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Przemysław Płociński
- grid.413454.30000 0001 1958 0162Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland ,grid.10789.370000 0000 9730 2769Department of Immunology and Infectious Biology, Faculty of Biology and Environmental Protection, University of Łódz, Łódź, Poland
| | - Anna Rumijowska-Galewicz
- grid.413454.30000 0001 1958 0162Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Dominik Strapagiel
- grid.10789.370000 0000 9730 2769Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - Jolanta Zakrzewska-Czerwińska
- grid.8505.80000 0001 1010 5103Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Jarosław Dziadek
- grid.413454.30000 0001 1958 0162Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
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Walter ND, Born SEM, Robertson GT, Reichlen M, Dide-Agossou C, Ektnitphong VA, Rossmassler K, Ramey ME, Bauman AA, Ozols V, Bearrows SC, Schoolnik G, Dolganov G, Garcia B, Musisi E, Worodria W, Huang L, Davis JL, Nguyen NV, Nguyen HV, Nguyen ATV, Phan H, Wilusz C, Podell BK, Sanoussi ND, de Jong BC, Merle CS, Affolabi D, McIlleron H, Garcia-Cremades M, Maidji E, Eshun-Wilson F, Aguilar-Rodriguez B, Karthikeyan D, Mdluli K, Bansbach C, Lenaerts AJ, Savic RM, Nahid P, Vásquez JJ, Voskuil MI. Mycobacterium tuberculosis precursor rRNA as a measure of treatment-shortening activity of drugs and regimens. Nat Commun 2021; 12:2899. [PMID: 34006838 PMCID: PMC8131613 DOI: 10.1038/s41467-021-22833-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/26/2021] [Indexed: 01/01/2023] Open
Abstract
There is urgent need for new drug regimens that more rapidly cure tuberculosis (TB). Existing TB drugs and regimens vary in treatment-shortening activity, but the molecular basis of these differences is unclear, and no existing assay directly quantifies the ability of a drug or regimen to shorten treatment. Here, we show that drugs historically classified as sterilizing and non-sterilizing have distinct impacts on a fundamental aspect of Mycobacterium tuberculosis physiology: ribosomal RNA (rRNA) synthesis. In culture, in mice, and in human studies, measurement of precursor rRNA reveals that sterilizing drugs and highly effective drug regimens profoundly suppress M. tuberculosis rRNA synthesis, whereas non-sterilizing drugs and weaker regimens do not. The rRNA synthesis ratio provides a readout of drug effect that is orthogonal to traditional measures of bacterial burden. We propose that this metric of drug activity may accelerate the development of shorter TB regimens.
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Affiliation(s)
- Nicholas D Walter
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA.
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- Consortium for Applied Microbial Metrics, Aurora, CO, USA.
| | - Sarah E M Born
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Gregory T Robertson
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Matthew Reichlen
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Victoria A Ektnitphong
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Karen Rossmassler
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Michelle E Ramey
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Allison A Bauman
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Victor Ozols
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Shelby C Bearrows
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Gary Schoolnik
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Palo Alto, CA, USA
| | - Gregory Dolganov
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Palo Alto, CA, USA
| | - Benjamin Garcia
- Integrated Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Emmanuel Musisi
- Infectious Disease Research Collaboration, Kampala, Uganda
- Department of Biochemistry, Makerere University, Kampala, Uganda
| | | | - Laurence Huang
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
- Division of HIV, Infectious Diseases and Global Medicine, University of California San Francisco, San Francisco, CA, USA
- Zuckerberg San Francisco General Hospital, San Francisco, CA, USA
| | - J Lucian Davis
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Pulmonary, Critical Care, and Sleep Medicine Section, Yale School of Medicine, New Haven, CT, USA
| | - Nhung V Nguyen
- Vietnam National TB Programme/UCSF Research Collaboration Unit, Hanoi, Vietnam
| | - Hung V Nguyen
- Vietnam National TB Programme/UCSF Research Collaboration Unit, Hanoi, Vietnam
| | - Anh T V Nguyen
- Vietnam National TB Programme/UCSF Research Collaboration Unit, Hanoi, Vietnam
| | - Ha Phan
- Vietnam National TB Programme/UCSF Research Collaboration Unit, Hanoi, Vietnam
| | - Carol Wilusz
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Brendan K Podell
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | | | - Bouke C de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Corinne S Merle
- London School of Hygiene and Tropical Medicine, London, UK
- UNICEF/UNDP/World Bank/WHO Special Programme on Research and Training in Tropical Disease, Geneva CH, Switzerland
| | | | - Helen McIlleron
- Division of Clinical Pharmacology, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Maria Garcia-Cremades
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Ekaterina Maidji
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Franceen Eshun-Wilson
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Dhuvarakesh Karthikeyan
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Khisimuzi Mdluli
- Bill & Melinda Gates Medical Research Institute, Cambridge, MA, USA
| | | | - Anne J Lenaerts
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Radojka M Savic
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- UCSF Center for Tuberculosis, University of California, San Francisco, CA, USA
| | - Payam Nahid
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
- Zuckerberg San Francisco General Hospital, San Francisco, CA, USA
- Vietnam National TB Programme/UCSF Research Collaboration Unit, Hanoi, Vietnam
- UCSF Center for Tuberculosis, University of California, San Francisco, CA, USA
| | - Joshua J Vásquez
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
- Zuckerberg San Francisco General Hospital, San Francisco, CA, USA
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF Center for Tuberculosis, University of California, San Francisco, CA, USA
| | - Martin I Voskuil
- Consortium for Applied Microbial Metrics, Aurora, CO, USA.
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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Lsr2 and Its Novel Paralogue Mediate the Adjustment of Mycobacterium smegmatis to Unfavorable Environmental Conditions. mSphere 2021; 6:6/3/e00290-21. [PMID: 33980681 PMCID: PMC8125055 DOI: 10.1128/msphere.00290-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Nucleoid-associated proteins (NAPs) are the most abundant proteins involved in bacterial chromosome organization and global transcription regulation. The mycobacterial NAP family includes many diverse proteins; some are unique to actinobacteria, and many are crucial for survival under stress (e.g., HupB and Lsr2) and/or optimal growth conditions (e.g., mycobacterial integration host factor [mIHF]). Lsr2 is a nucleoid-associated protein (NAP) that has been found strictly in actinobacteria, including mycobacteria. It is a functional homolog of histone-like nucleoid-structuring protein (H-NS); it acts as a DNA-bridging protein that plays a role in chromosomal organization and transcriptional regulation. To date, the studies on Lsr2 have focused mainly on Mycobacterium tuberculosis. In this study, we analyze the role of Lsr2 as a transcription factor in Mycobacterium smegmatis, a saprophytic bacterium whose natural habitat (soil and water) substantially differs from those of the obligatory mycobacterial pathogens. Our chromatin immunoprecipitation-sequencing (ChIP-seq) data revealed that Lsr2 binds preferentially to AT-rich regions of the M. smegmatis chromosome. We found that Lsr2 acts mainly as a repressor, controlling gene expression either directly by binding promoter regions or indirectly through DNA loop formation and DNA coating. One of the Lsr2-repressed genes encodes polyketide synthase (MSMEG_4727), which is involved in the synthesis of lipooligosaccharides (LOSs). An M. smegmatis strain deprived of Lsr2 produces more LOSs, which is mirrored by changes in the smoothness of cells and their susceptibilities to antibiotics. Unlike M. tuberculosis, M. smegmatis additionally encodes a paralogue of Lsr2, MSMEG_1060, which is a novel member of the mycobacterial NAP family. The Lsr2 and MSMEG_1060 proteins exhibit different DNA binding specificities and chromosomal localizations. Our results suggest that these proteins help M. smegmatis cells cope with stress conditions, including hypoxia and exposure to antibiotics. Thus, the present work provides novel insight into the role of Lsr2 paralogues in the ability of a saprophytic mycobacterial species to adjust to environmental changes. IMPORTANCE Nucleoid-associated proteins (NAPs) are the most abundant proteins involved in bacterial chromosome organization and global transcription regulation. The mycobacterial NAP family includes many diverse proteins; some are unique to actinobacteria, and many are crucial for survival under stress (e.g., HupB and Lsr2) and/or optimal growth conditions (e.g., mycobacterial integration host factor [mIHF]). Here, we present a comprehensive study concerning two functional homologues of mycobacterial H-NS: Lsr2 and its paralogue from M. smegmatis, MSMEG_1060. We found that Lsr2 plays a role in transcriptional regulation, mainly by repressing gene expression via DNA loop formation and/or DNA-coating mechanisms. Intriguingly, the number of Lsr2-mediated genes was found to increase under hypoxia. Compared to Lsr2, MSMEG_1060 exhibits a different DNA binding specificity and chromosomal localization. Since tuberculosis remains a serious worldwide health problem, studies on stress response-mediating agents, such as Lsr2, may contribute to the development of novel antituberculosis drugs.
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Abstract
Carbon monoxide has an infamous reputation as a toxic gas, and it has been suggested that it has potential as an antibacterial agent. Despite this, how bacteria resist its toxic effects is not well understood. Carbon monoxide (CO) gas is infamous for its acute toxicity. This toxicity predominantly stems from its tendency to form carbonyl complexes with transition metals, thus inhibiting the heme-prosthetic groups of proteins, including respiratory terminal oxidases. While CO has been proposed as an antibacterial agent, the evidence supporting its toxicity toward bacteria is equivocal, and its cellular targets remain poorly defined. In this work, we investigate the physiological response of mycobacteria to CO. We show that Mycobacterium smegmatis is highly resistant to the toxic effects of CO, exhibiting only minor inhibition of growth when cultured in its presence. We profiled the proteome of M. smegmatis during growth in CO, identifying strong induction of cytochrome bd oxidase and members of the dos regulon, but relatively few other changes. We show that the activity of cytochrome bd oxidase is resistant to CO, whereas cytochrome bcc-aa3 oxidase is strongly inhibited by this gas. Consistent with these findings, growth analysis shows that M. smegmatis lacking cytochrome bd oxidase displays a significant growth defect in the presence of CO, while induction of the dos regulon appears to be unimportant for adaptation to CO. Altogether, our findings indicate that M. smegmatis has considerable resistance to CO and benefits from respiratory flexibility to withstand its inhibitory effects. IMPORTANCE Carbon monoxide has an infamous reputation as a toxic gas, and it has been suggested that it has potential as an antibacterial agent. Despite this, how bacteria resist its toxic effects is not well understood. In this study, we investigated how CO influences growth, proteome, and aerobic respiration of wild-type and mutant strains of Mycobacterium smegmatis. We show that this bacterium produces the CO-resistant cytochrome bd oxidase to tolerate poisoning of its CO-sensitive complex IV homolog. Further, we show that aside from this remodeling of its respiratory chain, M. smegmatis makes few other functional changes to its proteome, suggesting it has a high level of inherent resistance to CO.
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Kundu M, Basu J. Applications of Transcriptomics and Proteomics for Understanding Dormancy and Resuscitation in Mycobacterium tuberculosis. Front Microbiol 2021; 12:642487. [PMID: 33868200 PMCID: PMC8044303 DOI: 10.3389/fmicb.2021.642487] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/19/2021] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium tuberculosis can survive within its host for extended periods of time without any clinical symptoms of disease and reactivate when the immune system is weakened. A detailed understanding of how M. tuberculosis enters into and exits out of dormancy, is necessary in order to develop new strategies for tackling tuberculosis. Omics methodologies are unsupervised and unbiased to any hypothesis, making them useful tools for the discovery of new drug targets. This review summarizes the findings of transcriptomic and proteomic approaches toward understanding dormancy and reactivation of M. tuberculosis. Within the granuloma of latently infected individuals, the bacteria are dormant, with a marked slowdown of growth, division and metabolism. In vitro models have attempted to simulate these features by subjecting the bacterium to hypoxia, nutrient starvation, potassium depletion, growth in the presence of vitamin C, or growth in the presence of long-chain fatty acids. The striking feature of all the models is the upregulation of the DosR regulon, which includes the transcriptional regulator Rv0081, one of the central hubs of dormancy. Also upregulated are chaperone proteins, fatty acid and cholesterol degrading enzymes, the sigma factors SigE and SigB, enzymes of the glyoxylate and the methylcitrate cycle, the Clp proteases and the transcriptional regulator ClgR. Further, there is increased expression of genes involved in mycobactin synthesis, fatty acid degradation, the glyoxylate shunt and gluconeogenesis, in granulomas formed in vitro from peripheral blood mononuclear cells from latently infected individuals compared to naïve individuals. Genes linked to aerobic respiration, replication, transcription, translation and cell division, are downregulated during dormancy in vitro, but upregulated during reactivation. Resuscitation in vitro is associated with upregulation of genes linked to the synthesis of mycolic acids, phthiocerol mycocerosate (PDIM) and sulfolipids; ribosome biosynthesis, replication, transcription and translation, cell division, and genes encoding the five resuscitation promoting factors (Rpfs). The expression of proteases, transposases and insertion sequences, suggests genome reorganization during reactivation.
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Affiliation(s)
| | - Joyoti Basu
- Department of Chemistry, Bose Institute, Kolkata, India
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47
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Lee IG, Lee BJ. How Bacterial Redox Sensors Transmit Redox Signals via Structural Changes. Antioxidants (Basel) 2021; 10:antiox10040502. [PMID: 33804871 PMCID: PMC8063818 DOI: 10.3390/antiox10040502] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/04/2021] [Accepted: 03/17/2021] [Indexed: 01/17/2023] Open
Abstract
Bacteria, like humans, face diverse kinds of stress during life. Oxidative stress, which is produced by cellular metabolism and environmental factors, can significantly damage cellular macromolecules, ultimately negatively affecting the normal growth of the cell. Therefore, bacteria have evolved a number of protective strategies to defend themselves and respond to imposed stress by changing the expression pattern of genes whose products are required to convert harmful oxidants into harmless products. Structural biology combined with biochemical studies has revealed the mechanisms by which various bacterial redox sensor proteins recognize the cellular redox state and transform chemical information into structural signals to regulate downstream signaling pathways.
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Affiliation(s)
- In-Gyun Lee
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14-gil, Seongbuk-gu, Seoul 02792, Korea;
| | - Bong-Jin Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
- Correspondence:
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48
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Deletion of pknG Abates Reactivation of Latent Mycobacterium tuberculosis in Mice. Antimicrob Agents Chemother 2021; 65:AAC.02095-20. [PMID: 33468473 DOI: 10.1128/aac.02095-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/12/2021] [Indexed: 01/10/2023] Open
Abstract
Eradication of tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), has been a challenge due to its uncanny ability to survive in a dormant state inside host granulomas for decades. Mtb rewires its metabolic and redox regulatory networks to survive in the hostile hypoxic and nutrient-limiting environment, facilitating the formation of drug-tolerant persisters. Previously, we showed that protein kinase G (PknG), a virulence factor required for lysosomal escape, aids in metabolic adaptation, thereby promoting the survival of nonreplicating mycobacteria. Here, we sought to investigate the therapeutic potential of PknG against latent mycobacterium. We show that inhibition of PknG by AX20017 reduces mycobacterial survival in in vitro latency models such as hypoxia, persisters, and nutrient starvation. Targeting PknG enhances the bactericidal activity of the frontline anti-TB drugs in peritoneal macrophages. Deletion of pknG resulted in 5- to 15-fold-reduced survival of Mtb in chronically infected mice treated with anti-TB drugs. Importantly, in the Cornell mouse model of latent TB, the deletion of pknG drastically attenuated Mtb's ability to resuscitate after antibiotic treatment compared with wild-type and complemented strains. This is the first study to investigate the sterilizing activity of pknG deletion and inhibition for adjunct therapy against latent TB in a preclinical model. Collectively, these results suggest that PknG may be a promising drug target for adjunct therapy to shorten the treatment duration and reduce disease relapse.
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Laval T, Chaumont L, Demangel C. Not too fat to fight: The emerging role of macrophage fatty acid metabolism in immunity to Mycobacterium tuberculosis. Immunol Rev 2021; 301:84-97. [PMID: 33559209 DOI: 10.1111/imr.12952] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/23/2022]
Abstract
While the existence of a special relationship between Mycobacterium tuberculosis (Mtb) and host lipids has long been known, it remains a challenging enigma. It was clearly established that Mtb requires host fatty acids (FAs) and cholesterol to produce energy, build its distinctive lipid-rich cell wall, and produce lipid virulence factors. It was also observed that in infected hosts, Mtb constantly resides in a FA-rich environment that the pathogen contributes to generate by inducing a lipid-laden "foamy" phenotype in host macrophages. These observations and the proximity between lipid droplets and phagosomes containing bacteria within infected macrophages gave rise to the hypothesis that Mtb reprograms host cell lipid metabolism to ensure a continuous supply of essential nutrients and its long-term persistence in vivo. However, recent studies question this principle by indicating that in Mtb-infected macrophages, lipid droplet formation prevents bacterial acquisition of host FAs while supporting the production of FA-derived protective lipid mediators. Further, in vivo investigations reveal discrete macrophage phenotypes linking the FA metabolisms of host cell and intracellular pathogen. Notably, FA storage within lipid droplets characterizes both macrophages controlling Mtb infection and dormant intracellular Mtb. In this review, we integrate findings from immunological and microbiological studies illustrating the new concept that cytoplasmic accumulation of FAs is a metabolic adaptation of macrophages to Mtb infection, which potentiates their antimycobacterial responses and forces the intracellular pathogen to shift into fat-saving, survival mode.
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Affiliation(s)
- Thomas Laval
- Immunobiology of Infection Unit, Institut Pasteur, INSERM U1221, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Lise Chaumont
- Immunobiology of Infection Unit, Institut Pasteur, INSERM U1221, Paris, France
| | - Caroline Demangel
- Immunobiology of Infection Unit, Institut Pasteur, INSERM U1221, Paris, France
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50
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Lsr2, a nucleoid-associated protein influencing mycobacterial cell cycle. Sci Rep 2021; 11:2910. [PMID: 33536448 PMCID: PMC7858621 DOI: 10.1038/s41598-021-82295-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/04/2021] [Indexed: 01/30/2023] Open
Abstract
Nucleoid-associated proteins (NAPs) are responsible for maintaining highly organized and yet dynamic chromosome structure in bacteria. The genus Mycobacterium possesses a unique set of NAPs, including Lsr2, which is a DNA-bridging protein. Importantly, Lsr2 is essential for the M. tuberculosis during infection exhibiting pleiotropic activities including regulation of gene expression (mainly as a repressor). Here, we report that deletion of lsr2 gene profoundly impacts the cell morphology of M. smegmatis, which is a model organism for studying the cell biology of M. tuberculosis and other mycobacterial pathogens. Cells lacking Lsr2 are shorter, wider, and more rigid than the wild-type cells. Using time-lapse fluorescent microscopy, we showed that fluorescently tagged Lsr2 forms large and dynamic nucleoprotein complexes, and that the N-terminal oligomerization domain of Lsr2 is indispensable for the formation of nucleoprotein complexes in vivo. Moreover, lsr2 deletion exerts a significant effect on the replication time and replisome dynamics. Thus, we propose that the Lsr2 nucleoprotein complexes may contribute to maintaining the proper organization of the newly synthesized DNA and therefore influencing mycobacterial cell cycle.
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