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Niculescu AG, Mük GR, Avram S, Vlad IM, Limban C, Nuta D, Grumezescu AM, Chifiriuc MC. Novel strategies based on natural products and synthetic derivatives to overcome resistance in Mycobacterium tuberculosis. Eur J Med Chem 2024; 269:116268. [PMID: 38460268 DOI: 10.1016/j.ejmech.2024.116268] [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: 02/09/2024] [Accepted: 02/18/2024] [Indexed: 03/11/2024]
Abstract
One of the biggest health challenges of today's world is the emergence of antimicrobial resistance (AMR), which renders conventional therapeutics insufficient and urgently demands the generation of novel antimicrobial strategies. Mycobacterium tuberculosis (M. tuberculosis), the pathogen causing tuberculosis (TB), is among the most successful bacteria producing drug-resistant infections. The versatility of M. tuberculosis allows it to evade traditional anti-TB agents through various acquired and intrinsic mechanisms, rendering TB among the leading causes of infectious disease-related mortality. In this context, researchers worldwide focused on establishing novel approaches to address drug resistance in M. tuberculosis, developing diverse alternative treatments with varying effectiveness and in different testing phases. Overviewing the current progress, this paper aims to briefly present the mechanisms involved in M. tuberculosis drug-resistance, further reviewing in more detail the under-development antibiotics, nanotechnological approaches, and natural therapeutic solutions that promise to overcome current treatment limitations.
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Affiliation(s)
- Adelina-Gabriela Niculescu
- Research Institute of the University of Bucharest, University of Bucharest, 90 Panduri Road, Bucharest, Romania; Department of Science and Engineering of Oxide Materials and Nanomaterials, National University of Science and Technology Politehnica Bucharest, 011061, Bucharest, Romania.
| | - Georgiana Ramona Mük
- Faculty of Biology, University of Bucharest, Splaiul Independenței 91-95, Bucharest, R-050095, Romania; St. Stephen's Pneumoftiziology Hospital, Șoseaua Ștefan cel Mare 11, Bucharest, 020122, Romania.
| | - Speranta Avram
- Faculty of Biology, University of Bucharest, Splaiul Independenței 91-95, Bucharest, R-050095, Romania.
| | - Ilinca Margareta Vlad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, 6 Traian Vuia, 020956, Bucharest, Romania.
| | - Carmen Limban
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, 6 Traian Vuia, 020956, Bucharest, Romania.
| | - Diana Nuta
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, 6 Traian Vuia, 020956, Bucharest, Romania.
| | - Alexandru Mihai Grumezescu
- Research Institute of the University of Bucharest, University of Bucharest, 90 Panduri Road, Bucharest, Romania; Department of Science and Engineering of Oxide Materials and Nanomaterials, National University of Science and Technology Politehnica Bucharest, 011061, Bucharest, Romania.
| | - Mariana-Carmen Chifiriuc
- Research Institute of the University of Bucharest, University of Bucharest, 90 Panduri Road, Bucharest, Romania; Faculty of Biology, University of Bucharest, Splaiul Independenței 91-95, Bucharest, R-050095, Romania.
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2
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Farhat M, Cox H, Ghanem M, Denkinger CM, Rodrigues C, Abd El Aziz MS, Enkh-Amgalan H, Vambe D, Ugarte-Gil C, Furin J, Pai M. Drug-resistant tuberculosis: a persistent global health concern. Nat Rev Microbiol 2024:10.1038/s41579-024-01025-1. [PMID: 38519618 DOI: 10.1038/s41579-024-01025-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2024] [Indexed: 03/25/2024]
Abstract
Drug-resistant tuberculosis (TB) is estimated to cause 13% of all antimicrobial resistance-attributable deaths worldwide and is driven by both ongoing resistance acquisition and person-to-person transmission. Poor outcomes are exacerbated by late diagnosis and inadequate access to effective treatment. Advances in rapid molecular testing have recently improved the diagnosis of TB and drug resistance. Next-generation sequencing of Mycobacterium tuberculosis has increased our understanding of genetic resistance mechanisms and can now detect mutations associated with resistance phenotypes. All-oral, shorter drug regimens that can achieve high cure rates of drug-resistant TB within 6-9 months are now available and recommended but have yet to be scaled to global clinical use. Promising regimens for the prevention of drug-resistant TB among high-risk contacts are supported by early clinical trial data but final results are pending. A person-centred approach is crucial in managing drug-resistant TB to reduce the risk of poor treatment outcomes, side effects, stigma and mental health burden associated with the diagnosis. In this Review, we describe current surveillance of drug-resistant TB and the causes, risk factors and determinants of drug resistance as well as the stigma and mental health considerations associated with it. We discuss recent advances in diagnostics and drug-susceptibility testing and outline the progress in developing better treatment and preventive therapies.
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Affiliation(s)
- Maha Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Helen Cox
- Institute of Infectious Disease and Molecular Medicine, Wellcome Centre for Infectious Disease Research and Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa
| | - Marwan Ghanem
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Claudia M Denkinger
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany
- German Center for Infection Research (DZIF), partner site Heidelberg University Hospital, Heidelberg, Germany
| | | | - Mirna S Abd El Aziz
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Debrah Vambe
- National TB Control Programme, Manzini, Eswatini
| | - Cesar Ugarte-Gil
- School of Public and Population Health, University of Texas Medical Branch, Galveston, TX, USA
| | - Jennifer Furin
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - Madhukar Pai
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada.
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3
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Hou K, Jabeen R, Sun L, Wei J. How do Mutations of Mycobacterium Genes Cause Drug Resistance in Tuberculosis? Curr Pharm Biotechnol 2024; 25:724-736. [PMID: 37888812 DOI: 10.2174/0113892010257816230920053547] [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: 05/05/2023] [Revised: 07/28/2023] [Accepted: 08/07/2023] [Indexed: 10/28/2023]
Abstract
A steady increase in the prevalence of drug-resistant tuberculosis (DR-TB) has already been reported in Pakistan. In addition, DR-TB is gradually changing from one-drug resistance to multi-drug resistance, which is a serious challenge for tuberculosis treatment. This review provides an overview of the anti-tuberculosis drugs and focuses on the molecular mechanisms of drug resistance in Mycobacterium tuberculosis, with the hope that it will contribute to the study of drug resistance in response to the emergence of multidrug-resistant tuberculosis.
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Affiliation(s)
- Kaiying Hou
- School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Riffat Jabeen
- School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Lin Sun
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004, China
| | - Jianshe Wei
- School of Life Sciences, Henan University, Kaifeng, 475004, China
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4
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Soni V, Rosenn EH, Venkataraman R. Insights into the central role of N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU) in peptidoglycan metabolism and its potential as a therapeutic target. Biochem J 2023; 480:1147-1164. [PMID: 37498748 DOI: 10.1042/bcj20230173] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023]
Abstract
Several decades after the discovery of the first antibiotic (penicillin) microbes have evolved novel mechanisms of resistance; endangering not only our abilities to combat future bacterial pandemics but many other clinical challenges such as acquired infections during surgeries. Antimicrobial resistance (AMR) is attributed to the mismanagement and overuse of these medications and is complicated by a slower rate of the discovery of novel drugs and targets. Bacterial peptidoglycan (PG), a three-dimensional mesh of glycan units, is the foundation of the cell wall that protects bacteria against environmental insults. A significant percentage of drugs target PG, however, these have been rendered ineffective due to growing drug resistance. Identifying novel druggable targets is, therefore, imperative. Uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) is one of the key building blocks in PG production, biosynthesized by the bifunctional enzyme N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU). UDP-GlcNAc metabolism has been studied in many organisms, but it holds some distinctive features in bacteria, especially regarding the bacterial GlmU enzyme. In this review, we provide an overview of different steps in PG biogenesis, discuss the biochemistry of GlmU, and summarize the characteristic structural elements of bacterial GlmU vital to its catalytic function. Finally, we will discuss various studies on the development of GlmU inhibitors and their significance in aiding future drug discoveries.
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Affiliation(s)
- Vijay Soni
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10065, U.S.A
| | - Eric H Rosenn
- Tel Aviv University School of Medicine, Tel Aviv 6997801, Israel
| | - Ramya Venkataraman
- Laboratory of Innate Immunity, National Institute of Immunology, New Delhi 110067, India
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5
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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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Baruzzo G, Serafini A, Finotello F, Sanavia T, Cioetto-Mazzabò L, Boldrin F, Lavezzo E, Barzon L, Toppo S, Provvedi R, Manganelli R, Di Camillo B. Role of the Extracytoplasmic Function Sigma Factor SigE in the Stringent Response of Mycobacterium tuberculosis. Microbiol Spectr 2023; 11:e0294422. [PMID: 36946740 PMCID: PMC10100808 DOI: 10.1128/spectrum.02944-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 02/15/2023] [Indexed: 03/23/2023] Open
Abstract
Bacteria respond to nutrient starvation implementing the stringent response, a stress signaling system resulting in metabolic remodeling leading to decreased growth rate and energy requirements. A well-characterized model of stringent response in Mycobacterium tuberculosis is the one induced by growth in low phosphate. The extracytoplasmic function (ECF) sigma factor SigE was previously suggested as having a key role in the activation of stringent response. In this study, we challenge this hypothesis by analyzing the temporal dynamics of the transcriptional response of a sigE mutant and its wild-type parental strain to low phosphate using RNA sequencing. We found that both strains responded to low phosphate with a typical stringent response trait, including the downregulation of genes encoding ribosomal proteins and RNA polymerase. We also observed transcriptional changes that support the occurring of an energetics imbalance, compensated by a reduced activity of the electron transport chain, decreased export of protons, and a remodeling of central metabolism. The most striking difference between the two strains was the induction in the sigE mutant of several stress-related genes, in particular, the genes encoding the ECF sigma factor SigH and the transcriptional regulator WhiB6. Since both proteins respond to redox unbalances, their induction suggests that the sigE mutant is not able to maintain redox homeostasis in response to the energetics imbalance induced by low phosphate. In conclusion, our data suggest that SigE is not directly involved in initiating stringent response but in protecting the cell from stress consequent to the low phosphate exposure and activation of stringent response. IMPORTANCE Mycobacterium tuberculosis can enter a dormant state enabling it to establish latent infections and to become tolerant to antibacterial drugs. Dormant bacteria's physiology and the mechanism(s) used by bacteria to enter dormancy during infection are still unknown due to the lack of reliable animal models. However, several in vitro models, mimicking conditions encountered during infection, can reproduce different aspects of dormancy (growth arrest, metabolic slowdown, drug tolerance). The stringent response, a stress response program enabling bacteria to cope with nutrient starvation, is one of them. In this study, we provide evidence suggesting that the sigma factor SigE is not directly involved in the activation of stringent response as previously hypothesized, but it is important to help the bacteria to handle the metabolic stress related to the adaptation to low phosphate and activation of stringent response, thus giving an important contribution to our understanding of the mechanism behind stringent response development.
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Affiliation(s)
- Giacomo Baruzzo
- Department of Information Engineering, University of Padova, Padua, Italy
| | - Agnese Serafini
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | - Tiziana Sanavia
- Department of Information Engineering, University of Padova, Padua, Italy
| | | | - Francesca Boldrin
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Enrico Lavezzo
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Luisa Barzon
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | | | - Barbara Di Camillo
- Department of Information Engineering, University of Padova, Padua, Italy
- Department of Comparative Biomedicine and Food Science, University of Padova, Padua, Italy
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7
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Waller NJE, Cheung CY, Cook GM, McNeil MB. The evolution of antibiotic resistance is associated with collateral drug phenotypes in Mycobacterium tuberculosis. Nat Commun 2023; 14:1517. [PMID: 36934122 PMCID: PMC10024696 DOI: 10.1038/s41467-023-37184-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/06/2023] [Indexed: 03/20/2023] Open
Abstract
The increasing incidence of drug resistance in Mycobacterium tuberculosis has diminished the efficacy of almost all available antibiotics, complicating efforts to combat the spread of this global health burden. Alongside the development of new drugs, optimised drug combinations are needed to improve treatment success and prevent the further spread of antibiotic resistance. Typically, antibiotic resistance leads to reduced sensitivity, yet in some cases the evolution of drug resistance can lead to enhanced sensitivity to unrelated drugs. This phenomenon of collateral sensitivity is largely unexplored in M. tuberculosis but has the potential to identify alternative therapeutic strategies to combat drug-resistant strains that are unresponsive to current treatments. Here, by using drug susceptibility profiling, genomics and evolutionary studies we provide evidence for the existence of collateral drug sensitivities in an isogenic collection M. tuberculosis drug-resistant strains. Furthermore, in proof-of-concept studies, we demonstrate how collateral drug phenotypes can be exploited to select against and prevent the emergence of drug-resistant strains. This study highlights that the evolution of drug resistance in M. tuberculosis leads to collateral drug responses that can be exploited to design improved drug regimens.
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Affiliation(s)
- Natalie J E Waller
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Matthew B McNeil
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
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8
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Zhang C, Ouyang Q, Zhou X, Huang Y, Zeng Y, Deng L, Lin D, Zheng W. In vitro activity of tetracycline analogs against multidrug-resistant and extensive drug resistance clinical isolates of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2023; 140:102336. [PMID: 36963294 DOI: 10.1016/j.tube.2023.102336] [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: 12/08/2022] [Revised: 02/27/2023] [Accepted: 03/10/2023] [Indexed: 03/13/2023]
Abstract
BACKGROUND Multidrug-resistant tuberculosis (MDR-TB) has become a big threaten to global health. The current strategy for treatment of MDR-TB and extensive drug resistant tuberculosis (XDR-TB) is with low efficacy and high side effect. While new drug is fundamental for cure MDR-TB, repurposing the Food and Drug Administration (FDA)-approved drugs represents an alternative soluation with less cost. METHODS The activity of 8 tetracycline-class antibiotics against mycobacterium tuberculosis (M.tb) were determined by Minimum Inhibitory Concentration (MIC) in vitro. A transposon M.smeg libraries was generated by using the Harm phage and then used to isolate the conditional growth mutants in doxycycline containing plate. Eleven mutants were isolated and genomic DNAs were extracted using the cetyltrimethyl ammonium bromide (CTAB) method and analyzed by whole genome sequencing. RESULTS We found that three of eight drugs efficiently inhibited mycobacteria growth under the peak plasma concentration in the human body. Further tests showed these three tetracycline analogs (demeclocycline, doxycycline and methacycline) had antimicrobial activity against seven clinical isolates, including MDR and XDR strains. Among them, Doxycycline had the lowest MICs in all mycobacteria strains tested in this study. By using a transposon library, we identify the insertion of transposon in two genes, porin and MshA, associatewith the resistant to doxycycline. CONCLUSIONS Our findings show that tetracycline analogs such as doxycycline, has bactericidal activity against not only drug sensitive M.tb, but also clinical MDR and XDR strains, provided proof of concept to repurpose doxycycline to fight MDR-TB and XDR-TB. Further investigations are warranted to clarify the underlying mechanism and optimize the strategy in combination with other anti-TB drugs.
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Affiliation(s)
- Chi Zhang
- Department of Laboratory Medicine, Shenzhen University General Hospital, Shenzhen University, Shenzhen, China
| | - Qi Ouyang
- Guangdong Key Lab of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen University, Shenzhen, China
| | - Xianyuan Zhou
- Department of Laboratory Medicine, Shenzhen University General Hospital, Shenzhen University, Shenzhen, China
| | - Yingfeng Huang
- Department of Laboratory Medicine, Shenzhen University General Hospital, Shenzhen University, Shenzhen, China
| | - Yu Zeng
- Department of Laboratory Medicine, Shenzhen University General Hospital, Shenzhen University, Shenzhen, China
| | - Li Deng
- Department of Laboratory Medicine, Shenzhen University General Hospital, Shenzhen University, Shenzhen, China
| | - Dachuan Lin
- Guangdong Key Lab of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen University, Shenzhen, China.
| | - Weidong Zheng
- Department of Laboratory Medicine, Shenzhen University General Hospital, Shenzhen University, Shenzhen, China.
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Truden S, Sodja E, Žolnir-Dovč M. Drug-Resistant Tuberculosis on the Balkan Peninsula: Determination of Drug Resistance Mechanisms with Xpert MTB/XDR and Whole-Genome Sequencing Analysis. Microbiol Spectr 2023; 11:e0276122. [PMID: 36877052 PMCID: PMC10100718 DOI: 10.1128/spectrum.02761-22] [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: 07/20/2022] [Accepted: 02/12/2023] [Indexed: 03/07/2023] Open
Abstract
The new molecular assay Xpert MTB/XDR (Cepheid, Sunnyvale, CA, USA) was launched in 2021 to detect Mycobacterium tuberculosis (MT) complex with mutations conferring resistance to isoniazid (INH), ethionamide (ETH), fluoroquinolone (FQ), and second-line injectable drugs (SLIDs). The aim of our study was to evaluate the performance of the Xpert MTB/XDR rapid molecular assay on rifampicin-resistant, multidrug-resistant, and pre-extensively resistant tuberculosis (TB) isolates in a clinical laboratory in the Balkan Peninsula compared to a phenotypic drug susceptibility test (pDST). Xpert MTB/XDR was used to test positive Bactec MGIT 960 (Becton, Dickinson and Co., Franklin Lakes, NJ, USA) cultures or DNA isolates. In the case of discrepant results between Xpert MTB/XDR and pDST, the usefulness of whole-genome sequencing (WGS) was emphasized. In our study, 80 MT isolates from different Balkan countries were selectively chosen from the National Mycobacterial Strain Collection in Golnik, Slovenia. Isolates were tested with the Xpert MTB/XDR assay, conventional pDST, and WGS. Xpert MTB/XDR showed high sensitivities of 91.9%, 100%, and 100% for detecting INH, FQ, and SLID resistance, respectively, compared to pDST. In contrast, low sensitivity (51.9%) for ETH resistance was achieved because isolates harbored widespread mutations across the ethA gene. The specificity of Xpert MTB/XDR was 100% for all drugs except for INH (66.7%). Further investigation with WGS revealed -57c→t mutations in the oxyR-ahpC region marked with uncertain significance, which caused the low specificity for detecting INH resistance with the new assay. Xpert MTB/XDR can be used in clinical laboratories for the rapid detection of INH, FQ, and SLID resistance. Moreover, it can be used to rule in resistance to ETH. Additional use of WGS is recommended in cases of discrepant results between pDST and Xpert MTB/XDR. Future improvements of Xpert MTB/XDR with the inclusion of additional genes may increase the usefulness of the assay. IMPORTANCE The Xpert MTB/XDR was tested on drug-resistant Mycobacterium tuberculosis complex isolates from the Balkan Peninsula. Positive Bactec MGIT 960 cultures or DNA isolates were tested as starting material. According to the results of our study with Xpert MTB/XDR, sensitivities for the detection of SLID, FQ, and INH resistance were sufficient (>90%) for the assay to be implemented into diagnostic algorithms. In our study, WGS revealed lesser-known mutations in genes conferring INH and ETH resistance, and their impact on resistance is still unknown. Mutations in the ethA gene causing resistance to ETH were scattered along structural gene without high-confidence markers for resistance. Therefore, resistance to ETH should be reported based on a combination of methods. Because the Xpert MTB/XDR assay was found to have good performance, we propose that it should be the method of choice for confirming resistance to INH, FQ, and SLID and conditionally for resistance to ETH.
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Affiliation(s)
- Sara Truden
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia
| | - Eva Sodja
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia
| | - Manca Žolnir-Dovč
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia
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10
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Sao Emani C, Richter A, Singh A, Bhatt A, Av-Gay Y. The ΔCysK 2 mutant of Mycobacterium tuberculosis is sensitive to vancomycin associated with changes in cell wall phospholipid profile. Biochem Biophys Res Commun 2022; 624:120-126. [PMID: 35940124 DOI: 10.1016/j.bbrc.2022.07.096] [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: 07/05/2022] [Revised: 07/11/2022] [Accepted: 07/25/2022] [Indexed: 11/26/2022]
Abstract
Cysteine plays a versatile role in cellular physiology and has previously been shown to be instrumental to Mycobacterium tuberculosis (M.tb) pathophysiology. In this study, we have generated mutants deficient in CysK2 and CysH, the key Cysteine, biosynthetic enzymes. In contrast to the ΔcysH mutant, the ΔcysK2 mutant is not an auxotroph and as such not essential for cysteine biosynthesis. Interestingly, the ΔcysK2 mutant shows increased sensitivity to cumene hydroperoxide, vitamin C, diamide, rifampicin and Vancomycin and shows alterations in phospholipid profile of Mtb cell wall. Our findings suggest that alteration in phospholipids content of M.tb cell wall by CysK2 may form a mode of defence against selected antibiotics and oxidative stress.
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Affiliation(s)
- Carine Sao Emani
- Division of Infectious Diseases, Department of Medicine/Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Adrian Richter
- Martin-Luther-University of Halle-Wittenberg, Kurt-Mothes-Straße 3, 06120, Halle, Germany
| | - Albel Singh
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Apoorva Bhatt
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Yossef Av-Gay
- Division of Infectious Diseases, Department of Medicine/Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada.
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11
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Rahman MM, Alam Tumpa MA, Zehravi M, Sarker MT, Yamin M, Islam MR, Harun-Or-Rashid M, Ahmed M, Ramproshad S, Mondal B, Dey A, Damiri F, Berrada M, Rahman MH, Cavalu S. An Overview of Antimicrobial Stewardship Optimization: The Use of Antibiotics in Humans and Animals to Prevent Resistance. Antibiotics (Basel) 2022; 11:667. [PMID: 35625311 PMCID: PMC9137991 DOI: 10.3390/antibiotics11050667] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 12/10/2022] Open
Abstract
Antimicrobials are a type of agent widely used to prevent various microbial infections in humans and animals. Antimicrobial resistance is a major cause of clinical antimicrobial therapy failure, and it has become a major public health concern around the world. Increasing the development of multiple antimicrobials has become available for humans and animals with no appropriate guidance. As a result, inappropriate use of antimicrobials has significantly produced antimicrobial resistance. However, an increasing number of infections such as sepsis are untreatable due to this antimicrobial resistance. In either case, life-saving drugs are rendered ineffective in most cases. The actual causes of antimicrobial resistance are complex and versatile. A lack of adequate health services, unoptimized use of antimicrobials in humans and animals, poor water and sanitation systems, wide gaps in access and research and development in healthcare technologies, and environmental pollution have vital impacts on antimicrobial resistance. This current review will highlight the natural history and basics of the development of antimicrobials, the relationship between antimicrobial use in humans and antimicrobial use in animals, the simplistic pathways, and mechanisms of antimicrobial resistance, and how to control the spread of this resistance.
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Affiliation(s)
- Md. Mominur Rahman
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh; (M.A.A.T.); (M.T.S.); (M.Y.); (M.R.I.); (M.H.-O.-R.); (M.A.)
| | - Mst. Afroza Alam Tumpa
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh; (M.A.A.T.); (M.T.S.); (M.Y.); (M.R.I.); (M.H.-O.-R.); (M.A.)
| | - Mehrukh Zehravi
- Department of Clinical Pharmacy Girls Section, Prince Sattam Bin Abdul Aziz University, Alkharj 11942, Saudi Arabia;
| | - Md. Taslim Sarker
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh; (M.A.A.T.); (M.T.S.); (M.Y.); (M.R.I.); (M.H.-O.-R.); (M.A.)
| | - Md. Yamin
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh; (M.A.A.T.); (M.T.S.); (M.Y.); (M.R.I.); (M.H.-O.-R.); (M.A.)
| | - Md. Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh; (M.A.A.T.); (M.T.S.); (M.Y.); (M.R.I.); (M.H.-O.-R.); (M.A.)
| | - Md. Harun-Or-Rashid
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh; (M.A.A.T.); (M.T.S.); (M.Y.); (M.R.I.); (M.H.-O.-R.); (M.A.)
| | - Muniruddin Ahmed
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh; (M.A.A.T.); (M.T.S.); (M.Y.); (M.R.I.); (M.H.-O.-R.); (M.A.)
| | - Sarker Ramproshad
- Department of Pharmacy, Ranada Prasad Shaha University, Narayanganj 1400, Bangladesh; (S.R.); (B.M.)
| | - Banani Mondal
- Department of Pharmacy, Ranada Prasad Shaha University, Narayanganj 1400, Bangladesh; (S.R.); (B.M.)
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata 700073, India;
| | - Fouad Damiri
- Labortory of Biomolecules and Organic Synthesis (BioSynthO), Department of Chemistry, Faculty of Sciences Ben M’Sick, University Hassan II of Casablanca, Casablanca 20000, Morocco; (F.D.); (M.B.)
| | - Mohammed Berrada
- Labortory of Biomolecules and Organic Synthesis (BioSynthO), Department of Chemistry, Faculty of Sciences Ben M’Sick, University Hassan II of Casablanca, Casablanca 20000, Morocco; (F.D.); (M.B.)
| | - Md. Habibur Rahman
- Department of Global Medical Science, Wonju College of Medicine, Yonsei University, Wonju 26426, Korea
| | - Simona Cavalu
- Faculty of Medicine and Pharmacy, University of Oradea, P-ta 1 Decembrie 10, 410087 Oradea, Romania
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12
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Anand PK, Kumar A, Saini A, Kaur J. Mutation in Eth A protein of Mycobacterium tuberculosis conferred drug tolerance against enthinoamide in Mycobacterium smegmatis mc2155. Comput Biol Chem 2022; 98:107677. [DOI: 10.1016/j.compbiolchem.2022.107677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 03/15/2022] [Accepted: 03/30/2022] [Indexed: 11/03/2022]
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13
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Espinosa-Pereiro J, Sánchez-Montalvá A, Aznar ML, Espiau M. MDR Tuberculosis Treatment. MEDICINA (KAUNAS, LITHUANIA) 2022; 58:188. [PMID: 35208510 PMCID: PMC8878254 DOI: 10.3390/medicina58020188] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/13/2022] [Accepted: 01/15/2022] [Indexed: 11/17/2022]
Abstract
Multidrug-resistant (MDR) tuberculosis (TB), resistant to isoniazid and rifampicin, continues to be one of the most important threats to controlling the TB epidemic. Over the last few years, there have been promising pharmacological advances in the paradigm of MDR TB treatment: new and repurposed drugs have shown excellent bactericidal and sterilizing activity against Mycobacterium tuberculosis and several all-oral short regimens to treat MDR TB have shown promising results. The purpose of this comprehensive review is to summarize the most important drugs currently used to treat MDR TB, the recommended regimens to treat MDR TB, and we also summarize new insights into the treatment of patients with MDR TB.
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Affiliation(s)
- Juan Espinosa-Pereiro
- Infectious Diseases Department, Vall d’Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, 08135 Barcelona, Spain; (J.E.-P.); (A.S.-M.)
- Mycobacteria Infection Study Group from Spanish Society of Infectious Diseases and Clinical Microbiology, 28003 Madrid, Spain
| | - Adrian Sánchez-Montalvá
- Infectious Diseases Department, Vall d’Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, 08135 Barcelona, Spain; (J.E.-P.); (A.S.-M.)
- Mycobacteria Infection Study Group from Spanish Society of Infectious Diseases and Clinical Microbiology, 28003 Madrid, Spain
| | - Maria Luisa Aznar
- Infectious Diseases Department, Vall d’Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, 08135 Barcelona, Spain; (J.E.-P.); (A.S.-M.)
- Mycobacteria Infection Study Group from Spanish Society of Infectious Diseases and Clinical Microbiology, 28003 Madrid, Spain
| | - Maria Espiau
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d’Hebron University Hospital, Universitat Autònoma de Barcelona, 08135 Barcelona, Spain;
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14
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Deng MR, Li Y, Luo X, Zheng XL, Chen Y, Zhang YL, Zhang W, Zhou H, Zhu H. Discovery of Mycothiogranaticins from Streptomyces vietnamensis GIMV4.0001 and the Regulatory Effect of Mycothiol on the Granaticin Biosynthesis. Front Chem 2021; 9:802279. [PMID: 35004619 PMCID: PMC8733708 DOI: 10.3389/fchem.2021.802279] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/06/2021] [Indexed: 11/24/2022] Open
Abstract
Granaticins are benzoisochromanequinone polyketides with remarkable antibacterial and anticancer activities. Three sulfur-containing granaticin congeners, mycothiogranaticins A (1), B (2) and granaticin MA (3) were discovered from a granaticin-producing strain of Streptomyces vietnamensis GIMV4.0001. Two of them were structurally determined with mycothiol or N-acetylcysteine moieties and found to be bio-actively reluctant. Disruption of the mshA gene (SVTN_RS20640) that encodes the D-inositol-3-phosphate glycosyltransferase crucial for mycothiol biosynthesis, fully abolished the production of mycothiogranaticins. The result substantiated that the newly discovered mycothiogranaticins are consequences of the combination of the granaticin and mycothiol biosynthetic pathways. The overall granaticin production of the ΔmshA mutant strain was unexpectedly decreased by at least more than 50%, while similar production level of granaticins to that of the wild type strain was observed in an mycothiol-S transferase gene (SVTN_RS22215) disruptant Δmst. These results indicated that the mycothiol deficiency was responsible for the decreased production of granaticins. Mycothiol may positively regulate the biosynthesis of granaticin possibly by maintaining the cellular redox balance. To the best of our knowledge, this is the first report that mycothiol can not only be a direct building block of polyketides but also play a regulatory role in the polyketide biosynthesis.
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Affiliation(s)
- Ming-Rong Deng
- Key Laboratory of Agricultural Microbiomics and Precision Application — Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yan Li
- Key Laboratory of Agricultural Microbiomics and Precision Application — Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiao Luo
- Key Laboratory of Agricultural Microbiomics and Precision Application — Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiang-Ling Zheng
- Key Laboratory of Agricultural Microbiomics and Precision Application — Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | | | - Yu-Lian Zhang
- Key Laboratory of Agricultural Microbiomics and Precision Application — Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | | | - Hao Zhou
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, China
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application — Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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15
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Drug Discovery for Mycobacterium tuberculosis Using Structure-Based Computer-Aided Drug Design Approach. Int J Mol Sci 2021; 22:ijms222413259. [PMID: 34948055 PMCID: PMC8703488 DOI: 10.3390/ijms222413259] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/09/2021] [Accepted: 11/14/2021] [Indexed: 12/12/2022] Open
Abstract
Developing new, more effective antibiotics against resistant Mycobacterium tuberculosis that inhibit its essential proteins is an appealing strategy for combating the global tuberculosis (TB) epidemic. Finding a compound that can target a particular cavity in a protein and interrupt its enzymatic activity is the crucial objective of drug design and discovery. Such a compound is then subjected to different tests, including clinical trials, to study its effectiveness against the pathogen in the host. In recent times, new techniques, which involve computational and analytical methods, enhanced the chances of drug development, as opposed to traditional drug design methods, which are laborious and time-consuming. The computational techniques in drug design have been improved with a new generation of software used to develop and optimize active compounds that can be used in future chemotherapeutic development to combat global tuberculosis resistance. This review provides an overview of the evolution of tuberculosis resistance, existing drug management, and the design of new anti-tuberculosis drugs developed based on the contributions of computational techniques. Also, we show an appraisal of available software and databases on computational drug design with an insight into the application of this software and databases in the development of anti-tubercular drugs. The review features a perspective involving machine learning, artificial intelligence, quantum computing, and CRISPR combination with available computational techniques as a prospective pathway to design new anti-tubercular drugs to combat resistant tuberculosis.
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16
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Sheikh BA, Bhat BA, Mehraj U, Mir W, Hamadani S, Mir MA. Development of New Therapeutics to Meet the Current Challenge of Drug Resistant Tuberculosis. Curr Pharm Biotechnol 2021; 22:480-500. [PMID: 32600226 DOI: 10.2174/1389201021666200628021702] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/01/2020] [Accepted: 05/13/2020] [Indexed: 11/22/2022]
Abstract
Tuberculosis (TB) is a prominent infective disease and a major reason of mortality/ morbidity globally. Mycobacterium tuberculosis causes a long-lasting latent infection in a significant proportion of human population. The increasing burden of tuberculosis is mainly caused due to multi drug-resistance. The failure of conventional treatment has been observed in large number of cases. Drugs that are used to treat extensively drug-resistant tuberculosis are expensive, have limited efficacy, and have more side effects for a longer duration of time and are often associated with poor prognosis. To regulate the emergence of multidrug resistant tuberculosis, extensively drug-resistant tuberculosis and totally drug resistant tuberculosis, efforts are being made to understand the genetic/molecular basis of target drug delivery and mechanisms of drug resistance. Understanding the molecular approaches and pathology of Mycobacterium tuberculosis through whole genome sequencing may further help in the improvement of new therapeutics to meet the current challenge of global health. Understanding cellular mechanisms that trigger resistance to Mycobacterium tuberculosis infection may expose immune associates of protection, which could be an important way for vaccine development, diagnostics, and novel host-directed therapeutic strategies. The recent development of new drugs and combinational therapies for drug-resistant tuberculosis through major collaboration between industry, donors, and academia gives an improved hope to overcome the challenges in tuberculosis treatment. In this review article, an attempt was made to highlight the new developments of drug resistance to the conventional drugs and the recent progress in the development of new therapeutics for the treatment of drugresistant and non-resistant cases.
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Affiliation(s)
- Bashir A Sheikh
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Basharat A Bhat
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Umar Mehraj
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Wajahat Mir
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Suhail Hamadani
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Manzoor A Mir
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
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17
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Rankine-Wilson LI, Shapira T, Sao Emani C, Av-Gay Y. From infection niche to therapeutic target: the intracellular lifestyle of Mycobacterium tuberculosis. MICROBIOLOGY (READING, ENGLAND) 2021; 167:001041. [PMID: 33826491 PMCID: PMC8289223 DOI: 10.1099/mic.0.001041] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/15/2021] [Indexed: 12/16/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is an obligate human pathogen killing millions of people annually. Treatment for tuberculosis is lengthy and complicated, involving multiple drugs and often resulting in serious side effects and non-compliance. Mtb has developed numerous complex mechanisms enabling it to not only survive but replicate inside professional phagocytes. These mechanisms include, among others, overcoming the phagosome maturation process, inhibiting the acidification of the phagosome and inhibiting apoptosis. Within the past decade, technologies have been developed that enable a more accurate understanding of Mtb physiology within its intracellular niche, paving the way for more clinically relevant drug-development programmes. Here we review the molecular biology of Mtb pathogenesis offering a unique perspective on the use and development of therapies that target Mtb during its intracellular life stage.
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Affiliation(s)
| | - Tirosh Shapira
- Division of Infectious Disease, Department of Medicine, The University of British Columbia, Vancouver, Canada
| | - Carine Sao Emani
- Division of Infectious Disease, Department of Medicine, The University of British Columbia, Vancouver, Canada
| | - Yossef Av-Gay
- Department of Microbiology & Immunology, The University of British Columbia, Vancouver, Canada
- Division of Infectious Disease, Department of Medicine, The University of British Columbia, Vancouver, Canada
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18
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Sertbas M, Ulgen KO. Genome-Scale Metabolic Modeling for Unraveling Molecular Mechanisms of High Threat Pathogens. Front Cell Dev Biol 2020; 8:566702. [PMID: 33251208 PMCID: PMC7673413 DOI: 10.3389/fcell.2020.566702] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/30/2020] [Indexed: 12/14/2022] Open
Abstract
Pathogens give rise to a wide range of diseases threatening global health and hence drawing public health agencies' attention to establish preventative and curative solutions. Genome-scale metabolic modeling is ever increasingly used tool for biomedical applications including the elucidation of antibiotic resistance, virulence, single pathogen mechanisms and pathogen-host interaction systems. With this approach, the sophisticated cellular system of metabolic reactions inside the pathogens as well as between pathogen and host cells are represented in conjunction with their corresponding genes and enzymes. Along with essential metabolic reactions, alternate pathways and fluxes are predicted by performing computational flux analyses for the growth of pathogens in a very short time. The genes or enzymes responsible for the essential metabolic reactions in pathogen growth are regarded as potential drug targets, as a priori guide to researchers in the pharmaceutical field. Pathogens alter the key metabolic processes in infected host, ultimately the objective of these integrative constraint-based context-specific metabolic models is to provide novel insights toward understanding the metabolic basis of the acute and chronic processes of infection, revealing cellular mechanisms of pathogenesis, identifying strain-specific biomarkers and developing new therapeutic approaches including the combination drugs. The reaction rates predicted during different time points of pathogen development enable us to predict active pathways and those that only occur during certain stages of infection, and thus point out the putative drug targets. Among others, fatty acid and lipid syntheses reactions are recent targets of new antimicrobial drugs. Genome-scale metabolic models provide an improved understanding of how intracellular pathogens utilize the existing microenvironment of the host. Here, we reviewed the current knowledge of genome-scale metabolic modeling in pathogen cells as well as pathogen host interaction systems and the promising applications in the extension of curative strategies against pathogens for global preventative healthcare.
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Affiliation(s)
- Mustafa Sertbas
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey.,Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Kutlu O Ulgen
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey
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19
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Modlin SJ, Conkle-Gutierrez D, Kim C, Mitchell SN, Morrissey C, Weinrick BC, Jacobs WR, Ramirez-Busby SM, Hoffner SE, Valafar F. Drivers and sites of diversity in the DNA adenine methylomes of 93 Mycobacterium tuberculosis complex clinical isolates. eLife 2020; 9:58542. [PMID: 33107429 PMCID: PMC7591249 DOI: 10.7554/elife.58542] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/15/2020] [Indexed: 12/20/2022] Open
Abstract
This study assembles DNA adenine methylomes for 93 Mycobacterium tuberculosis complex (MTBC) isolates from seven lineages paired with fully-annotated, finished, de novo assembled genomes. Integrative analysis yielded four key results. First, methyltransferase allele-methylome mapping corrected methyltransferase variant effects previously obscured by reference-based variant calling. Second, heterogeneity analysis of partially active methyltransferase alleles revealed that intracellular stochastic methylation generates a mosaic of methylomes within isogenic cultures, which we formalize as ‘intercellular mosaic methylation’ (IMM). Mutation-driven IMM was nearly ubiquitous in the globally prominent Beijing sublineage. Third, promoter methylation is widespread and associated with differential expression in the ΔhsdM transcriptome, suggesting promoter HsdM-methylation directly influences transcription. Finally, comparative and functional analyses identified 351 sites hypervariable across isolates and numerous putative regulatory interactions. This multi-omic integration revealed features of methylomic variability in clinical isolates and provides a rational basis for hypothesizing the functions of DNA adenine methylation in MTBC physiology and adaptive evolution.
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Affiliation(s)
- Samuel J Modlin
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
| | - Derek Conkle-Gutierrez
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
| | - Calvin Kim
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
| | - Scott N Mitchell
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
| | - Christopher Morrissey
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
| | | | - William R Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, United States
| | - Sarah M Ramirez-Busby
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
| | - Sven E Hoffner
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States.,Department of Public Health Sciences, Karolinska Institute, Stockholm, Sweden
| | - Faramarz Valafar
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
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20
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Tiwari S, Dutt TS, Chen B, Chen M, Kim J, Dai AZ, Lukose R, Shanley C, Fox A, Karger BR, Porcelli SA, Chan J, Podell BK, Obregon-Henao A, Orme IM, Jacobs WR, Henao-Tamayo M. BCG-Prime and boost with Esx-5 secretion system deletion mutant leads to better protection against clinical strains of Mycobacterium tuberculosis. Vaccine 2020; 38:7156-7165. [PMID: 32978002 PMCID: PMC7755135 DOI: 10.1016/j.vaccine.2020.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/07/2020] [Accepted: 08/03/2020] [Indexed: 10/23/2022]
Abstract
Although vaccination with BCG prevents disseminated forms of childhood tuberculosis (TB), it does not protect against pulmonary infection or Mycobacterium tuberculosis (Mtb) transmission. In this study, we generated a complete deletion mutant of the Mtb Esx-5 type VII secretion system (Mtb Δesx-5). Mtb Δesx-5 was highly attenuated and safe in immunocompromised mice. When tested as a vaccine candidate to boost BCG-primed immunity, Mtb Δesx-5 improved protection against highly virulent Mtb strains in the murine and guinea pig models of TB. Enhanced protection provided by heterologous BCG-prime plus Mtb Δesx-5 boost regimen was associated with increased pulmonary influx of central memory T cells (TCM), follicular helper T cells (TFH) and activated monocytes. Conversely, lower numbers of T cells expressing exhaustion markers were observed in vaccinated animals. Our results suggest that boosting BCG-primed immunity with Mtb Δesx-5 is a potential approach to improve protective immunity against Mtb. Further insight into the mechanism of action of this novel prime-boost approach is warranted.
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Affiliation(s)
- Sangeeta Tiwari
- Department of Biological Sciences & Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX 79968, United States.
| | - Taru S Dutt
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, United States
| | - Bing Chen
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, United States
| | - Mei Chen
- Department of Biological Sciences & Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX 79968, United States; Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, United States
| | - John Kim
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, United States
| | - Annie Zhi Dai
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, United States
| | - Regy Lukose
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, United States
| | - Crystal Shanley
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, United States
| | - Amy Fox
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, United States
| | - Burton R Karger
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, United States
| | - Steven A Porcelli
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, United States; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, United States
| | - John Chan
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, United States; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, United States
| | - Brendan K Podell
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, United States
| | - Andres Obregon-Henao
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, United States
| | - Ian M Orme
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, United States
| | - William R Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, United States.
| | - Marcela Henao-Tamayo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, United States.
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Abstract
Multi-omics strategies are indispensable tools in the search for new anti-tuberculosis drugs. Omics methodologies, where the ensemble of a class of biological molecules are measured and evaluated together, enable drug discovery programs to answer two fundamental questions. Firstly, in a discovery biology approach, to find new targets in druggable pathways for target-based investigation, advancing from target to lead compound. Secondly, in a discovery chemistry approach, to identify the mode of action of lead compounds derived from high-throughput screens, progressing from compound to target. The advantage of multi-omics methodologies in both of these settings is that omics approaches are unsupervised and unbiased to a priori hypotheses, making omics useful tools to confirm drug action, reveal new insights into compound activity, and discover new avenues for inquiry. This review summarizes the application of Mycobacterium tuberculosis omics technologies to the early stages of tuberculosis antimicrobial drug discovery.
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22
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Insights into the Mechanism of Ethionamide Resistance in Mycobacterium tuberculosis through an in silico Structural Evaluation of EthA and Mutants Identified in Clinical Isolates. Catalysts 2020. [DOI: 10.3390/catal10050543] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Mutation in the ethionamide (ETH) activating enzyme, EthA, is the main factor determining resistance to this drug, used to treat TB patients infected with MDR and XDR Mycobacterium tuberculosis isolates. Many mutations in EthA of ETH resistant (ETH-R) isolates have been described but their roles in resistance remain uncharacterized, partly because structural studies on the enzyme are lacking. Thus, we took a two-tier approach to evaluate two mutations (Y50C and T453I) found in ETH-R clinical isolates. First, we used a combination of comparative modeling, molecular docking, and molecular dynamics to build an EthA model in complex with ETH that has hallmark features of structurally characterized homologs. Second, we used free energy computational calculations for the reliable prediction of relative free energies between the wild type and mutant enzymes. The ΔΔG values for Y50C and T453I mutant enzymes in complex with FADH2-NADP-ETH were 3.34 (+/−0.55) and 8.11 (+/−0.51) kcal/mol, respectively, compared to the wild type complex. The positive ΔΔG values indicate that the wild type complex is more stable than the mutants, with the T453I complex being the least stable. These are the first results shedding light on the molecular basis of ETH resistance, namely reduced complex stability of mutant EthA.
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Mycobacterial Cell Wall: A Source of Successful Targets for Old and New Drugs. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10072278] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Eighty years after the introduction of the first antituberculosis (TB) drug, the treatment of drug-susceptible TB remains very cumbersome, requiring the use of four drugs (isoniazid, rifampicin, ethambutol and pyrazinamide) for two months followed by four months on isoniazid and rifampicin. Two of the drugs used in this “short”-course, six-month chemotherapy, isoniazid and ethambutol, target the mycobacterial cell wall. Disruption of the cell wall structure can enhance the entry of other TB drugs, resulting in a more potent chemotherapy. More importantly, inhibition of cell wall components can lead to mycobacterial cell death. The complexity of the mycobacterial cell wall offers numerous opportunities to develop drugs to eradicate Mycobacterium tuberculosis, the causative agent of TB. In the past 20 years, researchers from industrial and academic laboratories have tested new molecules to find the best candidates that will change the face of TB treatment: drugs that will shorten TB treatment and be efficacious against active and latent, as well as drug-resistant TB. Two of these new TB drugs block components of the mycobacterial cell wall and have reached phase 3 clinical trial. This article reviews TB drugs targeting the mycobacterial cell wall in use clinically and those in clinical development.
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Tateishi Y, Minato Y, Baughn AD, Ohnishi H, Nishiyama A, Ozeki Y, Matsumoto S. Genome-wide identification of essential genes in Mycobacterium intracellulare by transposon sequencing - Implication for metabolic remodeling. Sci Rep 2020; 10:5449. [PMID: 32214196 PMCID: PMC7096427 DOI: 10.1038/s41598-020-62287-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 03/10/2020] [Indexed: 12/20/2022] Open
Abstract
The global incidence of the human nontuberculous mycobacteria (NTM) disease is rapidly increasing. However, knowledge of gene essentiality under optimal growth conditions and conditions relevant to the natural ecology of NTM, such as hypoxia, is lacking. In this study, we utilized transposon sequencing to comprehensively identify genes essential for growth in Mycobacterium intracellulare. Of 5126 genes of M. intracellulare ATCC13950, 506 genes were identified as essential genes, of which 280 and 158 genes were shared with essential genes of M. tuberculosis and M. marinum, respectively. The shared genes included target genes of existing antituberculous drugs including SQ109, which targets the trehalose monomycolate transporter MmpL3. From 175 genes showing decreased fitness as conditionally essential under hypoxia, preferential carbohydrate metabolism including gluconeogenesis, glyoxylate cycle and succinate production was suggested under hypoxia. Virulence-associated genes including proteasome system and mycothiol redox system were also identified as conditionally essential under hypoxia, which was further supported by the higher effective suppression of bacterial growth under hypoxia compared to aerobic conditions in the presence of these inhibitors. This study has comprehensively identified functions essential for growth of M. intracellulare under conditions relevant to the host environment. These findings provide critical functional genomic information for drug discovery.
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Affiliation(s)
- Yoshitaka Tateishi
- Department of Bacteriology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757, Asahimachi-Dori, Chuo-ku, Niigata, 951-8510, Japan.
| | - Yusuke Minato
- Department of Microbiology and Immunology, University of Minnesota Medical School, 689 23rd Avenue S.E. Microbiology Research Facility, Minneapolis, 55455, MN, USA
| | - Anthony D Baughn
- Department of Microbiology and Immunology, University of Minnesota Medical School, 689 23rd Avenue S.E. Microbiology Research Facility, Minneapolis, 55455, MN, USA
| | - Hiroaki Ohnishi
- Department of Laboratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Akihito Nishiyama
- Department of Bacteriology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757, Asahimachi-Dori, Chuo-ku, Niigata, 951-8510, Japan
| | - Yuriko Ozeki
- Department of Bacteriology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757, Asahimachi-Dori, Chuo-ku, Niigata, 951-8510, Japan
| | - Sohkichi Matsumoto
- Department of Bacteriology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757, Asahimachi-Dori, Chuo-ku, Niigata, 951-8510, Japan
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Minakshi P, Ghosh M, Brar B, Kumar R, Lambe UP, Ranjan K, Manoj J, Prasad G. Nano-antimicrobials: A New Paradigm for Combating Mycobacterial Resistance. Curr Pharm Des 2020; 25:1554-1579. [PMID: 31218956 DOI: 10.2174/1381612825666190620094041] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/11/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Mycobacterium group contains several pathogenic bacteria including M. tuberculosis where the emergence of multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) is alarming for human and animal health around the world. The condition has further aggravated due to the speed of discovery of the newer drugs has been outpaced by the rate of resistance developed in microorganisms, thus requiring alternative combat strategies. For this purpose, nano-antimicrobials have emerged as a potential option. OBJECTIVE The current review is focused on providing a detailed account of nanocarriers like liposome, micelles, dendrimers, solid lipid NPs, niosomes, polymeric nanoparticles, nano-suspensions, nano-emulsion, mesoporous silica and alginate-based drug delivery systems along with the recent updates on developments regarding nanoparticle-based therapeutics, vaccines and diagnostic methods developed or under pipeline with their potential benefits and limitations to combat mycobacterial diseases for their successful eradication from the world in future. RESULTS Distinct morphology and the underlying mechanism of pathogenesis and resistance development in this group of organisms urge improved and novel methods for the early and efficient diagnosis, treatment and vaccination to eradicate the disease. Recent developments in nanotechnology have the potential to meet both the aspects: nano-materials are proven components of several efficient targeted drug delivery systems and the typical physicochemical properties of several nano-formulations have shown to possess distinct bacteriocidal properties. Along with the therapeutic aspects, nano-vaccines and theranostic applications of nano-formulations have grown in popularity in recent times as an effective alternative means to combat different microbial superbugs. CONCLUSION Nanomedicine holds a bright prospect to perform a key role in global tuberculosis elimination program.
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Affiliation(s)
- Prasad Minakshi
- Department of Animal Biotechnology, LLR University of Veterinary and Animal Sciences, Hisar-125 004, Haryana, India
| | - Mayukh Ghosh
- Department of Veterinary Biochemistry, Ranchi Veterinary College, Birsa Agricultural University, Ranchi-834 006, Jharkhand, India
| | - Basanti Brar
- Department of Animal Biotechnology, LLR University of Veterinary and Animal Sciences, Hisar-125 004, Haryana, India
| | - Rajesh Kumar
- Department of Veterinary Physiology, COVAS, KVASU, Pookode, Wayanad- 673576, Kerala, India
| | - Upendra P Lambe
- Department of Animal Biotechnology, LLR University of Veterinary and Animal Sciences, Hisar-125 004, Haryana, India
| | | | - Jinu Manoj
- RVDEC Mahendergarh, LUVAS, Haryana, India
| | - Gaya Prasad
- SVP University of Agriculture and Technology, Meerut, India
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Rizvi A, Shankar A, Chatterjee A, More TH, Bose T, Dutta A, Balakrishnan K, Madugulla L, Rapole S, Mande SS, Banerjee S, Mande SC. Rewiring of Metabolic Network in Mycobacterium tuberculosis During Adaptation to Different Stresses. Front Microbiol 2019; 10:2417. [PMID: 31736886 PMCID: PMC6828651 DOI: 10.3389/fmicb.2019.02417] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/07/2019] [Indexed: 12/15/2022] Open
Abstract
Metabolic adaptation of Mycobacterium tuberculosis (M. tuberculosis) to microbicidal intracellular environment of host macrophages is fundamental to its pathogenicity. However, an in-depth understanding of metabolic adjustments through key reaction pathways and networks is limited. To understand how such changes occur, we measured the cellular metabolome of M. tuberculosis subjected to four microbicidal stresses using liquid chromatography-mass spectrometric multiple reactions monitoring (LC-MRM/MS). Overall, 87 metabolites were identified. The metabolites best describing the separation between stresses were identified through multivariate analysis. The coupling of the metabolite measurements with existing genome-scale metabolic model, and using constraint-based simulation led to several new concepts and unreported observations in M. tuberculosis; such as (i) the high levels of released ammonia as an adaptive response to acidic stress was due to increased flux through L-asparaginase rather than urease activity; (ii) nutrient starvation-induced anaplerotic pathway for generation of TCA intermediates from phosphoenolpyruvate using phosphoenolpyruvate kinase; (iii) quenching of protons through GABA shunt pathway or sugar alcohols as possible mechanisms of early adaptation to acidic and oxidative stresses; and (iv) usage of alternate cofactors by the same enzyme as a possible mechanism of rewiring metabolic pathways to overcome stresses. Besides providing new leads and important nodes that can be used for designing intervention strategies, the study advocates the strength of applying flux balance analyses coupled with metabolomics to get a global picture of complex metabolic adjustments.
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Affiliation(s)
- Arshad Rizvi
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Arvind Shankar
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, India
| | | | | | - Tungadri Bose
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, India
| | - Anirban Dutta
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, India
| | - Kannan Balakrishnan
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Lavanya Madugulla
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | | | - Sharmila S Mande
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, India
| | - Sharmistha Banerjee
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
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The role of low molecular weight thiols in Mycobacterium tuberculosis. Tuberculosis (Edinb) 2019; 116:44-55. [PMID: 31153518 DOI: 10.1016/j.tube.2019.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 04/16/2019] [Accepted: 04/22/2019] [Indexed: 02/06/2023]
Abstract
Low molecular weight (LMW) thiols are molecules with a functional sulfhydryl group that enable them to detoxify reactive oxygen species, reactive nitrogen species and other free radicals. Their roles range from their ability to modulate the immune system to their ability to prevent damage of biological molecules such as DNA and proteins by protecting against oxidative, nitrosative and acidic stress. LMW thiols are synthesized and found in both eukaryotes and prokaryotes. Due to their beneficial role to both eukaryotes and prokaryotes, their specific functions need to be elucidated, most especially in pathogenic prokaryotes such as Mycobacterium tuberculosis (M.tb), in order to provide a rationale for targeting their biosynthesis for drug development. Ergothioneine (ERG), mycothiol (MSH) and gamma-glutamylcysteine (GGC) are LMW thiols that have been shown to interplay to protect M.tb against cellular stress. Though ERG, MSH and GGC seem to have overlapping functions, studies are gradually revealing their unique physiological roles. Understanding their unique physiological role during the course of tuberculosis (TB) infection, would pave the way for the development of drugs that target their biosynthetic pathway. This review identifies the knowledge gap in the unique physiological roles of LMW thiols and proposes their mechanistic roles based on previous studies. In addition, it gives an update on identified inhibitors of their biosynthetic enzymes.
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Guo Y, Gong W, Wang L, Guo J, Jin G, Gu G, Guo Z. Characterization and biochemical investigation of the potential inositol monophosphate phosphatase involved in bacterial mycothiol biosynthesis. J Carbohydr Chem 2019. [DOI: 10.1080/07328303.2018.1559326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Yuchuan Guo
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Jinan, China
- Department of Chemistry, University of Florida, Gainesville, USA
| | - Wei Gong
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Jinan, China
| | - Lizhen Wang
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Jinan, China
| | - Jiatong Guo
- Department of Chemistry, University of Florida, Gainesville, USA
| | - Guoxia Jin
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, China
| | - Guofeng Gu
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Jinan, China
| | - Zhongwu Guo
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Jinan, China
- Department of Chemistry, University of Florida, Gainesville, USA
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Mulik BB, Dhumal ST, Sapner VS, Rehman NNMA, Dixit PP, Sathe BR. Graphene oxide-based electrochemical activation of ethionamide towards enhanced biological activity. RSC Adv 2019; 9:35463-35472. [PMID: 35528088 PMCID: PMC9074427 DOI: 10.1039/c9ra06681k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 10/15/2019] [Indexed: 01/03/2023] Open
Abstract
The electrochemical behavior of ethionamide (ETO) was investigated on GO (∼500 nm) using the linear sweep voltammetric (LSV) technique at the sweep rate of 10 mV s−1 in 1 M PBS buffer solution, and the characteristic anodic signal was examined at 0.240 V over the potential range of −0.4 to 1 V vs. SCE. However, linearity was observed with the increase in scan rate (2–300 mV s−1) and concentration of ETO (1 μM to 100 mM), suggesting that the process involved diffusion-controlled electron transfer. The results also exhibited excellent current and potential stability, limit of detection (LOD 1.33) and limit of quantification (LOQ 4.4) at optimized experimental conditions. This electrochemical oxidation method was successfully applied in the complete oxidation of ETO to its oxidized form, which was further confirmed by high resolution mass spectroscopy (HRMS) and Fourier transform infrared (FTIR) spectroscopic measurements. Interestingly, the comparative biological evaluation of ETO and ETO-O (oxidised form) showed good enhancement in the activity of oxidised ETO against some Gram-negative pathogens, such as E. aerogenes, S. abony, S. boydii, and E. coli. Electrochemical oxidative activation of ethionamide (ETO) on GO (∼500 nm) confirmed by HRMS and FTIR analysis. The ETO-O (oxidized form) showed enhancement in activity over ETO against Gram negative pathogens (E. aerogenes, S. abony, S. boydii, E. coli).![]()
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Affiliation(s)
- Balaji B. Mulik
- Department of Chemistry
- Dr Babasaheb Ambedkar Marathwada University
- Aurangabad 431004
- India
| | - Sambhaji T. Dhumal
- Department of Chemistry
- Dr Babasaheb Ambedkar Marathwada University
- Aurangabad 431004
- India
| | - Vijay S. Sapner
- Department of Chemistry
- Dr Babasaheb Ambedkar Marathwada University
- Aurangabad 431004
- India
| | - Naziya N. M. A. Rehman
- Department of Microbiology
- Dr Babasaheb Ambedkar Marathwada University Aurangabad
- Sub-Campus
- Osmanabad
- India
| | - Prashant P. Dixit
- Department of Microbiology
- Dr Babasaheb Ambedkar Marathwada University Aurangabad
- Sub-Campus
- Osmanabad
- India
| | - Bhaskar R. Sathe
- Department of Chemistry
- Dr Babasaheb Ambedkar Marathwada University
- Aurangabad 431004
- India
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Shur KV, Bekker OB, Zaichikova MV, Maslov DA, Akimova NI, Zakharevich NV, Chekalina MS, Danilenko VN. Genetic Aspects of Drug Resistance and Virulence in Mycobacterium tuberculosis. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418120141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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31
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Integrated analysis of ethionamide resistance loci in Mycobacterium tuberculosis clinical isolates. Tuberculosis (Edinb) 2018; 113:163-174. [DOI: 10.1016/j.tube.2018.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 08/15/2018] [Accepted: 08/22/2018] [Indexed: 01/31/2023]
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Kavvas ES, Catoiu E, Mih N, Yurkovich JT, Seif Y, Dillon N, Heckmann D, Anand A, Yang L, Nizet V, Monk JM, Palsson BO. Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance. Nat Commun 2018; 9:4306. [PMID: 30333483 PMCID: PMC6193043 DOI: 10.1038/s41467-018-06634-y] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 09/06/2018] [Indexed: 11/09/2022] Open
Abstract
Mycobacterium tuberculosis is a serious human pathogen threat exhibiting complex evolution of antimicrobial resistance (AMR). Accordingly, the many publicly available datasets describing its AMR characteristics demand disparate data-type analyses. Here, we develop a reference strain-agnostic computational platform that uses machine learning approaches, complemented by both genetic interaction analysis and 3D structural mutation-mapping, to identify signatures of AMR evolution to 13 antibiotics. This platform is applied to 1595 sequenced strains to yield four key results. First, a pan-genome analysis shows that M. tuberculosis is highly conserved with sequenced variation concentrated in PE/PPE/PGRS genes. Second, the platform corroborates 33 genes known to confer resistance and identifies 24 new genetic signatures of AMR. Third, 97 epistatic interactions across 10 resistance classes are revealed. Fourth, detailed structural analysis of these genes yields mechanistic bases for their selection. The platform can be used to study other human pathogens.
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Affiliation(s)
- Erol S Kavvas
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Edward Catoiu
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Nathan Mih
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.,Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - James T Yurkovich
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.,Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Yara Seif
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Nicholas Dillon
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - David Heckmann
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Amitesh Anand
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Laurence Yang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Victor Nizet
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Jonathan M Monk
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA. .,Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA. .,Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
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Sao Emani C, Williams MJ, Van Helden PD, Taylor MJC, Carolis C, Wiid IJ, Baker B. Generation and characterization of thiol-deficient Mycobacterium tuberculosis mutants. Sci Data 2018; 5:180184. [PMID: 30251996 PMCID: PMC6154287 DOI: 10.1038/sdata.2018.184] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/03/2018] [Indexed: 12/23/2022] Open
Abstract
Mycothiol (MSH) and ergothioneine (ERG) are thiols able to compensate for each other to protect mycobacteria against oxidative stress. Gamma-glutamylcysteine (GGC), another thiol and an intermediate in ERG biosynthesis has detoxification abilities. Five enzymes are involved in ERG biosynthesis, namely EgtA, EgtB, EgtC, EgtD and EgtE. The role of these enzymes in the production of ERG had been unclear. On the other hand, the enzyme MshA is known to be essential for MSH biosynthesis. In this manuscript, we describe the raw data of the generation and characterization of Mycobacterium tuberculosis (M.tb) mutants harbouring a deletion of the gene coding for each of these enzymes, and the raw data of the phenotypic characterization of the obtained thiol-deficient M.tb mutants. High throughput screening (HTS) of off-patent drugs and natural compounds revealed few compounds that displayed a higher activity against the thiol-deficient mutants relative to the wild-type strain. The mode of action of these drugs was further investigated. Raw data displaying these results are described here.
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Affiliation(s)
- C Sao Emani
- NRF/DST 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, Tygerberg 8000, Cape Town, South Africa.,Barcelona Biomedical Research Park, Centre for Genomic Regulation, Biomolecular Screening & Protein Technologies Unit, 88 Dr.aiguider, 08003 Barcelona, Spain
| | - M J Williams
- NRF/DST 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, Tygerberg 8000, Cape Town, South Africa
| | - P D Van Helden
- NRF/DST 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, Tygerberg 8000, Cape Town, South Africa
| | - M J C Taylor
- Central Analytical Facilities, Mass Spectrometry Unit, Stellenbosch University, Stellenbosch 7600, Cape Town, South Africa
| | - C Carolis
- Barcelona Biomedical Research Park, Centre for Genomic Regulation, Biomolecular Screening & Protein Technologies Unit, 88 Dr.aiguider, 08003 Barcelona, Spain
| | - I J Wiid
- NRF/DST 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, Tygerberg 8000, Cape Town, South Africa
| | - B Baker
- NRF/DST 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, Tygerberg 8000, Cape Town, South Africa
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Arginine-deprivation-induced oxidative damage sterilizes Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2018; 115:9779-9784. [PMID: 30143580 PMCID: PMC6166831 DOI: 10.1073/pnas.1808874115] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Reactive oxygen species (ROS)-mediated oxidative stress and DNA damage have recently been recognized as contributing to the efficacy of most bactericidal antibiotics, irrespective of their primary macromolecular targets. Inhibitors of targets involved in both combating oxidative stress as well as being required for in vivo survival may exhibit powerful synergistic action. This study demonstrates that the de novo arginine biosynthetic pathway in Mycobacterium tuberculosis (Mtb) is up-regulated in the early response to the oxidative stress-elevating agent isoniazid or vitamin C. Arginine deprivation rapidly sterilizes the Mtb de novo arginine biosynthesis pathway mutants ΔargB and ΔargF without the emergence of suppressor mutants in vitro as well as in vivo. Transcriptomic and flow cytometry studies of arginine-deprived Mtb have indicated accumulation of ROS and extensive DNA damage. Metabolomics studies following arginine deprivation have revealed that these cells experienced depletion of antioxidant thiols and accumulation of the upstream metabolite substrate of ArgB or ArgF enzymes. ΔargB and ΔargF were unable to scavenge host arginine and were quickly cleared from both immunocompetent and immunocompromised mice. In summary, our investigation revealed in vivo essentiality of the de novo arginine biosynthesis pathway for Mtb and a promising drug target space for combating tuberculosis.
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Chawla M, Mishra S, Anand K, Parikh P, Mehta M, Vij M, Verma T, Singh P, Jakkala K, Verma HN, AjitKumar P, Ganguli M, Narain Seshasayee AS, Singh A. Redox-dependent condensation of the mycobacterial nucleoid by WhiB4. Redox Biol 2018; 19:116-133. [PMID: 30149290 PMCID: PMC6111044 DOI: 10.1016/j.redox.2018.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/02/2018] [Accepted: 08/11/2018] [Indexed: 12/22/2022] Open
Abstract
Oxidative stress response in bacteria is mediated through coordination between the regulators of oxidant-remediation systems (e.g. OxyR, SoxR) and nucleoid condensation (e.g. Dps, Fis). However, these genetic factors are either absent or rendered non-functional in the human pathogen Mycobacterium tuberculosis (Mtb). Therefore, how Mtb organizes genome architecture and regulates gene expression to counterbalance oxidative imbalance is unknown. Here, we report that an intracellular redox-sensor, WhiB4, dynamically links genome condensation and oxidative stress response in Mtb. Disruption of WhiB4 affects the expression of genes involved in maintaining redox homeostasis, central metabolism, and respiration under oxidative stress. Notably, disulfide-linked oligomerization of WhiB4 in response to oxidative stress activates the protein’s ability to condense DNA. Further, overexpression of WhiB4 led to hypercondensation of nucleoids, redox imbalance and increased susceptibility to oxidative stress, whereas WhiB4 disruption reversed this effect. In accordance with the findings in vitro, ChIP-Seq data demonstrated non-specific binding of WhiB4 to GC-rich regions of the Mtb genome. Lastly, data indicate that WhiB4 deletion affected the expression of ~ 30% of genes preferentially bound by the protein, suggesting both direct and indirect effects on gene expression. We propose that WhiB4 structurally couples Mtb’s response to oxidative stress with genome organization and transcription. Genome condensation is involved in the management of oxidative stress in bacteria. A relation between the genome condensation and oxidative stress is unclear in Mtb. A redox sensor WhiB4 calibrates genome-condensation and antioxidants in Mtb. Over-expression of WhiB4 hyper-condensed genome and induced killing by oxidants. WhiB4 deficiency delayed genome condensation and promoted oxidative stress survival.
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Affiliation(s)
- Manbeena Chawla
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Saurabh Mishra
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Kushi Anand
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Pankti Parikh
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Mansi Mehta
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Manika Vij
- Department of Structural Biology, CSIR-Institute of Genomics and Integrative Biology, South Campus, Mathura Road, New Delhi 110020, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | - Taru Verma
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India; Centre for BioSystems Science and Engineering (BSSE), Indian Institute of Science, Bangalore 560012, India
| | - Parul Singh
- National Centre for Biological Science, Bangalore 560065, India; SASTRA University, Thanjavur 613401, Tamil Nadu, India
| | - Kishor Jakkala
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - H N Verma
- Jaipur National University, Jagatpura, Jaipur 302017, India
| | - Parthasarathi AjitKumar
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Munia Ganguli
- Department of Structural Biology, CSIR-Institute of Genomics and Integrative Biology, South Campus, Mathura Road, New Delhi 110020, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | | | - Amit Singh
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India.
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Sao Emani C, Williams MJ, Wiid IJ, Baker B. The functional interplay of low molecular weight thiols in Mycobacterium tuberculosis. J Biomed Sci 2018; 25:55. [PMID: 30001196 PMCID: PMC6042322 DOI: 10.1186/s12929-018-0458-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 07/05/2018] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Three low molecular weight thiols are synthesized by Mycobacterium tuberculosis (M.tb), namely ergothioneine (ERG), mycothiol (MSH) and gamma-glutamylcysteine (GGC). They are able to counteract reactive oxygen species (ROS) and/or reactive nitrogen species (RNS). In addition, the production of ERG is elevated in the MSH-deficient M.tb mutant, while the production of MSH is elevated in the ERG-deficient mutants. Furthermore, the production of GGC is elevated in the MSH-deficient mutant and the ERG-deficient mutants. The propensity of one thiol to be elevated in the absence of the other prompted further investigations into their interplay in M.tb. METHODS To achieve that, we generated two M.tb mutants that are unable to produce ERG nor MSH but are able to produce a moderate (ΔegtD-mshA) or significantly high (ΔegtB-mshA) amount of GGC relative to the wild-type strain. In addition, we generated an M.tb mutant that is unable to produce GGC nor MSH but is able to produce a significantly low level of ERG (ΔegtA-mshA) relative to the wild-type strain. The susceptibilities of these mutants to various in vitro and ex vivo stress conditions were investigated and compared. RESULTS The ΔegtA-mshA mutant was the most susceptible to cellular stress relative to its parent single mutant strains (ΔegtA and ∆mshA) and the other double mutants. In addition, it displayed a growth-defect in vitro, in mouse and human macrophages suggesting; that the complete inhibition of ERG, MSH and GGC biosynthesis is deleterious for the growth of M.tb. CONCLUSIONS This study indicates that ERG, MSH and GGC are able to compensate for each other to maximize the protection and ensure the fitness of M.tb. This study therefore suggests that the most effective strategy to target thiol biosynthesis for anti-tuberculosis drug development would be the simultaneous inhibition of the biosynthesis of ERG, MSH and GGC.
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Affiliation(s)
- C. Sao Emani
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; SAMRC Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics; Department of Biomedical Sciences, Faculty of Medicine and Health Sciences; Stellenbosch University, PO Box 241, Francie van Zijl Drive, Tygerberg 8000, Cape Town, South Africa
| | - M. J. Williams
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; SAMRC Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics; Department of Biomedical Sciences, Faculty of Medicine and Health Sciences; Stellenbosch University, PO Box 241, Francie van Zijl Drive, Tygerberg 8000, Cape Town, South Africa
| | - I. J. Wiid
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; SAMRC Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics; Department of Biomedical Sciences, Faculty of Medicine and Health Sciences; Stellenbosch University, PO Box 241, Francie van Zijl Drive, Tygerberg 8000, Cape Town, South Africa
| | - B. Baker
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; SAMRC Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics; Department of Biomedical Sciences, Faculty of Medicine and Health Sciences; Stellenbosch University, PO Box 241, Francie van Zijl Drive, Tygerberg 8000, Cape Town, South Africa
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Sarkar R, Mdladla C, Macingwana L, Pietersen RD, Ngwane A, Tabb D, van Helden P, Wiid I, Baker B. Proteomic analysis reveals that sulfamethoxazole induces oxidative stress in M. tuberculosis. Tuberculosis (Edinb) 2018; 111:78-85. [DOI: 10.1016/j.tube.2018.05.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/27/2018] [Accepted: 05/15/2018] [Indexed: 02/04/2023]
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Pacl HT, Reddy VP, Saini V, Chinta KC, Steyn AJC. Host-pathogen redox dynamics modulate Mycobacterium tuberculosis pathogenesis. Pathog Dis 2018; 76:4972762. [PMID: 29873719 PMCID: PMC5989597 DOI: 10.1093/femspd/fty036] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/13/2018] [Indexed: 12/18/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, encounters variable and hostile environments within the host. A major component of these hostile conditions is reductive and oxidative stresses induced by factors modified by the host immune response, such as oxygen tension, NO or CO gases, reactive oxygen and nitrogen intermediates, the availability of different carbon sources and changes in pH. It is therefore essential for Mtb to continuously monitor and appropriately respond to the microenvironment. To this end, Mtb has developed various redox-sensitive systems capable of monitoring its intracellular redox environment and coordinating a response essential for virulence. Various aspects of Mtb physiology are regulated by these systems, including drug susceptibility, secretion systems, energy metabolism and dormancy. While great progress has been made in understanding the mechanisms and pathways that govern the response of Mtb to the host's redox environment, many questions in this area remain unanswered. The answers to these questions are promising avenues for addressing the tuberculosis crisis.
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Affiliation(s)
- Hayden T Pacl
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35205, USA
| | - Vineel P Reddy
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35205, USA
| | - Vikram Saini
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35205, USA
| | - Krishna C Chinta
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35205, USA
| | - Adrie J C Steyn
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35205, USA
- Centers for AIDS Research and Free Radical Biology, University of Alabama at Birmingham, Birmingham, Alabama 35205, USA
- Africa Health Research Institute, K-RITH Tower Building, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
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39
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Zeng X, Kwok JSL, Yang KY, Leung KSS, Shi M, Yang Z, Yam WC, Tsui SKW. Whole genome sequencing data of 1110 Mycobacterium tuberculosis isolates identifies insertions and deletions associated with drug resistance. BMC Genomics 2018; 19:365. [PMID: 29769016 PMCID: PMC5956929 DOI: 10.1186/s12864-018-4734-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 04/26/2018] [Indexed: 12/22/2022] Open
Abstract
Background Drug resistance in Mycobacterium tuberculosis (MTB) is one of the major challenges in tuberculosis (TB) treatment. However, known mutations cannot explain all of the cases of resistance and little research has focused on the relationship between insertions / deletions (indels) and drug resistance. Results Here, we retrieved whole genome sequencing data of 743 drug-resistant MTB strains and 367 pan-susceptible strains from TB patients from the public domain to identify novel genomic markers of drug resistance. A total of 20 region markers containing genes and intergenic regions (IGRs) with significant statistical correlation with antibiotic resistance were revealed, four of which have been previously reported to be associated with drug resistance. In addition, 83 point markers containing frameshift (FS) mutations and IGR indels were also identified independently based on differences in their incidence rates between drug-sensitive and -resistant strains. Among the 83 point markers, eight indels were detected in known drug-associated genes or IGRs. Furthermore, the overlap between 20 region markers and 83 point markers further indicated their associations with drug resistance. The markers identified were involved in essential bacterial metabolic functions, including cell wall and transmembrane transporter functions. A strong correlation between FS mutations and mutations in DNA repair genes including I21V in alkA, R48G in mutT4 and P2R in nth was also found. Conclusions This study identified a set of novel genetic markers with FS mutations and IGR indels associated with MTB drug resistance, which greatly broadens the pool of mutations related to MTB drug resistance. This insight may be important in identifying novel mechanisms of drug resistance in MTB. Electronic supplementary material The online version of this article (10.1186/s12864-018-4734-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xi Zeng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jamie Sui-Lam Kwok
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kevin Yi Yang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kenneth Siu-Sing Leung
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Mai Shi
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zhiyuan Yang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wing-Cheong Yam
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China. .,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China. .,Centre for Microbial Genomics and Proteomics, The Chinese University of Hong Kong, Hong Kong SAR, China.
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40
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Kulkarni A, Sharma AK, Chakrapani H. Redox-guided small molecule antimycobacterials. IUBMB Life 2018; 70:826-835. [DOI: 10.1002/iub.1867] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/14/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Amogh Kulkarni
- Department of Chemistry; Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road; Pune Maharashtra India
| | - Ajay Kumar Sharma
- Department of Chemistry; Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road; Pune Maharashtra India
| | - Harinath Chakrapani
- Department of Chemistry; Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road; Pune Maharashtra India
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41
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Negri A, Javidnia P, Mu R, Zhang X, Vendome J, Gold B, Roberts J, Barman D, Ioerger T, Sacchettini JC, Jiang X, Burns-Huang K, Warrier T, Ling Y, Warren JD, Oren DA, Beuming T, Wang H, Wu J, Li H, Rhee KY, Nathan CF, Liu G, Somersan-Karakaya S. Identification of a Mycothiol-Dependent Nitroreductase from Mycobacterium tuberculosis. ACS Infect Dis 2018; 4:771-787. [PMID: 29465985 PMCID: PMC5952258 DOI: 10.1021/acsinfecdis.7b00111] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
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The success of Mycobacterium tuberculosis (Mtb) as a pathogen depends on
the redundant and complex mechanisms it has evolved for resisting
nitrosative and oxidative stresses inflicted by host immunity. Improving
our understanding of these defense pathways can reveal vulnerable
points in Mtb pathogenesis. In this study, we combined genetic, structural,
computational, biochemical, and biophysical approaches to identify
a novel enzyme class represented by Rv2466c. We show that Rv2466c
is a mycothiol-dependent nitroreductase of Mtb and can reduce the
nitro group of a novel mycobactericidal compound using mycothiol as
a cofactor. In addition to its function as a nitroreductase, Rv2466c
confers partial protection to menadione stress.
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Affiliation(s)
- Ana Negri
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Prisca Javidnia
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, United States
| | | | | | - Jeremie Vendome
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | | | | | | | | | | | | | | | | | | | | | - Deena A. Oren
- Structural Biology Resource Center, Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Thijs Beuming
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | | | | | | | - Kyu Y. Rhee
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, United States
| | | | | | - Selin Somersan-Karakaya
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, United States
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42
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Kerry RG, Gouda S, Sil B, Das G, Shin HS, Ghodake G, Patra JK. Cure of tuberculosis using nanotechnology: An overview. J Microbiol 2018; 56:287-299. [PMID: 29721825 DOI: 10.1007/s12275-018-7414-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/04/2018] [Accepted: 01/04/2018] [Indexed: 02/03/2023]
Abstract
Mycobacterium tuberculosis is the causative agent of tuberculosis (TB), a major health issue of the present era. The bacterium inhabits the host macrophage and other immune cells where it modulates the lysosome trafficking protein, hinders the formation of phagolysosome, and blocks the TNF receptor-dependent apoptosis of host macrophage/monocytes. Other limitations such as resistance to and low bioavailability and bio-distribution of conventional drugs aid to their high virulence and human mortality. This review highlights the use of nanotechnology-based approaches for drug formulation and delivery which could open new avenues to limit the pathogenicity of tuberculosis. Moreover phytochemicals, such as alkaloids, phenols, saponins, steroids, tannins, and terpenoids, extracted from terrestrial plants and mangroves seem promising against M. tuberculosis through different molecular mechanisms. Further understanding of the genomics and proteomics of this pathogenic microbe could also help overcome various research gaps in the path of developing a suitable therapy against tuberculosis.
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Affiliation(s)
- Rout George Kerry
- Department of Biotechnology, AMIT College, Khurda, 752057, Odisha, India
| | - Sushanto Gouda
- Amity Institute of Wildlife Science, Amity University, Noida, 201313, Uttar Pradesh, India
| | - Bikram Sil
- Department of Biotechnology, AMIT College, Khurda, 752057, Odisha, India
| | - Gitishree Das
- Research Institute of Biotechnology & Medical Converged Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Han-Seung Shin
- Department of Food Science and Biotechnology, Dongguk University-Seoul, Goyang, 10326, Republic of Korea.
| | - Gajanan Ghodake
- Department of Biological and Environmental Science, College of Life Science and Biotechnology, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Jayanta Kumar Patra
- Research Institute of Biotechnology & Medical Converged Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea.
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43
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Dookie N, Rambaran S, Padayatchi N, Mahomed S, Naidoo K. Evolution of drug resistance in Mycobacterium tuberculosis: a review on the molecular determinants of resistance and implications for personalized care. J Antimicrob Chemother 2018; 73:1138-1151. [PMID: 29360989 PMCID: PMC5909630 DOI: 10.1093/jac/dkx506] [Citation(s) in RCA: 165] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Drug-resistant TB (DR-TB) remains a significant challenge in TB treatment and control programmes worldwide. Advances in sequencing technology have significantly increased our understanding of the mechanisms of resistance to anti-TB drugs. This review provides an update on advances in our understanding of drug resistance mechanisms to new, existing drugs and repurposed agents. Recent advances in WGS technology hold promise as a tool for rapid diagnosis and clinical management of TB. Although the standard approach to WGS of Mycobacterium tuberculosis is slow due to the requirement for organism culture, recent attempts to sequence directly from clinical specimens have improved the potential to diagnose and detect resistance within days. The introduction of new databases may be helpful, such as the Relational Sequencing TB Data Platform, which contains a collection of whole-genome sequences highlighting key drug resistance mutations and clinical outcomes. Taken together, these advances will help devise better molecular diagnostics for more effective DR-TB management enabling personalized treatment, and will facilitate the development of new drugs aimed at improving outcomes of patients with this disease.
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Affiliation(s)
- Navisha Dookie
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Santhuri Rambaran
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC) - CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Sharana Mahomed
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC) - CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
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Hameed HMA, Islam MM, Chhotaray C, Wang C, Liu Y, Tan Y, Li X, Tan S, Delorme V, Yew WW, Liu J, Zhang T. Molecular Targets Related Drug Resistance Mechanisms in MDR-, XDR-, and TDR- Mycobacterium tuberculosis Strains. Front Cell Infect Microbiol 2018; 8:114. [PMID: 29755957 PMCID: PMC5932416 DOI: 10.3389/fcimb.2018.00114] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 03/23/2018] [Indexed: 01/08/2023] Open
Abstract
Tuberculosis (TB) is a formidable infectious disease that remains a major cause of death worldwide today. Escalating application of genomic techniques has expedited the identification of increasing number of mutations associated with drug resistance in Mycobacterium tuberculosis. Unfortunately the prevalence of bacillary resistance becomes alarming in many parts of the world, with the daunting scenarios of multidrug-resistant tuberculosis (MDR-TB), extensively drug-resistant tuberculosis (XDR-TB) and total drug-resistant tuberculosis (TDR-TB), due to number of resistance pathways, alongside some apparently obscure ones. Recent advances in the understanding of the molecular/ genetic basis of drug targets and drug resistance mechanisms have been steadily made. Intriguing findings through whole genome sequencing and other molecular approaches facilitate the further understanding of biology and pathology of M. tuberculosis for the development of new therapeutics to meet the immense challenge of global health.
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Affiliation(s)
- H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Md Mahmudul Islam
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Changwei Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yang Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Institute of Health Sciences, Anhui University, Hefei, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Xinjie Li
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Vincent Delorme
- Tuberculosis Research Laboratory, Institut Pasteur Korea, Seongnam-si, South Korea
| | - Wing W Yew
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
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45
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Compounds with Potential Activity against Mycobacterium tuberculosis. Antimicrob Agents Chemother 2018; 62:AAC.02236-17. [PMID: 29437626 DOI: 10.1128/aac.02236-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/01/2018] [Indexed: 12/26/2022] Open
Abstract
The high acquisition rate of drug resistance by Mycobacterium tuberculosis necessitates the ongoing search for new drugs to be incorporated in the tuberculosis (TB) regimen. Compounds used for the treatment of other diseases have the potential to be repurposed for the treatment of TB. In this study, a high-throughput screening of compounds against thiol-deficient Mycobacterium smegmatis strains and subsequent validation with thiol-deficient M. tuberculosis strains revealed that ΔegtA and ΔmshA mutants had increased susceptibility to azaguanine (Aza) and sulfaguanidine (Su); ΔegtB and ΔegtE mutants had increased susceptibility to bacitracin (Ba); and ΔegtA, ΔmshA, and ΔegtB mutants had increased susceptibility to fusaric acid (Fu). Further analyses revealed that some of these compounds were able to modulate the levels of thiols and oxidative stress in M. tuberculosis This study reports the activities of Aza, Su, Fu, and Ba against M. tuberculosis and provides a rationale for further investigations.
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46
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Kavvas ES, Seif Y, Yurkovich JT, Norsigian C, Poudel S, Greenwald WW, Ghatak S, Palsson BO, Monk JM. Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions. BMC SYSTEMS BIOLOGY 2018; 12:25. [PMID: 29499714 PMCID: PMC5834885 DOI: 10.1186/s12918-018-0557-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 02/21/2018] [Indexed: 11/10/2022]
Abstract
BACKGROUND The efficacy of antibiotics against M. tuberculosis has been shown to be influenced by experimental media conditions. Investigations of M. tuberculosis growth in physiological conditions have described an environment that is different from common in vitro media. Thus, elucidating the interplay between available nutrient sources and antibiotic efficacy has clear medical relevance. While genome-scale reconstructions of M. tuberculosis have enabled the ability to interrogate media differences for the past 10 years, recent reconstructions have diverged from each other without standardization. A unified reconstruction of M. tuberculosis H37Rv would elucidate the impact of different nutrient conditions on antibiotic efficacy and provide new insights for therapeutic intervention. RESULTS We present a new genome-scale model of M. tuberculosis H37Rv, named iEK1011, that unifies and updates previous M. tuberculosis H37Rv genome-scale reconstructions. We functionally assess iEK1011 against previous models and show that the model increases correct gene essentiality predictions on two different experimental datasets by 6% (53% to 60%) and 18% (60% to 71%), respectively. We compared simulations between in vitro and approximated in vivo media conditions to examine the predictive capabilities of iEK1011. The simulated differences recapitulated literature defined characteristics in the rewiring of TCA metabolism including succinate secretion, gluconeogenesis, and activation of both the glyoxylate shunt and the methylcitrate cycle. To assist efforts to elucidate mechanisms of antibiotic resistance development, we curated 16 metabolic genes related to antimicrobial resistance and approximated evolutionary drivers of resistance. Comparing simulations of these antibiotic resistance features between in vivo and in vitro media highlighted condition-dependent differences that may influence the efficacy of antibiotics. CONCLUSIONS iEK1011 provides a computational knowledge base for exploring the impact of different environmental conditions on the metabolic state of M. tuberculosis H37Rv. As more experimental data and knowledge of M. tuberculosis H37Rv become available, a unified and standardized M. tuberculosis model will prove to be a valuable resource to the research community studying the systems biology of M. tuberculosis.
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Affiliation(s)
- Erol S. Kavvas
- Department of Bioengineering, University of California, San Diego, La Jolla, CA USA
| | - Yara Seif
- Department of Bioengineering, University of California, San Diego, La Jolla, CA USA
| | - James T. Yurkovich
- Department of Bioengineering, University of California, San Diego, La Jolla, CA USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, USA
| | - Charles Norsigian
- Department of Bioengineering, University of California, San Diego, La Jolla, CA USA
| | - Saugat Poudel
- Department of Bioengineering, University of California, San Diego, La Jolla, CA USA
| | - William W. Greenwald
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, USA
| | - Sankha Ghatak
- Department of Bioengineering, University of California, San Diego, La Jolla, CA USA
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens Lyngby, Denmark
| | - Jonathan M. Monk
- Department of Bioengineering, University of California, San Diego, La Jolla, CA USA
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Reyes AM, Pedre B, De Armas MI, Tossounian MA, Radi R, Messens J, Trujillo M. Chemistry and Redox Biology of Mycothiol. Antioxid Redox Signal 2018; 28:487-504. [PMID: 28372502 DOI: 10.1089/ars.2017.7074] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
SIGNIFICANCE Mycothiol (MSH, AcCys-GlcN-Ins) is the main low-molecular weight (LMW) thiol of most Actinomycetes, including the human pathogen Mycobacterium tuberculosis that affects millions of people worldwide. Strains with decreased MSH content show increased susceptibilities to hydroperoxides and electrophilic compounds. In M. tuberculosis, MSH modulates the response to several antituberculosis drugs. Enzymatic routes involving MSH could provide clues for specific drug design. Recent Advances: Physicochemical data argue against a rapid, nonenzymatic reaction of MSH with oxidants, disulfides, or electrophiles. Moreover, exposure of the bacteria to high concentrations of two-electron oxidants resulted in protein mycothiolation. The recently described glutaredoxin-like protein mycoredoxin-1 (Mrx-1) provides a route for catalytic reduction of mycothiolated proteins, protecting critical cysteines from irreversible oxidation. The description of MSH/Mrx-1-dependent activities of peroxidases helped to explain the higher susceptibility to oxidants observed in Actinomycetes lacking MSH. Moreover, the first mycothiol-S-transferase, member of the DinB superfamily of proteins, was described. In Corynebacterium, both the MSH/Mrx-1 and the thioredoxin pathways reduce methionine sulfoxide reductase A. A novel tool for in vivo imaging of the MSH/mycothiol disulfide (MSSM) status allows following changes in the mycothiol redox state during macrophage infection and its relationship with antibiotic sensitivity. CRITICAL ISSUES Redundancy of MSH with other LMW thiols is starting to be unraveled and could help to rationalize the differences in the reported importance of MSH synthesis observed in vitro versus in animal infection models. FUTURE DIRECTIONS Future work should be directed to establish the structural bases of the specificity of MSH-dependent enzymes, thus facilitating drug developments. Antioxid. Redox Signal. 28, 487-504.
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Affiliation(s)
- Aníbal M Reyes
- 1 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,2 Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
| | - Brandán Pedre
- 3 Center for Structural Biology , VIB, Brussels, Belgium .,4 Brussels Center for Redox Biology , Brussels, Belgium .,5 Structural Biology Brussels, Vrije Universiteit Brussel , Brussels, Belgium
| | - María Inés De Armas
- 1 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,2 Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
| | - Maria-Armineh Tossounian
- 3 Center for Structural Biology , VIB, Brussels, Belgium .,4 Brussels Center for Redox Biology , Brussels, Belgium .,5 Structural Biology Brussels, Vrije Universiteit Brussel , Brussels, Belgium
| | - Rafael Radi
- 1 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,2 Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
| | - Joris Messens
- 3 Center for Structural Biology , VIB, Brussels, Belgium .,4 Brussels Center for Redox Biology , Brussels, Belgium .,5 Structural Biology Brussels, Vrije Universiteit Brussel , Brussels, Belgium
| | - Madia Trujillo
- 1 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,2 Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
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Abstract
SIGNIFICANCE L-ergothioneine is synthesized in actinomycetes, cyanobacteria, methylobacteria, and some fungi. In contrast to other low-molecular-weight redox buffers, glutathione and mycothiol, ergothioneine is primarily present as a thione rather than a thiol at physiological pH, which makes it resistant to autoxidation. Ergothioneine regulates microbial physiology and enables the survival of microbes under stressful conditions encountered in their natural environments. In particular, ergothioneine enables pathogenic microbes, such as Mycobacterium tuberculosis (Mtb), to withstand hostile environments within the host to establish infection. Recent Advances: Ergothioneine has been reported to maintain bioenergetic homeostasis in Mtb and protect Mtb against oxidative stresses, thereby enhancing the virulence of Mtb in a mouse model. Furthermore, ergothioneine augments the resistance of Mtb to current frontline anti-TB drugs. Recently, an opportunistic fungus, Aspergillus fumigatus, which infects immunocompromised individuals, has been found to produce ergothioneine, which is important in conidial health and germination, and contributes to the fungal resistance against redox stresses. CRITICAL ISSUES The molecular mechanisms of the functions of ergothioneine in microbial physiology and pathogenesis are poorly understood. It is currently not known if ergothioneine is used in detoxification or antioxidant enzymatic pathways. As ergothioneine is involved in bioenergetic and redox homeostasis and antibiotic susceptibility of Mtb, it is of utmost importance to advance our understanding of these mechanisms. FUTURE DIRECTIONS A clear understanding of the role of ergothioneine in microbes will advance our knowledge of how this thione enhances microbial virulence and resistance to the host's defense mechanisms to avoid complete eradication. Antioxid. Redox Signal. 28, 431-444.
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Affiliation(s)
| | - Krishna C Chinta
- 2 Deptartment of Microbiology, University of Alabama at Birmingham , Birmingham, Alabama
| | - Vineel P Reddy
- 2 Deptartment of Microbiology, University of Alabama at Birmingham , Birmingham, Alabama
| | - Adrie J C Steyn
- 1 Africa Health Research Institute , Durban, South Africa .,2 Deptartment of Microbiology, University of Alabama at Birmingham , Birmingham, Alabama.,3 UAB Center for Free Radical Biology, University of Alabama at Birmingham , Birmingham, Alabama
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Sao Emani C, Williams M, Van Helden P, Taylor M, Wiid I, Baker B. Gamma-glutamylcysteine protects ergothioneine-deficient Mycobacterium tuberculosis mutants against oxidative and nitrosative stress. Biochem Biophys Res Commun 2018; 495:174-178. [DOI: 10.1016/j.bbrc.2017.10.163] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 10/29/2017] [Indexed: 11/15/2022]
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50
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Tan Y, Su B, Zheng H, Song Y, Wang Y, Pang Y. Molecular Characterization of Prothionamide-Resistant Mycobacterium tuberculosis Isolates in Southern China. Front Microbiol 2017; 8:2358. [PMID: 29250048 PMCID: PMC5714880 DOI: 10.3389/fmicb.2017.02358] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 11/15/2017] [Indexed: 01/08/2023] Open
Abstract
Prothionamide (PTH) has been widely used in the treatment of tuberculosis (TB), especially multidrug resistant tuberculosis (MDR-TB), while data regarding prevalence of resistance-causing mutation is limited. In this study, we aimed to investigate the molecular characteristics of PTH-resistant MTB isolates, and also analyzed the risk factors for PTH resistance among Mycobacterium tuberculosis (MTB) isolates in southern China. A total of 282 MTB isolates were enrolled in from Guangzhou Chest Hospital. Among these isolates, 46 (16.3%) were resistant to PTH. Statistical analysis revealed that PTH resistance was more likely to be associated with resistance to levofloxacin (LFX; OR: 2.18, 95% CI: 1.02–4.63; P = 0.04). Of the 46 PTH-resistant MTB isolates, 37 (80.4%) isolates harbored 19 different mutation types, including 10 (21.7%) isolates with double nucleotide substitutions and 27 (58.7%) with single nucleotide substitution. The mutations in ethA (51.4%, 19/37) were most frequently observed among PTH-resistant isolates, followed by 16 (43.2%) in the promoter of inhA and 6 (16.2%) in inhA. In addition, no significant difference was found in the distribution of isolates with different mutation types between Beijing and non-Beijing genotypes (P > 0.05). In conclusion, our data demonstrate that high diversity of genetic mutations conferring PTH resistance is identified among MTB isolates from southern China. Mutations in inhA, ethA, mshA, and ndh genes confer increased resistance of MTB to PTH. Ancient Beijing genotype strains have higher proportion of drug resistance compared with modern Beijing strains. In addition, PTH resistance is more likely to be observed in the LFX-resistant MTB isolates.
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Affiliation(s)
- Yaoju Tan
- Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou, China
| | - Biyi Su
- Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou, China
| | - Huiwen Zheng
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China.,National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuanyuan Song
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yufeng Wang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yu Pang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
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