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Luo G, Ming T, Yang L, He L, Tao T, Wang Y. Modulators targeting protein-protein interactions in Mycobacterium tuberculosis. Microbiol Res 2024; 284:127675. [PMID: 38636239 DOI: 10.1016/j.micres.2024.127675] [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: 09/27/2023] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 04/20/2024]
Abstract
Tuberculosis (TB) is a chronic infectious disease caused by Mycobacterium tuberculosis (M. tuberculosis), mainly transmitted through droplets to infect the lungs, and seriously affecting patients' health and quality of life. Clinically, anti-TB drugs often entail side effects and lack efficacy against resistant strains. Thus, the exploration and development of novel targeted anti-TB medications are imperative. Currently, protein-protein interactions (PPIs) offer novel avenues for anti-TB drug development, and the study of targeted modulators of PPIs in M. tuberculosis has become a prominent research focus. Furthermore, a comprehensive PPI network has been constructed using computational methods and bioinformatics tools. This network allows for a more in-depth analysis of the structural biology of PPIs and furnishes essential insights for the development of targeted small-molecule modulators. Furthermore, this article provides a detailed overview of the research progress and regulatory mechanisms of PPI modulators in M. tuberculosis, the causative agent of TB. Additionally, it summarizes potential targets for anti-TB drugs and discusses the prospects of existing PPI modulators.
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Affiliation(s)
- Guofeng Luo
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tianqi Ming
- State Key Laboratory of Southwestern Chinese Medicine Resources, Department of Pharmacology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Luchuan Yang
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China
| | - Lei He
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China
| | - Tao Tao
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China
| | - Yanmei Wang
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China.
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Płocińska R, Wasik K, Płociński P, Lechowicz E, Antczak M, Błaszczyk E, Dziadek B, Słomka M, Rumijowska-Galewicz A, Dziadek J. The Orphan Response Regulator Rv3143 Modulates the Activity of the NADH Dehydrogenase Complex (Nuo) in Mycobacterium tuberculosis via Protein–Protein Interactions. Front Cell Infect Microbiol 2022; 12:909507. [PMID: 35837472 PMCID: PMC9274095 DOI: 10.3389/fcimb.2022.909507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Two-component signal transduction systems enable mycobacterial cells to quickly adapt and adequately respond to adverse environmental conditions encountered at various stages of host infection. We attempted to determine the role of the Rv3143 “orphan” response regulator in the physiology of Mycobacterium tuberculosis and its orthologue Msmeg_2064 in Mycobacterium smegmatis. We identified the Rv3143 protein as an interaction partner for NuoD, a member of the type I NADH dehydrogenase complex involved in oxidative phosphorylation. The mutants Δrv3143 and Δmsmeg_2064 were engineered in M. tuberculosis and M. smegmatis cells, respectively. The Δmsmeg_2064 strain exhibited a significant reduction in growth and viability in the presence of reactive nitrogen species. The Rv3143-deficient strain was sensitive to valinomycin, which is known to reduce the electrochemical potential of the cell and overexpressed genes required for nitrate respiration. An increased level of reduction of the 2,3,5-triphenyltetrazolium chloride (TTC) electron acceptor in Δrv3143 and Δmsmeg_2064 cells was also evident. The silencing of ndh expression using CRISPRi/dCas9 affected cell survival under limited oxygen conditions. Oxygen consumption during entry to hypoxia was most severely affected in the double-mutant Δmsmeg_2064 ndhCRISPRi/dCas9. We propose that the regulatory protein Rv3143 is a component of the Nuo complex and modulates its activity.
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Affiliation(s)
- Renata Płocińska
- Department of Genetics and Physiology of Mycobacteria, Institute of Medical Biology of the Polish Academy of Sciences, Łódź, Poland
| | - Karolina Wasik
- Department of Genetics and Physiology of Mycobacteria, Institute of Medical Biology of the Polish Academy of Sciences, Łódź, Poland
| | - Przemysław Płociński
- Department of Genetics and Physiology of Mycobacteria, Institute of Medical Biology of the Polish Academy of Sciences, Łódź, Poland
- Department of Immunology and Infectious Biology, Faculty of Biology and Environmental Protection, University of Łódz, Łódź, Poland
| | - Ewelina Lechowicz
- Department of Genetics and Physiology of Mycobacteria, Institute of Medical Biology of the Polish Academy of Sciences, Łódź, Poland
| | - Magdalena Antczak
- Department of Genetics and Physiology of Mycobacteria, Institute of Medical Biology of the Polish Academy of Sciences, Łódź, Poland
| | - Ewelina Błaszczyk
- Department of Genetics and Physiology of Mycobacteria, Institute of Medical Biology of the Polish Academy of Sciences, Łódź, Poland
| | - Bożena Dziadek
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Łódz, Łódź, Poland
| | - Marcin Słomka
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Anna Rumijowska-Galewicz
- Department of Genetics and Physiology of Mycobacteria, Institute of Medical Biology of the Polish Academy of Sciences, Łódź, Poland
| | - Jarosław Dziadek
- Department of Genetics and Physiology of Mycobacteria, Institute of Medical Biology of the Polish Academy of Sciences, Łódź, Poland
- *Correspondence: Jarosław Dziadek,
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Bhattacharjee A, Sarma S, Sen T, Singh AK. Alterations in molecular response of Mycobacterium tuberculosis against anti-tuberculosis drugs. Mol Biol Rep 2022; 49:3987-4002. [PMID: 35066765 DOI: 10.1007/s11033-021-07095-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/16/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Tuberculosis (TB), an infectious disease caused by Mycobacterium tuberculosis, has plagued humans since the early middle-ages. More than one million deaths are recorded annually due to TB, even in present times. These deaths are primarily attributed to the constant appearance of resistant TB strains. Even with the advent of new therapeutics and diagnostics techniques, tuberculosis remains challenging to control due to resistant M. tuberculosis strains. Aided by various molecular changes, these strains adapt to stress created by anti-tuberculosis drugs. MATERIALS AND METHODS The review thus is an overview of ongoing research in the genome and transcriptome of antibiotic-resistant TB. It explores omics-based research to identify mutation and utilization of differential gene expression. CONCLUSIONS This study shows several mutations distinctive in the first- and second-line drug-resistant M. tuberculosis strains. It also explores the expressional differences of genes involved in the fundamental process of the cells and how they help in drug resistance. With the development of transcriptomics-based studies, a new insight has developed to inquire about gene expression changes in drug resistance. This information on expressional pattern changes can be utilized to design the basic platform of anti-TB treatments and therapeutic approaches. These novel insights can be instrumental in disease diagnosis and global containment of resistant TB.
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Affiliation(s)
- Abhilash Bhattacharjee
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sangita Sarma
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Tejosmita Sen
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Anil Kumar Singh
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, 785006, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Waturuocha UW, P. J. A, Singh KK, Malhotra V, Krishna MS, Saini DK. A high-frequency single nucleotide polymorphism in the MtrB sensor kinase in clinical strains of Mycobacterium tuberculosis alters its biochemical and physiological properties. PLoS One 2021; 16:e0256664. [PMID: 34529706 PMCID: PMC8445491 DOI: 10.1371/journal.pone.0256664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/11/2021] [Indexed: 11/19/2022] Open
Abstract
The DNA polymorphisms found in clinical strains of Mycobacterium tuberculosis drive altered physiology, virulence, and pathogenesis in them. Although the lineages of these clinical strains can be traced back to common ancestor/s, there exists a plethora of difference between them, compared to those that have evolved in the laboratory. We identify a mutation present in ~80% of clinical strains, which maps in the HATPase domain of the sensor kinase MtrB and alters kinase and phosphatase activities, and affects its physiological role. The changes conferred by the mutation were probed by in-vitro biochemical assays which revealed changes in signaling properties of the sensor kinase. These changes also affect bacterial cell division rates, size and membrane properties. The study highlights the impact of DNA polymorphisms on the pathophysiology of clinical strains and provides insights into underlying mechanisms that drive signal transduction in pathogenic bacteria.
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Affiliation(s)
- Uchenna Watson Waturuocha
- Department of Studies in Zoology, Manasagangotri, University of Mysore, Mysore, India
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Athira P. J.
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Krishna Kumar Singh
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Vandana Malhotra
- Department of Biochemistry, Sri Venkateswara College, University of Delhi, Delhi, India
| | - M. S. Krishna
- Department of Studies in Zoology, Manasagangotri, University of Mysore, Mysore, India
| | - Deepak Kumar Saini
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
- Center for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
- * E-mail:
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Yang J, Zhang T, Xian X, Li Y, Wang R, Wang P, Zhang M, Wang J. Molecular Characteristics and Drug Resistance of Mycobacterium tuberculosis Isolate Circulating in Shaanxi Province, Northwestern China. Microb Drug Resist 2021; 27:1207-1217. [PMID: 33794134 DOI: 10.1089/mdr.2020.0496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Objective: Shaanxi is the most highly populated province with high burdens of tuberculosis in northwestern China. The aim of this study was to investigate the molecular characteristics and drug resistance of Mycobacterium tuberculosis isolates from Shaanxi province of China in 2018. Methods: Phenotypic drug susceptibility testing and spoligotyping methods were performed on 518 M. tuberculosis isolates; drug-resistant isolates were sequenced in 11 drug loci, including katG, inhA, oxyR-ahpC, rpoB, embB, rpsL, rrs1 (nucleotides 388-1084), gyrA, gyrB, rrs2 (nucleotides 1158-1674), and eis. Results: The prevalences of isoniazid, rifampicin, ethambutol, streptomycin, ofloxacin, and kanamycin resistance were 22.0%, 19.3%, 7.9%, 23.8%, 10.4%, and 3.3%, respectively. The Beijing family (82.8%) was the predominant genotype, followed by the T (9.3%), H (0.6%), CAS (0.4%), LAM (0.4%), and U (0.4%) families. The percentage of Beijing genotype in a central area (88.1%) was higher than in the south (77.3%) and the north area (80.1%) (p < 0.05), while the sex, age, and treatment history between Beijing and non-Beijing family were not statistically different. Mutation analysis found that the most prevalent mutations were katG315, rpoB531, embB306, rpsL43, gyrA94, and rrs1401; the Beijing family exhibited a high rate of isoniazid-resistant isolates carrying katG315 mutations (p < 0.05). Furthermore, compared with the phenotypic data, the sensitivities of isoniazid, rifampicin, ethambutol, streptomycin, ofloxacin, and kanamycin resistance by sequencing base on 11 loci were 85.1%, 94.0%, 53.7%, 74.8%, 77.8%, and 64.7%, respectively. Conclusions: Shaanxi has a serious epidemic of drug-resistant tuberculosis, Beijing family is the predominant genotype, and the distribution showed geographic diversity. The prevalence of Beijing genotypes has a tendency to promote the transmission of high-level isoniazid-resistant M. tuberculosis. Besides, the hot spot regions localized in the embB, rrs2, and eis gene appear not to serve as excellent biomarkers for predicting ethambutol and kanamycin resistance in Shaanxi.
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Affiliation(s)
- Jian Yang
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Clinical Laboratory and Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, China
| | - Tianhua Zhang
- Administration Office, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, China
| | - Xiaoping Xian
- Administration Office, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, China
| | - Yan Li
- Clinical Laboratory and Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, China
| | - Rui Wang
- Clinical Laboratory and Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, China
| | - Panting Wang
- Clinical Laboratory and Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, China
| | - Meng Zhang
- Clinical Laboratory and Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, China
| | - Junyang Wang
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
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Dong W, Wang R, Li P, Wang G, Ren X, Feng J, Lu H, Lu W, Wang X, Chen H, Tan C. Orphan response regulator Rv3143 increases antibiotic sensitivity by regulating cell wall permeability in Mycobacterium smegmatis. Arch Biochem Biophys 2020; 692:108522. [PMID: 32781051 DOI: 10.1016/j.abb.2020.108522] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/23/2020] [Accepted: 07/28/2020] [Indexed: 12/20/2022]
Abstract
About one quarter of people worldwide are infected with tuberculosis, and multi-drug resistant tuberculosis (MDR-TB) remains a health threat. It is known that two-Component Signal Transduction Systems (TCSs) of Mycobacterium tuberculosis are closely related to tuberculosis resistance, but the mechanism by which orphan response protein Rv3143 regulates strain sensitivity to drug is still unclear. This study found that Rv3143 overexpression resulted in approximately two-fold increase in Mycobacterium smegmatis antibiotic sensitivity. Transcriptome sequencing indicated that 198 potential genes were regulated by Rv3143, affecting the sensitivity of the strain to rifampicin (RIF). MSMEG_4740 promoter binding with Rv3143, was screened out by surface plasmon resonance (SPR). Rv1524, the homologous gene of MSMEG_4740, belonging to the glycosyltransferase (Gtf) family, was related to cell wall modification. By measuring ethidium bromide (EB) accumulation, we found when Rv3143 or MSMEG_4740, or Rv1524 was overexpressed, the cell wall permeability of Mycobacterium smegmatis was increased. In addition, a combination of Rv3143 and RIF was observed. Our findings provide a new strategy for treating drug-resistant tuberculosis by increasing the expression of Rv3143 to enhance the strain sensitivity to antibiotics.
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Affiliation(s)
- Wenqi Dong
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Rui Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Pei Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Department of Gastrointestinal Surgery, The Second Clinical Medical College of Jinan University, Shenzhen, Guangdong, 518020, China
| | - Gaoyan Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xuanxiu Ren
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jiajia Feng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Hao Lu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Wenjia Lu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xiangru Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei, 430070, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, Hubei, 430070, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei, 430070, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, Hubei, 430070, China
| | - Chen Tan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei, 430070, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, Hubei, 430070, China.
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Yang J, Pang Y, Zhang T, Xian X, Li Y, Wang R, Wang P, Zhang M, Wang J. Molecular characteristics and in vitro susceptibility to bedaquiline of Mycobacterium tuberculosis isolates circulating in Shaanxi, China. Int J Infect Dis 2020; 99:163-170. [PMID: 32738481 DOI: 10.1016/j.ijid.2020.07.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/10/2020] [Accepted: 07/24/2020] [Indexed: 10/23/2022] Open
Abstract
OBJECTIVE The aim of this study was to investigate the molecular characteristics and in vitro susceptibility to bedaquiline of Mycobacterium tuberculosis (MTB) isolates from Shaanxi, China. METHODS The minimum inhibitory concentration (MIC) of bedaquiline was determined using the microplate alamarBlue assay for 518 MTB isolates from Shaanxi. Isolates with MIC values of bedaquiline ≥0.12 μg/mL were sequenced for the atpE, Rv0678, and pepQ genes. Drug susceptibility testing and spoligotyping were also conducted for all strains. RESULTS Ten (1.93%) bedaquiline-resistant strains were isolated from 518 tuberculosis patients. The resistance rate of bedaquiline was not correlated to sex, age, treatment history, region, or genotype. Five bedaquiline-resistant isolates and one bedaquiline-susceptible isolate were found to carry Rv0678 mutations; six mutation types were identified, including G5T, A263G, C185T, G19deletion, C265T, and T323C. No mutations within the atpE and pepQ genes were observed. CONCLUSIONS Bedaquiline showed strong in vitro antibacterial activity against MTB isolates, and the Rv0678 gene serves as the major mechanism contributing to bedaquiline resistance among MTB isolates from Shaanxi, China. Three novel mutation types (G19deletion, C265T, and T323C) of the Rv0678 gene were associated with resistance to bedaquiline. Furthermore, in addition to the current three resistance-associated genes (atpE, Rv0678, and pepQ), other mechanisms of resistance to bedaquiline may exist that need further study.
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Affiliation(s)
- Jian Yang
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China; Clinical Laboratory, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, Shaanxi 710048, China.
| | - Yu Pang
- National Clinical Laboratory on Tuberculosis, BeijingKey Laboratory for Drug Resistant Tuberculosis Research, BeijingChest Hospital, Capital Medical University, BeijingTuberculosis and Thoracic Tumor Institute, Beijing, 102206, China
| | - Tianhua Zhang
- Administration Office, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, Shaanxi 710048, China
| | - Xiaoping Xian
- Administration Office, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, Shaanxi 710048, China
| | - Yan Li
- Clinical Laboratory, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, Shaanxi 710048, China
| | - Rui Wang
- Clinical Laboratory, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, Shaanxi 710048, China
| | - Panting Wang
- Clinical Laboratory, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, Shaanxi 710048, China
| | - Meng Zhang
- Clinical Laboratory, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, Shaanxi 710048, China
| | - Junyang Wang
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China.
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Yang X, Wang J, Bing G, Bie P, De Y, Lyu Y, Wu Q. Ortholog-based screening and identification of genes related to intracellular survival. Gene 2018; 651:134-142. [DOI: 10.1016/j.gene.2018.01.059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 10/29/2017] [Accepted: 01/17/2018] [Indexed: 12/29/2022]
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A temporal proteome dynamics study reveals the molecular basis of induced phenotypic resistance in Mycobacterium smegmatis at sub-lethal rifampicin concentrations. Sci Rep 2017; 7:43858. [PMID: 28262820 PMCID: PMC5338346 DOI: 10.1038/srep43858] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 01/31/2017] [Indexed: 12/24/2022] Open
Abstract
In the last 40 years only one new antitubercular drug has been approved, whilst resistance to current drugs, including rifampicin, is spreading. Here, we used the model organism Mycobacterium smegmatis to study mechanisms of phenotypic mycobacterial resistance, employing quantitative mass spectrometry-based proteomics to investigate the temporal effects of sub-lethal concentrations of rifampicin on the mycobacterial proteome at time-points corresponding to early response, onset of bacteriostasis and early recovery. Across 18 samples, a total of 3,218 proteins were identified from 31,846 distinct peptides averaging 16,250 identified peptides per sample. We found evidence that two component signal transduction systems (e.g. MprA/MprB) play a major role during initial mycobacterial adaptive responses to sub-lethal rifampicin and that, after dampening an initial SOS response, the bacteria supress the DevR (DosR) regulon and also upregulate their transcriptional and translational machineries. Furthermore, we found a co-ordinated dysregulation in haeme and mycobactin synthesis. Finally, gradual upregulation of the M. smegmatis-specific rifampin ADP-ribosyl transferase was observed which, together with upregulation of transcriptional and translational machinery, likely explains recovery of normal growth. Overall, our data indicates that in mycobacteria, sub-lethal rifampicin triggers a concerted phenotypic response that contrasts significantly with that observed at higher antimicrobial doses.
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Wang T, Feng GD, Pang Y, Liu JY, Zhou Y, Yang YN, Dai W, Zhang L, Li Q, Gao Y, Chen P, Zhan LP, Marais BJ, Zhao YL, Zhao G. High rate of drug resistance among tuberculous meningitis cases in Shaanxi province, China. Sci Rep 2016; 6:25251. [PMID: 27143630 PMCID: PMC4855176 DOI: 10.1038/srep25251] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 04/12/2016] [Indexed: 11/18/2022] Open
Abstract
The clinical and mycobacterial features of tuberculous meningitis (TBM) cases in China are not well described; especially in western provinces with poor tuberculosis control. We prospectively enrolled patients in whom TBM was considered in Shaanxi Province, northwestern China, over a 2-year period (September 2010 to December 2012). Cerebrospinal fluid specimens were cultured for Mycobacterium tuberculosis; with phenotypic and genotypic drug susceptibility testing (DST), as well as genotyping of all positive cultures. Among 350 patients included in the study, 27 (7.7%) had culture-confirmed TBM; 84 (24.0%) had probable and 239 (68.3%) had possible TBM. DST was performed on 25/27 (92.3%) culture positive specimens; 12/25 (48.0%) had "any resistance" detected and 3 (12.0%) were multi-drug resistant (MDR). Demographic and clinical features of drug resistant and drug susceptible TBM cases were similar. Beijing was the most common genotype (20/25; 80.0%) with 9/20 (45%) of the Beijing strains exhibiting drug resistance; including all 3 MDR strains. All (4/4) isoniazid resistant strains had mutations in the katG gene; 75% (3/4) of strains with phenotypic rifampicin resistance had mutations in the rpoB gene detected by Xpert MTB/RIF®. High rates of drug resistance were found among culture-confirmed TBM cases; most were Beijing strains.
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Affiliation(s)
- Ting Wang
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
- Department of Neurology, Kunming Medical University affiliated Yan’an Hospital, 245 Renming East Road, Kunming, Yunnan, 650200, P.R.China
| | - Guo-Dong Feng
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
| | - Yu Pang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, no.155 Changbai Road, Beijing, 102206, P.R.China
| | - Jia-Yun Liu
- Department of Inspection, Xijing Hospital, Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
| | - Yang Zhou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, no.155 Changbai Road, Beijing, 102206, P.R.China
| | - Yi-Ning Yang
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
| | - Wen Dai
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
| | - Lin Zhang
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
| | - Qiao Li
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
| | - Yu Gao
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
| | - Ping Chen
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
| | - Li-Ping Zhan
- Department of Neurology, Kunming Medical University affiliated Yan’an Hospital, 245 Renming East Road, Kunming, Yunnan, 650200, P.R.China
| | - Ben J Marais
- The Children’s Hospital at Westmead and the Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Australia
| | - Yan-Lin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, no.155 Changbai Road, Beijing, 102206, P.R.China
| | - Gang Zhao
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
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Benjak A, Uplekar S, Zhang M, Piton J, Cole ST, Sala C. Genomic and transcriptomic analysis of the streptomycin-dependent Mycobacterium tuberculosis strain 18b. BMC Genomics 2016; 17:190. [PMID: 26944551 PMCID: PMC4779234 DOI: 10.1186/s12864-016-2528-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 02/24/2016] [Indexed: 12/05/2022] Open
Abstract
Background The ability of Mycobacterium tuberculosis to establish a latent infection (LTBI) in humans confounds the treatment of tuberculosis. Consequently, there is a need to discover new therapeutic agents that can kill M. tuberculosis both during active disease and LTBI. The streptomycin-dependent strain of M. tuberculosis, 18b, provides a useful tool for this purpose since upon removal of streptomycin (STR) it enters a non-replicating state that mimics latency both in vitro and in animal models. Results The 4.41 Mb genome sequence of M. tuberculosis 18b was determined and this revealed the strain to belong to clade 3 of the ancient ancestral lineage of the Beijing family. STR-dependence was attributable to insertion of a single cytosine in the 530 loop of the 16S rRNA and to a single amino acid insertion in the N-terminal domain of initiation factor 3. RNA-seq was used to understand the genetic programme activated upon STR-withdrawal and hence to gain insight into LTBI. This revealed reconfiguration of gene expression and metabolic pathways showing strong similarities between non-replicating 18b and M. tuberculosis residing within macrophages, and with the core stationary phase and microaerophilic responses. Conclusion The findings of this investigation confirm the validity of 18b as a model for LTBI, and provide insight into both the evolution of tubercle bacilli and the functioning of the ribosome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2528-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrej Benjak
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland.
| | - Swapna Uplekar
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland. .,Current addresses: Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA.
| | - Ming Zhang
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland. .,Current addresses: Department of Biochemistry, University of Lausanne, Quartier UNIL-Epalinges, Ch. des Boveresses 155, CH-1066, Epalinges, Switzerland.
| | - Jérémie Piton
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland.
| | - Stewart T Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland.
| | - Claudia Sala
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland.
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Differential roles of the hemerythrin-like proteins of Mycobacterium smegmatis in hydrogen peroxide and erythromycin susceptibility. Sci Rep 2015; 5:16130. [PMID: 26607739 PMCID: PMC4660385 DOI: 10.1038/srep16130] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/08/2015] [Indexed: 11/09/2022] Open
Abstract
Hemerythrin-like proteins are oxygen-carrying non-heme di-iron binding proteins and their functions have effect on oxidation-reduction regulation and antibiotic resistance. Recent studies using bioinformatic analyses suggest that multiple hemerythrin-like protein coding sequences might have been acquired by lateral gene transfer and the number of hemerythrin-like proteins varies amongst different species. Mycobacterium smegmatis contains three hemerythrin-like proteins, MSMEG_3312, MSMEG_2415 and MSMEG_6212. In this study, we have systematically analyzed all three hemerythrin-like proteins in M. smegmatis and our results identified and characterized two functional classes: MSMEG_2415 plays an important role in H2O2 susceptibility, and MSMEG_3312 and MSMEG_6212 are associated with erythromycin susceptibility. Phylogenetic analysis indicated that these three proteins have different evolutionary origins, possibly explaining their different physiological functions. Here, combined with biological and phylogenetic analyses, our results provide new insights into the evolutionary divergence of the hemerythrin-like proteins in M. smegmatis.
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