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Xu M, Liu M, Liu T, Pan X, Ren Q, Han T, Gou L. HigA2 (Rv2021c) Is a Transcriptional Regulator with Multiple Regulatory Targets in Mycobacterium tuberculosis. Microorganisms 2024; 12:1244. [PMID: 38930627 PMCID: PMC11205783 DOI: 10.3390/microorganisms12061244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
Toxin-antitoxin (TA) systems are the major mechanism for persister formation in Mycobacterium tuberculosis (Mtb). Previous studies found that HigBA2 (Rv2022c-Rv2021c), a predicted type II TA system of Mtb, could be activated for transcription in response to multiple stresses such as anti-tuberculosis drugs, nutrient starvation, endure hypoxia, acidic pH, etc. In this study, we determined the binding site of HigA2 (Rv2021c), which is located in the coding region of the upstream gene higB2 (Rv2022c), and the conserved recognition motif of HigA2 was characterized via oligonucleotide mutation. Eight binding sites of HigA2 were further found in the Mtb genome according to the conserved motif. RT-PCR showed that HigA2 can regulate the transcription level of all eight of these genes and three adjacent downstream genes. DNA pull-down experiments showed that twelve functional regulators sense external regulatory signals and may regulate the transcription of the HigBA2 system. Of these, Rv0903c, Rv0744c, Rv0474, Rv3124, Rv2603c, and Rv3583c may be involved in the regulation of external stress signals. In general, we identified the downstream target genes and possible upstream regulatory genes of HigA2, which paved the way for the illustration of the persistence establishment mechanism in Mtb.
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Affiliation(s)
- Mingyan Xu
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan 063210, China; (M.X.); (M.L.); (T.L.); (X.P.); (Q.R.)
| | - Meikun Liu
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan 063210, China; (M.X.); (M.L.); (T.L.); (X.P.); (Q.R.)
| | - Tong Liu
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan 063210, China; (M.X.); (M.L.); (T.L.); (X.P.); (Q.R.)
| | - Xuemei Pan
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan 063210, China; (M.X.); (M.L.); (T.L.); (X.P.); (Q.R.)
| | - Qi Ren
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan 063210, China; (M.X.); (M.L.); (T.L.); (X.P.); (Q.R.)
| | - Tiesheng Han
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan 063210, China; (M.X.); (M.L.); (T.L.); (X.P.); (Q.R.)
| | - Lixia Gou
- School of Life Science, North China University of Science and Technology, Tangshan 063210, China
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Singh P, Jamal S, Ahmed F, Saqib N, Mehra S, Ali W, Roy D, Ehtesham NZ, Hasnain SE. Computational modeling and bioinformatic analyses of functional mutations in drug target genes in Mycobacterium tuberculosis. Comput Struct Biotechnol J 2021; 19:2423-2446. [PMID: 34025934 PMCID: PMC8113780 DOI: 10.1016/j.csbj.2021.04.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 11/29/2022] Open
Abstract
MycoTRAP-DB, a database of mutations and their impact on normal functionality of protein in M.tb genes. Several secondary mutations were identified with significant impact on protein structure and function. Comprehensive information gives insight for screening of suspected hotspots in advance to combat drug resistant TB.
Tuberculosis (TB) continues to be the leading cause of deaths due to its persistent drug resistance and the consequent ineffectiveness of anti-TB treatment. Recent years witnessed huge amount of sequencing data, revealing mutations responsible for drug resistance. However, the lack of an up-to-date repository remains a barrier towards utilization of these data and identifying major mutations-associated with resistance. Amongst all mutations, non-synonymous mutations alter the amino acid sequence of a protein and have a much greater effect on pathogenicity. Hence, this type of gene mutation is of prime interest of the present study. The purpose of this study is to develop an updated database comprising almost all reported substitutions within the Mycobacterium tuberculosis (M.tb) drug target genes rpoB, inhA, katG, pncA, gyrA and gyrB. Various bioinformatics prediction tools were used to assess the structural and biophysical impacts of the resistance causing non-synonymous single nucleotide polymorphisms (nsSNPs) at the molecular level. This was followed by evaluating the impact of these mutations on binding affinity of the drugs to target proteins. We have developed a comprehensive online resource named MycoTRAP-DB (Mycobacterium tuberculosis Resistance Associated Polymorphisms Database) that connects mutations in genes with their structural, functional and pathogenic implications on protein. This database is accessible at http://139.59.12.92. This integrated platform would enable comprehensive analysis and prioritization of SNPs for the development of improved diagnostics and antimycobacterial medications. Moreover, our study puts forward secondary mutations that can be important for prognostic assessments of drug-resistance mechanism and actionable anti-TB drugs.
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Affiliation(s)
- Pooja Singh
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Salma Jamal
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Faraz Ahmed
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Najumu Saqib
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Seema Mehra
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Waseem Ali
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Deodutta Roy
- Department of Environmental and Occupational Health, Florida International University, Miami 33029, USA
| | - Nasreen Z Ehtesham
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | - Seyed E Hasnain
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida 201301, India.,Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi (IIT-D), Hauz Khas, New Delhi 110016, India
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Hameed HA, Tan Y, Islam MM, Lu Z, Chhotaray C, Wang S, Liu Z, Fang C, Tan S, Yew WW, Zhong N, Liu J, Zhang T. Detection of Novel Gene Mutations Associated with Pyrazinamide Resistance in Multidrug-Resistant Mycobacterium tuberculosis Clinical Isolates in Southern China. Infect Drug Resist 2020; 13:217-227. [PMID: 32158237 PMCID: PMC6986415 DOI: 10.2147/idr.s230774] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 12/20/2019] [Indexed: 12/19/2022] Open
Abstract
Objective Pyrazinamide (PZA) is a cornerstone of modern tuberculosis regimens. This study aimed to investigate the performance of genotypic testing of pncA + upstream region, rpsA, panD, Rv2783c, and clpC1 genes to add insights for more accurate molecular diagnosis of PZA-resistant (R) Mycobacterium tuberculosis. Methods Drug susceptibility testing, sequencing analysis of PZA-related genes including the entire operon of pncA (Rv2044c-pncA-Rv2042c) and PZase assay were performed for 448 M. tuberculosis clinical isolates. Results Our data showed that among 448 M. tuberculosis clinical isolates, 113 were MDR, 195 pre-XDR and 70 XDR TB, while the remaining 70 strains had other combinations of drug-resistance. A total of 60.04% (269/448) M. tuberculosis clinical isolates were resistant to PZA, of which 78/113 were MDR, 119/195 pre-XDR and 29/70 XDR TB strains. PZAR isolates have predominance (83.3%) of Beijing genotype. Genotypic characterization of Rv2044c-pncA-Rv2042c revealed novel nonsynonymous mutations in Rv2044c with negative PZase activity which led to confer PZAR. Compared with phenotypic data, 84.38% (227/269) PZAR strains with mutations in pncA + upstream region exhibited 83.64% sensitivity but the combined evaluation of the mutations in rpsA 2.60% (7/269), panD 1.48% (4/269), Rv2783c 1.11% (3/269) and Rv2044c 0.74% (2/269) increased the sensitivity to 89.59%. Fifty-seven novel mutations were identified in this study. Interestingly, a frameshift deletion (C-114del) in upstream of pncAwt nullified the effect of A-11G mutation and induced positive PZase activity, divergent from five PZase negative A-11G PZAR mutants. Twenty-six PZAR strains having wild-type-sequenced genes with positive or negative PZase suggest the existence of unknown resistance mechanisms. Conclusion Our study revealed that PZAR rate in MDR and pre-XDR TB was markedly higher in southern China. The concomitant evaluation of pncA + UFR, rpsA, panD, Rv2783c, and Rv2044c provides more dependable genotypic results of PZA resistance. Fifty-seven novel mutations/indels in this study may play a vital role as diagnostic markers. The upstream region of pncA and PZase regulation are valuable to explore the unknown mechanism of PZA-resistance.
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Affiliation(s)
- Hm Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People's Republic of China.,University of Chinese Academy of Sciences (UCAS), Beijing, People's Republic of China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, People's Republic of China
| | - Md Mahmudul Islam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People's Republic of China.,University of Chinese Academy of Sciences (UCAS), Beijing, People's Republic of China
| | - Zhili Lu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People's Republic of China
| | - Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People's Republic of China.,University of Chinese Academy of Sciences (UCAS), Beijing, People's Republic of China
| | - Shuai Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People's Republic of China.,University of Chinese Academy of Sciences (UCAS), Beijing, People's Republic of China
| | - Zhiyong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People's Republic of China
| | - Cuiting Fang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People's Republic of China.,University of Chinese Academy of Sciences (UCAS), Beijing, People's Republic of China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, People's Republic of China
| | - Wing Wai Yew
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Nanshan Zhong
- National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, People's Republic of China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People's Republic of China.,University of Chinese Academy of Sciences (UCAS), Beijing, People's Republic of China.,National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
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Karmakar M, Globan M, Fyfe JAM, Stinear TP, Johnson PDR, Holmes NE, Denholm JT, Ascher DB. Analysis of a Novel pncA Mutation for Susceptibility to Pyrazinamide Therapy. Am J Respir Crit Care Med 2019; 198:541-544. [PMID: 29694240 DOI: 10.1164/rccm.201712-2572le] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
| | - Maria Globan
- 1 University of Melbourne Melbourne, Victoria, Australia and.,2 Melbourne Health Melbourne, Victoria, Australia
| | - Janet A M Fyfe
- 1 University of Melbourne Melbourne, Victoria, Australia and.,2 Melbourne Health Melbourne, Victoria, Australia
| | | | - Paul D R Johnson
- 1 University of Melbourne Melbourne, Victoria, Australia and.,3 World Health Organization Collaborating Centre for Mycobacterium ulcerans Melbourne, Victoria, Australia
| | - Natasha E Holmes
- 1 University of Melbourne Melbourne, Victoria, Australia and.,4 Austin Health Heidelberg, Victoria, Australia
| | | | - David B Ascher
- 1 University of Melbourne Melbourne, Victoria, Australia and.,5 University of Cambridge Cambridge, United Kingdom
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Munir A, Kumar N, Ramalingam SB, Tamilzhalagan S, Shanmugam SK, Palaniappan AN, Nair D, Priyadarshini P, Natarajan M, Tripathy S, Ranganathan UD, Peacock SJ, Parkhill J, Blundell TL, Malhotra S. Identification and Characterization of Genetic Determinants of Isoniazid and Rifampicin Resistance in Mycobacterium tuberculosis in Southern India. Sci Rep 2019; 9:10283. [PMID: 31311987 PMCID: PMC6635374 DOI: 10.1038/s41598-019-46756-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/28/2019] [Indexed: 02/02/2023] Open
Abstract
Drug-resistant tuberculosis (TB), one of the leading causes of death worldwide, arises mainly from spontaneous mutations in the genome of Mycobacterium tuberculosis. There is an urgent need to understand the mechanisms by which the mutations confer resistance in order to identify new drug targets and to design new drugs. Previous studies have reported numerous mutations that confer resistance to anti-TB drugs, but there has been little systematic analysis to understand their genetic background and the potential impacts on the drug target stability and/or interactions. Here, we report the analysis of whole-genome sequence data for 98 clinical M. tuberculosis isolates from a city in southern India. The collection was screened for phenotypic resistance and sequenced to mine the genetic mutations conferring resistance to isoniazid and rifampicin. The most frequent mutation among isoniazid and rifampicin isolates was S315T in katG and S450L in rpoB respectively. The impacts of mutations on protein stability, protein-protein interactions and protein-ligand interactions were analysed using both statistical and machine-learning approaches. Drug-resistant mutations were predicted not only to target active sites in an orthosteric manner, but also to act through allosteric mechanisms arising from distant sites, sometimes at the protein-protein interface.
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Affiliation(s)
- Asma Munir
- 0000000121885934grid.5335.0Department of Biochemistry, University of Cambridge, Tennis Court. Rd., Cambridge, CB2 1GA UK
| | - Narender Kumar
- 0000000121885934grid.5335.0Department of Medicine, University of Cambridge, Hills Rd., Cambridge, CB2 0QQ UK
| | - Suresh Babu Ramalingam
- 0000 0004 1767 6138grid.417330.2ICMR-National Institute for Research in Tuberculosis, Chennai, 600031 India
| | - Sembulingam Tamilzhalagan
- 0000 0004 1767 6138grid.417330.2ICMR-National Institute for Research in Tuberculosis, Chennai, 600031 India
| | - Siva Kumar Shanmugam
- 0000 0004 1767 6138grid.417330.2ICMR-National Institute for Research in Tuberculosis, Chennai, 600031 India
| | | | - Dina Nair
- 0000 0004 1767 6138grid.417330.2ICMR-National Institute for Research in Tuberculosis, Chennai, 600031 India
| | - Padma Priyadarshini
- 0000 0004 1767 6138grid.417330.2ICMR-National Institute for Research in Tuberculosis, Chennai, 600031 India
| | - Mohan Natarajan
- 0000 0004 1767 6138grid.417330.2ICMR-National Institute for Research in Tuberculosis, Chennai, 600031 India
| | - Srikanth Tripathy
- 0000 0004 1767 6138grid.417330.2ICMR-National Institute for Research in Tuberculosis, Chennai, 600031 India
| | - Uma Devi Ranganathan
- 0000 0004 1767 6138grid.417330.2ICMR-National Institute for Research in Tuberculosis, Chennai, 600031 India
| | - Sharon J. Peacock
- 0000000121885934grid.5335.0Department of Medicine, University of Cambridge, Hills Rd., Cambridge, CB2 0QQ UK ,0000 0004 0425 469Xgrid.8991.9London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Julian Parkhill
- 0000 0004 0606 5382grid.10306.34Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA UK
| | - Tom L. Blundell
- 0000000121885934grid.5335.0Department of Biochemistry, University of Cambridge, Tennis Court. Rd., Cambridge, CB2 1GA UK
| | - Sony Malhotra
- 0000000121885934grid.5335.0Department of Biochemistry, University of Cambridge, Tennis Court. Rd., Cambridge, CB2 1GA UK ,0000 0001 2161 2573grid.4464.2Present Address: Birkbeck College, University of London, Malet Street, WC1E7HX London, UK
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