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Su F, Cao L, Ren X, Hu J, Tavengana G, Wu H, Zhou Y, Fu Y, Jiang M, Wen Y. The mutation rate of rpoB gene showed an upward trend with the increase of MIRU10, MIRU39 and QUB4156 repetitive number. BMC Genomics 2023; 24:26. [PMID: 36646991 PMCID: PMC9843906 DOI: 10.1186/s12864-023-09120-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 01/06/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) is a frequently used typing method for identifying the Beijing genotype of Mycobacterium tuberculosis (Mtb), which is easily transformed into rifampicin (RIF) resistance. The RIF resistance of Mtb is considered to be highly related with the mutation of rpoB gene. Therefore, this study aimed to analyze the relationship between the repetitive number of MIRU loci and the mutation of rpoB gene. METHODS An open-source whole-genome sequencing data of Mtb was used to detect the mutation of rpoB gene and the repetitive number of MIRU loci by bioinformatics methods. Cochran-Armitage analysis was performed to analyze the trend of the rpoB gene mutation rate and the repetitive number of MIRU loci. RESULTS Among 357 rifampicin-resistant tuberculosis (RR-TB), 304 strains with mutated rpoB genes were detected, and 6 of 67 rifampicin susceptible strains were detected mutations. The rpoB gene mutational rate showed an upward trend with the increase of MIRU10, MIRU39, QUB4156 and MIRU16 repetitive number, but only the repetitive number of MIRU10, MRIU39 and QUB4156 were risk factors for rpoB gene mutation. The Hunter-Gaston discriminatory index (HGDI) of MIRU10 (0.65) and QUB4156 (0.62) was high in the overall sample, while MIRU39 (0.39) and MIRU16 (0.43) showed a moderate discriminatory Power. CONCLUSION The mutation rate of rpoB gene increases with the addition of repetitive numbers of MIRU10, QUB4156 and MIRU39 loci.
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Affiliation(s)
- Fan Su
- grid.443626.10000 0004 1798 4069School of Public Health, Wannan Medical College, Wuhu, Anhui Province China
| | - Lei Cao
- grid.443626.10000 0004 1798 4069School of Public Health, Wannan Medical College, Wuhu, Anhui Province China
| | - Xia Ren
- grid.443626.10000 0004 1798 4069School of Public Health, Wannan Medical College, Wuhu, Anhui Province China
| | - Jian Hu
- grid.443626.10000 0004 1798 4069School of Public Health, Wannan Medical College, Wuhu, Anhui Province China
| | - Grace Tavengana
- grid.443626.10000 0004 1798 4069School of Public Health, Wannan Medical College, Wuhu, Anhui Province China
| | - Huan Wu
- grid.443626.10000 0004 1798 4069School of Laboratory Medicine, Wannan Medical College, Wuhu, Anhui Province China
| | - Yumei Zhou
- grid.443626.10000 0004 1798 4069School of Public Health, Wannan Medical College, Wuhu, Anhui Province China
| | - Yuhan Fu
- grid.443626.10000 0004 1798 4069School of Public Health, Wannan Medical College, Wuhu, Anhui Province China
| | - Mingfei Jiang
- grid.443626.10000 0004 1798 4069School of Clinical Medicine, Wannan Medical College, Wuhu, Anhui Province China
| | - Yufeng Wen
- grid.443626.10000 0004 1798 4069School of Public Health, Wannan Medical College, Wuhu, Anhui Province China
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Dwivedi M, Bajpai K. The chamber of secretome in Mycobacterium tuberculosis as a potential therapeutic target. Biotechnol Genet Eng Rev 2022; 39:1-44. [PMID: 35613080 DOI: 10.1080/02648725.2022.2076031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Mycobacterium tuberculosis (MTB) causes one of the ancient diseases, Tuberculosis, affects people around the globe and its severity can be understood by its classification as a second infectious disease after COVID-19 and the 13th leading cause of death according to a WHO report. Despite having advanced diagnostic approaches and therapeutic strategies, unfortunately, TB is still spreading across the population due to the emergence of drug-resistance MTB and Latent TB infection (LTBI). We are seeking for effective approaches to overcome these hindrances and efficient treatment for this perilous disease. Therefore, there is an urgent need to develop drugs based on operative targeting of the bacterial system that could result in both efficient treatment and lesser emergence of MDR-TB. One such promising target could be the secretory systems and especially the Type 7 secretory system (T7SS-ESX) of Mycobacterium tuberculosis, which is crucial for the secretion of effector proteins as well as in establishing host-pathogen interactions of the tubercle bacilli. The five paralogous ESX systems (ESX-1 to EXS-5) have been observed by in silico genome analysis of MTB, among which ESX-1 and ESX-5 are substantial for virulence and mediating host cellular inflammasome. The bacterium growth and virulence can be modulated by targeting the T7SS. In the present review, we demonstrate the current status of therapeutics against MTB and focus on the function and cruciality of T7SS along with other secretory systems as a promising therapeutic target against Tuberculosis.
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Affiliation(s)
- Manish Dwivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
| | - Kriti Bajpai
- Department of Biotechnology, Himachal Pradesh University, Shimla, India
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Drever K, Lim ZL, Zriba S, Chen JM. Protein Synthesis and Degradation Inhibitors Potently Block Mycobacterium tuberculosis type-7 Secretion System ESX-1 Activity. ACS Infect Dis 2021; 7:273-280. [PMID: 33534536 DOI: 10.1021/acsinfecdis.0c00741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mycobacterium tuberculosis (M. tb) uses its type-7 secretion system ESX-1 to translocate key virulence effector proteins. Taking a chemical genetics approach, we demonstrate for the first time the importance of mycobacterial proteostasis to ESX-1. We show that individual treatment with inhibitors of protein synthesis (chloramphenicol and kanamycin) and protein degradation (lassomycin and bortezomib), at concentrations that only reduce M. tb growth by 50% and less, specifically block ESX-1 secretion activity in the tubercle bacillus. In contrast, the mycobacterial cell-wall synthesis inhibitor isoniazid, even at a concentration that reduces M. tb growth by 90% has no effect on ESX-1 secretion activity. We also show that chloramphenicol but not isoniazid at subinhibitory concentrations specifically attenuates ESX-1-mediated M. tb virulence in macrophages. Taken together, the results of our study identify a novel vulnerability in the ESX-1 system and offer new avenues of anti-TB drug research to neutralize this critical virulence-mediating protein secretion apparatus.
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Affiliation(s)
- Kylee Drever
- Vaccine and Infectious Disease Organization, Saskatoon, Saskatchewan S7N 5E3, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B4, Canada
| | - Ze Long Lim
- Vaccine and Infectious Disease Organization, Saskatoon, Saskatchewan S7N 5E3, Canada
| | - Slim Zriba
- Vaccine and Infectious Disease Organization, Saskatoon, Saskatchewan S7N 5E3, Canada
- Vaccinology and Immunotherapeutics Program, School of Public Health, University of Saskatchewan, Saskatoon, Saskatchewan S7N 2Z4, Canada
| | - Jeffrey M. Chen
- Vaccine and Infectious Disease Organization, Saskatoon, Saskatchewan S7N 5E3, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B4, Canada
- Vaccinology and Immunotherapeutics Program, School of Public Health, University of Saskatchewan, Saskatoon, Saskatchewan S7N 2Z4, Canada
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Yu L, Fang W, He Y, Cai W, Wei W, Tian C. Secondary structure and transmembrane topology analysis of the N-terminal domain of the inner membrane protein EccE 1 from M. smegmatis using site-directed spin labeling EPR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183515. [PMID: 33245893 DOI: 10.1016/j.bbamem.2020.183515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/29/2020] [Accepted: 11/20/2020] [Indexed: 10/22/2022]
Abstract
Protein EccE1 is an essential component of the mycobacterial ESX-1 secretion system, which plays a crucial part in the process of virulence factors secretion, especially for pathogenic mycobacteria such as Mycobacterium tuberculosis. While EccE1 was previously postulated to be the inner membrane pore-forming unit of a membrane complex through which substrates are transported, the structural properties of EccE1 remains to be explored. In the present study, systematic Site-Directed Spin Labeling (SDSL) and Electron Paramagnetic Resonance (EPR) spectroscopic studies was carried out to reveal the secondary structure and transmembrane topology of the N-terminal Domain of EccE1 protein (EccE1-NTD) from M. smegmatis in detergent micelles. EPR-based mobility and accessibility analysis of the R1 side chain for 64 residue positions of EccE1-NTD indicates that the transmembrane domain adopts two α-helices spanning Phe7-Cys30 and Leu36-Ile54. A tentative structural topology model of EccE1-NTD embedded in membrane is also suggested based on EPR spectroscopic data in this study, which will provide further insights into this protein and the ESX secretion systems of mycobacteria.
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Affiliation(s)
- Lu Yu
- High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui 230031, China.
| | - Wei Fang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yao He
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Wenguang Cai
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui 230601, China
| | - Wei Wei
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Changlin Tian
- High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui 230031, China; Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China.
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The ESX-1 Virulence Factors Downregulate miR-147-3p in Mycobacterium marinum-Infected Macrophages. Infect Immun 2020; 88:IAI.00088-20. [PMID: 32253249 DOI: 10.1128/iai.00088-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 03/30/2020] [Indexed: 02/06/2023] Open
Abstract
As important virulence factors of Mycobacterium tuberculosis, EsxA and EsxB not only play a role in phagosome rupture and M. tuberculosis cytosolic translocation but also function as modulators of host immune responses by modulating numerous microRNAs (miRNAs). Recently, we have found that mycobacterial infection downregulated miR-148a-3p (now termed miR-148) in macrophages in an ESX-1-dependent manner. The upregulation of miR-148 reduced mycobacterial intracellular survival. Here, we investigated miR-147-3p (now termed miR-147), a negative regulator of inflammatory cytokines (e.g., interleukin-6 [IL-6] and IL-10), in mycobacterial infection. We infected murine RAW264.7 macrophages with Mycobacterium marinum, a surrogate model organism for M. tuberculosis, and found that the esxBA-knockout strain (M. marinum ΔesxBA) upregulated miR-147 to a level that was significantly higher than that induced by the M. marinum wild-type (WT) strain or by the M. marinum ΔesxBA complemented strain, M. marinum ΔesxBA/pesxBA, suggesting that the ESX-1 system (potentially EsxBA and/or other codependently secreted factors) is the negative regulator of miR-147. miR-147 was also downregulated by directly incubating the macrophages with the purified recombinant EsxA or EsxB protein or the EsxBA heterodimer, which further confirms the role of the EsxBA proteins in the downregulation of miR-147. The upregulation of miR-147 inhibited the production of IL-6 and IL-10 and significantly reduced M. marinum intracellular survival. Interestingly, inhibitors of either miR-147 or miR-148 reciprocally compromised the effects of the mimics of their counterparts on M. marinum intracellular survival. This suggests that miR-147 and miR-148 share converged downstream pathways in response to mycobacterial infection, which was supported by data indicating that miR-147 upregulation inhibits the Toll-like receptor 4/NF-κB pathway.
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Johansen MD, Herrmann JL, Kremer L. Non-tuberculous mycobacteria and the rise of Mycobacterium abscessus. Nat Rev Microbiol 2020; 18:392-407. [PMID: 32086501 DOI: 10.1038/s41579-020-0331-1] [Citation(s) in RCA: 364] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2020] [Indexed: 12/17/2022]
Abstract
Infections caused by non-tuberculous mycobacteria (NTM) are increasing globally and are notoriously difficult to treat due to intrinsic resistance of these bacteria to many common antibiotics. NTM are diverse and ubiquitous in the environment, with only a few species causing serious and often opportunistic infections in humans, including Mycobacterium abscessus. This rapidly growing mycobacterium is one of the most commonly identified NTM species responsible for severe respiratory, skin and mucosal infections in humans. It is often regarded as one of the most antibiotic-resistant mycobacteria, leaving us with few therapeutic options. In this Review, we cover the proposed infection process of M. abscessus, its virulence factors and host interactions and highlight the commonalities and differences of M. abscessus with other NTM species. Finally, we discuss drug resistance mechanisms and future therapeutic options. Taken together, this knowledge is essential to further our understanding of this overlooked and neglected global threat.
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Affiliation(s)
- Matt D Johansen
- Institut de Recherche en Infectiologie de Montpellier, Centre National de la Recherche Scientifique UMR 9004, Université de Montpellier, Montpellier, France
| | - Jean-Louis Herrmann
- Université Paris-Saclay, UVSQ, Inserm, Infection et Inflammation, Montigny-Le-Bretonneux, France.,AP-HP. GHU Paris Saclay, Hôpital Raymond Poincaré, Garches, France
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier, Centre National de la Recherche Scientifique UMR 9004, Université de Montpellier, Montpellier, France. .,Inserm, Institut de Recherche en Infectiologie de Montpellier, Montpellier, France.
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