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Feldman C, Theron AJ, Cholo MC, Anderson R. Cigarette Smoking as a Risk Factor for Tuberculosis in Adults: Epidemiology and Aspects of Disease Pathogenesis. Pathogens 2024; 13:151. [PMID: 38392889 PMCID: PMC10892798 DOI: 10.3390/pathogens13020151] [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: 11/22/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
It has been noted by the World Health Organisation that cases of tuberculosis in 2022 globally numbered 10.6 million, resulting in 1.3 million deaths, such that TB is one of the infectious diseases causing the greatest morbidity and mortality worldwide. Since as early as 1918, there has been an ongoing debate as to the relationship between cigarette smoking and TB. However, numerous epidemiological studies, as well as meta-analyses, have indicated that both active and passive smoking are independent risk factors for TB infection, development of reactivation TB, progression of primary TB, increased severity of cavitary disease, and death from TB, among several other considerations. With this considerable body of evidence confirming the association between smoking and TB, it is not surprising that TB control programmes represent a key potential preventative intervention. In addition to coverage of the epidemiology of TB and its compelling causative link with smoking, the current review is also focused on evidence derived from clinical- and laboratory-based studies of disease pathogenesis, most prominently the protective anti-mycobacterial mechanisms of the alveolar macrophage, the primary intracellular refuge of M. tuberculosis. This section of the review is followed by an overview of the major strategies utilised by the pathogen to subvert these antimicrobial mechanisms in the airway, which are intensified by the suppressive effects of smoke inhalation on alveolar macrophage function. Finally, consideration is given to a somewhat under-explored, pro-infective activity of cigarette smoking, namely augmentation of antibiotic resistance due to direct effects of smoke per se on the pathogen. These include biofilm formation, induction of cellular efflux pumps, which eliminate both smoke-derived toxicants and antibiotics, as well as gene modifications that underpin antibiotic resistance.
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Affiliation(s)
- Charles Feldman
- Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, York Road, Parktown, Johannesburg 2193, South Africa;
| | - Annette J. Theron
- Department of Immunology, School of Medicine, Faculty of Health Sciences, University of Pretoria, Bophelo Road, Prinshof, Pretoria 0083, South Africa; (A.J.T.); (M.C.C.)
| | - Moloko C. Cholo
- Department of Immunology, School of Medicine, Faculty of Health Sciences, University of Pretoria, Bophelo Road, Prinshof, Pretoria 0083, South Africa; (A.J.T.); (M.C.C.)
| | - Ronald Anderson
- Department of Immunology, School of Medicine, Faculty of Health Sciences, University of Pretoria, Bophelo Road, Prinshof, Pretoria 0083, South Africa; (A.J.T.); (M.C.C.)
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Niu H, Cao Q, Zhang T, Du Y, He P, Jiao L, Wang B, Zhu B, Hu L, Zhang Y. Construction and evaluation of a novel multi-antigenic Mycobacterium tuberculosis subunit vaccine candidate BfrB-GrpE/DPC. Int Immunopharmacol 2023; 124:111060. [PMID: 37862738 DOI: 10.1016/j.intimp.2023.111060] [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: 07/16/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 10/22/2023]
Abstract
Tuberculosis poses a significant threat to human health due to the lack of an effective vaccine. Although promising progress has been made in the development of tuberculosis vaccines, new vaccines that broaden the antigenic repertoire need to be developed to eradicate this illness. In this study, we used Mycobacterium tuberculosis ferritin BfrB and heat-shock protein GrpE to construct a novel multi-antigenic fusion protein, BfrB-GrpE (BG). BG protein was stably overexpressed in the soluble form in Escherichia coli at a high yield and purified via sequential salt fractionation and hydrophobic chromatography. Purified BG was emulsified in an adjuvant containing N, N'-dimethyl-N, N'-dioctadecylammonium bromide, polyinosinic-polycytidylic acid, and cholesterol (DPC) to construct the BG/DPC vaccine, which stimulated strong cellular and humoral immune responses in mice. Moreover, combination of BG with our previously developed vaccine, Mtb10.4-HspX (MH), containing antigens from both the proliferating and dormant stages, significantly reduced the bacterial counts in the lungs and spleens of M. tuberculosis-infected mice. Importantly, mice that received BG + MH/DPC after M. tuberculosis H37Rv infection survived slightly better (100% survival) than those that received the BCG vaccine (80% survival), although the difference was not statistically significant. Our findings can aid in the selection of antigens and optimization of vaccination regimens to improve the efficacy of tuberculosis vaccines.
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Affiliation(s)
- Hongxia Niu
- School of Basic Medical Sciences & Key Laboratory of Blood-stasis-toxin Syndrome of Zhejiang Province, Zhejiang Chinese Medical University, Hangzhou, China; School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - Qianqian Cao
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - Tingting Zhang
- Lanzhou Institute of Biological Products Co., Ltd., Lanzhou, China
| | - Yunjie Du
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - Pu He
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - Lei Jiao
- Lanzhou Institute of Biological Products Co., Ltd., Lanzhou, China
| | - Bingxiang Wang
- Lanzhou Institute of Biological Products Co., Ltd., Lanzhou, China
| | - Bingdong Zhu
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - Lina Hu
- Lanzhou Institute of Biological Products Co., Ltd., Lanzhou, China.
| | - Ying Zhang
- The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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Pereira MMR, de Oliveira FM, da Costa AC, Junqueira-Kipnis AP, Kipnis A. Ferritin from Mycobacterium abscessus is involved in resistance to antibiotics and oxidative stress. Appl Microbiol Biotechnol 2023; 107:2577-2595. [PMID: 36862179 DOI: 10.1007/s00253-023-12420-8] [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: 11/02/2022] [Revised: 01/22/2023] [Accepted: 01/30/2023] [Indexed: 03/03/2023]
Abstract
Mycobacterium abscessus subsp. massiliense (Mycma) is a rapidly growing Mycobacterium belonging to the M. abscessus complex that is often associated with lung and soft tissue infection outbreaks. Mycma is resistant to many antimicrobials, including those used for treating tuberculosis. Therefore, Mycma infections are difficult to treat and may lead to high infectious complication rates. Iron is essential for bacterial growth and establishment of infection. During infection, the host reduces iron concentrations as a defense mechanism. To counteract the host-induced iron deficiency, Mycma produces siderophores to capture iron. Mycma has two ferritins (encoded by mycma_0076 and mycma_0077) modulated by different iron concentrations, which allow the survival of this pathogen during iron scarcity. In this study, we constructed knockout (Mycma 0076KO) and complemented (Mycma 0076KOc) gene strains for mycma_0076 to understand the function of 0076 ferritin. Deletion of mycma_0076 in Mycma led to the transition in colony morphology from smooth to rough, alteration of the glycopeptidolipids spectra, increased permeability of the envelope, reduction in biofilm formation, increased susceptibility to antimicrobials and hydrogen peroxide-induced oxidative stress, and decreased internalization by macrophages. This study shows that Mycma_0076 ferritin in Mycma is involved in resistance to oxidative stress and antimicrobials, and alteration of cell envelope architecture. KEY POINTS: • Deletion of the mycma_0076 gene altered colony morphology to rough; • Mycma 0076KO changed GPL profile; • Absence of Mycma_0076 ferritin results in increased susceptibility to antimicrobials and oxidative stress in Mycma. Legend: a In wild-type M. abscessus subsp. massiliense strain, iron is captured from the environment by carboxymycobactins and mycobactins (1). Iron-dependent regulator (IdeR) proteins bind to ferrous iron (Fe+2) in the bacterial cytoplasm leading to the activation of the IdeR-Fe+2 complex (2). The activated complex binds to the promoter regions of iron-dependent genes, called iron box, which in turn help in the recruitment of RNA polymerase to promote transcription of genes such as mycma_0076 and mycma_0077 ferritin genes (3). Mycma_0076 and Mycma_0077 ferritins bind to excess iron in the medium and promote Fe2+ oxidation into ferric iron (Fe3+) and store iron molecules to be released under iron scarcity conditions. (4) Genes related to biosynthesis and transport of glycopeptidolipids (GPL) are expressed normally and the cell envelope is composed of different GPL species (colored squares represented on the cell surface (GPLs). Consequently, WT Mycma present smooth colony phenotype (5). b In Mycma 0076KO strain, the lack of ferritin 0076 causes overexpression of mycma_0077 (6), but does not restore wild-type iron homeostasis and thus may result in free intracellular iron, even in the presence of miniferritins (MaDps). The excess iron potentiates oxidative stress (7) by generating hydroxyl radicals through Fenton Reaction. During this process, through an unknown mechanism, that could involve Lsr2 (8), the expression of GPL synthesis locus is regulated positively and/or negatively, resulting in alteration of GPL composition in the membrane (as represented by different colors of squares on the cell surface), resulting in a rough colony phenotype (9). The changes of GPL can increase cell wall permeability, contributing to antimicrobial susceptibility (10).
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Affiliation(s)
- Maria Micaella Rodrigues Pereira
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, GO, Brazil
- Tropical Medicine and Public Health Graduate Program at Federal, University of Goiás, Goiânia, GO, Brazil
| | - Fábio Muniz de Oliveira
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, GO, Brazil
- Tropical Medicine and Public Health Graduate Program at Federal, University of Goiás, Goiânia, GO, Brazil
- Indiana Center for Regenerative Medicine and Engineering, School of Medicine, Indiana University, Indianapolis, IN, USA
| | | | | | - André Kipnis
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, GO, Brazil.
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Pattanaik KP, Sengupta S, Jit BP, Kotak R, Sonawane A. Host-Mycobacteria conflict: Immune responses of the host vs. the mycobacteria TLR2 and TLR4 ligands and concomitant host-directed therapy. Microbiol Res 2022; 264:127153. [DOI: 10.1016/j.micres.2022.127153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/21/2022] [Accepted: 07/29/2022] [Indexed: 12/15/2022]
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Distribution of Common and Rare Genetic Markers of Second-Line-Injectable-Drug Resistance in Mycobacterium tuberculosis Revealed by a Genome-Wide Association Study. Antimicrob Agents Chemother 2022; 66:e0207521. [PMID: 35532237 DOI: 10.1128/aac.02075-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Point mutations in the rrs gene and the eis promoter are known to confer resistance to the second-line injectable drugs (SLIDs) amikacin (AMK), capreomycin (CAP), and kanamycin (KAN). While mutations in these canonical genes confer the majority of SLID resistance, alternative mechanisms of resistance are not uncommon and threaten effective treatment decisions when using conventional molecular diagnostics. In total, 1,184 clinical Mycobacterium tuberculosis isolates from 7 countries were studied for genomic markers associated with phenotypic resistance. The markers rrs:A1401G and rrs:G1484T were associated with resistance to all three SLIDs, and three known markers in the eis promoter (eis:G-10A, eis:C-12T, and eis:C-14T) were similarly associated with kanamycin resistance (KAN-R). Among 325, 324, and 270 AMK-R, CAP-R, and KAN-R isolates, 274 (84.3%), 250 (77.2%), and 249 (92.3%) harbored canonical mutations, respectively. Thirteen isolates harbored more than one canonical mutation. Canonical mutations did not account for 103 of the phenotypically resistant isolates. A genome-wide association study identified three genes and promoters with mutations that, on aggregate, were associated with unexplained resistance to at least one SLID. Our analysis associated whiB7 5'-untranslated-region mutations with KAN resistance, supporting clinical relevance for this previously demonstrated mechanism of KAN resistance. We also provide evidence for the novel association of CAP resistance with the promoter of the Rv2680-Rv2681 operon, which encodes an exoribonuclease that may influence the binding of CAP to the ribosome. Aggregating mutations by gene can provide additional insight and therefore is recommended for identifying rare mechanisms of resistance when individual mutations carry insufficient statistical power.
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Willemse D, Moodley C, Mehra S, Kaushal D. Transcriptional Response of Mycobacterium tuberculosis to Cigarette Smoke Condensate. Front Microbiol 2021; 12:744800. [PMID: 34721344 PMCID: PMC8554204 DOI: 10.3389/fmicb.2021.744800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
Smoking is known to be an added risk factor for tuberculosis (TB), with nearly a quarter of the TB cases attributed to cigarette smokers in the 22 countries with the highest TB burden. Many studies have indicated a link between risk of active TB and cigarette smoke. Smoking is also known to significantly decrease TB cure and treatment completion rate and increase mortality rates. Cigarette smoke contains thousands of volatile compounds including carcinogens, toxins, reactive solids, and oxidants in both particulate and gaseous phase. Yet, to date, limited studies have analyzed the impact of cigarette smoke components on Mycobacterium tuberculosis (Mtb), the causative agent of TB. Here we report the impact of cigarette smoke condensate (CSC) on survival, mutation frequency, and gene expression of Mtb in vitro. We show that exposure of virulent Mtb to cigarette smoke increases the mutation frequency of the pathogen and strongly induces the expression of the regulon controlled by SigH—a global transcriptional regulator of oxidative stress. SigH has previously been shown to be required for Mtb to respond to oxidative stress, survival, and granuloma formation in vivo. A high-SigH expression phenotype is known to be associated with greater virulence of Mtb. In patients with pulmonary TB who smoke, these changes may therefore play an important, yet unexplored, role in the treatment efficacy by potentially enhancing the virulence of tubercle bacilli.
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Affiliation(s)
- Danicke Willemse
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Chivonne Moodley
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States.,Tulane National Primate Research Center, Tulane University Health Sciences Center, Covington, LA, United States
| | - Smriti Mehra
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States.,Tulane National Primate Research Center, Tulane University Health Sciences Center, Covington, LA, United States
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States
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Choi S, Choi HG, Back YW, Park HS, Lee KI, Gurmessa SK, Pham TA, Kim HJ. A Dendritic Cell-Activating Rv1876 Protein Elicits Mycobacterium Bovis BCG-Prime Effect via Th1-Immune Response. Biomolecules 2021; 11:1306. [PMID: 34572519 PMCID: PMC8465531 DOI: 10.3390/biom11091306] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 01/03/2023] Open
Abstract
The widely administered tuberculosis (TB) vaccine, Bacillus Calmette-Guerin (BCG), is the only licensed vaccine, but has highly variable efficiency against childhood and pulmonary TB. Therefore, the BCG prime-boost strategy is a rational solution for the development of new TB vaccines. Studies have shown that Mycobacterium tuberculosis (Mtb) culture filtrates contain proteins that have promising vaccine potential. In this study, Rv1876 bacterioferritin was identified from the culture filtrate fraction with strong immunoreactivity. Its immunobiological potential has not been reported previously. We found that recombinant Rv1876 protein induced dendritic cells' (DCs) maturation by MAPK and NF-κB signaling activation, induced a T helper type 1 cell-immune response, and expanded the population of the effector/memory T cell. Boosting BCG with Rv1876 protein enhanced the BCG-primed Th1 immune response and reduced the bacterial load in the lung compared to those of BCG alone. Thus, Rv1876 is a good target for the prime-boost strategy.
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Affiliation(s)
- Seunga Choi
- Department of Microbiology, College of Medicine, Chungnam National University, Daejeon 35015, Korea; (S.C.); (H.-G.C.); (Y.W.B.); (H.-S.P.); (K.-I.L.); (S.K.G.); (T.A.P.)
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea
| | - Han-Gyu Choi
- Department of Microbiology, College of Medicine, Chungnam National University, Daejeon 35015, Korea; (S.C.); (H.-G.C.); (Y.W.B.); (H.-S.P.); (K.-I.L.); (S.K.G.); (T.A.P.)
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea
| | - Yong Woo Back
- Department of Microbiology, College of Medicine, Chungnam National University, Daejeon 35015, Korea; (S.C.); (H.-G.C.); (Y.W.B.); (H.-S.P.); (K.-I.L.); (S.K.G.); (T.A.P.)
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea
| | - Hye-Soo Park
- Department of Microbiology, College of Medicine, Chungnam National University, Daejeon 35015, Korea; (S.C.); (H.-G.C.); (Y.W.B.); (H.-S.P.); (K.-I.L.); (S.K.G.); (T.A.P.)
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea
| | - Kang-In Lee
- Department of Microbiology, College of Medicine, Chungnam National University, Daejeon 35015, Korea; (S.C.); (H.-G.C.); (Y.W.B.); (H.-S.P.); (K.-I.L.); (S.K.G.); (T.A.P.)
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea
| | - Sintayehu Kebede Gurmessa
- Department of Microbiology, College of Medicine, Chungnam National University, Daejeon 35015, Korea; (S.C.); (H.-G.C.); (Y.W.B.); (H.-S.P.); (K.-I.L.); (S.K.G.); (T.A.P.)
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea
| | - Thuy An Pham
- Department of Microbiology, College of Medicine, Chungnam National University, Daejeon 35015, Korea; (S.C.); (H.-G.C.); (Y.W.B.); (H.-S.P.); (K.-I.L.); (S.K.G.); (T.A.P.)
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea
| | - Hwa-Jung Kim
- Department of Microbiology, College of Medicine, Chungnam National University, Daejeon 35015, Korea; (S.C.); (H.-G.C.); (Y.W.B.); (H.-S.P.); (K.-I.L.); (S.K.G.); (T.A.P.)
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea
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Sharma D, Sharma S, Sharma J. Potential strategies for the management of drug-resistant tuberculosis. J Glob Antimicrob Resist 2020; 22:210-214. [PMID: 32169684 DOI: 10.1016/j.jgar.2020.02.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 12/18/2019] [Accepted: 02/26/2020] [Indexed: 12/30/2022] Open
Abstract
In the current scenario, the emergence of drug resistance in Mycobacterium tuberculosis is the consequence of the failure of conventional diagnostic and treatment approaches. To combat this global emergence of drug resistance, alternative approaches such as pathogen-centric (use of repurposed drugs, novel analogues of existing anti-TB drugs and novel compounds with a different mechanism of action), host-centric (immunomodulatory agents, therapeutic vaccines, immune and cellular therapies) and nano-based drug/vaccine delivery should be used singly or in combination. Diverse types of nano-carriers have assessed as auspicious diagnostic and drug delivery systems. In this focused review, we have suggested a long-term solution for combating antimicrobial resistance and also an attractive means to increase patient compliance and reduce treatment duration.
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Affiliation(s)
- Divakar Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India.
| | - Sandeep Sharma
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medical Laboratory Sciences, Division of Research and Development, Lovely Professional University, Phagwara, Punjab 144411, India
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Sharma D, Lata M, Faheem M, Khan AU, Joshi B, Venkatesan K, Shukla S, Bisht D. Role of M.tuberculosis protein Rv2005c in the aminoglycosides resistance. Microb Pathog 2019; 132:150-155. [PMID: 31059757 DOI: 10.1016/j.micpath.2019.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/02/2019] [Accepted: 05/02/2019] [Indexed: 10/26/2022]
Abstract
Tuberculosis is an airborne infectious disease caused by Mycobacterium tuberculosis which threatens the globe. Aminoglycosides {Amikacin (AK) & Kanamycin (KM)} are WHO recommended second-line anti-TB drugs used against the treatment of drug-resistant tuberculosis. Aminoglycosides target the steps of protein translation machinery of M.tuberculosis. Several mechanisms have been put forward to elucidate the phenomena of aminoglycosides resistance but our knowledge is still insufficient. The aim of the study was to understand the involvement of Mycobacterium tuberculosis universal stress protein (Rv2005c) in aminoglycosides resistance and virulence. To establish the relationship of universal stress protein Rv2005c with AK & KM resistance, Rv2005c was cloned, expressed in E.coli BL21 using pQE2 expression vector and antimicrobial drug susceptibility testing (DST) was carried out. STRING-10 was also used to predict the interacting protein partners of Rv2005c. DST showed that the minimum inhibitory concentration of induced recombinant cells (Rv2005c) were five and four folds shifted with AK and KM E-strips, respectively. STRING-10 showed the interacting protein partners of Rv2005c. Overexpression of Rv2005c leads to shifting in MIC which might be signifying its involvement in the survival/resistance of Mycobacteria by inhibiting/modulating the effects of AK and KM released from the E-strips. Interactome also suggests that Rv2005c and its interacting protein partners are cumulatively involved in M.tuberculosis resistance, stresses, and latency.
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Affiliation(s)
- Divakar Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, 282004, India; Interdisciplinary Biotechnology Unit, Aligarh Muslim University Aligarh, 202002, India.
| | - Manju Lata
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, 282004, India
| | - Mohammad Faheem
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University Aligarh, 202002, India
| | - Asad Ullah Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University Aligarh, 202002, India
| | - Beenu Joshi
- Department of Immunology, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, 282004, India
| | - Krishnamurthy Venkatesan
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, 282004, India
| | - Sangeeta Shukla
- School of Studies (SOS) Zoology, Jiwaji University, Gwalior, 474011, India
| | - Deepa Bisht
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, 282004, India.
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Sharma D, Garg A, Kumar M, Khan AU. Proteome profiling of carbapenem-resistant K. pneumoniae clinical isolate (NDM-4): Exploring the mechanism of resistance and potential drug targets. J Proteomics 2019; 200:102-110. [PMID: 30953729 DOI: 10.1016/j.jprot.2019.04.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/28/2019] [Accepted: 04/02/2019] [Indexed: 02/06/2023]
Abstract
The emergence of carbapenem resistance has become a major problem worldwide. This has made treatment of K. pneumoniae infections a difficult task. In this study, we have explored the whole proteome of the carbapenem-resistant Klebsiella pneumonia clinical isolate (NDM-4) under the meropenem stress. Proteomics (LC-MS/MS) and bioinformatics approaches were employed to uncover the novel mystery of the resistance over the existing mechanisms. Gene ontology, KEGG and STRING were used for functional annotation, pathway enrichment and protein-protein interaction (PPI) network respectively. LC-MS/MS analysis revealed that 52 proteins were overexpressed (≥10 log folds) under meropenem stress. These proteins belong to four major groups namely protein translational machinery complex, DNA/RNA modifying enzymes or proteins, proteins involved in carbapenems cleavage, modifications & transport and energy metabolism & intermediary metabolism-related proteins. Among the total 52 proteins 38 {matched to Klebsiella pneumonia subsp. pneumoniae (strain ATCC 700721/MGH 78578)} were used for functional annotation, pathways enrichment and protein-protein interaction. These were significantly enriched in the "intracellular" (14 of 38), "cytoplasm" (12 of 38) and "ribosome" (10 of 38). We suggest that these 52 over expressed proteins and their interactive proteins cumulatively contributed in survival of bacteria and meropenem resistance through various mechanisms or enriched pathways. These proteins targets and their pathways might be used for development of novel therapeutics against the resistance; therefore, the situation of the emergence of "bad-bugs" could be controlled.
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Affiliation(s)
- Divakar Sharma
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Anjali Garg
- Department of Biophysics, University of Delhi South Campus, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi South Campus, India
| | - Asad U Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India.
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Qayyum S, Sharma D, Bisht D, Khan AU. Identification of factors involved in Enterococcus faecalis biofilm under quercetin stress. Microb Pathog 2019; 126:205-211. [DOI: 10.1016/j.micpath.2018.11.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/08/2018] [Accepted: 11/09/2018] [Indexed: 10/27/2022]
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12
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Sharma D, Khan AU. Role of cell division protein divIVA in Enterococcus faecalis pathogenesis, biofilm and drug resistance: A future perspective by in silico approaches. Microb Pathog 2018; 125:361-365. [PMID: 30290265 DOI: 10.1016/j.micpath.2018.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/01/2018] [Accepted: 10/01/2018] [Indexed: 12/18/2022]
Abstract
Antibiotics resistance is the major problem in clinical settings which leads to the emergence of drug resistant bacteria. Biofilm formation is one of the grounds for the emergence of antibiotics resistant strains of Enterococcus faecalis. Our group previously reported in a comparative proteomic study of biofilm and planktonic state of E. faecalis that cell division protein divIVA was two folds overexpressed in biofilm state as compared to planktonic one and suggested its involvement in biofilm formation and antibiotics resistance. In this in silico study molecular docking showed that DNA bind to the conserved amino acid residues of divIVA domain and suggested that divIVA possibly secretes DNA into extra polymeric substance (EPS) which is the part of biofilm. We also performed the STRING analysis of cell division protein divIVA and predicted their interactive partners {cell division proteins/divisome complex (ftsZ, ftsA, divIV, ftsL, & gpsB), hypothetical proteins (sepF, EF_0261, EF_1000, EF_0998, EF_1006 & EF_1040), isoleucyl-tRNA synthetase (ileS), septation ring formation regulator (ezrA), S4 domain-containing protein (EF_1001), rod shape-determining protein (mreC), UDP-N-acetylmuramoyl-L-alanyl-d-glutamate synthetase (murD), UDP-diphospho-muramoyl-pentapeptide beta-N- acetylglucosaminyltransferase (murG), Lipoprotein signal peptidase (lspA), adenylate kinase (adk) and DNA-binding response regulator (vicR)}. We suggest that cumulatively divIVA and its interactive partners might be directly or indirectly involved in E. faecalis cell division, growth, biofilm formation, virulence and resistance.
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Affiliation(s)
- Divakar Sharma
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Asad U Khan
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India.
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13
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Interactome analysis of Rv0148 to predict potential targets and their pathways linked to aminoglycosides drug resistance: An insilico approach. Microb Pathog 2018; 121:179-183. [DOI: 10.1016/j.micpath.2018.05.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/12/2018] [Accepted: 05/22/2018] [Indexed: 12/22/2022]
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14
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Oliveira FM, Da Costa AC, Procopio VO, Garcia W, Araújo JN, Da Silva RA, Junqueira-Kipnis AP, Kipnis A. Mycobacterium abscessus subsp. massiliense mycma_0076 and mycma_0077 Genes Code for Ferritins That Are Modulated by Iron Concentration. Front Microbiol 2018; 9:1072. [PMID: 29910777 PMCID: PMC5992710 DOI: 10.3389/fmicb.2018.01072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/04/2018] [Indexed: 12/19/2022] Open
Abstract
Mycobacterium abscessus complex has been characterized in the last decade as part of a cluster of mycobacteria that evolved from an opportunistic to true human pathogen; however, the factors responsible for pathogenicity are still undefined. It appears that the success of mycobacterial infection is intrinsically related with the capacity of the bacteria to regulate intracellular iron levels, mostly using iron storage proteins. This study evaluated two potential M. abscessus subsp. massiliense genes involved in iron storage. Unlike other opportunist or pathogenic mycobacteria studied, M. abscessus complex has two genes similar to ferritins from M. tuberculosis (Rv3841), and in M. abscessus subsp. massiliense, those genes are annotated as mycma_0076 and mycma_0077. Molecular dynamic analysis of the predicted expressed proteins showed that they have a ferroxidase center. The expressions of mycma_0076 and mycma_0077 genes were modulated by the iron levels in both in vitro cultures as well as infected macrophages. Structural studies using size-exclusion chromatography, circular dichroism spectroscopy and dynamic light scattering showed that r0076 protein has a structure similar to those observed in the ferritin family. The r0076 forms oligomers in solution most likely composed of 24 subunits. Functional studies with recombinant proteins, obtained from heterologous expression of mycma_0076 and mycma_0077 genes in Escherichia coli, showed that both proteins were capable of oxidizing Fe2+ into Fe3+, demonstrating that these proteins have a functional ferroxidase center. In conclusion, two ferritins proteins were shown, for the first time, to be involved in iron storage in M. abscessus subsp. massiliense and their expressions were modulated by the iron levels.
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Affiliation(s)
- Fábio M. Oliveira
- Tropical Institute of Pathology and Public Health, Department of Microbiology, Immunology, Parasitology and Pathology, Federal University of Goiás, Goiânia, Brazil
| | - Adeliane C. Da Costa
- Tropical Institute of Pathology and Public Health, Department of Microbiology, Immunology, Parasitology and Pathology, Federal University of Goiás, Goiânia, Brazil
| | - Victor O. Procopio
- Tropical Institute of Pathology and Public Health, Department of Microbiology, Immunology, Parasitology and Pathology, Federal University of Goiás, Goiânia, Brazil
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas, Federal University of ABC (UFABC), Santo André, Brazil
| | - Juscemácia N. Araújo
- Centro de Ciências Naturais e Humanas, Federal University of ABC (UFABC), Santo André, Brazil
| | - Roosevelt A. Da Silva
- Collaborative Center of Biosystems, Regional Jataí, Federal University of Goiás, Goiânia, Brazil
| | - Ana Paula Junqueira-Kipnis
- Tropical Institute of Pathology and Public Health, Department of Microbiology, Immunology, Parasitology and Pathology, Federal University of Goiás, Goiânia, Brazil
| | - André Kipnis
- Tropical Institute of Pathology and Public Health, Department of Microbiology, Immunology, Parasitology and Pathology, Federal University of Goiás, Goiânia, Brazil
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15
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Sharma D, Bisht D, Khan AU. Potential Alternative Strategy against Drug Resistant Tuberculosis: A Proteomics Prospect. Proteomes 2018; 6:E26. [PMID: 29843395 PMCID: PMC6027512 DOI: 10.3390/proteomes6020026] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 05/24/2018] [Accepted: 05/26/2018] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis is one of the deadliest human pathogen of the tuberculosis diseases. Drug resistance leads to emergence of multidrug-resistant and extremely drug resistant strains of M. tuberculosis. Apart from principal targets of resistance, many explanations have been proposed for drug resistance but some resistance mechanisms are still unknown. Recently approved line probe assay (LPA) diagnostics for detecting the resistance to first and second line drugs are unable to diagnose the drug resistance in M. tuberculosis isolates which do not have the mutations in particular genes responsible for resistance. Proteomics and bioinformatic tools emerged as direct approaches for identification and characterization of novel proteins which are directly and indirectly involved in drug resistance that could be used as potential targets in future. In future, these novel targets might reveal new mechanism of resistance and can be used in diagnostics or as drug targets.
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Affiliation(s)
- Divakar Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India.
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India.
| | - Deepa Bisht
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India.
| | - Asad U Khan
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India.
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16
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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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17
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Mycobacterium tuberculosis Protein Rv3841 Activates Dendritic Cells and Contributes to a T Helper 1 Immune Response. J Immunol Res 2018; 2018:3525302. [PMID: 29736404 PMCID: PMC5875036 DOI: 10.1155/2018/3525302] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 01/02/2018] [Accepted: 01/10/2018] [Indexed: 12/15/2022] Open
Abstract
The attenuated vaccine Mycobacterium bovis BCG (Bacille Calmette Guerin) has limited protective efficacy against TB. The development of more effective TB vaccines has focused on the mycobacterial antigens that cause strong T helper 1 (Th1) responses. Mtb protein Rv3841 (bacterioferritin B; BfrB) is known to play a crucial role in the growth of Mtb. Nonetheless, it is unclear whether Rv3841 can induce protective immunity against Mtb. Here, we studied the action of Rv3841 in maturation of dendritic cells (DCs) and its engagement in the development of T-cell immunity. We found that Rv3841 functionally activated DCs by upregulating costimulatory molecules and increased secretion of proinflammatory cytokines. Activation of DCs by Rv3841 was mediated by Toll-like receptor 4 (TLR4), followed by triggering of mitogen-activated protein kinase and nuclear factor-κB signaling pathways. In addition, Rv3841-matured DCs effectively proliferated and polarized Th1 immune response of naïve CD4+ and CD8+ T-cells. Moreover, Rv3841 specifically caused the expansion of CD4+CD44highCD62Llow T-cells from Mtb-infected mice; besides, the T-cells activated by Rv3841-matured DCs inhibited intracellular mycobacterial growth. Our data suggest that Rv3841 induces DC maturation and protective immune responses, a finding that may provide candidate of effective TB vaccines.
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18
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Sharma D, Dhuriya YK, Deo N, Bisht D. Repurposing and Revival of the Drugs: A New Approach to Combat the Drug Resistant Tuberculosis. Front Microbiol 2017; 8:2452. [PMID: 29321768 PMCID: PMC5732208 DOI: 10.3389/fmicb.2017.02452] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/27/2017] [Indexed: 01/15/2023] Open
Abstract
Emergence of drug resistant tuberculosis like multi drug resistant tuberculosis (MDR-TB), extensively drug-resistant tuberculosis (XDR-TB) and totally drug resistant tuberculosis (TDR-TB) has created a new challenge to fight against these bad bugs of Mycobacterium tuberculosis. Repurposing and revival of the drugs are the new trends/options to combat these worsen situations of tuberculosis in the antibiotics resistance era or in the situation of global emergency. Bactericidal and synergistic effect of repurposed/revived drugs along with the latest drugs bedaquiline and delamanid used in the treatment of MDR-TB, XDR-TB, and TDR-TB might be the choice for future promising combinatorial chemotherapy against these bad bugs.
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Affiliation(s)
- Divakar Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India.,Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Yogesh K Dhuriya
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow, India
| | - Nirmala Deo
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Deepa Bisht
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
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19
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Singh P, Kumar SK, Maurya VK, Mehta BK, Ahmad H, Dwivedi AK, Chaturvedi V, Thakur TS, Sinha S. S-Enantiomer of the Antitubercular Compound S006-830 Complements Activity of Frontline TB Drugs and Targets Biogenesis of Mycobacterium tuberculosis Cell Envelope. ACS OMEGA 2017; 2:8453-8465. [PMID: 30023583 PMCID: PMC6045410 DOI: 10.1021/acsomega.7b01281] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/31/2017] [Indexed: 05/15/2023]
Abstract
A synthetic molecule S006-830, belonging to the class of thiophene-containing trisubstituted methanes, had shown good in vitro and in vivo bactericidal activity against drug-sensitive and drug-resistant Mycobacterium tuberculosis (Mtb). The molecule had also shown good druglike pharmacokinetic properties. However, S006-830 is a racemic mixture of two enantiomers, one of which could possess a better pharmacological profile than the other. We purified both the enantiomers on a chiral column and observed that S-enantiomer has a significantly higher inhibitory and cidal activity against Mtb than the R-enantiomer. Action of S-S006-830 was "synergistic" for rifampicin and "additive" for isoniazid and ethambutol. The combination of S-S006-830 and rifampicin produced 100% kill of Mtb within 8 days. In a chemical proteomics approach using matrix-bound compound to pull down its target protein(s) from Mtb membrane, FabG4 (β-ketoacyl CoA reductase, EC 1.1.1.100) emerged as the most likely target for S-S006-830. In target validation assays, the compound exhibited 2-fold higher inhibitory concentration for an Mtb construct overexpressing FabG4. In addition, it inhibited mycolic acid biosynthesis and formation of biofilms by Mtb. Molecular docking of S-S006-830 with FabG4 was consistent with the experimental data. These results support the development of S-S006-830 as a novel lead against tuberculosis.
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Affiliation(s)
- Padam Singh
- Division
of Biochemistry, Division of Molecular and Structural Biology, and Division of Pharmaceutics, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow 226031, India
| | - Shashi Kant Kumar
- Division
of Biochemistry, Division of Molecular and Structural Biology, and Division of Pharmaceutics, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow 226031, India
| | - Vineet Kumar Maurya
- Division
of Biochemistry, Division of Molecular and Structural Biology, and Division of Pharmaceutics, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow 226031, India
- Department
of Botany and Microbiology, HNB Garhwal
University, Srinagar, Uttarakhand 246174, India
| | - Basant Kumar Mehta
- Division
of Biochemistry, Division of Molecular and Structural Biology, and Division of Pharmaceutics, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow 226031, India
| | - Hafsa Ahmad
- Division
of Biochemistry, Division of Molecular and Structural Biology, and Division of Pharmaceutics, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow 226031, India
| | - Anil Kumar Dwivedi
- Division
of Biochemistry, Division of Molecular and Structural Biology, and Division of Pharmaceutics, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow 226031, India
| | - Vinita Chaturvedi
- Division
of Biochemistry, Division of Molecular and Structural Biology, and Division of Pharmaceutics, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow 226031, India
- E-mail: (V.C.)
| | - Tejender S. Thakur
- Division
of Biochemistry, Division of Molecular and Structural Biology, and Division of Pharmaceutics, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow 226031, India
- E-mail: (T.S.T.)
| | - Sudhir Sinha
- Division
of Biochemistry, Division of Molecular and Structural Biology, and Division of Pharmaceutics, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow 226031, India
- Department
of Clinical Immunology, SGPG Institute of
Medical Sciences, Raebareli Road, Lucknow 226014, India
- E-mail: (S.S.)
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20
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Capolupo A, Cassiano C, Casapullo A, Andreotti G, Cubellis MV, Riccio A, Riccio R, Monti MC. Identification of Trombospondin-1 as a Novel Amelogenin Interactor by Functional Proteomics. Front Chem 2017; 5:74. [PMID: 29057222 PMCID: PMC5635807 DOI: 10.3389/fchem.2017.00074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/25/2017] [Indexed: 11/15/2022] Open
Abstract
Amelogenins are a set of low molecular-weight enamel proteins belonging to a group of extracellular matrix (ECM) proteins with a key role in tooth enamel development and in other regeneration processes, such as wound healing and angiogenesis. Since only few data are actually available to unravel amelogenin mechanism of action in chronic skin healing restoration, we moved to the full characterization of the human amelogenin isoform 2 interactome in the secretome and lysate of Human Umbilical Vein Endothelial cells (HUVEC), using a functional proteomic approach. Trombospondin-1 has been identified as a novel and interesting partner of human amelogenin isoform 2 and their direct binding has been validated thought biophysical orthogonal approaches.
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Affiliation(s)
- Angela Capolupo
- Department of Pharmacy, University of Salerno, Salerno, Italy.,PhD Program in Drug Discovery and Development, University of Salerno, Salerno, Italy
| | - Chiara Cassiano
- Department of Pharmacy, University of Salerno, Salerno, Italy
| | | | - Giuseppina Andreotti
- Istituto di Chimica Biomolecolare, Consiglio Nazionale Delle Ricerche (CNR), Napoli, Italy
| | - Maria V Cubellis
- Department of Biology, University of Naples Federico II, Napoli, Italy
| | - Andrea Riccio
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Raffaele Riccio
- Department of Pharmacy, University of Salerno, Salerno, Italy
| | - Maria C Monti
- Department of Pharmacy, University of Salerno, Salerno, Italy
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21
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Kumar G, Shankar H, Sharma D, Sharma P, Bisht D, Katoch VM, Joshi B. Proteomics of Culture Filtrate of Prevalent Mycobacterium tuberculosis Strains: 2D-PAGE Map and MALDI-TOF/MS Analysis. SLAS DISCOVERY 2017; 22:1142-1149. [PMID: 28683213 DOI: 10.1177/2472555217717639] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Although diverse efforts have been done to identify biomarkers for control of tuberculosis using laboratory strain Mycobacterium tuberculosis H37Rv, the disease still poses a threat to mankind. There are many emerging M. tuberculosis strains, and proteomic profiling of these strains might be important to find out potential targets for diagnosis and/or prevention of tuberculosis. We evaluated the comparative proteomic profiling of culture filtrate (CF) proteins from prevalent M. tuberculosis strains (Central Asian or Delhi type; CAS1_Del, East African-Indian; EAI-3 and Beijing family) by 2D polyacrylamide gel electrophoresis and matrix-assisted laser desorption ionization-time-of-flight mass spectrometry. As a result, we could identify 12 CF proteins (Rv0066c, Rv1310, Rv3375, Rv1415, Rv0567, Rv1886c, Rv3803c, Rv3804c, Rv2031c, Rv1038c, Rv2809, and Rv1911c), which were consistently increased in all prevalent M. tuberculosis strains, and interestingly, two CF proteins (Rv2809, Rv1911c) were identified with unknown functions. Consistent increased intensity of these proteins suggests their critical role for survival of prevalent M. tuberculosis isolates, and some of these proteins may also have potential as diagnostic and vaccine candidates for tuberculosis, which needs to be further explored by immunological analysis.
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Affiliation(s)
- Gavish Kumar
- Department of Immunology, National JALMA Institute for Leprosy and Other Mycobacterial Diseases (ICMR), Taj Ganj, Agra, Uttar Pradesh, India.,Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi, India
| | - Hari Shankar
- Department of Immunology, National JALMA Institute for Leprosy and Other Mycobacterial Diseases (ICMR), Taj Ganj, Agra, Uttar Pradesh, India
| | - Divakar Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases (ICMR), Taj Ganj, Agra, Uttar Pradesh, India
| | - Prashant Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases (ICMR), Taj Ganj, Agra, Uttar Pradesh, India
| | - Deepa Bisht
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases (ICMR), Taj Ganj, Agra, Uttar Pradesh, India
| | - Vishwa M Katoch
- Department of Health Research (Ministry of Health and Family Welfare), Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi, India
| | - Beenu Joshi
- Department of Immunology, National JALMA Institute for Leprosy and Other Mycobacterial Diseases (ICMR), Taj Ganj, Agra, Uttar Pradesh, India
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22
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Sharma D, Bisht D. Role of Bacterioferritin & Ferritin in M. tuberculosis Pathogenesis and Drug Resistance: A Future Perspective by Interactomic Approach. Front Cell Infect Microbiol 2017. [PMID: 28642844 PMCID: PMC5462900 DOI: 10.3389/fcimb.2017.00240] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Tuberculosis is caused by Mycobacterium tuberculosis, one of the most successful and deadliest human pathogen. Aminoglycosides resistance leads to emergence of extremely drug resistant strains of M. tuberculosis. Iron is crucial for the biological functions of the cells. Iron assimilation, storage and their utilization is not only involved in pathogenesis but also in emergence of drug resistance strains. We previously reported that iron storing proteins (bacterioferritin and ferritin) were found to be overexpressed in aminoglycosides resistant isolates. In this study we performed the STRING analysis of bacterioferritin & ferritin proteins and predicted their interactive partners [ferrochelatase (hemH), Rv1877 (hypothetical protein/probable conserved integral membrane protein), uroporphyrinogen decarboxylase (hemE) trigger factor (tig), transcriptional regulatory protein (MT3948), hypothetical protein (MT1928), glnA3 (glutamine synthetase), molecular chaperone GroEL (groEL1 & hsp65), and hypothetical protein (MT3947)]. We suggested that interactive partners of bacterioferritin and ferritin are directly or indirectly involved in M. tuberculosis growth, homeostasis, iron assimilation, virulence, resistance, and stresses.
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Affiliation(s)
- Divakar Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial DiseasesAgra, India
| | - Deepa Bisht
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial DiseasesAgra, India
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23
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Sharma D, Bisht D. M. tuberculosis Hypothetical Proteins and Proteins of Unknown Function: Hope for Exploring Novel Resistance Mechanisms as well as Future Target of Drug Resistance. Front Microbiol 2017; 8:465. [PMID: 28377758 PMCID: PMC5359272 DOI: 10.3389/fmicb.2017.00465] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 03/07/2017] [Indexed: 01/22/2023] Open
Abstract
Drug resistance in tuberculosis predominantly, mono-resistance, multi drug resistance, extensively drug resistance and totally drug resistance have emerged as a major problem in the chemotherapy of tuberculosis. Failures of first and second line anti-tuberculosis drugs treatment leads to emergence of resistant Mycobacterium tuberculosis. Few genes are reported as the principal targets of the resistance and apart from the primary targets many explanations have been proposed for drug resistance but still some resistance mechanisms are unknown. As proteins involved in most of the biological processes, these are potentially explored the unknown mechanism of drug resistance and attractive targets for diagnostics/future therapeutics against drug resistance. In last decade a panel of studies on expression proteomics of drug resistant M. tuberculosis isolates reported the differential expression of uncharacterized proteins and suggested these might be involved in resistance. Here we emphasize that detailed bioinformatics analysis (like molecular docking, pupylation, and proteins-proteins interaction) of these uncharacterized and hypothetical proteins might predict their interactive partners (other proteins) which are involved in various pathways of M. tuberculosis system biology and might give a clue for novel mechanism of drug resistance or future drug targets. In future these uncharacterized targets might be open the new resistance mechanism and used as potential drug targets against drug resistant tuberculosis.
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Affiliation(s)
- Divakar Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Deepa Bisht
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
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Sharma D, Bisht D. Secretory Proteome Analysis of Streptomycin-Resistant Mycobacterium tuberculosis Clinical Isolates. SLAS DISCOVERY 2017; 22:1229-1238. [PMID: 28314116 DOI: 10.1177/2472555217698428] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Tuberculosis still remains one of the most fatal infectious diseases. Streptomycin (SM) is the drug of choice, especially for patients with multidrug-resistant tuberculosis or category II patients, because it targets the protein synthesis machinery by interacting with steps of translation. Several mechanisms have been proposed to explain the resistance, but our knowledge is inadequate. Secretome often plays an important role in pathogenesis and is considered an attractive reservoir for the development of novel diagnostic markers and targets. In this study, we analyze the secretory proteins of streptomycin-resistant Mycobacterium tuberculosis isolates by 2-dimensional gel electrophoresis-matrix assisted laser desorption/ionization-time-of-flight mass spectrometry and bioinformatic tools. Fifteen overexpressed proteins were identified in a resistant isolate that belonged to various categories such as virulence/detoxification/adaptation, intermediary metabolism and respiration, and conserved hypotheticals. Among them, Rv1860, Rv1980c, Rv2140c, Rv1636, and Rv1926c were proteins of an undefined role. Molecular docking of these proteins with SM showed that it binds to their conserved domains and suggests that these might neutralize/compensate the effect of the drug. The interactome also suggests that overexpressed proteins along with their interactive partner might be involved in M. tuberculosis virulence and resistance. The cumulative effect of these overexpressed proteins could involve SM resistance, and these might be used as diagnostic markers or potential drug targets.
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Affiliation(s)
- Divakar Sharma
- 1 Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, India
| | - Deepa Bisht
- 1 Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, India
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Proteomic analysis of a carbapenem-resistant Klebsiella pneumoniae strain in response to meropenem stress. J Glob Antimicrob Resist 2017; 8:172-178. [PMID: 28219823 DOI: 10.1016/j.jgar.2016.12.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/12/2016] [Accepted: 12/14/2016] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVES Antibiotic resistance has become a major problem in treating bacterial infections. The aim of this study was to elucidate the effects of meropenem on a blaKPC-2-harbouring multidrug-resistant clinical strain of Klebsiella pneumoniae through a proteomics approach in order to attain a deeper understanding of bacterial resistance strategies. METHODS Analysis was performed by two-dimensional gel electrophoresis of whole-cell extracts of bacteria exposed to a sublethal concentration of meropenem compared with the untreated control. Differentially expressed proteins were identified by matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF). RESULTS Based on Quantity One® software and MALDI-TOF analysis, 16 overexpressed proteins were identified in meropenem-treated bacteria. These proteins were primarily enzymes involved in defence against oxidative stress as well as glycolytic enzymes. LysM domain/BON superfamily protein was found overexpressed by >12-fold. STRING-10 was used to determine protein-protein interaction among the overexpressed proteins and to predict their functional associations. This study demonstrated that treatment with meropenem resulted in upregulation of various proteins involved in defence and repair mechanisms along with enzymes of energy metabolism. CONCLUSIONS These overexpressed proteins may play an important role in bacterial resistance mechanisms against carbapenems, however their role in resistance needs to be further validated. High expression of lysine M domain/BON superfamily protein may indicate its possible involvement in modulating the bacterial response to antibiotic stress, but its actual role requires more investigation. These findings may also help in the development of newer therapeutic agents or diagnostic markers against carbapenem resistance.
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Sharma D, Lata M, Singh R, Deo N, Venkatesan K, Bisht D. Cytosolic Proteome Profiling of Aminoglycosides Resistant Mycobacterium tuberculosis Clinical Isolates Using MALDI-TOF/MS. Front Microbiol 2016; 7:1816. [PMID: 27895634 PMCID: PMC5108770 DOI: 10.3389/fmicb.2016.01816] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/28/2016] [Indexed: 12/25/2022] Open
Abstract
Emergence of extensively drug resistant tuberculosis (XDR-TB) is the consequence of the failure of second line TB treatment. Aminoglycosides are the important second line anti-TB drugs used to treat the multi drug resistant tuberculosis (MDR-TB). Main known mechanism of action of aminoglycosides is to inhibit the protein synthesis by inhibiting the normal functioning of ribosome. Primary target of aminoglycosides are the ribosomal RNA and its associated proteins. Various mechanisms have been proposed for aminoglycosides resistance but still some are unsolved. As proteins are involved in most of the biological processes, these act as a potential diagnostic markers and drug targets. In the present study we analyzed the purely cytosolic proteome of amikacin (AK) and kanamycin (KM) resistant Mycobacterium tuberculosis isolates by proteomic and bioinformatic approaches. Twenty protein spots were found to have over expressed in resistant isolates and were identified. Among these Rv3208A, Rv2623, Rv1360, Rv2140c, Rv1636, and Rv2185c are six proteins with unknown functions or undefined role. Docking results showed that AK and KM binds to the conserved domain (DUF, USP-A, Luciferase, PEBP and Polyketidecyclase/dehydrase domain) of these hypothetical proteins and over expression of these proteins might neutralize/modulate the effect of drug molecules. TBPred and GPS-PUP predicted cytoplasmic nature and potential pupylation sites within these identified proteins, respectively. String analysis also suggested that over expressed proteins along with their interactive partners might be involved in aminoglycosides resistance. Cumulative effect of these over expressed proteins could be involved in AK and KM resistance by mitigating the toxicity, repression of drug target and neutralizing affect. These findings need further exploitation for the expansion of newer therapeutics or diagnostic markers against AK and KM resistance so that an extreme condition like XDR-TB can be prevented.
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Affiliation(s)
- Divakar Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases Agra, India
| | - Manju Lata
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases Agra, India
| | - Rananjay Singh
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases Agra, India
| | - Nirmala Deo
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases Agra, India
| | - Krishnamurthy Venkatesan
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases Agra, India
| | - Deepa Bisht
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases Agra, India
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