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Shee S, Veetil RT, Mohanraj K, Das M, Malhotra N, Bandopadhyay D, Beig H, Birua S, Niphadkar S, Nagarajan SN, Sinha VK, Thakur C, Rajmani RS, Chandra N, Laxman S, Singh M, Samal A, Seshasayee AN, Singh A. Biosensor-integrated transposon mutagenesis reveals rv0158 as a coordinator of redox homeostasis in Mycobacterium tuberculosis. eLife 2023; 12:e80218. [PMID: 37642294 PMCID: PMC10501769 DOI: 10.7554/elife.80218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/25/2023] [Indexed: 08/31/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is evolutionarily equipped to resist exogenous reactive oxygen species (ROS) but shows vulnerability to an increase in endogenous ROS (eROS). Since eROS is an unavoidable consequence of aerobic metabolism, understanding how Mtb manages eROS levels is essential yet needs to be characterized. By combining the Mrx1-roGFP2 redox biosensor with transposon mutagenesis, we identified 368 genes (redoxosome) responsible for maintaining homeostatic levels of eROS in Mtb. Integrating redoxosome with a global network of transcriptional regulators revealed a hypothetical protein (Rv0158) as a critical node managing eROS in Mtb. Disruption of rv0158 (rv0158 KO) impaired growth, redox balance, respiration, and metabolism of Mtb on glucose but not on fatty acids. Importantly, rv0158 KO exhibited enhanced growth on propionate, and the Rv0158 protein directly binds to methylmalonyl-CoA, a key intermediate in propionate catabolism. Metabolite profiling, ChIP-Seq, and gene-expression analyses indicate that Rv0158 manages metabolic neutralization of propionate toxicity by regulating the methylcitrate cycle. Disruption of rv0158 enhanced the sensitivity of Mtb to oxidative stress, nitric oxide, and anti-TB drugs. Lastly, rv0158 KO showed poor survival in macrophages and persistence defect in mice. Our results suggest that Rv0158 is a metabolic integrator for carbon metabolism and redox balance in Mtb.
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Affiliation(s)
- Somnath Shee
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | | | - Karthikeyan Mohanraj
- The Institute of Mathematical Sciences, A CI of Homi Bhabha National InstituteChennaiIndia
| | - Mayashree Das
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | | | | | - Hussain Beig
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | - Shalini Birua
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | - Shreyas Niphadkar
- Institute for Stem Cell Science and Regenerative MedicineBangaloreIndia
| | - Sathya Narayanan Nagarajan
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | - Vikrant Kumar Sinha
- Molecular Biophysics Unit, Indian Institute of Science BangaloreBangaloreIndia
| | - Chandrani Thakur
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Raju S Rajmani
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative MedicineBangaloreIndia
| | - Mahavir Singh
- Molecular Biophysics Unit, Indian Institute of Science BangaloreBangaloreIndia
| | - Areejit Samal
- The Institute of Mathematical Sciences, A CI of Homi Bhabha National InstituteChennaiIndia
| | | | - Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
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Chattopadhyay G, Bhasin M, Ahmed S, Gosain TP, Ganesan S, Das S, Thakur C, Chandra N, Singh R, Varadarajan R. Functional and Biochemical Characterization of the MazEF6 Toxin-Antitoxin System of Mycobacterium tuberculosis. J Bacteriol 2022; 204:e0005822. [PMID: 35357163 PMCID: PMC9053165 DOI: 10.1128/jb.00058-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/07/2022] [Indexed: 12/15/2022] Open
Abstract
The Mycobacterium tuberculosis genome harbors nine toxin-antitoxin (TA) systems that are members of the mazEF family, unlike other prokaryotes, which have only one or two. Although the overall tertiary folds of MazF toxins are predicted to be similar, it is unclear how they recognize structurally different RNAs and antitoxins with divergent sequence specificity. Here, we have expressed and purified the individual components and complex of the MazEF6 TA system from M. tuberculosis. Size exclusion chromatography-multiangle light scattering (SEC-MALS) was performed to determine the oligomerization status of the toxin, antitoxin, and the complex in different stoichiometric ratios. The relative stabilities of the proteins were determined by nano-differential scanning fluorimetry (nano-DSF). Microscale thermophoresis (MST) and yeast surface display (YSD) were performed to measure the relative affinities between the cognate toxin-antitoxin partners. The interaction between MazEF6 complexes and cognate promoter DNA was also studied using MST. Analysis of paired-end RNA sequencing data revealed that the overexpression of MazF6 resulted in differential expression of 323 transcripts in M. tuberculosis. Network analysis was performed to identify the nodes from the top-response network. The analysis of mRNA protection ratios resulted in identification of putative MazF6 cleavage site in its native host, M. tuberculosis. IMPORTANCE M. tuberculosis harbors a large number of type II toxin-antitoxin (TA) systems, the exact roles for most of which are unclear. Prior studies have reported that overexpression of several of these type II toxins inhibits bacterial growth and contributes to the formation of drug-tolerant populations in vitro. To obtain insights into M. tuberculosis MazEF6 type II TA system function, we determined stability, oligomeric states, and binding affinities of cognate partners with each other and with their promoter operator DNA. Using RNA-seq data obtained from M. tuberculosis overexpression strains, we have identified putative MazF6 cleavage sites and targets in its native, cellular context.
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Affiliation(s)
| | - Munmun Bhasin
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Shahbaz Ahmed
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Tannu Priya Gosain
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Srivarshini Ganesan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Sayan Das
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Chandrani Thakur
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Ramandeep Singh
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
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3
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Tripathi A, Anand K, Das M, O'Niel RA, P S S, Thakur C, R L RR, Rajmani RS, Chandra N, Laxman S, Singh A. Mycobacterium tuberculosis requires SufT for Fe-S cluster maturation, metabolism, and survival in vivo. PLoS Pathog 2022; 18:e1010475. [PMID: 35427399 PMCID: PMC9045647 DOI: 10.1371/journal.ppat.1010475] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 04/27/2022] [Accepted: 03/25/2022] [Indexed: 11/18/2022] Open
Abstract
Iron-sulfur (Fe-S) cluster proteins carry out essential cellular functions in diverse organisms, including the human pathogen Mycobacterium tuberculosis (Mtb). The mechanisms underlying Fe-S cluster biogenesis are poorly defined in Mtb. Here, we show that Mtb SufT (Rv1466), a DUF59 domain-containing essential protein, is required for the Fe-S cluster maturation. Mtb SufT homodimerizes and interacts with Fe-S cluster biogenesis proteins; SufS and SufU. SufT also interacts with the 4Fe-4S cluster containing proteins; aconitase and SufR. Importantly, a hyperactive cysteine in the DUF59 domain mediates interaction of SufT with SufS, SufU, aconitase, and SufR. We efficiently repressed the expression of SufT to generate a SufT knock-down strain in Mtb (SufT-KD) using CRISPR interference. Depleting SufT reduces aconitase's enzymatic activity under standard growth conditions and in response to oxidative stress and iron limitation. The SufT-KD strain exhibited defective growth and an altered pool of tricarboxylic acid cycle intermediates, amino acids, and sulfur metabolites. Using Seahorse Extracellular Flux analyzer, we demonstrated that SufT depletion diminishes glycolytic rate and oxidative phosphorylation in Mtb. The SufT-KD strain showed defective survival upon exposure to oxidative stress and nitric oxide. Lastly, SufT depletion reduced the survival of Mtb in macrophages and attenuated the ability of Mtb to persist in mice. Altogether, SufT assists in Fe-S cluster maturation and couples this process to bioenergetics of Mtb for survival under low and high demand for Fe-S clusters.
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Affiliation(s)
- Ashutosh Tripathi
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Kushi Anand
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Mayashree Das
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Ruchika Annie O'Niel
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India
| | - Sabarinath P S
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India
| | - Chandrani Thakur
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Raghunatha Reddy R L
- Regional Horticultural Research and Extension Centre (RHREK), GKVK, Bengaluru, India
| | - Raju S Rajmani
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India
| | - Amit Singh
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
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Thakur C, Tripathi A, Ravichandran S, Shivananjaiah A, Chakraborty A, Varadappa S, Chikkavenkatappa N, Nagarajan D, Lakshminarasimhaiah S, Singh A, Chandra N. A new blood-based RNA signature (R 9), for monitoring effectiveness of tuberculosis treatment in a South Indian longitudinal cohort. iScience 2022; 25:103745. [PMID: 35118358 PMCID: PMC8800112 DOI: 10.1016/j.isci.2022.103745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 03/31/2021] [Accepted: 01/06/2022] [Indexed: 11/17/2022] Open
Abstract
Tuberculosis (TB) treatment involves a multidrug regimen for six months, and until two months, it is unclear if treatment is effective. This delay can lead to the evolution of drug resistance, lung damage, disease spread, and transmission. We identify a blood-based 9-gene signature using a computational pipeline that constructs and interrogates a genome-wide transcriptome-integrated protein-interaction network. The identified signature is able to determine treatment response at week 1-2 in three independent public datasets. Signature-based R9-score correctly detected treatment response at individual timepoints (204 samples) from a newly developed South Indian longitudinal cohort involving 32 patients with pulmonary TB. These results are consistent with conventional clinical metrics and can discriminate good from poor treatment responders at week 2 (AUC 0.93(0.81-1.00)). In this work, we provide proof of concept that the R9-score can determine treatment effectiveness, making a case for designing a larger clinical study.
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Affiliation(s)
- Chandrani Thakur
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Ashutosh Tripathi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | | | - Akshatha Shivananjaiah
- SDS Tuberculosis Research Centre and Rajiv Gandhi Institute of Chest Diseases, Bangalore, India
| | - Anushree Chakraborty
- SDS Tuberculosis Research Centre and Rajiv Gandhi Institute of Chest Diseases, Bangalore, India
| | - Sreekala Varadappa
- SDS Tuberculosis Research Centre and Rajiv Gandhi Institute of Chest Diseases, Bangalore, India
| | | | - Deepesh Nagarajan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | | | - Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
- National Mathematics Initiative, Indian Institute of Science, Bangalore, India
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
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5
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Hariharan VN, Yadav R, Thakur C, Singh A, Gopinathan R, Singh DP, Sankhe G, Malhotra V, Chandra N, Bhatt A, Saini DK. Cyclic di-GMP sensing histidine kinase PdtaS controls mycobacterial adaptation to carbon sources. FASEB J 2021; 35:e21475. [PMID: 33772870 DOI: 10.1096/fj.202002537rr] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 11/11/2022]
Abstract
Cell signaling relies on second messengers to transduce signals from the sensory apparatus to downstream signaling pathway components. In bacteria, one of the most important and ubiquitous second messenger is the small molecule cyclic diguanosine monophosphate (c-di-GMP). While the biosynthesis, degradation, and regulatory pathways controlled by c-di-GMP are well characterized, the mechanisms through which c-di-GMP controls these processes are not entirely understood. Herein we present the report of a c-di-GMP sensing sensor histidine kinase PdtaS (Rv3220c), which binds to c-di-GMP at submicromolar concentrations, subsequently perturbing signaling of the PdtaS-PdtaR (Rv1626) two-component system. Aided by biochemical analysis, genetics, molecular docking, FRET microscopy, and structural modelling, we have characterized the binding of c-di-GMP in the GAF domain of PdtaS. We show that a pdtaS knockout in Mycobacterium smegmatis is severely compromised in growth on amino acid deficient media and exhibits global transcriptional dysregulation. The perturbation of the c-di-GMP-PdtaS-PdtaR axis results in a cascade of cellular changes recorded by a multiparametric systems' approach of transcriptomics, unbiased metabolomics, and lipid analyses.
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Affiliation(s)
- Vignesh Narayan Hariharan
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Rahul Yadav
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Chandrani Thakur
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Albel Singh
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Renu Gopinathan
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Devendra Pratap Singh
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Gaurav Sankhe
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Vandana Malhotra
- Department of Biochemistry, Sri Venkateswara College, Delhi University, Delhi, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Apoorva Bhatt
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Deepak Kumar Saini
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India.,Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
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6
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Ravichandran S, Banerjee U, Dr GD, Kandukuru R, Thakur C, Chakravortty D, Balaji KN, Singh A, Chandra N. VB 10, a new blood biomarker for differential diagnosis and recovery monitoring of acute viral and bacterial infections. EBioMedicine 2021; 67:103352. [PMID: 33906069 PMCID: PMC8099739 DOI: 10.1016/j.ebiom.2021.103352] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 04/04/2021] [Accepted: 04/07/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Precise differential diagnosis between acute viral and bacterial infections is important to enable appropriate therapy, avoid unnecessary antibiotic prescriptions and optimize the use of hospital resources. A systems view of host response to infections provides opportunities for discovering sensitive and robust molecular diagnostics. METHODS We combine blood transcriptomes from six independent datasets (n = 756) with a knowledge-based human protein-protein interaction network, identifies subnetworks capturing host response to each infection class, and derives common response cores separately for viral and bacterial infections. We subject the subnetworks to a series of computational filters to identify a parsimonious gene panel and a standalone diagnostic score that can be applied to individual samples. We rigorously validate the panel and the diagnostic score in a wide range of publicly available datasets and in a newly developed Bangalore-Viral Bacterial (BL-VB) cohort. FINDING We discover a 10-gene blood-based biomarker panel (Panel-VB) that demonstrates high predictive performance to distinguish viral from bacterial infections, with a weighted mean AUROC of 0.97 (95% CI: 0.96-0.99) in eleven independent datasets (n = 898). We devise a new stand-alone patient-wise score (VB10) based on the panel, which shows high diagnostic accuracy with a weighted mean AUROC of 0.94 (95% CI 0.91-0.98) in 2996 patient samples from 56 public datasets from 19 different countries. Further, we evaluate VB10 in a newly generated South Indian (BL-VB, n = 56) cohort and find 97% accuracy in the confirmed cases of viral and bacterial infections. We find that VB10 is (a) capable of accurately identifying the infection class in culture-negative indeterminate cases, (b) reflects recovery status, and (c) is applicable across different age groups, covering a wide spectrum of acute bacterial and viral infections, including uncharacterized pathogens. We tested our VB10 score on publicly available COVID-19 data and find that our score detected viral infection in patient samples. INTERPRETATION Our results point to the promise of VB10 as a diagnostic test for precise diagnosis of acute infections and monitoring recovery status. We expect that it will provide clinical decision support for antibiotic prescriptions and thereby aid in antibiotic stewardship efforts. FUNDING Grand Challenges India, Biotechnology Industry Research Assistance Council (BIRAC), Department of Biotechnology, Govt. of India.
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Affiliation(s)
| | - Ushashi Banerjee
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Gayathri Devi Dr
- Department of Microbiology, M S Ramaiah Medical College, Bangalore 560054, Karnataka, India
| | - Rooparani Kandukuru
- Department of Microbiology, M S Ramaiah Medical College, Bangalore 560054, Karnataka, India
| | - Chandrani Thakur
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Dipshikha Chakravortty
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India; Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | | | - Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India; Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Nagasuma Chandra
- IISc Mathematics Initiative, Indian Institute of Science, Bangalore 560012, India; Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India; Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India.
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7
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Sharma A, Chattopadhyay G, Chopra P, Bhasin M, Thakur C, Agarwal S, Ahmed S, Chandra N, Varadarajan R, Singh R. VapC21 Toxin Contributes to Drug-Tolerance and Interacts With Non-cognate VapB32 Antitoxin in Mycobacterium tuberculosis. Front Microbiol 2020; 11:2037. [PMID: 33042034 PMCID: PMC7517352 DOI: 10.3389/fmicb.2020.02037] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/31/2020] [Indexed: 12/13/2022] Open
Abstract
The prokaryotic ubiquitous Toxin-antitoxin (TA) modules encodes for a stable toxin and an unstable antitoxin. VapBC subfamily is the most abundant Type II TA system in M. tuberculosis genome. However, the exact physiological role for most of these Type II TA systems are still unknown. Here, we have comprehensively characterized the VapBC21 TA locus from M. tuberculosis. The overexpression of VapC21 inhibited mycobacterial growth in a bacteriostatic manner and as expected, growth inhibition was abrogated upon co-expression of the cognate antitoxin, VapB21. We observed that the deletion of vapC21 had no noticeable influence on the in vitro and in vivo growth of M. tuberculosis. Using co-expression and biophysical studies, we observed that in addition to VapB21, VapC21 is also able to interact with non-cognate antitoxin, VapB32. The strength of interaction varied between the cognate and non-cognate TA pairs. The overexpression of VapC21 resulted in differential expression of approximately 435 transcripts in M. tuberculosis. The transcriptional profiles obtained upon ectopic expression of VapC21 was similar to those reported in M. tuberculosis upon exposure to stress conditions such as nutrient starvation and enduring hypoxic response. Further, VapC21 overexpression also led to increased expression of WhiB7 regulon and bacterial tolerance to aminoglycosides and ethambutol. Taken together, these results indicate that a complex network of interactions exists between non-cognate TA pairs and VapC21 contributes to drug tolerance in vitro.
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Affiliation(s)
- Arun Sharma
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | | | - Pankaj Chopra
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Munmun Bhasin
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India
| | - Chandrani Thakur
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Sakshi Agarwal
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Shahbaz Ahmed
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Ramandeep Singh
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
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8
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Nagarajan D, Roy N, Kulkarni O, Nanajkar N, Datey A, Ravichandran S, Thakur C, T. S, Aprameya IV, Sarma SP, Chakravortty D, Chandra N. Ω76: A designed antimicrobial peptide to combat carbapenem- and tigecycline-resistant Acinetobacter baumannii. Sci Adv 2019; 5:eaax1946. [PMID: 31355341 PMCID: PMC6656545 DOI: 10.1126/sciadv.aax1946] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 06/17/2019] [Indexed: 05/12/2023]
Abstract
Drug resistance is a public health concern that threatens to undermine decades of medical progress. ESKAPE pathogens cause most nosocomial infections, and are frequently resistant to carbapenem antibiotics, usually leaving tigecycline and colistin as the last treatment options. However, increasing tigecycline resistance and colistin's nephrotoxicity severely restrict use of these antibiotics. We have designed antimicrobial peptides using a maximum common subgraph approach. Our best peptide (Ω76) displayed high efficacy against carbapenem and tigecycline-resistant Acinetobacter baumannii in mice. Mice treated with repeated sublethal doses of Ω76 displayed no signs of chronic toxicity. Sublethal Ω76 doses co-administered alongside sublethal colistin doses displayed no additive toxicity. These results indicate that Ω76 can potentially supplement or replace colistin, especially where nephrotoxicity is a concern. To our knowledge, no other existing antibiotics occupy this clinical niche. Mechanistically, Ω76 adopts an α-helical structure in membranes, causing rapid membrane disruption, leakage, and bacterial death.
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Affiliation(s)
- Deepesh Nagarajan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Natasha Roy
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore 560012, India
| | - Omkar Kulkarni
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Neha Nanajkar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Akshay Datey
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | | | - Chandrani Thakur
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sandeep T.
- Department of Microbiology, M.S. Ramaiah Medical College, Bangalore 560054, India
| | | | - Siddhartha P. Sarma
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore 560012, India
- NMR Research Center, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
- Corresponding author. (N.C.); (D.C.)
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
- Corresponding author. (N.C.); (D.C.)
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9
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Padiadpu J, Baloni P, Anand K, Munshi M, Thakur C, Mohan A, Singh A, Chandra N. Identifying and Tackling Emergent Vulnerability in Drug-Resistant Mycobacteria. ACS Infect Dis 2016; 2:592-607. [PMID: 27759382 DOI: 10.1021/acsinfecdis.6b00004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The global mechanisms and associated molecular alterations that occur in drug-resistant mycobacteria are poorly understood. To address this, we obtain genomics data and then construct a genome-scale response network in isoniazid-resistant Mycobacterium smegmatis and apply a network-mining algorithm. Through this, we decipher global alterations in an unbiased manner and identify emergent vulnerabilities in resistant bacilli, of which redox response was prominent. Using phenotypic profiling, we find that resistant bacilli exhibit collateral sensitivity to several compounds that block antioxidant responses. We find that nanogram/milliliter concentrations of ebselen, vancomycin, and phenylarsine oxide, in combination with isoniazid, are highly effective against Mycobacterium tuberculosis H37Rv and three clinical drug-resistant strains. Dynamic measurements of cytoplasmic redox potential revealed a surprisingly diminished capacity of clinical drug-resistant strains to counteract oxidative stress, providing a mechanistic basis for efficient and synergistic mycobactericidal activity of the drug combinations. Ebselen and vancomycin appear to be promising repurposable drugs.
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Affiliation(s)
- Jyothi Padiadpu
- Department of Biochemistry, ‡Supercomputer Education and Research Centre, #Molecular Biophysics Unit, ΔMicrobiology and
Cellular Biology, and ⊥Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Priyanka Baloni
- Department of Biochemistry, ‡Supercomputer Education and Research Centre, #Molecular Biophysics Unit, ΔMicrobiology and
Cellular Biology, and ⊥Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Kushi Anand
- Department of Biochemistry, ‡Supercomputer Education and Research Centre, #Molecular Biophysics Unit, ΔMicrobiology and
Cellular Biology, and ⊥Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - MohamedHusen Munshi
- Department of Biochemistry, ‡Supercomputer Education and Research Centre, #Molecular Biophysics Unit, ΔMicrobiology and
Cellular Biology, and ⊥Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Chandrani Thakur
- Department of Biochemistry, ‡Supercomputer Education and Research Centre, #Molecular Biophysics Unit, ΔMicrobiology and
Cellular Biology, and ⊥Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Abhilash Mohan
- Department of Biochemistry, ‡Supercomputer Education and Research Centre, #Molecular Biophysics Unit, ΔMicrobiology and
Cellular Biology, and ⊥Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Amit Singh
- Department of Biochemistry, ‡Supercomputer Education and Research Centre, #Molecular Biophysics Unit, ΔMicrobiology and
Cellular Biology, and ⊥Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Nagasuma Chandra
- Department of Biochemistry, ‡Supercomputer Education and Research Centre, #Molecular Biophysics Unit, ΔMicrobiology and
Cellular Biology, and ⊥Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
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Sharma S, Arshad M, Sharma A, Dharwal K, Ekramuddin, Singh T, Thakur C. To study the anatomic variant of foramen ovale and spinosum – In dried human skulls. J ANAT SOC INDIA 2016. [DOI: 10.1016/j.jasi.2016.08.206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Verma S, Sharma V, Mokta K, Thakur C, Angrup A, Singh D, Kanga A. Outbreak of enteric fever due to Salmonella Paratyphi A variety durazzo (2,12:a:-) in a hilly region of North India: A report of 43 cases. Indian J Med Microbiol 2016; 34:387-9. [PMID: 27514969 DOI: 10.4103/0255-0857.188366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Enteric fever due to Salmonella Paratyphi A (SPA) is a global problem occurring as outbreaks at times. An unusual SPA (2,12:a:-) variety durazzo has been reported rarely. We report an outbreak of enteric fever due to this variety affecting 43 individuals. The blood samples grew unusual mucoid, lactose non-fermenting colonies with atypical biochemical reactions in sugar fermentation and amino acid decarboxylation. Isolates had sensitivity to ceftriaxone, chloramphenical, cotrimoxazole, intermediate susceptibility to ciprofloxacin and resistance to ampicillin and nalidixic acid. Identification was confirmed as SPA (2,12:a:-) at the National Salmonella Centre.
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Affiliation(s)
- S Verma
- Department of Microbiology, Indira Gandhi Medical College, Shimla, Himachal Pradesh, India
| | - V Sharma
- Department of Microbiology, Indira Gandhi Medical College, Shimla, Himachal Pradesh, India
| | - K Mokta
- Department of Microbiology, Indira Gandhi Medical College, Shimla, Himachal Pradesh, India
| | - C Thakur
- Department of Microbiology, Indira Gandhi Medical College, Shimla, Himachal Pradesh, India
| | - A Angrup
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - D Singh
- Department of Microbiology, Indira Gandhi Medical College, Shimla, Himachal Pradesh, India
| | - A Kanga
- Department of Microbiology, Indira Gandhi Medical College, Shimla, Himachal Pradesh, India
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Thakur C, Kumar V, Gupta AK. Detecting mutation pattern of drug-resistant Mycobacterium tuberculosis isolates in Himachal Pradesh using GenoType(®) MTBDRplus assay. Indian J Med Microbiol 2016; 33:547-53. [PMID: 26470962 DOI: 10.4103/0255-0857.167336] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
CONTEXT Tuberculosis (TB) is a major public health problem in India and a principal cause of death in adults, especially among the economically productive age group. India accounts for one-fifth of the global burden of TB. It is estimated that about 40% of Indian population is infected with TB bacillus. The GenoType® MTBDRplus molecular method allows rapid diagnosis of the clinical samples and detection of the most common mutations in the genes associated with rifampicin (R) and isoniazid (H) resistance. AIMS To study the drug resistance and mutational patterns in multidrug-resistant (MDR) suspects clinical strains using GenoType® MTBDRplus assay. SUBJECTS AND METHODS A total of 770 sputum samples of the MDR-TB suspects were included in this study, which were received at Intermediate Reference Laboratory, Government TB Sanatorium, Dharampur, Solan, Himachal Pradesh from the Designated Microscopy Centres of Himachal Pradesh for the culture and susceptibility testing. All the 521 Mycobacterium tuberculosis complex (MTBC) strains were subjected to GenoType® MTBDRplus (HAIN Lifescience) assay to detect molecular resistance pattern to first line anti-tubercular drugs (isoniazid and rifampicin). RESULTS Of 770 samples, 556 (72.20%) were from male and 214 (27.80%) were from female. Among the 521 MTBC strains, 19.76% were found to be MDR and mono-resistance to isoniazid and rifampicin was detected in 8.63% and 6.14% strains respectively. About 74.81%, 76.35% and 5.40% strains harboured known mutation in rpoB, katG and inhA genes respectively. CONCLUSIONS In rpoB gene, the most common mutation is associated with S531 L region. The GenoType® MTBDRplus assay is a rapid test for the detection of the most common mutations in MDR-TB strains. In our study, unknown rpoB gene mutations were found in 25.18% strains that may further be detected by gene sequencing.
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Affiliation(s)
- C Thakur
- Intermediate Reference Laboratory, Government Tuberculosis Sanatorium, Dharampur, Solan, Himachal Pradesh, India
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Dhar N, Mohan A, Thakur C, Chandra NR, Dighe RR. Dissecting the structural and functional features of the Luteinizing hormone receptor using receptor specific single chain fragment variables. Mol Cell Endocrinol 2016; 427:1-12. [PMID: 26940038 DOI: 10.1016/j.mce.2016.02.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 02/27/2016] [Accepted: 02/27/2016] [Indexed: 01/16/2023]
Abstract
The Luteinizing hormone receptor (LHR) has a large extracellular domain (amino acid residues, a.a.1-355) and a transmembrane domain (TMD; a.a. 356-699), essential for hormone binding and signaling, respectively. The LHR hinge region (a.a. 256-355) connects the two domains and acts as an activating switch for the receptor by an unknown mechanism. LHR hinge-specific Single chain fragment variables (ScFv) stimulated cAMP production by the stable and transiently transfected cell lines expressing LHR in a hormone-independent manner and the C-terminal region of LHR hinge (a.a. 313-349) was identified as the probable epitope for one agonistic ScFv. This epitope attained a helical conformation upon agonistic ScFv binding and the activity of the ScFv was dependent on Y331 sulfation. ScFv was also able to activate TMD mutants, D578Y and A593P, reemphasizing the role of TM helix VI in LHR activation.
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Affiliation(s)
- Neha Dhar
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Abhilash Mohan
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Chandrani Thakur
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Nagasuma R Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Rajan R Dighe
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, Karnataka 560012, India.
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Thakur C, Saikia TC, Yadav RN. Total serum levels of triiodothyronine (T3) thyroxine (T4) and thyrotropine (TSH) in school going children of Dibrugarh district: an endemic goitre region of Assam. Indian J Physiol Pharmacol 1997; 41:167-70. [PMID: 9142564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The Thyroid Status was studied by estimating the total serum levels of T3 and T4 by radioimmunoassay (RIA) and TSH by radioimmunometric Assay (IRMA) from 635 school children (8-20 years; male 129, female 506) of the Dibrugarh district: a chronic endemic goitrous region of India. The results were compared with the control group of 147 (male 48, female 99) of healthy medical students of the same geographical area. The average values of T3 and TSH of school children were found higher and T4 lower than the control; the difference were only significant for T3 and TSH. T3/T4 ratio is more in school children than the control. The findings of low T4 and high TSH indicate that the school children (Pubertal stage) from chronic iodine deficients areas suffer from poor thyroid status; the male seemed to have been affected more than the female. As age advances the thyroid status improves in female.
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Affiliation(s)
- C Thakur
- Department of Physiology, Assam Medical College, Dibrugarh
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Nuzum E, White F, Thakur C, Dietze R, Wages J, Grogl M, Berman J. Diagnosis of symptomatic visceral leishmaniasis by use of the polymerase chain reaction on patient blood. J Infect Dis 1995; 171:751-4. [PMID: 7876635 DOI: 10.1093/infdis/171.3.751] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
To diagnose symptomatic visceral leishmaniasis (kala-azar) using peripheral blood rather than tissue aspirates, a polymerase chain reaction (PCR) technique was developed for which the detection limit is 1 Leishmania-infected macrophage in 8 mL of blood. For Indian, Kenyan, or Brazilian patients with parasitologically confirmed kala-azar, 57 of 63 cases before treatment had blood that was PCR-positive (90% sensitivity). None of 40 clinically healthy persons had PCR-positive blood (100% specificity). Twelve (92%) of 13 clinically cured Indian patients had negative PCR reactions 1-6 months after treatment. This PCR procedure can provide a parasitologic diagnosis for the vast majority of kala-azar cases before therapy, may identify patients who have been successfully treated by chemotherapy, and should substantially reduce the need for invasive tests.
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Affiliation(s)
- E Nuzum
- Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Washington, DC 20307-5100
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