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Tulin G, Figueroa NR, Checa SK, Soncini FC. The multifarious MerR family of transcriptional regulators. Mol Microbiol 2024; 121:230-242. [PMID: 38105009 DOI: 10.1111/mmi.15212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/28/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023]
Abstract
The MerR family of transcriptional regulators includes a variety of bacterial cytoplasmic proteins that respond to a wide range of signals, including toxins, metal ions, and endogenous metabolites. Its best-characterized members share similar structural and functional features with the family founder, the mercury sensor MerR, although most of them do not respond to metal ions. The group of "canonical" MerR homologs displays common molecular mechanisms for controlling the transcriptional activation of their target genes in response to inducer signals. This includes the recognition of distinctive operator sequences located at suboptimal σ70 -dependent promoters. Interestingly, an increasing number of proteins assigned to the MerR family based on their DNA-binding domain do not match in structure, sequence, or mode of action with any of the canonical MerR-like regulators. Here, we analyzed several members of the family, including this last group. Based on a phylogenetic analysis, and similarities in structural/functional features and position of their target operators relative to the promoter elements, we propose to assign these "atypical/divergent" MerR regulators to a phylogenetically separated group. These atypical/divergent homologs represent a new class of transcriptional regulators with novel regulatory mechanisms.
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Affiliation(s)
- Gonzalo Tulin
- Instituto de Biología Molecular y Celular de Rosario, Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - Nicolás R Figueroa
- Centro de Estudios Fotosintéticos y Bioquímicos, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - Susana K Checa
- Instituto de Biología Molecular y Celular de Rosario, Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - Fernando C Soncini
- Instituto de Biología Molecular y Celular de Rosario, Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
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2
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Zeng R, He L, Zhang B, Hu Y, Yu J, Yang S, Gu J, Wu Z, Deng J. Association between mutations in a thyX-hsdS.1 region and para-aminosalicylic acid resistance in Mycobacterium tuberculosis clinical isolates. Emerg Microbes Infect 2023; 12:2276339. [PMID: 38029724 PMCID: PMC10769527 DOI: 10.1080/22221751.2023.2276339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
Although para-aminosalicylic acid (PAS) has been used to treat tuberculosis agent for decades, its mechanisms of resistance are still not thoroughly understood. Previously, sporadic studies showed that certain mutations in the thyX-hsdS.1 region caused PAS resistance in M. tuberculosis, but a comprehensive analysis is lacking. Recently, we found a G-10A mutation in thyX-hsdS.1 in a PAS-resistant clinical isolate, but it did not cause PAS resistance. SNPs in thyX-hsdS.1 in 6550 clinical isolates were analyzed, and 153 SNPs were identified. C-16 T was the most common SNP identified (54.25%, 83/153), followed by C-4T (7.19%, 11/153) and G-9A (6.54%, 10/153). Subsequently, the effects of those SNPs on the promoter activity of thyX were tested, and the results showed that mutations C-1T, G-3A, C-4T, C-4G, G-7A, G-9A, C-16T, G-18C, and C-19G led to increased promoter activity compared with the wild-type sequence, but other mutations did not. Then, thyX and wild-type thyX-hsdS.1, or thyX-hsdS.1 containing specific SNPs, were overexpressed in M. tuberculosis H37Ra. The results showed that mutations resulting in increased promoter activity also caused PAS resistance. Moreover, the results of an electrophoretic mobility shift assay showed that thyX-hsdS.1 containing the C-16T mutation had a higher binding capacity to RNA polymerase than did the wild-type sequence. Taken together, our data demonstrated that among the SNPs identified in thyX-hsdS.1 of M. tuberculosis clinical isolates, only those able to increase the promoter activity of thyX caused PAS resistance and therefore can be considered as molecular markers for PAS resistance.
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Affiliation(s)
- Rong Zeng
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Lina He
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Baoyue Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Yangbo Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Jifang Yu
- Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People’s Republic of China
| | - Shanshan Yang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Jing Gu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Zhilong Wu
- Department of Tuberculosis Control, The Fourth People’s Hospital of Foshan City, Foshan, People’s Republic of China
| | - Jiaoyu Deng
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
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3
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Gopi Reji J, K Edison L, Raghunandanan S, Pushparajan AR, Kurthkoti K, Ajay Kumar R. Rv1255c, a dormancy-related transcriptional regulator of TetR family in Mycobacterium tuberculosis, enhances isoniazid tolerance in Mycobacterium smegmatis. J Antibiot (Tokyo) 2023; 76:720-727. [PMID: 37821540 DOI: 10.1038/s41429-023-00661-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 08/29/2023] [Accepted: 09/12/2023] [Indexed: 10/13/2023]
Abstract
Mycobacterium tuberculosis is exposed to diverse stresses inside the host during dormancy. Meanwhile, many metabolic and transcriptional regulatory changes occur, resulting in physiological modifications that help M. tuberculosis to adapt to these stresses. The same physiological changes also cause antibiotic tolerance in dormant M. tuberculosis. However, the transcriptional regulatory mechanism of antibiotic tolerance during dormancy remains unclear. Here, we showed that the expression of Rv1255c, an uncharacterised member of the tetracycline repressor family of transcriptional regulators, is upregulated during different stresses and hypoxia-induced dormancy. Antibiotic tolerance and efflux activities of Mycobacterium smegmatis constitutively expressing Rv1255c were analysed, and interestingly, it showed increased isoniazid tolerance and efflux activity. The intrabacterial isoniazid concentrations were found to be low in M. smegmatis expressing Rv1255c. Moreover, orthologs of the M. tuberculosis katG, gene of the enzyme which activates the first-line prodrug isoniazid, are overexpressed in this strain. Structural analysis of isoforms of KatG enzymes in M. smegmatis identified major amino acid substitutions associated with isoniazid resistance. Thus, we showed that Rv1255c helps M. smegmatis tolerate isoniazid by orchestrating drug efflux machinery. In addition, we showed that Rv1255c also causes overexpression of katG isoform in M. smegmatis which has amino acid substitutions as found in isoniazid-resistant katG in M. tuberculosis.
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Affiliation(s)
- Jijimole Gopi Reji
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Lakshmi K Edison
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Sajith Raghunandanan
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Akhil Raj Pushparajan
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Krishna Kurthkoti
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Ramakrsihnan Ajay Kumar
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India.
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4
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Pushparajan AR, Edison LK, Ajay Kumar R. Mycobacterium tuberculosis transcriptional regulator Rv1019 is upregulated in hypoxia, and negatively regulates Rv3230c-Rv3229c operon encoding enzymes in the oleic acid biosynthetic pathway. FEBS J 2023; 290:1583-1595. [PMID: 36209365 DOI: 10.1111/febs.16647] [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: 04/25/2022] [Revised: 07/19/2022] [Accepted: 10/05/2022] [Indexed: 11/05/2022]
Abstract
The main obstacle in eradicating tuberculosis is the ability of Mycobacterium tuberculosis to remain dormant in the host, and then to get reactivated even years later under immunocompromised conditions. Transcriptional regulation in intracellular pathogens plays an important role in their adapting to the challenging environment inside the host cells. Previously, we demonstrated that Rv1019, a putative transcriptional regulator of M. tuberculosis H37Rv, is an autorepressor. We showed that Rv1019 is cotranscribed with Rv1020 (mfd) and Rv1021 (mazG) which encode DNA repair proteins and negatively regulates the expression of these genes. In the present study, we show that Rv1019 regulates the expression of the genes Rv3230c and Rv3229c (desA3) also which form a two-gene operon in M. tuberculosis. Overexpression of Rv1019 in M. tuberculosis significantly downregulated the expression of these genes. Employing Wayne's hypoxia-induced dormancy model of M. tuberculosis, we show that Rv1019 is upregulated three-fold under hypoxia. Finally, by reporter assay, using Mycobacterium smegmatis as a model, we validate that Rv1019 is recruited to the promoter of Rv3230c-Rv3229c during hypoxia, and negatively regulates this operon which is involved in the biosynthesis of oleic acid.
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Affiliation(s)
- Akhil Raj Pushparajan
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India.,Department of Biotechnology, Faculty of Applied Sciences and Technology, University of Kerala, Thiruvananthapuram, India
| | - Lekshmi K Edison
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Ramakrishnan Ajay Kumar
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
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5
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Investigating a putative transcriptional regulatory protein encoded by Rv1719 gene of Mycobacterium tuberculosis. Protein J 2022; 41:424-433. [PMID: 35715720 DOI: 10.1007/s10930-022-10062-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2022] [Indexed: 10/18/2022]
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis, demonstrates immense plasticity with which it adapts to a highly dynamic and hostile host environment. This is facilitated by a web of signalling pathways constantly modulated by a multitude of proteins that regulate the flow of genetic information inside the pathogen. Transcription factors (TFs) belongs to one such family of proteins that modulate the signalling by regulating the abundance of proteins at the transcript level. In the current study, we have characterized the putative transcriptional regulatory protein encoded by the Rv1719 gene of Mycobacterium tuberculosis. This TF belongs to the IclR family of proteins with orthologs found in both bacterial and archaeal species. We cloned the Rv1719 gene into the pET28a expression vector and performed heterologous expression of the recombinant protein with E coli as the host. Further, optimization of the purification protocol by affinity chromatography and characterization of proteins for their functional viability has been demonstrated using various biochemical and/or biophysical approaches. Scale-up of purification yielded approximately 30 mg of ~ 28 kDa protein per litre of culture. In-silico protein domain analysis of Rv1719 protein predicted the presence of the helix-turn-helix (HTH) domain suggesting its ability to bind DNA sequence and modulate transcription; a hallmark of a transcriptional regulatory protein. Further, by performing electrophoretic mobility shift assay (EMSA) we demonstrated that the protein binds to a specific DNA fragment harboring the probable binding site of one of the predicted promoters.
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6
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Fang C, Zhang Y. Bacterial MerR family transcription regulators: activationby distortion. Acta Biochim Biophys Sin (Shanghai) 2021; 54:25-36. [PMID: 35130613 PMCID: PMC9909328 DOI: 10.3724/abbs.2021003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Transcription factors (TFs) modulate gene expression by regulating the accessibility of promoter DNA to RNA polymerases (RNAPs) in bacteria. The MerR family TFs are a large class of bacterial proteins unique in their physiological functions and molecular action: they function as transcription repressors under normal circumstances, but rapidly transform to transcription activators under various cellular triggers, including oxidative stress, imbalance of cellular metal ions, and antibiotic challenge. The promoters regulated by MerR TFs typically contain an abnormal long spacer between the -35 and -10 elements, where MerR TFs bind and regulate transcription activity through unique mechanisms. In this review, we summarize the function, ligand reception, DNA recognition, and molecular mechanism of transcription regulation of MerR-family TFs.
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Affiliation(s)
- Chengli Fang
- Key Laboratory of Synthetic BiologyCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
| | - Yu Zhang
- Key Laboratory of Synthetic BiologyCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
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Sousa EH, Carepo MS, Moura JJ. Nitrate-nitrite fate and oxygen sensing in dormant Mycobacterium tuberculosis: A bioinorganic approach highlighting the importance of transition metals. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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Anand K, Tripathi A, Shukla K, Malhotra N, Jamithireddy A, Jha RK, Chaudhury SN, Rajmani RS, Ramesh A, Nagaraja V, Gopal B, Nagaraju G, Seshasayee ASN, Singh A. Mycobacterium tuberculosis SufR Responds to Nitric oxide via its 4Fe-4S cluster and Regulates Fe-S cluster Biogenesis for Persistence in Mice.. [DOI: 10.1101/2020.08.10.245365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
Abstract
The persistence of Mycobacterium tuberculosis (Mtb) is a major problem in managing tuberculosis. Host–generated nitric oxide (NO) is perceived as one of the signals by Mtb to reprogram metabolism and respiration for persistence. However, the mechanisms involved in NO sensing and reorganizing Mtb′s physiology are not fully understood. Since NO damages iron–sulfur (Fe–S) clusters of essential enzymes, the mechanism(s) involved in regulating Fe–S cluster biogenesis could help Mtb persist in host tissues. Here, we show that a transcription factor SufR (Rv1460) senses NO via its 4Fe–4S cluster and promotes persistence of Mtb by mobilizing the Fe-S cluster biogenesis system; suf operon (Rv1460–Rv1466). Analysis of anaerobically purified SufR by UV-visible spectroscopy, circular dichroism, and iron-sulfide estimation confirms the presence of a 4Fe–4S cluster. Atmospheric O2 and H2O2 gradually degrade the 4Fe–4S cluster of SufR. Furthermore, electron paramagnetic resonance (EPR) analysis demonstrates that NO directly targets SufR 4Fe–4S cluster by forming a protein-bound dinitrosyl–iron–dithiol complex. DNase I footprinting, gel–shift, and in vitro transcription assays confirm that SufR directly regulates the expression of the suf operon in response to NO. Consistent with this, RNA–sequencing of Mtb ΔsufR demonstrates deregulation of the suf operon under NO stress. Strikingly, NO inflicted irreversible damage upon Fe–S clusters to exhaust respiratory and redox buffering capacity of MtbΔsufR. Lastly, Mtb ΔsufR failed to recover from a NO-induced non-growing state and displayed persistence defect inside immune–activated macrophages and murine lungs in a NO–dependent manner. Data suggest that SufR is a sensor of NO that supports persistence by reprogramming Fe–S cluster metabolism and bioenergetics.
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Pushparajan AR, Ramachandran R, Gopi Reji J, Ajay Kumar R. Mycobacterium
tuberculosis
TetR family transcriptional regulator Rv1019 is a negative regulator of the
mfd‐mazG
operon encoding DNA repair proteins. FEBS Lett 2020; 594:2867-2880. [DOI: 10.1002/1873-3468.13861] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/28/2020] [Accepted: 05/31/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Akhil Raj Pushparajan
- Mycobacterium Research Laboratory Rajiv Gandhi Centre for Biotechnology Thiruvananthapuram Kerala India
- Department of Biotechnology Faculty of Applied Sciences and Technology University of Kerala Thiruvananthapuram Kerala India
| | - Ranjit Ramachandran
- Mycobacterium Research Laboratory Rajiv Gandhi Centre for Biotechnology Thiruvananthapuram Kerala India
- Department of Biotechnology Faculty of Applied Sciences and Technology University of Kerala Thiruvananthapuram Kerala India
| | - Jijimole Gopi Reji
- Mycobacterium Research Laboratory Rajiv Gandhi Centre for Biotechnology Thiruvananthapuram Kerala India
- Department of Biotechnology Faculty of Applied Sciences and Technology University of Kerala Thiruvananthapuram Kerala India
| | - Ramakrishnan Ajay Kumar
- Mycobacterium Research Laboratory Rajiv Gandhi Centre for Biotechnology Thiruvananthapuram Kerala India
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Song N, Li Z, Cui Z, Chen L, Cui Y, Dang G, Li Z, Li H, Liu S. The prominent alteration in transcriptome and metabolome of Mycobacterium bovis BCG str. Tokyo 172 induced by vitamin B 1. BMC Microbiol 2019; 19:104. [PMID: 31117936 PMCID: PMC6530141 DOI: 10.1186/s12866-019-1492-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 05/14/2019] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Vitamin B1 (VB1) is a crucial dietary nutrient and essential cofactor for several key enzymes in the regulation of cellular and metabolic processes, and more importantly in the activation of immune system. To date, the precise role of VB1 in Mycobacterium tuberculosis remains to be fully understood. RESULTS In this study, the transcriptional and metabolic profiles of VB1-treated Mycobacterium. bovis BCG were analyzed by RNA-sequencing and LC-MS (Liquid chromatography coupled to mass spectrometry). The selection of BCG strain was based on its common physiological features shared with M. tuberculosis. The results of cell growth assays demonstrated that VB1 inhibited the BCG growth rate in vitro. Transcriptomic analysis revealed that the expression levels of genes related to fatty acid metabolism, cholesterol metabolism, glycolipid catabolism, DNA replication, protein translation, cell division and cell wall formation were significantly downregulated in M. bovis BCG treated with VB1. In addition, the metabolomics LC-MS data indicated that most of the amino acids and adenosine diphosphate (ADP) were decreased in M. bovis BCG strain after VB1 treatment. CONCLUSIONS This study provides the molecular and metabolic bases to understand the impacts of VB1 on M.bovis BCG.
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Affiliation(s)
- Ningning Song
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhaoli Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ziyin Cui
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Liping Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yingying Cui
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Guanghui Dang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhe Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - He Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Siguo Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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11
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Sun X, Zhang L, Jiang J, Ng M, Cui Z, Mai J, Ahn SK, Liu J, Zhang J, Liu J, Li Y. Transcription factors Rv0081 and Rv3334 connect the early and the enduring hypoxic response of Mycobacterium tuberculosis. Virulence 2019; 9:1468-1482. [PMID: 30165798 PMCID: PMC6177252 DOI: 10.1080/21505594.2018.1514237] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The ability of Mycobacterium tuberculosis (M. tb) to survive and persist in the host for decades in an asymptomatic state is an important aspect of tuberculosis pathogenesis. Although adaptation to hypoxia is thought to play a prominent role underlying M. tb persistence, how the bacteria achieve this goal is largely unknown. Rv0081, a member of the DosR regulon, is induced at the early stage of hypoxia while Rv3334 is one of the enduring hypoxic response genes. In this study, we uncovered genetic interactions between these two transcription factors. RNA-seq analysis of ΔRv0081 and ΔRv3334 revealed that the gene expression profiles of these two mutants were highly similar. We also found that under hypoxia, Rv0081 positively regulated the expression of Rv3334 while Rv3334 repressed transcription of Rv0081. In addition, we demonstrated that Rv0081 formed dimer and bound to the promoter region of Rv3334. Taken together, these data suggest that Rv0081 and Rv3334 work in the same regulatory pathway and that Rv3334 functions immediately downstream of Rv0081. We also found that Rv3334 is a bona fide regulator of the enduring hypoxic response genes. Our study has uncovered a regulatory pathway that connects the early and the enduring hypoxic response, revealing a transcriptional cascade that coordinates the temporal response of M. tb to hypoxia.
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Affiliation(s)
- Xian Sun
- a State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science , Fudan University , Shanghai , China
| | - Lu Zhang
- a State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science , Fudan University , Shanghai , China
| | - Jun Jiang
- a State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science , Fudan University , Shanghai , China
| | - Mark Ng
- b Department of Molecular Genetics , University of Toronto , Toronto , Canada
| | - Zhenling Cui
- c Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Medical School , Tongji University , Shanghai , China
| | - Juntao Mai
- b Department of Molecular Genetics , University of Toronto , Toronto , Canada
| | - Sang Kyun Ahn
- b Department of Molecular Genetics , University of Toronto , Toronto , Canada
| | - Jingqian Liu
- b Department of Molecular Genetics , University of Toronto , Toronto , Canada
| | - Jinyu Zhang
- a State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science , Fudan University , Shanghai , China
| | - Jun Liu
- a State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science , Fudan University , Shanghai , China.,b Department of Molecular Genetics , University of Toronto , Toronto , Canada
| | - Yao Li
- a State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science , Fudan University , Shanghai , China
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12
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Singh S, Sevalkar RR, Sarkar D, Karthikeyan S. Characteristics of the essential pathogenicity factor Rv1828, a MerR family transcription regulator from Mycobacterium tuberculosis. FEBS J 2018; 285:4424-4444. [PMID: 30306715 DOI: 10.1111/febs.14676] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 09/02/2018] [Accepted: 10/08/2018] [Indexed: 01/16/2023]
Abstract
The gene Rv1828 in Mycobacterium tuberculosis is shown to be essential for the pathogen and encodes for an uncharacterized protein. In this study, we have carried out biochemical and structural characterization of Rv1828 at the molecular level to understand its mechanism of action. The Rv1828 is annotated as helix-turn-helix (HTH)-type MerR family transcription regulator based on its N-terminal amino acid sequence similarity. The MerR family protein binds to a specific DNA sequence in the spacer region between -35 and -10 elements of a promoter through its N-terminal domain (NTD) and acts as transcriptional repressor or activator depending on the absence or presence of effector that binds to its C-terminal domain (CTD). A characteristic feature of MerR family protein is its ability to bind to 19 ± 1 bp DNA sequence in the spacer region between -35 and -10 elements which is otherwise a suboptimal length for transcription initiation by RNA polymerase. Here, we show the Rv1828 through its NTD binds to a specific DNA sequence that exists on its own as well as in other promoter regions. Moreover, the crystal structure of CTD of Rv1828, determined by single-wavelength anomalous diffraction method, reveals a distinctive dimerization. The biochemical and structural analysis reveals that Rv1828 specifically binds to an everted repeat through its winged-HTH motif. Taken together, we demonstrate that the Rv1828 encodes for a MerR family transcription regulator.
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Affiliation(s)
- Suruchi Singh
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Ritesh Rajesh Sevalkar
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Dibyendu Sarkar
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Subramanian Karthikeyan
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
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13
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Raghunandanan S, Ramachandran R, Gomez RL, Devanarayanan S, Bommakanti A, Kondapi AK, Varadarajan R, Kumar RA. Rv0474 is a copper-responsive transcriptional regulator that negatively regulates expression of RNA polymerase β subunit in Mycobacterium tuberculosis. FEBS J 2018; 285:3849-3869. [PMID: 30120904 DOI: 10.1111/febs.14637] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/03/2018] [Accepted: 08/15/2018] [Indexed: 11/28/2022]
Abstract
We characterize Rv0474, a putative transcriptional regulatory protein of Mycobacterium tuberculosis, which is found to function as a copper-responsive transcriptional regulator at toxic levels of copper. It is an autorepressor, but at elevated levels (10-250 μm) of copper ions the repression is relieved resulting in an increase in Rv0474 expression. Copper-bound Rv0474 is recruited to the rpoB promoter leading to its repression resulting in the growth arrest of the bacterium. Mutational analysis showed that the helix-turn-helix and leucine zipper domains of Rv0474 are essential for its binding to Rv0474 and rpoB promoters, respectively. The mechanism of Rv0474-mediated rpoB regulation seems to be operational only in pathogenic mycobacteria that can persist inside the host.
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Affiliation(s)
- Sajith Raghunandanan
- Mycobacterium Research Laboratory, Tropical Disease Biology Division, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Ranjit Ramachandran
- Mycobacterium Research Laboratory, Tropical Disease Biology Division, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Roshna Lawrence Gomez
- Mycobacterium Research Laboratory, Tropical Disease Biology Division, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | | | - Akhila Bommakanti
- Department of Biotechnology and Bioinformatics, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Anand Kumar Kondapi
- Department of Biotechnology and Bioinformatics, School of Life Science, University of Hyderabad, Hyderabad, India
| | | | - Ramakrishnan Ajay Kumar
- Mycobacterium Research Laboratory, Tropical Disease Biology Division, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
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The transcriptional regulator LysG (Rv1985c) of Mycobacterium tuberculosis activates lysE (Rv1986) in a lysine-dependent manner. PLoS One 2017; 12:e0186505. [PMID: 29049397 PMCID: PMC5648196 DOI: 10.1371/journal.pone.0186505] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 10/03/2017] [Indexed: 12/20/2022] Open
Abstract
The Mycobacterium tuberculosis protein encoded by the Rv1986 gene is a target for memory T cells in patients with tuberculosis, and shows strong similarities to a lysine exporter LysE of Corynebacterium glutamicum. During infection, the pathogen Mycobacterium tuberculosis adapts its metabolism to environmental changes. In this study, we found that the expression of Rv1986 is controlled by Rv1985c. Rv1985c is located directly upstream of Rv1986 with an overlapping promoter region between both genes. Semiquantitative reverse transcription PCR using an isogenic mutant of Mycobacterium tuberculosis lacking Rv1985c showed that in the presence of lysine, Rv1985c protein positively upregulated the expression of Rv1986. RNA sequencing revealed the transcription start points for both transcripts and overlapping promoters. An inverted repeat in the center of the intergenic region was identified, and binding of Rv1985c protein to the intergenic region was confirmed by electrophoretic mobility shift assays. Whole transcriptome expression analysis and RNAsequencing showed downregulated transcription of ppsBCD in the Rv1985c-mutant compared to the wild type strain. Taken together, our findings characterize the regulatory network of Rv1985c in Mycobacterium tuberculosis. Due to their similarity of an orthologous gene pair in Corynebacterium glutamicum, we suggest to rename Rv1985c to lysG(Mt), and Rv1986 to lysE(Mt).
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