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Dubey S, Maurya RK, Shree S, Kumar S, Jahan F, Krishnan MY, Ramachandran R. Mycobacterium tuberculosis Rv2324 is a multifunctional feast/famine regulatory protein involved in growth, DNA replication and damage control. Int J Biol Macromol 2023; 252:126459. [PMID: 37634786 DOI: 10.1016/j.ijbiomac.2023.126459] [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: 02/02/2023] [Revised: 06/20/2023] [Accepted: 08/20/2023] [Indexed: 08/29/2023]
Abstract
Feast/famine regulatory proteins (FFRPs) are multifunctional regulators. We show that Mtb Rv2324 is important for growth, survival, and countering DNA damage in Mycobacterium tuberculosis (Mtb). DNA-relaxation activity against linear and supercoiled substrates suggest its involvement in transcription activation, while its high affinity for recombination, replication and repair substrates suggest a role there too. Small-Angle-X-ray scattering supports the adoption of an 'open' quaternary association in response to amino-acid binding. Size-exclusion-chromatography and glutaraldehyde cross-linking identify the adoption of diverse oligomers modulated by amino-acid binding, and DNA interactions. We tested G52A, G101T and D104A mutants which correspond to highly conserved residues, distal to the DNA-binding site, and are important for amino acids binding. G101T exhibits increased DNA affinity, while G52A and D104A exhibit weak DNA-binding thereby suggesting that they mediate effector-binding, and DNA binding activities. Gain and loss-of-function studies show that Rv2324 overexpression promotes growth-rate, while its knock-down leads to retarded growth. Rv2324 down-regulation lowers Mtb survival inside resting and IFN-ϒ-activated macrophages. Rv2324 protects the pathogen from DNA damage, as evidenced by the reduction in the knockdown strain's survival following treatment with H2O2 and UV light. Overall, we show that Rv2324 plays a crucial role in regulating survival and growth of Mtb.
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Affiliation(s)
- Shikha Dubey
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Uttar Pradesh 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rahul Kumar Maurya
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Uttar Pradesh 226031, India
| | - Sonal Shree
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Uttar Pradesh 226031, India; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
| | - Sanjay Kumar
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Uttar Pradesh 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Farheen Jahan
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Uttar Pradesh 226031, India
| | - Manju Yasoda Krishnan
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Uttar Pradesh 226031, India
| | - Ravishankar Ramachandran
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Uttar Pradesh 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Base excision repair pathways of bacteria: new promise for an old problem. Future Med Chem 2020; 12:339-355. [PMID: 32031026 DOI: 10.4155/fmc-2019-0267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Infectious diseases continue to be a major cause of human mortality. With the emergence of drug resistance, diseases that were long thought to have been curable by antibiotics are resurging. There is an urgent clinical need for newer antibiotics that target novel cellular pathways to overcome resistance to currently used therapeutics. The base excision repair (BER) pathways of the pathogen restore altered bases and safeguard the genomic integrity of the pathogen from the host's immune response. Although the BER machinery is of paramount importance to the survival of the pathogens, its potential as a drug target is largely unexplored. In this review, we discuss the importance of BER in different pathogenic organisms and the potential of its inhibition with small molecules.
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Catarina Teodoro Castro B, Cançado de Faria R, Faria BF, Azevedo V, Lara Dos Santos L, Júnior MC, Machado CR, de Oliveira Lopes D. UvrB protein of Corynebacterium pseudotuberculosis complements the phenotype of knockout Escherichia coli and recognizes DNA damage caused by UV radiation but not 8-oxoguanine in vitro. Gene 2018; 639:34-43. [PMID: 28974474 DOI: 10.1016/j.gene.2017.09.068] [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: 07/11/2017] [Revised: 09/17/2017] [Accepted: 09/29/2017] [Indexed: 11/27/2022]
Abstract
In prokaryotic cells, the UvrB protein plays a central role in nucleotide excision repair, which is involved in the recognition of bulky DNA lesions generated by chemical or physical agents. The present investigation aimed to characterize the uvrB gene of Corynebacterium pseudotuberculosis (CpuvrB) and evaluate its involvement in the DNA repair system of this pathogenic organism. In computational analysis, the alignment of the UvrB protein sequences of Escherichia coli, Mycobacterium tuberculosis, Bacillus caldotenax and Corynebacterium pseudotuberculosis showed high similarity and the catalytic amino acid residues and functional domains are preserved. A CpUvrB model was constructed by comparative modeling and presented structural similarity with the UvrB of E. coli. Moreover, in molecular docking analysis CpUvrB showed favorable interaction with EcUvrA and revealed a preserved ATP incorporation site. Heterologous functional complementation assays using E. coli uvrB-deficient cells exposed to UV irradiation showed that the CpUvrB protein contributed to an increased survival rate in relation to those in the absence of CpUvrB. Damaged oligonucleotides containing thymine dimer or 8-oxoguanine lesion were synthesized and incubated with CpUvrB protein, which was able to recognize and excise UV irradiation damage but not 8-oxoguanine. These results suggest that CpUvrB is involved in repairing lesions derived from UV light and encodes a protein orthologous to EcUvrB.
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Affiliation(s)
- Bárbara Catarina Teodoro Castro
- Laboratory of Molecular Biology, Federal University of São João Del-Rei (CCO), Av. Sebastião Gonçalves Coelho, 400, Divinópolis, MG 35501-296, Brazil.
| | - Rafael Cançado de Faria
- Laboratory of Molecular Biology, Federal University of São João Del-Rei (CCO), Av. Sebastião Gonçalves Coelho, 400, Divinópolis, MG 35501-296, Brazil.
| | - Bruna Franciele Faria
- Laboratory of Molecular Modeling, Federal University of São João Del-Rei (CCO), Av. Sebastião Gonçalves Coelho, 400, Divinópolis, MG 35501-296, Brazil.
| | - Vasco Azevedo
- Laboratory of Cell and Molecular Genetics, Department of General Biology, ICB, Federal University of Minas Gerais, Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil.
| | - Luciana Lara Dos Santos
- Laboratory of Molecular Biology, Federal University of São João Del-Rei (CCO), Av. Sebastião Gonçalves Coelho, 400, Divinópolis, MG 35501-296, Brazil.
| | - Moacyr Comar Júnior
- Laboratory of Molecular Modeling, Federal University of São João Del-Rei (CCO), Av. Sebastião Gonçalves Coelho, 400, Divinópolis, MG 35501-296, Brazil.
| | - Carlos Renato Machado
- Laboratory of Genetics and Biochemistry, Department of Biochemistry, ICB, Federal University of Minas Gerais, Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil.
| | - Débora de Oliveira Lopes
- Laboratory of Molecular Biology, Federal University of São João Del-Rei (CCO), Av. Sebastião Gonçalves Coelho, 400, Divinópolis, MG 35501-296, Brazil.
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Antimycobacterial mechanism of vanillin involves disruption of cell-surface integrity, virulence attributes, and iron homeostasis. Int J Mycobacteriol 2016; 5:460-468. [PMID: 27931688 DOI: 10.1016/j.ijmyco.2016.06.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 06/06/2016] [Accepted: 06/14/2016] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVE/BACKGROUND Tuberculosis (TB) remains a global threat, claiming one-third of the population annually. The ever increasing emergence of multidrug-resistant TB (MDR-TB) is the major impediment to effective anti-TB therapy. Under such circumstances, deciphering the antimycobacterial potential of natural compounds has gained considerable prominence. This study evaluated the antimycobacterial activity of vanillin (Van), a natural food-flavoring agent and preservative, along with its potential mechanisms of action. METHODS Drug susceptibilities were performed using broth microdilution, spot, and filter-disc assays. Membrane damage was studied by nitrocefin hydrolysis and electron microscopy. Virulence attributes were assessed by biofilm formation and cell adherence. Iron availability was estimated by enzymatic (ferroxidase) assay. RESULTS We found that the antimycobacterial activity of Van against Mycobacterium smegmatis (a surrogate of Mycobacterium tuberculosis) is 125μg/mL. Additionally, we observed disruption of membrane homeostasis in the presence of Van, as revealed by enhanced membrane permeability and transmission electron microscopy images showing a disturbed cell envelope. Concomitant with our findings, we also observed that Van leads to enhanced drug susceptibility to membrane targeting known anti-TB drugs. Furthermore, Van affects significant virulence traits of Mycobacterium by inhibiting biofilm formation and cell adhesion. Finally, we observed that Van disrupted iron homeostasis as displayed by hypersensitivity to iron deprivation. CONCLUSION The results established for the first time that Van could be an effective antimycobacterial agent that could be exploited further in treating mycobacterial infections.
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Devasundaram S, Raja A. Variable transcriptional adaptation between the laboratory (H37Rv) and clinical strains (S7 and S10) of Mycobacterium tuberculosis under hypoxia. INFECTION GENETICS AND EVOLUTION 2016; 40:21-28. [PMID: 26780642 DOI: 10.1016/j.meegid.2016.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Revised: 11/12/2015] [Accepted: 01/07/2016] [Indexed: 11/28/2022]
Abstract
Tuberculosis continues to be a major public health problem in many parts of the world, despite intensified efforts taken to control the disease. The remarkable success of M. tuberculosis as a pathogen is largely due to its ability to persist within the host for long periods. To develop the effective intervention strategies, understanding the biology of persistence is highly required. Accumulating evidences showed oxygen deprivation (hypoxia) as a potential stimulus for triggering the transition of M. tuberculosis to a non-replicating persistent state analogous to latency in vivo. To date, in vitro hypoxia experimental models used the laboratory adapted isolate H37Rv and very little is known about the behavior of clinical isolates that are involved during disease outbreaks. Hence, we compared the transcription profiles of H37Rv and two south Indian clinical isolates (S7 and S10) under hypoxia to find differences in gene expression pattern. The main objective of this current work is to find "differentially regulated genes" (genes that are down regulated in H37Rv but upregulated in both the clinical isolates) under hypoxia. Microarray results showed, a total of 502 genes were down regulated in H37Rv under hypoxia and 10 out of 502 genes were upregulated in both the clinical isolates. Thus, giving less importance to down regulated genes based on H37Rv model strain might exclude the true representative gene candidates in clinical isolates. Our study suggests the use of most prevalent clinical isolates for in vitro experimental model to minimize the variation in understanding the adaptation mechanisms of the strains.
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Affiliation(s)
- Santhi Devasundaram
- Department of Immunology, National Institute for Research in Tuberculosis (ICMR) (Formerly Tuberculosis Research Centre), No.1, Mayor Sathiyamoorthy Road, Chetpet, Chennai 600 031, India
| | - Alamelu Raja
- Department of Immunology, National Institute for Research in Tuberculosis (ICMR) (Formerly Tuberculosis Research Centre), No.1, Mayor Sathiyamoorthy Road, Chetpet, Chennai 600 031, India.
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Iron Deprivation Affects Drug Susceptibilities of Mycobacteria Targeting Membrane Integrity. J Pathog 2015; 2015:938523. [PMID: 26779346 PMCID: PMC4686683 DOI: 10.1155/2015/938523] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/19/2015] [Accepted: 11/23/2015] [Indexed: 12/28/2022] Open
Abstract
Multidrug resistance (MDR) acquired by Mycobacterium tuberculosis (MTB) through continuous deployment of antitubercular drugs warrants immediate search for novel targets and mechanisms. The ability of MTB to sense and become accustomed to changes in the host is essential for survival and confers the basis of infection. A crucial condition that MTB must surmount is iron limitation, during the establishment of infection, since iron is required by both bacteria and humans. This study focuses on how iron deprivation affects drug susceptibilities of known anti-TB drugs in Mycobacterium smegmatis, a "surrogate of MTB." We showed that iron deprivation leads to enhanced potency of most commonly used first line anti-TB drugs that could be reverted upon iron supplementation. We explored that membrane homeostasis is disrupted upon iron deprivation as revealed by enhanced membrane permeability and hypersensitivity to membrane perturbing agent leading to increased passive diffusion of drug and TEM images showing detectable differences in cell envelope thickness. Furthermore, iron seems to be indispensable to sustain genotoxic stress suggesting its possible role in DNA repair machinery. Taken together, we for the first time established a link between cellular iron and drug susceptibility of mycobacteria suggesting iron as novel determinant to combat MDR.
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Sang PB, Srinath T, Patil AG, Woo EJ, Varshney U. A unique uracil-DNA binding protein of the uracil DNA glycosylase superfamily. Nucleic Acids Res 2015; 43:8452-63. [PMID: 26304551 PMCID: PMC4787834 DOI: 10.1093/nar/gkv854] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 08/11/2015] [Indexed: 11/19/2022] Open
Abstract
Uracil DNA glycosylases (UDGs) are an important group of DNA repair enzymes, which pioneer the base excision repair pathway by recognizing and excising uracil from DNA. Based on two short conserved sequences (motifs A and B), UDGs have been classified into six families. Here we report a novel UDG, UdgX, from Mycobacterium smegmatis and other organisms. UdgX specifically recognizes uracil in DNA, forms a tight complex stable to sodium dodecyl sulphate, 2-mercaptoethanol, urea and heat treatment, and shows no detectable uracil excision. UdgX shares highest homology to family 4 UDGs possessing Fe-S cluster. UdgX possesses a conserved sequence, KRRIH, which forms a flexible loop playing an important role in its activity. Mutations of H in the KRRIH sequence to S, G, A or Q lead to gain of uracil excision activity in MsmUdgX, establishing it as a novel member of the UDG superfamily. Our observations suggest that UdgX marks the uracil-DNA for its repair by a RecA dependent process. Finally, we observed that the tight binding activity of UdgX is useful in detecting uracils in the genomes.
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Affiliation(s)
- Pau Biak Sang
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Thiruneelakantan Srinath
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Aravind Goud Patil
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Eui-Jeon Woo
- Functional Genomic Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahakro, Yuseongu, Daejeon, South Korea
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560064, India
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