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Kiran K, Patil KN. Characterization of Staphylococcus aureus RecX protein: Molecular insights into negative regulation of RecA protein and implications in HR processes. J Biochem 2023; 174:227-237. [PMID: 37115499 DOI: 10.1093/jb/mvad039] [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: 10/13/2022] [Revised: 04/11/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Homologous recombination (HR) is essential for genome stability and for maintaining genetic diversity. In eubacteria, RecA protein plays a key role during DNA repair, transcription, and HR. RecA is regulated at multiple levels, but majorly by RecX protein. Moreover, studies have shown RecX is a potent inhibitor of RecA and thus acts as an antirecombinase. Staphylococcus aureus is a major food-borne pathogen that causes skin, bone joint, and bloodstream infections. To date, RecX's role in S. aureus has remained enigmatic. Here, we show that S. aureus RecX (SaRecX) is expressed during exposure to DNA-damaging agents, and purified RecX protein directly interacts physically with RecA protein. The SaRecX is competent to bind with single-stranded DNA preferentially and double-stranded DNA feebly. Significantly, SaRecX impedes the RecA-driven displacement loop and inhibits formation of the strand exchange. Notably, SaRecX also abrogates adenosine triphosphate hydrolysis and abolishes the LexA coprotease activity. These findings highlight the role of the RecX protein as an antirecombinase during HR and play a pivotal role in regulation of RecA during the DNA transactions.
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Affiliation(s)
- Kajal Kiran
- Department of Microbiology and Fermentation Technology, Council of Scientific and Industrial Research-Central Food Technological Research Institute (CSIR-CFTRI), Mysuru 570 020, Karnataka, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - K Neelakanteshwar Patil
- Department of Microbiology and Fermentation Technology, Council of Scientific and Industrial Research-Central Food Technological Research Institute (CSIR-CFTRI), Mysuru 570 020, Karnataka, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
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Tharappel AM, Li Z, Li H. Inteins as Drug Targets and Therapeutic Tools. Front Mol Biosci 2022; 9:821146. [PMID: 35211511 PMCID: PMC8861304 DOI: 10.3389/fmolb.2022.821146] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/10/2022] [Indexed: 12/12/2022] Open
Abstract
Multidrug-resistant pathogens are of significant concern in recent years. Hence new antifungal and anti-bacterial drug targets are urgently needed before the situation goes beyond control. Inteins are polypeptides that self-splice from exteins without the need for cofactors or external energy, resulting in joining of extein fragments. Inteins are present in many organisms, including human pathogens such as Mycobacterium tuberculosis, Cryptococcus neoformans, C. gattii, and Aspergillus fumigatus. Because intein elements are not present in human genes, they are attractive drug targets to develop antifungals and antibiotics. Thus far, a few inhibitors of intein splicing have been reported. Metal-ions such as Zn2+ and Cu2+, and platinum-containing compound cisplatin inhibit intein splicing in M. tuberculosis and C. neoformans by binding to the active site cysteines. A small-molecule inhibitor 6G-318S and its derivative 6G-319S are found to inhibit intein splicing in C. neoformans and C. gattii with a MIC in nanomolar concentrations. Inteins have also been used in many other applications. Intein can be used in activating a protein inside a cell using small molecules. Moreover, split intein can be used to deliver large genes in experimental gene therapy and to kill selected species in a mixed population of microbes by taking advantage of the toxin-antitoxin system. Furthermore, split inteins are used in synthesizing cyclic peptides and in developing cell culture model to study infectious viruses including SARS-CoV-2 in the biosafety level (BSL) 2 facility. This mini-review discusses the recent research developments of inteins in drug discovery and therapeutic research.
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Affiliation(s)
- Anil Mathew Tharappel
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, United States
| | - Zhong Li
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, United States
| | - Hongmin Li
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, United States
- BIO5 Institute, The University of Arizona, Tucson, AZ, United States
- *Correspondence: Hongmin Li,
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Kiran K, Patil KN. Expression and Characterization of the Staphylococcus aureus RecA protein: A mapping of canonical functions. Protein Expr Purif 2021; 189:105967. [PMID: 34481085 DOI: 10.1016/j.pep.2021.105967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/27/2021] [Accepted: 08/27/2021] [Indexed: 11/16/2022]
Abstract
Recombinases are responsible for homologous recombination (HR), proper genome maintenance, and accurate deoxyribonucleic acid (DNA) duplication. Moreover, HR plays a determining role in DNA transaction processes such as DNA replication, repair, recombination, and transcription. Staphylococcus aureus, an opportunistic pathogen, usually causes respiratory infections such as sinusitis, skin infections, and food poisoning. To date, the role of the RecA gene product in S. aureus remains obscure. In this study, we attempted to map the functional properties of the RecA protein. S. aureus expresses the recA gene product in vivo upon exposure to the DNA-damaging agents, ultraviolet radiation, and methyl methanesulfonate. The recombinant purified S. aureus RecA protein displayed strong single-stranded DNA affinity compared to feeble binding to double-stranded DNA. Interestingly, the RecA protein is capable of invasion and formed displacement loops and readily performed strand-exchange activities with an oligonucleotide-based substrate. Notably, the S. aureus RecA protein hydrolyzed the DNA-dependent adenosine triphosphate and cleaved LexA, showing the conserved function of coprotease. This study provides the functional characterization of the S. aureus RecA protein and sheds light on the canonical processes of homologous recombination, which are conserved in the gram-positive foodborne pathogen S. aureus.
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Affiliation(s)
- Kajal Kiran
- Department of Protein Chemistry and Technology, Council of Scientific & Industrial Research-Central Food Technological Research Institute (CSIR-CFTRI), Mysuru, 570 020, Karnataka, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - K Neelakanteshwar Patil
- Department of Protein Chemistry and Technology, Council of Scientific & Industrial Research-Central Food Technological Research Institute (CSIR-CFTRI), Mysuru, 570 020, Karnataka, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India.
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Ojha D, Patil KN. Molecular and functional characterization of the Listeria monocytogenes RecA protein: Insights into the homologous recombination process. Int J Biochem Cell Biol 2019; 119:105642. [PMID: 31698090 DOI: 10.1016/j.biocel.2019.105642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 10/20/2019] [Accepted: 10/31/2019] [Indexed: 12/28/2022]
Abstract
The recombinases present in the all kingdoms in nature play a crucial role in DNA metabolism processes such as replication, repair, recombination and transcription. However, till date, the role of RecA in the deadly foodborne pathogen Listeria monocytogenes remains unknown. In this study, the authors show that L. monocytogenes expresses recA more than two-fold in vivo upon exposure to the DNA damaging agents, methyl methanesulfonate and ultraviolet radiation. The purified L. monocytogenes RecA protein show robust binding to single stranded DNA. The RecA is capable of forming displacement loop and hydrolyzes ATP, whereas the mutant LmRecAK70A fails to hydrolyze ATP, showing conserved walker A and B motifs. Interestingly, L. monocytogenes RecA and LmRecAK70A perform the DNA strand transfer activity, which is the hallmark feature of RecA protein with an oligonucleotide-based substrate. Notably, L. monocytogenes RecA readily cleaves L. monocytogenes LexA, the SOS regulon and protects the presynaptic filament from the exonuclease I activity. Altogether, this study provides the first detailed characterization of L. monocytogenes RecA and presents important insights into the process of homologous recombination in the gram-positive foodborne bacteria L. monocytogenes.
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Affiliation(s)
- Debika Ojha
- Department of Protein Chemistry and Technology, Council of Scientific & Industrial Research-Central Food Technological Research Institute (CSIR-CFTRI), Mysuru, 570 020, Karnataka, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - K Neelakanteshwar Patil
- Department of Protein Chemistry and Technology, Council of Scientific & Industrial Research-Central Food Technological Research Institute (CSIR-CFTRI), Mysuru, 570 020, Karnataka, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India.
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Rastogi R, Kaur G, Maan P, Bhatnagar A, Narang T, Dogra S, Kaur J. Molecular characterization and immunogenic function of ML1899 (LipG) of Mycobacterium leprae. J Med Microbiol 2019; 68:1629-1640. [PMID: 31553301 DOI: 10.1099/jmm.0.001080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. ML1899 is conserved in all mycobacterium sp. and is a middle member of mle-ML1898 operon involved in mycolic acid modification.Aim. In the present study attempts were made to characterize ML1899 in detail.Methodology. Bioinformatics tools were used for prediction of active-site residues, antigenic epitopes and a three-dimensional model of protein. The gene was cloned, expressed and purified as His-tagged protein in Escherichia coli for biophysical/biochemical characterization. Recombinant protein was used to treat THP-1 cells to study change in production of nitric oxide (NO), reactive oxygen species (ROS), cytokines and chemokines using flowcytometry/ELISA.Results. In silico analysis predicted ML1899 as a member of α/β hydrolase family with GXSXG-motif and Ser126, His282, Asp254 as active-site residues that were confirmed by site-directed mutagensis. ML1899 exhibited esterase activity. It hydrolysed pNP-butyrate as optimum substrate at pH 8.0 and 50 °C with 5.56 µM-1 min-1 catalytic efficiency. The enzyme exhibited stability up to 60 °C temperature and between pH 6.0 to 9.0. K m, V max and specific activity of ML1899 were calculated to be 400 µM, 40 µmoles min-1 ml-1 and 27 U mg- 1, respectively. ML1899 also exhibited phospholipase activity. The protein affected the survival of macrophages when treated at higher concentration. ML1899 enhanced ROS/NO production and up-regulated pro-inflammatory cytokines and chemokine including TNF-α, IFN-γ, IL-6 and IL-8 in macrophages. ML1899 was also observed to elicit humoral response in 69 % of leprosy patients.Conclusion. These results suggested that ML1899, an esterase could up-regulate the immune responses in favour of macrophages at a low concentration but kills the THP-1 macrophages cells at a higher concentration.
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Affiliation(s)
- Ruchi Rastogi
- Department of Biochemistry, BMS Block 2, South Campus, Panjab University, Sector 25, Chandigarh 160014, India
| | - Gurkamaljit Kaur
- Department of Biotechnology, BMS Block 1, South Campus, Panjab University, Sector 25, Chandigarh 160014, India
| | - Pratibha Maan
- Present address: Department of Experimental Medicine and Biotechnology, PGIMER, Chandigarh, 160012, India.,Department of Biotechnology, BMS Block 1, South Campus, Panjab University, Sector 25, Chandigarh 160014, India
| | - Archana Bhatnagar
- Department of Biochemistry, BMS Block 2, South Campus, Panjab University, Sector 25, Chandigarh 160014, India
| | - Tarun Narang
- Department of Dermatology, Veberology and Leprology, PGIMER, Chandigarh, 160012, India
| | - Sunil Dogra
- Department of Dermatology, Veberology and Leprology, PGIMER, Chandigarh, 160012, India
| | - Jagdeep Kaur
- Department of Biotechnology, BMS Block 1, South Campus, Panjab University, Sector 25, Chandigarh 160014, India
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Expression, purification and biochemical characterization of Listeria monocytogenes single stranded DNA binding protein 1. Protein Expr Purif 2019; 161:63-69. [DOI: 10.1016/j.pep.2019.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/22/2019] [Accepted: 04/22/2019] [Indexed: 11/22/2022]
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Ojha D, Patil KN. p-Coumaric acid inhibits the Listeria monocytogenes RecA protein functions and SOS response: An antimicrobial target. Biochem Biophys Res Commun 2019; 517:655-661. [PMID: 31416617 DOI: 10.1016/j.bbrc.2019.07.093] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 07/24/2019] [Indexed: 11/17/2022]
Abstract
Bacterial RecA plays an important role in the evaluation of antibiotic resistance via stress-induced DNA repair mechanism; SOS response. Accordingly, RecA became an important therapeutic target against antimicrobial resistance. Small molecule inhibitors of RecA may prevent adaptation of antibiotic resistance mutations and the emergence of antimicrobial resistance. In our study, we observed that phenolic compound p-Coumaric acid as potent RecA inhibitor. It inhibited RecA driven biochemical activities in vitro such as ssDNA binding, strand exchange, ATP hydrolysis and RecA coprotease activity of E. coli and L. monocytogenes RecA proteins. The mechanism underlying such inhibitory action of p-Coumaric acid involves its ability to interfere with the DNA binding domain of RecA protein. p-Coumaric acid also potentiates the activity of ciprofloxacin by inhibiting drastic cell survival of L. monocytogenes as well as filamentation process; the bacteria defensive mechanism in response to DNA damage. Additionally, it also blocked the ciprofloxacin induced RecA expression leading to suppression of SOS response in L. monocytogenes. These findings revealed that p-Coumaric acid is a potent RecA inhibitor, and can be used as an adjuvant to the existing antibiotics which not only enhance the shelf-life but also slow down the emergence of antibiotic resistance in bacteria.
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Affiliation(s)
- Debika Ojha
- Department of Protein Chemistry and Technology, Council of Scientific & Industrial Research-Central Food Technological Research Institute (CSIR-CFTRI), Mysuru, 570 020, Karnataka, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - K Neelakanteshwar Patil
- Department of Protein Chemistry and Technology, Council of Scientific & Industrial Research-Central Food Technological Research Institute (CSIR-CFTRI), Mysuru, 570 020, Karnataka, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India.
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Singh A, Bhagavat R, Vijayan M, Chandra N. A comparative analysis of the DNA recombination repair pathway in mycobacterial genomes. Tuberculosis (Edinb) 2016; 99:109-119. [PMID: 27450012 DOI: 10.1016/j.tube.2016.04.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/19/2016] [Accepted: 04/28/2016] [Indexed: 10/21/2022]
Abstract
In prokaryotes, repair by homologous recombination provides a major means to reinstate the genetic information lost in DNA damage. Recombination repair pathway in mycobacteria has multiple differences as compared to that in Escherichia coli. Of about 20 proteins known to be involved in the pathway, a set of 9 proteins, namely, RecF, RecO, RecR, RecA, SSBa, RuvA, RuvB and RuvC was found to be indispensable among the 43 mycobacterial strains. A domain level analysis indicated that most domains involved in recombination repair are unique to these proteins and are present as single copies in the genomes. Synteny analysis reveals that the gene order of proteins involved in the pathway is not conserved, suggesting that they may be regulated differently in different species. Sequence conservation among the same protein from different strains suggests the importance of RecO-RecA and RecFOR-RecA presynaptic pathways in the repair of double strand-breaks and single strand-breaks respectively. New annotations obtained from the analysis, include identification of a protein with a probable Holliday junction binding role present in 41 mycobacterial genomes and that of a RecB-like nuclease, containing a cas4 domain, present in 42 genomes. New insights into the binding of small molecules to the relevant proteins are provided by binding pocket analysis using three dimensional structural models. Analysis of the various features of the recombination repair pathway, presented here, is likely to provide a framework for further exploring stress response and emergence of drug resistance in mycobacteria.
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Affiliation(s)
- Amandeep Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Raghu Bhagavat
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - M Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India.
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Akinola RO, Mazandu GK, Mulder NJ. A Quantitative Approach to Analyzing Genome Reductive Evolution Using Protein-Protein Interaction Networks: A Case Study of Mycobacterium leprae. Front Genet 2016; 7:39. [PMID: 27066064 PMCID: PMC4809885 DOI: 10.3389/fgene.2016.00039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Accepted: 03/08/2016] [Indexed: 01/18/2023] Open
Abstract
The advance in high-throughput sequencing technologies has yielded complete genome sequences of several organisms, including complete bacterial genomes. The growing number of these available sequenced genomes has enabled analyses of their dynamics, as well as the molecular and evolutionary processes which these organisms are under. Comparative genomics of different bacterial genomes have highlighted their genome size and gene content in association with lifestyles and adaptation to various environments and have contributed to enhancing our understanding of the mechanisms of their evolution. Protein–protein functional interactions mediate many essential processes for maintaining the stability of the biological systems under changing environmental conditions. Thus, these interactions play crucial roles in the evolutionary processes of different organisms, especially for obligate intracellular bacteria, proven to generally have reduced genome sizes compared to their nearest free-living relatives. In this study, we used the approach based on the Renormalization Group (RG) analysis technique and the Maximum-Excluded-Mass-Burning (MEMB) model to investigate the evolutionary process of genome reduction in relation to the organization of functional networks of two organisms. Using a Mycobacterium leprae (MLP) network in comparison with a Mycobacterium tuberculosis (MTB) network as a case study, we show that reductive evolution in MLP was as a result of removal of important proteins from neighbors of corresponding orthologous MTB proteins. While each orthologous MTB protein had an increase in number of interacting partners in most instances, the corresponding MLP protein had lost some of them. This work provides a quantitative model for mapping reductive evolution and protein–protein functional interaction network organization in terms of roles played by different proteins in the network structure.
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Affiliation(s)
- Richard O Akinola
- Computational Biology Group, Department of Integrative Biomedical Sciences, Medical School, Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape Town, South Africa; Department of Mathematics, Faculty of Natural Sciences, University of JosJos, Nigeria
| | - Gaston K Mazandu
- Computational Biology Group, Department of Integrative Biomedical Sciences, Medical School, Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape Town, South Africa; African Institute for Mathematical SciencesCape Town, South Africa; African Institute for Mathematical SciencesCape Coast, Ghana
| | - Nicola J Mulder
- Computational Biology Group, Department of Integrative Biomedical Sciences, Medical School, Institute of Infectious Disease and Molecular Medicine, University of Cape Town Cape Town, South Africa
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Thakur RS, Desingu A, Basavaraju S, Subramanya S, Rao DN, Nagaraju G. Mycobacterium tuberculosis DinG is a structure-specific helicase that unwinds G4 DNA: implications for targeting G4 DNA as a novel therapeutic approach. J Biol Chem 2014; 289:25112-36. [PMID: 25059658 DOI: 10.1074/jbc.m114.563569] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The significance of G-quadruplexes and the helicases that resolve G4 structures in prokaryotes is poorly understood. The Mycobacterium tuberculosis genome is GC-rich and contains >10,000 sequences that have the potential to form G4 structures. In Escherichia coli, RecQ helicase unwinds G4 structures. However, RecQ is absent in M. tuberculosis, and the helicase that participates in G4 resolution in M. tuberculosis is obscure. Here, we show that M. tuberculosis DinG (MtDinG) exhibits high affinity for ssDNA and ssDNA translocation with a 5' → 3' polarity. Interestingly, MtDinG unwinds overhangs, flap structures, and forked duplexes but fails to unwind linear duplex DNA. Our data with DNase I footprinting provide mechanistic insights and suggest that MtDinG is a 5' → 3' polarity helicase. Notably, in contrast to E. coli DinG, MtDinG catalyzes unwinding of replication fork and Holliday junction structures. Strikingly, we find that MtDinG resolves intermolecular G4 structures. These data suggest that MtDinG is a multifunctional structure-specific helicase that unwinds model structures of DNA replication, repair, and recombination as well as G4 structures. We finally demonstrate that promoter sequences of M. tuberculosis PE_PGRS2, mce1R, and moeB1 genes contain G4 structures, implying that G4 structures may regulate gene expression in M. tuberculosis. We discuss these data and implicate targeting G4 structures and DinG helicase in M. tuberculosis could be a novel therapeutic strategy for culminating the infection with this pathogen.
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Affiliation(s)
- Roshan Singh Thakur
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Ambika Desingu
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Shivakumar Basavaraju
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | | | - Desirazu N Rao
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Ganesh Nagaraju
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
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