1
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Bandyopadhyay D, Mishra PP. Revealing the DNA Unwinding Activity and Mechanism of Fork Reversal by RecG While Exposed to Variants of Stalled Replication-fork at Single-Molecular Resolution. J Mol Biol 2022; 434:167822. [PMID: 36108776 DOI: 10.1016/j.jmb.2022.167822] [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: 01/27/2022] [Revised: 08/23/2022] [Accepted: 09/06/2022] [Indexed: 11/25/2022]
Abstract
RecG, belonging to the category of Superfamily-2 plays a vital role in rescuing different kinds of stalled fork. The elemental mechanism of the helicase activity of RecG with several non-homologous stalled fork structures resembling intermediates formed during the process of DNA repair has been investigated in the present study to capture the dynamic stages of genetic rearrangement. The functional characterization has been exemplified through quantifying the response of the substrate in terms of their molecular heterogeneity and dynamical response by employing single-molecule fluorescence methods. An elevated processivity of RecG is observed for the stalled fork where progression of lagging daughter strand is ahead as compared to that of the leading strand. Through precise alteration of its function in terms of unwinding, depending upon the substrate DNA, RecG catalyzes the formation of Holliday junction from a stalled fork DNA. RecG is found to adopt an asymmetric mode of locomotion to unwind the lagging daughter strand for facilitating formation of Holliday junction that acts as a suitable intermediate for recombinational repair pathway. Our results emphasize the mechanism adopted by RecG during its 'sliding back' mode along the lagging daughter strand to be 'active translocation and passive unwinding'. This also provide clues as to how this helicase decides and controls the mode of translocation along the DNA to unwind.
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Affiliation(s)
- Debolina Bandyopadhyay
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Homi Bhaba National Institute, Mumbai, India. https://twitter.com/DebolinaBandyo2
| | - Padmaja Prasad Mishra
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Homi Bhaba National Institute, Mumbai, India.
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2
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López-Fernández H, Vieira CP, Ferreira P, Gouveia P, Fdez-Riverola F, Reboiro-Jato M, Vieira J. On the Identification of Clinically Relevant Bacterial Amino Acid Changes at the Whole Genome Level Using Auto-PSS-Genome. Interdiscip Sci 2021; 13:334-343. [PMID: 34009546 DOI: 10.1007/s12539-021-00439-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 03/21/2021] [Accepted: 05/07/2021] [Indexed: 11/26/2022]
Abstract
The identification of clinically relevant bacterial amino acid changes can be performed using different methods aimed at the identification of genes showing positively selected amino acid sites (PSS). Nevertheless, such analyses are time consuming, and the frequency of genes showing evidence for PSS can be low. Therefore, the development of a pipeline that allows the quick and efficient identification of the set of genes that show PSS is of interest. Here, we present Auto-PSS-Genome, a Compi-based pipeline distributed as a Docker image, that automates the process of identifying genes that show PSS using three different methods, namely codeML, FUBAR, and omegaMap. Auto-PSS-Genome accepts as input a set of FASTA files, one per genome, containing all coding sequences, thus minimizing the work needed to conduct positively selected sites analyses. The Auto-PSS-Genome pipeline identifies orthologous gene sets and corrects for multiple possible problems in input FASTA files that may prevent the automated identification of genes showing PSS. A FASTA file containing all coding sequences can also be given as an external global reference, thus easing the comparison of results across species, when gene names are different. In this work, we use Auto-PSS-Genome to analyse Mycobacterium leprae (that causes leprosy), and the closely related species M. haemophilum, that mainly causes ulcerating skin infections and arthritis in persons who are severely immunocompromised, and in children causes cervical and perihilar lymphadenitis. The genes identified in these two species as showing PSS may be those that are partially responsible for virulence and resistance to drugs.
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Affiliation(s)
- Hugo López-Fernández
- Department of Computer Science, University of Vigo, ESEI, Campus As Lagoas, 32004, Ourense, Spain
- The Biomedical Research Centre (CINBIO), Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Cristina P Vieira
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Pedro Ferreira
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Paula Gouveia
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Florentino Fdez-Riverola
- Department of Computer Science, University of Vigo, ESEI, Campus As Lagoas, 32004, Ourense, Spain
- The Biomedical Research Centre (CINBIO), Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Miguel Reboiro-Jato
- Department of Computer Science, University of Vigo, ESEI, Campus As Lagoas, 32004, Ourense, Spain
- The Biomedical Research Centre (CINBIO), Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Jorge Vieira
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.
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3
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Mittal P, Sinha R, Kumar A, Singh P, Ngasainao MR, Singh A, Singh IK. Focusing on DNA Repair and Damage Tolerance Mechanisms in Mycobacterium tuberculosis: An Emerging Therapeutic Theme. Curr Top Med Chem 2020; 20:390-408. [PMID: 31924156 DOI: 10.2174/1568026620666200110114322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/02/2019] [Accepted: 10/10/2019] [Indexed: 11/22/2022]
Abstract
Tuberculosis (TB) is one such disease that has become a nuisance in the world scenario and one of the most deadly diseases of the current times. The etiological agent of tuberculosis, Mycobacterium tuberculosis (M. tb) kills millions of people each year. Not only 1.7 million people worldwide are estimated to harbor M. tb in the latent form but also 5 to 15 percent of which are expected to acquire an infection during a lifetime. Though curable, a long duration of drug regimen and expense leads to low patient adherence. The emergence of multi-, extensive- and total- drug-resistant strains of M. tb further complicates the situation. Owing to high TB burden, scientists worldwide are trying to design novel therapeutics to combat this disease. Therefore, to identify new drug targets, there is a growing interest in targeting DNA repair pathways to fight this infection. Thus, this review aims to explore DNA repair and damage tolerance as an efficient target for drug development by understanding M. tb DNA repair and tolerance machinery and its regulation, its role in pathogenesis and survival, mutagenesis, and consequently, in the development of drug resistance.
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Affiliation(s)
- Pooja Mittal
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Rajesh Sinha
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Amit Kumar
- Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India
| | - Pooja Singh
- Public Health Research Institute, NJMS-Rutgers University, New Jersey, United States
| | - Moses Rinchui Ngasainao
- Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India.,Department of Molecular Ecology, Max-Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Indrakant K Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India.,Department of Molecular Ecology, Max-Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
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4
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Saha T, Shukla K, Thakur RS, Desingu A, Nagaraju G. Mycobacterium tuberculosis UvrD1 and UvrD2 helicases unwind G-quadruplex DNA. FEBS J 2019; 286:2062-2086. [PMID: 30821905 DOI: 10.1111/febs.14798] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 01/07/2019] [Accepted: 02/28/2019] [Indexed: 01/31/2023]
Abstract
Unresolved G-quadruplex (G4) DNA secondary structures impede DNA replication and can lead to DNA breaks and to genome instability. Helicases are known to unwind G4 structures and thereby facilitate genome duplication. Escherichia coli UvrD is a multifunctional helicase that participates in DNA repair, recombination and replication. Previously, we had demonstrated a novel role of E. coli UvrD helicase in resolving G4 structures. Mycobacterium tuberculosis genome encodes two orthologs of E. coli UvrD helicase, UvrD1 and UvrD2. It is unclear whether UvrD1 or UvrD2 or both helicases unwind G4 DNA structures. Here, we demonstrate that M. tuberculosis UvrD1 and UvrD2 unwind G4 tetraplexes. Both helicases were proficient in resolving previously characterized tetramolecular G4 structures in an ATP hydrolysis and single-stranded 3'-tail-dependent manner. Notably, M. tuberculosis UvrD1 and UvrD2 were efficient in unwinding G4 structures derived from the potential G4 forming sequences present in the M. tuberculosis genome. These data suggest an extended role for M. tuberculosis UvrD1 and UvrD2 helicases in resolving G4 DNA structures and provide insights into the maintenance of genome integrity via G4 DNA resolution.
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Affiliation(s)
- Tias Saha
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Kaustubh Shukla
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | | | - Ambika Desingu
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Ganesh Nagaraju
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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5
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Deciphering Within-Host Microevolution of Mycobacterium tuberculosis through Whole-Genome Sequencing: the Phenotypic Impact and Way Forward. Microbiol Mol Biol Rev 2019; 83:83/2/e00062-18. [PMID: 30918049 DOI: 10.1128/mmbr.00062-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Mycobacterium tuberculosis genome is more heterogenous and less genetically stable within the host than previously thought. Currently, only limited data exist on the within-host microevolution, diversity, and genetic stability of M. tuberculosis As a direct consequence, our ability to infer M. tuberculosis transmission chains and to understand the full complexity of drug resistance profiles in individual patients is limited. Furthermore, apart from the acquisition of certain drug resistance-conferring mutations, our knowledge on the function of genetic variants that emerge within a host and their phenotypic impact remains scarce. We performed a systematic literature review of whole-genome sequencing studies of serial and parallel isolates to summarize the knowledge on genetic diversity and within-host microevolution of M. tuberculosis We identified genomic loci of within-host emerged variants found across multiple studies and determined their functional relevance. We discuss important remaining knowledge gaps and finally make suggestions on the way forward.
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6
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Singh A, Vijayan M, Nagaraju G. RecG wed : A probable novel regulator in the resolution of branched DNA structures in mycobacteria. IUBMB Life 2018; 70:786-794. [PMID: 30240108 DOI: 10.1002/iub.1881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/02/2018] [Accepted: 05/04/2018] [Indexed: 01/31/2023]
Abstract
Structure-specific helicases, such as RecG, play an important role in the resolution of recombination intermediates. A bioinformatic analysis of mycobacterial genomes led to the identification of a protein (RecGwed ) with a C-terminal "edge" domain, similar to the wedge domain of RecG. RecGwed is predominately found in the phylum Actinobacteria and in few human pathogens. Mycobacterium smegmatis RecGwed was able to bind branched DNA structures in vitro but failed to interact with single- or double-stranded DNA. The expression of recGwed in M. smegmatis cells was up-regulated during stationary phase/UV damage and down-regulated during MMS/H2 O2 treatment. These observations indicate the possible involvement of RecGwed in transactions during recombination events, that proceed though branched DNA intermediates. © 2018 IUBMB Life, 70(8):786-794, 2018.
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Affiliation(s)
- Amandeep Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - M Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Ganesh Nagaraju
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
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7
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Singh A. Guardians of the mycobacterial genome: A review on DNA repair systems in Mycobacterium tuberculosis. MICROBIOLOGY-SGM 2017; 163:1740-1758. [PMID: 29171825 DOI: 10.1099/mic.0.000578] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The genomic integrity of Mycobacterium tuberculosis is continuously threatened by the harsh survival conditions inside host macrophages, due to immune and antibiotic stresses. Faithful genome maintenance and repair must be accomplished under stress for the bacillus to survive in the host, necessitating a robust DNA repair system. The importance of DNA repair systems in pathogenesis is well established. Previous examination of the M. tuberculosis genome revealed homologues of almost all the major DNA repair systems, i.e. nucleotide excision repair (NER), base excision repair (BER), homologous recombination (HR) and non-homologous end joining (NHEJ). However, recent developments in the field have pointed to the presence of novel proteins and pathways in mycobacteria. Homologues of archeal mismatch repair proteins were recently reported in mycobacteria, a pathway previously thought to be absent. RecBCD, the major nuclease-helicase enzymes involved in HR in E. coli, were implicated in the single-strand annealing (SSA) pathway. Novel roles of archeo-eukaryotic primase (AEP) polymerases, previously thought to be exclusive to NHEJ, have been reported in BER. Many new proteins with a probable role in DNA repair have also been discovered. It is now realized that the DNA repair systems in M. tuberculosis are highly evolved and have redundant backup mechanisms to mend the damage. This review is an attempt to summarize our current understanding of the DNA repair systems in M. tuberculosis.
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Affiliation(s)
- Amandeep Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
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8
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Escherichia coli and Neisseria gonorrhoeae UvrD helicase unwinds G4 DNA structures. Biochem J 2017; 474:3579-3597. [PMID: 28916651 DOI: 10.1042/bcj20170587] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/06/2017] [Accepted: 09/07/2017] [Indexed: 11/17/2022]
Abstract
G-quadruplex (G4) secondary structures have been implicated in various biological processes, including gene expression, DNA replication and telomere maintenance. However, unresolved G4 structures impede replication progression which can lead to the generation of DNA double-strand breaks and genome instability. Helicases have been shown to resolve G4 structures to facilitate faithful duplication of the genome. Escherichia coli UvrD (EcUvrD) helicase plays a crucial role in nucleotide excision repair, mismatch repair and in the regulation of homologous recombination. Here, we demonstrate a novel role of E. coli and Neisseria gonorrhoeae UvrD in resolving G4 tetraplexes. EcUvrD and Ngonorrhoeae UvrD were proficient in unwinding previously characterized tetramolecular G4 structures. Notably, EcUvrD was equally efficient in resolving tetramolecular and bimolecular G4 DNA that were derived from the potential G4-forming sequences from the genome of E. coli Interestingly, in addition to resolving intermolecular G4 structures, EcUvrD was robust in unwinding intramolecular G4 structures. These data for the first time provide evidence for the role of UvrD in the resolution of G4 structures, which has implications for the in vivo role of UvrD helicase in G4 DNA resolution and genome maintenance.
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9
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Azeroglu B, Leach DRF. RecG controls DNA amplification at double-strand breaks and arrested replication forks. FEBS Lett 2017; 591:1101-1113. [PMID: 28155219 PMCID: PMC5412681 DOI: 10.1002/1873-3468.12583] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 01/13/2017] [Accepted: 01/28/2017] [Indexed: 12/16/2022]
Abstract
DNA amplification is a powerful mutational mechanism that is a hallmark of cancer and drug resistance. It is therefore important to understand the fundamental pathways that cells employ to avoid over‐replicating sections of their genomes. Recent studies demonstrate that, in the absence of RecG, DNA amplification is observed at sites of DNA double‐strand break repair (DSBR) and of DNA replication arrest that are processed to generate double‐strand ends. RecG also plays a role in stabilising joint molecules formed during DSBR. We propose that RecG prevents a previously unrecognised mechanism of DNA amplification that we call reverse‐restart, which generates DNA double‐strand ends from incorrect loading of the replicative helicase at D‐loops formed by recombination, and at arrested replication forks.
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Affiliation(s)
- Benura Azeroglu
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, UK
| | - David R F Leach
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, UK
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10
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Beyene GT, Balasingham SV, Frye SA, Namouchi A, Homberset H, Kalayou S, Riaz T, Tønjum T. Characterization of the Neisseria meningitidis Helicase RecG. PLoS One 2016; 11:e0164588. [PMID: 27736945 PMCID: PMC5063381 DOI: 10.1371/journal.pone.0164588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 09/27/2016] [Indexed: 11/19/2022] Open
Abstract
Neisseria meningitidis (Nm) is a Gram-negative oral commensal that opportunistically can cause septicaemia and/or meningitis. Here, we overexpressed, purified and characterized the Nm DNA repair/recombination helicase RecG (RecGNm) and examined its role during genotoxic stress. RecGNm possessed ATP-dependent DNA binding and unwinding activities in vitro on a variety of DNA model substrates including a Holliday junction (HJ). Database searching of the Nm genomes identified 49 single nucleotide polymorphisms (SNPs) in the recGNm including 37 non-synonymous SNPs (nsSNPs), and 7 of the nsSNPs were located in the codons for conserved active site residues of RecGNm. A transient reduction in transformation of DNA was observed in the Nm ΔrecG strain as compared to the wildtype. The gene encoding recGNm also contained an unusually high number of the DNA uptake sequence (DUS) that facilitate transformation in neisserial species. The differentially abundant protein profiles of the Nm wildtype and ΔrecG strains suggest that expression of RecGNm might be linked to expression of other proteins involved in DNA repair, recombination and replication, pilus biogenesis, glycan biosynthesis and ribosomal activity. This might explain the growth defect that was observed in the Nm ΔrecG null mutant.
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Affiliation(s)
| | | | - Stephan A. Frye
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
| | - Amine Namouchi
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
| | | | - Shewit Kalayou
- Department of Microbiology, University of Oslo, Oslo, Norway
| | - Tahira Riaz
- Department of Microbiology, University of Oslo, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, University of Oslo, Oslo, Norway
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
- * E-mail:
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11
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Gaidutšik I, Sedman T, Sillamaa S, Sedman J. Irc3 is a mitochondrial DNA branch migration enzyme. Sci Rep 2016; 6:26414. [PMID: 27194389 PMCID: PMC4872236 DOI: 10.1038/srep26414] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 05/03/2016] [Indexed: 01/03/2023] Open
Abstract
Integrity of mitochondrial DNA (mtDNA) is essential for cellular energy metabolism. In the budding yeast Saccharomyces cerevisiae, a large number of nuclear genes influence the stability of mitochondrial genome; however, most corresponding gene products act indirectly and the actual molecular mechanisms of mtDNA inheritance remain poorly characterized. Recently, we found that a Superfamily II helicase Irc3 is required for the maintenance of mitochondrial genome integrity. Here we show that Irc3 is a mitochondrial DNA branch migration enzyme. Irc3 modulates mtDNA metabolic intermediates by preferential binding and unwinding Holliday junctions and replication fork structures. Furthermore, we demonstrate that the loss of Irc3 can be complemented with mitochondrially targeted RecG of Escherichia coli. We suggest that Irc3 could support the stability of mtDNA by stimulating fork regression and branch migration or by inhibiting the formation of irregular branched molecules.
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Affiliation(s)
- Ilja Gaidutšik
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b, Tartu 51010, Estonia
| | - Tiina Sedman
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b, Tartu 51010, Estonia
| | - Sirelin Sillamaa
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b, Tartu 51010, Estonia
| | - Juhan Sedman
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b, Tartu 51010, Estonia
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12
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Nautiyal A, Rani PS, Sharples GJ, Muniyappa K. Mycobacterium tuberculosis RuvX is a Holliday junction resolvase formed by dimerisation of the monomeric YqgF nuclease domain. Mol Microbiol 2016; 100:656-74. [PMID: 26817626 DOI: 10.1111/mmi.13338] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2016] [Indexed: 01/07/2023]
Abstract
The Mycobacterium tuberculosis genome possesses homologues of the ruvC and yqgF genes that encode putative Holliday junction (HJ) resolvases. However, their gene expression profiles and enzymatic properties have not been experimentally defined. Here we report that expression of ruvC and yqgF is induced in response to DNA damage. Protein-DNA interaction assays with purified M. tuberculosis RuvC (MtRuvC) and YqgF (MtRuvX) revealed that both associate preferentially with HJ DNA, albeit with differing affinities. Although both MtRuvC and MtRuvX cleaved HJ DNA in vitro, the latter displayed robust HJ resolution activity by symmetrically related, paired incisions. MtRuvX showed a higher binding affinity for the HJ structure over other branched recombination and replication intermediates. An MtRuvX(D28N) mutation, eliminating one of the highly conserved catalytic residues in this class of endonucleases, dramatically reduced its ability to cleave HJ DNA. Furthermore, a unique cysteine (C38) fulfils a crucial role in HJ cleavage, consistent with disulfide-bond mediated dimerization being essential for MtRuvX activity. In contrast, E. coli YqgF is monomeric and exhibits no branched DNA binding or cleavage activity. These results fit with a functional modification of YqgF in M. tuberculosis so that it can act as a dimeric HJ resolvase analogous to that of RuvC.
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Affiliation(s)
- Astha Nautiyal
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - P Sandhya Rani
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Gary J Sharples
- Department of Chemistry, School of Biological and Biomedical Sciences, Biophysical Sciences Institute, University of Durham, DH1 3LE, UK
| | - K Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
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13
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Abstract
Discontinuity of both strands of the chromosome is a lethal event in all living organisms because it compromises chromosome replication. As such, a diversity of DNA repair systems has evolved to repair double-strand DNA breaks (DSBs). In part, this diversity of DSB repair systems has evolved to repair breaks that arise in diverse physiologic circumstances or sequence contexts, including cellular states of nonreplication or breaks that arise between repeats. Mycobacteria elaborate a set of three genetically distinct DNA repair pathways: homologous recombination, nonhomologous end joining, and single-strand annealing. As such, mycobacterial DSB repair diverges substantially from the standard model of prokaryotic DSB repair and represents an attractive new model system. In addition, the presence in mycobacteria of a DSB repair system that can repair DSBs in nonreplicating cells (nonhomologous end joining) or when DSBs arise between repeats (single-strand annealing) has clear potential relevance to Mycobacterium tuberculosis pathogenesis, although the exact role of these systems in M. tuberculosis pathogenesis is still being elucidated. In this article we will review the genetics of mycobacterial DSB repair systems, focusing on recent insights.
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14
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Thakur RS, Basavaraju S, Khanduja JS, Muniyappa K, Nagaraju G. Mycobacterium tuberculosis RecG protein but not RuvAB or RecA protein is efficient at remodeling the stalled replication forks: implications for multiple mechanisms of replication restart in mycobacteria. J Biol Chem 2015; 290:24119-39. [PMID: 26276393 DOI: 10.1074/jbc.m115.671164] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Indexed: 11/06/2022] Open
Abstract
Aberrant DNA replication, defects in the protection, and restart of stalled replication forks are major causes of genome instability in all organisms. Replication fork reversal is emerging as an evolutionarily conserved physiological response for restart of stalled forks. Escherichia coli RecG, RuvAB, and RecA proteins have been shown to reverse the model replication fork structures in vitro. However, the pathways and the mechanisms by which Mycobacterium tuberculosis, a slow growing human pathogen, responds to different types of replication stress and DNA damage are unclear. Here, we show that M. tuberculosis RecG rescues E. coli ΔrecG cells from replicative stress. The purified M. tuberculosis RecG (MtRecG) and RuvAB (MtRuvAB) proteins catalyze fork reversal of model replication fork structures with and without a leading strand single-stranded DNA gap. Interestingly, single-stranded DNA-binding protein suppresses the MtRecG- and MtRuvAB-mediated fork reversal with substrates that contain lagging strand gap. Notably, our comparative studies with fork structures containing template damage and template switching mechanism of lesion bypass reveal that MtRecG but not MtRuvAB or MtRecA is proficient in driving the fork reversal. Finally, unlike MtRuvAB, we find that MtRecG drives efficient reversal of forks when fork structures are tightly bound by protein. These results provide direct evidence and valuable insights into the underlying mechanism of MtRecG-catalyzed replication fork remodeling and restart pathways in vivo.
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Affiliation(s)
- Roshan Singh Thakur
- 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
| | - Jasbeer Singh Khanduja
- From the Department of Biochemistry, Indian Institute of Science, Bangalore-560012, India
| | - K Muniyappa
- 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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15
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Mycobacterium smegmatis HelY Is an RNA-Activated ATPase/dATPase and 3'-to-5' Helicase That Unwinds 3'-Tailed RNA Duplexes and RNA:DNA Hybrids. J Bacteriol 2015; 197:3057-65. [PMID: 26170411 DOI: 10.1128/jb.00418-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/07/2015] [Indexed: 12/30/2022] Open
Abstract
UNLABELLED Mycobacteria have a large and distinctive ensemble of DNA helicases that function in DNA replication, repair, and recombination. Little is known about the roster of RNA helicases in mycobacteria or their roles in RNA transactions. The 912-amino-acid Mycobacterium smegmatis HelY (MSMEG_3885) protein is a bacterial homolog of the Mtr4 and Ski2 helicases that regulate RNA 3' processing and turnover by the eukaryal exosome. Here we characterize HelY as an RNA-stimulated ATPase/dATPase and an ATP/dATP-dependent 3'-to-5' helicase. HelY requires a 3' single-strand RNA tail (a loading RNA strand) to displace the complementary strand of a tailed RNA:RNA or RNA:DNA duplex. The findings that HelY ATPase is unresponsive to a DNA polynucleotide cofactor and that HelY is unable to unwind a 3'-tailed duplex in which the loading strand is DNA distinguish HelY from other mycobacterial nucleoside triphosphatases/helicases characterized previously. The biochemical properties of HelY, which resemble those of Mtr4/Ski2, hint at a role for HelY in mycobacterial RNA catabolism. IMPORTANCE RNA helicases play crucial roles in transcription, RNA processing, and translation by virtue of their ability to alter RNA secondary structure or remodel RNA-protein interactions. In eukarya, the RNA helicases Mtr4 and Ski2 regulate RNA 3' resection by the exosome. Mycobacterium smegmatis HelY, a bacterial homolog of Mtr4/Ski2, is characterized here as a unidirectional helicase, powered by RNA-dependent ATP/dATP hydrolysis, that tracks 3' to 5' along a loading RNA strand to displace the complementary strand of a tailed RNA:RNA or RNA:DNA duplex. The biochemical properties of HelY suggest a role in bacterial RNA transactions. HelY homologs are present in pathogenic mycobacteria (e.g., M. tuberculosis and M. leprae) and are widely prevalent in Actinobacteria and Cyanobacteria but occur sporadically elsewhere in the bacterial domain.
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16
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Sharadamma N, Harshavardhana Y, Ravishankar A, Anand P, Chandra N, Muniyappa K. Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction. Biochemistry 2015; 54:4142-60. [DOI: 10.1021/acs.biochem.5b00447] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Apoorva Ravishankar
- Department of
Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Praveen Anand
- Department of
Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Nagasuma Chandra
- Department of
Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - K. Muniyappa
- Department of
Biochemistry, Indian Institute of Science, Bangalore 560012, India
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17
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Sharadamma N, Harshavardhana Y, Ravishankar A, Anand P, Chandra N, Muniyappa K. Molecular dissection of Mycobacterium tuberculosis integration host factor reveals novel insights into the mode of DNA binding and nucleoid compaction. J Biol Chem 2014; 289:34325-40. [PMID: 25324543 DOI: 10.1074/jbc.m114.608596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The annotated whole-genome sequence of Mycobacterium tuberculosis revealed that Rv1388 (Mtihf) is likely to encode for a putative 20-kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or the organization of the mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg-170, Arg-171, and Arg-173, which might be involved in DNA binding, and a conserved proline (Pro-150) in the tight turn. The phenotypic sensitivity of Escherichia coli ΔihfA and ΔihfB strains to UV and methyl methanesulfonate could be complemented with the wild-type Mtihf but not its alleles bearing mutations in the DNA-binding residues. Protein-DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, binds with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHFαβ. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes DNA compaction into nucleoid-like or higher order filamentous structures. We therefore propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins.
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Affiliation(s)
| | | | - Apoorva Ravishankar
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Praveen Anand
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Nagasuma Chandra
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - K Muniyappa
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
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18
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Mawer JSP, Leach DRF. Branch migration prevents DNA loss during double-strand break repair. PLoS Genet 2014; 10:e1004485. [PMID: 25102287 PMCID: PMC4125073 DOI: 10.1371/journal.pgen.1004485] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 05/18/2014] [Indexed: 11/19/2022] Open
Abstract
The repair of DNA double-strand breaks must be accurate to avoid genomic rearrangements that can lead to cell death and disease. This can be accomplished by promoting homologous recombination between correctly aligned sister chromosomes. Here, using a unique system for generating a site-specific DNA double-strand break in one copy of two replicating Escherichia coli sister chromosomes, we analyse the intermediates of sister-sister double-strand break repair. Using two-dimensional agarose gel electrophoresis, we show that when double-strand breaks are formed in the absence of RuvAB, 4-way DNA (Holliday) junctions are accumulated in a RecG-dependent manner, arguing against the long-standing view that the redundancy of RuvAB and RecG is in the resolution of Holliday junctions. Using pulsed-field gel electrophoresis, we explain the redundancy by showing that branch migration catalysed by RuvAB and RecG is required for stabilising the intermediates of repair as, when branch migration cannot take place, repair is aborted and DNA is lost at the break locus. We demonstrate that in the repair of correctly aligned sister chromosomes, an unstable early intermediate is stabilised by branch migration. This reliance on branch migration may have evolved to help promote recombination between correctly aligned sister chromosomes to prevent genomic rearrangements. Genetic recombination is critically important for the repair of DNA double-strand breaks and is the only repair mechanism available to the bacterium Escherichia coli. Repair requires that the appropriate location on an unbroken sister chromosome is recognised as a repair template, and this can be accomplished by a system that detects the presence of extensive DNA sequence identity. We show here that the two known branch migration activities of the cell, RuvAB and RecG, provide alternative mechanisms for stabilising early recombination intermediates. In their absence, broken DNA is extensively degraded at the site of the break consistent with abortion of recombination. It has previously been proposed that RuvABC and RecG can substitute for each other in the resolution of four-way Holliday junctions, whereas we show that they play a synergistic role in the formations of these junctions. Our results demonstrate that branch migration provides a mechanism capable of stabilising recombination intermediates when extensive DNA sequence homology is available, a reaction that may contribute to ensuring that repair occurs at an appropriate location on a sister chromosome.
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Affiliation(s)
- Julia S. P. Mawer
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Kings Buildings, Edinburgh, United Kingdom
| | - David R. F. Leach
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Kings Buildings, Edinburgh, United Kingdom
- * E-mail:
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19
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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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20
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Cañas C, Suzuki Y, Marchisone C, Carrasco B, Freire-Benéitez V, Takeyasu K, Alonso JC, Ayora S. Interaction of branch migration translocases with the Holliday junction-resolving enzyme and their implications in Holliday junction resolution. J Biol Chem 2014; 289:17634-46. [PMID: 24770420 DOI: 10.1074/jbc.m114.552794] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Double-strand break repair involves the formation of Holliday junction (HJ) structures that need to be resolved to promote correct replication and chromosomal segregation. The molecular mechanisms of HJ branch migration and/or resolution are poorly characterized in Firmicutes. Genetic evidence suggested that the absence of the RuvAB branch migration translocase and the RecU HJ resolvase is synthetically lethal in Bacillus subtilis, whereas a recU recG mutant was viable. In vitro RecU, which is restricted to bacteria of the Firmicutes phylum, binds HJs with high affinity. In this work we found that RecU does not bind simultaneously with RecG to a HJ. RuvB by interacting with RecU bound to the central region of HJ DNA, loses its nonspecific association with DNA, and re-localizes with RecU to form a ternary complex. RecU cannot stimulate the ATPase or branch migration activity of RuvB. The presence of RuvB·ATPγS greatly stimulates RecU-mediated HJ resolution, but the addition of ATP or RuvA abolishes this stimulatory effect. A RecU·HJ·RuvAB complex might be formed. RecU does not increase the RuvAB activities but slightly inhibits them.
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Affiliation(s)
- Cristina Cañas
- From the Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Departamento de Biotecnología Microbiana, 28049 Madrid, Spain and
| | - Yuki Suzuki
- Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Chiara Marchisone
- From the Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Departamento de Biotecnología Microbiana, 28049 Madrid, Spain and
| | - Begoña Carrasco
- From the Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Departamento de Biotecnología Microbiana, 28049 Madrid, Spain and
| | - Verónica Freire-Benéitez
- From the Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Departamento de Biotecnología Microbiana, 28049 Madrid, Spain and
| | - Kunio Takeyasu
- Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Juan C Alonso
- From the Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Departamento de Biotecnología Microbiana, 28049 Madrid, Spain and
| | - Silvia Ayora
- From the Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Departamento de Biotecnología Microbiana, 28049 Madrid, Spain and
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21
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Zegeye ED, Balasingham SV, Laerdahl JK, Homberset H, Kristiansen PE, Tønjum T. Effects of conserved residues and naturally occurring mutations on Mycobacterium tuberculosis RecG helicase activity. MICROBIOLOGY-SGM 2013; 160:217-227. [PMID: 24169816 DOI: 10.1099/mic.0.072140-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
RecG is a helicase that is conserved in nearly all bacterial species. The prototypical Escherichia coli RecG promotes regression of stalled replication forks, participates in DNA recombination and DNA repair, and prevents aberrant replication. Mycobacterium tuberculosis RecG (RecGMtb) is a DNA-dependent ATPase that unwinds a variety of DNA substrates, although its preferred substrate is a Holliday junction. Here, we performed site-directed mutagenesis of selected residues in the wedge domain and motifs Q, I, Ib and VI of RecGMtb. Three of the 10 substitution mutations engineered were detected previously as naturally occurring SNPs in the gene encoding RecGMtb. Alanine substitution mutations at residues Q292, F286, K321 and R627 abolished the RecGMtb unwinding activity, whilst RecGMtb F99A, P285S and T408A mutants exhibited ~25-50 % lower unwinding activity than WT. We also found that RecGMtb bound ATP in the absence of a DNA cofactor.
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Affiliation(s)
- Ephrem Debebe Zegeye
- Centre for Molecular Biology and Neuroscience and Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway.,Centre for Molecular Biology and Neuroscience and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Seetha V Balasingham
- Centre for Molecular Biology and Neuroscience and Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway.,Centre for Molecular Biology and Neuroscience and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Jon K Laerdahl
- Bioinformatics Core Facility, Department of Informatics, University of Oslo, Oslo, Norway.,Centre for Molecular Biology and Neuroscience and Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway.,Centre for Molecular Biology and Neuroscience and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Håvard Homberset
- Centre for Molecular Biology and Neuroscience and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Per E Kristiansen
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
| | - Tone Tønjum
- Centre for Molecular Biology and Neuroscience and Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway.,Centre for Molecular Biology and Neuroscience and Department of Microbiology, University of Oslo, Oslo, Norway
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