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Petropoulos V, Uboldi L, Maiuri M, Cerullo G, Martinez-Fernandez L, Balanikas E, Markovitsi D. Effect of the DNA Polarity on the Relaxation of Its Electronic Excited States. J Phys Chem Lett 2023; 14:10219-10224. [PMID: 37931204 DOI: 10.1021/acs.jpclett.3c02580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
The DNA polarity, i.e., the order in which nucleobases are connected together via the phosphodiester backbone, is crucial for several biological processes. But, so far, there has not been experimental evidence regarding its effect on the relaxation of DNA electronic excited states. Here we examine this aspect for two dinucleotides containing adenine and guanine: 5'-dApdG-3' and 5'-dGpdA-3' in water. We used two different femtosecond transient absorption setups: one providing high temporal resolution and broad spectral coverage (330-650 nm) between 30 fs and 50 ps, and the other recording decays at selected wavelengths until 1.2 ns. The transient absorption spectra corresponding to the minima in the potential energy surface of the first excited state were computed by quantum chemistry methods. Our results show that the excited charge transfer state in 5'-dGpdA-3' is formed with a ∼75% higher quantum yield and exhibits slower decay (170 ± 10 ps vs 112 ± 12 ps) compared to 5'-dApdG-3'.
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Affiliation(s)
- Vasilis Petropoulos
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Lorenzo Uboldi
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Margherita Maiuri
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Giulio Cerullo
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemical Sciences (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Evangelos Balanikas
- Department of Physical Chemistry, University of Geneva, CH-1211 Geneva-4, Switzerland
| | - Dimitra Markovitsi
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
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2
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Matern WM, Harris HT, Danchik C, McDonald M, Patel G, Srivastava A, Ioerger TR, Bader JS, Karakousis PC. Functional Whole Genome Screen of Nutrient-Starved Mycobacterium tuberculosis Identifies Genes Involved in Rifampin Tolerance. Microorganisms 2023; 11:2269. [PMID: 37764112 PMCID: PMC10534295 DOI: 10.3390/microorganisms11092269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), poses a global health challenge and is responsible for over a million deaths each year. Current treatment is lengthy and complex, and new, abbreviated regimens are urgently needed. Mtb adapts to nutrient starvation, a condition experienced during host infection, by shifting its metabolism and becoming tolerant to the killing activity of bactericidal antibiotics. An improved understanding of the mechanisms mediating antibiotic tolerance in Mtb can serve as the basis for developing more effective therapies. We performed a forward genetic screen to identify candidate Mtb genes involved in tolerance to the two key first-line antibiotics, rifampin and isoniazid, under nutrient-rich and nutrient-starved conditions. In nutrient-rich conditions, we found 220 mutants with differential antibiotic susceptibility (218 in the rifampin screen and 2 in the isoniazid screen). Following Mtb adaptation to nutrient starvation, 82 mutants showed differential antibiotic susceptibility (80 in the rifampin screen and 2 in the isoniazid screen). Using targeted mutagenesis, we validated the rifampin-hypersusceptible phenotype under nutrient starvation in Mtb mutants lacking the following genes: ercc3, moeA1, rv0049, and rv2179c. These findings shed light on potential therapeutic targets, which could help shorten the duration and complexity of antitubercular regimens.
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Affiliation(s)
- William M. Matern
- Department of Biomedical Engineering, Institute for Computational Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA; (W.M.M.)
- Center for Systems Approaches to Infectious Diseases (C-SAID), School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA; (H.T.H.)
- Tuberculosis Research Advancement Center, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Harley T. Harris
- Center for Systems Approaches to Infectious Diseases (C-SAID), School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA; (H.T.H.)
- Tuberculosis Research Advancement Center, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Carina Danchik
- Center for Systems Approaches to Infectious Diseases (C-SAID), School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA; (H.T.H.)
- Tuberculosis Research Advancement Center, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Marissa McDonald
- Center for Systems Approaches to Infectious Diseases (C-SAID), School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA; (H.T.H.)
- Tuberculosis Research Advancement Center, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Gopi Patel
- Center for Systems Approaches to Infectious Diseases (C-SAID), School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA; (H.T.H.)
- Tuberculosis Research Advancement Center, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Aashish Srivastava
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA;
| | - Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Joel S. Bader
- Department of Biomedical Engineering, Institute for Computational Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA; (W.M.M.)
- Center for Systems Approaches to Infectious Diseases (C-SAID), School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA; (H.T.H.)
| | - Petros C. Karakousis
- Center for Systems Approaches to Infectious Diseases (C-SAID), School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA; (H.T.H.)
- Tuberculosis Research Advancement Center, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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3
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Matern WM, Harris HT, Danchik C, McDonald M, Patel G, Srivastava A, Ioerger TR, Bader JS, Karakousis PC. Functional whole genome screen of nutrient-starved Mycobacterium tuberculosis identifies genes involved in antibiotic tolerance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536593. [PMID: 37090629 PMCID: PMC10120713 DOI: 10.1101/2023.04.12.536593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Mycobacterium tuberculosis ( Mtb ), the causative agent of tuberculosis (TB), poses a global health challenge and is responsible for over a million deaths each year. Current treatment is lengthy and complex, and new, abbreviated regimens are urgently needed. Mtb adapts to nutrient starvation, a condition experienced during host infection, by shifting its metabolism and becoming tolerant to the killing activity of bactericidal antibiotics. An improved understanding of the mechanisms mediating antibiotic tolerance in Mtb can serve as the basis for developing more effective therapies. We performed a forward genetic screen to identify candidate Mtb genes involved in tolerance to the two key first-line antibiotics, rifampin and isoniazid, under nutrient-rich and nutrient-starved conditions. In nutrient-rich conditions, we found 220 mutants with differential antibiotic susceptibility (218 in the rifampin screen and 2 in the isoniazid screen). Following Mtb adaptation to nutrient starvation, 82 mutants showed differential antibiotic susceptibility (80 in the rifampin screen and 2 in the isoniazid screen). Using targeted mutagenesis, we validated the rifampin-hypersusceptible phenotype under nutrient starvation in Mtb mutants lacking the following genes: ercc3 , moeA1 , rv0049 , and rv2179c . These findings shed light on potential therapeutic targets, which could help shorten the duration and complexity of antitubercular regimens. Importance Treatment of Mtb infection requires a long course of combination antibiotics, likely due to subpopulations of tolerant bacteria exhibiting decreased susceptibility to antibiotics. Identifying and characterizing the genetic pathways involved in antibiotic tolerance is expected to yield therapeutic targets for the development of novel TB treatment-shortening regimens.
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Kapoor I, Shaw A, Naha A, Emam EAF, Varshney U. Role of the nucleotide excision repair pathway proteins (UvrB and UvrD2) in recycling UdgB, a base excision repair enzyme in Mycobacterium smegmatis. DNA Repair (Amst) 2022; 113:103316. [PMID: 35306347 DOI: 10.1016/j.dnarep.2022.103316] [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: 10/19/2021] [Revised: 01/30/2022] [Accepted: 03/02/2022] [Indexed: 11/24/2022]
Abstract
Cross-talks between DNA repair pathways are emerging as a crucial strategy in the maintenance of the genomic integrity. A double-stranded (ds) DNA specific DNA glycosylase, UdgB is known to excise uracil, hypoxanthine and ethenocytosine. We earlier showed that Mycobacterium smegmatis (Msm) UdgB stays back on the AP-sites it generates in the DNA upon excision of the damaged bases. Here, we show that in an Msm strain deleted for a nucleotide excision repair (NER) protein, UvrB (uvrB-), UdgB expression is toxic, and its deletion from the genome (udgB-) rescues the strain from the genotoxic stress. However, UdgB bound AP-site is not a direct substrate for NER in vitro. We show that UvrD2 and UvrB, known helicases with single-stranded (ss) DNA translocase activity, facilitate recycling of UdgB from AP-DNA. Our studies reveal that the helicases play an important role in exposing the AP-sites in DNA and make them available for further repair.
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Affiliation(s)
- Indu Kapoor
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Abhirup Shaw
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Arindam Naha
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Elhassan Ali Fathi Emam
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - 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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5
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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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6
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Ejaz A, Ordonez H, Jacewicz A, Ferrao R, Shuman S. Structure of mycobacterial 3'-to-5' RNA:DNA helicase Lhr bound to a ssDNA tracking strand highlights distinctive features of a novel family of bacterial helicases. Nucleic Acids Res 2019; 46:442-455. [PMID: 29165676 PMCID: PMC5758891 DOI: 10.1093/nar/gkx1163] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 11/06/2017] [Indexed: 01/17/2023] Open
Abstract
Mycobacterial Lhr is a DNA damage-inducible superfamily 2 helicase that uses adenosine triphosphate (ATP) hydrolysis to drive unidirectional 3′-to-5′ translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes en route. ATPase, translocase and helicase activities are encompassed within the N-terminal 856-amino acid segment. The crystal structure of Lhr-(1–856) in complex with AMPPNP•Mg2+ and ssDNA defines a new helicase family. The enzyme comprises two N-terminal RecA-like modules, a winged helix (WH) domain and a unique C-terminal domain. The 3′ ssDNA end binds in a crescent-shaped groove at the interface between the first RecA domain and the WH domain and tracks 5′ into a groove between the second RecA and C domains. A kissing interaction between the second RecA and C domains forms an aperture that demarcates a putative junction between the loading strand tail and the duplex, with the first duplex nucleoside bookended by stacking on Trp597. Intercalation of Ile528 between nucleosides of the loading strand creates another bookend. Coupling of ATP hydrolysis to RNA:DNA unwinding is dependent on Trp597 and Ile528, and on Thr145 and Arg279 that contact phosphates of the loading strand. The structural and functional data suggest a ratchet mechanism of translocation and unwinding coupled to ATP-driven domain movements.
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Affiliation(s)
- Anam Ejaz
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Heather Ordonez
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Agata Jacewicz
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ryan Ferrao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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Sandoz J, Nagy Z, Catez P, Caliskan G, Geny S, Renaud JB, Concordet JP, Poterszman A, Tora L, Egly JM, Le May N, Coin F. Functional interplay between TFIIH and KAT2A regulates higher-order chromatin structure and class II gene expression. Nat Commun 2019; 10:1288. [PMID: 30894545 PMCID: PMC6426930 DOI: 10.1038/s41467-019-09270-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 03/01/2019] [Indexed: 12/21/2022] Open
Abstract
The TFIIH subunit XPB is involved in combined Xeroderma Pigmentosum and Cockayne syndrome (XP-B/CS). Our analyses reveal that XPB interacts functionally with KAT2A, a histone acetyltransferase (HAT) that belongs to the hSAGA and hATAC complexes. XPB interacts with KAT2A-containing complexes on chromatin and an XP-B/CS mutation specifically elicits KAT2A-mediated large-scale chromatin decondensation. In XP-B/CS cells, the abnormal recruitment of TFIIH and KAT2A to chromatin causes inappropriate acetylation of histone H3K9, leading to aberrant formation of transcription initiation complexes on the promoters of several hundred genes and their subsequent overexpression. Significantly, this cascade of events is similarly sensitive to KAT2A HAT inhibition or to the rescue with wild-type XPB. In agreement, the XP-B/CS mutation increases KAT2A HAT activity in vitro. Our results unveil a tight connection between TFIIH and KAT2A that controls higher-order chromatin structure and gene expression and provide new insights into transcriptional misregulation in a cancer-prone DNA repair-deficient disorder.
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Affiliation(s)
- Jérémy Sandoz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Zita Nagy
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Philippe Catez
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Gizem Caliskan
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Sylvain Geny
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Muséum national d'Histoire naturelle, 43 rue Cuvier, 75005, Paris, France
| | - Jean-Baptiste Renaud
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Muséum national d'Histoire naturelle, 43 rue Cuvier, 75005, Paris, France
| | - Jean-Paul Concordet
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Muséum national d'Histoire naturelle, 43 rue Cuvier, 75005, Paris, France
| | - Arnaud Poterszman
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Laszlo Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Jean-Marc Egly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Nicolas Le May
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Frédéric Coin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France.
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France.
- Université de Strasbourg, 67404, Illkirch, France.
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Greber BJ, Toso DB, Fang J, Nogales E. The complete structure of the human TFIIH core complex. eLife 2019; 8:e44771. [PMID: 30860024 PMCID: PMC6422496 DOI: 10.7554/elife.44771] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 03/03/2019] [Indexed: 01/26/2023] Open
Abstract
Transcription factor IIH (TFIIH) is a heterodecameric protein complex critical for transcription initiation by RNA polymerase II and nucleotide excision DNA repair. The TFIIH core complex is sufficient for its repair functions and harbors the XPB and XPD DNA-dependent ATPase/helicase subunits, which are affected by human disease mutations. Transcription initiation additionally requires the CdK activating kinase subcomplex. Previous structural work has provided only partial insight into the architecture of TFIIH and its interactions within transcription pre-initiation complexes. Here, we present the complete structure of the human TFIIH core complex, determined by phase-plate cryo-electron microscopy at 3.7 Å resolution. The structure uncovers the molecular basis of TFIIH assembly, revealing how the recruitment of XPB by p52 depends on a pseudo-symmetric dimer of homologous domains in these two proteins. The structure also suggests a function for p62 in the regulation of XPD, and allows the mapping of previously unresolved human disease mutations.
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Affiliation(s)
- Basil J Greber
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyUnited States
- Molecular Biophysics and Integrative Bio-Imaging DivisionLawrence Berkeley National LaboratoryBerkeleyUnited States
| | - Daniel B Toso
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyUnited States
| | - Jie Fang
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyUnited States
| | - Eva Nogales
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyUnited States
- Molecular Biophysics and Integrative Bio-Imaging DivisionLawrence Berkeley National LaboratoryBerkeleyUnited States
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyUnited States
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyUnited States
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9
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Kolesnikova O, Radu L, Poterszman A. TFIIH: A multi-subunit complex at the cross-roads of transcription and DNA repair. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 115:21-67. [PMID: 30798933 DOI: 10.1016/bs.apcsb.2019.01.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Transcription factor IIH (TFIIH) is a multiprotein complex involved in both eukaryotic transcription and DNA repair, revealing a tight connection between these two processes. Composed of 10 subunits, it can be resolved into a 7-subunits core complex with the XPB translocase and the XPD helicase, and the 3-subunits kinase complex CAK, which also exists as a free complex with a distinct function. Initially identified as basal transcription factor, TFIIH also participates in transcription regulation and plays a key role in nucleotide excision repair (NER) for opening DNA at damaged sites, lesion verification and recruitment of additional repair factors. Our understanding of TFIIH function in eukaryotic cells has greatly benefited from studies of the genetic rare diseases xeroderma pigmentosum (XP), Cockayne syndrome (CS) and trichothiodystrophy (TTD), that are not only characterized by cancer and aging predispositions but also by neurological and developmental defects. Although much remains unknown about TFIIH function, significant progresses have been done regarding the structure of the complex, the functions of its catalytic subunits and the multiple roles of the regulatory core-TFIIH subunits. This review provides a non-exhaustive survey of key discoveries on the structure and function of this pivotal factor, which can be considered as a promising target for therapeutic strategies.
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Affiliation(s)
- Olga Kolesnikova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Laura Radu
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Arnaud Poterszman
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France.
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10
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Frye SA, Beyene GT, Namouchi A, Gómez-Muñoz M, Homberset H, Kalayou S, Riaz T, Tønjum T, Balasingham SV. The helicase DinG responds to stress due to DNA double strand breaks. PLoS One 2017; 12:e0187900. [PMID: 29121674 PMCID: PMC5679670 DOI: 10.1371/journal.pone.0187900] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 10/27/2017] [Indexed: 12/20/2022] Open
Abstract
Neisseria meningitidis (Nm) is a Gram-negative nasopharyngeal commensal that can cause septicaemia and meningitis. The neisserial DNA damage-inducible protein DinG is a helicase related to the mammalian helicases XPD and FANCJ. These helicases belong to superfamily 2, are ATP dependent and exert 5′ → 3′ directionality. To better understand the role of DinG in neisserial genome maintenance, the Nm DinG (DinGNm) enzymatic activities were assessed in vitro and phenotypical characterization of a dinG null mutant (NmΔdinG) was performed. Like its homologues, DinGNm possesses 5′ → 3′ directionality and prefers DNA substrates containing a 5′-overhang. ATPase activity of DinGNm is strictly DNA-dependent and DNA unwinding activity requires nucleoside triphosphate and divalent metal cations. DinGNm directly binds SSBNm with a Kd of 313 nM. Genotoxic stress analysis demonstrated that NmΔdinG was more sensitive to double-strand DNA breaks (DSB) induced by mitomycin C (MMC) than the Nm wildtype, defining the role of neisserial DinG in DSB repair. Notably, when NmΔdinG cells grown under MMC stress assessed by quantitative mass spectrometry, 134 proteins were shown to be differentially abundant (DA) compared to unstressed NmΔdinG cells. Among the DNA replication, repair and recombination proteins affected, polymerase III subunits and recombinational repair proteins RuvA, RuvB, RecB and RecD were significantly down regulated while TopA and SSB were upregulated under stress condition. Most of the other DA proteins detected are involved in metabolic functions. The present study shows that the helicase DinG is probably involved in regulating metabolic pathways as well as in genome maintenance.
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Affiliation(s)
- Stephan A. Frye
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
- * E-mail: (SVB); (SAF)
| | | | - Amine Namouchi
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | | | | | - Shewit Kalayou
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Tahira Riaz
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
- Department of Microbiology, University of Oslo, Oslo, Norway
| | - Seetha V. Balasingham
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
- * E-mail: (SVB); (SAF)
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11
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Hovland E, Beyene GT, Frye SA, Homberset H, Balasingham SV, Gómez-Muñoz M, Derrick JP, Tønjum T, Ambur OH. DprA from Neisseria meningitidis: properties and role in natural competence for transformation. MICROBIOLOGY-SGM 2017; 163:1016-1029. [PMID: 28696187 PMCID: PMC5817196 DOI: 10.1099/mic.0.000489] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
DNA processing chain A (DprA) is a DNA-binding protein that is ubiquitous in bacteria and expressed in some archaea. DprA is active in many bacterial species that are competent for transformation of DNA, but its role in Neisseriameningitidis (Nm) is not well characterized. An Nm mutant lacking DprA was constructed, and the phenotypes of the wild-type and ΔdprA mutant were compared. The salient feature of the phenotype of dprA null cells is the total lack of competence for genetic transformation shown by all of the donor DNA substrates tested in this study. Here, Nm wild-type and dprA null cells appeared to be equally resistant to genotoxic stress. The gene encoding DprANm was cloned and overexpressed, and the biological activities of DprANm were further investigated. DprANm binds ssDNA more strongly than dsDNA, but lacks DNA uptake sequence-specific DNA binding. DprANm dimerization and interaction with the C-terminal part of the single-stranded binding protein SSBNmwere demonstrated. dprA is co-expressed with smg, a downstream gene of unknown function, and the gene encoding topoisomerase 1, topA.
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Affiliation(s)
- Eirik Hovland
- Department of Microbiology, University of Oslo, Oslo, Norway.,Present address: Lovisenberg Diaconal Hospital, Oslo, Norway
| | | | - Stephan A Frye
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | | | | | | | - Jeremy P Derrick
- Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester, UK
| | - Tone Tønjum
- Department of Microbiology, Oslo University Hospital, Oslo, Norway.,Department of Microbiology, University of Oslo, Oslo, Norway
| | - Ole H Ambur
- Department of Microbiology, Oslo University Hospital, Oslo, Norway.,Present address: Department of Life Sciences and Health, Oslo and Akershus University College of Applied Sciences, Norway
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12
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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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13
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Identification of in vivo-induced bacterial protein antigens during calf infection with Chlamydia psittaci. Int J Med Microbiol 2015; 305:310-21. [DOI: 10.1016/j.ijmm.2014.12.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 11/19/2014] [Accepted: 12/20/2014] [Indexed: 01/21/2023] Open
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14
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Fan L, DuPrez KT. XPB: An unconventional SF2 DNA helicase. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 117:174-181. [PMID: 25641424 DOI: 10.1016/j.pbiomolbio.2014.12.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 12/24/2014] [Accepted: 12/29/2014] [Indexed: 11/27/2022]
Abstract
XPB is a 3'-5' DNA helicase belonging to the superfamily 2 (SF2) of helicases. XPB is an essential core subunit of the eukaryotic basal transcription factor complex TFIIH which plays a dual role in transcription and DNA repair: 1) to facilitate the melting of the promoter during the initiation of RNA polymerase II transcription; 2) to unwind double stranded DNA (dsDNA) around a DNA lesion during nucleotide excision repair (NER). NER is a highly versatile DNA repair process which is able to remove a broad spectrum of structurally unrelated DNA helix-distorting lesions. The importance of a fully functional XPB is clearly illustrated by the severe clinical consequences associated with inherited defects in XPB including UV-hypersensitive syndromes xeroderma pigmentosum (XP), Cockayne syndrome (CS), combined XP and CS (XP/CS), and trichothiodystrophy (TTD). Here we discuss the structure and function of XPB in NER as well as the impact of a disease mutation in XP11BE patients with XP/CS complex manifestations.
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Affiliation(s)
- Li Fan
- 900 University Ave, Biochemistry Department, University of California, Riverside, CA 92521, USA.
| | - Kevin T DuPrez
- 900 University Ave, Biochemistry Department, University of California, Riverside, CA 92521, USA
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15
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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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16
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Badjatia N, Nguyen TN, Lee JH, Günzl A. Trypanosoma brucei harbours a divergent XPB helicase paralogue that is specialized in nucleotide excision repair and conserved among kinetoplastid organisms. Mol Microbiol 2013; 90:1293-308. [PMID: 24134817 DOI: 10.1111/mmi.12435] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2013] [Indexed: 12/21/2022]
Abstract
Conserved from yeast to humans, TFIIH is essential for RNA polymerase II transcription and nucleotide excision repair (NER). TFIIH consists of a core that includes the DNA helicase Xeroderma pigmentosum B (XPB) and a kinase subcomplex. Trypanosoma brucei TFIIH harbours all core complex components and is indispensable for RNA polymerase II transcription of spliced leader RNA genes (SLRNAs). Kinetoplastid organisms, however, possess two highly divergent XPB paralogues with only the larger being identified as a TFIIH subunit in T. brucei. Here we show that a knockout of the gene for the smaller paralogue, termed XPB-R (R for repair) resulted in viable cultured trypanosomes that grew slower than normal. XPB-R depletion did not affect transcription in vivo or in vitro and XPB-R was not found to occupy the SLRNA promoter which assembles a RNA polymerase II transcription pre-initiation complex including TFIIH. However, XPB-R(-/-) cells were much less tolerant than wild-type cells to UV light- and cisplatin-induced DNA damage, which require NER. Since XPB-R(-/-) cells were not impaired in DNA base excision repair, XPB-R appears to function specifically in NER. Interestingly, several other protists possess highly divergent XPB paralogues suggesting that XPBs specialized in transcription or NER exist beyond the Kinetoplastida.
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Affiliation(s)
- Nitika Badjatia
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT, 06030-6403, USA
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17
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Ordonez H, Shuman S. Mycobacterium smegmatis Lhr Is a DNA-dependent ATPase and a 3'-to-5' DNA translocase and helicase that prefers to unwind 3'-tailed RNA:DNA hybrids. J Biol Chem 2013; 288:14125-14134. [PMID: 23549043 DOI: 10.1074/jbc.m113.466854] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We are interested in the distinctive roster of helicases of Mycobacterium, a genus of the phylum Actinobacteria that includes the human pathogen Mycobacterium tuberculosis and its avirulent relative Mycobacterium smegmatis. Here, we identify and characterize M. smegmatis Lhr as the exemplar of a novel clade of superfamily II helicases, by virtue of its biochemical specificities and signature domain organization. Lhr is a 1507-amino acid monomeric nucleic acid-dependent ATPase that uses the energy of ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single strand DNA and to unwind duplexes en route. The ATPase is more active in the presence of calcium than magnesium. ATP hydrolysis is triggered by either single strand DNA or single strand RNA, yet the apparent affinity for a DNA activator is 11-fold higher than for an RNA strand of identical size and nucleobase sequence. Lhr is 8-fold better at unwinding an RNA:DNA hybrid than it is at displacing a DNA:DNA duplex of identical nucleobase sequence. The truncated derivative Lhr-(1-856) is an autonomous ATPase, 3'-to-5' translocase, and RNA:DNA helicase. Lhr-(1-856) is 100-fold better RNA:DNA helicase than DNA:DNA helicase. Lhr homologs are found in bacteria representing eight different phyla, being especially prevalent in Actinobacteria (including M. tuberculosis) and Proteobacteria (including Escherichia coli).
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Affiliation(s)
- Heather Ordonez
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065.
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18
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Abstract
Fundamental aspects of the lifestyle of Mycobacterium tuberculosis implicate DNA metabolism in bacillary survival and adaptive evolution. The environments encountered by M. tuberculosis during successive cycles of infection and transmission are genotoxic. Moreover, as an obligate pathogen, M. tuberculosis has the ability to persist for extended periods in a subclinical state, suggesting that active DNA repair is critical to maintain genome integrity and bacterial viability during prolonged infection. In this chapter, we provide an overview of the major DNA metabolic pathways identified in M. tuberculosis, and situate key recent findings within the context of mycobacterial pathogenesis. Unlike many other bacterial pathogens, M. tuberculosis is genetically secluded, and appears to rely solely on chromosomal mutagenesis to drive its microevolution within the human host. In turn, this implies that a balance between high versus relaxed fidelity mechanisms of DNA metabolism ensures the maintenance of genome integrity, while accommodating the evolutionary imperative to adapt to hostile and fluctuating environments. The inferred relationship between mycobacterial DNA repair and genome dynamics is considered in the light of emerging data from whole-genome sequencing studies of clinical M. tuberculosis isolates which have revealed the potential for considerable heterogeneity within and between different bacterial and host populations.
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19
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Unwinding and rewinding: double faces of helicase? J Nucleic Acids 2012; 2012:140601. [PMID: 22888405 PMCID: PMC3409536 DOI: 10.1155/2012/140601] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 05/28/2012] [Indexed: 12/29/2022] Open
Abstract
Helicases are enzymes that use ATP-driven motor force to unwind double-stranded DNA or RNA. Recently, increasing evidence demonstrates that some helicases also possess rewinding activity—in other words, they can anneal two complementary single-stranded nucleic acids. All five members of the human RecQ helicase family, helicase PIF1, mitochondrial helicase TWINKLE, and helicase/nuclease Dna2 have been shown to possess strand-annealing activity. Moreover, two recently identified helicases—HARP and AH2 have only ATP-dependent rewinding activity. These findings not only enhance our understanding of helicase enzymes but also establish the presence of a new type of protein: annealing helicases. This paper discusses what is known about these helicases, focusing on their biochemical activity to zip and unzip double-stranded DNA and/or RNA, their possible regulation mechanisms, and biological functions.
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20
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Zegeye ED, Balasingham SV, Laerdahl JK, Homberset H, Tønjum T. Mycobacterium tuberculosis RecG binds and unwinds model DNA substrates with a preference for Holliday junctions. MICROBIOLOGY-SGM 2012; 158:1982-1993. [PMID: 22628485 PMCID: PMC3542137 DOI: 10.1099/mic.0.058693-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The RecG enzyme, a superfamily 2 helicase, is present in nearly all bacteria. Here we report for the first time that the recG gene is also present in the genomes of most vascular plants as well as in green algae, but is not found in other eukaryotes or archaea. The precise function of RecG is poorly understood, although ample evidence shows that it plays critical roles in DNA repair, recombination and replication. We further demonstrate that Mycobacterium tuberculosis RecG (RecGMtb) DNA binding activity had a broad substrate specificity, whereas it only unwound branched-DNA substrates such as Holliday junctions (HJs), replication forks, D-loops and R-loops, with a strong preference for the HJ as a helicase substrate. In addition, RecGMtb preferentially bound relatively long (≥40 nt) ssDNA, exhibiting a higher affinity for the homopolymeric nucleotides poly(dT), poly(dG) and poly(dC) than for poly(dA). RecGMtb helicase activity was supported by hydrolysis of ATP or dATP in the presence of Mg2+, Mn2+, Cu2+ or Fe2+. Like its Escherichia coli orthologue, RecGMtb is also a strictly DNA-dependent ATPase.
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Affiliation(s)
- Ephrem Debebe Zegeye
- Centre for Molecular Biology and Neuroscience and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Seetha V Balasingham
- 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.,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
| | - Tone Tønjum
- 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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