1
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Łazowski K, Woodgate R, Fijalkowska IJ. Escherichia coli DNA replication: the old model organism still holds many surprises. FEMS Microbiol Rev 2024; 48:fuae018. [PMID: 38982189 PMCID: PMC11253446 DOI: 10.1093/femsre/fuae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/26/2024] [Accepted: 07/08/2024] [Indexed: 07/11/2024] Open
Abstract
Research on Escherichia coli DNA replication paved the groundwork for many breakthrough discoveries with important implications for our understanding of human molecular biology, due to the high level of conservation of key molecular processes involved. To this day, it attracts a lot of attention, partially by virtue of being an important model organism, but also because the understanding of factors influencing replication fidelity might be important for studies on the emergence of antibiotic resistance. Importantly, the wide access to high-resolution single-molecule and live-cell imaging, whole genome sequencing, and cryo-electron microscopy techniques, which were greatly popularized in the last decade, allows us to revisit certain assumptions about the replisomes and offers very detailed insight into how they work. For many parts of the replisome, step-by-step mechanisms have been reconstituted, and some new players identified. This review summarizes the latest developments in the area, focusing on (a) the structure of the replisome and mechanisms of action of its components, (b) organization of replisome transactions and repair, (c) replisome dynamics, and (d) factors influencing the base and sugar fidelity of DNA synthesis.
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Affiliation(s)
- Krystian Łazowski
- Laboratory of DNA Replication and Genome Stability, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, United States
| | - Iwona J Fijalkowska
- Laboratory of DNA Replication and Genome Stability, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
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2
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Tsao N, Ashour ME, Mosammaparast N. How RNA impacts DNA repair. DNA Repair (Amst) 2023; 131:103564. [PMID: 37776841 PMCID: PMC11232704 DOI: 10.1016/j.dnarep.2023.103564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 10/02/2023]
Abstract
The central dogma of molecular biology posits that genetic information flows unidirectionally, from DNA, to RNA, and finally to protein. However, this directionality is broken in some cases, such as reverse transcription where RNA is converted to DNA by retroviruses and certain transposable elements. Our genomes have evolved and adapted to the presence of reverse transcription. Similarly, our genome is continuously maintained by several repair pathways to reverse damage due to various endogenous and exogenous sources. More recently, evidence has revealed that RNA, while in certain contexts may be detrimental for genome stability, is involved in promoting certain types of DNA repair. Depending on the pathway in question, the size of these DNA repair-associated RNAs range from one or a few ribonucleotides to long fragments of RNA. Moreover, RNA is highly modified, and RNA modifications have been revealed to be functionally associated with specific DNA repair pathways. In this review, we highlight aspects of this unexpected layer of genomic maintenance, demonstrating how RNA may influence DNA integrity.
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Affiliation(s)
- Ning Tsao
- Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Mohamed E Ashour
- Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nima Mosammaparast
- Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA.
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3
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Schroeder JW, Hurto RL, Randall JR, Wozniak KJ, Timko TA, Nye TM, Wang JD, Freddolino PL, Simmons LA. RNase H genes cause distinct impacts on RNA:DNA hybrid formation and mutagenesis genome wide. SCIENCE ADVANCES 2023; 9:eadi5945. [PMID: 37494439 PMCID: PMC10371020 DOI: 10.1126/sciadv.adi5945] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 06/23/2023] [Indexed: 07/28/2023]
Abstract
RNA:DNA hybrids compromise replication fork progression and genome integrity in all cells. The overall impacts of naturally occurring RNA:DNA hybrids on genome integrity, and the relative contributions of ribonucleases H to mitigating the negative effects of hybrids, remain unknown. Here, we investigate the contributions of RNases HII (RnhB) and HIII (RnhC) to hybrid removal, DNA replication, and mutagenesis genome wide. Deletion of either rnhB or rnhC triggers RNA:DNA hybrid accumulation but with distinct patterns of mutagenesis and hybrid accumulation. Across all cells, hybrids accumulate strongly in noncoding RNAs and 5'-UTRs of coding sequences. For ΔrnhB, hybrids accumulate preferentially in untranslated regions and early in coding sequences. We show that hybrid accumulation is particularly sensitive to gene expression in ΔrnhC cells. DNA replication in ΔrnhC cells is disrupted, leading to transversions and structural variation. Our results resolve the outstanding question of how hybrids in native genomic contexts cause mutagenesis and shape genome organization.
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Affiliation(s)
- Jeremy W. Schroeder
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Rebecca L. Hurto
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Justin R. Randall
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Katherine J. Wozniak
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Room 743E, Houston, TX 77030, USA
| | - Taylor A. Timko
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Taylor M. Nye
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jue D. Wang
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Peter L. Freddolino
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Lyle A. Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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4
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Hao Z, Gowder M, Proshkin S, Bharati BK, Epshtein V, Svetlov V, Shamovsky I, Nudler E. RNA polymerase drives ribonucleotide excision DNA repair in E. coli. Cell 2023; 186:2425-2437.e21. [PMID: 37196657 PMCID: PMC10515295 DOI: 10.1016/j.cell.2023.04.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/21/2022] [Accepted: 04/20/2023] [Indexed: 05/19/2023]
Abstract
Ribonuclease HII (RNaseHII) is the principal enzyme that removes misincorporated ribonucleoside monophosphates (rNMPs) from genomic DNA. Here, we present structural, biochemical, and genetic evidence demonstrating that ribonucleotide excision repair (RER) is directly coupled to transcription. Affinity pull-downs and mass-spectrometry-assisted mapping of in cellulo inter-protein cross-linking reveal the majority of RNaseHII molecules interacting with RNA polymerase (RNAP) in E. coli. Cryoelectron microscopy structures of RNaseHII bound to RNAP during elongation, with and without the target rNMP substrate, show specific protein-protein interactions that define the transcription-coupled RER (TC-RER) complex in engaged and unengaged states. The weakening of RNAP-RNaseHII interactions compromises RER in vivo. The structure-functional data support a model where RNaseHII scans DNA in one dimension in search for rNMPs while "riding" the RNAP. We further demonstrate that TC-RER accounts for a significant fraction of repair events, thereby establishing RNAP as a surveillance "vehicle" for detecting the most frequently occurring replication errors.
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Affiliation(s)
- Zhitai Hao
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Manjunath Gowder
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Sergey Proshkin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Binod K Bharati
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Vitaly Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Vladimir Svetlov
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ilya Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA.
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5
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Schroeder JW, Hurto RL, Randall JR, Wozniak KJ, Timko TA, Nye TM, Wang JD, Freddolino PL, Simmons LA. RNase H genes cause distinct impacts on RNA:DNA hybrid formation and mutagenesis genome-wide. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539860. [PMID: 37214986 PMCID: PMC10197577 DOI: 10.1101/2023.05.08.539860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
RNA:DNA hybrids such as R-loops affect genome integrity and DNA replication fork progression. The overall impacts of naturally occurring RNA:DNA hybrids on genome integrity, and the relative contributions of ribonucleases H to mitigating the negative effects of hybrids, remain unknown. Here, we investigate the contributions of RNases HII (RnhB) and HIII (RnhC) to hybrid removal, DNA replication, and mutagenesis genome-wide. Deletion of either rnhB or rnhC triggers RNA:DNA hybrid accumulation, but with distinct patterns of mutagenesis and hybrid accumulation. Across all cells, hybrids accumulate most strongly in non-coding RNAs and 5'-UTRs of coding sequences. For Δ rnhB , hybrids accumulate preferentially in untranslated regions and early in coding sequences. Hybrid accumulation is particularly sensitive to gene expression in Δ rnhC ; in cells lacking RnhC, DNA replication is disrupted leading to transversions and structural variation. Our results resolve the outstanding question of how hybrids in native genomic contexts interact with replication to cause mutagenesis and shape genome organization.
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Affiliation(s)
- Jeremy W. Schroeder
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI 53706
| | - Rebecca L. Hurto
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Justin R. Randall
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Katherine J. Wozniak
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Taylor A. Timko
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Taylor M. Nye
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
- Department of Molecular Microbiology and Center for Women’s Infectious Disease Research, Washington University School of Medicine, Saint Louis, MO 63110-1093, USA
| | - Jue D. Wang
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI 53706
| | - Peter L. Freddolino
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Lyle A. Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
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6
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Łazowski K, Faraz M, Vaisman A, Ashton NW, Jonczyk P, Fijalkowska IJ, Clausen AR, Woodgate R, Makiela-Dzbenska K. Strand specificity of ribonucleotide excision repair in Escherichia coli. Nucleic Acids Res 2023; 51:1766-1782. [PMID: 36762476 PMCID: PMC9976901 DOI: 10.1093/nar/gkad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/03/2023] [Accepted: 01/12/2023] [Indexed: 02/11/2023] Open
Abstract
In Escherichia coli, replication of both strands of genomic DNA is carried out by a single replicase-DNA polymerase III holoenzyme (pol III HE). However, in certain genetic backgrounds, the low-fidelity TLS polymerase, DNA polymerase V (pol V) gains access to undamaged genomic DNA where it promotes elevated levels of spontaneous mutagenesis preferentially on the lagging strand. We employed active site mutants of pol III (pol IIIα_S759N) and pol V (pol V_Y11A) to analyze ribonucleotide incorporation and removal from the E. coli chromosome on a genome-wide scale under conditions of normal replication, as well as SOS induction. Using a variety of methods tuned to the specific properties of these polymerases (analysis of lacI mutational spectra, lacZ reversion assay, HydEn-seq, alkaline gel electrophoresis), we present evidence that repair of ribonucleotides from both DNA strands in E. coli is unequal. While RNase HII plays a primary role in leading-strand Ribonucleotide Excision Repair (RER), the lagging strand is subject to other repair systems (RNase HI and under conditions of SOS activation also Nucleotide Excision Repair). Importantly, we suggest that RNase HI activity can also influence the repair of single ribonucleotides incorporated by the replicase pol III HE into the lagging strand.
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Affiliation(s)
- Krystian Łazowski
- Laboratory of DNA Replication and Genome Stability, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Mahmood Faraz
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Alexandra Vaisman
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
| | - Nicholas W Ashton
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
| | - Piotr Jonczyk
- Laboratory of DNA Replication and Genome Stability, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Iwona J Fijalkowska
- Laboratory of DNA Replication and Genome Stability, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Anders R Clausen
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
| | - Karolina Makiela-Dzbenska
- Laboratory of DNA Replication and Genome Stability, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
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7
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Nieto NS, Parrott EE, Nelson SW. Ribonucleotide Misincorporation and Reverse Transcriptase Activities of Plasmodium falciparum Apicoplast DNA Polymerase. Biochemistry 2022; 61:2742-2750. [DOI: 10.1021/acs.biochem.2c00450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nicholas S. Nieto
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa50011, United States
| | - Eric E. Parrott
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa50011, United States
| | - Scott W. Nelson
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa50011, United States
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8
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McLean EK, Nye TM, Lowder FC, Simmons LA. The Impact of RNA-DNA Hybrids on Genome Integrity in Bacteria. Annu Rev Microbiol 2022; 76:461-480. [PMID: 35655343 PMCID: PMC9527769 DOI: 10.1146/annurev-micro-102521-014450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2023]
Abstract
During the essential processes of DNA replication and transcription, RNA-DNA hybrid intermediates are formed that pose significant risks to genome integrity when left unresolved. To manage RNA-DNA hybrids, all cells rely on RNase H family enzymes that specifically cleave the RNA portion of the many different types of hybrids that form in vivo. Recent experimental advances have provided new insight into how RNA-DNA hybrids form and the consequences to genome integrity that ensue when persistent hybrids remain unresolved. Here we review the types of RNA-DNA hybrids, including R-loops, RNA primers, and ribonucleotide misincorporations, that form during DNA replication and transcription and discuss how each type of hybrid can contribute to genome instability in bacteria. Further, we discuss how bacterial RNase HI, HII, and HIII and bacterial FEN enzymes contribute to genome maintenance through the resolution of hybrids.
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Affiliation(s)
- Emma K McLean
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA;
| | - Taylor M Nye
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA;
- Current affiliation: Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Frances C Lowder
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA;
| | - Lyle A Simmons
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA;
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9
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Abstract
Bacteria are continuously exposed to numerous endogenous and exogenous DNA-damaging agents. To maintain genome integrity and ensure cell survival, bacteria have evolved several DNA repair pathways to correct different types of DNA damage and non-canonical bases, including strand breaks, nucleotide modifications, cross-links, mismatches and ribonucleotide incorporations. Recent advances in genome-wide screens, the availability of thousands of whole-genome sequences and advances in structural biology have enabled the rapid discovery and characterization of novel bacterial DNA repair pathways and new enzymatic activities. In this Review, we discuss recent advances in our understanding of base excision repair and nucleotide excision repair, and we discuss several new repair processes including the EndoMS mismatch correction pathway and the MrfAB excision repair system.
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Affiliation(s)
- Katherine J Wozniak
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lyle A Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
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10
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In vitro reconstitution of an efficient nucleotide excision repair system using mesophilic enzymes from Deinococcus radiodurans. Commun Biol 2022; 5:127. [PMID: 35149830 PMCID: PMC8837605 DOI: 10.1038/s42003-022-03064-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 01/18/2022] [Indexed: 11/08/2022] Open
Abstract
Nucleotide excision repair (NER) is a universal and versatile DNA repair pathway, capable of removing a very wide range of lesions, including UV-induced pyrimidine dimers and bulky adducts. In bacteria, NER involves the sequential action of the UvrA, UvrB and UvrC proteins to release a short 12- or 13-nucleotide DNA fragment containing the damaged site. Although bacterial NER has been the focus of numerous studies over the past 40 years, a number of key questions remain unanswered regarding the mechanisms underlying DNA damage recognition by UvrA, the handoff to UvrB and the site-specific incision by UvrC. In the present study, we have successfully reconstituted in vitro a robust NER system using the UvrABC proteins from the radiation resistant bacterium, Deinococcus radiodurans. We have investigated the influence of various parameters, including temperature, salt, protein and ATP concentrations, protein purity and metal cations, on the dual incision by UvrABC, so as to find the optimal conditions for the efficient release of the short lesion-containing oligonucleotide. This newly developed assay relying on the use of an original, doubly-labelled DNA substrate has allowed us to probe the kinetics of repair on different DNA substrates and to determine the order and precise sites of incisions on the 5′ and 3′ sides of the lesion. This new assay thus constitutes a valuable tool to further decipher the NER pathway in bacteria. Reconstitution of D radiodurans nucleotide excision repair provides insights into the kinetics of repair on different DNA substrates and determines the order and precise sites of incisions on the 5’ and 3’ sides of the lesion.
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11
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Campion C, Charbon G, Thomsen TT, Nielsen PE, Løbner-Olesen A. Antisense inhibition of the Escherichia coli NrdAB aerobic ribonucleotide reductase is bactericidal due to induction of DNA strand breaks. J Antimicrob Chemother 2021; 76:2802-2814. [PMID: 34450639 PMCID: PMC8521395 DOI: 10.1093/jac/dkab305] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/16/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Antisense peptide nucleic acids (PNAs) constitute an alternative to traditional antibiotics, by their ability to silence essential genes. OBJECTIVES To evaluate the antibacterial effects of antisense PNA-peptide conjugates that target the gene encoding the alpha subunit (NrdA) of the Escherichia coli ribonucleotide reductase (RNR). METHODS Bacterial susceptibility of a series of NrdA-targeting PNAs was studied by MIC determination and time-kill analysis. Western-blot analysis, gene complementation and synergy with hydroxyurea were employed to determine the efficiency of NrdA-PNA antisense treatment. The effect on chromosome replication was addressed by determining the DNA synthesis rate, by flow cytometry analysis, by quantitative PCR and by fluorescence microscopy. The use of DNA repair mutants provided insight into the bactericidal action of NrdA-PNA. RESULTS Treatment with NrdA-PNA specifically inhibited growth of E. coli, as well as NrdA protein translation at 4 μM. Also, the DNA synthesis rate was reduced, preventing completion of chromosome replication and resulting in formation of double-stranded DNA breaks and cell death. CONCLUSIONS These data present subunits of the NrdAB RNR as a target for future antisense microbial agents and provide insight into the bacterial physiological response to RNR-targeting antimicrobials.
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Affiliation(s)
- Christopher Campion
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, Center for Peptide-Based Antibiotics, The Panum Institute, University of Copenhagen, Blegdamsvej 3c, 2200 Copenhagen N, Denmark.,Department of Biology, Faculty of Science, Section for Functional Genomics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Godefroid Charbon
- Department of Biology, Faculty of Science, Section for Functional Genomics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Thomas T Thomsen
- Department of Biology, Faculty of Science, Section for Functional Genomics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark.,Department of Clinical Microbiology, Rigshospitalet, Henrik Harpestreng Vej 4A, 2100 Copenhagen, Denmark
| | - Peter E Nielsen
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, Center for Peptide-Based Antibiotics, The Panum Institute, University of Copenhagen, Blegdamsvej 3c, 2200 Copenhagen N, Denmark
| | - Anders Løbner-Olesen
- Department of Biology, Faculty of Science, Section for Functional Genomics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
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12
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Vaisman A, Łazowski K, Reijns MAM, Walsh E, McDonald JP, Moreno KC, Quiros DR, Schmidt M, Kranz H, Yang W, Makiela-Dzbenska K, Woodgate R. Novel Escherichia coli active site dnaE alleles with altered base and sugar selectivity. Mol Microbiol 2021; 116:909-925. [PMID: 34181784 PMCID: PMC8485763 DOI: 10.1111/mmi.14779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/25/2021] [Accepted: 06/26/2021] [Indexed: 11/26/2022]
Abstract
The Escherichia coli dnaE gene encodes the α‐catalytic subunit (pol IIIα) of DNA polymerase III, the cell’s main replicase. Like all high‐fidelity DNA polymerases, pol III possesses stringent base and sugar discrimination. The latter is mediated by a so‐called “steric gate” residue in the active site of the polymerase that physically clashes with the 2′‐OH of an incoming ribonucleotide. Our structural modeling data suggest that H760 is the steric gate residue in E.coli pol IIIα. To understand how H760 and the adjacent S759 residue help maintain genome stability, we generated DNA fragments in which the codons for H760 or S759 were systematically changed to the other nineteen naturally occurring amino acids and attempted to clone them into a plasmid expressing pol III core (α‐θ‐ε subunits). Of the possible 38 mutants, only nine were successfully sub‐cloned: three with substitutions at H760 and 6 with substitutions at S759. Three of the plasmid‐encoded alleles, S759C, S759N, and S759T, exhibited mild to moderate mutator activity and were moved onto the chromosome for further characterization. These studies revealed altered phenotypes regarding deoxyribonucleotide base selectivity and ribonucleotide discrimination. We believe that these are the first dnaE mutants with such phenotypes to be reported in the literature.
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Affiliation(s)
- Alexandra Vaisman
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Krystian Łazowski
- Laboratory of DNA Replication and Genome Stability, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Martin A M Reijns
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Erin Walsh
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - John P McDonald
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Kristiniana C Moreno
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Dominic R Quiros
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Marlen Schmidt
- Gen-H Genetic Engineering Heidelberg GmbH, Heidelberg, Germany
| | - Harald Kranz
- Gen-H Genetic Engineering Heidelberg GmbH, Heidelberg, Germany
| | - Wei Yang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Karolina Makiela-Dzbenska
- Laboratory of DNA Replication and Genome Stability, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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13
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High Flexibility of RNaseH2 Catalytic Activity with Respect to Non-Canonical DNA Structures. Int J Mol Sci 2021; 22:ijms22105201. [PMID: 34068992 PMCID: PMC8155979 DOI: 10.3390/ijms22105201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/17/2022] Open
Abstract
Ribonucleotides misincorporated in the human genome are the most abundant DNA lesions. The 2'-hydroxyl group makes them prone to spontaneous hydrolysis, potentially resulting in strand breaks. Moreover, their presence may decrease the rate of DNA replication causing replicative fork stalling and collapse. Ribonucleotide removal is initiated by Ribonuclease H2 (RNase H2), the key player in Ribonucleotide Excision Repair (RER). Its absence leads to embryonic lethality in mice, while mutations decreasing its activity cause Aicardi-Goutières syndrome. DNA geometry can be altered by DNA lesions or by peculiar sequences forming secondary structures, like G-quadruplex (G4) and trinucleotide repeats (TNR) hairpins, which significantly differ from canonical B-form. Ribonucleotides pairing to lesioned nucleotides, or incorporated within non-B DNA structures could avoid RNase H2 recognition, potentially contributing to genome instability. In this work, we investigate the ability of RNase H2 to process misincorporated ribonucleotides in a panel of DNA substrates showing different geometrical features. RNase H2 proved to be a flexible enzyme, recognizing as a substrate the majority of the constructs we generated. However, some geometrical features and non-canonical DNA structures severely impaired its activity, suggesting a relevant role of misincorporated ribonucleotides in the physiological instability of specific DNA sequences.
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14
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Kouzminova EA, Kuzminov A. Ultraviolet-induced RNA:DNA hybrids interfere with chromosomal DNA synthesis. Nucleic Acids Res 2021; 49:3888-3906. [PMID: 33693789 PMCID: PMC8053090 DOI: 10.1093/nar/gkab147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 02/14/2021] [Accepted: 02/23/2021] [Indexed: 12/28/2022] Open
Abstract
Ultraviolet (UV) induces pyrimidine dimers (PDs) in DNA and replication-dependent fragmentation in chromosomes. The rnhAB mutants in Escherichia coli, accumulating R-loops and single DNA-rNs, are generally resistant to DNA damage, but are surprisingly UV-sensitive, even though they remove PDs normally, suggesting irreparable chromosome lesions. We show here that the RNase H defect does not cause additional chromosome fragmentation after UV, but inhibits DNA synthesis after replication restart. Genetic analysis implies formation of R-loop-anchored transcription elongation complexes (R-loop-aTECs) in UV-irradiated rnhAB mutants, predicting that their chromosomal DNA will accumulate: (i) RNA:DNA hybrids; (ii) a few slow-to-remove PDs. We confirm both features and also find that both, surprisingly, depend on replication restart. Finally, enriching for the UV-induced RNA:DNA hybrids in the rnhAB uvrA mutants also co-enriches for PDs, showing their co-residence in the same structures. We propose that PD-triggered R-loop-aTECs block head-on replication in RNase H-deficient mutants.
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Affiliation(s)
- Elena A Kouzminova
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrei Kuzminov
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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15
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Moreno-del Álamo M, Carrasco B, Torres R, Alonso JC. Bacillus subtilis PcrA Helicase Removes Trafficking Barriers. Cells 2021; 10:935. [PMID: 33920686 PMCID: PMC8074105 DOI: 10.3390/cells10040935] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/27/2022] Open
Abstract
Bacillus subtilis PcrA interacts with the RNA polymerase and might contribute to mitigate replication-transcription conflicts (RTCs). We show that PcrA depletion lethality is partially suppressed by rnhB inactivation, but cell viability is significantly reduced by rnhC or dinG inactivation. Following PcrA depletion, cells lacking RnhC or DinG are extremely sensitive to DNA damage. Chromosome segregation is not further impaired by rnhB or dinG inactivation but is blocked by rnhC or recA inactivation upon PcrA depletion. Despite our efforts, we could not construct a ΔrnhC ΔrecA strain. These observations support the idea that PcrA dismantles RTCs. Purified PcrA, which binds single-stranded (ss) DNA over RNA, is a ssDNA-dependent ATPase and preferentially unwinds DNA in a 3'→5'direction. PcrA unwinds a 3'-tailed RNA of an RNA-DNA hybrid significantly faster than that of a DNA substrate. Our results suggest that a replicative stress, caused by mis-incorporated rNMPs, indirectly increases cell viability upon PcrA depletion. We propose that PcrA, in concert with RnhC or DinG, contributes to removing spontaneous or enzyme-driven R-loops, to counteract deleterious trafficking conflicts and preserve to genomic integrity.
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Affiliation(s)
| | | | | | - Juan Carlos Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 28049 Madrid, Spain; (M.M.-d.Á.); (B.C.); (R.T.)
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16
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Malfatti MC, Antoniali G, Codrich M, Burra S, Mangiapane G, Dalla E, Tell G. New perspectives in cancer biology from a study of canonical and non-canonical functions of base excision repair proteins with a focus on early steps. Mutagenesis 2021; 35:129-149. [PMID: 31858150 DOI: 10.1093/mutage/gez051] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022] Open
Abstract
Alterations of DNA repair enzymes and consequential triggering of aberrant DNA damage response (DDR) pathways are thought to play a pivotal role in genomic instabilities associated with cancer development, and are further thought to be important predictive biomarkers for therapy using the synthetic lethality paradigm. However, novel unpredicted perspectives are emerging from the identification of several non-canonical roles of DNA repair enzymes, particularly in gene expression regulation, by different molecular mechanisms, such as (i) non-coding RNA regulation of tumour suppressors, (ii) epigenetic and transcriptional regulation of genes involved in genotoxic responses and (iii) paracrine effects of secreted DNA repair enzymes triggering the cell senescence phenotype. The base excision repair (BER) pathway, canonically involved in the repair of non-distorting DNA lesions generated by oxidative stress, ionising radiation, alkylation damage and spontaneous or enzymatic deamination of nucleotide bases, represents a paradigm for the multifaceted roles of complex DDR in human cells. This review will focus on what is known about the canonical and non-canonical functions of BER enzymes related to cancer development, highlighting novel opportunities to understand the biology of cancer and representing future perspectives for designing new anticancer strategies. We will specifically focus on APE1 as an example of a pleiotropic and multifunctional BER protein.
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Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Marta Codrich
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Silvia Burra
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giovanna Mangiapane
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Emiliano Dalla
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
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17
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Zhou ZX, Williams JS, Lujan SA, Kunkel TA. Ribonucleotide incorporation into DNA during DNA replication and its consequences. Crit Rev Biochem Mol Biol 2021; 56:109-124. [PMID: 33461360 DOI: 10.1080/10409238.2020.1869175] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Ribonucleotides are the most abundant non-canonical nucleotides in the genome. Their vast presence and influence over genome biology is becoming increasingly appreciated. Here we review the recent progress made in understanding their genomic presence, incorporation characteristics and usefulness as biomarkers for polymerase enzymology. We also discuss ribonucleotide processing, the genetic consequences of unrepaired ribonucleotides in DNA and evidence supporting the significance of their transient presence in the nuclear genome.
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Affiliation(s)
- Zhi-Xiong Zhou
- Genome Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, NC, USA
| | - Jessica S Williams
- Genome Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, NC, USA
| | - Scott A Lujan
- Genome Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, NC, USA
| | - Thomas A Kunkel
- Genome Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, NC, USA
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18
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Silva RMB, Grodick MA, Barton JK. UvrC Coordinates an O 2-Sensitive [4Fe4S] Cofactor. J Am Chem Soc 2020; 142:10964-10977. [PMID: 32470300 DOI: 10.1021/jacs.0c01671] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent advances have led to numerous landmark discoveries of [4Fe4S] clusters coordinated by essential enzymes in repair, replication, and transcription across all domains of life. The cofactor has notably been challenging to observe for many nucleic acid processing enzymes due to several factors, including a weak bioinformatic signature of the coordinating cysteines and lability of the metal cofactor. To overcome these challenges, we have used sequence alignments, an anaerobic purification method, iron quantification, and UV-visible and electron paramagnetic resonance spectroscopies to investigate UvrC, the dual-incision endonuclease in the bacterial nucleotide excision repair (NER) pathway. The characteristics of UvrC are consistent with [4Fe4S] coordination with 60-70% cofactor incorporation, and additionally, we show that, bound to UvrC, the [4Fe4S] cofactor is susceptible to oxidative degradation with aggregation of apo species. Importantly, in its holo form with the cofactor bound, UvrC forms high affinity complexes with duplexed DNA substrates; the apparent dissociation constants to well-matched and damaged duplex substrates are 100 ± 20 nM and 80 ± 30 nM, respectively. This high affinity DNA binding contrasts reports made for isolated protein lacking the cofactor. Moreover, using DNA electrochemistry, we find that the cluster coordinated by UvrC is redox-active and participates in DNA-mediated charge transport chemistry with a DNA-bound midpoint potential of 90 mV vs NHE. This work highlights that the [4Fe4S] center is critical to UvrC.
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Affiliation(s)
- Rebekah M B Silva
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Michael A Grodick
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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19
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Processing of a single ribonucleotide embedded into DNA by human nucleotide excision repair and DNA polymerase η. Sci Rep 2019; 9:13910. [PMID: 31558768 PMCID: PMC6763444 DOI: 10.1038/s41598-019-50421-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/05/2019] [Indexed: 12/18/2022] Open
Abstract
DNA polymerases often incorporate non-canonical nucleotide, i.e., ribonucleoside triphosphates into the genomic DNA. Aberrant accumulation of ribonucleotides in the genome causes various cellular abnormalities. Here, we show the possible role of human nucleotide excision repair (NER) and DNA polymerase η (Pol η) in processing of a single ribonucleotide embedded into DNA. We found that the reconstituted NER system can excise the oxidized ribonucleotide on the plasmid DNA. Taken together with the evidence that Pol η accurately bypasses a ribonucleotide, i.e., riboguanosine (rG) or its oxidized derivative (8-oxo-rG) in vitro, we further assessed the mutagenic potential of the embedded ribonucleotide in human cells lacking NER or Pol η. A single rG on the supF reporter gene predominantly induced large deletion mutations. An embedded 8-oxo-rG caused base substitution mutations at the 3′-neighboring base rather than large deletions in wild-type cells. The disruption of XPA, an essential factor for NER, or Pol η leads to the increased mutant frequency of 8-oxo-rG. Furthermore, the frequency of 8-oxo-rG-mediated large deletions was increased by the loss of Pol η, but not XPA. Collectively, our results suggest that base oxidation of the embedded ribonucleotide enables processing of the ribonucleotide via alternative DNA repair and damage tolerance pathways.
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20
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Walsh E, Henrikus SS, Vaisman A, Makiela-Dzbenska K, Armstrong TJ, Łazowski K, McDonald JP, Goodman MF, van Oijen AM, Jonczyk P, Fijalkowska IJ, Robinson A, Woodgate R. Role of RNase H enzymes in maintaining genome stability in Escherichia coli expressing a steric-gate mutant of pol V ICE391. DNA Repair (Amst) 2019; 84:102685. [PMID: 31543434 DOI: 10.1016/j.dnarep.2019.102685] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 07/31/2019] [Accepted: 08/03/2019] [Indexed: 11/18/2022]
Abstract
pol VICE391 (RumA'2B) is a low-fidelity polymerase that promotes considerably higher levels of spontaneous "SOS-induced" mutagenesis than the related E. coli pol V (UmuD'2C). The molecular basis for the enhanced mutagenesis was previously unknown. Using single molecule fluorescence microscopy to visualize pol V enzymes, we discovered that the elevated levels of mutagenesis are likely due, in part, to prolonged binding of RumB to genomic DNA leading to increased levels of DNA synthesis compared to UmuC. We have generated a steric gate pol VICE391 variant (pol VICE391_Y13A) that readily misincorporates ribonucleotides into the E. coli genome and have used the enzyme to investigate the molecular mechanisms of Ribonucleotide Excision Repair (RER) under conditions of increased ribonucleotide-induced stress. To do so, we compared the extent of spontaneous mutagenesis promoted by pol V and pol VICE391 to that of their respective steric gate variants. Levels of mutagenesis promoted by the steric gate variants that are lower than that of the wild-type enzyme are indicative of active RER that removes misincorporated ribonucleotides, but also misincorporated deoxyribonucleotides from the genome. Using such an approach, we confirmed that RNase HII plays a pivotal role in RER. In the absence of RNase HII, Nucleotide Excision Repair (NER) proteins help remove misincorporated ribonucleotides. However, significant RER occurs in the absence of RNase HII and NER. Most of the RNase HII and NER-independent RER occurs on the lagging strand during genome duplication. We suggest that this is most likely due to efficient RNase HI-dependent RER which recognizes the polyribonucleotide tracts generated by pol VICE391_Y13A. These activities are critical for the maintenance of genomic integrity when RNase HII is overwhelmed, or inactivated, as ΔrnhB or ΔrnhB ΔuvrA strains expressing pol VICE391_Y13A exhibit genome and plasmid instability in the absence of RNase HI.
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Affiliation(s)
- Erin Walsh
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
| | - Sarah S Henrikus
- Molecular Horizons Institute and School of Chemistry and Biomolecular Science, University of Wollongong, Australia; Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Alexandra Vaisman
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
| | | | - Thomas J Armstrong
- Molecular Horizons Institute and School of Chemistry and Biomolecular Science, University of Wollongong, Australia; Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Krystian Łazowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - John P McDonald
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
| | - Myron F Goodman
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089-2910 USA
| | - Antoine M van Oijen
- Molecular Horizons Institute and School of Chemistry and Biomolecular Science, University of Wollongong, Australia; Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Piotr Jonczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Iwona J Fijalkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Andrew Robinson
- Molecular Horizons Institute and School of Chemistry and Biomolecular Science, University of Wollongong, Australia; Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA.
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21
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Zatopek KM, Potapov V, Maduzia LL, Alpaslan E, Chen L, Evans TC, Ong JL, Ettwiller LM, Gardner AF. RADAR-seq: A RAre DAmage and Repair sequencing method for detecting DNA damage on a genome-wide scale. DNA Repair (Amst) 2019; 80:36-44. [PMID: 31247470 DOI: 10.1016/j.dnarep.2019.06.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/13/2019] [Accepted: 06/19/2019] [Indexed: 12/19/2022]
Abstract
RAre DAmage and Repair sequencing (RADAR-seq) is a highly adaptable sequencing method that enables the identification and detection of rare DNA damage events for a wide variety of DNA lesions at single-molecule resolution on a genome-wide scale. In RADAR-seq, DNA lesions are replaced with a patch of modified bases that can be directly detected by Pacific Biosciences Single Molecule Real-Time (SMRT) sequencing. RADAR-seq enables dynamic detection over a wide range of DNA damage frequencies, including low physiological levels. Furthermore, without the need for DNA amplification and enrichment steps, RADAR-seq provides sequencing coverage of damaged and undamaged DNA across an entire genome. Here, we use RADAR-seq to measure the frequency and map the location of ribonucleotides in wild-type and RNaseH2-deficient E. coli and Thermococcus kodakarensis strains. Additionally, by tracking ribonucleotides incorporated during in vivo lagging strand DNA synthesis, we determined the replication initiation point in E. coli, and its relation to the origin of replication (oriC). RADAR-seq was also used to map cyclobutane pyrimidine dimers (CPDs) in Escherichia coli (E. coli) genomic DNA exposed to UV-radiation. On a broader scale, RADAR-seq can be applied to understand formation and repair of DNA damage, the correlation between DNA damage and disease initiation and progression, and complex biological pathways, including DNA replication.
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Affiliation(s)
- Kelly M Zatopek
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938 USA
| | - Vladimir Potapov
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938 USA
| | - Lisa L Maduzia
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938 USA
| | - Ece Alpaslan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938 USA
| | - Lixin Chen
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938 USA
| | - Thomas C Evans
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938 USA
| | - Jennifer L Ong
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938 USA.
| | | | - Andrew F Gardner
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938 USA.
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22
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Randall JR, Nye TM, Wozniak KJ, Simmons LA. RNase HIII Is Important for Okazaki Fragment Processing in Bacillus subtilis. J Bacteriol 2019; 201:e00686-18. [PMID: 30670546 PMCID: PMC6416905 DOI: 10.1128/jb.00686-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/18/2019] [Indexed: 01/15/2023] Open
Abstract
RNA-DNA hybrids are common in chromosomal DNA. Persistent RNA-DNA hybrids result in replication fork stress, DNA breaks, and neurological disorders in humans. During replication, Okazaki fragment synthesis relies on frequent RNA primer placement, providing one of the most prominent forms of covalent RNA-DNA strands in vivo The mechanism of Okazaki fragment maturation, which involves RNA removal and subsequent DNA replacement, in bacteria lacking RNase HI remains unclear. In this work, we reconstituted repair of a linear model Okazaki fragment in vitro using purified recombinant enzymes from Bacillus subtilis We showed that RNase HII and HIII are capable of incision on Okazaki fragments in vitro and that both enzymes show mild stimulation by single-stranded DNA binding protein (SSB). We also showed that RNase HIII and DNA polymerase I provide the primary pathway for Okazaki fragment maturation in vitro Furthermore, we found that YpcP is a 5' to 3' nuclease that can act on a wide variety of RNA- and DNA-containing substrates and exhibits preference for degrading RNA in model Okazaki fragments. Together, our data showed that RNase HIII and DNA polymerase I provide the primary pathway for Okazaki fragment maturation, whereas YpcP also contributes to the removal of RNA from an Okazaki fragment in vitroIMPORTANCE All cells are required to resolve the different types of RNA-DNA hybrids that form in vivo When RNA-DNA hybrids persist, cells experience an increase in mutation rate and problems with DNA replication. Okazaki fragment synthesis on the lagging strand requires an RNA primer to begin synthesis of each fragment. The mechanism of RNA removal from Okazaki fragments remains unknown in bacteria that lack RNase HI. We examined Okazaki fragment processing in vitro and found that RNase HIII in conjunction with DNA polymerase I represent the most efficient repair pathway. We also assessed the contribution of YpcP and found that YpcP is a 5' to 3' exonuclease that prefers RNA substrates with activity on Okazaki and flap substrates in vitro.
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Affiliation(s)
- Justin R Randall
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Taylor M Nye
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Katherine J Wozniak
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Lyle A Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
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23
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Kreisel K, Engqvist MKM, Kalm J, Thompson LJ, Boström M, Navarrete C, McDonald JP, Larsson E, Woodgate R, Clausen AR. DNA polymerase η contributes to genome-wide lagging strand synthesis. Nucleic Acids Res 2019; 47:2425-2435. [PMID: 30597049 PMCID: PMC6411934 DOI: 10.1093/nar/gky1291] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/11/2018] [Accepted: 12/14/2018] [Indexed: 12/14/2022] Open
Abstract
DNA polymerase η (pol η) is best known for its ability to bypass UV-induced thymine-thymine (T-T) dimers and other bulky DNA lesions, but pol η also has other cellular roles. Here, we present evidence that pol η competes with DNA polymerases α and δ for the synthesis of the lagging strand genome-wide, where it also shows a preference for T-T in the DNA template. Moreover, we found that the C-terminus of pol η, which contains a PCNA-Interacting Protein motif is required for pol η to function in lagging strand synthesis. Finally, we provide evidence that a pol η dependent signature is also found to be lagging strand specific in patients with skin cancer. Taken together, these findings provide insight into the physiological role of DNA synthesis by pol η and have implications for our understanding of how our genome is replicated to avoid mutagenesis, genome instability and cancer.
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Affiliation(s)
- Katrin Kreisel
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Martin K M Engqvist
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Josephine Kalm
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Liam J Thompson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Martin Boström
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Clara Navarrete
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - John P McDonald
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erik Larsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anders R Clausen
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden
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24
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Sassa A, Yasui M, Honma M. Current perspectives on mechanisms of ribonucleotide incorporation and processing in mammalian DNA. Genes Environ 2019; 41:3. [PMID: 30700998 PMCID: PMC6346524 DOI: 10.1186/s41021-019-0118-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/08/2019] [Indexed: 01/09/2023] Open
Abstract
Ribonucleotides, which are RNA precursors, are often incorporated into DNA during replication. Although embedded ribonucleotides in the genome are efficiently removed by canonical ribonucleotide excision repair (RER), inactivation of RER causes genomic ribonucleotide accumulation, leading to various abnormalities in cells. Mutation of genes encoding factors involved in RER is associated with the neuroinflammatory autoimmune disorder Aicardi–Goutières syndrome. Over the last decade, the biological impact of ribonucleotides in the genome has attracted much attention. In the present review, we particularly focus on recent studies that have elucidated possible mechanisms of ribonucleotide incorporation and repair and their significance in mammals.
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Affiliation(s)
- Akira Sassa
- 1Department of Biology, Graduate School of Science, Chiba University, Chiba, 263-8522 Japan
| | - Manabu Yasui
- 2Division of Genetics and Mutagenesis, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki 210-9501 Japan
| | - Masamitsu Honma
- 2Division of Genetics and Mutagenesis, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki 210-9501 Japan
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25
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Lemor M, Kong Z, Henry E, Brizard R, Laurent S, Bossé A, Henneke G. Differential Activities of DNA Polymerases in Processing Ribonucleotides during DNA Synthesis in Archaea. J Mol Biol 2018; 430:4908-4924. [PMID: 30342933 DOI: 10.1016/j.jmb.2018.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/09/2018] [Accepted: 10/12/2018] [Indexed: 12/11/2022]
Abstract
Consistent with the fact that ribonucleotides (rNTPs) are in excess over deoxyribonucleotides (dNTPs) in vivo, recent findings indicate that replicative DNA polymerases (DNA Pols) are able to insert ribonucleotides (rNMPs) during DNA synthesis, raising crucial questions about the fidelity of DNA replication in both Bacteria and Eukarya. Here, we report that the level of rNTPs is 20-fold higher than that of dNTPs in Pyrococcus abyssi cells. Using dNTP and rNTP concentrations present in vivo, we recorded rNMP incorporation in a template-specific manner during in vitro synthesis, with the family-D DNA Pol (PolD) having the highest propensity compared with the family-B DNA Pol and the p41/p46 complex. We also showed that ribonucleotides accumulate at a relatively high frequency in the genome of wild-type Thermococcales cells, and this frequency significantly increases upon deletion of RNase HII, the major enzyme responsible for the removal of RNA from DNA. Because ribonucleotides remain in genomic DNA, we then analyzed the effects on polymerization activities by the three DNA Pols. Depending on the identity of the base and the sequence context, all three DNA Pols bypass rNMP-containing DNA templates with variable efficiency and nucleotide (mis)incorporation ability. Unexpectedly, we found that PolD correctly base-paired a single ribonucleotide opposite rNMP-containing DNA templates. An evolutionary scenario is discussed concerning rNMP incorporation into DNA and genome stability.
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Affiliation(s)
- Mélanie Lemor
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Ziqing Kong
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Etienne Henry
- CNRS, Ifremer, Univ Brest, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280, Plouzané, France
| | - Raphaël Brizard
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Sébastien Laurent
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Audrey Bossé
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Ghislaine Henneke
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France.
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Vaisman A, Woodgate R. Ribonucleotide discrimination by translesion synthesis DNA polymerases. Crit Rev Biochem Mol Biol 2018; 53:382-402. [PMID: 29972306 DOI: 10.1080/10409238.2018.1483889] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The well-being of all living organisms relies on the accurate duplication of their genomes. This is usually achieved by highly elaborate replicase complexes which ensure that this task is accomplished timely and efficiently. However, cells often must resort to the help of various additional "specialized" DNA polymerases that gain access to genomic DNA when replication fork progression is hindered. One such specialized polymerase family consists of the so-called "translesion synthesis" (TLS) polymerases; enzymes that have evolved to replicate damaged DNA. To fulfill their main cellular mission, TLS polymerases often must sacrifice precision when selecting nucleotide substrates. Low base-substitution fidelity is a well-documented inherent property of these enzymes. However, incorrect nucleotide substrates are not only those which do not comply with Watson-Crick base complementarity, but also those whose sugar moiety is incorrect. Does relaxed base-selectivity automatically mean that the TLS polymerases are unable to efficiently discriminate between ribonucleoside triphosphates and deoxyribonucleoside triphosphates that differ by only a single atom? Which strategies do TLS polymerases employ to select suitable nucleotide substrates? In this review, we will collate and summarize data accumulated over the past decade from biochemical and structural studies, which aim to answer these questions.
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Affiliation(s)
- Alexandra Vaisman
- a Laboratory of Genomic Integrity , National Institute of Child Health and Human Development, National Institutes of Health , Bethesda , MD , USA
| | - Roger Woodgate
- a Laboratory of Genomic Integrity , National Institute of Child Health and Human Development, National Institutes of Health , Bethesda , MD , USA
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Randall JR, Hirst WG, Simmons LA. Substrate Specificity for Bacterial RNases HII and HIII Is Influenced by Metal Availability. J Bacteriol 2018; 200:e00401-17. [PMID: 29084857 PMCID: PMC5786700 DOI: 10.1128/jb.00401-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 10/23/2017] [Indexed: 12/27/2022] Open
Abstract
We tested the activities of four predicated RNase H enzymes, including two RNase HI-type enzymes, in addition to RNase HII (RnhB) and RNase HIII (RnhC), on several RNA-DNA hybrid substrates with different divalent metal cations. We found that the two RNase HI-type enzymes, YpdQ and YpeP, failed to show activity on the three substrates tested. RNase HII and RNase HIII cleaved all the substrates tested, although the activity was dependent on the metal made available. We show that Bacillus subtilis RNase HII and RNase HIII are both able to incise 5' to a single ribonucleoside monophosphate (rNMP). We show that RNase HIII incision at a single rNMP occurs most efficiently with Mn2+, an activity we found to be conserved among other Gram-positive RNase HIII enzymes. Characterization of RNases HII and HIII with metal concentrations in the physiological range showed that RNase HII can cleave at single rNMPs embedded in DNA while RNase HIII is far less effective. Further, using metal concentrations within the physiological range, RNase HIII efficiently cleaved longer RNA-DNA hybrids lacking an RNA-DNA junction, while RNase HII was much less effective. Phenotypic analysis showed that cells with an rnhC deletion were sensitive to hydroxyurea (HU). In contrast, cells with an rnhB deletion showed wild-type growth in the presence of HU, supporting the hypothesis that RNases HII and HIII have distinct substrate specificities in vivo This work demonstrates how metal availability influences the substrate recognition and activity of RNases HII and HIII, providing insight into their functions in vivoIMPORTANCE RNase H represents a class of proteins that cleave RNA-DNA hybrids, helping resolve R-loops and Okazaki fragments, as well as initiating the process of ribonucleotide excision repair (RER). We investigated the activities of four Bacillus subtilis RNase H enzymes and found that only RNases HII and HIII have activity and that their substrate preference is dependent on metal availability. To understand the factors that contribute to RNase HII and RNase HIII substrate preference, we show that in the presence of metal concentrations within the physiological range, RNases HII and HIII have distinct activities on different RNA-DNA hybrids. This work provides insight into how RNases HII and HIII repair the broad range of RNA-DNA hybrids that form in Gram-positive bacteria.
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Affiliation(s)
- Justin R Randall
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - William G Hirst
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Lyle A Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
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Malfatti MC, Balachander S, Antoniali G, Koh KD, Saint-Pierre C, Gasparutto D, Chon H, Crouch RJ, Storici F, Tell G. Abasic and oxidized ribonucleotides embedded in DNA are processed by human APE1 and not by RNase H2. Nucleic Acids Res 2017; 45:11193-11212. [PMID: 28977421 PMCID: PMC5737539 DOI: 10.1093/nar/gkx723] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 08/11/2017] [Indexed: 12/13/2022] Open
Abstract
Ribonucleoside 5′-monophosphates (rNMPs) are the most common non-standard nucleotides found in DNA of eukaryotic cells, with over 100 million rNMPs transiently incorporated in the mammalian genome per cell cycle. Human ribonuclease (RNase) H2 is the principal enzyme able to cleave rNMPs in DNA. Whether RNase H2 may process abasic or oxidized rNMPs incorporated in DNA is unknown. The base excision repair (BER) pathway is mainly responsible for repairing oxidized and abasic sites into DNA. Here we show that human RNase H2 is unable to process an abasic rNMP (rAP site) or a ribose 8oxoG (r8oxoG) site embedded in DNA. On the contrary, we found that recombinant purified human apurinic/apyrimidinic endonuclease-1 (APE1) and APE1 from human cell extracts efficiently process an rAP site in DNA and have weak endoribonuclease and 3′-exonuclease activities on r8oxoG substrate. Using biochemical assays, our results provide evidence of a human enzyme able to recognize and process abasic and oxidized ribonucleotides embedded in DNA.
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Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, Udine, Italy
| | - Sathya Balachander
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, Udine, Italy
| | - Kyung Duk Koh
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,University of California, San Francisco, UCSF, School of Medicine, San Francisco, CA, USA
| | - Christine Saint-Pierre
- Chimie Reconnaissance & Etude Assemblages Biologiques, Université Grenoble Alpes, SPrAM UMR5819 CEA CNRS UGA, INAC/CEA, Grenoble, France
| | - Didier Gasparutto
- Chimie Reconnaissance & Etude Assemblages Biologiques, Université Grenoble Alpes, SPrAM UMR5819 CEA CNRS UGA, INAC/CEA, Grenoble, France
| | - Hyongi Chon
- Developmental Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Robert J Crouch
- Developmental Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, Udine, Italy
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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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30
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Schroeder JW, Yeesin P, Simmons LA, Wang JD. Sources of spontaneous mutagenesis in bacteria. Crit Rev Biochem Mol Biol 2017; 53:29-48. [PMID: 29108429 DOI: 10.1080/10409238.2017.1394262] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mutations in an organism's genome can arise spontaneously, that is, in the absence of exogenous stress and prior to selection. Mutations are often neutral or deleterious to individual fitness but can also provide genetic diversity driving evolution. Mutagenesis in bacteria contributes to the already serious and growing problem of antibiotic resistance. However, the negative impacts of spontaneous mutagenesis on human health are not limited to bacterial antibiotic resistance. Spontaneous mutations also underlie tumorigenesis and evolution of drug resistance. To better understand the causes of genetic change and how they may be manipulated in order to curb antibiotic resistance or the development of cancer, we must acquire a mechanistic understanding of the major sources of mutagenesis. Bacterial systems are particularly well-suited to studying mutagenesis because of their fast growth rate and the panoply of available experimental tools, but efforts to understand mutagenic mechanisms can be complicated by the experimental system employed. Here, we review our current understanding of mutagenic mechanisms in bacteria and describe the methods used to study mutagenesis in bacterial systems.
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Affiliation(s)
- Jeremy W Schroeder
- a Department of Bacteriology , University of Wisconsin - Madison , Madison , WI , USA
| | - Ponlkrit Yeesin
- a Department of Bacteriology , University of Wisconsin - Madison , Madison , WI , USA
| | - Lyle A Simmons
- b Department of Molecular, Cellular, and Developmental Biology , University of Michigan , Ann Arbor , MI , USA
| | - Jue D Wang
- a Department of Bacteriology , University of Wisconsin - Madison , Madison , WI , USA
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31
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Schroeder JW, Randall JR, Hirst WG, O'Donnell ME, Simmons LA. Mutagenic cost of ribonucleotides in bacterial DNA. Proc Natl Acad Sci U S A 2017; 114:11733-11738. [PMID: 29078353 PMCID: PMC5676920 DOI: 10.1073/pnas.1710995114] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Replicative DNA polymerases misincorporate ribonucleoside triphosphates (rNTPs) into DNA approximately once every 2,000 base pairs synthesized. Ribonucleotide excision repair (RER) removes ribonucleoside monophosphates (rNMPs) from genomic DNA, replacing the error with the appropriate deoxyribonucleoside triphosphate (dNTP). Ribonucleotides represent a major threat to genome integrity with the potential to cause strand breaks. Furthermore, it has been shown in the bacterium Bacillus subtilis that loss of RER increases spontaneous mutagenesis. Despite the high rNTP error rate and the effect on genome integrity, the mechanism underlying mutagenesis in RER-deficient bacterial cells remains unknown. We performed mutation accumulation lines and genome-wide mutational profiling of B. subtilis lacking RNase HII, the enzyme that incises at single rNMP residues initiating RER. We show that loss of RER in B. subtilis causes strand- and sequence-context-dependent GC → AT transitions. Using purified proteins, we show that the replicative polymerase DnaE is mutagenic within the sequence context identified in RER-deficient cells. We also found that DnaE does not perform strand displacement synthesis. Given the use of nucleotide excision repair (NER) as a backup pathway for RER in RNase HII-deficient cells and the known mutagenic profile of DnaE, we propose that misincorporated ribonucleotides are removed by NER followed by error-prone resynthesis with DnaE.
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Affiliation(s)
- Jeremy W Schroeder
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Justin R Randall
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - William G Hirst
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Michael E O'Donnell
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065
| | - Lyle A Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109;
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32
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Kouzminova EA, Kadyrov FF, Kuzminov A. RNase HII Saves rnhA Mutant Escherichia coli from R-Loop-Associated Chromosomal Fragmentation. J Mol Biol 2017; 429:2873-2894. [PMID: 28821455 DOI: 10.1016/j.jmb.2017.08.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 01/02/2023]
Abstract
The rnhAB mutant Escherichia coli, deficient in two RNase H enzymes that remove both R-loops and incorporated ribonucleotides (rNs) from DNA, grow slowly, suggesting accumulation of rN-containing DNA lesions (R-lesions). We report that the rnhAB mutants have reduced viability, form filaments with abnormal nucleoids, induce SOS, and fragment their chromosome, revealing replication and/or segregation stress. R-loops are known to interfere with replication forks, and sensitivity of the double rnhAB mutants to translation inhibition points to R-loops as precursors for R-lesions. However, the strict specificity of bacterial RNase HII for RNA-DNA junctions indicates that R-lesions have rNs integrated into DNA. Indeed, instead of relieving problems of rnhAB mutants, transient inhibition of replication from oriC kills them, suggesting that oriC-initiated replication removes R-loops instead of compounding them to R-lesions. Yet, replication from an R-loop-initiating plasmid origin kills the double rnhAB mutant, revealing generation of R-lesions by R-loop-primed DNA synthesis. These R-lesions could be R-tracts, contiguous runs of ≥4 RNA nucleotides within DNA strand and the only common substrate between the two bacterial RNase H enzymes. However, a plasmid relaxation test failed to detect R-tracts in DNA of the rnhAB mutants, although it readily detected R-patches (runs of 1-3 rNs). Instead, we detected R-gaps, single-strand gaps containing rNs, in the chromosomal DNA of the rnhAB mutant. Therefore, we propose that RNase H-deficient mutants convert some R-loops into R-tracts, which progress into R-gaps and then to double-strand breaks-explaining why R-tracts do not accumulate in RNase H-deficient cells, while double-strand breaks do.
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Affiliation(s)
- Elena A Kouzminova
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Farid F Kadyrov
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrei Kuzminov
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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33
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Antoniali G, Malfatti MC, Tell G. Unveiling the non-repair face of the Base Excision Repair pathway in RNA processing: A missing link between DNA repair and gene expression? DNA Repair (Amst) 2017. [DOI: 10.1016/j.dnarep.2017.06.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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34
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Sassa A, Çağlayan M, Rodriguez Y, Beard WA, Wilson SH, Nohmi T, Honma M, Yasui M. Impact of Ribonucleotide Backbone on Translesion Synthesis and Repair of 7,8-Dihydro-8-oxoguanine. J Biol Chem 2016; 291:24314-24323. [PMID: 27660390 DOI: 10.1074/jbc.m116.738732] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 08/28/2016] [Indexed: 12/21/2022] Open
Abstract
Numerous ribonucleotides are incorporated into the genome during DNA replication. Oxidized ribonucleotides can also be erroneously incorporated into DNA. Embedded ribonucleotides destabilize the structure of DNA and retard DNA synthesis by DNA polymerases (pols), leading to genomic instability. Mammalian cells possess translesion DNA synthesis (TLS) pols that bypass DNA damage. The mechanism of TLS and repair of oxidized ribonucleotides remains to be elucidated. To address this, we analyzed the miscoding properties of the ribonucleotides riboguanosine (rG) and 7,8-dihydro-8-oxo-riboguanosine (8-oxo-rG) during TLS catalyzed by the human TLS pols κ and η in vitro The primer extension reaction catalyzed by human replicative pol α was strongly blocked by 8-oxo-rG. pol κ inefficiently bypassed rG and 8-oxo-rG compared with dG and 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxo-dG), whereas pol η easily bypassed the ribonucleotides. pol α exclusively inserted dAMP opposite 8-oxo-rG. Interestingly, pol κ preferentially inserted dCMP opposite 8-oxo-rG, whereas the insertion of dAMP was favored opposite 8-oxo-dG. In addition, pol η accurately bypassed 8-oxo-rG. Furthermore, we examined the activity of the base excision repair (BER) enzymes 8-oxoguanine DNA glycosylase (OGG1) and apurinic/apyrimidinic endonuclease 1 on the substrates, including rG and 8-oxo-rG. Both BER enzymes were completely inactive against 8-oxo-rG in DNA. However, OGG1 suppressed 8-oxo-rG excision by RNase H2, which is involved in the removal of ribonucleotides from DNA. These results suggest that the different sugar backbones between 8-oxo-rG and 8-oxo-dG alter the capacity of TLS and repair of 8-oxoguanine.
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Affiliation(s)
- Akira Sassa
- From the Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan and
| | - Melike Çağlayan
- the Genome Integrity and Structural Biology Laboratory, National Institutes of Health, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Yesenia Rodriguez
- the Genome Integrity and Structural Biology Laboratory, National Institutes of Health, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - William A Beard
- the Genome Integrity and Structural Biology Laboratory, National Institutes of Health, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Samuel H Wilson
- the Genome Integrity and Structural Biology Laboratory, National Institutes of Health, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Takehiko Nohmi
- From the Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan and
| | - Masamitsu Honma
- From the Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan and
| | - Manabu Yasui
- From the Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan and
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Cho JE, Jinks-Robertson S. Ribonucleotides and Transcription-Associated Mutagenesis in Yeast. J Mol Biol 2016; 429:3156-3167. [PMID: 27511624 DOI: 10.1016/j.jmb.2016.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 08/01/2016] [Accepted: 08/03/2016] [Indexed: 12/26/2022]
Abstract
High levels of transcription stimulate mutation rates in microorganisms, and this occurs primarily through an enhanced accumulation of DNA damage. The major source of transcription-associated damage in yeast is Topoisomerase I (Top1), an enzyme that removes torsional stress that accumulates when DNA strands are separated. Top1 relieves torsional stress by nicking and resealing one DNA strand, and some Top1-dependent mutations are due to trapping and processing of the covalent cleavage intermediate. Most, however, reflect enzyme incision at ribonucleotides, which are the most abundant noncanonical component of DNA. In either case, Top1 generates a distinctive mutation signature composed of short deletions in tandem repeats; in the specific case of ribonucleotide-initiated events, mutations reflect sequential cleavage by the enzyme. Top1-dependent mutations do not require highly activated transcription, but their levels are greatly increased by transcription, which partially reflects an interaction of Top1 with RNA polymerase. Recent studies have demonstrated that Top1-dependent mutations exhibit a strand bias, with the nature of the bias differing depending on the transcriptional status of the underlying DNA. Under low-transcription conditions, most Top1-dependent mutations arise in the context of replication and reflect incision at ribonucleotides incorporated during leading-strand synthesis. Under high-transcription conditions, most Top1-dependent events arise when the enzyme cleaves the non-transcribed strand of DNA. In addition to increasing genetic instability in growing cells, Top1 activity in transcriptionally active regions may be a source of mutations in quiescent cells.
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Affiliation(s)
- Jang-Eun Cho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA.
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36
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Erill I, Campoy S, Kılıç S, Barbé J. The Verrucomicrobia LexA-Binding Motif: Insights into the Evolutionary Dynamics of the SOS Response. Front Mol Biosci 2016; 3:33. [PMID: 27489856 PMCID: PMC4951493 DOI: 10.3389/fmolb.2016.00033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 07/04/2016] [Indexed: 12/20/2022] Open
Abstract
The SOS response is the primary bacterial mechanism to address DNA damage, coordinating multiple cellular processes that include DNA repair, cell division, and translesion synthesis. In contrast to other regulatory systems, the composition of the SOS genetic network and the binding motif of its transcriptional repressor, LexA, have been shown to vary greatly across bacterial clades, making it an ideal system to study the co-evolution of transcription factors and their regulons. Leveraging comparative genomics approaches and prior knowledge on the core SOS regulon, here we define the binding motif of the Verrucomicrobia, a recently described phylum of emerging interest due to its association with eukaryotic hosts. Site directed mutagenesis of the Verrucomicrobium spinosum recA promoter confirms that LexA binds a 14 bp palindromic motif with consensus sequence TGTTC-N4-GAACA. Computational analyses suggest that recognition of this novel motif is determined primarily by changes in base-contacting residues of the third alpha helix of the LexA helix-turn-helix DNA binding motif. In conjunction with comparative genomics analysis of the LexA regulon in the Verrucomicrobia phylum, electrophoretic shift assays reveal that LexA binds to operators in the promoter region of DNA repair genes and a mutagenesis cassette in this organism, and identify previously unreported components of the SOS response. The identification of tandem LexA-binding sites generating instances of other LexA-binding motifs in the lexA gene promoter of Verrucomicrobia species leads us to postulate a novel mechanism for LexA-binding motif evolution. This model, based on gene duplication, successfully addresses outstanding questions in the intricate co-evolution of the LexA protein, its binding motif and the regulatory network it controls.
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Affiliation(s)
- Ivan Erill
- Erill Lab, Department of Biological Sciences, University of Maryland Baltimore County Baltimore, MD, USA
| | - Susana Campoy
- Unitat de Microbiologia, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona Barcelona, Spain
| | - Sefa Kılıç
- Erill Lab, Department of Biological Sciences, University of Maryland Baltimore County Baltimore, MD, USA
| | - Jordi Barbé
- Unitat de Microbiologia, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona Barcelona, Spain
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37
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Williams JS, Lujan SA, Kunkel TA. Processing ribonucleotides incorporated during eukaryotic DNA replication. Nat Rev Mol Cell Biol 2016; 17:350-63. [PMID: 27093943 PMCID: PMC5445644 DOI: 10.1038/nrm.2016.37] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The information encoded in DNA is influenced by the presence of non-canonical nucleotides, the most frequent of which are ribonucleotides. In this Review, we discuss recent discoveries about ribonucleotide incorporation into DNA during replication by the three major eukaryotic replicases, DNA polymerases α, δ and ε. The presence of ribonucleotides in DNA causes short deletion mutations and may result in the generation of single- and double-strand DNA breaks, leading to genome instability. We describe how these ribonucleotides are removed from DNA through ribonucleotide excision repair and by topoisomerase I. We discuss the biological consequences and the physiological roles of ribonucleotides in DNA, and consider how deficiencies in their removal from DNA may be important in the aetiology of disease.
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Affiliation(s)
- Jessica S. Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, United States
| | - Scott A. Lujan
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, United States
| | - Thomas A. Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, United States
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A DinB Ortholog Enables Mycobacterial Growth under dTTP-Limiting Conditions Induced by the Expression of a Mycobacteriophage-Derived Ribonucleotide Reductase Gene. J Bacteriol 2015; 198:352-62. [PMID: 26527643 DOI: 10.1128/jb.00669-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/24/2015] [Indexed: 01/30/2023] Open
Abstract
UNLABELLED Mycobacterium species such as M. smegmatis and M. tuberculosis encode at least two translesion synthesis (TLS) polymerases, DinB1 and DinB2, respectively. Although predicted to be linked to DNA repair, their role in vivo remains enigmatic. M. smegmatis mc(2)155, a strain commonly used to investigate mycobacterial genetics, has two copies of dinB2, the gene that codes for DinB2, by virtue of a 56-kb chromosomal duplication. Expression of a mycobacteriophage D29 gene (gene 50) encoding a class II ribonucleotide reductase in M. smegmatis ΔDRKIN, a strain derived from mc(2)155 in which one copy of the duplication is lost, resulted in DNA replication defects and growth inhibition. The inhibitory effect could be linked to the deficiency of dTTP that resulted under these circumstances. The selective inhibition observed in the ΔDRKIN strain was found to be due solely to a reduced dosage of dinB2 in this strain. Mycobacterium bovis, which is closely related to M. tuberculosis, the tuberculosis pathogen, was found to be highly susceptible to gene 50 overexpression. Incidentally, these slow-growing pathogens harbor one copy of dinB2. The results indicate that the induction of a dTTP-limiting state can lead to growth inhibition in mycobacteria, with the effect being maximum in cells deficient in DinB2. IMPORTANCE Mycobacterium species, such as M. tuberculosis, the tuberculosis pathogen, are known to encode several Y family DNA polymerases, one of which is DinB2, an ortholog of the DNA repair-related protein DinP of Escherichia coli. Although this protein has been biochemically characterized previously and found to be capable of translesion synthesis in vitro, its in vivo function remains unknown. Using a novel method to induce dTTP deficiency in mycobacteria, we demonstrate that DinB2 can aid mycobacterial survival under such conditions. Apart from unraveling a specific role for the mycobacterial Y family DNA polymerase DinB2 for the first time, this study also paves the way for the development of drugs that can kill mycobacteria by inducing a dTTP-deficient state.
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Donigan KA, Cerritelli SM, McDonald JP, Vaisman A, Crouch RJ, Woodgate R. Unlocking the steric gate of DNA polymerase η leads to increased genomic instability in Saccharomyces cerevisiae. DNA Repair (Amst) 2015; 35:1-12. [PMID: 26340535 PMCID: PMC4651834 DOI: 10.1016/j.dnarep.2015.07.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/18/2015] [Accepted: 07/21/2015] [Indexed: 11/26/2022]
Abstract
DNA polymerase η (pol η) is best characterized for its ability to perform accurate and efficient translesion DNA synthesis (TLS) through cyclobutane pyrimidine dimers (CPDs). To ensure accurate bypass the polymerase is not only required to select the correct base, but also discriminate between NTPs and dNTPs. Most DNA polymerases have a conserved "steric gate" residue which functions to prevent incorporation of NMPs during DNA synthesis. Here, we demonstrate that the Phe35 residue of Saccharomyces cerevisiae pol η functions as a steric gate to limit the use of ribonucleotides during polymerization both in vitro and in vivo. Unlike the related pol ι enzyme, wild-type pol η does not readily incorporate NMPs in vitro. In contrast, a pol η F35A mutant incorporates NMPs on both damaged and undamaged DNA in vitro with a high degree of base selectivity. An S.cerevisiae strain expressing pol η F35A (rad30-F35A) that is also deficient for nucleotide excision repair (rad1Δ) and the TLS polymerase, pol ζ (rev3Δ), is extremely sensitive to UV-light. The sensitivity is due, in part, to RNase H2 activity, as an isogenic rnh201Δ strain is roughly 50-fold more UV-resistant than its RNH201(+) counterpart. Interestingly the rad1Δ rev3Δ rad30-F35A rnh201Δ strain exhibits a significant increase in the extent of spontaneous mutagenesis with a spectrum dominated by 1bp deletions at runs of template Ts. We hypothesize that the increased mutagenesis is due to rA incorporation at these sites and that the short poly rA tract is subsequently repaired in an error-prone manner by a novel repair pathway that is specifically targeted to polyribonucleotide tracks. These data indicate that under certain conditions, pol η can compete with the cell's replicases and gain access to undamaged genomic DNA. Such observations are consistent with a role for pol η in replicating common fragile sites (CFS) in human cells.
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Affiliation(s)
- Katherine A Donigan
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
| | - Susana M Cerritelli
- Program in Genomics of Differentiation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - John P McDonald
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
| | - Alexandra Vaisman
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
| | - Robert J Crouch
- Program in Genomics of Differentiation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA.
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40
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Lindsey-Boltz LA, Kemp MG, Hu J, Sancar A. Analysis of Ribonucleotide Removal from DNA by Human Nucleotide Excision Repair. J Biol Chem 2015; 290:29801-7. [PMID: 26491008 DOI: 10.1074/jbc.m115.695254] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Indexed: 11/06/2022] Open
Abstract
Ribonucleotides are incorporated into the genome during DNA replication. The enzyme RNase H2 plays a critical role in targeting the removal of these ribonucleotides from DNA, and defects in RNase H2 activity are associated with both genomic instability and the human autoimmune/inflammatory disorder Aicardi-Goutières syndrome. Whether additional general DNA repair mechanisms contribute to ribonucleotide removal from DNA in human cells is not known. Because of its ability to act on a wide variety of substrates, we examined a potential role for canonical nucleotide excision repair in the removal of ribonucleotides from DNA. However, using highly sensitive dual incision/excision assays, we find that ribonucleotides are not efficiently targeted by the human nucleotide excision repair system in vitro or in cultured human cells. These results suggest that nucleotide excision repair is unlikely to play a major role in the cellular response to ribonucleotide incorporation in genomic DNA in human cells.
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Affiliation(s)
- Laura A Lindsey-Boltz
- From the Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
| | - Michael G Kemp
- From the Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
| | - Jinchuan Hu
- From the Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
| | - Aziz Sancar
- From the Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
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41
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Abstract
The demonstration of DNA damage excision and repair replication by Setlow, Howard-Flanders, Hanawalt and their colleagues in the early 1960s, constituted the discovery of the ubiquitous pathway of nucleotide excision repair (NER). The serial steps in NER are similar in organisms from unicellular bacteria to complex mammals and plants, and involve recognition of lesions, adducts or structures that disrupt the DNA double helix, removal of a short oligonucleotide containing the offending lesion, synthesis of a repair patch copying the opposite undamaged strand, and ligation, to restore the DNA to its original form. The transcription-coupled repair (TCR) subpathway of NER, discovered nearly two decades later, is dedicated to the removal of lesions from the template DNA strands of actively transcribed genes. In this review I will outline the essential factors and complexes involved in NER in humans, and will comment on additional factors and metabolic processes that affect the efficiency of this important process.
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Affiliation(s)
- Graciela Spivak
- Department of Biology, Stanford University, Stanford, CA 94305-5020,USA.
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42
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Ding J, Taylor MS, Jackson AP, Reijns MAM. Genome-wide mapping of embedded ribonucleotides and other noncanonical nucleotides using emRiboSeq and EndoSeq. Nat Protoc 2015; 10:1433-44. [PMID: 26313479 DOI: 10.1038/nprot.2015.099] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Ribonucleotides are the most common noncanonical nucleotides incorporated into the genome of replicating cells. They are efficiently removed by ribonucleotide excision repair initiated by RNase H2 cleavage. In the absence of RNase H2, such embedded ribonucleotides can be used to track DNA polymerase activity in vivo. To determine their precise location in Saccharomyces cerevisiae, we developed embedded ribonucleotide sequencing (emRiboSeq), which uses recombinant RNase H2 to selectively create ligatable 3'-hydroxyl groups, in contrast to alternative methods that use alkaline hydrolysis. EmRiboSeq allows reproducible, strand-specific and potentially quantitative detection of embedded ribonucleotides at single-nucleotide resolution. For the genome-wide mapping of other noncanonical bases, RNase H2 can be replaced with specific nicking endonucleases in this protocol; we term this method endonuclease sequencing (EndoSeq). With the protocol taking <5 d to complete, these methods allow the in vivo study of DNA replication and repair, including the identification of replication origins and termination regions.
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Affiliation(s)
- James Ding
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Martin S Taylor
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Andrew P Jackson
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Martin A M Reijns
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
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43
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Jiang C, Shen F, Du J, Wang X, Su J, Liu Z, Huang X. DNA repair gene ERCC1 polymorphisms and glioma susceptibility among Chinese population: a meta-analysis. Int J Clin Exp Med 2015; 8:10248-10255. [PMID: 26379816 PMCID: PMC4565199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 06/10/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Excision repair cross complementation group 1 (ERCC1) has been shown to be involved in the progression of glioma susceptibility. However, the results remain conflict. The aim of this study was to systematically review and evaluate the role of ERCC1 C118T and C8092A polymorphisms in glioma risk among Chinese population. METHODS Related case-control studies were searched in online electronic databases. Odds ratio (OR) with its 95% confidence interval (CI) were employed to calculate the extracted data. RESULTS Total seven articles were retrieved, including 4426 subjects (1926 were glioma patients and 2500 were matched controls). No significant heterogeneity was found between studies (I(2)=0%, P>0.01). Our results demonstrated that A allele and AA genotype of ERCC1 C8092A polymorphism have a positive association with increasing the risk of glioma in the fixed-effect model (A vs. C: OR=1.13, 95% CI=1.02-1.25, P=0.02; AA vs. CC: OR=1.29, 95% CI=1.04-1.61, P=0.02; AA vs. CA+CC: OR=1.25, 95% CI=1.01-1.55, P=0.04). However, no significant relationship was found between C118T variant and glioma susceptibility. CONCLUSIONS Our results indicated that ERCC1 C8092A, not C118T polymorphism might be a biomarker for patients with glioma among Chinese population. Future studies with more ethnicities are needed to explore the precise association.
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Affiliation(s)
- Chunming Jiang
- Department of Pediatrics, Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou First People’s HospitalHangzhou 301103, Zhejiang, P. R. China
| | - Fang Shen
- Department of psychiatry, Tongde Hospital of Zhejiang ProvinceHangzhou 301103, Zhejiang, P. R. China
| | - Jianmin Du
- Department of Pediatrics, Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou First People’s HospitalHangzhou 301103, Zhejiang, P. R. China
| | - Xiaohua Wang
- Nanjing First Hospital, Nanjing Medical UniversityNanjing 210029, Jiangsu, P. R. China
| | - Jin Su
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical UniversityNanjing 210029, Jiangsu, P. R. China
| | - Zhanli Liu
- Department of Pediatrics, Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou First People’s HospitalHangzhou 301103, Zhejiang, P. R. China
| | - Xianmei Huang
- Department of Pediatrics, Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou First People’s HospitalHangzhou 301103, Zhejiang, P. R. China
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Abstract
Innate immune sensing of nucleic acids provides resistance against viral infection and is important in the aetiology of autoimmune diseases. AGS (Aicardi-Goutières syndrome) is a monogenic autoinflammatory disorder mimicking in utero viral infection of the brain. Phenotypically and immunologically, it also exhibits similarities to SLE (systemic lupus erythaematosus). Three of the six genes identified to date encode components of the ribonuclease H2 complex. As all six encode enzymes involved in nucleic acid metabolism, it is thought that pathogenesis involves the accumulation of nucleic acids to stimulate an inappropriate innate immune response. Given that AGS is a monogenic disorder with a defined molecular basis, we use it as a model for common autoimmune disease to investigate cellular processes and molecular pathways responsible for nucleic-acid-mediated autoimmunity. These investigations have also provided fundamental insights into the biological roles of the RNase H2 endonuclease enzyme. In the present article, we describe how human RNase H2 and its role in AGS were first identified, and give an overview of subsequent structural, biochemical, cellular and developmental studies of this enzyme. These investigations have culminated in establishing this enzyme as a key genome-surveillance enzyme required for mammalian genome stability.
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45
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Huang SYN, Ghosh S, Pommier Y. Topoisomerase I alone is sufficient to produce short DNA deletions and can also reverse nicks at ribonucleotide sites. J Biol Chem 2015; 290:14068-76. [PMID: 25887397 DOI: 10.1074/jbc.m115.653345] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Indexed: 11/06/2022] Open
Abstract
Ribonucleotide monophosphates (rNMPs) are among the most frequent form of DNA aberration, as high ratios of ribonucleotide triphosphate:deoxyribonucleotide triphosphate pools result in approximately two misincorporated rNMPs/kb of DNA. The main pathway for the removal of rNMPs is by RNase H2. However, in a RNase H2 knock-out yeast strain, a topoisomerase I (Top1)-dependent mutator effect develops with accumulation of short deletions within tandem repeats. Proposed models for these deletions implicated processing of Top1-generated nicks at rNMP sites and/or sequential Top1 binding, but experimental support has been lacking thus far. Here, we investigated the biochemical mechanism of the Top1-induced short deletions at the rNMP sites by generating nicked DNA substrates bearing 2',3'-cyclic phosphates at the nick sites, mimicking the Top1-induced nicks. We demonstrate that a second Top1 cleavage complex adjacent to the nick and subsequent faulty Top1 religation led to the short deletions. Moreover, when acting on the nicked DNA substrates containing 2',3'-cyclic phosphates, Top1 generated not only the short deletion, but also a full-length religated DNA product. A catalytically inactive Top1 mutant (Top1-Y723F) also induced the full-length products, indicating that Top1 binding independent of its enzymatic activity promotes the sealing of DNA backbones via nucleophilic attacks by the 5'-hydroxyl on the 2',3'-cyclic phosphate. The resealed DNA would allow renewed attempt for repair by the error-free RNase H2-dependent pathway in vivo. Our results provide direct evidence for the generation of short deletions by sequential Top1 cleavage events and for the promotion of nick religation at rNMP sites by Top1.
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Affiliation(s)
- Shar-Yin Naomi Huang
- From the Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Sanchari Ghosh
- From the Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Yves Pommier
- From the Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
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46
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Million-Weaver S, Samadpour AN, Moreno-Habel DA, Nugent P, Brittnacher MJ, Weiss E, Hayden HS, Miller SI, Liachko I, Merrikh H. An underlying mechanism for the increased mutagenesis of lagging-strand genes in Bacillus subtilis. Proc Natl Acad Sci U S A 2015; 112:E1096-105. [PMID: 25713353 PMCID: PMC4364195 DOI: 10.1073/pnas.1416651112] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We previously reported that lagging-strand genes accumulate mutations faster than those encoded on the leading strand in Bacillus subtilis. Although we proposed that orientation-specific encounters between replication and transcription underlie this phenomenon, the mechanism leading to the increased mutagenesis of lagging-strand genes remained unknown. Here, we report that the transcription-dependent and orientation-specific differences in mutation rates of genes require the B. subtilis Y-family polymerase, PolY1 (yqjH). We find that without PolY1, association of the replicative helicase, DnaC, and the recombination protein, RecA, with lagging-strand genes increases in a transcription-dependent manner. These data suggest that PolY1 promotes efficient replisome progression through lagging-strand genes, thereby reducing potentially detrimental breaks and single-stranded DNA at these loci. Y-family polymerases can alleviate potential obstacles to replisome progression by facilitating DNA lesion bypass, extension of D-loops, or excision repair. We find that the nucleotide excision repair (NER) proteins UvrA, UvrB, and UvrC, but not RecA, are required for transcription-dependent asymmetry in mutation rates of genes in the two orientations. Furthermore, we find that the transcription-coupling repair factor Mfd functions in the same pathway as PolY1 and is also required for increased mutagenesis of lagging-strand genes. Experimental and SNP analyses of B. subtilis genomes show mutational footprints consistent with these findings. We propose that the interplay between replication and transcription increases lesion susceptibility of, specifically, lagging-strand genes, activating an Mfd-dependent error-prone NER mechanism. We propose that this process, at least partially, underlies the accelerated evolution of lagging-strand genes.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ivan Liachko
- Genome Sciences, University of Washington, Seattle, WA 98195
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47
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Vaisman A, Woodgate R. Redundancy in ribonucleotide excision repair: Competition, compensation, and cooperation. DNA Repair (Amst) 2015; 29:74-82. [PMID: 25753809 DOI: 10.1016/j.dnarep.2015.02.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 02/07/2015] [Accepted: 02/09/2015] [Indexed: 10/24/2022]
Abstract
The survival of all living organisms is determined by their ability to reproduce, which in turn depends on accurate duplication of chromosomal DNA. In order to ensure the integrity of genome duplication, DNA polymerases are equipped with stringent mechanisms by which they select and insert correctly paired nucleotides with a deoxyribose sugar ring. However, this process is never 100% accurate. To fix occasional mistakes, cells have evolved highly sophisticated and often redundant mechanisms. A good example is mismatch repair (MMR), which corrects the majority of mispaired bases and which has been extensively studied for many years. On the contrary, pathways leading to the replacement of nucleotides with an incorrect sugar that is embedded in chromosomal DNA have only recently attracted significant attention. This review describes progress made during the last few years in understanding such pathways in both prokaryotes and eukaryotes. Genetic studies in Escherichia coli and Saccharomyces cerevisiae demonstrated that MMR has the capacity to replace errant ribonucleotides, but only when the base is mispaired. In contrast, the major evolutionarily conserved ribonucleotide repair pathway initiated by the ribonuclease activity of type 2 Rnase H has broad specificity. In yeast, this pathway also requires the concerted action of Fen1 and pol δ, while in bacteria it can be successfully completed by DNA polymerase I. Besides these main players, all organisms contain alternative enzymes able to accomplish the same tasks, although with differing efficiency and fidelity. Studies in bacteria have very recently demonstrated that isolated rNMPs can be removed from genomic DNA by error-free nucleotide excision repair (NER), while studies in yeast suggest the involvement of topoisomerase 1 in alternative mutagenic ribonucleotide processing. This review summarizes the most recent progress in understanding the ribonucleotide repair mechanisms in prokaryotes and eukaryotes.
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Affiliation(s)
- Alexandra Vaisman
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA.
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48
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Minias AE, Brzostek AM, Minias P, Dziadek J. The deletion of rnhB in Mycobacterium smegmatis does not affect the level of RNase HII substrates or influence genome stability. PLoS One 2015; 10:e0115521. [PMID: 25603150 PMCID: PMC4300193 DOI: 10.1371/journal.pone.0115521] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 11/25/2014] [Indexed: 11/24/2022] Open
Abstract
RNase HII removes RNA from RNA/DNA hybrids, such as single ribonucleotides and RNA primers generated during DNA synthesis. Both, RNase HII substrates and RNase HII deficiency have been associated with genome instability in several organisms, and genome instability is a major force leading to the acquisition of drug resistance in bacteria. Understanding the mechanisms that underlie this phenomenon is one of the challenges in identifying efficient methods to combat bacterial pathogens. The aim of the present study was set to investigate the role of rnhB, presumably encoding RNase HII, in maintaining genome stability in the M. tuberculosis model organism Mycobacterium smegmatis. We performed gene replacement through homologous recombination to obtain mutant strains of Mycobacterium smegmatis lacking the rnhB gene. The mutants did not present an altered phenotype, according to the growth rate in liquid culture or susceptibility to hydroxyurea, and did not show an increase in the spontaneous mutation rate, determined using the Luria-Delbrück fluctuation test for streptomycin resistance in bacteria. The mutants also did not present an increase in the level of RNase HII substrates, measured as the level of alkaline degradation of chromosomal DNA or determined through immunodetection. We conclude that proteins other than RnhB proteins efficiently remove RNase HII substrates in M. smegmatis. These results highlight differences in the basic biology between Mycobacteria and eukaryotes and between different species of bacteria.
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Affiliation(s)
- Alina E. Minias
- Department of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- Department of Microbiology, Biotechnology and Immunology, University of Lodz, Lodz, Poland
- * E-mail: (AM); (JD)
| | - Anna M. Brzostek
- Department of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Piotr Minias
- Department of Teacher Training and Biodiversity Studies, University of Lodz, Lodz, Poland
| | - Jaroslaw Dziadek
- Department of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- * E-mail: (AM); (JD)
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49
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Sidorenko J, Ukkivi K, Kivisaar M. NER enzymes maintain genome integrity and suppress homologous recombination in the absence of exogenously induced DNA damage in Pseudomonas putida. DNA Repair (Amst) 2015; 25:15-26. [DOI: 10.1016/j.dnarep.2014.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 10/29/2014] [Accepted: 11/05/2014] [Indexed: 02/04/2023]
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50
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Abstract
In all living cells, DNA is the storage medium for genetic information. Being quite stable, DNA is well-suited for its role in storage and propagation of information, but RNA is also covalently included in DNA through various mechanisms. Recent studies also demonstrate useful aspects of including ribonucleotides in the genome during repair. Therefore, our understanding of the consequences of RNA inclusion into bacterial genomic DNA is just beginning, but with its high frequency of occurrence the consequences and potential benefits are likely to be numerous and diverse. In this review, we discuss the processes that cause ribonucleotide inclusion in genomic DNA, the pathways important for ribonucleotide removal and the consequences that arise should ribonucleotides remain nested in genomic DNA.
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Affiliation(s)
- Jeremy W. Schroeder
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Justin R. Randall
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lindsay A. Matthews
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lyle A. Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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