1
|
Hoitsma NM, Norris J, Khoang TH, Kaushik V, Chadda R, Antony E, Hedglin M, Freudenthal BD. Mechanistic insight into AP-endonuclease 1 cleavage of abasic sites at stalled replication fork mimics. Nucleic Acids Res 2023; 51:6738-6753. [PMID: 37264933 PMCID: PMC10359615 DOI: 10.1093/nar/gkad481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 05/13/2023] [Accepted: 05/31/2023] [Indexed: 06/03/2023] Open
Abstract
Many types of damage, including abasic sites, block replicative DNA polymerases causing replication fork uncoupling and generating ssDNA. AP-Endonuclease 1 (APE1) has been shown to cleave abasic sites in ssDNA. Importantly, APE1 cleavage of ssDNA at a replication fork has significant biological implications by generating double strand breaks that could collapse the replication fork. Despite this, the molecular basis and efficiency of APE1 processing abasic sites at replication forks remain elusive. Here, we investigate APE1 cleavage of abasic substrates that mimic APE1 interactions at stalled replication forks or gaps. We determine that APE1 has robust activity on these substrates, like dsDNA, and report rates for cleavage and product release. X-ray structures visualize the APE1 active site, highlighting an analogous mechanism is used to process ssDNA substrates as canonical APE1 activity on dsDNA. However, mutational analysis reveals R177 to be uniquely critical for the APE1 ssDNA cleavage mechanism. Additionally, we investigate the interplay between APE1 and Replication Protein A (RPA), the major ssDNA-binding protein at replication forks, revealing that APE1 can cleave an abasic site while RPA is still bound to the DNA. Together, this work provides molecular level insights into abasic ssDNA processing by APE1, including the presence of RPA.
Collapse
Affiliation(s)
- Nicole M Hoitsma
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jessica Norris
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Thu H Khoang
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Vikas Kaushik
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Rahul Chadda
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| |
Collapse
|
2
|
Cox MM, Goodman MF, Keck JL, van Oijen A, Lovett ST, Robinson A. Generation and Repair of Postreplication Gaps in Escherichia coli. Microbiol Mol Biol Rev 2023; 87:e0007822. [PMID: 37212693 PMCID: PMC10304936 DOI: 10.1128/mmbr.00078-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
When replication forks encounter template lesions, one result is lesion skipping, where the stalled DNA polymerase transiently stalls, disengages, and then reinitiates downstream to leave the lesion behind in a postreplication gap. Despite considerable attention in the 6 decades since postreplication gaps were discovered, the mechanisms by which postreplication gaps are generated and repaired remain highly enigmatic. This review focuses on postreplication gap generation and repair in the bacterium Escherichia coli. New information to address the frequency and mechanism of gap generation and new mechanisms for their resolution are described. There are a few instances where the formation of postreplication gaps appears to be programmed into particular genomic locations, where they are triggered by novel genomic elements.
Collapse
Affiliation(s)
- Michael M. Cox
- Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Myron F. Goodman
- Department of Biological Sciences, University of Southern California, University Park, Los Angeles, California, USA
- Department of Chemistry, University of Southern California, University Park, Los Angeles, California, USA
| | - James L. Keck
- Department of Biological Chemistry, University of Wisconsin—Madison School of Medicine, Madison, Wisconsin, USA
| | - Antoine van Oijen
- Molecular Horizons, University of Wollongong, Wollongong, New South Wales, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
| | - Susan T. Lovett
- Department of Biology, Brandeis University, Waltham, Massachusetts, USA
| | - Andrew Robinson
- Molecular Horizons, University of Wollongong, Wollongong, New South Wales, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
| |
Collapse
|
3
|
Dyrkheeva NS, Malakhova AA, Zakharenko AL, Okorokova LS, Shtokalo DN, Pavlova SV, Medvedev SP, Zakian SM, Nushtaeva AA, Tupikin AE, Kabilov MR, Khodyreva SN, Luzina OA, Salakhutdinov NF, Lavrik OI. Transcriptomic Analysis of CRISPR/Cas9-Mediated PARP1-Knockout Cells under the Influence of Topotecan and TDP1 Inhibitor. Int J Mol Sci 2023; 24:ijms24065148. [PMID: 36982223 PMCID: PMC10049738 DOI: 10.3390/ijms24065148] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/04/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
Topoisomerase 1 (TOP1) is an enzyme that regulates DNA topology and is essential for replication, recombination, and other processes. The normal TOP1 catalytic cycle involves the formation of a short-lived covalent complex with the 3' end of DNA (TOP1 cleavage complex, TOP1cc), which can be stabilized, resulting in cell death. This fact substantiates the effectiveness of anticancer drugs-TOP1 poisons, such as topotecan, that block the relegation of DNA and fix TOP1cc. Tyrosyl-DNA phosphodiesterase 1 (TDP1) is able to eliminate TOP1cc. Thus, TDP1 interferes with the action of topotecan. Poly(ADP-ribose) polymerase 1 (PARP1) is a key regulator of many processes in the cell, such as maintaining the integrity of the genome, regulation of the cell cycle, cell death, and others. PARP1 also controls the repair of TOP1cc. We performed a transcriptomic analysis of wild type and PARP1 knockout HEK293A cells treated with topotecan and TDP1 inhibitor OL9-119 alone and in combination. The largest number of differentially expressed genes (DEGs, about 4000 both up- and down-regulated genes) was found in knockout cells. Topotecan and OL9-119 treatment elicited significantly fewer DEGs in WT cells and negligible DEGs in PARP1-KO cells. A significant part of the changes caused by PARP1-KO affected the synthesis and processing of proteins. Differences under the action of treatment with TOP1 or TDP1 inhibitors alone were found in the signaling pathways for the development of cancer, DNA repair, and the proteasome. The drug combination resulted in DEGs in the ribosome, proteasome, spliceosome, and oxidative phosphorylation pathways.
Collapse
Affiliation(s)
- Nadezhda S Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Anastasia A Malakhova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
- Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Aleksandra L Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | | | - Dmitriy N Shtokalo
- AcademGene LLC, 6 Lavrentyeva Ave., 630090 Novosibirsk, Russia
- A.P. Ershov Institute of Informatics Systems SB RAS, 6 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Sophia V Pavlova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
- Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Sergey P Medvedev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
- Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Suren M Zakian
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
- Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Anna A Nushtaeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Alexey E Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Svetlana N Khodyreva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Olga A Luzina
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Nariman F Salakhutdinov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
- Department of Molecular Biology and Biotechnology, Novosibirsk State University, 630090 Novosibirsk, Russia
| |
Collapse
|
4
|
Zakharenko AL, Malakhova AA, Dyrkheeva NS, Okorokova LS, Medvedev SP, Zakian SM, Kabilov MR, Tupikin AA, Lavrik OI. PARP1 Gene Knockout Suppresses Expression of DNA Base Excision Repair Genes. DOKL BIOCHEM BIOPHYS 2023; 508:6-11. [PMID: 36653586 PMCID: PMC10042944 DOI: 10.1134/s1607672922700028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 01/20/2023]
Abstract
The effect of PARP1 knockout in HEK293 cells on the gene expression of DNA base excision repair (BER) proteins was studied. It was shown that the expression of all differentially expressed genes (DEGs) of BER was reduced by knockout. The expression of the DNA glycosylase gene NEIL1, which is considered to be one of the common "hubs" for binding BER proteins, has changed the most. The expression of genes of auxiliary subunits of DNA polymerases δ and ε is also significantly reduced. The PARP1 gene knockout cell line obtained is an adequate cell model for studying the activity of the BER process in the absence of PARP1 and testing drugs aimed at inhibiting repair processes. It has been found for the first time that knockout of the PARP1 gene results in a significant change in the level of expression of proteins responsible for ribosome biogenesis and the functioning of the proteasome.
Collapse
Affiliation(s)
- A L Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Malakhova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Meshalkin National Medical Research Center of the Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - N S Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | - S P Medvedev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Meshalkin National Medical Research Center of the Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - S M Zakian
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Meshalkin National Medical Research Center of the Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - M R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - O I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
| |
Collapse
|
5
|
Rechkunova NI, Zhdanova PV, Lebedeva NA, Maltseva EA, Koval VV, Lavrik OI. Structural features of DNA polymerases β and λ in complex with benzo[a]pyrene-adducted DNA cause a difference in lesion tolerance. DNA Repair (Amst) 2022; 116:103353. [DOI: 10.1016/j.dnarep.2022.103353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 05/31/2022] [Indexed: 11/28/2022]
|
6
|
Hreusova M, Brabec V, Novakova O. Processing and Bypass of a Site-Specific DNA Adduct of the Cytotoxic Platinum-Acridinylthiourea Conjugate by Polymerases Involved in DNA Repair: Biochemical and Thermodynamic Aspects. Int J Mol Sci 2021; 22:ijms221910838. [PMID: 34639179 PMCID: PMC8509567 DOI: 10.3390/ijms221910838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 11/24/2022] Open
Abstract
DNA-dependent DNA and RNA polymerases are important modulators of biological functions such as replication, transcription, recombination, or repair. In this work performed in cell-free media, we studied the ability of selected DNA polymerases to overcome a monofunctional adduct of the cytotoxic/antitumor platinum–acridinylthiourea conjugate [PtCl(en)(L)](NO3)2 (en = ethane-1,2-diamine, L = 1-[2-(acridin-9-ylamino)ethyl]-1,3-dimethylthiourea) (ACR) in its favored 5′-CG sequence. We focused on how a single site-specific ACR adduct with intercalation potency affects the processivity and fidelity of DNA-dependent DNA polymerases involved in translesion synthesis (TLS) and repair. The ability of the G(N7) hybrid ACR adduct formed in the 5′-TCGT sequence of a 24-mer DNA template to inhibit the synthesis of a complementary DNA strand by the exonuclease-deficient Klenow fragment of DNA polymerase I (KFexo−) and human polymerases eta, kappa, and iota was supplemented by thermodynamic analysis of the polymerization process. Thermodynamic parameters of a simulated translesion synthesis across the ACR adduct were obtained by using microscale thermophoresis (MST). Our results show a strong inhibitory effect of an ACR adduct on enzymatic TLS: there was only small synthesis of a full-length product (less than 10%) except polymerase eta (~20%). Polymerase eta was able to most efficiently bypass the ACR hybrid adduct. Incorporation of a correct dCMP opposite the modified G residue is preferred by all the four polymerases tested. On the other hand, the frequency of misinsertions increased. The relative efficiency of misinsertions is higher than that of matched cytidine monophosphate but still lower than for the nonmodified control duplex. Thermodynamic inspection of the simulated TLS revealed a significant stabilization of successively extended primer/template duplexes containing an ACR adduct. Moreover, no significant decrease of dissociation enthalpy change behind the position of the modification can contribute to the enzymatic TLS observed with the DNA-dependent, repair-involved polymerases. This TLS could lead to a higher tolerance of cancer cells to the ACR conjugate compared to its enhanced analog, where thiourea is replaced by an amidine group: [PtCl(en)(L)](NO3)2 (complex AMD, en = ethane-1,2-diamine, L = N-[2-(acridin-9-ylamino)ethyl]-N-methylpropionamidine).
Collapse
Affiliation(s)
- Monika Hreusova
- Czech Academy of Sciences, Institute of Biophysics, Kralovopolska 135, CZ 61265 Brno, Czech Republic; (M.H.); (V.B.)
| | - Viktor Brabec
- Czech Academy of Sciences, Institute of Biophysics, Kralovopolska 135, CZ 61265 Brno, Czech Republic; (M.H.); (V.B.)
- Department of Biophysics, Faculty of Science, Palacky University, Slechtitelu 27, CZ 78371 Olomouc, Czech Republic
| | - Olga Novakova
- Czech Academy of Sciences, Institute of Biophysics, Kralovopolska 135, CZ 61265 Brno, Czech Republic; (M.H.); (V.B.)
- Correspondence: ; Tel.: +420-541-517-135
| |
Collapse
|
7
|
Kavli B, Iveland TS, Buchinger E, Hagen L, Liabakk NB, Aas PA, Obermann TS, Aachmann FL, Slupphaug G. RPA2 winged-helix domain facilitates UNG-mediated removal of uracil from ssDNA; implications for repair of mutagenic uracil at the replication fork. Nucleic Acids Res 2021; 49:3948-3966. [PMID: 33784377 PMCID: PMC8053108 DOI: 10.1093/nar/gkab195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/04/2021] [Accepted: 03/10/2021] [Indexed: 01/14/2023] Open
Abstract
Uracil occurs at replication forks via misincorporation of deoxyuridine monophosphate (dUMP) or via deamination of existing cytosines, which occurs 2-3 orders of magnitude faster in ssDNA than in dsDNA and is 100% miscoding. Tethering of UNG2 to proliferating cell nuclear antigen (PCNA) allows rapid post-replicative removal of misincorporated uracil, but potential 'pre-replicative' removal of deaminated cytosines in ssDNA has been questioned since this could mediate mutagenic translesion synthesis and induction of double-strand breaks. Here, we demonstrate that uracil-DNA glycosylase (UNG), but not SMUG1 efficiently excises uracil from replication protein A (RPA)-coated ssDNA and that this depends on functional interaction between the flexible winged-helix (WH) domain of RPA2 and the N-terminal RPA-binding helix in UNG. This functional interaction is promoted by mono-ubiquitination and diminished by cell-cycle regulated phosphorylations on UNG. Six other human proteins bind the RPA2-WH domain, all of which are involved in DNA repair and replication fork remodelling. Based on this and the recent discovery of the AP site crosslinking protein HMCES, we propose an integrated model in which templated repair of uracil and potentially other mutagenic base lesions in ssDNA at the replication fork, is orchestrated by RPA. The UNG:RPA2-WH interaction may also play a role in adaptive immunity by promoting efficient excision of AID-induced uracils in transcribed immunoglobulin loci.
Collapse
Affiliation(s)
- Bodil Kavli
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
| | - Tobias S Iveland
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,Cancer Clinic, St. Olavs Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
| | - Edith Buchinger
- NOBIPOL, Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, N-7034 Trondheim, Norway
| | - Lars Hagen
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway.,PROMEC Proteomics and Modomics Experimental Core at NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
| | - Nina B Liabakk
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
| | - Per A Aas
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
| | - Tobias S Obermann
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
| | - Finn L Aachmann
- NOBIPOL, Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, N-7034 Trondheim, Norway
| | - Geir Slupphaug
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway.,PROMEC Proteomics and Modomics Experimental Core at NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
| |
Collapse
|
8
|
Romero ZJ, Armstrong TJ, Henrikus SS, Chen SH, Glass DJ, Ferrazzoli AE, Wood EA, Chitteni-Pattu S, van Oijen AM, Lovett ST, Robinson A, Cox MM. Frequent template switching in postreplication gaps: suppression of deleterious consequences by the Escherichia coli Uup and RadD proteins. Nucleic Acids Res 2020; 48:212-230. [PMID: 31665437 PMCID: PMC7145654 DOI: 10.1093/nar/gkz960] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 10/03/2019] [Accepted: 10/16/2019] [Indexed: 12/21/2022] Open
Abstract
When replication forks encounter template DNA lesions, the lesion is simply skipped in some cases. The resulting lesion-containing gap must be converted to duplex DNA to permit repair. Some gap filling occurs via template switching, a process that generates recombination-like branched DNA intermediates. The Escherichia coli Uup and RadD proteins function in different pathways to process the branched intermediates. Uup is a UvrA-like ABC family ATPase. RadD is a RecQ-like SF2 family ATPase. Loss of both functions uncovers frequent and RecA-independent deletion events in a plasmid-based assay. Elevated levels of crossing over and repeat expansions accompany these deletion events, indicating that many, if not most, of these events are associated with template switching in postreplication gaps as opposed to simple replication slippage. The deletion data underpin simulations indicating that multiple postreplication gaps may be generated per replication cycle. Both Uup and RadD bind to branched DNAs in vitro. RadD protein suppresses crossovers and Uup prevents nucleoid mis-segregation. Loss of Uup and RadD function increases sensitivity to ciprofloxacin. We present Uup and RadD as genomic guardians. These proteins govern two pathways for resolution of branched DNA intermediates such that potentially deleterious genome rearrangements arising from frequent template switching are averted.
Collapse
Affiliation(s)
- Zachary J Romero
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Thomas J Armstrong
- Molecular Horizons Institute and School of Chemistry, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Sarah S Henrikus
- Molecular Horizons Institute and School of Chemistry, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Stefanie H Chen
- Biotechnology Program, North Carolina State University, Raleigh, NC 27695, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - David J Glass
- Department of Biology and Rosenstiel Center, Brandeis University, Waltham, MA 02453, USA
| | - Alexander E Ferrazzoli
- Department of Biology and Rosenstiel Center, Brandeis University, Waltham, MA 02453, USA
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Antoine M van Oijen
- Molecular Horizons Institute and School of Chemistry, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Susan T Lovett
- Department of Biology and Rosenstiel Center, Brandeis University, Waltham, MA 02453, USA
| | - Andrew Robinson
- Molecular Horizons Institute and School of Chemistry, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| |
Collapse
|
9
|
Jiang Z, Lai Y, Beaver JM, Tsegay PS, Zhao ML, Horton JK, Zamora M, Rein HL, Miralles F, Shaver M, Hutcheson JD, Agoulnik I, Wilson SH, Liu Y. Oxidative DNA Damage Modulates DNA Methylation Pattern in Human Breast Cancer 1 (BRCA1) Gene via the Crosstalk between DNA Polymerase β and a de novo DNA Methyltransferase. Cells 2020; 9:E225. [PMID: 31963223 PMCID: PMC7016758 DOI: 10.3390/cells9010225] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/15/2019] [Accepted: 01/13/2020] [Indexed: 12/13/2022] Open
Abstract
DNA damage and base excision repair (BER) are actively involved in the modulation of DNA methylation and demethylation. However, the underlying molecular mechanisms remain unclear. In this study, we seek to understand the mechanisms by exploring the effects of oxidative DNA damage on the DNA methylation pattern of the tumor suppressor breast cancer 1 (BRCA1) gene in the human embryonic kidney (HEK) HEK293H cells. We found that oxidative DNA damage simultaneously induced DNA demethylation and generation of new methylation sites at the CpGs located at the promoter and transcribed regions of the gene ranging from -189 to +27 in human cells. We demonstrated that DNA damage-induced demethylation was mediated by nucleotide misincorporation by DNA polymerase β (pol β). Surprisingly, we found that the generation of new DNA methylation sites was mediated by coordination between pol β and the de novo DNA methyltransferase, DNA methyltransferase 3b (DNMT3b), through the interaction between the two enzymes in the promoter and encoding regions of the BRCA1 gene. Our study provides the first evidence that oxidative DNA damage can cause dynamic changes in DNA methylation in the BRCA1 gene through the crosstalk between BER and de novo DNA methylation.
Collapse
Affiliation(s)
- Zhongliang Jiang
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA; (Z.J.); (J.M.B.); (P.S.T.)
| | - Yanhao Lai
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (Y.L.); (M.Z.); (H.L.R.); (F.M.)
| | - Jill M. Beaver
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA; (Z.J.); (J.M.B.); (P.S.T.)
| | - Pawlos S. Tsegay
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA; (Z.J.); (J.M.B.); (P.S.T.)
| | - Ming-Lang Zhao
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA; (M.-L.Z.); (J.K.H.); (S.H.W.)
| | - Julie K. Horton
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA; (M.-L.Z.); (J.K.H.); (S.H.W.)
| | - Marco Zamora
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (Y.L.); (M.Z.); (H.L.R.); (F.M.)
| | - Hayley L. Rein
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (Y.L.); (M.Z.); (H.L.R.); (F.M.)
| | - Frank Miralles
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (Y.L.); (M.Z.); (H.L.R.); (F.M.)
| | - Mohammad Shaver
- Department of Biomedical Engineering, Florida International University, Miami, FL 33199, USA; (M.S.); (J.D.H.)
| | - Joshua D. Hutcheson
- Department of Biomedical Engineering, Florida International University, Miami, FL 33199, USA; (M.S.); (J.D.H.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA;
| | - Irina Agoulnik
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA;
- Department of Human and Molecular Genetics, Florida International University, Miami, FL 33199, USA
| | - Samuel H. Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA; (M.-L.Z.); (J.K.H.); (S.H.W.)
| | - Yuan Liu
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA; (Z.J.); (J.M.B.); (P.S.T.)
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (Y.L.); (M.Z.); (H.L.R.); (F.M.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA;
| |
Collapse
|
10
|
Translesion DNA Synthesis Across Lesions Induced by Oxidative Products of Pyrimidines: An Insight into the Mechanism by Microscale Thermophoresis. Int J Mol Sci 2019; 20:ijms20205012. [PMID: 31658654 PMCID: PMC6829345 DOI: 10.3390/ijms20205012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 01/02/2023] Open
Abstract
Oxidative stress in cells can lead to the accumulation of reactive oxygen species and oxidation of DNA precursors. Oxidized nucleotides such as 2'-deoxyribo-5-hydroxyuridin (HdU) and 2'-deoxyribo-5-hydroxymethyluridin (HMdU) can be inserted into DNA during replication and repair. HdU and HMdU have attracted particular interest because they have different effects on damaged-DNA processing enzymes that control the downstream effects of the lesions. Herein, we studied the chemically simulated translesion DNA synthesis (TLS) across the lesions formed by HdU or HMdU using microscale thermophoresis (MST). The thermodynamic changes associated with replication across HdU or HMdU show that the HdU paired with the mismatched deoxyribonucleoside triphosphates disturbs DNA duplexes considerably less than thymidine (dT) or HMdU. Moreover, we also demonstrate that TLS by DNA polymerases across the lesion derived from HdU was markedly less extensive and potentially more mutagenic than that across the lesion formed by HMdU. Thus, DNA polymerization by DNA polymerase η (polη), the exonuclease-deficient Klenow fragment of DNA polymerase I (KF-), and reverse transcriptase from human immunodeficiency virus type 1 (HIV-1 RT) across these pyrimidine lesions correlated with the different stabilization effects of the HdU and HMdU in DNA duplexes revealed by MST. The equilibrium thermodynamic data obtained by MST can explain the influence of the thermodynamic alterations on the ability of DNA polymerases to bypass lesions induced by oxidative products of pyrimidines. The results also highlighted the usefulness of MST in evaluating the impact of oxidative products of pyrimidines on the processing of these lesions by damaged DNA processing enzymes.
Collapse
|
11
|
Variable termination sites of DNA polymerases encountering a DNA-protein cross-link. PLoS One 2018; 13:e0198480. [PMID: 29856874 PMCID: PMC5983568 DOI: 10.1371/journal.pone.0198480] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/18/2018] [Indexed: 11/19/2022] Open
Abstract
DNA-protein cross-links (DPCs) are important DNA lesions induced by endogenous crosslinking agents such as formaldehyde or acetaldehyde, as well as ionizing radiation, cancer chemotherapeutic drugs, and abortive action of some enzymes. Due to their very bulky nature, they are expected to interfere with DNA and RNA synthesis and DNA repair. DPCs are highly genotoxic and the ability of cells to deal with them is relevant for many chemotherapeutic interventions. However, interactions of DNA polymerases with DPCs have been poorly studied due to the lack of a convenient experimental model. We have used NaBH4-induced trapping of E. coli formamidopyrimidine-DNA glycosylase with DNA to construct model DNA polymerase substrates containing a DPC in single-stranded template, or in the template strand of double-stranded DNA, or in the non-template (displaced) strand of double-stranded DNA. Nine DNA polymerases belonging to families A, B, X, and Y were studied with respect to their behavior upon encountering a DPC: Klenow fragment of E. coli DNA polymerase I, Thermus aquaticus DNA polymerase I, Pyrococcus furiosus DNA polymerase, Sulfolobus solfataricus DNA polymerase IV, human DNA polymerases β, κ and λ, and DNA polymerases from bacteriophages T4 and RB69. Although none were able to fully bypass DPCs in any context, Family B DNA polymerases (T4, RB69) and Family Y DNA polymerase IV were able to elongate the primer up to the site of the cross-link if a DPC was located in single-stranded template or in the displaced strand. In other cases, DNA synthesis stopped 4-5 nucleotides before the site of the cross-link in single-stranded template or in double-stranded DNA if the polymerases could displace the downstream strand. We suggest that termination of DNA polymerases on a DPC is mostly due to the unrelieved conformational strain experienced by the enzyme when pressing against the cross-linked protein molecule.
Collapse
|
12
|
Abstract
Life as we know it, simply would not exist without DNA replication. All living organisms utilize a complex machinery to duplicate their genomes and the central role in this machinery belongs to replicative DNA polymerases, enzymes that are specifically designed to copy DNA. "Hassle-free" DNA duplication exists only in an ideal world, while in real life, it is constantly threatened by a myriad of diverse challenges. Among the most pressing obstacles that replicative polymerases often cannot overcome by themselves are lesions that distort the structure of DNA. Despite elaborate systems that cells utilize to cleanse their genomes of damaged DNA, repair is often incomplete. The persistence of DNA lesions obstructing the cellular replicases can have deleterious consequences. One of the mechanisms allowing cells to complete replication is "Translesion DNA Synthesis (TLS)". TLS is intrinsically error-prone, but apparently, the potential downside of increased mutagenesis is a healthier outcome for the cell than incomplete replication. Although most of the currently identified eukaryotic DNA polymerases have been implicated in TLS, the best characterized are those belonging to the "Y-family" of DNA polymerases (pols η, ι, κ and Rev1), which are thought to play major roles in the TLS of persisting DNA lesions in coordination with the B-family polymerase, pol ζ. In this review, we summarize the unique features of these DNA polymerases by mainly focusing on their biochemical and structural characteristics, as well as potential protein-protein interactions with other critical factors affecting TLS regulation.
Collapse
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
| |
Collapse
|
13
|
Kozhukhar N, Spadafora D, Fayzulin R, Shokolenko IN, Alexeyev M. The efficiency of the translesion synthesis across abasic sites by mitochondrial DNA polymerase is low in mitochondria of 3T3 cells. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4390-4396. [PMID: 26470640 DOI: 10.3109/19401736.2015.1089539] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Translesion synthesis by specialized DNA polymerases is an important strategy for mitigating DNA damage that cannot be otherwise repaired either due to the chemical nature of the lesion. Apurinic/Apyrimidinic (abasic, AP) sites represent a block to both transcription and replication, and are normally repaired by the base excision repair (BER) pathway. However, when the number of abasic sites exceeds BER capacity, mitochondrial DNA is targeted for degradation. Here, we used two uracil-N-glycosylase (UNG1) mutants, Y147A or N204D, to generate AP sites directly in the mtDNA of NIH3T3 cells in vivo at sites normally occupied by T or C residues, respectively, and to study repair of these lesions in their native context. We conclude that mitochondrial DNA polymerase γ (Pol γ) is capable of translesion synthesis across AP sites in mitochondria of the NIH3T3 cells, and obeys the A-rule. However, in our system, base excision repair (BER) and mtDNA degradation occur more frequently than translesion bypass of AP sites.
Collapse
Affiliation(s)
- Natalya Kozhukhar
- a Department of Physiology and Cell Biology , University of South Alabama , Mobile , AL , USA
| | - Domenico Spadafora
- b Department of Pharmacology , University of South Alabama , Mobile , AL , USA and
| | - Rafik Fayzulin
- a Department of Physiology and Cell Biology , University of South Alabama , Mobile , AL , USA
| | - Inna N Shokolenko
- c Department of Biomedical Sciences , University of South Alabama, Patt Capps Covey College of Allied Health Professions , Mobile , AL , USA
| | - Mikhail Alexeyev
- a Department of Physiology and Cell Biology , University of South Alabama , Mobile , AL , USA
| |
Collapse
|
14
|
Jiang Z, Xu M, Lai Y, Laverde EE, Terzidis MA, Masi A, Chatgilialoglu C, Liu Y. Bypass of a 5',8-cyclopurine-2'-deoxynucleoside by DNA polymerase β during DNA replication and base excision repair leads to nucleotide misinsertions and DNA strand breaks. DNA Repair (Amst) 2015; 33:24-34. [PMID: 26123757 DOI: 10.1016/j.dnarep.2015.06.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/23/2015] [Accepted: 06/09/2015] [Indexed: 12/18/2022]
Abstract
5',8-Cyclopurine-2'-deoxynucleosides including 5',8-cyclo-dA (cdA) and 5',8-cyclo-dG (cdG) are induced by hydroxyl radicals resulting from oxidative stress such as ionizing radiation. 5',8-cyclopurine-2'-deoxynucleoside lesions are repaired by nucleotide excision repair with low efficiency, thereby leading to their accumulation in the human genome and lesion bypass by DNA polymerases during DNA replication and base excision repair (BER). In this study, for the first time, we discovered that DNA polymerase β (pol β) efficiently bypassed a 5'R-cdA, but inefficiently bypassed a 5'S-cdA during DNA replication and BER. We found that cell extracts from pol β wild-type mouse embryonic fibroblasts exhibited significant DNA synthesis activity in bypassing a cdA lesion located in replication and BER intermediates. However, pol β knock-out cell extracts exhibited little DNA synthesis to bypass the lesion. This indicates that pol β plays an important role in bypassing a cdA lesion during DNA replication and BER. Furthermore, we demonstrated that pol β inserted both a correct and incorrect nucleotide to bypass a cdA at a low concentration. Nucleotide misinsertion was significantly stimulated by a high concentration of pol β, indicating a mutagenic effect induced by pol β lesion bypass synthesis of a 5',8-cyclopurine-2'-deoxynucleoside. Moreover, we found that bypass of a 5'S-cdA by pol β generated an intermediate that failed to be extended by pol β, resulting in accumulation of single-strand DNA breaks. Our study provides the first evidence that pol β plays an important role in bypassing a 5',8-cyclo-dA during DNA replication and repair, as well as new insight into mutagenic effects and genome instability resulting from pol β bypassing of a cdA lesion.
Collapse
Affiliation(s)
- Zhongliang Jiang
- Department of Chemistry and Biochemistry, USA; Biochemistry Ph.D. Program, USA
| | - Meng Xu
- Department of Chemistry and Biochemistry, USA
| | - Yanhao Lai
- Department of Chemistry and Biochemistry, USA
| | | | - Michael A Terzidis
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Annalisa Masi
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Chryssostomos Chatgilialoglu
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy; Institute of Nanoscience and Nanotechnology, N.C.S.R. "Demokritos", 15341, Agia Paraskevi, Athens, Greece
| | - Yuan Liu
- Department of Chemistry and Biochemistry, USA; Biochemistry Ph.D. Program, USA; Biomolecular Sciences Institute, School of Integrated Sciences and Humanities, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA.
| |
Collapse
|
15
|
Starostenko LV, Rechkunova NI, Lebedeva NA, Kolbanovskiy A, Geacintov NE, Lavrik OI. Human DNA polymerases catalyze lesion bypass across benzo[ a ]pyrene-derived DNA adduct clustered with an abasic site. DNA Repair (Amst) 2014; 24:1-9. [DOI: 10.1016/j.dnarep.2014.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 09/10/2014] [Accepted: 10/03/2014] [Indexed: 01/30/2023]
|
16
|
Xu M, Lai Y, Jiang Z, Terzidis MA, Masi A, Chatgilialoglu C, Liu Y. A 5', 8-cyclo-2'-deoxypurine lesion induces trinucleotide repeat deletion via a unique lesion bypass by DNA polymerase β. Nucleic Acids Res 2014; 42:13749-63. [PMID: 25428354 PMCID: PMC4267656 DOI: 10.1093/nar/gku1239] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
5',8-cyclo-2'-deoxypurines (cdPus) are common forms of oxidized DNA lesions resulting from endogenous and environmental oxidative stress such as ionizing radiation. The lesions can only be repaired by nucleotide excision repair with a low efficiency. This results in their accumulation in the genome that leads to stalling of the replication DNA polymerases and poor lesion bypass by translesion DNA polymerases. Trinucleotide repeats (TNRs) consist of tandem repeats of Gs and As and therefore are hotspots of cdPus. In this study, we provided the first evidence that both (5'R)- and (5'S)-5',8-cyclo-2'-deoxyadenosine (cdA) in a CAG repeat tract caused CTG repeat deletion exclusively during DNA lagging strand maturation and base excision repair. We found that a cdA induced the formation of a CAG loop in the template strand, which was skipped over by DNA polymerase β (pol β) lesion bypass synthesis. This subsequently resulted in the formation of a long flap that was efficiently cleaved by flap endonuclease 1, thereby leading to repeat deletion. Our study indicates that accumulation of cdPus in the human genome can lead to TNR instability via a unique lesion bypass by pol β.
Collapse
Affiliation(s)
- Meng Xu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW, 8th Street, Miami, FL 33199, USA
| | - Yanhao Lai
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW, 8th Street, Miami, FL 33199, USA
| | - Zhongliang Jiang
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW, 8th Street, Miami, FL 33199, USA
| | - Michael A Terzidis
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Annalisa Masi
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Chryssostomos Chatgilialoglu
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy Institute of Nanoscience and Nanotechnology, N.C.S.R. 'Demokritos', 15341 Agia, Paraskevi, Athens, Greece
| | - Yuan Liu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW, 8th Street, Miami, FL 33199, USA Biomolecular Sciences Institute, School of Integrated Sciences and Humanities, Florida International University, 11200 SW, 8th Street, Miami, FL 33199, USA
| |
Collapse
|
17
|
Villani G, Shevelev I, Orlando E, Pospiech H, Syvaoja JE, Markkanen E, Hubscher U, Le Gac NT. Gap-directed translesion DNA synthesis of an abasic site on circular DNA templates by a human replication complex. PLoS One 2014; 9:e93908. [PMID: 24710081 PMCID: PMC3977967 DOI: 10.1371/journal.pone.0093908] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/08/2014] [Indexed: 12/02/2022] Open
Abstract
DNA polymerase ε (pol ε) is believed to be the leading strand replicase in eukaryotes whereas pols λ and β are thought to be mainly involved in re-synthesis steps of DNA repair. DNA elongation by the human pol ε is halted by an abasic site (apurinic/apyrimidinic (AP) site). We have previously reported that human pols λ, β and η can perform translesion synthesis (TLS) of an AP site in the presence of pol ε. In the case of pol λ and β, this TLS requires the presence of a gap downstream from the product synthetized by the ε replicase. However, since these studies were conducted exclusively with a linear DNA template, we decided to test whether the structure of the template could influence the capacity of the pols ε, λ, β and η to perform TLS of an AP site. Therefore, we have investigated the replication of damaged “minicircle” DNA templates. In addition, replication of circular DNA requires, beyond DNA pols, the processivity clamp PCNA, the clamp loader replication factor C (RFC), and the accessory proteins replication protein A (RPA). Finally we have compared the capacity of unmodified versus monoubiquitinated PCNA in sustaining TLS by pols λ and η on a circular template. Our results indicate that in vitro gap-directed TLS synthesis by pols λ and β in the presence of pol ε, RPA and PCNA is unaffected by the structure of the DNA template. Moreover, monoubiquitination of PCNA does not affect TLS by pol λ while it appears to slightly stimulate TLS by pol η.
Collapse
Affiliation(s)
- Giuseppe Villani
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
| | - Igor Shevelev
- Leibniz Institute for Age Research - Fritz Lipman Institute, Jena, Germany
- Department of Biochemistry, University of Oulu, Oulu, Finland
| | - Eleonora Orlando
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
| | - Helmut Pospiech
- Leibniz Institute for Age Research - Fritz Lipman Institute, Jena, Germany
- Department of Biochemistry, University of Oulu, Oulu, Finland
| | - Juhani E. Syvaoja
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Enni Markkanen
- Biochemistry Group, Department of Oncology, Gray Institute for Radiation Oncology and Biology, Oxford, United Kingdom
| | - Ulrich Hubscher
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zürich-Irchel, Zürich, Switzerland
| | - Nicolas Tanguy Le Gac
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
- * E-mail:
| |
Collapse
|
18
|
Skosareva LV, Lebedeva NA, Lavrik OI, Rechkunova NI. Repair of bulky DNA lesions deriving from polycyclic aromatic hydrocarbons. Mol Biol 2013. [DOI: 10.1134/s002689331305018x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
19
|
Furrer A, van Loon B. Handling the 3-methylcytosine lesion by six human DNA polymerases members of the B-, X- and Y-families. Nucleic Acids Res 2013; 42:553-66. [PMID: 24097443 PMCID: PMC3874200 DOI: 10.1093/nar/gkt889] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Alkylating agents often generate 3-methylcytosine (3meC) lesions that are efficiently repaired by AlkB homologues. If AlkB homologue proteins are not functional, or the number of 3meC lesions exceeds the cellular repair capacity, the damage will persist in the genome and become substrate of DNA polymerases (Pols). Though alkylating agents are present in our environment and used in the clinics, currently nothing is known about the impact of 3meC on the accuracy and efficiency of human Pols. Here we compared the 3meC bypass properties of six human Pols belonging to the three families: B (Pol δ), X (Pols β and λ) and Y (Pols κ, ι and η). We show that under replicative conditions 3meC impairs B-family, blocks X-family, but not Y-family Pols, in particular Pols η and ι. These Pols successfully synthesize opposite 3meC; Pol ι preferentially misincorporates dTTP and Pol η dATP. The most efficient extenders from 3meC base-paired primers are Pols κ and η. Finally, using xeroderma pigmentosum variant patient cell extracts, we provide evidence that the presence of functional Pol η is mandatory to efficiently overcome 3meC by mediating complete bypass or extension. Our data suggest that Pol η is crucial for efficient 3meC bypass.
Collapse
Affiliation(s)
- Antonia Furrer
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | | |
Collapse
|
20
|
Abstract
Living cells are continually exposed to DNA-damaging agents that threaten their genomic integrity. Although DNA repair processes rapidly target the damaged DNA for repair, some lesions nevertheless persist and block genome duplication by the cell's replicase. To avoid the deleterious consequence of a stalled replication fork, cells use specialized polymerases to traverse the damage. This process, termed "translesion DNA synthesis" (TLS), affords the cell additional time to repair the damage before the replicase returns to complete genome duplication. In many cases, this damage-tolerance mechanism is error-prone, and cell survival is often associated with an increased risk of mutagenesis and carcinogenesis. Despite being tightly regulated by a variety of transcriptional and posttranslational controls, the low-fidelity TLS polymerases also gain access to undamaged DNA where their inaccurate synthesis may actually be beneficial for genetic diversity and evolutionary fitness.
Collapse
Affiliation(s)
- Myron F Goodman
- Department of Biological Sciences and Department of Chemistry, University of Southern California, University Park, Los Angeles, California 90089-2910
| | | |
Collapse
|
21
|
siRNA screening identifies differences in the Fanconi anemia pathway in BALB/c-Trp53+/- with susceptibility versus C57BL/6-Trp53+/- mice with resistance to mammary tumors. Oncogene 2013; 32:5458-70. [PMID: 23435420 PMCID: PMC3898496 DOI: 10.1038/onc.2013.38] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 12/18/2012] [Accepted: 12/27/2012] [Indexed: 12/24/2022]
Abstract
BALB/c mice heterozygous for Trp53 develop a high proportion of spontaneous mammary tumors, a phenotype distinct from other mouse strains. BALB/c-Trp53+/- female mice, thus, resemble the hereditary Li-Fraumeni syndrome (LFS) characterized by early-onset of breast cancer, even though LFS involves TP53 mutations, which may involve not only loss- but also gain-of-function. Previous analysis of tumors in BALB/c-Trp53+/- females showed frequent loss of heterozygosity involving the wild-type allele of Trp53 and displayed characteristics indicative of mitotic recombination. Critical involvement of DNA double-strand break (DSB) repair dysfunction, particularly of homologous recombination (HR), was also noticed in the etiology of human breast cancer. To better define functional alterations in BALB/c-Trp53+/- mice, we applied a fluorescence-based DSB repair assay on mouse embryonic fibroblasts (MEFs) from BALB/c-Trp53+/- versus C57BL/6J-Trp53+/- mice. This approach revealed deregulation of HR but not non-homologous end-joining (NHEJ) in BALB/c-Trp53+/-, which was further confirmed for mammary epithelial cells. Screening of a small interfering RNA-library targeting DSB repair, recombination, replication and signaling genes, identified 25 genes causing differences between homologous DSB repair in the two strains upon silencing. Interactome analysis of the hits revealed clustering of replication-related and fanconi anemia (FA)/breast cancer susceptibility (BRCA) genes. Further dissection of the functional change in BALB/c-Trp53+/- by immunofluorescence microscopy of nuclear 53BP1, Replication protein A (RPA) and Rad51 foci uncovered differences in crosslink and replication-associated repair. Chromosome breakage, G2 arrest and biochemical analyses indicated a FA pathway defect downstream of FancD2 associated with reduced levels of BRCA2. Consistent with polygenic models for BRCA, mammary carcinogenesis in BALB/c-Trp53+/- mice may, therefore, be promoted by a BRCA modifier allele in the FA pathway in the context of partial p53 loss-of-function.
Collapse
|
22
|
Menezes MR, Sweasy JB. Mouse models of DNA polymerases. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2012; 53:645-665. [PMID: 23001998 DOI: 10.1002/em.21731] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 08/01/2012] [Accepted: 08/07/2012] [Indexed: 06/01/2023]
Abstract
In 1956, Arthur Kornberg discovered the mechanism of the biological synthesis of DNA and was awarded the Nobel Prize in Physiology or Medicine in 1959 for this contribution, which included the isolation and characterization of Escherichia coli DNA polymerase I. Now there are 15 known DNA polymerases in mammalian cells that belong to four different families. These DNA polymerases function in many different cellular processes including DNA replication, DNA repair, and damage tolerance. Several biochemical and cell biological studies have provoked a further investigation of DNA polymerase function using mouse models in which polymerase genes have been altered using gene-targeting techniques. The phenotypes of mice harboring mutant alleles reveal the prominent role of DNA polymerases in embryogenesis, prevention of premature aging, and cancer suppression.
Collapse
Affiliation(s)
- Miriam R Menezes
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
| | | |
Collapse
|
23
|
Fenske AE, Glaesener S, Bokemeyer C, Thomale J, Dahm-Daphi J, Honecker F, Dartsch DC. Cisplatin resistance induced in germ cell tumour cells is due to reduced susceptibility towards cell death but not to altered DNA damage induction or repair. Cancer Lett 2012; 324:171-8. [DOI: 10.1016/j.canlet.2012.05.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 05/09/2012] [Accepted: 05/11/2012] [Indexed: 11/26/2022]
|
24
|
Wang JL, Guo HL, Wang PC, Liu CG. Age-dependent down-regulation of DNA polymerase δ1 in human lymphocytes. Mol Cell Biochem 2012; 371:157-63. [PMID: 22915169 DOI: 10.1007/s11010-012-1432-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Accepted: 08/03/2012] [Indexed: 01/19/2023]
Abstract
Aging progress and degeneracy of functional activity are mainly attributed to the decreased DNA repair potential. DNA polymerase (pol) δ activity plays an essential role in genome stability by virtue of its crucial DNA replication and repair capacity. To order to clarify the role of DNA pol δ in aging progression, we firstly examined the expressions of its catalytic subunit named DNA pol δ1 in human lymphocytes at different age stages, respectively, and then observed the effect of diseases on DNA pol δ1 in vivo and of nutriture on its expressions in 2BS cells in vitro. Blood samples from the healthy subjects and patients with diabetes mellitus and coronary heart disease were collected, respectively, for analysis of transcription and protein expressions of DNA pol δ1 by RT-PCR and western blot. 2BS cells of PD30 and PD47 were incubated in both normal medium and other mediums of different nutritures for verifying the differential expressions of DNA pol δ1. Results showed that the mRNA expression of DNA pol δ1 decreased substantially with age and the protein levels were well consistent with gene levels. Furthermore, there were no significant differences in DNA pol δ1 expressions between the groups of healthy individuals and the age matched patients. In addition, DNA pol δ1 gene expression levels were not affected by nutritional status in vitro. Our findings collectively confirmed that the down-regulations of DNA pol δ1 are age-related and have little bearing on diseases and nutritures. DNA pol δ1 has great potential for a new biomarker of aging.
Collapse
Affiliation(s)
- Jin-Ling Wang
- Department of Clinical Laboratory, Xuanwu Hospital, Capital Medical University, Beijing 100053, People's Republic of China
| | | | | | | |
Collapse
|
25
|
Skosareva LV, Lebedeva NA, Rechkunova NI, Kolbanovskiy A, Geacintov NE, Lavrik OI. Human DNA polymerase λ catalyzes lesion bypass across benzo[a]pyrene-derived DNA adduct during base excision repair. DNA Repair (Amst) 2012; 11:367-73. [PMID: 22317757 DOI: 10.1016/j.dnarep.2012.01.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 11/15/2011] [Accepted: 01/03/2012] [Indexed: 11/17/2022]
Abstract
The combined action of oxidative stress and genotoxic polycyclic aromatic hydrocarbons derivatives can lead to cluster-type DNA damage that includes both a modified nucleotide and a bulky lesion. As an example, we investigated the possibility of repair of an AP site located opposite a minor groove-positioned (+)-trans-BPDE-dG or a base-displaced intercalated (+)-cis-BPDE-dG adduct (BP lesion) by a BER system. Oligonucleotides with single uracil residues in certain positions were annealed with complementary oligonucleotides bearing either a cis- or trans-BP adduct. The resulting DNA duplexes contained dU either directly opposite the modified dG or shifted to adjacent 5' (-1) or 3' (+1) positions. Digestion with uracil DNA glycosylase was utilized to generate AP sites which were then hydrolyzed by APE1, and the resulting gaps were processed by DNA polymerase β (Polβ) or λ (Polλ). The AP sites in position -1 can be repaired effectively using APE1 and Polβ or Polλ. The AP sites opposite the BP lesions can be repaired using Polλ in the case of cis- but not the trans-isomeric adduct. The AP sites in position +1 are the most difficult to repair. In the case of the AP site located in position +1, the activity of Polλ does not depend on the stereoisomeric properties of the BP lesions and dCTP is the preferred inserted substrate in both cases. The capability of Polλ to introduce the correct dNTP opposite the cis-BP-dG adduct in gap filling reactions suggests that this polymerase may play a specialized role in the process of repair of these kinds of lesions.
Collapse
Affiliation(s)
- Lidia V Skosareva
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | | | | | | | | | | |
Collapse
|