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Hurben AK, Zhang Q, Galligan JJ, Tretyakova N, Erber L. Endogenous Cellular Metabolite Methylglyoxal Induces DNA-Protein Cross-Links in Living Cells. ACS Chem Biol 2024; 19:1291-1302. [PMID: 38752800 DOI: 10.1021/acschembio.4c00100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Methylglyoxal (MGO) is an electrophilic α-oxoaldehyde generated endogenously through metabolism of carbohydrates and exogenously due to autoxidation of sugars, degradation of lipids, and fermentation during food and drink processing. MGO can react with nucleophilic sites within proteins and DNA to form covalent adducts. MGO-induced advanced glycation end-products such as protein and DNA adducts are thought to be involved in oxidative stress, inflammation, diabetes, cancer, renal failure, and neurodegenerative diseases. Additionally, MGO has been hypothesized to form toxic DNA-protein cross-links (DPC), but the identities of proteins participating in such cross-linking in cells have not been determined. In the present work, we quantified DPC formation in human cells exposed to MGO and identified proteins trapped on DNA upon MGO exposure using mass spectrometry-based proteomics. A total of 265 proteins were found to participate in MGO-derived DPC formation including gene products engaged in telomere organization, nucleosome assembly, and gene expression. In vitro experiments confirmed DPC formation between DNA and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), as well as histone proteins H3.1 and H4. Collectively, our study provides the first evidence for MGO-mediated DNA-protein cross-linking in living cells, prompting future studies regarding the relevance of these toxic lesions in cancer, diabetes, and other diseases linked to elevated MGO levels.
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Affiliation(s)
- Alexander K Hurben
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Qi Zhang
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - James J Galligan
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Natalia Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Luke Erber
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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2
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Bacurio JHT, Yawson P, Thomforde J, Zhang Q, Kumar HV, Den Hartog H, Tretyakova NY, Basu AK. 5-Formylcytosine mediated DNA-peptide cross-link induces predominantly semi-targeted mutations in both Escherichia coli and human cells. J Biol Chem 2024; 300:105786. [PMID: 38401843 PMCID: PMC10966706 DOI: 10.1016/j.jbc.2024.105786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/12/2024] [Accepted: 02/19/2024] [Indexed: 02/26/2024] Open
Abstract
Histone proteins can become trapped on DNA in the presence of 5-formylcytosine (5fC) to form toxic DNA-protein conjugates. Their repair may involve proteolytic digestion resulting in DNA-peptide cross-links (DpCs). Here, we have investigated replication of a model DpC comprised of an 11-mer peptide (NH2-GGGKGLGK∗GGA) containing an oxy-lysine residue (K∗) conjugated to 5fC in DNA. Both CXG and CXT (where X = 5fC-DpC) sequence contexts were examined. Replication of both constructs gave low viability (<10%) in Escherichia coli, whereas TLS efficiency was high (72%) in HEK 293T cells. In E. coli, the DpC was bypassed largely error-free, inducing only 2 to 3% mutations, which increased to 4 to 5% with SOS. For both sequences, semi-targeted mutations were dominant, and for CXG, the predominant mutations were G→T and G→C at the 3'-base to the 5fC-DpC. In HEK 293T cells, 7 to 9% mutations occurred, and the dominant mutations were the semi-targeted G → T for CXG and T → G for CXT. These mutations were reduced drastically in cells deficient in hPol η, hPol ι or hPol ζ, suggesting a role of these TLS polymerases in mutagenic TLS. Steady-state kinetics studies using hPol η confirmed that this polymerase induces G → T and T → G transversions at the base immediately 3' to the DpC. This study reveals a unique replication pattern of 5fC-conjugated DpCs, which are bypassed largely error-free in both E. coli and human cells and induce mostly semi-targeted mutations at the 3' position to the lesion.
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Affiliation(s)
| | - Priscilla Yawson
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Jenna Thomforde
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Qi Zhang
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Honnaiah Vijay Kumar
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Holly Den Hartog
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Natalia Y Tretyakova
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ashis K Basu
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA.
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3
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Essawy MM, Campbell C. Enzymatic Processing of DNA-Protein Crosslinks. Genes (Basel) 2024; 15:85. [PMID: 38254974 PMCID: PMC10815813 DOI: 10.3390/genes15010085] [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: 12/01/2023] [Revised: 12/30/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
DNA-protein crosslinks (DPCs) represent a unique and complex form of DNA damage formed by covalent attachment of proteins to DNA. DPCs are formed through a variety of mechanisms and can significantly impede essential cellular processes such as transcription and replication. For this reason, anti-cancer drugs that form DPCs have proven effective in cancer therapy. While cells rely on numerous different processes to remove DPCs, the molecular mechanisms responsible for orchestrating these processes remain obscure. Having this insight could potentially be harnessed therapeutically to improve clinical outcomes in the battle against cancer. In this review, we describe the ways cells enzymatically process DPCs. These processing events include direct reversal of the DPC via hydrolysis, nuclease digestion of the DNA backbone to delete the DPC and surrounding DNA, proteolytic processing of the crosslinked protein, as well as covalent modification of the DNA-crosslinked proteins with ubiquitin, SUMO, and Poly(ADP) Ribose (PAR).
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Affiliation(s)
| | - Colin Campbell
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA;
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Zhang Q, Tretyakova N. Incorporation of inosine into DNA by human polymerase eta (Polη): kinetics of nucleotide misincorporation and structural basis for the mutagenicity. Biochem J 2023; 480:1479-1483. [PMID: 37746864 PMCID: PMC10586757 DOI: 10.1042/bcj20230159] [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: 08/04/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/26/2023]
Abstract
Inosine, a purine nucleoside containing the hypoxanthine (HX) nucleobase, can form in DNA via hydrolytic deamination of adenine. Due to its structural similarity to guanine and the geometry of Watson-Crick base pairs, inosine can mispair with cytosine upon catalysis by DNA polymerases, leading to AT → GC mutations. Additionally, inosine plays an essential role in purine nucleotide biosynthesis, and inosine triphosphate is present in living cells. In a recent publication, Averill and Jung examined the possibility of polη catalyzed incorporation of deoxyinosine triphosphate (dITP) across dC and dT in a DNA template. They found that dITP can be incorporated across C or T, with the ratio of 13.7. X ray crystallography studies revealed that the mutagenic incorporation of dITP by human polη was affected by several factors including base pair geometry in the active site of the polymerase, tautomerization of nucleobases, and the interaction of the incoming dITP nucleotide with active site residues of polη. This study demonstrates that TLS incorporation of inosine monophosphate (IMP) into growing DNA chains contributes to its mutagenic potential in cells.
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Affiliation(s)
- Qi Zhang
- Department of Medicinal Chemistry, University of Minnesota-Twin Cities, Minneapolis, U.S.A
| | - Natalia Tretyakova
- Department of Medicinal Chemistry, University of Minnesota-Twin Cities, Minneapolis, U.S.A
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Richie-Jannetta R, Pallan P, Kingsley PJ, Kamdar N, Egli M, Marnett LJ. The peroxidation-derived DNA adduct, 6-oxo-M 1dG, is a strong block to replication by human DNA polymerase η. J Biol Chem 2023; 299:105067. [PMID: 37468099 PMCID: PMC10450521 DOI: 10.1016/j.jbc.2023.105067] [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: 03/22/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023] Open
Abstract
The DNA adduct 6-oxo-M1dG, (3-(2'-deoxy-β-D-erythro-pentofuranosyl)-6-oxo-pyrimido(1,2alpha)purin-10(3H)-one) is formed in the genome via oxidation of the peroxidation-derived adduct M1dG. However, the effect of 6-oxo-M1dG adducts on subsequent DNA replication is unclear. Here we investigated the ability of the human Y-family polymerase hPol η to bypass 6-oxo-M1dG. Using steady-state kinetics and analysis of DNA extension products by liquid chromatography-tandem mass spectrometry, we found hPol η preferentially inserts a dAMP or dGMP nucleotide into primer-templates across from the 6-oxo-M1dG adduct, with dGMP being slightly preferred. We also show primer-templates with a 3'-terminal dGMP or dAMP across from 6-oxo-M1dG were extended to a greater degree than primers with a dCMP or dTMP across from the adduct. In addition, we explored the structural basis for bypass of 6-oxo-M1dG by hPol η using X-ray crystallography of both an insertion-stage and an extension-stage complex. In the insertion-stage complex, we observed that the incoming dCTP opposite 6-oxo-M1dG, although present during crystallization, was not present in the active site. We found the adduct does not interact with residues in the hPol η active site but rather forms stacking interactions with the base pair immediately 3' to the adduct. In the extension-stage complex, we observed the 3' hydroxyl group of the primer strand dGMP across from 6-oxo-M1dG is not positioned correctly to form a phosphodiester bond with the incoming dCTP. Taken together, these results indicate 6-oxo-M1dG forms a strong block to DNA replication by hPol η and provide a structural basis for its blocking ability.
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Affiliation(s)
- Robyn Richie-Jannetta
- A. B. Hancock, Jr, Memorial Laboratory for Cancer Research, Departments of Biochemistry, Chemistry and Pharmacology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Pradeep Pallan
- Department of Biochemistry, Center for Structural Biology and Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Philip J Kingsley
- A. B. Hancock, Jr, Memorial Laboratory for Cancer Research, Departments of Biochemistry, Chemistry and Pharmacology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Nikhil Kamdar
- A. B. Hancock, Jr, Memorial Laboratory for Cancer Research, Departments of Biochemistry, Chemistry and Pharmacology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Martin Egli
- Department of Biochemistry, Center for Structural Biology and Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Lawrence J Marnett
- A. B. Hancock, Jr, Memorial Laboratory for Cancer Research, Departments of Biochemistry, Chemistry and Pharmacology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
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Kaszubowski JD, Trakselis MA. Beyond the Lesion: Back to High Fidelity DNA Synthesis. Front Mol Biosci 2022; 8:811540. [PMID: 35071328 PMCID: PMC8766770 DOI: 10.3389/fmolb.2021.811540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/16/2021] [Indexed: 12/16/2022] Open
Abstract
High fidelity (HiFi) DNA polymerases (Pols) perform the bulk of DNA synthesis required to duplicate genomes in all forms of life. Their structural features, enzymatic mechanisms, and inherent properties are well-described over several decades of research. HiFi Pols are so accurate that they become stalled at sites of DNA damage or lesions that are not one of the four canonical DNA bases. Once stalled, the replisome becomes compromised and vulnerable to further DNA damage. One mechanism to relieve stalling is to recruit a translesion synthesis (TLS) Pol to rapidly synthesize over and past the damage. These TLS Pols have good specificities for the lesion but are less accurate when synthesizing opposite undamaged DNA, and so, mechanisms are needed to limit TLS Pol synthesis and recruit back a HiFi Pol to reestablish the replisome. The overall TLS process can be complicated with several cellular Pols, multifaceted protein contacts, and variable nucleotide incorporation kinetics all contributing to several discrete substitution (or template hand-off) steps. In this review, we highlight the mechanistic differences between distributive equilibrium exchange events and concerted contact-dependent switching by DNA Pols for insertion, extension, and resumption of high-fidelity synthesis beyond the lesion.
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Pujari SS, Wu M, Thomforde J, Wang ZA, Chao C, Olson NM, Erber L, Pomerantz WCK, Cole P, Tretyakova NY. Site‐Specific 5‐Formyl Cytosine Mediated DNA‐Histone Cross‐Links: Synthesis and Polymerase Bypass by Human DNA Polymerase η. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Suresh S. Pujari
- Department of Medicinal Chemistry College of Pharmacy, and Masonic Cancer Center University of Minnesota Minneapolis MN 55455 USA
| | - Mingxuan Wu
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston, MA 02115 USA
- Current address: School of Science Westlake University Institute of Natural Sciences, Westlake Institute for Advanced Study 18 Shilongshan Road, 310024 Hangzhou Zhejiang Province China
| | - Jenna Thomforde
- Department of Medicinal Chemistry College of Pharmacy, and Masonic Cancer Center University of Minnesota Minneapolis MN 55455 USA
| | - Zhipeng A. Wang
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston, MA 02115 USA
| | - Christopher Chao
- Department of Medicinal Chemistry College of Pharmacy, and Masonic Cancer Center University of Minnesota Minneapolis MN 55455 USA
| | - Noelle M. Olson
- Department of Chemistry University of Minnesota Minneapolis MN 55455 USA
| | - Luke Erber
- Department of Medicinal Chemistry College of Pharmacy, and Masonic Cancer Center University of Minnesota Minneapolis MN 55455 USA
| | | | - Philip Cole
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston, MA 02115 USA
| | - Natalia Y. Tretyakova
- Department of Medicinal Chemistry College of Pharmacy, and Masonic Cancer Center University of Minnesota Minneapolis MN 55455 USA
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8
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Pujari SS, Wu M, Thomforde J, Wang ZA, Chao C, Olson N, Erber L, Pomerantz WCK, Cole P, Tretyakova NY. Site-Specific 5-Formyl Cytosine Mediated DNA-Histone Cross-Links: Synthesis and Polymerase Bypass by Human DNA Polymerase η. Angew Chem Int Ed Engl 2021; 60:26489-26494. [PMID: 34634172 PMCID: PMC8775767 DOI: 10.1002/anie.202109418] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/06/2021] [Indexed: 01/16/2023]
Abstract
DNA-protein cross-links (DPCs) between DNA epigenetic mark 5-formylC and lysine residues of histone proteins spontaneously form in human cells. Such conjugates are likely to influence chromatin structure and mediate DNA replication, transcription, and repair, but are challenging to study due to their reversible nature. Here we report the construction of site specific, hydrolytically stable DPCs between 5fdC in DNA and K4 of histone H3 and an investigation of their effects on DNA replication. Our approach employs oxime ligation, allowing for site-specific conjugation of histones to DNA under physiological conditions. Primer extension experiments revealed that histone H3-DNA crosslinks blocked DNA synthesis by hPol η polymerase, but were bypassed following proteolytic processing.
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Affiliation(s)
- Suresh S. Pujari
- Department of Medicinal Chemistry, College of Pharmacy, and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Mingxuan Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA. 02115, USA
| | - Jenna Thomforde
- Department of Medicinal Chemistry, College of Pharmacy, and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Zhipeng A. Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA. 02115, USA
| | - Christopher Chao
- Department of Medicinal Chemistry, College of Pharmacy, and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Noelle Olson
- Department of Chemistry, University of Minnesota, Minnesota 55455, USA
| | - Luke Erber
- Department of Medicinal Chemistry, College of Pharmacy, and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | | | - Philip Cole
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA. 02115, USA
| | - Natalia Y. Tretyakova
- Department of Medicinal Chemistry, College of Pharmacy, and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Pujari SS, Tretyakova N. Synthesis and polymerase bypass studies of DNA-peptide and DNA-protein conjugates. Methods Enzymol 2021; 661:363-405. [PMID: 34776221 PMCID: PMC10159213 DOI: 10.1016/bs.mie.2021.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
DNA-peptide (DpCs) and DNA-protein cross-links (DPCs) are DNA lesions formed when polypeptides and nuclear proteins become covalently trapped on DNA strands. DNA-protein cross-links are of enormous size and hence pose challenges to cell survival by blocking DNA replication, transcription, and repair. However, DPCs can undergo proteolytic degradation via various pathways to give shorter polypeptide chains (DpCs). The resulting DpC lesions are efficiently bypassed by translesion synthesis (TLS) DNA polymerases like κ, η, δ, etc., although polymerase bypass efficiency as well as correct base insertion depends heavily on size, sequence context, and position of peptides in DpCs. This chapter explores various synthetic methods to generate these lesions including detailed experimental procedures for the construction of DpCs and DPCs via reductive amination and oxime ligation. Further we describe biochemical experiments to investigate the effects of these lesions on DNA polymerase activity and fidelity.
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Affiliation(s)
- Suresh S Pujari
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States.
| | - Natalia Tretyakova
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States.
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