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Sugiyama T. Biochemical reconstitution of a major age-related cancer mutational signature by heat-induced spontaneous deamination of 5-methylcytosine residues, repair of uracil residues, and DNA replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595323. [PMID: 38826364 PMCID: PMC11142167 DOI: 10.1101/2024.05.22.595323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Non-enzymatic spontaneous deamination of 5-methylcytosine, producing thymine, is the proposed etiology of cancer mutational signature 1, which is the most predominant signature in all cancers. Here, the proposed mutational process was reconstituted using synthetic DNA and purified proteins. First, single-stranded DNA containing 5-methylcytosine at CpG context was incubated at an elevated temperature to accelerate spontaneous DNA damage. Then, the DNA was treated with uracil DNA glycosylase to remove uracil residues that were formed by deamination of cytosine. The resulting DNA was then used as a template for DNA synthesis by yeast DNA polymerase δ. The DNA products were analyzed by next-generation DNA sequencing, and mutation frequencies were quantified. The observed mutations after this process were exclusively C>T mutations at CpG context, which was very similar to signature 1. When 5-methylcytosine modification and uracil DNA glycosylase were both omitted, C>T mutations were produced on C residues in all sequence contexts, but these mutations were diminished by uracil DNA glycosylase-treatment. These results indicate that the CpG>TpG mutations were produced by the deamination of 5-methylcytosine. Additional mutations, mainly C>G, were introduced by yeast DNA polymerase ζ on the heat-damaged DNA, indicating that G residues of the templates were also damaged. However, the damage on G residues was not converted to mutations with DNA polymerase δ or ε. These results provide biochemical evidence to support that the majority of mutations in cancers are produced by ordinary DNA replication on spontaneously damaged DNA.
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2
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Liang C, Yang Y, Ning P, Chang C, Cao W. Structural and functional coupling in cross-linking uracil-DNA glycosylase UDGX. Biosci Rep 2024; 44:BSR20231551. [PMID: 38059429 PMCID: PMC10776899 DOI: 10.1042/bsr20231551] [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: 09/11/2023] [Revised: 11/14/2023] [Accepted: 12/05/2023] [Indexed: 12/08/2023] Open
Abstract
Enzymes in uracil-DNA glycosylase (UDG) superfamily are involved in removal of deaminated nucleobases such as uracil, methylcytosine derivatives such as formylcytosine and carboxylcytosine, and other base damage in DNA repair. UDGX is the latest addition of a new class to the UDG superfamily with a sporadic distribution in bacteria. UDGX type enzymes have a distinct biochemical property of cross-linking itself to the resulting AP site after uracil removal. Built on previous biochemical and structural analyses, this work comprehensively investigated the kinetic and enzymatic properties of Mycobacterium smegmatis UDGX. Kinetics and mutational analyses, coupled with structural information, defined the roles of E52, D56, D59, F65 of motif 1, H178 of motif 2 and N91, K94, R107 and H109 of motif 3 play in uracil excision and cross-linking. More importantly, a series of quantitative analyses underscored the structural coupling through inter-motif and intra-motif interactions and subsequent functional coupling of the uracil excision and cross-linking reactions. A catalytic model is proposed, which underlies this catalytic feature unique to UDGX type enzymes. This study offers new insight on the catalytic mechanism of UDGX and provides a unique example of enzyme evolution.
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Affiliation(s)
- Chuan Liang
- Department of Genetics and Biochemistry, Clemson University, Room 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, U.S.A
| | - Ye Yang
- Department of Genetics and Biochemistry, Clemson University, Room 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, U.S.A
| | - Ping Ning
- Department of Genetics and Biochemistry, Clemson University, Room 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, U.S.A
| | - Chenyan Chang
- Department of Genetics and Biochemistry, Clemson University, Room 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, U.S.A
| | - Weiguo Cao
- Department of Genetics and Biochemistry, Clemson University, Room 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, U.S.A
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3
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Li J, Yang Y, Chang C, Cao W. DR0022 from Deinococcus radiodurans is an acid uracil-DNA glycosylase. FEBS J 2022; 289:6420-6434. [PMID: 35607831 PMCID: PMC9796141 DOI: 10.1111/febs.16533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/08/2022] [Accepted: 05/23/2022] [Indexed: 01/02/2023]
Abstract
Uracil-DNA glycosylase (UDG) initiates base excision repair (BER) by removing damaged or modified nucleobases during DNA repair or mammalian demethylation. The UDG superfamily consists of at least six families with a variety of catalytic specificities and functions. Deinococcus radiodurans, an extreme radiation resistant bacterium, contains multiple members of UDG enzymes within its genome. The present study reveals that the putative protein, DR0022, is a uracil-DNA glycosylase that requires acidic conditions for its glycosylase activity, which is the first case of such an enzyme within the UDG superfamily. The key residues in the catalytic motifs are investigated by biochemical, enzyme kinetics, and de novo structural prediction, as well as molecular modeling analyses. The structural and catalytic roles of several distinct residues are discussed in light of predicted and modeled DR0022 glycosylase structures. The spontaneous mutation rate analysis performed in a dr0022 deficient D. radiodurans strain indicated that the dr0022 gene plays a role in mutation prevention. Furthermore, survival rate analysis in a dr0022 deficient D. radiodurans strain demonstrated its role in stress resistance, including γ-irradiation. Additionally, the novel acid UDG activity in relationship to its in vivo roles is discussed. This work underscores the functional diversity in the UDG superfamily.
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Affiliation(s)
- Jing Li
- Department of Genetics and BiochemistryClemson UniversityClemsonSCUSA
| | - Ye Yang
- Department of Genetics and BiochemistryClemson UniversityClemsonSCUSA
| | - Chenyan Chang
- Department of Genetics and BiochemistryClemson UniversityClemsonSCUSA
| | - Weiguo Cao
- Department of Genetics and BiochemistryClemson UniversityClemsonSCUSA
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4
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A novel Family V uracil DNA glycosylase from Sulfolobus islandicus REY15A. DNA Repair (Amst) 2022; 120:103420. [DOI: 10.1016/j.dnarep.2022.103420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/09/2022] [Accepted: 10/16/2022] [Indexed: 11/18/2022]
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5
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Lirussi L, Ayyildiz D, Liu Y, Montaldo NP, Carracedo S, Aure MR, Jobert L, Tekpli X, Touma J, Sauer T, Dalla E, Kristensen VN, Geisler J, Piazza S, Tell G, Nilsen H. A regulatory network comprising let-7 miRNA and SMUG1 is associated with good prognosis in ER+ breast tumours. Nucleic Acids Res 2022; 50:10449-10468. [PMID: 36156150 PMCID: PMC9561369 DOI: 10.1093/nar/gkac807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/31/2022] [Accepted: 09/09/2022] [Indexed: 11/13/2022] Open
Abstract
Single-strand selective uracil-DNA glycosylase 1 (SMUG1) initiates base excision repair (BER) of uracil and oxidized pyrimidines. SMUG1 status has been associated with cancer risk and therapeutic response in breast carcinomas and other cancer types. However, SMUG1 is a multifunctional protein involved, not only, in BER but also in RNA quality control, and its function in cancer cells is unclear. Here we identify several novel SMUG1 interaction partners that functions in many biological processes relevant for cancer development and treatment response. Based on this, we hypothesized that the dominating function of SMUG1 in cancer might be ascribed to functions other than BER. We define a bad prognosis signature for SMUG1 by mapping out the SMUG1 interaction network and found that high expression of genes in the bad prognosis network correlated with lower survival probability in ER+ breast cancer. Interestingly, we identified hsa-let-7b-5p microRNA as an upstream regulator of the SMUG1 interactome. Expression of SMUG1 and hsa-let-7b-5p were negatively correlated in breast cancer and we found an inhibitory auto-regulatory loop between SMUG1 and hsa-let-7b-5p in the MCF7 breast cancer cells. We conclude that SMUG1 functions in a gene regulatory network that influence the survival and treatment response in several cancers.
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Affiliation(s)
- Lisa Lirussi
- Institute of Clinical Medicine, Department of Clinical Molecular Biology, University of Oslo, N-0318 Oslo, Norway.,Section of Clinical Molecular Biology, Akershus University Hospital (AHUS), 1478 Lørenskog, Norway
| | - Dilara Ayyildiz
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, p.le M. Kolbe 4, 33100 Udine, Italy
| | - Yan Liu
- Section of Clinical Molecular Biology, Akershus University Hospital (AHUS), 1478 Lørenskog, Norway
| | - Nicola P Montaldo
- Institute of Clinical Medicine, Department of Clinical Molecular Biology, University of Oslo, N-0318 Oslo, Norway
| | - Sergio Carracedo
- Institute of Clinical Medicine, Department of Clinical Molecular Biology, University of Oslo, N-0318 Oslo, Norway.,Section of Clinical Molecular Biology, Akershus University Hospital (AHUS), 1478 Lørenskog, Norway
| | - Miriam R Aure
- Department of Medical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo and Oslo University Hospital, 0450 Oslo, Norway
| | - Laure Jobert
- Institute of Clinical Medicine, Department of Clinical Molecular Biology, University of Oslo, N-0318 Oslo, Norway
| | - Xavier Tekpli
- Department of Medical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo and Oslo University Hospital, 0450 Oslo, Norway
| | - Joel Touma
- Department of Breast and Endocrine Surgery, Akershus University Hospital (AHUS), 1478 Lørenskog, Norway.,Institute of Clinical Medicine, University of Oslo, Campus AHUS, 1478 Lørenskog, Norway
| | - Torill Sauer
- Institute of Clinical Medicine, University of Oslo, Campus AHUS, 1478 Lørenskog, Norway.,Department of Pathology, Akershus University Hospital, 1478 Lørenskog, Norway
| | - Emiliano Dalla
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, p.le M. Kolbe 4, 33100 Udine, Italy
| | - Vessela N Kristensen
- Department of Medical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo and Oslo University Hospital, 0450 Oslo, Norway.,Department of Pathology, Akershus University Hospital, 1478 Lørenskog, Norway
| | - Jürgen Geisler
- Institute of Clinical Medicine, University of Oslo, Campus AHUS, 1478 Lørenskog, Norway.,Department of Oncology, Akershus University Hospital (AHUS), 1478 Lørenskog, Norway
| | - Silvano Piazza
- Bioinformatics Core Facility, Centre for Integrative Biology (CIBIO), University of Trento, via Sommarive 18, 38123, Povo (Trento), Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, p.le M. Kolbe 4, 33100 Udine, Italy
| | - Hilde Nilsen
- Institute of Clinical Medicine, Department of Clinical Molecular Biology, University of Oslo, N-0318 Oslo, Norway.,Section of Clinical Molecular Biology, Akershus University Hospital (AHUS), 1478 Lørenskog, Norway.,Department of Microbiology, Oslo University Hospital, N-0424 Oslo, Norway
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6
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Screening of glycosylase activity on oxidative derivatives of methylcytosine: Pedobacter heparinus SMUG2 as a formylcytosine- and carboxylcytosine-DNA glycosylase. DNA Repair (Amst) 2022; 119:103408. [PMID: 36179537 DOI: 10.1016/j.dnarep.2022.103408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 11/22/2022]
Abstract
5-Methylcytosine (mC) is an epigenetic mark that impacts transcription, development, diseases including cancer and aging. The demethylation process involves Tet-mediated stepwise oxidation of mC to hmC, fC, or caC, excision of fC or caC by thymine-DNA glycosylase (TDG), and subsequent base excision repair. Thymine-DNA glycosylase (TDG) belongs to uracil-DNA glycosylase (UDG) superfamily, which is a group of enzymes that are initially found to be responsible for excising the deaminated bases from DNA and generating apurinic/apyrimidinic (AP) sites. mC oxidative derivatives may also be generated from Fenton chemistry and γ-irradiation. In screening DNA glycosylase activity in UDG superfamily, we identified new activity on fC- and caC-containing DNA in family 2 MUG/TDG and family 6 HDG enzymes. Surprisingly, we found a glycosylase SMUG2 from bacterium Pedobacter heparinus (Phe), a subfamily of family 3 SMUG1 DNA glycosylase, displayed catalytic activity towards not only DNA containing uracil, but also fC and caC. Given the sequence and structural differences between the family 3 and other family enzymes, we investigated the catalytic mechanism using mutational, enzyme kinetics and molecular modeling approaches. Mutational analysis and kinetics measurements identified I62, N63 and F76 of motif 1, and H205 of motif 2 in Phe SMUG2 as important catalytic residues, of which H205 of motif 2 played a critical role in catalyzing the removal of fC and caC. A catalytic model underlying the roles of these residues was proposed. The structural and catalytic differences between Phe SMUG2 and human TDG were compared by molecular modeling and molecular dynamics simulations. This study expands our understanding of DNA glycosylase capacity in UDG superfamily and provides insights into the molecular mechanism of fC and caC excision in Phe SMUG2.
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7
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Yang Y, Park SH, Alford-Zappala M, Lee HW, Li J, Cunningham RP, Cao W. Role of endonuclease III enzymes in uracil repair. Mutat Res 2019; 813:20-30. [PMID: 30590231 PMCID: PMC6378108 DOI: 10.1016/j.mrfmmm.2018.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/07/2018] [Accepted: 12/10/2018] [Indexed: 06/09/2023]
Abstract
Endonuclease III is a DNA glycosylase previously known for its repair activity on oxidative pyrimidine damage. Uracil is a deamination product derived from cytosine. Uracil DNA N-glycosylase (UNG) and mismatch-specific uracil DNA glycosylase (MUG) are two known repair enzymes with enzymatic activity on uracil in E. coli. Here we report a G/U specific uracil DNA glycosylase activity in E. coli endonuclease III (endo III, Nth), which is comparable to MUG but significantly lower than its thymine glycol DNA glycosylase activity. The possibility that the novel activity is due to contamination is ruled out by expressing the wild type nth gene and an active site mutant in a uracil-repair-deficient genetic background. Consistent with the biochemical analysis, analyses of lac+ reversion and mutation frequencies in the presence of human AID induced cytosine deamination indicate the endo III can play a role in repair of cytosine deamination. In addition to E. coli, UDG activity is found in endo III homologs from other organisms. E. coli nucleoside diphosphate kinase (Ndk) was also tested for UDG activity because it was previously reported as an uracil repair enzyme. Under the assay conditions, very limited UDG activity was detected in single-stranded uracil-containing DNA from E. coli Ndk and no UDG activity was detected in human Ndk homologs. This study provides definitive clarification on uracil repair by endo III and reveals that endonuclease III is a G/U-specific UDG that can be viewed as a prototype for the human MBD4 uracil DNA glycosylase.
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Affiliation(s)
- Ye Yang
- Department of Genetics and Biochemistry, Clemson University, Room 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA
| | - Sung-Hyun Park
- Department of Genetics and Biochemistry, Clemson University, Room 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA
| | - Maria Alford-Zappala
- Department of Biological Sciences, The University at Albany, SUNY, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Hyun-Wook Lee
- Department of Genetics and Biochemistry, Clemson University, Room 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA
| | - Jing Li
- Department of Genetics and Biochemistry, Clemson University, Room 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA
| | - Richard P Cunningham
- Department of Biological Sciences, The University at Albany, SUNY, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Weiguo Cao
- Department of Genetics and Biochemistry, Clemson University, Room 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA.
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8
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Li J, Chen R, Yang Y, Zhang Z, Fang GC, Xie W, Cao W. An unconventional family 1 uracil DNA glycosylase in Nitratifractor salsuginis. FEBS J 2017; 284:4017-4034. [PMID: 28977725 DOI: 10.1111/febs.14285] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 08/10/2017] [Accepted: 09/29/2017] [Indexed: 11/30/2022]
Abstract
The uracil DNA glycosylase superfamily consists of at least six families with a diverse specificity toward DNA base damage. Family 1 uracil N-glycosylase (UNG) exhibits exclusive specificity on uracil-containing DNA. Here, we report a family 1 UNG homolog from Nitratifractor salsuginis with distinct biochemical features that differentiate it from conventional family 1 UNGs. Globally, the crystal structure of N. salsuginisUNG shows a few additional secondary structural elements. Biochemical and enzyme kinetic analysis, coupled with structural determination, molecular modeling, and molecular dynamics simulations, shows that N. salsuginisUNG contains a salt bridge network that plays an important role in DNA backbone interactions. Disruption of the amino acid residues involved in the salt bridges greatly impedes the enzymatic activity. A tyrosine residue in motif 1 (GQDPY) is one of the distinct sequence features setting family 1 UNG apart from other families. The crystal structure of Y81G mutant indicates that several subtle changes may account for its inactivity. Unlike the conventional family 1 UNG enzymes, N. salsuginisUNG is not inhibited by Ugi, a potent inhibitor specific for family 1 UNG. This study underscores the diversity of paths that a uracil DNA glycosylase may take to acquire its unique structural and biochemical properties during evolution. DATABASE Structure data are available in the PDB under accession numbers 5X3G and 5X3H.
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Affiliation(s)
- Jing Li
- Department of Genetics and Biochemistry, Clemson University, SC, USA
| | - Ran Chen
- State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Ye Yang
- Department of Genetics and Biochemistry, Clemson University, SC, USA
| | - Zhemin Zhang
- State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Guang-Chen Fang
- Department of Genetics and Biochemistry, Clemson University, SC, USA
| | - Wei Xie
- State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Weiguo Cao
- Department of Genetics and Biochemistry, Clemson University, SC, USA
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9
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Li J, Yang Y, Guevara J, Wang L, Cao W. Identification of a prototypical single-stranded uracil DNA glycosylase from Listeria innocua. DNA Repair (Amst) 2017; 57:107-115. [PMID: 28719838 PMCID: PMC5568478 DOI: 10.1016/j.dnarep.2017.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/04/2017] [Accepted: 07/05/2017] [Indexed: 12/23/2022]
Abstract
A recent phylogenetic study on UDG superfamily estimated a new clade of family 3 enzymes (SMUG1-like), which shares a lower homology with canonic SMUG1 enzymes. The enzymatic properties of the newly found putative DNA glycosylase are unknown. To test the potential UDG activity and evaluate phylogenetic classification, we isolated one SMUG1-like glycosylase representative from Listeria innocua (Lin). A biochemical screening of DNA glycosylase activity in vitro indicates that Lin SMUG1-like glycosylase is a single-strand selective uracil DNA glycosylase. The UDG activity on DNA bubble structures provides clue to its physiological significance in vivo. Mutagenesis and molecular modeling analyses reveal that Lin SMUG1-like glycosylase has similar functional motifs with SMUG1 enzymes; however, it contains a distinct catalytic doublet S67-S68 in motif 1 that is not found in any families in the UDG superfamily. Experimental investigation shows that the S67M-S68N double mutant is catalytically more active than either S67M or S68N single mutant. Coupled with mutual information analysis, the results indicate a high degree of correlation in the evolution of SMUG1-like enzymes. This study underscores the functional and catalytic diversity in the evolution of enzymes in UDG superfamily.
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Affiliation(s)
- Jing Li
- Department of Genetics and Biochemistry, Clemson University, Room 060 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA
| | - Ye Yang
- Department of Genetics and Biochemistry, Clemson University, Room 060 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA
| | - Jose Guevara
- Department of Genetics and Biochemistry, Clemson University, Room 060 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA
| | - Liangjiang Wang
- Department of Genetics and Biochemistry, Clemson University, Room 060 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA
| | - Weiguo Cao
- Department of Genetics and Biochemistry, Clemson University, Room 060 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA.
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10
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Correlated Mutation in the Evolution of Catalysis in Uracil DNA Glycosylase Superfamily. Sci Rep 2017; 7:45978. [PMID: 28397787 PMCID: PMC5387724 DOI: 10.1038/srep45978] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/07/2017] [Indexed: 02/07/2023] Open
Abstract
Enzymes in Uracil DNA glycosylase (UDG) superfamily are essential for the removal of uracil. Family 4 UDGa is a robust uracil DNA glycosylase that only acts on double-stranded and single-stranded uracil-containing DNA. Based on mutational, kinetic and modeling analyses, a catalytic mechanism involving leaving group stabilization by H155 in motif 2 and water coordination by N89 in motif 3 is proposed. Mutual Information analysis identifies a complexed correlated mutation network including a strong correlation in the EG doublet in motif 1 of family 4 UDGa and in the QD doublet in motif 1 of family 1 UNG. Conversion of EG doublet in family 4 Thermus thermophilus UDGa to QD doublet increases the catalytic efficiency by over one hundred-fold and seventeen-fold over the E41Q and G42D single mutation, respectively, rectifying the strong correlation in the doublet. Molecular dynamics simulations suggest that the correlated mutations in the doublet in motif 1 position the catalytic H155 in motif 2 to stabilize the leaving uracilate anion. The integrated approach has important implications in studying enzyme evolution and protein structure and function.
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11
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SMUG2 DNA glycosylase from Pedobacter heparinus as a new subfamily of the UDG superfamily. Biochem J 2017; 474:923-938. [PMID: 28049757 DOI: 10.1042/bcj20160934] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/11/2016] [Accepted: 01/03/2017] [Indexed: 11/17/2022]
Abstract
Base deamination is a common type of DNA damage that occurs in all organisms. DNA repair mechanisms are essential to maintain genome integrity, in which the base excision repair (BER) pathway plays a major role in the removal of base damage. In the BER pathway, the uracil DNA glycosylase superfamily is responsible for excising the deaminated bases from DNA and generates apurinic/apyrimidinic (AP) sites. Using bioinformatics tools, we identified a family 3 SMUG1-like DNA glycoyslase from Pedobacter heparinus (named Phe SMUG2), which displays catalytic activities towards DNA containing uracil or hypoxanthine/xanthine. Phylogenetic analyses show that SMUG2 enzymes are closely related to family 3 SMUG1s but belong to a distinct branch of the family. The high-resolution crystal structure of the apoenzyme reveals that the general fold of Phe SMUG2 resembles SMUG1s, yet with several distinct local structural differences. Mutational studies, coupled with structural modeling, identified several important amino acid residues for glycosylase activity. Substitution of G65 with a tyrosine results in loss of all glycosylase activity. The crystal structure of the G65Y mutant suggests a potential misalignment at the active site due to the mutation. The relationship between the new subfamily and other families in the UDG superfamily is discussed. The present study provides new mechanistic insight into the molecular mechanism of the UDG superfamily.
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12
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part V. {[Fe4S4](SCysγ)4} proteins. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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13
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Sulfolobus acidocaldarius UDG Can Remove dU from the RNA Backbone: Insight into the Specific Recognition of Uracil Linked with Deoxyribose. Genes (Basel) 2017; 8:genes8010038. [PMID: 28106786 PMCID: PMC5295032 DOI: 10.3390/genes8010038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 01/01/2017] [Accepted: 01/11/2017] [Indexed: 12/12/2022] Open
Abstract
Sulfolobus acidocaldarius encodes family 4 and 5 uracil-DNA glycosylase (UDG). Two recombinant S. acidocaldarius UDGs (SacUDG) were prepared and biochemically characterized using oligonucleotides carrying a deaminated base. Both SacUDGs can remove deoxyuracil (dU) base from both double-stranded DNA and single-stranded DNA. Interestingly, they can remove U linked with deoxyribose from single-stranded RNA backbone, suggesting that the riboses on the backbone have less effect on the recognition of dU and hydrolysis of the C-N glycosidic bond. However, the removal of rU from DNA backbone is inefficient, suggesting strong steric hindrance comes from the 2′ hydroxyl of ribose linked to uracil. Both SacUDGs cannot remove 2,2′-anhydro uridine, hypoxanthine, and 7-deazaxanthine from single-stranded DNA and single-stranded DNA. Compared with the family 2 MUG, other family UDGs have an extra N-terminal structure consisting of about 50 residues. Removal of the 46 N-terminal residues of family 5 SacUDG resulted in only a 40% decrease in activity, indicating that the [4Fe-4S] cluster and truncated secondary structure are not the key elements in hydrolyzing the glycosidic bond. Combining our biochemical and structural results with those of other groups, we discussed the UDGs’ catalytic mechanism and the possible repair reactions of deaminated bases in prokaryotes.
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Zhang Z, Shen J, Yang Y, Li J, Cao W, Xie W. Structural Basis of Substrate Specificity in Geobacter metallireducens SMUG1. ACS Chem Biol 2016; 11:1729-36. [PMID: 27071000 DOI: 10.1021/acschembio.6b00164] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Base deamination is a common type of DNA damage that occurs in all organisms. DNA repair mechanisms are critical to maintain genome integrity, in which the base excision repair pathway plays an essential role. In the BER pathway, the uracil DNA glycosylase superfamily is responsible for removing the deaminated bases from DNA and generates apurinic/apyrimidinic (AP) sites. Geobacter metallireducens SMUG1 (GmeSMUG1) is an interesting family 3 enzyme in the UDG superfamily, with dual substrate specificities for DNA with uracil or xanthine. In contrast, the mutant G63P of GmeSMUG1 has exclusive activity for uracil, while N58D is inactive for both substrates, as we have reported previously. However, the structural bases for these substrate specificities are not well understood. In this study, we solved a series of crystal structures of WT and mutants of GmeSMUG1 at relatively high resolutions. These structures provide insight on the molecular mechanism of xanthine recognition for GmeSMUG1 and indicate that H210 plays a key role in xanthine recognition, which is in good agreement with the results of our EMSA and activity assays. More importantly, our mutant structures allow us to build models to rationalize our previous experimental observations of altered substrate activities of these mutants.
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Affiliation(s)
- Zhemin Zhang
- State
Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, 135 W. Xingang Rd., Guangzhou, Guangdong 510275, People’s Republic of China
- Center for Cellular & Structural Biology, The Sun Yat-Sen University, 132 E. Circle Rd., University City, Guangzhou, Guangdong 510006, People’s Republic of China
| | - Jiemin Shen
- State
Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, 135 W. Xingang Rd., Guangzhou, Guangdong 510275, People’s Republic of China
- Center for Cellular & Structural Biology, The Sun Yat-Sen University, 132 E. Circle Rd., University City, Guangzhou, Guangdong 510006, People’s Republic of China
| | - Ye Yang
- Department
of Genetics and Biochemistry, Clemson University, South Carolina Experiment Station,
190 Collings Street, Clemson, South Carolina 29634, United States
| | - Jing Li
- Department
of Genetics and Biochemistry, Clemson University, South Carolina Experiment Station,
190 Collings Street, Clemson, South Carolina 29634, United States
| | - Weiguo Cao
- Department
of Genetics and Biochemistry, Clemson University, South Carolina Experiment Station,
190 Collings Street, Clemson, South Carolina 29634, United States
| | - Wei Xie
- State
Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, 135 W. Xingang Rd., Guangzhou, Guangdong 510275, People’s Republic of China
- Center for Cellular & Structural Biology, The Sun Yat-Sen University, 132 E. Circle Rd., University City, Guangzhou, Guangdong 510006, People’s Republic of China
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15
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Bauer NC, Corbett AH, Doetsch PW. The current state of eukaryotic DNA base damage and repair. Nucleic Acids Res 2015; 43:10083-101. [PMID: 26519467 PMCID: PMC4666366 DOI: 10.1093/nar/gkv1136] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/16/2015] [Indexed: 12/15/2022] Open
Abstract
DNA damage is a natural hazard of life. The most common DNA lesions are base, sugar, and single-strand break damage resulting from oxidation, alkylation, deamination, and spontaneous hydrolysis. If left unrepaired, such lesions can become fixed in the genome as permanent mutations. Thus, evolution has led to the creation of several highly conserved, partially redundant pathways to repair or mitigate the effects of DNA base damage. The biochemical mechanisms of these pathways have been well characterized and the impact of this work was recently highlighted by the selection of Tomas Lindahl, Aziz Sancar and Paul Modrich as the recipients of the 2015 Nobel Prize in Chemistry for their seminal work in defining DNA repair pathways. However, how these repair pathways are regulated and interconnected is still being elucidated. This review focuses on the classical base excision repair and strand incision pathways in eukaryotes, considering both Saccharomyces cerevisiae and humans, and extends to some important questions and challenges facing the field of DNA base damage repair.
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Affiliation(s)
- Nicholas C Bauer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Paul W Doetsch
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
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16
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Drohat AC, Maiti A. Mechanisms for enzymatic cleavage of the N-glycosidic bond in DNA. Org Biomol Chem 2015; 12:8367-78. [PMID: 25181003 DOI: 10.1039/c4ob01063a] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA glycosylases remove damaged or enzymatically modified nucleobases from DNA, thereby initiating the base excision repair (BER) pathway, which is found in all forms of life. These ubiquitous enzymes promote genomic integrity by initiating repair of mutagenic and/or cytotoxic lesions that arise continuously due to alkylation, deamination, or oxidation of the normal bases in DNA. Glycosylases also perform essential roles in epigenetic regulation of gene expression, by targeting enzymatically-modified forms of the canonical DNA bases. Monofunctional DNA glycosylases hydrolyze the N-glycosidic bond to liberate the target base, while bifunctional glycosylases mediate glycosyl transfer using an amine group of the enzyme, generating a Schiff base intermediate that facilitates their second activity, cleavage of the DNA backbone. Here we review recent advances in understanding the chemical mechanism of monofunctional DNA glycosylases, with an emphasis on how the reactions are influenced by the properties of the nucleobase leaving-group, the moiety that varies across the vast range of substrates targeted by these enzymes.
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Affiliation(s)
- Alexander C Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA.
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17
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Lee DH, Liu Y, Lee HW, Xia B, Brice AR, Park SH, Balduf H, Dominy BN, Cao W. A structural determinant in the uracil DNA glycosylase superfamily for the removal of uracil from adenine/uracil base pairs. Nucleic Acids Res 2014; 43:1081-9. [PMID: 25550433 PMCID: PMC4333384 DOI: 10.1093/nar/gku1332] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The uracil DNA glycosylase superfamily consists of several distinct families. Family 2 mismatch-specific uracil DNA glycosylase (MUG) from Escherichia coli is known to exhibit glycosylase activity on three mismatched base pairs, T/U, G/U and C/U. Family 1 uracil N-glycosylase (UNG) from E. coli is an extremely efficient enzyme that can remove uracil from any uracil-containing base pairs including the A/U base pair. Here, we report the identification of an important structural determinant that underlies the functional difference between MUG and UNG. Substitution of a Lys residue at position 68 with Asn in MUG not only accelerates the removal of uracil from mismatched base pairs but also enables the enzyme to gain catalytic activity on A/U base pairs. Binding and kinetic analysis demonstrate that the MUG-K68N substitution results in enhanced ground state binding and transition state interactions. Molecular modeling reveals that MUG-K68N, UNG-N123 and family 5 Thermus thermophiles UDGb-A111N can form bidentate hydrogen bonds with the N3 and O4 moieties of the uracil base. Genetic analysis indicates the gain of function for A/U base pairs allows the MUG-K68N mutant to remove uracil incorporated into the genome during DNA replication. The implications of this study in the origin of life are discussed.
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Affiliation(s)
- Dong-Hoon Lee
- Department of Genetics and Biochemistry, South Carolina Experiment Station, Clemson University, 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA
| | - Yinling Liu
- 367 Hunter Laboratories, Department of Chemistry, Clemson University, Clemson, SC 29634, USA
| | - Hyun-Wook Lee
- Department of Genetics and Biochemistry, South Carolina Experiment Station, Clemson University, 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA
| | - Bo Xia
- Department of Genetics and Biochemistry, South Carolina Experiment Station, Clemson University, 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA
| | - Allyn R Brice
- 367 Hunter Laboratories, Department of Chemistry, Clemson University, Clemson, SC 29634, USA
| | - Sung-Hyun Park
- Department of Genetics and Biochemistry, South Carolina Experiment Station, Clemson University, 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA
| | - Hunter Balduf
- Department of Genetics and Biochemistry, South Carolina Experiment Station, Clemson University, 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA
| | - Brian N Dominy
- 367 Hunter Laboratories, Department of Chemistry, Clemson University, Clemson, SC 29634, USA
| | - Weiguo Cao
- Department of Genetics and Biochemistry, South Carolina Experiment Station, Clemson University, 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA
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18
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Uracil DNA glycosylase BKRF3 contributes to Epstein-Barr virus DNA replication through physical interactions with proteins in viral DNA replication complex. J Virol 2014; 88:8883-99. [PMID: 24872582 DOI: 10.1128/jvi.00950-14] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Epstein-Barr virus (EBV) BKRF3 shares sequence homology with members of the uracil-N-glycosylase (UNG) protein family and has DNA glycosylase activity. Here, we explored how BKRF3 participates in the DNA replication complex and contributes to viral DNA replication. Exogenously expressed Flag-BKRF3 was distributed mostly in the cytoplasm, whereas BKRF3 was translocated into the nucleus and colocalized with the EBV DNA polymerase BALF5 in the replication compartment during EBV lytic replication. The expression level of BKRF3 increased gradually during viral replication, coupled with a decrease of cellular UNG2, suggesting BKRF3 enzyme activity compensates for UNG2 and ensures the fidelity of viral DNA replication. In immunoprecipitation-Western blotting, BKRF3 was coimmuno-precipitated with BALF5, the polymerase processivity factor BMRF1, and the immediate-early transactivator Rta. Coexpression of BMRF1 appeared to facilitate the nuclear targeting of BKRF3 in immunofluorescence staining. Residues 164 to 255 of BKRF3 were required for interaction with Rta and BALF5, whereas residues 81 to 166 of BKRF3 were critical for BMRF1 interaction in glutathione S-transferase (GST) pulldown experiments. Viral DNA replication was defective in cells harboring BKRF3 knockout EBV bacmids. In complementation assays, the catalytic mutant BKRF3(Q90L,D91N) restored viral DNA replication, whereas the leucine loop mutant BKRF3(H213L) only partially rescued viral DNA replication, coupled with a reduced ability to interact with the viral DNA polymerase and Rta. Our data suggest that BKRF3 plays a critical role in viral DNA synthesis predominantly through its interactions with viral proteins in the DNA replication compartment, while its enzymatic activity may be supplementary for uracil DNA glycosylase (UDG) function during virus replication. IMPORTANCE Catalytic activities of both cellular UDG UNG2 and viral UDGs contribute to herpesviral DNA replication. To ensure that the enzyme activity executes at the right time and the right place in DNA replication forks, complex formation with other components in the DNA replication machinery provides an important regulation for UDG function. In this study, we provide the mechanism for EBV UDG BKRF3 nuclear targeting and the interacting domains of BKRF3 with viral DNA replication proteins. Through knockout and complementation approaches, we further demonstrate that in addition to UDG activity, the interaction of BKRF3 with viral proteins in the replication compartment is crucial for efficient viral DNA replication.
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19
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Xia B, Liu Y, Li W, Brice AR, Dominy BN, Cao W. Specificity and catalytic mechanism in family 5 uracil DNA glycosylase. J Biol Chem 2014; 289:18413-26. [PMID: 24838246 DOI: 10.1074/jbc.m114.567354] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
UDGb belongs to family 5 of the uracil DNA glycosylase (UDG) superfamily. Here, we report that family 5 UDGb from Thermus thermophilus HB8 is not only a uracil DNA glycosyase acting on G/U, T/U, C/U, and A/U base pairs, but also a hypoxanthine DNA glycosylase acting on G/I, T/I, and A/I base pairs and a xanthine DNA glycosylase acting on all double-stranded and single-stranded xanthine-containing DNA. Analysis of potentials of mean force indicates that the tendency of hypoxanthine base flipping follows the order of G/I > T/I, A/I > C/I, matching the trend of hypoxanthine DNA glycosylase activity observed in vitro. Genetic analysis indicates that family 5 UDGb can also act as an enzyme to remove uracil incorporated into DNA through the existence of dUTP in the nucleotide pool. Mutational analysis coupled with molecular modeling and molecular dynamics analysis reveals that although hydrogen bonding to O2 of uracil underlies the UDG activity in a dissociative fashion, Tth UDGb relies on multiple catalytic residues to facilitate its excision of hypoxanthine and xanthine. This study underscores the structural and functional diversity in the UDG superfamily.
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Affiliation(s)
- Bo Xia
- From the Department of Genetics and Biochemistry, South Carolina Experiment Station and
| | - Yinling Liu
- the Department of Chemistry, Clemson University, Clemson, South Carolina 29634
| | - Wei Li
- From the Department of Genetics and Biochemistry, South Carolina Experiment Station and
| | - Allyn R Brice
- the Department of Chemistry, Clemson University, Clemson, South Carolina 29634
| | - Brian N Dominy
- the Department of Chemistry, Clemson University, Clemson, South Carolina 29634
| | - Weiguo Cao
- From the Department of Genetics and Biochemistry, South Carolina Experiment Station and
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20
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Jobert L, Nilsen H. Regulatory mechanisms of RNA function: emerging roles of DNA repair enzymes. Cell Mol Life Sci 2014; 71:2451-65. [PMID: 24496644 PMCID: PMC4055861 DOI: 10.1007/s00018-014-1562-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 01/05/2014] [Accepted: 01/10/2014] [Indexed: 12/13/2022]
Abstract
The acquisition of an appropriate set of chemical modifications is required in order to establish correct structure of RNA molecules, and essential for their function. Modification of RNA bases affects RNA maturation, RNA processing, RNA quality control, and protein translation. Some RNA modifications are directly involved in the regulation of these processes. RNA epigenetics is emerging as a mechanism to achieve dynamic regulation of RNA function. Other modifications may prevent or be a signal for degradation. All types of RNA species are subject to processing or degradation, and numerous cellular mechanisms are involved. Unexpectedly, several studies during the last decade have established a connection between DNA and RNA surveillance mechanisms in eukaryotes. Several proteins that respond to DNA damage, either to process or to signal the presence of damaged DNA, have been shown to participate in RNA quality control, turnover or processing. Some enzymes that repair DNA damage may also process modified RNA substrates. In this review, we give an overview of the DNA repair proteins that function in RNA metabolism. We also discuss the roles of two base excision repair enzymes, SMUG1 and APE1, in RNA quality control.
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Affiliation(s)
- Laure Jobert
- Division of Medicine, Department of Clinical Molecular Biology, Akershus University Hospital, Nordbyhagen, 1478 Lørenskog, Norway
| | - Hilde Nilsen
- Division of Medicine, Department of Clinical Molecular Biology, Akershus University Hospital, Nordbyhagen, 1478 Lørenskog, Norway
- Department of Clinical Molecular Biology, Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Blindern, P.O.Box 1171, 0318 Oslo, Norway
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21
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Cao W. Endonuclease V: an unusual enzyme for repair of DNA deamination. Cell Mol Life Sci 2013; 70:3145-56. [PMID: 23263163 PMCID: PMC11114013 DOI: 10.1007/s00018-012-1222-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2012] [Revised: 11/25/2012] [Accepted: 11/26/2012] [Indexed: 10/27/2022]
Abstract
Endonuclease V (endo V) was first discovered as the fifth endonuclease in Escherichia coli in 1977 and later rediscovered as a deoxyinosine 3' endonuclease. Decades of biochemical and genetic investigations have accumulated rich information on its role as a DNA repair enzyme for the removal of deaminated bases. Structural and biochemical analyses have offered invaluable insights on its recognition capacity, catalytic mechanism, and multitude of enzymatic activities. The roles of endo V in genome maintenance have been validated in both prokaryotic and eukaryotic organisms. The ubiquitous nature of endo V in the three domains of life: Bacteria, Archaea, and Eukaryotes, indicates its existence in the early evolutionary stage of cellular life. The application of endo V in mutation detection and DNA manipulation underscores its value beyond cellular DNA repair. This review is intended to provide a comprehensive account of the historic aspects, biochemical, structural biological, genetic and biotechnological studies of this unusual DNA repair enzyme.
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Affiliation(s)
- Weiguo Cao
- Department of Genetics and Biochemistry, South Carolina Experiment Station, Clemson University, Room 049 Life Science Building, 190 Collings Street, Clemson, SC, 29634, USA.
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22
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Lee HW, Dominy BN, Cao W. New family of deamination repair enzymes in uracil-DNA glycosylase superfamily. J Biol Chem 2011; 286:31282-7. [PMID: 21642431 DOI: 10.1074/jbc.m111.249524] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA glycosylases play a major role in the repair of deaminated DNA damage. Previous investigations identified five families within the uracil-DNA glycosylase (UDG) superfamily. All enzymes within the superfamily studied thus far exhibit uracil-DNA glycosylase activity. Here we identify a new class of DNA glycosylases in the UDG superfamily that lacks UDG activity. Instead, these enzymes act as hypoxanthine-DNA glycosylases in vitro and in vivo. Molecular modeling and structure-guided mutational analysis allowed us to identify a unique catalytic center in this class of DNA glycosylases. Based on unprecedented biochemical properties and phylogenetic analysis, we propose this new class of DNA repair glycosylases that exists in bacteria, archaea, and eukaryotes as family 6 and designate it as the hypoxanthine-DNA glycosylase family. This study demonstrates the structural evolvability that underlies substrate specificity and catalytic flexibility in the evolution of enzymatic function.
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Affiliation(s)
- Hyun-Wook Lee
- Department of Genetics and Biochemistry, South Carolina Experiment Station, Clemson University, Clemson, South Carolina 29634, USA
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23
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Lee HW, Brice AR, Wright CB, Dominy BN, Cao W. Identification of Escherichia coli mismatch-specific uracil DNA glycosylase as a robust xanthine DNA glycosylase. J Biol Chem 2010; 285:41483-90. [PMID: 20852254 DOI: 10.1074/jbc.m110.150003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The gene for the mismatch-specific uracil DNA glycosylase (MUG) was identified in the Escherichia coli genome as a sequence homolog of the human thymine DNA glycosylase with activity against mismatched uracil base pairs. Examination of cell extracts led us to detect a previously unknown xanthine DNA glycosylase (XDG) activity in E. coli. DNA glycosylase assays with purified enzymes indicated the novel XDG activity is attributable to MUG. Here, we report a biochemical characterization of xanthine DNA glycosylase activity in MUG. The wild type MUG possesses more robust activity against xanthine than uracil and is active against all xanthine-containing DNA (C/X, T/X, G/X, A/X and single-stranded X). Analysis of potentials of mean force indicates that the double-stranded xanthine base pairs have a relatively narrow energetic difference in base flipping, whereas the tendency for uracil base flipping follows the order of C/U > G/U > T/U > A/U. Site-directed mutagenesis performed on conserved motifs revealed that Asn-140 and Ser-23 are important determinants for XDG activity in E. coli MUG. Molecular modeling and molecular dynamics simulations reveal distinct hydrogen-bonding patterns in the active site of E. coli MUG that account for the specificity differences between E. coli MUG and human thymine DNA glycosylase as well as that between the wild type MUG and the Asn-140 and Ser-23 mutants. This study underscores the role of the favorable binding interactions in modulating the specificity of DNA glycosylases.
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Affiliation(s)
- Hyun-Wook Lee
- Department of Genetics and Biochemistry, South Carolina Experiment Station, Clemson, South Carolina 29634, USA
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