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Ahn WC, Aroli S, Kim JH, Moon JH, Lee GS, Lee MH, Sang PB, Oh BH, Varshney U, Woo EJ. Covalent binding of uracil DNA glycosylase UdgX to abasic DNA upon uracil excision. Nat Chem Biol 2019; 15:607-614. [PMID: 31101917 DOI: 10.1038/s41589-019-0289-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 04/10/2019] [Indexed: 11/09/2022]
Abstract
Uracil DNA glycosylases (UDGs) are important DNA repair enzymes that excise uracil from DNA, yielding an abasic site. Recently, UdgX, an unconventional UDG with extremely tight binding to DNA containing uracil, was discovered. The structure of UdgX from Mycobacterium smegmatis in complex with DNA shows an overall similarity to that of family 4 UDGs except for a protruding loop at the entrance of the uracil-binding pocket. Surprisingly, H109 in the loop was found to make a covalent bond to the abasic site to form a stable intermediate, while the excised uracil remained in the pocket of the active site. H109 functions as a nucleophile to attack the oxocarbenium ion, substituting for the catalytic water molecule found in other UDGs. To our knowledge, this change from a catalytic water attack to a direct nucleophilic attack by the histidine residue is unprecedented. UdgX utilizes a unique mechanism of protecting cytotoxic abasic sites from exposure to the cellular environment.
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Affiliation(s)
- Woo-Chan Ahn
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.,Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Shashanka Aroli
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Jin-Hahn Kim
- Creative Research Initiative Center for Chemical Dynamics in Living Cells, Department of Chemistry, Chung-Ang University, Seoul, Korea
| | - Jeong Hee Moon
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Ga Seal Lee
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Min-Ho Lee
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Pau Biak Sang
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Byung-Ha Oh
- Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.
| | - Eui-Jeon Woo
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea. .,University of Science and Technology, Daejeon, Republic of Korea.
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Taylor EL, Kesavan PM, Wolfe AE, O'Brien PJ. Distinguishing Specific and Nonspecific Complexes of Alkyladenine DNA Glycosylase. Biochemistry 2018; 57:4440-4454. [PMID: 29940097 DOI: 10.1021/acs.biochem.8b00531] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Human alkyladenine DNA glycosylase (AAG) recognizes many alkylated and deaminated purine lesions and excises them to initiate the base excision DNA repair pathway. AAG employs facilitated diffusion to rapidly scan nonspecific sites and locate rare sites of damage. Nonspecific DNA binding interactions are critical to the efficiency of this search for damage, but little is known about the binding footprint or the affinity of AAG for nonspecific sites. We used biochemical and biophysical approaches to characterize the binding of AAG to both undamaged and damaged DNA. Although fluorescence anisotropy is routinely used to study DNA binding, we found unexpected complexities in the data for binding of AAG to DNA. Systematic comparison of different fluorescent labels and different lengths of DNA allowed binding models to be distinguished and demonstrated that AAG can bind with high affinity and high density to nonspecific DNA. Fluorescein-labeled DNA gave the most complex behavior but also showed the greatest potential to distinguish specific and nonspecific binding modes. We suggest a unified model that is expected to apply to many DNA binding proteins that exhibit affinity for nonspecific DNA. Although AAG strongly prefers to excise lesions from duplex DNA, nonspecific binding is comparable for single- and double-stranded nonspecific sites. The electrostatically driven binding of AAG to small DNA sites (∼5 nucleotides of single-stranded and ∼6 base pairs of duplex) facilitates the search for DNA damage in chromosomal DNA, which is bound by nucleosomes and other proteins.
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Affiliation(s)
- Erin L Taylor
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Preethi M Kesavan
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Abigail E Wolfe
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Patrick J O'Brien
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
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Róna G, Scheer I, Nagy K, Pálinkás HL, Tihanyi G, Borsos M, Békési A, Vértessy BG. Detection of uracil within DNA using a sensitive labeling method for in vitro and cellular applications. Nucleic Acids Res 2016; 44:e28. [PMID: 26429970 PMCID: PMC4756853 DOI: 10.1093/nar/gkv977] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 09/10/2015] [Accepted: 09/15/2015] [Indexed: 11/14/2022] Open
Abstract
The role of uracil in genomic DNA has been recently re-evaluated. It is now widely accepted to be a physiologically important DNA element in diverse systems from specific phages to antibody maturation and Drosophila development. Further relevant investigations would largely benefit from a novel reliable and fast method to gain quantitative and qualitative information on uracil levels in DNA both in vitro and in situ, especially since current techniques does not allow in situ cellular detection. Here, starting from a catalytically inactive uracil-DNA glycosylase protein, we have designed several uracil sensor fusion proteins. The designed constructs can be applied as molecular recognition tools that can be detected with conventional antibodies in dot-blot applications and may also serve as in situ uracil-DNA sensors in cellular techniques. Our method is verified on numerous prokaryotic and eukaryotic cellular systems. The method is easy to use and can be applied in a high-throughput manner. It does not require expensive equipment or complex know-how, facilitating its easy implementation in any basic molecular biology laboratory. Elevated genomic uracil levels from cells of diverse genetic backgrounds and/or treated with different drugs can be demonstrated also in situ, within the cell.
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Affiliation(s)
- Gergely Róna
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok Str. 2, H-1117 Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Szt Gellért Square 4, H-1111 Budapest, Hungary
| | - Ildikó Scheer
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok Str. 2, H-1117 Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Szt Gellért Square 4, H-1111 Budapest, Hungary
| | - Kinga Nagy
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok Str. 2, H-1117 Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Szt Gellért Square 4, H-1111 Budapest, Hungary
| | - Hajnalka L Pálinkás
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok Str. 2, H-1117 Budapest, Hungary Doctoral School of Multidisciplinary Medical Science, University of Szeged, H-6720 Szeged, Hungary
| | - Gergely Tihanyi
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok Str. 2, H-1117 Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Szt Gellért Square 4, H-1111 Budapest, Hungary
| | - Máté Borsos
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok Str. 2, H-1117 Budapest, Hungary
| | - Angéla Békési
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok Str. 2, H-1117 Budapest, Hungary
| | - Beáta G Vértessy
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok Str. 2, H-1117 Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Szt Gellért Square 4, H-1111 Budapest, Hungary
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Ferreira E, Giménez R, Cañas MA, Aguilera L, Aguilar J, Badia J, Baldomà L. Glyceraldehyde-3-phosphate dehydrogenase is required for efficient repair of cytotoxic DNA lesions in Escherichia coli. Int J Biochem Cell Biol 2015; 60:202-12. [PMID: 25603270 DOI: 10.1016/j.biocel.2015.01.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 12/04/2014] [Accepted: 01/12/2015] [Indexed: 01/07/2023]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a multifunctional protein with diverse biological functions in human cells. In bacteria, moonlighting GAPDH functions have only been described for the secreted protein in pathogens or probiotics. At the intracellular level, we previously reported the interaction of Escherichia coli GAPDH with phosphoglycolate phosphatase, a protein involved in the metabolism of the DNA repair product 2-phosphoglycolate, thus suggesting a putative role of GAPDH in DNA repair processes. Here, we provide evidence that GAPDH is required for the efficient repair of DNA lesions in E. coli. We show that GAPDH-deficient cells are more sensitive to bleomycin or methyl methanesulfonate. In cells challenged with these genotoxic agents, GAPDH deficiency results in reduced cell viability and filamentous growth. In addition, the gapA knockout mutant accumulates a higher number of spontaneous abasic sites and displays higher spontaneous mutation frequencies than the parental strain. Pull-down experiments in different genetic backgrounds show interaction between GAPDH and enzymes of the base excision repair pathway, namely the AP-endonuclease Endo IV and uracil DNA glycosylase. This finding suggests that GAPDH is a component of a protein complex dedicated to the maintenance of genomic DNA integrity. Our results also show interaction of GAPDH with the single-stranded DNA binding protein. This interaction may recruit GAPDH to the repair sites and implicates GAPDH in DNA repair pathways activated by profuse DNA damage, such as homologous recombination or the SOS response.
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Affiliation(s)
- Elaine Ferreira
- Departament de Bioquímica i Biología Molecular, Institut de Biomedicina de la Universitat de Barcelona, Facultat de Farmàcia, Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Rosa Giménez
- Departament de Bioquímica i Biología Molecular, Institut de Biomedicina de la Universitat de Barcelona, Facultat de Farmàcia, Universitat de Barcelona, E-08028 Barcelona, Spain
| | - María Alexandra Cañas
- Departament de Bioquímica i Biología Molecular, Institut de Biomedicina de la Universitat de Barcelona, Facultat de Farmàcia, Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Laura Aguilera
- Departament de Bioquímica i Biología Molecular, Institut de Biomedicina de la Universitat de Barcelona, Facultat de Farmàcia, Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Juan Aguilar
- Departament de Bioquímica i Biología Molecular, Institut de Biomedicina de la Universitat de Barcelona, Facultat de Farmàcia, Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Josefa Badia
- Departament de Bioquímica i Biología Molecular, Institut de Biomedicina de la Universitat de Barcelona, Facultat de Farmàcia, Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Laura Baldomà
- Departament de Bioquímica i Biología Molecular, Institut de Biomedicina de la Universitat de Barcelona, Facultat de Farmàcia, Universitat de Barcelona, E-08028 Barcelona, Spain.
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Abstract
In all domains of life, initiator tRNA functions exclusively at the first step of protein synthesis while elongator tRNAs extend the polypeptide chain. Unique features of initiator tRNA enable it to preferentially bind the ribosomal P site and initiate translation. Recently, we showed that the abundance of initiator tRNA also contributes to its specialized role. This motivates the question, can a cell also use elongator tRNA to initiate translation under certain conditions? To address this, we introduced non-AUG initiation codons CCC (Pro), GAG (Glu), GGU (Gly), UCU (Ser), UGU (Cys), ACG (Thr), AAU (Asn), and AGA (Arg) into the uracil DNA glycosylase gene (ung) used as a reporter gene. Enzyme assays from log-phase cells revealed initiation from non-AUG codons when intracellular initiator tRNA levels were reduced. The activity increased significantly in stationary phase. Further increases in initiation from non-AUG codons occurred in both growth phases upon introduction of plasmid-borne genes of cognate elongator tRNAs. Since purine-rich Shine-Dalgarno sequences occur frequently on mRNAs (in places other than the canonical AUG codon initiation contexts), initiation with elongator tRNAs from the alternate contexts may generate proteome diversity under stress without compromising genomic integrity. Thus, by changing the relative amounts of initiator and elongator tRNAs within the cell, we have blurred the distinction between the two classes of tRNAs thought to be frozen through years of evolution.
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Base excision and nucleotide excision repair pathways in mycobacteria. Tuberculosis (Edinb) 2011; 91:533-43. [DOI: 10.1016/j.tube.2011.06.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 06/01/2011] [Accepted: 06/12/2011] [Indexed: 01/13/2023]
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