1
|
Liu QW, Yang ZW, Tang QH, Wang WE, Chu DS, Ji JF, Fan QY, Jiang H, Yang QX, Zhang H, Liu XY, Xu XS, Wang XF, Liu JB, Fu D, Tao K, Yu H. The power and the promise of synthetic lethality for clinical application in cancer treatment. Biomed Pharmacother 2024; 172:116288. [PMID: 38377739 DOI: 10.1016/j.biopha.2024.116288] [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: 01/04/2024] [Revised: 02/08/2024] [Accepted: 02/17/2024] [Indexed: 02/22/2024] Open
Abstract
Synthetic lethality is a phenomenon wherein the simultaneous deficiency of two or more genes results in cell death, while the deficiency of any individual gene does not lead to cell death. In recent years, synthetic lethality has emerged as a significant topic in the field of targeted cancer therapy, with certain drugs based on this concept exhibiting promising outcomes in clinical trials. Nevertheless, the presence of tumor heterogeneity and the intricate DNA repair mechanisms pose challenges to the effective implementation of synthetic lethality. This review aims to explore the concepts, development, and ethical quandaries surrounding synthetic lethality. Additionally, it will provide an in-depth analysis of the clinical application and underlying mechanism of synthetic lethality.
Collapse
Affiliation(s)
- Qian-Wen Liu
- Department of Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu Province 225300, China; General Surgery, Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Zhi-Wen Yang
- Department of Pharmacy, Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai, Shanghai 200050, China
| | - Qing-Hai Tang
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region and College of Life Sciences, Hengyang Normal University, Hengyang, Hunan Province 421008, China
| | - Wen-Er Wang
- General Surgery, the Fourth Hospital Of Changsha, Changsha Hospital Of Hunan Normal University, Changsha, Hunan Province 410006, China
| | - Da-Sheng Chu
- Second Cadre Rest Medical and Health Center of Changning District, Shanghai Garrison, Shanghai226631, China
| | - Jin-Feng Ji
- Department of Integrated Traditional Chinese and Western Internal Medicine, Affiliated Tumor Hospital of Nantong University, Nantong Tumor Hospital, Nantong, Jiangsu Province 226631, China
| | - Qi-Yu Fan
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu Province 226631, China
| | - Hong Jiang
- Department of Thoracic Surgery, the 905th Hospital of Chinese People's Liberation Army Navy, Shanghai 200050, China
| | - Qin-Xin Yang
- Department of Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu Province 225300, China
| | - Hui Zhang
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu Province 226631, China
| | - Xin-Yun Liu
- Department of Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu Province 225300, China
| | - Xiao-Sheng Xu
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China.
| | - Xiao-Feng Wang
- Department of Orthopedics, Xiamen Hospital, Zhongshan Hospital, Fudan University, Xiamen, Fujian Province 361015, China.
| | - Ji-Bin Liu
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu Province 226631, China.
| | - Da Fu
- General Surgery, Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China.
| | - Kun Tao
- Department of Pathology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China.
| | - Hong Yu
- Department of Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu Province 225300, China; Department of Pathology, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, Jiangsu Province 225300, China.
| |
Collapse
|
2
|
Fang Q. The Versatile Attributes of MGMT: Its Repair Mechanism, Crosstalk with Other DNA Repair Pathways, and Its Role in Cancer. Cancers (Basel) 2024; 16:331. [PMID: 38254819 PMCID: PMC10814553 DOI: 10.3390/cancers16020331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
O6-methylguanine-DNA methyltransferase (MGMT or AGT) is a DNA repair protein with the capability to remove alkyl groups from O6-AlkylG adducts. Moreover, MGMT plays a crucial role in repairing DNA damage induced by methylating agents like temozolomide and chloroethylating agents such as carmustine, and thereby contributes to chemotherapeutic resistance when these agents are used. This review delves into the structural roles and repair mechanisms of MGMT, with emphasis on the potential structural and functional roles of the N-terminal domain of MGMT. It also explores the development of cancer therapeutic strategies that target MGMT. Finally, it discusses the intriguing crosstalk between MGMT and other DNA repair pathways.
Collapse
Affiliation(s)
- Qingming Fang
- Department of Biochemistry and Structural Biology, Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| |
Collapse
|
3
|
T. G. S, Siddiqui SA, Dubey KD. Unraveling key interactions and the mechanism of demethylation during hAGT-mediated DNA repair via simulations. Front Mol Biosci 2022; 9:975046. [PMID: 36188219 PMCID: PMC9515978 DOI: 10.3389/fmolb.2022.975046] [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: 06/21/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Alkylating agents pose the biggest threat to the genomic integrity of cells by damaging DNA bases through regular alkylation. Such damages are repaired by several automated types of machinery inside the cell. O6-alkylguanine-DNA alkyltransferase (AGT) is an enzyme that performs the direct repair of an alkylated guanine base by transferring the alkyl group to a cysteine residue. In the present study, using extensive MD simulations and hybrid QM/MM calculations, we have investigated the key interactions between the DNA lesion and the hAGT enzyme and elucidated the mechanisms of the demethylation of the guanine base. Our simulation shows that the DNA lesion is electrostatically stabilized by the enzyme and the Arg135 of hAGT enzyme provides the main driving force to flip the damaged base into the enzyme. The QM/MM calculations show demethylation of the damaged base as a three-step process in a thermodynamically feasible and irreversible manner. Our calculations show that the final product forms via Tyr114 in a facile way in contrast to the previously proposed Lys-mediated route.
Collapse
Affiliation(s)
- Shruti T. G.
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence Delhi-NCR, Uttar Pradesh, India
| | - Shakir Ali Siddiqui
- Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence Delhi-NCR, Uttar Pradesh, India
| | - Kshatresh Dutta Dubey
- Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence Delhi-NCR, Uttar Pradesh, India
- *Correspondence: Kshatresh Dutta Dubey,
| |
Collapse
|
4
|
Davies CP, Jurkiw T, Haendiges J, Reed E, Anderson N, Grasso-Kelley E, Hoffmann M, Zheng J. Changes in the genomes and methylomes of three Salmonella enterica serovars after long-term storage in ground black pepper. Front Microbiol 2022; 13:970135. [PMID: 36160197 PMCID: PMC9507087 DOI: 10.3389/fmicb.2022.970135] [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: 06/15/2022] [Accepted: 08/16/2022] [Indexed: 11/28/2022] Open
Abstract
Low moisture foods (LMFs) have traditionally been recognized as safe for consumption, as most bacteria require higher water content to grow. However, outbreaks due to LMF foods are increasing, and the microbial pathogen Salmonella enterica is frequently implicated. S. enterica can survive in LMFs for years, but few serovars have been studied, and the mechanisms which underlie this longevity are not well understood. Here, we determine that S. enterica serovars S. Tennessee, S. Anatum, and S. Reading but not S. Oranienburg can survive in the ground black pepper for 6 years. S. Reading was not previously associated with any LMF. Using both Illumina and Pacific Biosciences sequencing technologies, we also document changes in the genomes and methylomes of the surviving serovars over this 6-year period. The three serovars acquired a small number of single nucleotide polymorphisms (SNPs) including seven substitutions (four synonymous, two non-synonymous, and one substitution in a non-coding region), and two insertion-deletions. Nine distinct N6-methyladenine (m6A) methylated motifs across the three serovars were identified including five which were previously known, Gm6ATC, CAGm6AG, BATGCm6AT, CRTm6AYN6CTC, and CCm6AN7TGAG, and four novel serovar-specific motifs, GRTm6AN8TTYG, GAm6ACN7GTA, GAA m6ACY, and CAAm6ANCC. Interestingly, the BATGCAT motif was incompletely methylated (35–64% sites across the genome methylated), suggesting a possible role in gene regulation. Furthermore, the number of methylated BATGCm6AT motifs increased after storage in ground black pepper for 6 years from 475 to 657 (S. Tennessee), 366 to 608 (S. Anatum), and 525 to 570 (S. Reading), thus warranting further study as an adaptive mechanism. This is the first long-term assessment of genomic changes in S. enterica in a low moisture environment, and the first study to examine the methylome of any bacteria over a period of years, to our knowledge. These data contribute to our understanding of S. enterica survival in LMFs, and coupled with further studies, will provide the information necessary to design effective interventions which reduce S. enterica in LMFs and maintain a healthy, safe food supply.
Collapse
Affiliation(s)
- Cary P. Davies
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, NEA, U.S. Department of Agriculture, Beltsville, MD, United States
- *Correspondence: Cary P. Davies,
| | - Thomas Jurkiw
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Julie Haendiges
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Elizabeth Reed
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Nathan Anderson
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Bedford Park, IL, United States
| | - Elizabeth Grasso-Kelley
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Bedford Park, IL, United States
| | - Maria Hoffmann
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Jie Zheng
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| |
Collapse
|
5
|
Kikuchi M, Yamauchi T, Iizuka Y, Tsunoda M. Roles of the hydroxy group of tyrosine in crystal structures of Sulfurisphaera tokodaiiO 6-methylguanine-DNA methyltransferase. Acta Crystallogr F Struct Biol Commun 2021; 77:444-451. [PMID: 34866599 PMCID: PMC8647212 DOI: 10.1107/s2053230x21011055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/21/2021] [Indexed: 12/02/2022] Open
Abstract
O6-Methylguanine-DNA methyltransferase (MGMT) removes cytotoxic O6-alkyl adducts on the guanine base and protects the cell from genomic damage induced by alkylating agents. Although there are reports of computational studies on the activity of the enzyme with mutations at tyrosine residues, no studies concerning the crystal structure of its mutants have been found. In this study, the function of Tyr91 was investigated in detail by comparing the crystal structures of mutants and their complexes with substrate analogs. In this study, tyrosine, a conserved amino acid near the active-site loop in the C-terminal domain of Sulfurisphaera tokodaii MGMT (StoMGMT), was mutated to phenylalanine to produce a Y91F mutant, and the cysteine which is responsible for receiving the methyl group in the active site was mutated to a serine to produce a C120S mutant. A Y91F/C120S double-mutant StoMGMT was also created. The function of tyrosine is discussed based on the crystal structure of Y91F mutant StoMGMT. The crystal structures of StoMGMT were determined at resolutions of 1.13-2.60 Å. They showed no structural changes except in the mutated part. No electron density for deoxyguanosine or methyl groups was observed in the structure of Y91F mutant crystals immersed in O6-methyl-2'-deoxyguanosine, nor was the group oxidized in wild-type StoMGMT. Therefore, the hydroxy group of Tyr91 may prevent the oxidant from entering the active site. This suggests that tyrosine, which is highly conserved at the N-terminus of the helix-turn-helix motif across species, protects the active site of MGMTs, which are deactivated after repairing only one alkyl adduct. Overall, the results may provide a basis for understanding the molecular mechanisms by which high levels of conserved amino acids play a role in ensuring the integrity of suicide enzymes, in addition to promoting their activity.
Collapse
Affiliation(s)
- Makiko Kikuchi
- Graduate School of Science and Engnieering, Iryo Sosei University, Iwaki, Fukushima, Japan
| | - Takahiro Yamauchi
- Graduate School of Life Science and Technology, Iryo Sosei University, Iwaki, Fukushima, Japan
- Department of Pharmacy, Fukushima Rosai Hospital, Iwaki, Fukushima, Japan
| | - Yasuhito Iizuka
- Graduate School of Life Science and Technology, Iryo Sosei University, Iwaki, Fukushima, Japan
- Faculty of Pharmacy, Iryo Sosei University, Iwaki, Fukushima, Japan
| | - Masaru Tsunoda
- Graduate School of Science and Engnieering, Iryo Sosei University, Iwaki, Fukushima, Japan
- Graduate School of Life Science and Technology, Iryo Sosei University, Iwaki, Fukushima, Japan
- Faculty of Pharmacy, Iryo Sosei University, Iwaki, Fukushima, Japan
| |
Collapse
|
6
|
The specific role of O 6-methylguanine-DNA methyltransferase inhibitors in cancer chemotherapy. Future Med Chem 2018; 10:1971-1996. [PMID: 30001630 DOI: 10.4155/fmc-2018-0069] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The DNA repair protein, O6-methylguanine DNA methyltransferase (MGMT), can confer resistance to guanine O6-alkylating agents. Therefore, inhibition of resistant MGMT protein is a practical approach to increase the anticancer effects of such alkylating agents. Numerous small molecule inhibitors were synthesized and exhibited potential MGMT inhibitory activities. Although they were nontoxic alone, they also inhibited MGMT in normal tissues, thereby enhancing the side effects of chemotherapy. Therefore, strategies for tumor-specific MGMT inhibition have been proposed, including local drug delivery and tumor-activated prodrugs. Over-expression of MGMT in hematopoietic stem cells to protect bone marrow from the toxic effects of chemotherapy is also a feasible selection. The future prospects and challenges of MGMT inhibitors in cancer chemotherapy were also discussed.
Collapse
|
7
|
Sacre L, O'Flaherty DK, Archambault P, Copp W, Peslherbe GH, Muchall HM, Wilds CJ. O 4 -Alkylated-2-Deoxyuridine Repair by O 6 -Alkylguanine DNA Alkyltransferase is Augmented by a C5-Fluorine Modification. Chembiochem 2018; 19:575-582. [PMID: 29243336 DOI: 10.1002/cbic.201700660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Indexed: 11/10/2022]
Abstract
Oligonucleotides containing various adducts, including ethyl, benzyl, 4-hydroxybutyl and 7-hydroxyheptyl groups, at the O4 atom of 5-fluoro-O4 -alkyl-2'-deoxyuridine were prepared by solid-phase synthesis. UV thermal denaturation studies demonstrated that these modifications destabilised the duplex by approximately 10 °C, relative to the control containing 5-fluoro-2'-deoxyuridine. Circular dichroism spectroscopy revealed that these modified duplexes all adopted a B-form DNA structure. O6 -Alkylguanine DNA alkyltransferase (AGT) from humans (hAGT) was most efficient at repair of the 5-fluoro-O4 -benzyl-2'-deoxyuridine adduct, whereas the thymidine analogue was refractory to repair. The Escherichia coli AGT variant (OGT) was also efficient at removing O4 -ethyl and benzyl adducts of 5-fluoro-2-deoxyuridine. Computational assessment of N1-methyl analogues of the O4 -alkylated nucleobases revealed that the C5-fluorine modification had an influence on reducing the electron density of the O4 -Cα bond, relative to thymine (C5-methyl) and uracil (C5-hydrogen). These results reveal the positive influence of the C5-fluorine atom on the repair of larger O4 -alkyl adducts to expand knowledge of the range of substrates able to be repaired by AGT.
Collapse
Affiliation(s)
- Lauralicia Sacre
- Department of Chemistry and Biochemistry and, Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke St. West, Montréal, Québec, H4B 1R6, Canada
| | - Derek K O'Flaherty
- Department of Chemistry and Biochemistry and, Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke St. West, Montréal, Québec, H4B 1R6, Canada.,Present address: Howard Hughes Medical Institute, Department of Molecular Biology and, Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Philippe Archambault
- Department of Chemistry and Biochemistry and, Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke St. West, Montréal, Québec, H4B 1R6, Canada
| | - William Copp
- Department of Chemistry and Biochemistry and, Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke St. West, Montréal, Québec, H4B 1R6, Canada
| | - Gilles H Peslherbe
- Department of Chemistry and Biochemistry and, Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke St. West, Montréal, Québec, H4B 1R6, Canada
| | - Heidi M Muchall
- Department of Chemistry and Biochemistry and, Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke St. West, Montréal, Québec, H4B 1R6, Canada
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry and, Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke St. West, Montréal, Québec, H4B 1R6, Canada
| |
Collapse
|
8
|
Mostofa A, Punganuru SR, Madala HR, Srivenugopal KS. S-phase Specific Downregulation of Human O 6-Methylguanine DNA Methyltransferase (MGMT) and its Serendipitous Interactions with PCNA and p21 cip1 Proteins in Glioma Cells. Neoplasia 2018; 20:305-323. [PMID: 29510343 PMCID: PMC5909491 DOI: 10.1016/j.neo.2018.01.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/17/2018] [Accepted: 01/21/2018] [Indexed: 01/28/2023] Open
Abstract
Whether the antimutagenic DNA repair protein MGMT works solo in human cells and if it has other cellular functions is not known. Here, we show that human MGMT associates with PCNA and in turn, with the cell cycle inhibitor, p21cip1 in glioblastoma and other cancer cell lines. MGMT protein was shown to harbor a nearly perfect PCNA-Interacting Protein (PIP box) motif. Isogenic p53-null H1299 cells were engineered to express the p21 protein by two different procedures. Reciprocal immunoprecipitation/western blotting, Far-western blotting, and confocal microscopy confirmed the specific association of MGMT with PCNA and the ability of p21 to strongly disrupt the MGMT-PCNA complexes in tumor cells. Alkylation DNA damage resulted in a greater colocalization of MGMT and PCNA proteins, particularly in HCT116 cells deficient in p21 expression. p21 expression in isogenic cell lines directly correlated with markedly higher levels of MGMT mRNA, protein, activity and greater resistance to alkylating agents. In other experiments, four glioblastoma cell lines synchronized at the G1/S phase using either double thymidine or thymidine-mimosine blocks and subsequent cycling consistently showed a loss of MGMT protein at mid- to late S-phase, irrespective of the cell line, suggesting such a downregulation is fundamental to cell cycle control. MGMT protein was also specifically degraded in extracts from S-phase cells and evidence strongly suggested the involvement of PCNA-dependent CRL4Cdt2 ubiquitin-ligase in the reaction. Overall, these data provide the first evidence for non-repair functions of MGMT in cell cycle and highlight the involvement of PCNA in MGMT downregulation, with p21 attenuating the process.
Collapse
Affiliation(s)
- Agm Mostofa
- Department of Biomedical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, 1406 S. Coulter Drive, Amarillo, TX 79106, USA
| | - Surendra R Punganuru
- Department of Biomedical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, 1406 S. Coulter Drive, Amarillo, TX 79106, USA
| | - Hanumantha Rao Madala
- Department of Biomedical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, 1406 S. Coulter Drive, Amarillo, TX 79106, USA
| | - Kalkunte S Srivenugopal
- Department of Biomedical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, 1406 S. Coulter Drive, Amarillo, TX 79106, USA.
| |
Collapse
|
9
|
Gutierrez R, Thompson Y, R. O’Connor T. DNA direct repair pathways in cancer. AIMS MEDICAL SCIENCE 2018. [DOI: 10.3934/medsci.2018.3.284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
10
|
Interdomain interactions rearrangements control the reaction steps of a thermostable DNA alkyltransferase. Biochim Biophys Acta Gen Subj 2016; 1861:86-96. [PMID: 27777086 DOI: 10.1016/j.bbagen.2016.10.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/07/2016] [Accepted: 10/20/2016] [Indexed: 12/18/2022]
Abstract
BACKGROUND Alkylated DNA-protein alkyltransferases (AGTs) are conserved proteins that repair alkylation damage in DNA by using a single-step mechanism leading to irreversible alkylation of the catalytic cysteine in the active site. Trans-alkylation induces inactivation and destabilization of the protein, both in vitro and in vivo, likely triggering conformational changes. A complete picture of structural rearrangements occurring during the reaction cycle is missing, despite considerable interest raised by the peculiarity of AGT reaction, and the contribution of a functional AGT in limiting the efficacy of chemotherapy with alkylating drugs. METHODS As a model for AGTs we have used a thermostable ortholog from the archaeon Sulfolobus solfataricus (SsOGT), performing biochemical, structural, molecular dynamics and in silico analysis of ligand-free, DNA-bound and mutated versions of the protein. RESULTS Conformational changes occurring during lesion recognition and after the reaction, allowed us to identify a novel interaction network contributing to SsOGT stability, which is perturbed when a bulky adduct between the catalytic cysteine and the alkyl group is formed, a mandatory step toward the permanent protein alkylation. CONCLUSIONS Our data highlighted conformational changes and perturbation of intramolecular interaction occurring during lesion recognition and catalysis, confirming our previous hypothesis that coordination between the N- and C-terminal domains of SsOGT is important for protein activity and stability. GENERAL SIGNIFICANCE A general model of structural rearrangements occurring during the reaction cycle of AGTs is proposed. If confirmed, this model might be a starting point to design strategies to modulate AGT activity in therapeutic settings.
Collapse
|
11
|
Serrano M, Crawshaw AD, Dembek M, Monteiro JM, Pereira FC, Pinho MG, Fairweather NF, Salgado PS, Henriques AO. The SpoIIQ-SpoIIIAH complex of Clostridium difficile controls forespore engulfment and late stages of gene expression and spore morphogenesis. Mol Microbiol 2016; 100:204-28. [PMID: 26690930 PMCID: PMC4982068 DOI: 10.1111/mmi.13311] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2015] [Indexed: 11/29/2022]
Abstract
Engulfment of the forespore by the mother cell is a universal feature of endosporulation. In Bacillus subtilis, the forespore protein SpoIIQ and the mother cell protein SpoIIIAH form a channel, essential for endosporulation, through which the developing spore is nurtured. The two proteins also form a backup system for engulfment. Unlike in B. subtilis, SpoIIQ of Clostridium difficile has intact LytM zinc‐binding motifs. We show that spoIIQ or spoIIIAH deletion mutants of C. difficile result in anomalous engulfment, and that disruption of the SpoIIQ LytM domain via a single amino acid substitution (H120S) impairs engulfment differently. SpoIIQ and SpoIIQH120S interact with SpoIIIAH throughout engulfment. SpoIIQ, but not SpoIIQH120S, binds Zn2+, and metal absence alters the SpoIIQ‐SpoIIIAH complex in vitro. Possibly, SpoIIQH120S supports normal engulfment in some cells but not a second function of the complex, required following engulfment completion. We show that cells of the spoIIQ or spoIIIAH mutants that complete engulfment are impaired in post‐engulfment, forespore and mother cell‐specific gene expression, suggesting a channel‐like function. Both engulfment and a channel‐like function may be ancestral functions of SpoIIQ‐SpoIIIAH while the requirement for engulfment was alleviated through the emergence of redundant mechanisms in B. subtilis and related organisms.
Collapse
Affiliation(s)
- Mónica Serrano
- Microbial Development, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, Avenida da República, 2780-157, Oeiras, Portugal
| | - Adam D Crawshaw
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Marcin Dembek
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - João M Monteiro
- Bacterial Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, Avenida da República, 2780-157, Oeiras, Portugal
| | - Fátima C Pereira
- Microbial Development, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, Avenida da República, 2780-157, Oeiras, Portugal
| | - Mariana Gomes Pinho
- Bacterial Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, Avenida da República, 2780-157, Oeiras, Portugal
| | - Neil F Fairweather
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - Paula S Salgado
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Adriano O Henriques
- Microbial Development, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, Avenida da República, 2780-157, Oeiras, Portugal
| |
Collapse
|
12
|
Perugino G, Miggiano R, Serpe M, Vettone A, Valenti A, Lahiri S, Rossi F, Rossi M, Rizzi M, Ciaramella M. Structure-function relationships governing activity and stability of a DNA alkylation damage repair thermostable protein. Nucleic Acids Res 2015; 43:8801-16. [PMID: 26227971 PMCID: PMC4605297 DOI: 10.1093/nar/gkv774] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 07/18/2015] [Indexed: 12/22/2022] Open
Abstract
Alkylated DNA-protein alkyltransferases repair alkylated DNA bases, which are among the most common DNA lesions, and are evolutionary conserved, from prokaryotes to higher eukaryotes. The human ortholog, hAGT, is involved in resistance to alkylating chemotherapy drugs. We report here on the alkylated DNA-protein alkyltransferase, SsOGT, from an archaeal species living at high temperature, a condition that enhances the harmful effect of DNA alkylation. The exceptionally high stability of SsOGT gave us the unique opportunity to perform structural and biochemical analysis of a protein of this class in its post-reaction form. This analysis, along with those performed on SsOGT in its ligand-free and DNA-bound forms, provides insights in the structure-function relationships of the protein before, during and after DNA repair, suggesting a molecular basis for DNA recognition, catalytic activity and protein post-reaction fate, and giving hints on the mechanism of alkylation-induced inactivation of this class of proteins.
Collapse
Affiliation(s)
- Giuseppe Perugino
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80125 Naples, Italy
| | - Riccardo Miggiano
- DiSF-Dipartimento di Scienze del Farmaco, University of Piemonte Orientale 'A. Avogadro', Via Bovio 6, 28100 Novara, Italy
| | - Mario Serpe
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80125 Naples, Italy
| | - Antonella Vettone
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80125 Naples, Italy
| | - Anna Valenti
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80125 Naples, Italy
| | - Samarpita Lahiri
- DiSF-Dipartimento di Scienze del Farmaco, University of Piemonte Orientale 'A. Avogadro', Via Bovio 6, 28100 Novara, Italy
| | - Franca Rossi
- DiSF-Dipartimento di Scienze del Farmaco, University of Piemonte Orientale 'A. Avogadro', Via Bovio 6, 28100 Novara, Italy
| | - Mosè Rossi
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80125 Naples, Italy
| | - Menico Rizzi
- DiSF-Dipartimento di Scienze del Farmaco, University of Piemonte Orientale 'A. Avogadro', Via Bovio 6, 28100 Novara, Italy
| | - Maria Ciaramella
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80125 Naples, Italy
| |
Collapse
|
13
|
Chikan NA, Bukhari S, Shabir N, Amin A, Shafi S, Qadri RA, Patel TNC. Atomic Insight into the Altered O6-Methylguanine-DNA Methyltransferase Protein Architecture in Gastric Cancer. PLoS One 2015; 10:e0127741. [PMID: 26011121 PMCID: PMC4444098 DOI: 10.1371/journal.pone.0127741] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/19/2015] [Indexed: 11/22/2022] Open
Abstract
O6-methylguanine-DNA methyltransferase (MGMT) is one of the major DNA repair protein that counteracts the alkalyting agent-induced DNA damage by replacing O6-methylguanine (mutagenic lesion) back to guanine, eventually suppressing the mismatch errors and double strand crosslinks. Exonic alterations in the form of nucleotide polymorphism may result in altered protein structure that in turn can lead to the loss of function. In the present study, we focused on the population feared for high exposure to alkylating agents owing to their typical and specialized dietary habits. To this end, gastric cancer patients pooled out from the population were selected for the mutational screening of a specific error prone region of MGMT gene. We found that nearly 40% of the studied neoplastic samples harbored missense mutation at codon151 resulting into Serine to Isoleucine variation. This variation resulted in bringing about the structural disorder, subsequently ensuing into a major stoichiometric variance in recognition domain, substrate binding and selectivity loop of the active site of the MGMT protein, as observed under virtual microscope of molecular dynamics simulation (MDS). The atomic insight into MGMT protein by computational approach showed a significant change in the intra molecular hydrogen bond pattern, thus leading to the observed structural anomalies. To further examine the mutational implications on regulatory plugs of MGMT that holds the protein in a DNA-Binding position, a MDS based analysis was carried out on, all known physically interacting amino acids essentially clustered into groups based on their position and function. The results generated by physical-functional clustering of protein indicated that the identified mutation in the vicinity of the active site of MGMT protein causes the local and global destabilization of a protein by either eliminating the stabilizing salt bridges in cluster C3, C4, and C5 or by locally destabilizing the “protein stabilizing hing” mapped on C3-C4 cluster, preceding the active site.
Collapse
Affiliation(s)
- Naveed Anjum Chikan
- Division of Medical Biotechnology, School of Bioscience and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
- Departments of Biotechnology, University of Kashmir, Srinagar, Kashmir, 190006, India
| | - Shoiab Bukhari
- Departments of Biotechnology, University of Kashmir, Srinagar, Kashmir, 190006, India
| | - Nadeem Shabir
- Department of Animal Biotechnology, College of Veterinary Sciences, Anand Agricultural University, Anand, Gujarat, India, 388 001
| | - Asif Amin
- Departments of Biotechnology, University of Kashmir, Srinagar, Kashmir, 190006, India
| | - Sheikh Shafi
- Department of Clinical Biochemistry, Sher-i- Kashmir Institute of Medical Sciences, Srinagar, Kashmir, 190011, India
| | - Raies Ahmad Qadri
- Departments of Biotechnology, University of Kashmir, Srinagar, Kashmir, 190006, India
| | - Trupti Navin Chandra Patel
- Division of Medical Biotechnology, School of Bioscience and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
- * E-mail:
| |
Collapse
|
14
|
Shyam K, Penketh PG, Baumann RP, Finch RA, Zhu R, Zhu YL, Sartorelli AC. Antitumor sulfonylhydrazines: design, structure-activity relationships, resistance mechanisms, and strategies for improving therapeutic utility. J Med Chem 2015; 58:3639-71. [PMID: 25612194 DOI: 10.1021/jm501459c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
1,2-Bis(sulfonyl)-1-alkylhydrazines (BSHs) were conceived as more specific DNA guanine O-6 methylating and chloroethylating agents lacking many of the undesirable toxicophores contained in antitumor nitrosoureas. O(6)-Alkylguanine-DNA alkyltransferase (MGMT) is the sole repair protein for O(6)-alkylguanine lesions in DNA and has been reported to be absent in 5-20% of most tumor types. Many BSHs exhibit highly selective cytotoxicity toward cells deficient in MGMT activity. The development of clinically useful MGMT assays should permit the identification of tumors with this vulnerability and allow for the preselection of patient subpopulations with a high probability of responding. The BSH system is highly versatile, permitting the synthesis of many prodrug types with the ability to incorporate an additional level of tumor-targeting due to preferential activation by tumor cells. Furthermore, it may be possible to expand the spectrum of activity of these agents to include tumors with MGMT activity by combining them with tumor-targeted MGMT inhibitors.
Collapse
Affiliation(s)
- Krishnamurthy Shyam
- †Department of Pharmacology and Developmental Therapeutics Program, Cancer Center, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520-8066, United States
| | - Philip G Penketh
- †Department of Pharmacology and Developmental Therapeutics Program, Cancer Center, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520-8066, United States
| | - Raymond P Baumann
- †Department of Pharmacology and Developmental Therapeutics Program, Cancer Center, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520-8066, United States
| | - Rick A Finch
- ‡Department of Veterinary Sciences, The University of Texas M.D. Anderson Cancer Center, 650 Cool Water Drive, Bastrop, Texas 78602, United States
| | - Rui Zhu
- †Department of Pharmacology and Developmental Therapeutics Program, Cancer Center, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520-8066, United States
| | - Yong-Lian Zhu
- †Department of Pharmacology and Developmental Therapeutics Program, Cancer Center, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520-8066, United States
| | - Alan C Sartorelli
- †Department of Pharmacology and Developmental Therapeutics Program, Cancer Center, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520-8066, United States
| |
Collapse
|
15
|
Leandro GS, Sykora P, Bohr VA. The impact of base excision DNA repair in age-related neurodegenerative diseases. Mutat Res 2015; 776:31-9. [PMID: 26255938 PMCID: PMC5576886 DOI: 10.1016/j.mrfmmm.2014.12.011] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 12/23/2014] [Accepted: 12/26/2014] [Indexed: 12/29/2022]
Abstract
The aging process and several age-related neurodegenerative disorders have been linked to elevated levels of DNA damage induced by ROS and deficiency in DNA repair mechanisms. DNA damage induced by ROS is a byproduct of cellular respiration and accumulation of damage over time, is a fundamental aspect of a main theory of aging. Mitochondria have a pivotal role in generating cellular oxidative stress, and mitochondrial dysfunction has been associated with several diseases. DNA base excision repair is considered the major pathway for repair of oxidized bases in DNA both in the nuclei and in mitochondria, and in neurons this mechanism is particularly important because non-diving cells have limited back-up DNA repair mechanisms. An association between elevated oxidative stress and a decrease in BER is strongly related to the aging process and has special relevance in age-related neurodegenerative diseases. Here, we review the role of DNA repair in aging, focusing on the implications of the DNA base excision repair pathways and how alterations in expression of these DNA repair proteins are related to the aging process and to age-related neurodegenerative diseases.
Collapse
Affiliation(s)
- Giovana S Leandro
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program (NIA IRP), Biomedical Research Center, 251 Bayview Blvd., Baltimore, MD 21224, United States; Department of Genetics, Ribeirao Preto Medical School, University of Sao Paulo, Avenida Bandeirantes, 3900, Ribeirao Preto, SP 14049-900, Brazil
| | - Peter Sykora
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program (NIA IRP), Biomedical Research Center, 251 Bayview Blvd., Baltimore, MD 21224, United States.
| | - Vilhelm A Bohr
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program (NIA IRP), Biomedical Research Center, 251 Bayview Blvd., Baltimore, MD 21224, United States.
| |
Collapse
|
16
|
Mielecki D, Wrzesiński M, Grzesiuk E. Inducible repair of alkylated DNA in microorganisms. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2014; 763:294-305. [PMID: 25795127 DOI: 10.1016/j.mrrev.2014.12.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 12/01/2014] [Accepted: 12/02/2014] [Indexed: 12/15/2022]
Abstract
Alkylating agents, which are widespread in the environment, also occur endogenously as primary and secondary metabolites. Such compounds have intrinsically extremely cytotoxic and frequently mutagenic effects, to which organisms have developed resistance by evolving multiple repair mechanisms to protect cellular DNA. One such defense against alkylation lesions is an inducible Adaptive (Ada) response. In Escherichia coli, the Ada response enhances cell resistance by the biosynthesis of four proteins: Ada, AlkA, AlkB, and AidB. The glycosidic bonds of the most cytotoxic lesion, N3-methyladenine (3meA), together with N3-methylguanine (3meG), O(2)-methylthymine (O(2)-meT), and O(2)-methylcytosine (O(2)-meC), are cleaved by AlkA DNA glycosylase. Lesions such as N1-methyladenine (1meA) and N3-methylcytosine (3meC) are removed from DNA and RNA by AlkB dioxygenase. Cytotoxic and mutagenic O(6)-methylguanine (O(6)meG) is repaired by Ada DNA methyltransferase, which transfers the methyl group onto its own cysteine residue from the methylated oxygen. We review (i) the individual Ada proteins Ada, AlkA, AlkB, AidB, and COG3826, with emphasis on the ubiquitous and versatile AlkB and its prokaryotic and eukaryotic homologs; (ii) the organization of the Ada regulon in several bacterial species; (iii) the mechanisms underlying activation of Ada transcription. In vivo and in silico analysis of various microorganisms shows the widespread existence and versatile organization of Ada regulon genes, including not only ada, alkA, alkB, and aidB but also COG3826, alkD, and other genes whose roles in repair of alkylated DNA remain to be elucidated. This review explores the comparative organization of Ada response and protein functions among bacterial species beyond the classical E. coli model.
Collapse
Affiliation(s)
- Damian Mielecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland
| | - Michał Wrzesiński
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland
| | - Elżbieta Grzesiuk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland.
| |
Collapse
|
17
|
Brooks PJ, Zakhari S. Acetaldehyde and the genome: beyond nuclear DNA adducts and carcinogenesis. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2014; 55:77-91. [PMID: 24282063 DOI: 10.1002/em.21824] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 10/01/2013] [Accepted: 10/02/2013] [Indexed: 06/02/2023]
Abstract
The designation of acetaldehyde associated with the consumption of alcoholic beverages as "carcinogenic to humans" (Group 1) by the International Agency for Research on Cancer (IARC) has brought renewed attention to the biological effects of acetaldehyde, as the primary oxidative metabolite of alcohol. Therefore, the overall focus of this review is on acetaldehyde and its direct and indirect effects on the nuclear and mitochondrial genome. We first consider different acetaldehyde-DNA adducts, including a critical assessment of the evidence supporting a role for acetaldehyde-DNA adducts in alcohol related carcinogenesis, and consideration of additional data needed to make a conclusion. We also review recent data on the role of the Fanconi anemia DNA repair pathway in protecting against acetaldehyde genotoxicity and carcinogenicity, as well as teratogenicity. We also review evidence from the older literature that acetaldehyde may impact the genome indirectly, via the formation of adducts with proteins that are themselves critically involved in the maintenance of genetic and epigenetic stability. Finally, we note the lack of information regarding acetaldehyde effects on the mitochondrial genome, which is notable since aldehyde dehydrogenase 2 (ALDH2), the primary acetaldehyde metabolic enzyme, is located in the mitochondrion, and roughly 30% of East Asian individuals are deficient in ALDH2 activity due to a genetic variant in the ALDH2 gene. In summary, a comprehensive understanding of all of the mechanisms by which acetaldehyde impacts the function of the genome has implications not only for alcohol and cancer, but types of alcohol related pathologies as well.
Collapse
Affiliation(s)
- Philip J Brooks
- Division of Metabolism and Health Effects, National Institute on Alcohol Abuse and Alcoholism, Bethesda, Maryland
| | | |
Collapse
|
18
|
Insight into the cooperative DNA binding of the O⁶-alkylguanine DNA alkyltransferase. DNA Repair (Amst) 2014; 20:14-22. [PMID: 24553127 DOI: 10.1016/j.dnarep.2014.01.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 01/18/2014] [Indexed: 11/22/2022]
Abstract
The O(6)-alkylguanine DNA alkyltransferase (AGT) is a highly conserved protein responsible for direct repair of alkylated guanine and to a lesser degree thymine bases. While specific DNA lesion-bound complexes in crystal structures consist of monomeric AGT, several solution studies have suggested that cooperative DNA binding plays a role in the physiological activities of AGT. Cooperative AGT-DNA complexes have been described by theoretical models, which can be tested by atomic force microscopy (AFM). Direct access to structural features of AGT-DNA complexes at the single molecule level by AFM imaging revealed non-specifically bound, cooperative complexes with limited cluster length. Implications of cooperative binding in AGT-DNA interactions are discussed.
Collapse
|
19
|
Gana R, Rao S, Huang H, Wu C, Vasudevan S. Structural and functional studies of S-adenosyl-L-methionine binding proteins: a ligand-centric approach. BMC STRUCTURAL BIOLOGY 2013; 13:6. [PMID: 23617634 PMCID: PMC3662625 DOI: 10.1186/1472-6807-13-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 04/09/2013] [Indexed: 12/31/2022]
Abstract
BACKGROUND The post-genomic era poses several challenges. The biggest is the identification of biochemical function for protein sequences and structures resulting from genomic initiatives. Most sequences lack a characterized function and are annotated as hypothetical or uncharacterized. While homology-based methods are useful, and work well for sequences with sequence identities above 50%, they fail for sequences in the twilight zone (<30%) of sequence identity. For cases where sequence methods fail, structural approaches are often used, based on the premise that structure preserves function for longer evolutionary time-frames than sequence alone. It is now clear that no single method can be used successfully for functional inference. Given the growing need for functional assignments, we describe here a systematic new approach, designated ligand-centric, which is primarily based on analysis of ligand-bound/unbound structures in the PDB. Results of applying our approach to S-adenosyl-L-methionine (SAM) binding proteins are presented. RESULTS Our analysis included 1,224 structures that belong to 172 unique families of the Protein Information Resource Superfamily system. Our ligand-centric approach was divided into four levels: residue, protein/domain, ligand, and family levels. The residue level included the identification of conserved binding site residues based on structure-guided sequence alignments of representative members of a family, and the identification of conserved structural motifs. The protein/domain level included structural classification of proteins, Pfam domains, domain architectures, and protein topologies. The ligand level included ligand conformations, ribose sugar puckering, and the identification of conserved ligand-atom interactions. The family level included phylogenetic analysis. CONCLUSION We found that SAM bound to a total of 18 different fold types (I-XVIII). We identified 4 new fold types and 11 additional topological arrangements of strands within the well-studied Rossmann fold Methyltransferases (MTases). This extends the existing structural classification of SAM binding proteins. A striking correlation between fold type and the conformation of the bound SAM (classified as types) was found across the 18 fold types. Several site-specific rules were created for the assignment of functional residues to families and proteins that do not have a bound SAM or a solved structure.
Collapse
Affiliation(s)
- Rajaram Gana
- Department of Biostatistics and Bioinformatics, Georgetown University Medical Center, Washington, DC 20007, USA
| | | | | | | | | |
Collapse
|
20
|
Uversky VN. The alphabet of intrinsic disorder: II. Various roles of glutamic acid in ordered and intrinsically disordered proteins. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e24684. [PMID: 28516010 PMCID: PMC5424795 DOI: 10.4161/idp.24684] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 03/27/2013] [Accepted: 04/12/2013] [Indexed: 11/19/2022]
Abstract
The ability of a protein to fold into unique functional state or to stay intrinsically disordered is encoded in its amino acid sequence. Both ordered and intrinsically disordered proteins (IDPs) are natural polypeptides that use the same arsenal of 20 proteinogenic amino acid residues as their major building blocks. The exceptional structural plasticity of IDPs, their capability to exist as heterogeneous structural ensembles and their wide array of important disorder-based biological functions that complements functional repertoire of ordered proteins are all rooted within the peculiar differential usage of these building blocks by ordered proteins and IDPs. In fact, some residues (so-called disorder-promoting residues) are noticeably more common in IDPs than in sequences of ordered proteins, which, in their turn, are enriched in several order-promoting residues. Furthermore, residues can be arranged according to their “disorder promoting potencies,” which are evaluated based on the relative abundances of various amino acids in ordered and disordered proteins. This review continues a series of publications on the roles of different amino acids in defining the phenomenon of protein intrinsic disorder and concerns glutamic acid, which is the second most disorder-promoting residue.
Collapse
Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; College of Medicine; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Moscow, Russia
| |
Collapse
|
21
|
Couvé S, Ishchenko AA, Fedorova OS, Ramanculov EM, Laval J, Saparbaev M. Direct DNA Lesion Reversal and Excision Repair in Escherichia coli. EcoSal Plus 2013; 5. [PMID: 26442931 DOI: 10.1128/ecosalplus.7.2.4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2012] [Indexed: 06/05/2023]
Abstract
Cellular DNA is constantly challenged by various endogenous and exogenous genotoxic factors that inevitably lead to DNA damage: structural and chemical modifications of primary DNA sequence. These DNA lesions are either cytotoxic, because they block DNA replication and transcription, or mutagenic due to the miscoding nature of the DNA modifications, or both, and are believed to contribute to cell lethality and mutagenesis. Studies on DNA repair in Escherichia coli spearheaded formulation of principal strategies to counteract DNA damage and mutagenesis, such as: direct lesion reversal, DNA excision repair, mismatch and recombinational repair and genotoxic stress signalling pathways. These DNA repair pathways are universal among cellular organisms. Mechanistic principles used for each repair strategies are fundamentally different. Direct lesion reversal removes DNA damage without need for excision and de novo DNA synthesis, whereas DNA excision repair that includes pathways such as base excision, nucleotide excision, alternative excision and mismatch repair, proceeds through phosphodiester bond breakage, de novo DNA synthesis and ligation. Cell signalling systems, such as adaptive and oxidative stress responses, although not DNA repair pathways per se, are nevertheless essential to counteract DNA damage and mutagenesis. The present review focuses on the nature of DNA damage, direct lesion reversal, DNA excision repair pathways and adaptive and oxidative stress responses in E. coli.
Collapse
|
22
|
Penketh PG, Shyam K, Baumann RP, Ishiguro K, Patridge EV, Zhu R, Sartorelli AC. A strategy for selective O(6)-alkylguanine-DNA alkyltransferase depletion under hypoxic conditions. Chem Biol Drug Des 2012; 80:279-90. [PMID: 22553921 DOI: 10.1111/j.1747-0285.2012.01401.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cellular resistance to chemotherapeutics that alkylate the O-6 position of guanine residues in DNA correlates with their O(6)-alkylguanine-DNA alkyltransferase activity. In normal cells high [O(6)-alkylguanine-DNA alkyltransferase] is beneficial, sparing the host from toxicity, whereas in tumor cells high [O(6)-alkylguanine-DNA alkyltransferase] prevents chemotherapeutic response. Therefore, it is necessary to selectively inactivate O(6)-alkylguanine-DNA alkyltransferase in tumors. The oxygen-deficient compartment unique to solid tumors is conducive to reduction, and could be utilized to provide this selectivity. Therefore, we synthesized 2-nitro-6-benzyloxypurine, an analog of O(6)-benzylguanine in which the essential 2-amino group is replaced by a nitro moiety, and 2-nitro-6-benzyloxypurine is >2000-fold weaker than O(6)-benzylguanine as an O(6)-alkylguanine-DNA alkyltransferase inhibitor. We demonstrate oxygen concentration sensitive net reduction of 2-nitro-6-benzyloxypurine by cytochrome P450 reductase, xanthine oxidase, and EMT6, DU145, and HL-60 cells to yield O(6)-benzylguanine. We show that 2-nitro-6-benzyloxypurine treatment depletes O(6)-alkylguanine-DNA alkyltransferase in intact cells under oxygen-deficient conditions and selectively sensitizes cells to laromustine (an agent that chloroethylates the O-6 position of guanine) under oxygen-deficient but not normoxic conditions. 2-Nitro-6-benzyloxypurine represents a proof of concept lead compound; however, its facile reduction (E(1/2) - 177 mV versus Ag/AgCl) may result in excessive oxidative stress and/or the generation of O(6)-alkylguanine-DNA alkyltransferase inhibitors in normoxic regions in vivo.
Collapse
Affiliation(s)
- Philip G Penketh
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.
| | | | | | | | | | | | | |
Collapse
|
23
|
Melikishvili M, Rodgers DW, Fried MG. 6-Carboxyfluorescein and structurally similar molecules inhibit DNA binding and repair by O⁶-alkylguanine DNA alkyltransferase. DNA Repair (Amst) 2011; 10:1193-202. [PMID: 21982443 DOI: 10.1016/j.dnarep.2011.09.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Revised: 09/06/2011] [Accepted: 09/09/2011] [Indexed: 11/18/2022]
Abstract
Human O⁶-alkylguanine-DNA alkyltransferase (AGT) repairs mutagenic O⁶-alkylguanine and O⁴-alkylthymine adducts in single-stranded and duplex DNAs. These activities protect normal cells and tumor cells against drugs that alkylate DNA; drugs that inactivate AGT are under test as chemotherapeutic enhancers. In studies using 6-carboxyfluorescein (FAM)-labeled DNAs, AGT reduced the fluorescence intensity by ∼40% at binding saturation, whether the FAM was located at the 5' or the 3' end of the DNA. AGT protected residual fluorescence from quenching, indicating a solute-inaccessible binding site for FAM. Sedimentation equilibrium analyses showed that saturating AGT-stoichiometries were higher with FAM-labeled DNAs than with unlabeled DNAs, suggesting that the FAM provides a protein binding site that is not present in unlabeled DNAs. Additional fluorescence and sedimentation measurements showed that AGT forms a 1:1 complex with free FAM. Active site benzylation experiments and docking calculations support models in which the primary binding site is located in or near the active site of the enzyme. Electrophoretic analyses show that FAM inhibits DNA binding (IC₅₀∼76μM) and repair of DNA containing an O⁶-methylguanine residue (IC₅₀∼63μM). Similar results were obtained with other polycyclic aromatic compounds. These observations demonstrate the existence of a new class of non-covalent AGT-inhibitors. After optimization for binding-affinity, members of this class might be useful in cancer chemotherapy.
Collapse
Affiliation(s)
- Manana Melikishvili
- Center for Structural Biology, Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536-0509, United States
| | | | | |
Collapse
|
24
|
Morita R, Nakane S, Shimada A, Inoue M, Iino H, Wakamatsu T, Fukui K, Nakagawa N, Masui R, Kuramitsu S. Molecular mechanisms of the whole DNA repair system: a comparison of bacterial and eukaryotic systems. J Nucleic Acids 2010; 2010:179594. [PMID: 20981145 PMCID: PMC2957137 DOI: 10.4061/2010/179594] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 07/27/2010] [Indexed: 11/20/2022] Open
Abstract
DNA is subjected to many endogenous and exogenous damages. All organisms have developed a complex network of DNA repair mechanisms. A variety of different DNA repair pathways have been reported: direct reversal, base excision repair, nucleotide excision repair, mismatch repair, and recombination repair pathways. Recent studies of the fundamental mechanisms for DNA repair processes have revealed a complexity beyond that initially expected, with inter- and intrapathway complementation as well as functional interactions between proteins involved in repair pathways. In this paper we give a broad overview of the whole DNA repair system and focus on the molecular basis of the repair machineries, particularly in Thermus thermophilus HB8.
Collapse
Affiliation(s)
- Rihito Morita
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Alkyltransferase-like proteins: molecular switches between DNA repair pathways. Cell Mol Life Sci 2010; 67:3749-62. [PMID: 20502938 DOI: 10.1007/s00018-010-0405-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 05/04/2010] [Accepted: 05/10/2010] [Indexed: 01/08/2023]
Abstract
Alkyltransferase-like proteins (ATLs) play a role in the protection of cells from the biological effects of DNA alkylation damage. Although ATLs share functional motifs with the DNA repair protein and cancer chemotherapy target O⁶-alkylguanine-DNA alkyltransferase, they lack the reactive cysteine residue required for alkyltransferase activity, so its mechanism for cell protection was previously unknown. Here we review recent advances in unraveling the enigmatic cellular protection provided by ATLs against the deleterious effects of DNA alkylation damage. We discuss exciting new evidence that ATLs aid in the repair of DNA O⁶-alkylguanine lesions through a novel repair cross-talk between DNA-alkylation base damage responses and the DNA nucleotide excision repair pathway.
Collapse
|
26
|
Morales-Ramírez P, Vallarino-Kelly T, Cruz-Vallejo VL. Effect of O6-chloroethylguanine DNA lesions on the kinetics and mechanism of micronucleus induction in vivo. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2010; 51:236-242. [PMID: 19844954 DOI: 10.1002/em.20538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The aim of this work was to determine the kinetics of micronucleus production because of an increase in O(6)-chloroethyl guanine (O6-ChlEt-G) DNA lesions in murine bone marrow cells in vivo. We increased the frequency of O6-ChlEt-G lesions by pretreatment with an inhibitor of O(6)-methylguanine-DNA methyltransferase (MGMT), O(6)-benzylguanine (O6BG), and subsequent treatment with bis-chloroethylnitrosourea (BCNU). The kinetics of micronucleated-polychromatic erythrocyte (MN-PCE) induction was established by scoring the frequency of MN-PCEs per 2000 PCEs in peripheral blood at 8-hr intervals from immediately prior to treatment to 72-hr post-treatment. We examined groups of five mice treated with (i) dimethylsulfoxide (DMSO), (ii) O6BG in DMSO, (iii) BCNU, or (iv) O6BG in DMSO plus BCNU. The data indicate that O6BG pretreatment causes: (i) ían increase in MN-PCEs induced by BCNU, (ii) a delay in the time of maximal MN-PCE induction produced by the different BCNU doses, and (iii) an increase in cytotoxicity. These data confirm that O6-ChlEt-G is a lesion involved in DNA break induction and in the subsequent production of micronuclei, and also that these lesions seem to be stoichiometrically reduced by MGMT. These data also show that induction of MN-PCEs by BCNU is delayed by pretreatment with O6BG for more than 6 hr, perhaps due to the time required for repair of crosslinks derived from O6-ChlEt-G and/or for DNA duplication, which is required for adduct transformation into crosslinks.
Collapse
Affiliation(s)
- P Morales-Ramírez
- Instituto Nacional de Investigaciones Nucleares, AP 18-1027 México, DF, México. pedro.morales@ inin.gob.mx
| | | | | |
Collapse
|
27
|
Flipping of alkylated DNA damage bridges base and nucleotide excision repair. Nature 2009; 459:808-13. [PMID: 19516334 PMCID: PMC2729916 DOI: 10.1038/nature08076] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Accepted: 04/17/2009] [Indexed: 01/01/2023]
Abstract
Alkyltransferase-like proteins (ATLs) share functional motifs with the cancer chemotherapy target O(6)-alkylguanine-DNA alkyltransferase (AGT) and paradoxically protect cells from the biological effects of DNA alkylation damage, despite lacking the reactive cysteine and alkyltransferase activity of AGT. Here we determine Schizosaccharomyces pombe ATL structures without and with damaged DNA containing the endogenous lesion O(6)-methylguanine or cigarette-smoke-derived O(6)-4-(3-pyridyl)-4-oxobutylguanine. These results reveal non-enzymatic DNA nucleotide flipping plus increased DNA distortion and binding pocket size compared to AGT. Our analysis of lesion-binding site conservation identifies new ATLs in sea anemone and ancestral archaea, indicating that ATL interactions are ancestral to present-day repair pathways in all domains of life. Genetic connections to mammalian XPG (also known as ERCC5) and ERCC1 in S. pombe homologues Rad13 and Swi10 and biochemical interactions with Escherichia coli UvrA and UvrC combined with structural results reveal that ATLs sculpt alkylated DNA to create a genetic and structural intersection of base damage processing with nucleotide excision repair.
Collapse
|
28
|
Telomerase and DNA repair in glioma. Biochim Biophys Acta Mol Basis Dis 2009; 1792:275-9. [DOI: 10.1016/j.bbadis.2009.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Revised: 02/06/2009] [Accepted: 02/06/2009] [Indexed: 02/07/2023]
|
29
|
Luke GA, Escuin H, Felipe PD, Ryan MD. 2A to the Fore – Research, Technology and Applications. Biotechnol Genet Eng Rev 2009; 26:223-60. [DOI: 10.5661/bger-26-223] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
30
|
Georgieva P, Himo F. Density functional theory study of the reaction mechanism of the DNA repairing enzyme alkylguanine alkyltransferase. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.08.043] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
31
|
Morita R, Nakagawa N, Kuramitsu S, Masui R. An O6-methylguanine-DNA methyltransferase-like protein from Thermus thermophilus interacts with a nucleotide excision repair protein. J Biochem 2008; 144:267-77. [PMID: 18483064 DOI: 10.1093/jb/mvn065] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The major damage to DNA caused by alkylating agents involves the formation of O6-methylguanine (O6-meG). Almost all species possess O6-methylguanine-DNA-methyltransferase (Ogt) to repair such damage. Ogt repairs O6-meG lesions in DNA by stoichiometric transfer of the methyl group to a cysteine residue in its active site (PCHR). Thermus thermophilus HB8 has an Ogt homologue, TTHA1564, but in this case an alanine residue replaces cysteine in the putative active site. To reveal the possible function of TTHA1564 in processing O6-meG-containing DNA, we characterized the biochemical properties of TTHA1564. No methyltransferase activity for synthetic O6-meG-containing DNA could be detected, indicating TTHA1564 is an alkyltransferase-like protein. Nevertheless, gel shift assays showed that TTHA1564 can bind to DNA containing O6-meG with higher affinity (9-fold) than normal (unmethylated) DNA. Experiments using a fluorescent oligonucleotide suggested that TTHA1564 recognizes O6-meG in DNA using the same mechanism as other Ogts. We then investigated whether TTHA1564 functions as a damage sensor. Pull-down assays identified 20 proteins, including a nucleotide excision repair protein UvrA, which interacts with TTHA1564. Interaction of TTHA1564 with UvrA was confirmed using a surface plasmon resonance assay. These results suggest the possible involvement of TTHA1564 in DNA repair pathways.
Collapse
Affiliation(s)
- Rihito Morita
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | | | | | | |
Collapse
|
32
|
Bugni JM, Han J, Tsai MS, Hunter DJ, Samson LD. Genetic association and functional studies of major polymorphic variants of MGMT. DNA Repair (Amst) 2007; 6:1116-26. [PMID: 17569599 DOI: 10.1016/j.dnarep.2007.03.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The DNA repair protein, O(6)-methylguanine DNA-methyltransferase (MGMT) prevents mutations and cell death that result from aberrant alkylation of DNA. The polymorphic variants Leu84Phe, Ile143Val, and Lys178Arg are frequent in the human population. We review here studies of these and other MGMT polymorphisms and their association with risk for lung, breast, colorectal and endometrial cancer with a consideration of gene-environment interactions. In addition, we review studies of the effects of polymorphic variation on alkyltransferase activity and expression. It is formally possible that polymorphic variation could modify functions of MGMT other than its alkyltransferase activity. While it was previously reported that an alkylated form of MGMT modifies Estrogen Receptor alpha activity, from our studies we conclude that this regulation is not a major function of MGMT. Overall, the effects of polymorphic variation on protein function are subtle, and further investigation is required to provide a comprehensive mechanism that explains the observed associations of these variants with risk for cancer.
Collapse
Affiliation(s)
- James M Bugni
- Biological Engineering Division, Biology Department, and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | | | | |
Collapse
|
33
|
Tubbs JL, Pegg AE, Tainer JA. DNA binding, nucleotide flipping, and the helix-turn-helix motif in base repair by O6-alkylguanine-DNA alkyltransferase and its implications for cancer chemotherapy. DNA Repair (Amst) 2007; 6:1100-15. [PMID: 17485252 PMCID: PMC1993358 DOI: 10.1016/j.dnarep.2007.03.011] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
O(6)-Alkylguanine-DNA alkyltransferase (AGT) is a crucial target both for the prevention of cancer and for chemotherapy, since it repairs mutagenic lesions in DNA, and it limits the effectiveness of alkylating chemotherapies. AGT catalyzes the unique, single-step, direct damage reversal repair of O(6)-alkylguanines by selectively transferring the O(6)-alkyl adduct to an internal cysteine residue. Recent crystal structures of human AGT alone and in complex with substrate DNA reveal a two-domain alpha/beta fold and a bound zinc ion. AGT uses its helix-turn-helix motif to bind substrate DNA via the minor groove. The alkylated guanine is then flipped out from the base stack into the AGT active site for repair by covalent transfer of the alkyl adduct to Cys145. An asparagine hinge (Asn137) couples the helix-turn-helix DNA binding and active site motifs. An arginine finger (Arg128) stabilizes the extrahelical DNA conformation. With this newly improved structural understanding of AGT and its interactions with biologically relevant substrates, we can now begin to unravel the role it plays in preserving genetic integrity and discover how it promotes resistance to anticancer therapies.
Collapse
Affiliation(s)
- Julie L. Tubbs
- The Scripps Research Institute, The Skaggs Institute for Chemical Biology and Department of Molecular Biology, 10550 North Torrey Pines Road, MB4, La Jolla, CA 92037
| | - Anthony E. Pegg
- Department of Cellular and Molecular Physiology, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine, Hershey, PA 17033
| | - John A. Tainer
- The Scripps Research Institute, The Skaggs Institute for Chemical Biology and Department of Molecular Biology, 10550 North Torrey Pines Road, MB4, La Jolla, CA 92037
- Life Sciences Division, Department of Molecular Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- *To whom correspondence should be addressed: Tel: +1-858-784-8119; fax: +1-858-784-2289;
| |
Collapse
|
34
|
Rasimas JJ, Kar SR, Pegg AE, Fried MG. Interactions of human O6-alkylguanine-DNA alkyltransferase (AGT) with short single-stranded DNAs. J Biol Chem 2007; 282:3357-66. [PMID: 17138560 PMCID: PMC1941669 DOI: 10.1074/jbc.m608876200] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The O6-alkylguanine-DNA alkyltransferase (AGT) repairs O6-alkylguanine and O4-alkylthymine adducts in single-stranded and duplex DNAs. Here we characterize the binding of AGT to single-stranded DNAs ranging in length from 5 to 78 nucleotides (nt). Binding is moderately cooperative (37.9 +/- 3.0
Collapse
Affiliation(s)
- Joseph J. Rasimas
- Department of Molecular Physiology, Penn State University
College of Medicine, Hershey, PA 17033 and
| | - Sambit R. Kar
- Department of Molecular Physiology, Penn State University
College of Medicine, Hershey, PA 17033 and
- Department of Molecular and Cellular Biochemistry and Center
for Structural Biology, University of Kentucky, Lexington, KY 40536
| | - Anthony E. Pegg
- Department of Molecular Physiology, Penn State University
College of Medicine, Hershey, PA 17033 and
| | - Michael G. Fried
- Department of Molecular and Cellular Biochemistry and Center
for Structural Biology, University of Kentucky, Lexington, KY 40536
| |
Collapse
|
35
|
Roberts A, Pelton JG, Wemmer DE. Structural studies of MJ1529, an O6-methylguanine-DNA methyltransferase. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2006; 44 Spec No:S71-82. [PMID: 16826543 DOI: 10.1002/mrc.1823] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The structure of an O6-methylguanine-DNA methyltransferase (MGMT) from the thermophile Methanococcus jannaschii has been determined using multinuclear multidimensional NMR spectroscopy. The structure is similar to homologs from other organisms that have been determined by crystallography, with some variation in the N-terminal domain. The C-terminal domain is more highly conserved in both sequence and structure. Regions of the protein show broadening, reflecting conformational flexibility that is likely related to function.
Collapse
Affiliation(s)
- Anne Roberts
- Department of Chemistry, University of California and Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, CA 94720-1460, USA
| | | | | |
Collapse
|
36
|
Tranah GJ, Bugni J, Giovannucci E, Ma J, Fuchs C, Hines L, Samson L, Hunter DJ. O6-Methylguanine-DNA Methyltransferase Leu84Phe and Ile143Val Polymorphisms and Risk of Colorectal Cancer in the Nurses’ Health Study and Physicians’ Health Study (United States). Cancer Causes Control 2006; 17:721-31. [PMID: 16633920 DOI: 10.1007/s10552-006-0005-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2005] [Accepted: 01/12/2006] [Indexed: 10/24/2022]
Abstract
OBJECTIVE O6-methylguanine-DNA methyltransferase (MGMT) removes mutagenic adducts from the O6-position of guanine in DNA. Unrepaired O6-methylguanines result in G:C to A:T transitions in mutated K-ras and p53 in colorectal tumors. Two non-synonymous MGMT coding region variants, Leu84Phe and Ile143Val, lie in close proximity to the reactive 145Cys residue and to a conserved estrogen receptor interacting helix. METHODS We assessed the association between the MGMT Leu84Phe and Ile143Val polymorphisms and risk of colorectal cancer in two nested case-control studies: one each in the Nurses' Health Study (NHS) and the Physicians' Health Study (PHS) cohorts. RESULTS Among 197 female cases and 2,500 controls from the NHS, the variant 143Val allele was significantly associated with reduced risk of colorectal cancer [odds ratio (OR) = 0.52, 95% confidence interval (CI) 0.33-0.80]. In women, statistically significant gene-environment interactions were found between the Leu84Phe polymorphism and alcohol intake (P = 0.03), BMI (P = 0.04) and postmenopausal hormone use (P = 0.03). The Leu84Phe and Ile143Val polymorphisms were not significantly associated with risk of colorectal cancer among 271 male cases and 451 controls from the PHS. CONCLUSIONS Our results suggest that the common Leu84Phe and Ile143Val polymorphisms in MGMT influence risk of colorectal cancer in women possibly through modulating estrogen receptor-dependent transcriptional activation, which has previously been shown to occur in response to DNA alkylation damage.
Collapse
Affiliation(s)
- Gregory J Tranah
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA.
| | | | | | | | | | | | | | | |
Collapse
|
37
|
Rabik CA, Njoku MC, Dolan ME. Inactivation of O6-alkylguanine DNA alkyltransferase as a means to enhance chemotherapy. Cancer Treat Rev 2006; 32:261-76. [PMID: 16698182 DOI: 10.1016/j.ctrv.2006.03.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Revised: 03/14/2006] [Accepted: 03/15/2006] [Indexed: 10/24/2022]
Abstract
DNA adducts at the O6-position of guanine are a result of the carcinogenic, mutagenic and cytotoxic actions of methylating and chloroethylating agents. The presence of the DNA repair protein O6-alkylguanine-DNA alkyltransferase (AGT) renders cells resistant to the biological effects induced by agents that attack at this position. O6-Benzylguanine (O6-BG) is a low molecular weight substrate of AGT and therefore, results in sensitizing cells and tumors to alkylating agent-induced cytotoxicity and antitumor activity. Presently, chemotherapy regimens of O6-BG in combination with BCNU, temozolomide and Gliadel are in clinical development. Other ongoing clinical trials include expression of mutant AGT proteins that confer resistance to O6-BG in bone marrow stem cells, in an effort to reduce the potential enhanced toxicity and mutagenicity of alkylating agents in the bone marrow. O6-BG has also been found to enhance the cytotoxicity of agents that do not form adducts at the O6-position of DNA, including platinating agents. O6-BG's mechanism of action with these agents is not fully understood; however, it is independent of AGT activity or AGT inactivation. A better understanding of the effects of this agent will contribute to its clinical usefulness and the design of better analogs to further improve cancer chemotherapy.
Collapse
Affiliation(s)
- Cara A Rabik
- Department of Medicine, Committee on Cancer Biology, Committee on Clinical Pharmacology and Pharmacogenomics, University of Chicago, Chicago, IL 60637, USA
| | | | | |
Collapse
|
38
|
Fontes AM, Davis BM, Encell LP, Lingas K, Covas DT, Zago MA, Loeb LA, Pegg AE, Gerson SL. Differential competitive resistance to methylating versus chloroethylating agents among five O6-alkylguanine DNA alkyltransferases in human hematopoietic cells. Mol Cancer Ther 2006; 5:121-8. [PMID: 16432170 DOI: 10.1158/1535-7163.mct-05-0236] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
P140K-MGMT and G156A-MGMT genes encode two O(6)-benzylguanine-resistant O(6)-alkylguanine DNA alkyltransferase proteins that confer a high degree of O(6)-benzylguanine and 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU) or O(6)-benzylguanine and temozolomide resistance to primary hematopoietic cells. In this study, we directly compared these and three other O(6)-benzylguanine-resistant MGMT genes for their ability to protect the human erythroleukemia cell line, K562, using a direct competitive selection strategy to identify the mutation that conferred the greatest degree of protection from O(6)-benzylguanine and either BCNU or temozolomide. MFG retroviral vector plasmids for each of these mutants [G156A-MGMT (ED(50) for O(6)-benzylguanine, 60 micromol/L); and P140K-MGMT, MGMT-2 (S152H, A154G, Y158H, G160S, L162V), MGMT-3 (C150Y, A154G, Y158F, L162P, K165R), and MGMT-5 (N157T, Y158H, A170S; ED(50) for benzylguanine, >1,000 micromol/L)] were mixed, and the virus produced from Phoenix cells was transduced into K562 cells. Stringent selection used high doses of O(6)-benzylguanine (800 micromol/L) and temozolomide (1,000 micromol/L) or BCNU (20 micromol/L) administered twice, and following regrowth, surviving clones were isolated, and the MGMT transgene was sequenced. None of the mutants was lost during selection. Using temozolomide, the enrichment factor was greatest for P140K-MGMT (1.7-fold). Using BCNU selection, the greatest enrichment was observed with MGMT-2 (1.5-fold). G156A-MGMT, which is the least O(6)-benzylguanine-resistant MGMT gene of the mutants tested, was not lost during selection but was selected against. The optimal mutant MGMT useful as a drug resistance gene may depend on whether a methylating or chloroethylating agent is used for drug selection.
Collapse
Affiliation(s)
- Aparecida Maria Fontes
- Division of Hematology/Oncology and Comprehensive Cancer Center, Case Western Reserve University and University Hospitals of Cleveland, OH 44106-4955, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Affiliation(s)
- Yukiko Mishina
- Department of Chemistry, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637
| | - Erica M. Duguid
- Department of Chemistry, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637
| | - Chuan He
- Department of Chemistry, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637
| |
Collapse
|
40
|
Li W, Wen L, Feng JA. RepairNET: A bioinformatics toolbox for functional exploration of DNA damage response. J Cell Physiol 2006; 207:293-9. [PMID: 16453295 DOI: 10.1002/jcp.20594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA damage response is one of the essential cellular mechanisms to maintaining the genomic integrity of the cell. Aberrations in the mechanism of DNA damage response often result in cancer. We describe here RepairNET, a protein-protein interaction network associated with the DNA damage response. RepairNET is assembled from the published literature by using a protocol that involved computational data mining of the MEDLINE and manual curation. This network represents the current knowledge on the intrinsic signaling pathways related to the DNA damage response process. RepairNET currently contains more than 1,200 proteins with over 2,300 functional interactions. A number of web-interface tools have been implemented to facilitate a user-friendly environment. The users can navigate through the cellular network associated with the DNA damage response via a Java-based interactive graphical interface. In order to help users explore the functional relationships between the interacting proteins, we have assigned functional domains to the proteins in RepairNET based on their sequences. A total of 365 unique functional domains are assigned. RepairNET is available online at http://guanyin.chem.temple.edu/RepairNET.html. It could become an essential resource center for cancer research, providing clues to understanding the functional relationship between proteins in the network, and to building scientific models for the mechanism of DNA damage response and cancer proliferation.
Collapse
Affiliation(s)
- Wei Li
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
| | | | | |
Collapse
|
41
|
O6-Benzylguanine Stimulates Regulatory Functions of the Ada Protein in Escherichia coli. RUSS J GENET+ 2005. [DOI: 10.1007/s11177-005-0220-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
42
|
Kufer SK, Dietz H, Albrecht C, Blank K, Kardinal A, Rief M, Gaub HE. Covalent immobilization of recombinant fusion proteins with hAGT for single molecule force spectroscopy. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2005; 35:72-8. [PMID: 16160825 DOI: 10.1007/s00249-005-0010-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Revised: 07/05/2005] [Accepted: 07/18/2005] [Indexed: 11/25/2022]
Abstract
A genetically modified form of the human DNA repair protein O(6)-alkylguanine-DNA-alkyltransferase (hAGT) was used to immobilize different recombinant hAGT fusion proteins covalently and selectively on gold and glass surfaces. Fusion proteins of hAGT with Glutathione S-Transferase and with tandem repeats of Titin Ig-domains, were produced and anchored via amino-polyethylene glycol benzylguanine. Anchoring was characterized and quantified with surface plasmon resonance, atomic force microscope and fluorescence measurements. Individual fusion proteins were unfolded by single molecule force spectroscopy corroborating the selectivity of the covalent attachment.
Collapse
Affiliation(s)
- Stefan K Kufer
- Lehrstuhl für Angewandte Physik, Sektion Physik, Ludwig-Maximilians-Universität München and Center for NanoScience, Amalienstrasse 54, 80799 Munich, Germany
| | | | | | | | | | | | | |
Collapse
|
43
|
Pearson SJ, Ferguson J, Santibanez-Koref M, Margison GP. Inhibition of O6-methylguanine-DNA methyltransferase by an alkyltransferase-like protein from Escherichia coli. Nucleic Acids Res 2005; 33:3837-44. [PMID: 16027108 PMCID: PMC1175458 DOI: 10.1093/nar/gki696] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The alkyltransferase-like (ATL) proteins contain primary sequence motifs resembling those found in DNA repair O6-alkylguanine-DNA alkyltransferase proteins. However, in the putative active site of ATL proteins, a tryptophan (W83) residue replaces the cysteine at the known active site of alkyltransferases. The Escherichia coli atl gene was expressed as a fusion protein and purified. Neither ATL nor C83 or A83 mutants transferred [3H] from [3H]-methylated DNA to themselves, and the levels of O6-methyl guanine (O6-meG) in substrate DNA were not affected by ATL. However, ATL inhibited the transfer of methyl groups to human alkyltransferase (MGMT). Inhibition was reduced by prolonged incubation in the presence of MGMT, again suggesting that O6-meG in the substrate is not changed by ATL. Gel-shift assays show that ATL binds to short single- or double-stranded oligonucleotides containing O6-meG, but not to oligonucleotides containing 8-oxoguanine, ethenoadenine, 5-hydroxycytosine or O4-methylthymine. There was no evidence of demethylation of O6-meG or of glycosylase or endonuclease activity. Overexpression of ATL in E.coli increased, or did not affect, the toxicity of N-methyl-N′-nitro-N-nitrosoguanidine in an alklyltransferase-proficient and -deficient strain, respectively. These results suggest that ATL may act as a damage sensor that flags O6-meG and possibly other O6-alkylation lesions for processing by other repair pathways.
Collapse
Affiliation(s)
| | | | | | - Geoffrey P. Margison
- To whom correspondence should be addressed. Tel: +44 161 446 3183; Fax: +44 161 446 3109;
| |
Collapse
|
44
|
|
45
|
Drabløs F, Feyzi E, Aas PA, Vaagbø CB, Kavli B, Bratlie MS, Peña-Diaz J, Otterlei M, Slupphaug G, Krokan HE. Alkylation damage in DNA and RNA--repair mechanisms and medical significance. DNA Repair (Amst) 2005; 3:1389-407. [PMID: 15380096 DOI: 10.1016/j.dnarep.2004.05.004] [Citation(s) in RCA: 443] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2004] [Indexed: 12/13/2022]
Abstract
Alkylation lesions in DNA and RNA result from endogenous compounds, environmental agents and alkylating drugs. Simple methylating agents, e.g. methylnitrosourea, tobacco-specific nitrosamines and drugs like temozolomide or streptozotocin, form adducts at N- and O-atoms in DNA bases. These lesions are mainly repaired by direct base repair, base excision repair, and to some extent by nucleotide excision repair (NER). The identified carcinogenicity of O(6)-methylguanine (O(6)-meG) is largely caused by its miscoding properties. Mutations from this lesion are prevented by O(6)-alkylG-DNA alkyltransferase (MGMT or AGT) that repairs the base in one step. However, the genotoxicity and cytotoxicity of O(6)-meG is mainly due to recognition of O(6)-meG/T (or C) mispairs by the mismatch repair system (MMR) and induction of futile repair cycles, eventually resulting in cytotoxic double-strand breaks. Therefore, inactivation of the MMR system in an AGT-defective background causes resistance to the killing effects of O(6)-alkylating agents, but not to the mutagenic effect. Bifunctional alkylating agents, such as chlorambucil or carmustine (BCNU), are commonly used anti-cancer drugs. DNA lesions caused by these agents are complex and require complex repair mechanisms. Thus, primary chloroethyl adducts at O(6)-G are repaired by AGT, while the secondary highly cytotoxic interstrand cross-links (ICLs) require nucleotide excision repair factors (e.g. XPF-ERCC1) for incision and homologous recombination to complete repair. Recently, Escherichia coli protein AlkB and human homologues were shown to be oxidative demethylases that repair cytotoxic 1-methyladenine (1-meA) and 3-methylcytosine (3-meC) residues. Numerous AlkB homologues are found in viruses, bacteria and eukaryotes, including eight human homologues (hABH1-8). These have distinct locations in subcellular compartments and their functions are only starting to become understood. Surprisingly, AlkB and hABH3 also repair RNA. An evaluation of the biological effects of environmental mutagens, as well as understanding the mechanism of action and resistance to alkylating drugs require a detailed understanding of DNA repair processes.
Collapse
Affiliation(s)
- Finn Drabløs
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7489 Trondheim, Norway
| | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Zhang F, Bartels MJ, Pottenger LH, Gollapudi BB. Differential adduction of proteins vs. deoxynucleosides by methyl methanesulfonate and 1-methyl-1-nitrosourea in vitro. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2005; 19:438-448. [PMID: 15655799 DOI: 10.1002/rcm.1806] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The reactions of two model mutagenic and carcinogenic alkylating agents, N-methyl-N-nitrosourea (MNU) and methyl methanesulfonate (MMS), with proteins and deoxynucleosides in vitro, were investigated. The protein work used an approach involving trypsin digestion and high-performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC/ESI-MS/MS). This technique permitted identification of the specific location of protein adduction by both MNU and MMS with commercial apomyoglobin and human hemoglobin, under physiological conditions. MNU treatment resulted in predominantly carbamoylation adducts on the proteins, but in contrast only methylated protein adducts were found following treatment with MMS. Further analyses, using TurboSequest, and the Scoring Algorithm for Spectral Analysis (SALSA), revealed that MNU carbamoylation was specific for modification of either the N-terminal valine or the free amino group in lysine residues of apomyglobin and human hemoglobin. However, MMS methylation modified the N-terminal valine and histidine residues of the proteins. Despite their clear differences in protein modifications, MNU and MMS formed qualitatively the same methylated deoxynucleoside adduct profiles with all four deoxynucleosides in vitro under physiological conditions. In light of their different biological potencies, where MMS is considered a 'super clastogen' while MNU is a 'super mutagen', these differences in reaction products with proteins vs. deoxynucleosides may indicate that these two model alkylating agents work via different mechanisms to produce their mutagenic and carcinogenic effects.
Collapse
Affiliation(s)
- Fagen Zhang
- Toxicology and Environmental Research & Consulting, The Dow Chemical Company, 1803 Building, Midland, MI 48674, USA.
| | | | | | | |
Collapse
|
47
|
Koivisto P, Robins P, Lindahl T, Sedgwick B. Demethylation of 3-Methylthymine in DNA by Bacterial and Human DNA Dioxygenases. J Biol Chem 2004; 279:40470-4. [PMID: 15269201 DOI: 10.1074/jbc.m407960200] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rare DNA lesions that are chemically stable and refractory to repair may add disproportionately to the accumulation of mutations in long lived cells. 3-Methylthymine is a minor lesion that is induced by DNA-methylating agents and for which no repair process has been described previously. Here we demonstrate that this lesion can be directly demethylated in vitro by bacterial and human DNA dioxygenases. The Escherichia coli AlkB and human ABH3 proteins repaired 3-methylthymine in both single-stranded and double-stranded polydeoxynucleotides, whereas the human ABH2 protein preferred a duplex substrate. Thus, the known substrates of these enzymes now include 3-methylthymine in DNA, as well as 1-methyladenine and 3-methylcytosine, which all have structurally similar sites of alkylation. Repair of 3-methylthymine by AlkB and ABH3 was optimal at pH 6, but inefficient. At physiological pH, 3-methylthymine, which is a minor methylated lesion, was more slowly repaired than the major lesion generated in single-stranded DNA, 3-methylcytosine. Our data suggest that 3-methylthymine residues in DNA will be repaired inefficiently in vivo and therefore may occur at a low steady-state level, but the residues should not gradually accumulate to high levels in long lived cells.
Collapse
Affiliation(s)
- Pertti Koivisto
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, Hertfordshire EN6 3LD, United Kingdom
| | | | | | | |
Collapse
|
48
|
Rasimas JJ, Dalessio PA, Ropson IJ, Pegg AE, Fried MG. Active-site alkylation destabilizes human O6-alkylguanine DNA alkyltransferase. Protein Sci 2004; 13:301-5. [PMID: 14691244 PMCID: PMC2286524 DOI: 10.1110/ps.03319404] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
O(6)-alkylguanine-DNA alkyltransferase (AGT) repairs pro-mutagenic O(6)-alkylguanine and O(4)-alkylthymine lesions in DNA. The alkylated form of the protein is not reactivated; instead, it is rapidly ubiquitinated and degraded. Here, we show that alkylation destabilizes the native fold of the protein by 0.5-1.2 kcal/mole and the DNA-binding function by 0.8-1.4 kcal/mole. On this basis, we propose that destabilization of the native conformational ensemble acts as a signal for ubiquitination.
Collapse
Affiliation(s)
- Joseph J Rasimas
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, USA
| | | | | | | | | |
Collapse
|
49
|
Daniels DS, Woo TT, Luu KX, Noll DM, Clarke ND, Pegg AE, Tainer JA. DNA binding and nucleotide flipping by the human DNA repair protein AGT. Nat Struct Mol Biol 2004; 11:714-20. [PMID: 15221026 DOI: 10.1038/nsmb791] [Citation(s) in RCA: 243] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2004] [Accepted: 05/19/2004] [Indexed: 01/09/2023]
Abstract
O(6)-alkylguanine-DNA alkyltransferase (AGT), or O(6)-methylguanine-DNA methyltransferase (MGMT), prevents mutations and apoptosis resulting from alkylation damage to guanines. AGT irreversibly transfers the alkyl lesion to an active site cysteine in a stoichiometric, direct damage reversal pathway. AGT expression therefore elicits tumor resistance to alkylating chemotherapies, and AGT inhibitors are in clinical trials. We report here structures of human AGT in complex with double-stranded DNA containing the biological substrate O(6)-methylguanine or crosslinked to the mechanistic inhibitor N(1),O(6)-ethanoxanthosine. The prototypical DNA major groove-binding helix-turn-helix (HTH) motif mediates unprecedented minor groove DNA binding. This binding architecture has advantages for DNA repair and nucleotide flipping, and provides a paradigm for HTH interactions in sequence-independent DNA-binding proteins like RecQ and BRCA2. Structural and biochemical results further support an unpredicted role for Tyr114 in nucleotide flipping through phosphate rotation and an efficient kinetic mechanism for locating alkylated bases.
Collapse
Affiliation(s)
- Douglas S Daniels
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, MB-4, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | | | | | | | | | | | | |
Collapse
|
50
|
Sancar A, Lindsey-Boltz LA, Unsal-Kaçmaz K, Linn S. Molecular Mechanisms of Mammalian DNA Repair and the DNA Damage Checkpoints. Annu Rev Biochem 2004; 73:39-85. [PMID: 15189136 DOI: 10.1146/annurev.biochem.73.011303.073723] [Citation(s) in RCA: 2324] [Impact Index Per Article: 116.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA damage is a relatively common event in the life of a cell and may lead to mutation, cancer, and cellular or organismic death. Damage to DNA induces several cellular responses that enable the cell either to eliminate or cope with the damage or to activate a programmed cell death process, presumably to eliminate cells with potentially catastrophic mutations. These DNA damage response reactions include: (a) removal of DNA damage and restoration of the continuity of the DNA duplex; (b) activation of a DNA damage checkpoint, which arrests cell cycle progression so as to allow for repair and prevention of the transmission of damaged or incompletely replicated chromosomes; (c) transcriptional response, which causes changes in the transcription profile that may be beneficial to the cell; and (d) apoptosis, which eliminates heavily damaged or seriously deregulated cells. DNA repair mechanisms include direct repair, base excision repair, nucleotide excision repair, double-strand break repair, and cross-link repair. The DNA damage checkpoints employ damage sensor proteins, such as ATM, ATR, the Rad17-RFC complex, and the 9-1-1 complex, to detect DNA damage and to initiate signal transduction cascades that employ Chk1 and Chk2 Ser/Thr kinases and Cdc25 phosphatases. The signal transducers activate p53 and inactivate cyclin-dependent kinases to inhibit cell cycle progression from G1 to S (the G1/S checkpoint), DNA replication (the intra-S checkpoint), or G2 to mitosis (the G2/M checkpoint). In this review the molecular mechanisms of DNA repair and the DNA damage checkpoints in mammalian cells are analyzed.
Collapse
Affiliation(s)
- Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7260, USA.
| | | | | | | |
Collapse
|