1
|
Nischwitz E, Schoonenberg VA, Fradera-Sola A, Dejung M, Vydzhak O, Levin M, Luke B, Butter F, Scheibe M. DNA damage repair proteins across the Tree of Life. iScience 2023; 26:106778. [PMID: 37250769 PMCID: PMC10220248 DOI: 10.1016/j.isci.2023.106778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/27/2023] [Accepted: 04/25/2023] [Indexed: 05/31/2023] Open
Abstract
Genome maintenance is orchestrated by a highly regulated DNA damage response with specific DNA repair pathways. Here, we investigate the phylogenetic diversity in the recognition and repair of three well-established DNA lesions, primarily repaired by base excision repair (BER) and ribonucleotide excision repair (RER): (1) 8-oxoguanine, (2) abasic site, and (3) incorporated ribonucleotide in DNA in 11 species: Escherichia coli, Bacillus subtilis, Halobacterium salinarum, Trypanosoma brucei, Tetrahymena thermophila, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans, Homo sapiens, Arabidopsis thaliana, and Zea mays. Using quantitative mass spectrometry, we identified 337 binding proteins across these species. Of these proteins, 99 were previously characterized to be involved in DNA repair. Through orthology, network, and domain analysis, we linked 44 previously unconnected proteins to DNA repair. Our study presents a resource for future study of the crosstalk and evolutionary conservation of DNA damage repair across all domains of life.
Collapse
Affiliation(s)
| | | | | | - Mario Dejung
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Olga Vydzhak
- Institute of Developmental Biology and Neurobiology (IDN), Johannes-Gutenberg-University, 55128 Mainz, Germany
| | - Michal Levin
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Brian Luke
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes-Gutenberg-University, 55128 Mainz, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Marion Scheibe
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| |
Collapse
|
2
|
Wang L, Zhang H, Chen W, Chen H, Xiao J, Chen X. Recent advances in DNA glycosylase assays. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.10.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
3
|
Liu X, Shao C, Fu J. Promising Biomarkers of Radiation-Induced Lung Injury: A Review. Biomedicines 2021; 9:1181. [PMID: 34572367 PMCID: PMC8470495 DOI: 10.3390/biomedicines9091181] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/05/2021] [Accepted: 09/06/2021] [Indexed: 12/15/2022] Open
Abstract
Radiation-induced lung injury (RILI) is one of the main dose-limiting side effects in patients with thoracic cancer during radiotherapy. No reliable predictors or accurate risk models are currently available in clinical practice. Severe radiation pneumonitis (RP) or pulmonary fibrosis (PF) will reduce the quality of life, even when the anti-tumor treatment is effective for patients. Thus, precise prediction and early diagnosis of lung toxicity are critical to overcome this longstanding problem. This review summarizes the primary mechanisms and preclinical animal models of RILI reported in recent decades, and analyzes the most promising biomarkers for the early detection of lung complications. In general, ideal integrated models considering individual genetic susceptibility, clinical background parameters, and biological variations are encouraged to be built up, and more prospective investigations are still required to disclose the molecular mechanisms of RILI as well as to discover valuable intervention strategies.
Collapse
Affiliation(s)
- Xinglong Liu
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China;
| | - Chunlin Shao
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China;
| | - Jiamei Fu
- Department of Radiation Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| |
Collapse
|
4
|
Chang HL, Su KY, Goodman SD, Yen RS, Cheng WC, Yang YC, Lin LI, Chang SY, Fang WH. Measurement of uracil-DNA glycosylase activity by matrix assisted laser desorption/ionization time-of-flight mass spectrometry technique. DNA Repair (Amst) 2020; 97:103028. [PMID: 33254084 DOI: 10.1016/j.dnarep.2020.103028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/19/2020] [Accepted: 11/19/2020] [Indexed: 11/26/2022]
Abstract
Uracil-DNA glycosylase (UDG) is a highly conserved DNA repair enzyme that acts as a key component in the base excision repair pathway to correct hydrolytic deamination of cytosine making it critical to genome integrity in living organisms. We report here a non-labeled, non-radio-isotopic and very specific method to measure UDG activity. Oligodeoxyribonucleotide duplex containing a site-specific G:U mismatch that is hydrolyzed by UDG then subjected to Matrix Assisted Laser Desorption/Ionization time-of-flight mass spectrometry analysis. A protocol was developed to maintain the AP product in DNA without strand break then the cleavage of uracil was identified by the mass change from uracil substrate to AP product. From UDG kinetic analysis, for G:U substrate the Km is 50 nM, Vmax is 0.98 nM/s and Kcat = 9.31 s-1. The method was applied to uracil glycosylase inhibitor measurement with an IC50 value of 7.6 pM. Single-stranded and double-stranded DNAs with uracil at various positions of the substrates were also tested for UDG activity albeit with different efficiencies. The simple, rapid, quantifiable, scalable and versatile method has potential to be the reference method for monofunctional glycosylase measurement, and can also be used as a tool for glycosylase inhibitors screening.
Collapse
Affiliation(s)
- Hui-Lan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan, ROC
| | - Kang-Yi Su
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan, ROC; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan, ROC
| | - Steven D Goodman
- Center for Microbial Pathogenesis, Nationwide Children's Hospital and the Department of Pediatrics, the Ohio State University, Columbus, OH, USA
| | - Rong-Syuan Yen
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan, ROC
| | - Wern-Cherng Cheng
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan, ROC
| | - Ya-Chien Yang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan, ROC; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan, ROC
| | - Liang-In Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan, ROC; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan, ROC
| | - Sui-Yuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan, ROC; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan, ROC
| | - Woei-Horng Fang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan, ROC; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan, ROC.
| |
Collapse
|