Review
Biochemistry & Molecular Biology
Inga R. Grin, Daria V. Petrova, Anton V. Endutkin, Chunquan Ma, Bing Yu, Haiying Li, Dmitry O. Zharkov
Summary: Base excision DNA repair is an important pathway in safeguarding the genome of plants, and understanding their repair mechanisms is crucial for developing new crop varieties.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Clinical Neurology
Mehmet Utku Kucuker, Aysegul Ozerdem, Deniz Ceylan, Alejandra Cabello-Arreola, Ada M. C. Ho, Boney Joseph, Lauren M. Webb, Paul E. Croarkin, Mark A. Frye, Marin Veldic
Summary: This systematic review examined the role of DNA repair enzymes, particularly base excision repair (BER), in mood disorders. The study found that SNPs of several BER genes are associated with MDD and BD, but conflicting findings and limited studies make it difficult to draw definitive conclusions about BER gene expression. Further research comparing DNA repair during episodes of mood disorders to remission may provide valuable insights into the role of DNA repair in these conditions.
JOURNAL OF AFFECTIVE DISORDERS
(2022)
Article
Agronomy
Shiwen Liu, Shuhua Zhu, Guangqin Jing
Summary: Excessive reactive oxygen species (ROS) during storage can lead to oxidative damage to mitochondrial DNA (mtDNA) in peaches, exacerbating fruit damage. Nitric oxide (NO) has been found to help maintain the storage quality of peaches. This study investigates the effects of NO on mtDNA damage and repair, focusing on the base excision repair (BER) pathway. The results show that NO reduces ROS levels and oxidative damage markers in mitochondria, increases mtDNA copy number, and enhances the BER pathway, leading to improved repair efficiency and maintenance of mtDNA integrity.
POSTHARVEST BIOLOGY AND TECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Polina Zhdanova, Alexander A. Ishchenko, Alexander A. Chernonosov, Dmitry O. Zharkov, Vladimir V. Koval
Summary: The study reveals the structural and dynamic features of human endonuclease VIII-like protein 2 (hNEIL2), showing its unique specificity for non-canonical DNA substrates and conformational flexibility in solution.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Jiahui Zhu, Lexin Liu, Xiaodi Ma, Xinyu Cao, Yu Chen, Xiangping Qu, Ming Ji, Huijun Liu, Chi Liu, Xiaoqun Qin, Yang Xiang
Summary: The mortality rate of idiopathic pulmonary fibrosis (IPF) increases yearly due to ineffective treatment. Oxidative stress, especially DNA stimulation, plays a crucial role in pulmonary fibrosis. DNA damage is important in the initiation of IPF and DNA repair systems targeting damage are crucial for lung cell survival. However, existing research has not focused on the role of DNA damage and repair pathways in IPF.
Review
Cell Biology
Mansour Akbari, Hilde Loge Nilsen, Nicola Pietro Montaldo
Summary: Mitochondria are essential for cellular energy production and play a crucial role in organismal development and normal function. Understanding the mechanisms of mtDNA maintenance and transcription can provide insights into the pathogenesis of various diseases.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Vladimir Shafirovich, Nicholas E. Geacintov
Summary: Base excision repair (BER) and nucleotide excision repair (NER) are two major mechanisms that remove DNA lesions. Experimental evidence shows that oxidatively generated DNA lesions can be repaired by both competitive BER and NER pathways. The interaction between BER and NER pathways in repairing oxidatively generated DNA lesions is crucial for understanding DNA repair mechanisms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Weiran Zhang, Ranwei Zhong, Xiangping Qu, Yang Xiang, Ming Ji
Summary: Excess reactive oxygen species (ROS) can lead to oxidative stress by disrupting the balance between oxidation and anti-oxidation. The main product of ROS-induced base damage is 8-hydroxyguanine (8-oxoG), which can cause mutations if not promptly removed during DNA replication. The OGG1-mediated oxidative damage repair pathway plays an important role in preventing dysfunction caused by oxidative stress.
Article
Microbiology
Filipe Rollo, Guilherme D. Martins, Andre G. Gouveia, Solenne Ithurbide, Pascale Servant, Celia V. Romao, Elin Moe
Summary: This study demonstrates the importance of three Endonuclease III-like enzymes encoded by genes in Deinococcus radiodurans. While DrEndoIII2 is the main enzyme in this bacterium, DrEndoIII1 and 3 show unusual and undetectable activity, respectively. The knockout mutants of these genes were more resistant to oxidative stress induced by methyl viologen, indicating the crucial role of all three EndoIII homologs for cell survival. The upregulation of EndoIII homologs gene expression in response to oxidative stress may compensate for the loss of one gene.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Immunology
Maria Belland Olsen, Camilla Huse, Mirta Mittelstedt Leal de Sousa, Sarah Louise Murphy, Antonio Sarno, Tobias Sebastian Obermann, Kuan Yang, Jan Cato Holter, Marte Jontvedt Jorgensen, Erik Egeland Christensen, Wei Wang, Ping Ji, Lars Heggelund, Hedda Hoel, Anne Margarita Dyrhol-Riise, Ida Gregersen, Pal Aukrust, Magnar Bjoras, Bente Halvorsen, Tuva Borresdatter Dahl
Summary: This study aimed to investigate DNA damage and repair in Covid-19 patients. The results showed that patients had comparable levels of DNA damage to healthy controls, but levels of DNA repair proteins were significantly increased, indicating enhanced DNA repair during acute infection. Gene expression analysis also revealed the involvement of DNA repair genes in respiratory failure. Furthermore, the regulation of DNA repair pathway was more significant during Covid-19 compared to other viral or bacterial infections.
JOURNAL OF INFLAMMATION RESEARCH
(2022)
Article
Genetics & Heredity
Heike Katrin Schreier, Rahel Stefanie Wiehe, Miria Ricchetti, Lisa Wiesmueller
Summary: This study identifies the role of polymerase zeta (POLZ) in maintaining mitochondrial DNA (mtDNA) under conditions of oxidative stress. POLZ knockdown leads to mtDNA accumulation and requires the activity of the base excision repair enzyme APE1. Additionally, POLZ is involved in the formation of mtDNA deletions independently of reactive oxygen species. These findings highlight the significance of POLZ in mtDNA turnover, particularly in the presence of oxidative stress.
Article
Plant Sciences
Jose Roberto Torres, Ignacio Lescano Lopez, Ana Maria Ayala, Maria Elena Alvarez
Summary: DNA glycosylases, such as MBD4L in plants, are responsible for removing mispaired or modified bases from DNA through the base excision repair (BER) pathway. This study investigates the role of Arabidopsis MBD4L in removing certain substrates from the nuclear genome in coordination with uracil DNA glycosylase (AtUNG). The findings suggest that MBD4L is critical for maintaining nuclear genome integrity and preventing cell death under genotoxic stress conditions.
Article
Geriatrics & Gerontology
Haixia Zhao, Laixin Song, Na Ma, Chaoqi Liu, Yaoyan Dun, Zhiyong Zhou, Ding Yuan, Changcheng Zhang
Summary: The study investigated the mechanisms underlying the decline in testicular function with aging, highlighting the roles of oxidative stress, DNA damage, and impaired repair. It was found that the weakening antioxidant ability mediated by the Nrf2 pathway and damage to the BER capacity may lead to increased DNA damage and subsequent decline in testicular function during aging.
EXPERIMENTAL GERONTOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Martina Fiumara, Samuele Ferrari, Attya Omer-Javed, Stefano Beretta, Luisa Albano, Daniele Canarutto, Angelica Varesi, Chiara Gaddoni, Chiara Brombin, Federica Cugnata, Erika Zonari, Matteo Maria Naldini, Matteo Barcella, Bernhard Gentner, Ivan Merelli, Luigi Naldini
Summary: Base and prime editors have shown potential for precise genetic engineering, but their cellular responses and genotoxicity are not well understood. This study compared the efficiency, toxicity, and genotoxicity between base and prime editors and Cas9 in human hematopoietic cells. The findings suggest that these editors can induce harmful effects and genotoxicity, raising concerns for their clinical applications.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Muneera Waheed Alfarhan, Heba Al-Hussaini, Narayana Kilarkaje
Summary: Type 2 diabetes negatively affects testicular structure and function, increasing oxidative DNA damage and BER protein levels. PPAR-γ modulation has minimal impact on testicular structural changes, but affects oxidative DNA damage and BER proteins.
CHEMICO-BIOLOGICAL INTERACTIONS
(2022)
Article
Biochemistry & Molecular Biology
Amy M. Whitaker, Mallory R. Smith, Matthew A. Schaich, Bret D. Freudenthal
NUCLEIC ACIDS RESEARCH
(2017)
Article
Biochemistry & Molecular Biology
Mallory R. Smith, David D. Shock, William A. Beard, Marc M. Greenberg, Bret D. Freudenthal, Samuel H. Wilson
NUCLEIC ACIDS RESEARCH
(2019)
Article
Toxicology
Jephte Y. Akakpo, Anup Ramachandran, Luqi Duan, Matthew A. Schaich, Matthew W. Jaeschke, Bret D. Freudenthal, Wen-Xing Ding, Barry H. Rumack, Hartmut Jaeschke
TOXICOLOGICAL SCIENCES
(2019)
Review
Biochemistry & Molecular Biology
Nicole M. Hoitsma, Amy M. Whitaker, Matthew A. Schaich, Mallory R. Smith, Max S. Fairlamb, Bret D. Freudenthal
CELLULAR AND MOLECULAR LIFE SCIENCES
(2020)
Article
Biochemistry & Molecular Biology
Mallory R. Smith, Khadijeh S. Alnajjar, Nicole M. Hoitsma, Joann B. Sweasy, Bret D. Freudenthal
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Chemistry, Multidisciplinary
Benjamin J. Ryan, Haozhe Yang, Jan Henric T. Bacurio, Mallory R. Smith, Ashis K. Basu, Marc M. Greenberg, Bret D. Freudenthal
Summary: This study presents the crystallographic characterization of Fapy•dG in duplex DNA and as the template base for DNA polymerase beta (Pol β). Fapy•dG adopts different anomers depending on the base pairing, and ring opening and epimerization occur in the crystalline state. The mutagenicity of Fapy•dG is influenced by Pol β, resulting in a decrease in polymerase fidelity. The kinetic studies reveal that dCMP incorporation opposite the beta-anomer is significantly faster than the alpha-anomer.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Medicinal
Matthew A. Schaich, Mallory R. Smith, Ashley S. Cloud, Sean M. Holloran, Bret D. Freudenthal
CHEMICAL RESEARCH IN TOXICOLOGY
(2017)
Article
Cell Biology
Prabhakar Bastola, Feng Wang, Matthew A. Schaich, Taiping Gan, Bret D. Freudenthal, Tsui-Fen Chou, Jeremy Chien
CELL DEATH DISCOVERY
(2017)