Review
Biochemistry & Molecular Biology
Joseph D. Kaszubowski, Michael A. Trakselis
Summary: High fidelity DNA polymerases are crucial for genome replication, but they can become stalled at damaged sites. Translesion synthesis polymerases can temporarily take over synthesis at these sites, but they are less accurate. Mechanisms are needed to recruit high fidelity polymerases back to ensure accurate synthesis.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Alexander A. Kruchinin, Alena V. Makarova
Summary: DNA polymerase theta belongs to the A family of DNA polymerases and plays a key role in DNA repair and damage tolerance, including double-strand break repair and DNA translesion synthesis. Pol theta is often overexpressed in cancer cells and promotes their resistance to chemotherapeutic agents. In this review, we discuss unique biochemical properties and structural features of Pol theta, its multiple roles in protection of genome stability and the potential of Pol theta as a target for cancer treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Daniel W. Conroy, Yu Xu, Honglue Shi, Nicole Gonzalez Salguero, Rudra N. Purusottam, Matthew D. Shannon, Hashim M. Al-Hashimi, Christopher P. Jaroniec
Summary: The majority of base pairs in DNA follow the canonical Watson-Crick geometry, but they can also adopt alternative Hoogsteen conformations which are important for biological function and mechanism. This study demonstrates that multidimensional dynamic nuclear polarization-enhanced solid-state NMR can be used as a spectroscopic tool to observe and distinguish between Watson-Crick and Hoogsteen base pairs in various DNA systems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Radhika Malik, Robert E. Johnson, Louise Prakash, Satya Prakash, Iban Ubarretxena-Belandia, Aneel K. Aggarwal
Summary: The study investigates the structure of the DNA-Pol zeta complex and its ability to extend DNA synthesis past mismatched base pairs. The results reveal the conformational changes in the Pol zeta active site and how it responds to mismatched DNA, allowing for the proper binding and extension of nucleotides. This study provides valuable insights into the regulation of DNA synthesis in eukaryotes.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Xu Feng, Baochang Zhang, Zhe Gao, Ruyi Xu, Xiaotong Liu, Sonoko Ishino, Mingxia Feng, Yulong Shen, Yoshizumi Ishino, Qunxin She
Summary: The study reveals that Sulfolobus islandicus Dpo2, previously predicted to be inactive, is actually a functional DNA polymerase involved in translesion synthesis. Dpo2 replicates undamaged DNA with high fidelity and efficiently extends mismatched and DNA lesion-containing substrates, highlighting its importance in DNA damage repair.
Article
Microbiology
Xu Feng, Baochang Zhang, Zhe Gao, Ruyi Xu, Xiaotong Liu, Sonoko Ishino, Mingxia Feng, Yulong Shen, Yoshizumi Ishino, Qunxin She
Summary: In this work, we discovered that Sulfolobus islandicus Dpo2, a B-family DNA polymerase once predicted to be inactive, is a functional DNA polymerase involved in translesion synthesis. S. islandicus Dpo2 belongs to a large group of B-family DNA polymerases (PolB2) that exists in many archaea and some bacteria, and they carry variations in conserved amino acids in the functional domains responsible for polymerization and proofreading. Contrary to predictions, this prokaryotic B-family DNA polymerase not only replicates undamaged DNA accurately, but also efficiently extends mismatched and DNA lesion-containing substrates. Based on our findings, we propose that this enzyme functions as an extender polymerase, representing the first prokaryotic enzyme of this type. Our data also suggests that this PolB2 enzyme serves as a functional counterpart of the eukaryotic DNA polymerase Pol zeta, which is dedicated to DNA damage repair.
Article
Biochemical Research Methods
Yu Wang, Dongdong Zhao, Letian Sun, Jie Wang, Liwen Fan, Guimin Cheng, Zhihui Zhang, Xiaomeng Ni, Jinhui Feng, Meng Wang, Ping Zheng, Changhao Bi, Xueli Zhang, Jibin Sun
Summary: Expanding base conversion types greatly broadens the application of base editing. The study discovered that the DNA polymerase V-mediated TLS pathway controls C-to-A editing in E. coli while C-to-G conversion is the main product in C. glutamicum. Introducing the E. coli TLS pathway into a TLS-deficient C. glutamicum mutant changes the GBE outcome from C-to-G to C-to-A. This study demonstrates the possibility of engineering TLS systems for advanced genome editing tools.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Thomas A. Guilliam, Joseph T. P. Yeeles
Summary: The study shows that a yeast replisome is inherently tolerant to the oxidative lesion Tg, efficiently bypassing leading-strand Tg even in the absence of TLS machinery. A switch from Pol epsilon to Pol delta after helicase-polymerase uncoupling promotes rapid, efficient, and error-free lesion bypass at physiological nucleotide levels. Replicase switching may facilitate continued leading-strand synthesis when Pol delta is more effective at bypassing damage than Pol epsilon.
Article
Chemistry, Physical
Ahmed M. Rozza, Imre Bako, Julianna Olah
Summary: Solvation plays a crucial role in maintaining the structure and function of biomolecules. In this study, the hydration patterns of DNA with different base pairings were investigated using molecular dynamics simulation and topological analysis of the hydrogen bond network. It was found that HG base pairing increased the solvation of the major groove and disrupted the water structure in the minor groove, which could contribute to the recognition of specific DNA binding proteins.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Cell Biology
Anna Schrempf, Sara Bernardo, Emili A. Arasa Verge, Miguel A. Ramirez Otero, Jordan Wilson, Dominik Kirchhofer, Gerald Timelthaler, Anna M. Ambros, Atilla Kaya, Marcus Wieder, Gerhard F. Ecker, Georg E. Winter, Vincenzo Costanzo, Joanna I. Loizou
Summary: Polymerase theta (POLO) is an error-prone DNA polymerase that is synthetically lethal in cancer cells with BRCA1/2 mutations. The study shows that POLO processes single-stranded DNA gaps in the absence of BRCA1, promoting replication fork progression and survival of BRCA1 mutant cells. The research also uncovers suppressors of the POLO-BRCA1 interaction, including NBN and CDK6, which contribute to ssDNA gap formation and exacerbate replication stress in BRCA1-deficient cells.
Article
Biochemistry & Molecular Biology
Alicia M. Crisalli, Yi-Tzai Chen, Ang Cai, Deyu Li, Bongsup P. Cho
Summary: This study investigates the impact of epigenetic modulation on conformational heterogeneity and bypass of DNA lesions in different sequence contexts. The results reveal that the bypass efficiency of DNA damage varies depending on the sequence context, particularly in sequences with 5mC modification. The conformational basis behind these variations differs between different sequence contexts, providing novel insights into how epigenetic modifications affect the repair of DNA adducts.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Mina Yeom, Jin-Kyung Hong, Joo-Ho Shin, Yunjong Lee, Frederick Peter Guengerich, Jeong-Yun Choi
Summary: Three variants of DNA polymerase, C34W, I147N, and R167Q, have been found to significantly decrease the repair function of cells, leading to increased sensitivity to UV radiation and cisplatin chemotherapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Domenico Maiorano, Jana El Etri, Camille Franchet, Jean-Sebastien Hoffmann
Summary: Genome instability plays a crucial role in tumor formation and treatment, but excessive instability may suppress tumorigenesis and be associated with a better prognosis. Specialized DNA polymerases play a key role in reducing extreme genetic instability, helping to avoid or repair DNA damage.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Radha Charan Dash, Kyle Hadden
Summary: Translesion synthesis (TLS) is an error-prone mechanism used by actively replicating cells to copy past DNA lesions, ensuring cells continue replication in the presence of damaged DNA bases. TLS plays a crucial role in rescuing cancer cells during chemotherapy and has emerged as an interesting target for drug discovery.
Review
Biochemistry & Molecular Biology
Carlos D. Ordonez, Modesto Redrejo-Rodriguez
Summary: Just like DNA polymerases (DNAPs) replicate cellular and viral genomes, a few dedicated proteins from natural origins and engineered versions are suitable for amplification of whole genomes and metagenomes (WGA). Different protocols based on various DNAPs have been developed for specific applications. Isothermal WGA using f29 DNA polymerase is widely used due to its high performance, but PCR-based methods are also available. Selection of a suitable enzyme for WGA should consider replication fidelity, processivity, thermostability, coupling replication, double helix unwinding, and maintaining replication opposite to damaged bases. This review provides an overview of the properties of DNAPs used in WGA, discusses their limitations, and suggests future research directions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Jung-Hoon Yoon, Mark J. McArthur, Jeseong Park, Debashree Basu, Maki Wakamiya, Louise Prakash, Satya Prakash
Article
Biochemistry & Molecular Biology
Jung-Hoon Yoon, Jayati Roy Choudhury, Louise Prakash, Satya Prakash
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Rinku Jain, William J. Rice, Radhika Malik, Robert E. Johnson, Louise Prakash, Satya Prakash, Iban Ubarretxena-Belandia, Aneel K. Aggarwal
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2019)
Article
Multidisciplinary Sciences
Olga Rechkoblit, Robert E. Johnson, Angeliki Buku, Louise Prakash, Satya Prakash, Aneel K. Aggarwal
SCIENTIFIC REPORTS
(2019)
Correction
Cell Biology
Jung-Hoon Yoon, Robert E. Johnson, Louise Prakash, Satya Prakash
GENES & DEVELOPMENT
(2020)
Article
Biochemistry & Molecular Biology
Jung-Hoon Yoon, Robert E. Johnson, Louise Prakash, Satya Prakash
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Biology
Jung-Hoon Yoon, Debashree Basu, Karthi Sellamuthu, Robert E. Johnson, Satya Prakash, Louise Prakash
Summary: Pol lambda can substitute for Rev1 as a scaffolding component of Polζ, enabling error-free translesion synthesis in human cells and maintaining genome integrity and cellular homeostasis.
LIFE SCIENCE ALLIANCE
(2021)
Article
Cell Biology
Jung-Hoon Yoon, Robert E. Johnson, Louise Prakash, Satya Prakash
Summary: Chemotherapy with cisplatin is limited by its toxicity and risk of secondary malignancies. Targeting translesion synthesis (TLS) mechanisms in cancer cells, as opposed to normal cells, can exacerbate the toxicity and tumorigenicity of cisplatin-based chemotherapeutics.
GENES & DEVELOPMENT
(2021)
Article
Biochemistry & Molecular Biology
Jung-Hoon Yoon, Debashree Basu, Jayati Roy Choudhury, Satya Prakash, Louise Prakash
Summary: The study demonstrates the essential role of Pol lambda in inserting the correct nucleotide T opposite 1-MeA, while Pol zeta is responsible for extending synthesis. The ability of Pol lambda to accommodate 1-MeA in a syn confirmation and form Hoogsteen base pair with T during DNA synthesis is highlighted. This adds a novel aspect to Pol lambda's function in translesion synthesis, in addition to its role as a scaffolding component for Pol zeta.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)