Copyright 2013-2019 Zhao Lab | Contact: linlin.zhao@ucr.edu

   Human genetic material DNA is susceptible to a variety of endogenous and foreign chemicals, producing as many as 100,000 chemically modified DNA lesions or DNA adducts per cell each day. DNA damage is safeguarded by an intricate DNA repair network and several DNA damage tolerance mechanisms; nonetheless, certain DNA lesions can escape repair or exceed the repair capacity and eventually accumulate in the genome. The persisted DNA lesions can interfere with DNA transactions, leading to cell cycle arrest, mutations, and cell death. An altered genetic content in key regions, such as proto-oncogenes and tumor suppressor genes, is a major driving force for human diseases including cancer.


   

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   This project focuses on understanding the molecular mechanisms by which specialized DNA polymerases catalyze nucleotide incorporation, interact with cognate proteins, and form faulty products. Translesion synthesis (TLS) is a conversed DNA damage tolerance mechanism, whereby specialized DNA polymerases participate in copying past obstructive DNA structures, such as DNA lesions or  non-canonical DNA structures. Because TLS is error-prone, it plays an important role in mutagenesis. We combine classic enzymology and biophysical approaches (e.g. enzyme kinetics and X-ray crystallography) with modern mass spectrometry-based methods to gain mechanistic insights into specialized DNA polymerases.


Representative publications:


  1. 1.Xu et al. Biochemistry, 2015, 54, 639-651.

  2. 2.Xu et al, J Mol. Biol. 2019, 431, 673-686.


    Mitochondria are subcellular compartments that are critical for energy production, cell signaling, and the biosynthesis of protein cofactors in higher eukaryotic cells. The mitochondrial DNA (mtDNA) genome is indispensable for mitochondrial function because it encodes protein subunits of the electron transport chain and a full set of transfer and ribosomal RNAs. mtDNA degradation is an essential mechanism in mitochondrial genomic maintenance. In addition, mtDNA degradation is an important quality control measure to cope with mitochondrial DNA damage sourced from endogenous and environmental chemicals. The project aims to decipher the chemical and molecular basis of mitochondrial DNA turnover. Mitochondrial transcription factor A (TFAM) is abundant DNA packaging protein and an important protein for transcription and mitochondrial DNA maintenance. We recently discovered a novel role of TFAM in facilitating the degradation of damaged DNA containing abasic sites. We found that TFAM could accelerate the strand breakage rate at abasic sites by 2 to 3-orders of magnitude relative to naked DNA. TFAM competes effectively with AP endonuclease, considering the abundance of TFAM in mitochondrial nucleoids.  Currently, we are investigating the mechanism of the reaction and confirming such a role of TFAM in cells.


Representative publications:


  1. 1.Xu et al. PNAS. 2019, 116, 17792-17799.

  2. 2.Zhao, The Enzymes. 2019, 45, 311-341.


DNA polymerase enzymology

Mitochondrial DNA degradation