Mutations play a dual role in life, bad and good. An understanding of the biochemical basis of mutation is fundamental to human health issues involving genetic disorders including birth defects, heritable and sporadic cancers, neurodegenerative disorders and numerous age-related diseases. Mutations, however, also play an essential role during evolution by ensuring competitive fitness at cellular and whole organism levels, including the generation of antibody diversity in higher vertebrates. An understanding of DNA polymerase fidelity is at the core of understanding how mutations are generated. We have been studying the biochemical and physical chemical basis of DNA polymerase fidelity for the past thirty-nine years. By studying high and low fidelity DNA polymerases, we have developed concepts and methods to analyze base selection, exonuclease proofreading, and translesion DNA synthesis (TLS). While investigating the biochemical basis of SOS damaged-induced mutagenesis in E. coli, we discovered DNA polymerase V, a founding member of a new family (Y-family) of "error-prone" DNA polymerases. We showed that Pol V is a heterotrimer (UmuD22C) of two proteins required for UV mutagenesis. In 2009, we resolved a long-standing issue in DNA damage-induced mutagenesis in E. coli, the direct role of a RecA nucleoprotein filament (RecA*) in the replication of damaged DNA templates by Pol V. We showed that the role of RecA* is to transfer a molecule of RecA-ATP from its 32-end to convert inactive Pol V into mutagenically active Pol V Mut (UmuD22C-RecA-ATP). The properties of Pol V Mut are regulated through a biochemical cycle of polymerase activation, TLS, deactivation and reactivation. Using bulk solution studies, we showed that RecA-ATP remains bound to UmuD22C in both activated and deactivated forms of Pol V Mut. Based on these studies, we proposed that Pol V Mut behaves as a conformational switch, with RecA-ATP changing positions relative to UmuC and UmuD22 in activated and deactivated states. Our competing renewal grant contains two major aims.
Both aims use state-of-the-art laser single molecule microscopy to visualize fundamental polymerase behavior, in vitro and in living cells, as the polymerase performs its functions in real-time.
In Aim 1, we use Total Internal Reflectance Microscopy (TIRF) in conjunction with Forster Resonance Energy Transfer (FRET) to watch, in real- time, as a single molecule of Pol V Mut makes transitions between activated and deactivated states, while synthesizing DNA, or while remaining quiescent in the absence of template DNA.
In Aim 2, we use live cell imaging to watch, in real-time, as a single molecule of Pol V, Pol II or Pol IV exchanges with the replicative DNA polymerase III at a replication fork that has stalled in the presence of DNA damage.
Each aim i n our proposal addresses an important new model.
Aim 1 addresses a new model for the regulation of DNA damaged-induced mutagenesis, where active and inactive forms of DNA polymerase are determined by an unprecedented on-off toggle switch mechanism, reflecting conformational changes of RecA-ATP within Pol V Mut. This new regulatory mechanism can act to ensure that error-prone Pol V Mut cannot mutate the cell unnecessarily by copying undamaged DNA templates.
Aim 2 addresses a new model for Pol V-Pol III exchange at a blocked replication fork, where we have found that the ? proofreading subunit of Pol III undergoes rapid degradation dependent on the induction of Pol V in living cells. This new polymerase exchange model suggests the possibility that Pol V gains access to damaged DNA by "attacking" a stalled Pol III at a blocked replication fork.

Public Health Relevance

In all organisms including bacteria and humans, mutations are generally harmful, causing numerous sporadic and inherited diseases. On the other hand, mutations are required for evolution and play an essential role ensuring immunological diversity and general cell and organismal fitness. The proposed research explores the biochemical mechanisms of a new type of error-prone DNA polymerase, which is activated when needed to copy damaged DNA, deactivated to keep it from mutating undamaged DNA, then reactivated again to deal with further DNA damage. This study explores biochemical mechanisms that govern the ability of error-prone DNA polymerases to copy damaged DNA that would otherwise cause a cessation of chromosome replication resulting in cell death.

Agency
National Institute of Health (NIH)
Institute
National Institute of Environmental Health Sciences (NIEHS)
Type
Research Project (R01)
Project #
5R01ES012259-25
Application #
8728853
Study Section
Molecular Genetics B Study Section (MGB)
Program Officer
Shaughnessy, Daniel
Project Start
1989-07-01
Project End
2018-05-31
Budget Start
2014-06-01
Budget End
2015-05-31
Support Year
25
Fiscal Year
2014
Total Cost
$345,978
Indirect Cost
$135,603
Name
University of Southern California
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
072933393
City
Los Angeles
State
CA
Country
United States
Zip Code
90089
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Jiang, Qingfei; Karata, Kiyonobu; Woodgate, Roger et al. (2009) The active form of DNA polymerase V is UmuD'(2)C-RecA-ATP. Nature 460:359-63
Minko, Irina G; Yamanaka, Kinrin; Kozekov, Ivan D et al. (2008) Replication bypass of the acrolein-mediated deoxyguanine DNA-peptide cross-links by DNA polymerases of the DinB family. Chem Res Toxicol 21:1983-90

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