Biochemical Basis of SOS-Induced Mutagenesis

University Of Southern California, Los Angeles CA

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Abstract

DESCRIPTION (provided by applicant): 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 in 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.