Failure to efficiently coordinate DNA replication with other cellular processes results in mutations and genome instability, contributing to numerous human disease states, including cancers. Mutations in human pathogens, particularly those caused by reactive oxygen species (ROS) generated by the host immune response, or exposure to antibiotics, promote their adaptation to the host (i.e., pathoadaptation), exacerbating treatment. The long-term goal of our research is to develop an integrated mechanistic understanding of how organisms coordinate the actions of their DNA replication machinery with those of other cellular factors that act in DNA repair and damage tolerance. Work in our lab over the last 10 years supported by this grant has had a major impact on our understanding of mechanisms coordinating the actions of the E. coli replicase with those of translesion DNA synthesis DNA polymerases (TLS Pols). Our findings successfully challenged the well- established tool belt model. We have also shown that errors catalyzed by Pseudomonas aeruginosa DNA polymerase IV (Pol IV) contribute to mutations that likely promote persistence of this pathogen in cystic fibrosis airways. A molecular understanding of the mechanisms that contribute to mutations is crucial to our understanding of the basis for genome instability, human disease, and pathoadaptation, as well as efforts to develop novel therapies. The proposed research addresses unanswered questions regarding mechanisms that organisms use to manage the actions of their diverse Pols. We will focus our efforts in two critical yet understudied areas. During the prior period of support, we discovered that specific E. coli beta-clamp-DNA interactions are required for DNA damage-induced mutagenesis, suggesting they impart a hierarchical order to Pol switches that may be exploited to control mutation rate.
In Aim 1, we will determine the contributions of the different beta-clamp-DNA interactions to replication fidelity and TLS using a combination of genetic, biochemical, biophysical, and single molecule approaches.
In Aim 2, we will use small angle X-ray scattering (SAXS), size exclusion chromatography-multi angle light scattering (SEC-MALS), molecular modeling, and biochemical approaches to structurally define complexes consisting of the 5 different E. coli Pols, clamp, and DNA. Using insights gained from these efforts, together with genetic, biochemical, biophysical, and single molecule approaches, we will define the mechanisms by which E. coli Pols switch. We will also determine whether an ability to impede Pol III processivity is shared by other proteins that switch with Pol III. Results from these experiments will provide unprecedented insight into the molecular mechanisms underlying coordinate regulation of DNA replication, DNA repair, and TLS. Furthermore, we anticipate that our results will identify critical steps in these evolutionarily conserved processes that can be targeted to control proficiency and fidelity of replication for therapeutic gain.

Public Health Relevance

Mutations contribute directly to human diseases, including cancers;they also complicate treatment of individuals infected with pathogenic bacteria by conferring antibiotic resistance and adaptation of these pathogens to their human host. We will define mechanisms by which low fidelity bacterial DNA polymerases gain access to the replication fork to catalyze mutations. We anticipate that our results will identify critical stepsin these control networks that may be targeted to control replication and mutagenesis for therapeutic gain, and will also serve as a framework for understanding similar control networks in humans, contributing to our understanding of mechanisms underlying human diseases such as cancer, as well as aging.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Prokaryotic Cell and Molecular Biology Study Section (PCMB)
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Janes, Daniel E
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State University of New York at Buffalo
Schools of Medicine
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Kath, James E; Jergic, Slobodan; Heltzel, Justin M H et al. (2014) Polymerase exchange on single DNA molecules reveals processivity clamp control of translesion synthesis. Proc Natl Acad Sci U S A 111:7647-52
Babu, Vignesh M P; Sutton, Mark D (2014) A dnaN plasmid shuffle strain for rapid in vivo analysis of mutant Escherichia coli ? clamps provides insight into the role of clamp in umuDC-mediated cold sensitivity. PLoS One 9:e98791
Sanders, Laurie H; Devadoss, Babho; Raja, Geraldine V et al. (2011) Epistatic roles for Pseudomonas aeruginosa MutS and DinB (DNA Pol IV) in coping with reactive oxygen species-induced DNA damage. PLoS One 6:e18824
Sanders, Laurie H; Sudhakaran, Julee; Sutton, Mark D (2009) The GO system prevents ROS-induced mutagenesis and killing in Pseudomonas aeruginosa. FEMS Microbiol Lett 294:89-96
Heltzel, Justin M H; Scouten Ponticelli, Sarah K; Sanders, Laurie H et al. (2009) Sliding clamp-DNA interactions are required for viability and contribute to DNA polymerase management in Escherichia coli. J Mol Biol 387:74-91
Maul, Robert W; Sanders, Laurie H; Lim, James B et al. (2007) Role of Escherichia coli DNA polymerase I in conferring viability upon the dnaN159 mutant strain. J Bacteriol 189:4688-95
Maul, Robert W; Ponticelli, Sarah K Scouten; Duzen, Jill M et al. (2007) Differential binding of Escherichia coli DNA polymerases to the beta-sliding clamp. Mol Microbiol 65:811-27
Sanders, Laurie H; Rockel, Andrea; Lu, Haiping et al. (2006) Role of Pseudomonas aeruginosa dinB-encoded DNA polymerase IV in mutagenesis. J Bacteriol 188:8573-85
Sutton, Mark D; Duzen, Jill M (2006) Specific amino acid residues in the beta sliding clamp establish a DNA polymerase usage hierarchy in Escherichia coli. DNA Repair (Amst) 5:312-23
Sutton, Mark D; Duzen, Jill M; Maul, Robert W (2005) Mutant forms of the Escherichia colibeta sliding clamp that distinguish between its roles in replication and DNA polymerase V-dependent translesion DNA synthesis. Mol Microbiol 55:1751-66

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