The long-term goal of this research is to understand how organisms accurately duplicate their genetic material by coordinating the actions of their DNA replication machinery with those of other cellular proteins involved in repair, damage tolerance, and cell cycle progression. Failure of an organism to do so can have catastrophic consequences ranging from disease, such as cancer, to death. The proposed research program utilizes both biochemical and genetic approaches to understand the roles played by the beta processivity clamp of the E. coli replicative DNA polymerase in coordinating DNA replication, repair, damage tolerance, and cell cycle progression. The beta clamp participates in a DNA damage checkpoint control as well as in translesion DNA synthesis (TLS). In addition, it interacts with a variety of proteins known to function in various aspects of DNA metabolism. As one Aim, we will test our hypothesis that unique interactions of beta with the different umuDC gene products influence the choice between replication, checkpoint, and TLS. These studies will have broad relevance to understanding integration of replication and TLS in both prokaryotic and eukaryotic cells. As a second Aim, we will test our proposal that beta participates in at least one DNA repair and/or umuDC-independent damage tolerance function by determining the molecular basis of the UV light sensitivity of a dnaN59 beta mutant. These studies will further our understanding of mechanisms that couple replication and repair. As a third Aim, we will test our hypothesis that certain partner proteins bind to overlapping surfaces on beta, and that by competing with each other for binding to the clamp, beta is able to regulate which proteins gain access to the replication fork. These studies will provide important insights into fundamental mechanisms of polymerase switching and replication fork management. In summation, we anticipate that the study of the coordinated regulation of DNA replication, DNA damage tolerance and repair, and cell cycle progression in E. coli will provide a valuable framework for understanding these same processes in humans, where the complexity of the events is far greater.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM066094-03
Application #
6887404
Study Section
Special Emphasis Panel (ZRG1-MBC-2 (01))
Program Officer
Portnoy, Matthew
Project Start
2003-05-01
Project End
2008-04-30
Budget Start
2005-05-01
Budget End
2006-04-30
Support Year
3
Fiscal Year
2005
Total Cost
$296,960
Indirect Cost
Name
State University of New York at Buffalo
Department
Biochemistry
Type
Schools of Medicine
DUNS #
038633251
City
Buffalo
State
NY
Country
United States
Zip Code
14260
Kim, Jin S; Nanfara, Michael T; Chodavarapu, Sundari et al. (2017) Dynamic assembly of Hda and the sliding clamp in the regulation of replication licensing. Nucleic Acids Res 45:3888-3905
Babu, Vignesh M P; Itsko, Mark; Baxter, Jamie C et al. (2017) Insufficient levels of the nrdAB-encoded ribonucleotide reductase underlie the severe growth defect of the ?hda E. coli strain. Mol Microbiol 104:377-399
Yuan, Quan; Dohrmann, Paul R; Sutton, Mark D et al. (2016) DNA Polymerase III, but Not Polymerase IV, Must Be Bound to a ?-Containing DnaX Complex to Enable Exchange into Replication Forks. J Biol Chem 291:11727-35
Nanfara, Michael T; Babu, Vignesh M P; Ghazy, Mohamed A et al. (2016) Identification of ? Clamp-DNA Interaction Regions That Impair the Ability of E. coli to Tolerate Specific Classes of DNA Damage. PLoS One 11:e0163643
Ly, Neang S; Bulman, Zackery P; Bulitta, Jürgen B et al. (2016) Optimization of Polymyxin B in Combination with Doripenem To Combat Mutator Pseudomonas aeruginosa. Antimicrob Agents Chemother 60:2870-80
Kath, James E; Chang, Seungwoo; Scotland, Michelle K et al. (2016) Exchange between Escherichia coli polymerases II and III on a processivity clamp. Nucleic Acids Res 44:1681-90
Scotland, Michelle K; Heltzel, Justin M H; Kath, James E et al. (2015) A Genetic Selection for dinB Mutants Reveals an Interaction between DNA Polymerase IV and the Replicative Polymerase That Is Required for Translesion Synthesis. PLoS Genet 11:e1005507
Pillon, Monica C; Babu, Vignesh M P; Randall, Justin R et al. (2015) The sliding clamp tethers the endonuclease domain of MutL to DNA. Nucleic Acids Res 43:10746-59
Bulman, Zackery P; Sutton, Mark D; Ly, Neang S et al. (2015) Emergence of polymyxin B resistance influences pathogenicity in Pseudomonas aeruginosa mutators. Antimicrob Agents Chemother 59:4343-6
Sutton, Mark D (2015) How MutS finds a needle in a haystack. Proc Natl Acad Sci U S A 112:15265-6

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