The long term goal of this research is to develop a detailed and integrated view of how organisms respond to damage to their genetic material. The proposed multidisciplinary research program places a particular emphasis on the roles of the SOS-regulated umuDC genes, which play roles in a DNA damage checkpoint and also encode the DNA polymerase (DNA po1 V) that acts in translesion synthesis, the molecular basis of most UV and chemical mutagenesis. It also includes analyses of the interactions and functions of the SOS-regulated DinB (DNA pol IV) protein and a new initiative to use the techniques of prokaryotic cell biology to determine how the subcellular organization of DNA repair and mutagenesis proteins changes in response to DNA damage. Our work on the structure of the various forms of the umuD gene product has already offered important insights into its mechanism of action and we will continue to investigate the structures of the umuDC and dinB gene products and explore structure-function relationships. To test our hypothesis that UmuD and UmuD' form part of a higher order regulatory system that controls the events that occur when DNA po1 III encounters a lesion, we will characterize the interactions of the umuDC gene products with subunits of DNA po1 III and other cellular proteins. To further our understanding of the molecular mechanisms involved in umuDC-dependent checkpoint control and umuDC-dependent translesion synthesis, we will carry out physiological experiments that test various hypotheses concerning umuDC function. We will identify proteins that interact with DinB (DNA po1 IV) and investigate its physiological role(s). We will carry out cell biological experiments designed to characterize umuC homologs in B. subtilis and determine their subcellular organization, to examine the effects of DNA damage on DNA replication factories, and examine the subcellular organization of other DNA repair systems. Since the process of translesion synthesis appears to be a universal process by which mutations are introduced as a consequence of DNA damage, further studies of the roles of the umuDC gene products in this process should yield insights that are relevant to the origin of cancer and aging. They should also be relevant to certain other human diseases and to evolution. Insights into the structure of UmuC-related DNA polymerases should help us understand the role of the Xeroderma pigmentosum variant (XP-V) product in cancer prevention. Our proposed research may also lead to the identification of new targets for drug development.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Project (R01)
Project #
5R01CA021615-26
Application #
6632955
Study Section
Microbial Physiology and Genetics Subcommittee 2 (MBC)
Program Officer
Okano, Paul
Project Start
1991-02-01
Project End
2006-05-31
Budget Start
2003-06-01
Budget End
2004-05-31
Support Year
26
Fiscal Year
2003
Total Cost
$338,116
Indirect Cost
Name
Massachusetts Institute of Technology
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
001425594
City
Cambridge
State
MA
Country
United States
Zip Code
02139
Gruber, Charley C; Walker, Graham C (2018) Incomplete base excision repair contributes to cell death from antibiotics and other stresses. DNA Repair (Amst) :
Takahashi, Noriko; Gruber, Charley C; Yang, Jason H et al. (2017) Lethality of MalE-LacZ hybrid protein shares mechanistic attributes with oxidative component of antibiotic lethality. Proc Natl Acad Sci U S A :
Dwyer, Daniel J; Collins, James J; Walker, Graham C (2015) Unraveling the physiological complexities of antibiotic lethality. Annu Rev Pharmacol Toxicol 55:313-32
Belenky, Peter; Ye, Jonathan D; Porter, Caroline B M et al. (2015) Bactericidal Antibiotics Induce Toxic Metabolic Perturbations that Lead to Cellular Damage. Cell Rep 13:968-80
Shrivastav, Nidhi; Fedeles, Bogdan I; Li, Deyu et al. (2014) A chemical genetics analysis of the roles of bypass polymerase DinB and DNA repair protein AlkB in processing N2-alkylguanine lesions in vivo. PLoS One 9:e94716
Opperman, Timothy J; Kwasny, Steven M; Kim, Hong-Suk et al. (2014) Characterization of a novel pyranopyridine inhibitor of the AcrAB efflux pump of Escherichia coli. Antimicrob Agents Chemother 58:722-33
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
Pandey, Shree P; Winkler, Jonathan A; Li, Hu et al. (2014) Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria. BMC Genomics 15:121
Penterman, Jon; Singh, Pradeep K; Walker, Graham C (2014) Biological cost of pyocin production during the SOS response in Pseudomonas aeruginosa. J Bacteriol 196:3351-9
Dwyer, Daniel J; Belenky, Peter A; Yang, Jason H et al. (2014) Antibiotics induce redox-related physiological alterations as part of their lethality. Proc Natl Acad Sci U S A 111:E2100-9

Showing the most recent 10 out of 92 publications