The goals of this project are to understand recombinational DNA repair, particularly the mechanisms of the central recombinases involved in this process and their regulation. Homologous genetic recombination is at once (a) a key DNA repair process, (b) one of the important cancer avoidance pathways in higher eukaryotes, and (c) one of the primary paths to the productive alteration/engineering of cellular genomes. The competing proposal is focused on the bacterial RecA protein and proteins that regulate or augment RecA function. We will also explore specific applications of these proteins in biotechnology. There are four specific aims.
Aim 1 is focused on RecA itself. One key initiative seeks to generate RecA variants with enhanced functionality.
Aim 2 is concerned with RecA regulators. These include the RecFOR proteins that load RecA onto ssDNA, the PsiB protein that binds to free RecA protein and inhibits its binding to DNA, the DprA protein that also helps load RecA onto DNA and enhances DNA transformation in vivo, and the UvrD helicase that is responsible for displacing RecA filaments from the DNA when they are no longer needed. As part of aim 2, we will also explore the function of MgsA, an AAA+ ATPase involved in genome maintenance that is highly conserved from bacteria to humans.
In Aim 3, we will explore the function of a novel RecA-dependent nuclease called Ref, discovered during the last grant period. Ref, encoded by P1, can be used as a kind of universal restriction enzyme. Deployed with RecA, Ref will efficiently introduce targeted double strand breaks at any chosen DNA location in an oligonucleotide- directed fashion. Finally, Aim 4 will continue our efforts to elucidate the role of RecA protein in the function of the mutagenic DNA polymerase V. Practical applications include the use of the Ref nuclease for targeted DNA cleavage, and the use of RecA-mediated double strand break repair for metagenomics, filling gaps in large genomic sequencing projects, and the enhancement of forensic DNA analysis. Ref may eventually be utilized in the genomic engineering of mammalian DNA, in the service of human gene therapy or the generation of mouse gene knockouts.

Public Health Relevance

Recombinational DNA repair is crucial to cancer avoidance in humans, and is also a major path for the productive alteration or engineering of cellular genomes. Specific tools being developed in this project may eventually find applications in some or all of the following: human gene therapy, bacterial genome engineering to produce useful pharmaceuticals, plant genome engineering, the exploration of complex bacterial populations by metagenomics (such as those endemic to the human intestine), the generation of knockout mouse or rat strains for research, and forensic DNA analysis.

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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Barski, Oleg
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University of Wisconsin Madison
Schools of Earth Sciences/Natur
United States
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Chen, Stefanie H; Byrne, Rose T; Wood, Elizabeth A et al. (2015) Escherichia coli radD?(yejH) gene: a novel function involved in radiation resistance and double-strand break repair. Mol Microbiol 95:754-68
Byrne, Rose T; Klingele, Audrey J; Cabot, Eric L et al. (2014) Evolution of extreme resistance to ionizing radiation via genetic adaptation of DNA repair. Elife 3:e01322
Byrne, Rose T; Chen, Stefanie H; Wood, Elizabeth A et al. (2014) Escherichia coli genes and pathways involved in surviving extreme exposure to ionizing radiation. J Bacteriol 196:3534-45
Ronayne, Erin A; Cox, Michael M (2014) RecA-dependent programmable endonuclease Ref cleaves DNA in two distinct steps. Nucleic Acids Res 42:3871-83
Tham, Khek-Chian; Hermans, Nicolaas; Winterwerp, Herrie H K et al. (2013) Mismatch repair inhibits homeologous recombination via coordinated directional unwinding of trapped DNA structures. Mol Cell 51:326-37
Norais, Cedric; Servant, Pascale; Bouthier-de-la-Tour, Claire et al. (2013) The Deinococcus radiodurans DR1245 protein, a DdrB partner homologous to YbjN proteins and reminiscent of type III secretion system chaperones. PLoS One 8:e56558
Ngo, Khanh V; Molzberger, Eileen T; Chitteni-Pattu, Sindhu et al. (2013) Regulation of Deinococcus radiodurans RecA protein function via modulation of active and inactive nucleoprotein filament states. J Biol Chem 288:21351-66
Britt, Rachel L; Chitteni-Pattu, Sindhu; Page, Asher N et al. (2011) RecA K72R filament formation defects reveal an oligomeric RecA species involved in filament extension. J Biol Chem 286:7830-40
Bouthier de la Tour, Claire; Boisnard, Stephanie; Norais, Cedric et al. (2011) The deinococcal DdrB protein is involved in an early step of DNA double strand break repair and in plasmid transformation through its single-strand annealing activity. DNA Repair (Amst) 10:1223-31
Fan, Hsiu-Fang; Cox, Michael M; Li, Hung-Wen (2011) Developing single-molecule TPM experiments for direct observation of successful RecA-mediated strand exchange reaction. PLoS One 6:e21359

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