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)
Project #
Application #
Study Section
Prokaryotic Cell and Molecular Biology Study Section (PCMB)
Program Officer
Barski, Oleg
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Wisconsin Madison
Schools of Earth Sciences/Natur
United States
Zip Code
Stanage, Tyler H; Page, Asher N; Cox, Michael M (2017) DNA flap creation by the RarA/MgsA protein of Escherichia coli. Nucleic Acids Res 45:2724-2735
Lewis, Jacob S; Spenkelink, Lisanne M; Jergic, Slobodan et al. (2017) Single-molecule visualization of fast polymerase turnover in the bacterial replisome. Elife 6:
Chen, Stefanie H; Byrne-Nash, Rose T; Cox, Michael M (2016) Escherichia coli RadD Protein Functionally Interacts with the Single-stranded DNA-binding Protein. J Biol Chem 291:20779-86
Bakhlanova, Irina V; Dudkina, Alexandra V; Wood, Elizabeth A et al. (2016) DNA Metabolism in Balance: Rapid Loss of a RecA-Based Hyperrec Phenotype. PLoS One 11:e0154137
Jaszczur, Malgorzata; Bertram, Jeffrey G; Robinson, Andrew et al. (2016) Mutations for Worse or Better: Low-Fidelity DNA Synthesis by SOS DNA Polymerase V Is a Tightly Regulated Double-Edged Sword. Biochemistry 55:2309-18
Ronayne, Erin A; Wan, Y C Serena; Boudreau, Beth A et al. (2016) P1 Ref Endonuclease: A Molecular Mechanism for Phage-Enhanced Antibiotic Lethality. PLoS Genet 12:e1005797
Leite, Wellington C; Galvão, Carolina W; Saab, Sérgio C et al. (2016) Structural and Functional Studies of H. seropedicae RecA Protein - Insights into the Polymerization of RecA Protein as Nucleoprotein Filament. PLoS One 11:e0159871
Gruber, Angela J; Olsen, Tayla M; Dvorak, Rachel H et al. (2015) Function of the N-terminal segment of the RecA-dependent nuclease Ref. Nucleic Acids Res 43:1795-803
Robinson, Andrew; McDonald, John P; Caldas, Victor E A et al. (2015) Regulation of Mutagenic DNA Polymerase V Activation in Space and Time. PLoS Genet 11:e1005482
Kim, Taejin; Chitteni-Pattu, Sindhu; Cox, Benjamin L et al. (2015) Directed Evolution of RecA Variants with Enhanced Capacity for Conjugational Recombination. PLoS Genet 11:e1005278

Showing the most recent 10 out of 120 publications