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. This competing proposal is focused on the bacterial RecA protein, proteins that regulate or augment RecA function, and proteins that function in closely related pathways. We will also explore specific applications of these proteins in biotechnology. There are four specific aims.
Aim 1 is focused on RecA itself. We will generate RecA variants with enhanced functionality, which may eventually find application in biotechnology.
Aims 2 and 3 focus on proteins that have a major role in maintaining genome stability, but address molecular functions that have been largely overlooked. The subject of Aim2 is the protein MgsA (maintenance of genome stability A). MgsA has close homologues in all organisms from bacteria to humans, but its function has been enigmatic. We have found that it opens up DNA ends, presumably to facilitate the productive loading of key helicases that function in DNA replication.
Aim 3 addresses a previously uncharacterized protein called RadD. This protein may play a role in removing barriers such as RNA polymerase from damaged DNA, clearing the way for DNA repair processes. Finally, Aim 4 will continue our efforts to elucidate the role of RecA protein in the function of the mutagenic DNA polymerase V. We have made much progress in the past 4 years on our understanding of this unusual DNA polymerase, and are now down to mapping the molecular interaction between RecA and the polymerase subunits. The RecA variants generated in Aim 1 may have some practical application as the subjects of new studies to explore RecA structure/function and as reagents in RecA applications in forensic science and genome engineering.
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. Proteins being studied in this project will provide new insights into pathways by which cells repair DNA and organisms avoid tumorigenesis. 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),and forensic DNA analysis.
| Henrikus, Sarah S; Wood, Elizabeth A; McDonald, John P et al. (2018) DNA polymerase IV primarily operates outside of DNA replication forks in Escherichia coli. PLoS Genet 14:e1007161 |
| 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: |
| 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 |
| 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 |
| 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 |
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