The repair of DNA lesions such as double strand breaks (DSBs) is crucial to the stability of the genome, and we are proposing to study two processes that are fundamental to the prevention and repair of DSBs in all cells. The first is recombination-dependent replication (RDR) that is now recognized as a central mechanism in DNA metabolism that operates in many DNA repair scenarios. The second process is replication fork progression and the rescue of stalled forks. Stalled forks can lead to DSBs, and they need to be rapidly dealt with in the cell. We are interested in the underlying mechanisms that operate in these two processes, and will therefore study them in a very simple, well characterized organism, namely bacteriophage T4. Phage T4 is an ideal system for the multidisciplinary approach that we have designed, and there are many similarities between T4 and eukaryotic proteins. Defects in repair mechanisms lead to the accumulation of mutations that eventually result in cancer, and the proposed studies in T4 are therefore directly relevant to human disease. Five T4 proteins will be studied, UvsX, UvsY, UvsW, Dda and MotA. The recombinatorial proteins UvsX and UvsY mediate the T4 homologous recombination reaction that is required for RDR. UvsW and Dda are helicases that translocate and/or unwind branched nucleic acid structures and have important roles in RDR and replication fork progression. Defects in helicases such as Bloom and Werner are known to cause cancer in humans, and there is evidence that UvsW and Dda may be functionally homologous to these molecules. Finally, structural studies suggest that the T4 transcription factor MotA binds DNA in a novel fashion that is shared by UvsW. The mechanisms of these five proteins will be studied at the molecular level by a coordinated approach involving X-ray crystallography and NMR spectroscopy to study their structures, in vitro methods to study their individual functions and interactions, and in vivo methods to understand their biological roles. A considerable body of preliminary data have been obtained for this project that includes two high resolution structures, crystals, purified proteins and functional information from T4 mutants. The P.I. will direct the structural studies, and the co-P.I. will direct the in vivo studies. The in vitro analyses will be performed in both laboratories as appropriate.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM066934-03
Application #
7099478
Study Section
Physiological Chemistry Study Section (PC)
Program Officer
Lewis, Catherine D
Project Start
2004-08-01
Project End
2008-07-31
Budget Start
2006-08-01
Budget End
2007-07-31
Support Year
3
Fiscal Year
2006
Total Cost
$348,076
Indirect Cost
Name
St. Jude Children's Research Hospital
Department
Type
DUNS #
067717892
City
Memphis
State
TN
Country
United States
Zip Code
38105
Gajewski, Stefan; Waddell, Michael Brett; Vaithiyalingam, Sivaraja et al. (2016) Structure and mechanism of the phage T4 recombination mediator protein UvsY. Proc Natl Acad Sci U S A 113:3275-80
Barfoot, Tasida; Herdendorf, Timothy J; Behning, Bryanna R et al. (2015) Functional Analysis of the Bacteriophage T4 Rad50 Homolog (gp46) Coiled-coil Domain. J Biol Chem 290:23905-15
Almond, Joshua R; Stohr, Bradley A; Panigrahi, Anil K et al. (2013) Coordination and processing of DNA ends during double-strand break repair: the role of the bacteriophage T4 Mre11/Rad50 (MR) complex. Genetics 195:739-55
Kreuzer, Kenneth N (2013) DNA damage responses in prokaryotes: regulating gene expression, modulating growth patterns, and manipulating replication forks. Cold Spring Harb Perspect Biol 5:a012674
Hsieh, Meng-Lun; James, Tamara D; Knipling, Leslie et al. (2013) Architecture of the bacteriophage T4 activator MotA/promoter DNA interaction during sigma appropriation. J Biol Chem 288:27607-18
He, Xiaoping; Byrd, Alicia K; Yun, Mi-Kyung et al. (2012) The T4 phage SF1B helicase Dda is structurally optimized to perform DNA strand separation. Structure 20:1189-200
Gajewski, Stefan; Webb, Michael R; Galkin, Vitold et al. (2011) Crystal structure of the phage T4 recombinase UvsX and its functional interaction with the T4 SF2 helicase UvsW. J Mol Biol 405:65-76
Long, David T; Kreuzer, Kenneth N (2009) Fork regression is an active helicase-driven pathway in bacteriophage T4. EMBO Rep 10:394-9
Kerr, Iain D; Sivakolundu, Sivashankar; Li, Zhenmei et al. (2007) Crystallographic and NMR analyses of UvsW and UvsW.1 from bacteriophage T4. J Biol Chem 282:34392-400
He, Xiaoping; van Waardenburg, Robert C A M; Babaoglu, Kerim et al. (2007) Mutation of a conserved active site residue converts tyrosyl-DNA phosphodiesterase I into a DNA topoisomerase I-dependent poison. J Mol Biol 372:1070-81

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