The general goal of the proposed research is to describe the molecular architecture of the eukaryotic DNA replication fork, its function during normal replication, and its response to stress or DNA damage, using S. cerevisiae as a model system. Recent studies have delineated the activities of DNA polymerase d and DNA polymerase e at the standard replication fork, and the role of DNA polymerase d in lagging strand DNA replication. Translesion synthesis (TLS) in response to DNA damage allows the cell to overcome damage that forms a terminal block for the regular replication machinery;TLS is associated with an increased frequency of mutations, hence mutagenesis. A ubiquitinated form of the replication clamp PCNA initiates its essential roles in TLS through recruitment of the Rev1 protein, a factor that organizes the TLS machinery. The DNA damage checkpoint is a signal transduction pathway that temporarily holds the cell cycle in response to DNA damage. The checkpoint clamp 9-1-1, when brought together onto DNA with the sensor kinase Mec1 (human ATR), activates Mec1 to phosphorylate downstream targets including Rad53 (human Chk1/2). Preliminary studies indicate that the replication initiation protein kinase Cdc7-Dbf4 uniquely phosphorylates critical factors in the mutagenesis and checkpoint pathways. These data suggest that the three pathways are more interconnected than they at first appear to be. The proposal will test specific hypotheses central to genome replication and maintenance.
In aim 1, the mechanistic and structural nature of strand displacement synthesis by DNA polymerase d, and its regulation by the flap endonuclease FEN1 will be investigated.
In aim 2, the efficiency and fidelity of TLS by DNA polymerase ? and associated factors, and the role of the Cdc7-Dbf4 protein kinase in TLS and mutagenesis will be studied.
In aim 3, the role of the checkpoint clamp 9-1-1 in checkpoint function and in mutagenesis will be addressed by biochemical studies and mutational analysis. The regulation of the 9-1-1 pathway by Cdc7-Dbf4 phosphorylation will also be studied. Proper replication of cellular DNA, and responses to stress and DNA damage is of the highest importance in maintaining the integrity of our genetic information. Patients with known defects in these pathways are at a highly increased risk for developing cancer. These pathways are conserved from human to yeast. The proposed studies will be carried out in yeast because this model organism is more approachable to genetic and biochemical analysis.
Proper replication of cellular DNA is of the highest importance in maintaining the integrity of our genetic information. In this application, we are proposing to study the process of DNA replication, and the responses of the cell to DNA damage that can lead to the generation of mutations and to cell death. Patients with known defects in these pathways are at a highly increased risk for developing cancer. These pathways are conserved from human to yeast, and we are proposing to study these pathways in yeast, because this model organism is more approachable to genetic and biochemical analysis.
| Burgers, Peter M J; Kunkel, Thomas A (2017) Eukaryotic DNA Replication Fork. Annu Rev Biochem 86:417-438 |
| Koc, Katrina N; Singh, Saurabh P; Stodola, Joseph L et al. (2016) Pif1 removes a Rap1-dependent barrier to the strand displacement activity of DNA polymerase ?. Nucleic Acids Res 44:3811-9 |
| Burgers, Peter M J; Gordenin, Dmitry; Kunkel, Thomas A (2016) Who Is Leading the Replication Fork, Pol ? or Pol ?? Mol Cell 61:492-493 |
| Stodola, Joseph L; Stith, Carrie M; Burgers, Peter M (2016) Proficient Replication of the Yeast Genome by a Viral DNA Polymerase. J Biol Chem 291:11698-705 |
| Stojkovi?, Gorazd; Makarova, Alena V; Wanrooij, Paulina H et al. (2016) Oxidative DNA damage stalls the human mitochondrial replisome. Sci Rep 6:28942 |
| Stodola, Joseph L; Burgers, Peter M (2016) Resolving individual steps of Okazaki-fragment maturation at a millisecond timescale. Nat Struct Mol Biol 23:402-8 |
| Kochenova, Olga V; Bezalel-Buch, Rachel; Tran, Phong et al. (2016) Yeast DNA polymerase ? maintains consistent activity and mutagenicity across a wide range of physiological dNTP concentrations. Nucleic Acids Res : |
| Cho, Jang-Eun; Huang, Shar-Yin N; Burgers, Peter M et al. (2016) Parallel analysis of ribonucleotide-dependent deletions produced by yeast Top1 in vitro and in vivo. Nucleic Acids Res 44:7714-21 |
| Wanrooij, Paulina H; Burgers, Peter M (2015) Yet another job for Dna2: Checkpoint activation. DNA Repair (Amst) 32:17-23 |
| Sparks, Justin L; Burgers, Peter M (2015) Error-free and mutagenic processing of topoisomerase 1-provoked damage at genomic ribonucleotides. EMBO J 34:1259-69 |
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