Article ; Online: Escherichia coli β-clamp slows down DNA polymerase I dependent nick translation while accelerating ligation.
PloS one
2018 Volume 13, Issue 6, Page(s) e0199559
Abstract: The nick translation property of DNA polymerase I (Pol I) ensures the maturation of Okazaki fragments by removing primer RNAs and facilitating ligation. However, prolonged nick translation traversing downstream DNA is an energy wasting futile process, as ...
| Abstract | The nick translation property of DNA polymerase I (Pol I) ensures the maturation of Okazaki fragments by removing primer RNAs and facilitating ligation. However, prolonged nick translation traversing downstream DNA is an energy wasting futile process, as Pol I simultaneously polymerizes and depolymerizes at the nick sites utilizing energy-rich dNTPs. Using an in vitro assay system, we demonstrate that the β-clamp of the Escherichia coli replisome strongly inhibits nick translation on the DNA substrate. To do so, β-clamp inhibits the strand displacement activity of Pol I by interfering with the interaction between the finger subdomain of Pol I and the downstream primer-template junction. Conversely, β-clamp stimulates the 5' exonuclease property of Pol I to cleave single nucleotides or shorter oligonucleotide flaps. This single nucleotide flap removal at high frequency increases the probability of ligation between the upstream and downstream DNA strands at an early phase, terminating nick translation. Besides β-clamp-mediated ligation helps DNA ligase to seal the nick promptly during the maturation of Okazaki fragments. |
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| MeSH term(s) | DNA/metabolism ; DNA Breaks, Single-Stranded ; DNA Polymerase I/metabolism ; DNA Polymerase III/metabolism ; DNA, Bacterial/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Models, Molecular ; Protein Biosynthesis ; Time Factors |
| Chemical Substances | DNA, Bacterial ; Okazaki fragments ; DNA (9007-49-2) ; DNA Polymerase I (EC 2.7.7.-) ; DNA Polymerase III (EC 2.7.7.-) ; beta subunit, DNA polymerase III (EC 2.7.7.-) |
| Language | English |
| Publishing date | 2018-06-20 |
| Publishing country | United States |
| Document type | Journal Article ; Research Support, Non-U.S. Gov't |
| ISSN | 1932-6203 |
| ISSN (online) | 1932-6203 |
| DOI | 10.1371/journal.pone.0199559 |
| Database | MEDical Literature Analysis and Retrieval System OnLINE |
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