title: Escherichia coli β-clamp slows down DNA polymerase I dependent nick translation while accelerating ligation.
creator: Bhardwaj, Amit
creator: Ghose, Debarghya
creator: Thakur, Krishan Gopal
creator: Dutta, Dipak
subject: QR Microbiology
description: 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.
publisher: Public Library of Science
date: 2018-06-20
type: Article
type: PeerReviewed
relation: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0199559
identifier:   Bhardwaj, Amit and Ghose, Debarghya and Thakur, Krishan Gopal and Dutta, Dipak  (2018) Escherichia coli β-clamp slows down DNA polymerase I dependent nick translation while accelerating ligation.  PloS one, 13 (6).  e0199559.  ISSN 1932-6203     
relation: http://crdd.osdd.net/open/2093/