Escherichia coli β-clamp slows down DNA polymerase I dependent nick translation while accelerating ligation

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 depolyme...

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Veröffentlicht in:PloS one 2018-06, Vol.13 (6), p.e0199559-e0199559
Hauptverfasser: Bhardwaj, Amit, Ghose, Debarghya, Thakur, Krishan Gopal, Dutta, Dipak
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Ghose, Debarghya
Thakur, Krishan Gopal
Dutta, Dipak
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.
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subjects Bacillus subtilis
Bacteria
Biology and Life Sciences
Deoxyribonucleic acid
Depolymerization
Displacement activity
DNA
DNA polymerase
DNA repair
DNA-directed DNA polymerase
E coli
Escherichia coli
Exonuclease
Flaps
Fragments
Maturation
Nucleotides
Okazaki fragments
Oligonucleotides
Physical Sciences
Polypeptides
Research and Analysis Methods
Substrate inhibition
Translation
title Escherichia coli β-clamp slows down DNA polymerase I dependent nick translation while accelerating ligation
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