The role of the DNA sliding clamp in Okazaki fragment maturation in archaea and eukaryotes

2011 ◽  
Vol 39 (1) ◽  
pp. 70-76 ◽  
Author(s):  
Thomas R. Beattie ◽  
Stephen D. Bell
Keyword(s):  
Proliferating Cell Nuclear Antigen ◽  
Genome Integrity ◽  
Nuclear Antigen ◽  
Structural Studies ◽  
Sliding Clamp ◽  
Efficient Processing ◽  
Covalently Linked ◽  
Proliferating Cell ◽  
Lagging Strand

Efficient processing of Okazaki fragments generated during discontinuous lagging-strand DNA replication is critical for the maintenance of genome integrity. In eukaryotes, a number of enzymes co-ordinate to ensure the removal of initiating primers from the 5′-end of each fragment and the generation of a covalently linked daughter strand. Studies in eukaryotic systems have revealed that the co-ordination of DNA polymerase δ and FEN-1 (Flap Endonuclease 1) is sufficient to remove the majority of primers. Other pathways such as that involving Dna2 also operate under certain conditions, although, notably, Dna2 is not universally conserved between eukaryotes and archaea, unlike the other core factors. In addition to the catalytic components, the DNA sliding clamp, PCNA (proliferating-cell nuclear antigen), plays a pivotal role in binding and co-ordinating these enzymes at sites of lagging-strand replication. Structural studies in eukaryotic and archaeal systems have revealed that PCNA-binding proteins can adopt different conformations when binding PCNA. This conformational malleability may be key to the co-ordination of these enzymes' activities.

scholarly journals Stability of the human polymerase δ holoenzyme and its implications in lagging strand DNA synthesis

2016 ◽  
Vol 113 (13) ◽  
pp. E1777-E1786 ◽  
Author(s):  
Mark Hedglin ◽  
Binod Pandey ◽  
Stephen J. Benkovic
Keyword(s):  
Dna Polymerase ◽  
Proliferating Cell Nuclear Antigen ◽  
Nuclear Antigen ◽  
Okazaki Fragment ◽  
Sliding Clamp ◽  
Dna Lesion ◽  
The Stability ◽  
Proliferating Cell ◽  
Lagging Strand ◽  
Extreme Stability

In eukaryotes, DNA polymerase δ (pol δ) is responsible for replicating the lagging strand template and anchors to the proliferating cell nuclear antigen (PCNA) sliding clamp to form a holoenzyme. The stability of this complex is integral to every aspect of lagging strand replication. Most of our understanding comes fromSaccharomyces cerevisaewhere the extreme stability of the pol δ holoenzyme ensures that every nucleobase within an Okazaki fragment is faithfully duplicated before dissociation but also necessitates an active displacement mechanism for polymerase recycling and exchange. However, the stability of the human pol δ holoenzyme is unknown. We designed unique kinetic assays to analyze the processivity and stability of the pol δ holoenzyme. Surprisingly, the results indicate that human pol δ maintains a loose association with PCNA while replicating DNA. Such behavior has profound implications on Okazaki fragment synthesis in humans as it limits the processivity of pol δ on undamaged DNA and promotes the rapid dissociation of pol δ from PCNA on stalling at a DNA lesion.

scholarly journals Structure of the processive human Pol δ holoenzyme

2019 ◽  
Author(s):  
Claudia Lancey ◽  
Muhammad Tehseen ◽  
Vlad-Stefan Raducanu ◽  
Fahad Rashid ◽  
Nekane Merino ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Proliferating Cell Nuclear Antigen ◽  
Nuclear Antigen ◽  
Structural Basis ◽  
Catalytic Core ◽  
Regulatory Subunits ◽  
Functional Interactions ◽  
Proliferating Cell ◽  
Lagging Strand ◽  
Catalytic Cleft

In eukaryotes, DNA polymerase δ (Pol δ) bound to the proliferating cell nuclear antigen (PCNA) replicates the lagging strand and cooperates with flap endonuclease 1 (FEN1) to process the Okazaki fragments for their ligation. We present the high-resolution cryo-EM structure of the human processive Pol δ-DNA-PCNA complex in the absence and presence of FEN1. Pol δ is anchored to one of the three PCNA monomers through the C-terminal domain of the catalytic subunit. The catalytic core sits on top of PCNA in an open configuration while the regulatory subunits project laterally. This arrangement allows PCNA to thread and stabilize the DNA exiting the catalytic cleft and recruit FEN1 to one unoccupied monomer in a toolbelt fashion. Alternative holoenzyme conformations reveal important functional interactions that maintain PCNA orientation during synthesis. This work sheds light on the structural basis of Pol δ’s activity in replicating the human genome.

scholarly journals The Effect of DNA Replication Mutations on CAG Tract Stability in Yeast

Genetics ◽  
1999 ◽  
Vol 152 (3) ◽  
pp. 953-963 ◽  
Author(s):  
Jill Kuglin Schweitzer ◽  
Dennis M Livingston
Keyword(s):  
Dna Replication ◽  
Proliferating Cell Nuclear Antigen ◽  
Cag Repeat ◽  
Cag Repeats ◽  
Nuclear Antigen ◽  
Temperature Sensitive ◽  
Simple Repeats ◽  
Proliferating Cell ◽  
Lagging Strand ◽  
Palindromic Sequences

AbstractCAG repeat tracts are unstable in yeast, leading to frequent contractions and infrequent expansions in repeat tract length. To compare CAG repeats to other simple repeats and palindromic sequences, we examined the effect of DNA replication mutations, including alleles of pol α, pol δ, pol ϵ, and PCNA (proliferating cell nuclear antigen), on tract stability. Among the polymerase mutations, the pol δ mutation (pol3-14) destabilizes tracts with either CAG or CTG as the lagging strand template. One pol α mutation, pol1-1, destabilizes the orientation with CAG as the lagging strand template, but it has little effect on the CTG orientation. In contrast, the pol1-17 mutation has no effect on either orientation. Similarly, mutations in the proofreading functions of pol δ and pol ϵ, as well as a temperature-sensitive pol ϵ mutation, pol2-18, have no effect on tract stability. Three PCNA mutations, pol30-52, pol30-79, and pol30-90, all have drastic effects on tract stability. Of the three, pol30-52 is unique in yielding small tract changes that are indicative of an impairment in mismatch repair. These results show that while CAG repeats are destabilized by many of the same mutations that destabilize other simple repeats, they also have some behaviors that are suggestive of their potential to form hairpin structures.

Characterization of cytosolic proliferating cell nuclear antigen (PCNA) in neutrophils: antiapoptotic role of the monomer

2013 ◽  
Vol 94 (4) ◽  
pp. 723-731 ◽  
Author(s):  
Alessia De Chiara ◽  
Magali Pederzoli-Ribeil ◽  
Julie Mocek ◽  
Céline Candalh ◽  
Patrick Mayeux ◽  
...  
Keyword(s):  
Proliferating Cell Nuclear Antigen ◽  
Nuclear Antigen ◽  
Proliferating Cell

scholarly journals DNA Polymerases BI and D from the Hyperthermophilic Archaeon Pyrococcus furiosus Both Bind to Proliferating Cell Nuclear Antigen with Their C-Terminal PIP-Box Motifs

2007 ◽  
Vol 189 (15) ◽  
pp. 5652-5657 ◽  
Author(s):  
Kazuo Tori ◽  
Megumi Kimizu ◽  
Sonoko Ishino ◽  
Yoshizumi Ishino
Keyword(s):  
Dna Synthesis ◽  
Proliferating Cell Nuclear Antigen ◽  
Pyrococcus Furiosus ◽  
Dna Polymerases ◽  
Nuclear Antigen ◽  
Hyperthermophilic Archaeon ◽  
Sliding Clamp ◽  
Replication Fork Progression ◽  
Proliferating Cell

ABSTRACT Proliferating cell nuclear antigen (PCNA) is the sliding clamp that is essential for the high processivity of DNA synthesis during DNA replication. Pyrococcus furiosus, a hyperthermophilic archaeon, has at least two DNA polymerases, polymerase BI (PolBI) and PolD. Both of the two DNA polymerases interact with the archaeal P. furiosus PCNA (PfuPCNA) and perform processive DNA synthesis in vitro. This phenomenon, in addition to the fact that both enzymes display 3′-5′ exonuclease activity, suggests that both DNA polymerases work in replication fork progression. We demonstrated here that both PolBI and PolD functionally interact with PfuPCNA at their C-terminal PIP boxes. The mutant PolBI and PolD enzymes lacking the PIP-box sequence do not respond to the PfuPCNA at all in an in vitro primer extension reaction. This is the first experimental evidence that the PIP-box motif, located at the C termini of the archaeal DNA polymerases, is actually critical for PCNA binding to form a processive DNA-synthesizing complex.

Sign in / Sign up

Export Citation Format

Share Document