scholarly journals Pif1 removes a Rap1-dependent barrier to the strand displacement activity of DNA polymerase δ

2016 ◽  
Vol 44 (8) ◽  
pp. 3811-3819 ◽  
Author(s):  
Katrina N. Koc ◽  
Saurabh P. Singh ◽  
Joseph L. Stodola ◽  
Peter M. Burgers ◽  
Roberto Galletto
Keyword(s):  
Dna Polymerase ◽  
Strand Displacement ◽  
Displacement Activity ◽  
Dna Polymerase Δ

scholarly journals Strand Displacement Activity of PrimPol

2020 ◽  
Vol 21 (23) ◽  
pp. 9027
Author(s):  
Elizaveta O. Boldinova ◽  
Ekaterina A. Belousova ◽  
Diana I. Gagarinskaya ◽  
Ekaterina A. Maltseva ◽  
Svetlana N. Khodyreva ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Strand Displacement ◽  
Displacement Activity

Human PrimPol is a unique enzyme possessing DNA/RNA primase and DNA polymerase activities. In this work, we demonstrated that PrimPol efficiently fills a 5-nt gap and possesses the conditional strand displacement activity stimulated by Mn2+ ions and accessory replicative proteins RPA and PolDIP2. The DNA displacement activity of PrimPol was found to be more efficient than the RNA displacement activity and FEN1 processed the 5′-DNA flaps generated by PrimPol in vitro.

scholarly journals 3′ to 5′ Exonuclease Activity of Herpes Simplex Virus Type 1 DNA Polymerase Modulates Its Strand Displacement Activity

2003 ◽  
Vol 77 (18) ◽  
pp. 10147-10153 ◽  
Author(s):  
Yali Zhu ◽  
Kelly S. Trego ◽  
Liping Song ◽  
Deborah S. Parris
Keyword(s):  
Herpes Simplex Virus ◽  
Herpes Simplex ◽  
Dna Polymerase ◽  
Virus Type ◽  
Herpes Simplex Virus Type ◽  
Strand Displacement ◽  
Displacement Activity ◽  
Simplex Virus ◽  
Hsv 1

ABSTRACT Using a minicircle DNA primer-template, the wild-type catalytic subunit of herpes simplex virus type 1 (HSV-1) DNA polymerase (pol) was shown to lack significant strand displacement activity with or without its processivity factor, UL42. However, an exonuclease-deficient (exo−) pol (D368A) was capable of slow strand displacement. Although UL42 increased the rate (2/s) and processivity of strand displacement by exo− pol, the rate was slower than that for gap-filling synthesis. High inherent excision rates on matched primer-templates and rapid idling-turnover (successive rounds of excision and polymerization) of exo-proficient polymerases correlated with poor strand displacement activity. The results suggest that the exo activity of HSV-1 pol modulates its ability to engage in strand displacement, a function that may be important to the viability and genome stability of the virus.

scholarly journals Pif1, RPA, and FEN1 modulate the ability of DNA polymerase δ to overcome protein barriers during DNA synthesis

2020 ◽  
Vol 295 (47) ◽  
pp. 15883-15891 ◽  
Author(s):  
Melanie A. Sparks ◽  
Peter M. Burgers ◽  
Roberto Galletto
Keyword(s):  
Transcription Factors ◽  
Dna Replication ◽  
Dna Binding ◽  
Dna Synthesis ◽  
Dna Polymerase ◽  
Strand Displacement ◽  
Chromosomal Dna ◽  
Dna Polymerase Δ ◽  
Lagging Strand ◽  
Stimulation Of

Successful DNA replication requires carefully regulated mechanisms to overcome numerous obstacles that naturally occur throughout chromosomal DNA. Scattered across the genome are tightly bound proteins, such as transcription factors and nucleosomes, that are necessary for cell function, but that also have the potential to impede timely DNA replication. Using biochemically reconstituted systems, we show that two transcription factors, yeast Reb1 and Tbf1, and a tightly positioned nucleosome, are strong blocks to the strand displacement DNA synthesis activity of DNA polymerase δ. Although the block imparted by Tbf1 can be overcome by the DNA-binding activity of the single-stranded DNA-binding protein RPA, efficient DNA replication through either a Reb1 or a nucleosome block occurs only in the presence of the 5'-3' DNA helicase Pif1. The Pif1-dependent stimulation of DNA synthesis across strong protein barriers may be beneficial during break-induced replication where barriers are expected to pose a problem to efficient DNA bubble migration. However, in the context of lagging strand DNA synthesis, the efficient disruption of a nucleosome barrier by Pif1 could lead to the futile re-replication of newly synthetized DNA. In the presence of FEN1 endonuclease, the major driver of nick translation during lagging strand replication, Pif1-dependent stimulation of DNA synthesis through a nucleosome or Reb1 barrier is prevented. By cleaving the short 5' tails generated during strand displacement, FEN1 eliminates the entry point for Pif1. We propose that this activity would protect the cell from potential DNA re-replication caused by unwarranted Pif1 interference during lagging strand replication.

scholarly journals Regulation of yeast DNA polymerase δ-mediated strand displacement synthesis by 5′-flaps

2015 ◽  
Vol 43 (8) ◽  
pp. 4179-4190 ◽  
Author(s):  
Katrina N. Koc ◽  
Joseph L. Stodola ◽  
Peter M. Burgers ◽  
Roberto Galletto
Keyword(s):  
Dna Polymerase ◽  
Strand Displacement ◽  
Dna Polymerase Δ

scholarly journals Pif1-family helicases cooperate to suppress widespread replication fork arrest at tRNA genes

2016 ◽  
Author(s):  
Joseph S. Osmundson ◽  
Jayashree Kumar ◽  
Rani Yeung ◽  
Duncan J. Smith
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Damage ◽  
Dna Polymerase ◽  
Replication Fork ◽  
Trna Genes ◽  
Strand Displacement ◽  
Dna Polymerase Δ ◽  
Replication Fork Arrest ◽  
Nuclear Processes ◽  
Lagging Strand

ABSTRACTSaccharomyces cerevisiaeencodes two distinct Pif1-family helicases – Pif1 and Rrm3 – which have been reported to play distinct roles in numerous nuclear processes. Here, we systematically characterize the roles of Pif1 helicases in replisome progression and lagging-strand synthesis inS. cerevisiae. We demonstrate that either Pif1 or Rrm3 redundantly stimulate strand-displacement by DNA polymerase δ during lagging-strand synthesis. By analyzing replisome mobility inpif1andrrm3mutants, we show that Rrm3, with a partially redundant contribution from Pif1, suppresses widespread terminal arrest of the replisome at tRNA genes. Although both head-on and codirectional collisions induce replication fork arrest at tRNA genes, head-on collisions arrest a higher proportion of replisomes; consistent with this observation, we find that head-on collisions between tRNA transcription and replisome progression are under-represented in theS. cerevisiaegenome. Further, we demonstrate that tRNA-mediated arrest is R-loop independent, and propose that replisome arrest and DNA damage are mechanistically separable.

scholarly journals A strong strand displacement activity of thermostable DNA polymerase markedly improves the results of DNA amplification

BioTechniques ◽  
2014 ◽  
Vol 57 (2) ◽  
Author(s):  
Konstantin B. Ignatov ◽  
Ekaterina V. Barsova ◽  
Arkady F. Fradkov ◽  
Konstantin A. Blagodatskikh ◽  
Tatiana V. Kramarova ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Dna Amplification ◽  
Strand Displacement ◽  
Displacement Activity ◽  
Thermostable Dna Polymerase

scholarly journals DNA-directed DNA Polymerase and Strand Displacement Activity of the Reverse Transcriptase Encoded by the R2 Retrotransposon

2007 ◽  
Vol 374 (2) ◽  
pp. 322-333 ◽  
Author(s):  
Anna Kurzynska-Kokorniak ◽  
Varuni K. Jamburuthugoda ◽  
Arkadiusz Bibillo ◽  
Thomas H. Eickbush
Keyword(s):  
Reverse Transcriptase ◽  
Dna Polymerase ◽  
Strand Displacement ◽  
Displacement Activity
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