Faculty Opinions recommendation of The Importance of Poly(ADP-Ribose) Polymerase as a Sensor of Unligated Okazaki Fragments during DNA Replication.

2019 ◽  
Author(s):  
Aura Carreira
Keyword(s):  
Dna Replication ◽  
Okazaki Fragments

scholarly journals Near-continuously synthesized leading strands inEscherichia coliare broken by ribonucleotide excision

2019 ◽  
Vol 116 (4) ◽  
pp. 1251-1260 ◽  
Author(s):  
Glen E. Cronan ◽  
Elena A. Kouzminova ◽  
Andrei Kuzminov
Keyword(s):  
Dna Replication ◽  
Excision Repair ◽  
Chromosomal Dna ◽  
E Coli ◽  
Okazaki Fragments ◽  
Leading Strand ◽  
Replication Intermediates ◽  
Lagging Strand

In vitro, purified replisomes drive model replication forks to synthesize continuous leading strands, even without ligase, supporting the semidiscontinuous model of DNA replication. However, nascent replication intermediates isolated from ligase-deficientEscherichia colicomprise only short (on average 1.2-kb) Okazaki fragments. It was long suspected that cells replicate their chromosomal DNA by the semidiscontinuous mode observed in vitro but that, in vivo, the nascent leading strand was artifactually fragmented postsynthesis by excision repair. Here, using high-resolution separation of pulse-labeled replication intermediates coupled with strand-specific hybridization, we show that excision-proficientE. coligenerates leading-strand intermediates >10-fold longer than lagging-strand Okazaki fragments. Inactivation of DNA-repair activities, including ribonucleotide excision, further increased nascent leading-strand size to ∼80 kb, while lagging-strand Okazaki fragments remained unaffected. We conclude that in vivo, repriming occurs ∼70× less frequently on the leading versus lagging strands, and that DNA replication inE. coliis effectively semidiscontinuous.

scholarly journals The Importance of Poly(ADP-Ribose) Polymerase as a Sensor of Unligated Okazaki Fragments during DNA Replication

2018 ◽  
Vol 71 (2) ◽  
pp. 319-331.e3 ◽  
Author(s):  
Hana Hanzlikova ◽  
Ilona Kalasova ◽  
Annie A. Demin ◽  
Lewis E. Pennicott ◽  
Zuzana Cihlarova ◽  
...  
Keyword(s):  
Dna Replication ◽  
Okazaki Fragments

scholarly journals Phosphorylation of PNKP mediated by CDKs promotes end-processing of Okazaki fragments during DNA replication

2021 ◽  
Author(s):  
Kaima Tsukada ◽  
Rikiya Imamura ◽  
Kotaro Saikawa ◽  
Mizuki Saito ◽  
Naoya Kase ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Dna Replication ◽  
Dna Synthesis ◽  
High Speed ◽  
Replication Forks ◽  
Cyclin Dependent Kinases ◽  
Okazaki Fragments ◽  
Dna Ligation ◽  
Polynucleotide Kinase ◽  
Dna Ends

Polynucleotide kinase phosphatase (PNKP) has enzymatic activities as 3′ phosphatase and 5′ kinase of DNA ends to promote DNA ligation. Here, we show that PNKP is involved in progression of DNA replication through end-processing of Okazaki fragments (OFs). Cyclin-dependent kinases (CDKs) regulate phosphorylation on threonine 118 (T118) of PNKP, and which phosphorylation allows it to be recruited to OFs. Loss of PNKP and T118 phosphorylation significantly increased unligated OFs and high-speed DNA synthesis in replication forks, suggesting that PNKP T118 phosphorylation is required for OFs ligation for its maturation. Furthermore, phosphatase-dead PNKP also exhibited an accumulation of unligated OFs and high-speed DNA synthesis. Overall, our data suggested that CDK-mediated PNKP phosphorylation at T118 is important for its recruitment to OFs and PNKP subsequently promotes end-processing for OFs maturation for stable cell proliferation.

scholarly journals On the time behaviour of Okazaki fragments

2006 ◽  
Vol 43 (02) ◽  
pp. 500-509
Author(s):  
Krzysztof Bartoszek ◽  
Wojciech Bartoszek
Keyword(s):  
Dna Replication ◽  
Probability Distribution ◽  
Time Dependence ◽  
Time Behaviour ◽  
Okazaki Fragments ◽  
Analytical Formulae ◽  
Asymptotic Probability

We find explicit analytical formulae for the time dependence of the probability of the number of Okazaki fragments produced during the process of DNA replication. This extends a result of Cowan on the asymptotic probability distribution of these fragments.

scholarly journals RNA primer–primase complexes serve as the signal for polymerase recycling and Okazaki fragment initiation in T4 phage DNA replication

2017 ◽  
Vol 114 (22) ◽  
pp. 5635-5640 ◽  
Author(s):  
Michelle M. Spiering ◽  
Philip Hanoian ◽  
Swathi Gannavaram ◽  
Stephen J. Benkovic
Keyword(s):  
Dna Replication ◽  
Okazaki Fragment ◽  
Signaling Mechanism ◽  
Okazaki Fragments ◽  
Phage Dna ◽  
T4 Bacteriophage ◽  
Opposite Strand ◽  
T4 Phage ◽  
Lagging Strand

The opposite strand polarity of duplex DNA necessitates that the leading strand is replicated continuously whereas the lagging strand is replicated in discrete segments known as Okazaki fragments. The lagging-strand polymerase sometimes recycles to begin the synthesis of a new Okazaki fragment before finishing the previous fragment, creating a gap between the Okazaki fragments. The mechanism and signal that initiate this behavior—that is, the signaling mechanism—have not been definitively identified. We examined the role of RNA primer–primase complexes left on the lagging ssDNA from primer synthesis in initiating early lagging-strand polymerase recycling. We show for the T4 bacteriophage DNA replication system that primer–primase complexes have a residence time similar to the timescale of Okazaki fragment synthesis and the ability to block a holoenzyme synthesizing DNA and stimulate the dissociation of the holoenzyme to trigger polymerase recycling. The collision with primer–primase complexes triggering the early termination of Okazaki fragment synthesis has distinct advantages over those previously proposed because this signal requires no transmission to the lagging-strand polymerase through protein or DNA interactions, the mechanism for rapid dissociation of the holoenzyme is always collision, and no unique characteristics need to be assigned to either identical polymerase in the replisome. We have modeled repeated cycles of Okazaki fragment initiation using a collision with a completed Okazaki fragment or primer–primase complexes as the recycling mechanism. The results reproduce experimental data, providing insights into events related to Okazaki fragment initiation and the overall functioning of DNA replisomes.

scholarly journals On the time behaviour of Okazaki fragments

2006 ◽  
Vol 43 (2) ◽  
pp. 500-509
Author(s):  
Krzysztof Bartoszek ◽  
Wojciech Bartoszek
Keyword(s):  
Dna Replication ◽  
Probability Distribution ◽  
Time Dependence ◽  
Time Behaviour ◽  
Okazaki Fragments ◽  
Analytical Formulae ◽  
Asymptotic Probability

We find explicit analytical formulae for the time dependence of the probability of the number of Okazaki fragments produced during the process of DNA replication. This extends a result of Cowan on the asymptotic probability distribution of these fragments.

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