Dynamics of Translesion DNA Synthesis Catalyzed by the Bacteriophage T4 Exonuclease-Deficient DNA Polymerase†

Biochemistry ◽  
2001 ◽  
Vol 40 (24) ◽  
pp. 7180-7191 ◽  
Author(s):  
Anthony J. Berdis
Keyword(s):  
Dna Synthesis ◽  
Dna Polymerase ◽  
Bacteriophage T4 ◽  
Translesion Dna Synthesis ◽  
Translesion Dna

scholarly journals Accessory proteins assist exonuclease-deficient bacteriophage T4 DNA polymerase in replicating past an abasic site

2007 ◽  
Vol 402 (2) ◽  
pp. 321-329 ◽  
Author(s):  
Giuseppina Blanca ◽  
Emmanuelle Delagoutte ◽  
Nicolas Tanguy le gac ◽  
Neil P. Johnson ◽  
Giuseppe Baldacci ◽  
...  
Keyword(s):  
Dna Damage ◽  
Dna Synthesis ◽  
Dna Polymerase ◽  
Bacteriophage T4 ◽  
Dna Polymerases ◽  
Accessory Proteins ◽  
Clamp Loader ◽  
Abasic Site ◽  
Translesion Dna Synthesis ◽  
Translesion Dna

Replicative DNA polymerases, such as T4 polymerase, possess both elongation and 3′–5′ exonuclease proofreading catalytic activities. They arrest at the base preceding DNA damage on the coding DNA strand and specialized DNA polymerases have evolved to replicate across the lesion by a process known as TLS (translesion DNA synthesis). TLS is considered to take place in two steps that often require different enzymes, insertion of a nucleotide opposite the damaged template base followed by extension from the inserted nucleotide. We and others have observed that inactivation of the 3′–5′ exonuclease function of T4 polymerase enables TLS across a single site-specific abasic [AP (apurinic/apyrimidinic)] lesion. In the present study we report a role for auxiliary replicative factors in this reaction. When replication is performed with a large excess of DNA template over DNA polymerase in the absence of auxiliary factors, the exo− polymerase (T4 DNA polymerase deficient in the 3′–5′ exonuclease activity) inserts one nucleotide opposite the AP site but does not extend past the lesion. Addition of the clamp processivity factor and the clamp loader complex restores primer extension across an AP lesion on a circular AP-containing DNA substrate by the exo− polymerase, but has no effect on the wild-type enzyme. Hence T4 DNA polymerase exhibits a variety of responses to DNA damage. It can behave as a replicative polymerase or (in the absence of proofreading activity) as a specialized DNA polymerase and carry out TLS. As a specialized polymerase it can function either as an inserter or (with the help of accessory proteins) as an extender. The capacity to separate these distinct functions in a single DNA polymerase provides insight into the biochemical requirements for translesion DNA synthesis.

Protein interactions in T7 DNA replisome inhibit the bypass of abasic site by DNA polymerase

Mutagenesis ◽  
2019 ◽  
Author(s):  
Zhenyu Zou ◽  
Tingting Liang ◽  
Zhongyan Xu ◽  
Jiayu Xie ◽  
Shuming Zhang ◽  
...  
Keyword(s):  
Dna Replication ◽  
Dna Synthesis ◽  
Dna Polymerase ◽  
Protein Interactions ◽  
Accessory Proteins ◽  
Abasic Site ◽  
Traditional Concept ◽  
Translesion Dna Synthesis ◽  
Dna Lesion ◽  
Translesion Dna

Abstract Abasic site as a common DNA lesion blocks DNA replication and is highly mutagenic. Protein interactions in T7 DNA replisome facilitate DNA replication and translesion DNA synthesis. However, bypass of an abasic site by T7 DNA replisome has never been investigated. In this work, we used T7 DNA replisome and T7 DNA polymerase alone as two models to study DNA replication on encountering an abasic site. Relative to unmodified DNA, abasic site strongly inhibited primer extension and completely blocked strand-displacement DNA synthesis, due to the decreased fraction of enzyme–DNA productive complex and the reduced average extension rates. Moreover, abasic site at DNA fork inhibited the binding of DNA polymerase or helicase onto fork and the binding between polymerase and helicase at fork. Notably and unexpectedly, we found DNA polymerase alone bypassed an abasic site on primer/template (P/T) substrate more efficiently than did polymerase and helicase complex bypass it at fork. The presence of gp2.5 further inhibited the abasic site bypass at DNA fork. Kinetic analysis showed that this inhibition at fork relative to that on P/T was due to the decreased fraction of productive complex instead of the average extension rates. Therefore, we found that protein interactions in T7 DNA replisome inhibited the bypass of DNA lesion, different from all the traditional concept that protein interactions or accessory proteins always promote DNA replication and DNA damage bypass, providing new insights in translesion DNA synthesis performed by DNA replisome.

scholarly journals Mechanism of Translesion DNA Synthesis by DNA Polymerase II

1996 ◽  
Vol 271 (40) ◽  
pp. 24662-24669 ◽  
Author(s):  
Tamar Paz-Elizur ◽  
Masaru Takeshita ◽  
Myron Goodman ◽  
Michael O'Donnell ◽  
Zvi Livneh
Keyword(s):  
Dna Synthesis ◽  
Dna Polymerase ◽  
Translesion Dna Synthesis ◽  
Translesion Dna ◽  
Dna Polymerase Ii

scholarly journals N-terminal domains of human DNA polymerase lambda promote primer realignment during translesion DNA synthesis

DNA Repair ◽  
2014 ◽  
Vol 22 ◽  
pp. 41-52 ◽  
Author(s):  
David J. Taggart ◽  
Daniel M. Dayeh ◽  
Saul W. Fredrickson ◽  
Zucai Suo
Keyword(s):  
Dna Synthesis ◽  
Dna Polymerase ◽  
Translesion Dna Synthesis ◽  
Human Dna ◽  
Translesion Dna ◽  
Terminal Domains

scholarly journals Investigating the role of the E. coli β‐sliding clamp in DNA polymerase V‐dependent translesion DNA synthesis

2006 ◽  
Vol 20 (5) ◽  
Author(s):  
Mark David Sutton ◽  
Laurie Sanders ◽  
Sarah Ponticelli ◽  
Jill Duzen ◽  
Robert Maul ◽  
...  
Keyword(s):  
Dna Synthesis ◽  
Dna Polymerase ◽  
Translesion Dna Synthesis ◽  
E Coli ◽  
Sliding Clamp ◽  
Dna Polymerase V ◽  
Translesion Dna

scholarly journals Transcriptional Modulator NusA Interacts with Translesion DNA Polymerases in Escherichia coli

2008 ◽  
Vol 191 (2) ◽  
pp. 665-672 ◽  
Author(s):  
Susan E. Cohen ◽  
Veronica G. Godoy ◽  
Graham C. Walker
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Dna Synthesis ◽  
Dna Polymerase ◽  
Temperature Sensitivity ◽  
Dna Polymerases ◽  
Rna Polymerases ◽  
Translesion Dna Synthesis ◽  
Catalytic Activities ◽  
Translesion Dna

ABSTRACT NusA, a modulator of RNA polymerase, interacts with the DNA polymerase DinB. An increased level of expression of dinB or umuDC suppresses the temperature sensitivity of the nusA11 strain, requiring the catalytic activities of these proteins. We propose that NusA recruits translesion DNA synthesis (TLS) polymerases to RNA polymerases stalled at gaps, coupling TLS to transcription.

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