Thermodynamic and Mechanistic Insights into Translesion DNA Synthesis Catalyzed by Y-Family DNA Polymerase Across a Bulky Double-Base Lesion of an Antitumor Platinum Drug

2012 ◽  
Vol 18 (48) ◽  
pp. 15439-15448 ◽  
Author(s):  
Viktor Brabec ◽  
Jaroslav Malina ◽  
Nicola Margiotta ◽  
Giovanni Natile ◽  
Jana Kasparkova
Keyword(s):  
Dna Synthesis ◽  
Dna Polymerase ◽  
Platinum Drug ◽  
Translesion Dna Synthesis ◽  
Translesion Dna ◽  
Double Base ◽  
Base Lesion ◽  
Y Family

scholarly journals Mechanism of double-base lesion bypass catalyzed by a Y-family DNA polymerase

2008 ◽  
Vol 36 (12) ◽  
pp. 3867-3878 ◽  
Author(s):  
Jessica A. Brown ◽  
Sean A. Newmister ◽  
Kevin A. Fiala ◽  
Zucai Suo
Keyword(s):  
Dna Polymerase ◽  
Lesion Bypass ◽  
Double Base ◽  
Base Lesion ◽  
Y Family

scholarly journals Heterotrimeric PCNA Increases the Activity and Fidelity of Dbh, a Y-family Translesion DNA Polymerase Prone to Creating Single-Base Deletion Mutations

2020 ◽  
Author(s):  
Yifeng Wu ◽  
William Jaremko ◽  
Ryan C. Wilson ◽  
Janice D. Pata
Keyword(s):  
Dna Synthesis ◽  
Dna Polymerase ◽  
Polymerase Activity ◽  
List Type ◽  
Single Base ◽  
Deletion Mutations ◽  
Single Base Deletion ◽  
Translesion Dna ◽  
Y Family

AbstractDbh is a Y-family translesion DNA polymerase from Sulfolobus acidocaldarius, an archaeal species that grows in harsh environmental conditions. Biochemically, Dbh displays a distinctive mutational profile, creating single-base deletion mutations at extraordinarily high frequencies (up to 50%) in specific repeat sequences. In cells, however, Dbh does not appear to contribute significantly to spontaneous frameshifts in these same sequence contexts. This suggests that either the error-prone DNA synthesis activity of Dbh is reduced in vivo and/or Dbh is restricted from replicating these sequences. Here, we test the hypothesis that the propensity for Dbh to make single base deletion mutations is reduced through interaction with the S. acidocaldarius heterotrimeric sliding clamp processivity factor, PCNA-123. We first confirm that Dbh physically interacts with PCNA-123, with the interaction requiring both the PCNA-1 subunit and the C-terminal 10 amino acids of Dbh, which contain a predicted PCNA-interaction peptide (PIP) motif. This interaction stimulates the polymerase activity of Dbh, even on short, linear primer-template DNA by increasing the rate of nucleotide incorporation. This stimulation requires an intact PCNA-123 heterotrimer and a DNA duplex length of at least 18 basepairs, the minimal length predicted from structural data to bind to both the polymerase and the clamp. Finally, we find that PCNA-123 increases the fidelity of Dbh on a single-base deletion hotspot sequence 3-fold by promoting an increase in the rate of correct, but not incorrect, nucleotide addition and propose that PCNA-123 induces Dbh to adopt a more active conformation that is less prone to creating deletions during DNA synthesis.HighlightsPCNA increases the fidelity of Dbh polymerase on a deletion-hotspot sequence.The interaction stimulates incorporation of the correct, but not incorrect, nucleotide.A minimal duplex length of 18 bp is required for PCNA to stimulate polymerase activity.Structural modeling suggests that PCNA induces a conformational change in Dbh.

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

Translesion DNA synthesis across double-base lesions derived from cross-links of an antitumor trinuclear platinum compound: primer extension, conformational and thermodynamic studies

Metallomics ◽  
2018 ◽  
Vol 10 (1) ◽  
pp. 132-144 ◽  
Author(s):  
O. Novakova ◽  
N. P. Farrell ◽  
V. Brabec
Keyword(s):  
Dna Synthesis ◽  
Dna Polymerases ◽  
Primer Extension ◽  
Platinum Compound ◽  
Thermodynamic Studies ◽  
Translesion Dna Synthesis ◽  
Cross Links ◽  
Translesion Dna ◽  
Compound Primer ◽  
Double Base

The central linker of antitumor polynuclear Triplatin represents an important factor responsible for the lowered tolerance of its DNA double-base adducts by DNA polymerases.

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 Division of labor of Y-family polymerases in translesion-DNA synthesis for distinct types of DNA damage

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252587
Author(s):  
Yuriko Inomata ◽  
Takuya Abe ◽  
Masataka Tsuda ◽  
Shunichi Takeda ◽  
Kouji Hirota
Keyword(s):  
Dna Damage ◽  
Dna Synthesis ◽  
Division Of Labor ◽  
Double Knockout ◽  
Translesion Dna Synthesis ◽  
Translesion Dna ◽  
Template Dna ◽  
Y Family ◽  
Higher Sensitivity

Living organisms are continuously under threat from a vast array of DNA-damaging agents, which impact genome DNA. DNA replication machinery stalls at damaged template DNA. The stalled replication fork is restarted via bypass replication by translesion DNA-synthesis polymerases, including the Y-family polymerases Polη, Polι, and Polκ, which possess the ability to incorporate nucleotides opposite the damaged template. To investigate the division of labor among these polymerases in vivo, we generated POLη−/−, POLι−/−, POLκ−/−, double knockout (KO), and triple knockout (TKO) mutants in all combinations from human TK6 cells. TKO cells exhibited a hypersensitivity to ultraviolet (UV), cisplatin (CDDP), and methyl methanesulfonate (MMS), confirming the pivotal role played by these polymerases in bypass replication of damaged template DNA. POLη−/− cells, but not POLι−/− or POLκ−/− cells, showed a strong sensitivity to UV and CDDP, while TKO cells showed a slightly higher sensitivity to UV and CDDP than did POLη−/− cells. On the other hand, TKO cells, but not all single KO cells, exhibited a significantly higher sensitivity to MMS than did wild-type cells. Consistently, DNA-fiber assay revealed that Polη plays a crucial role in bypassing lesions caused by UV-mimetic agent 4-nitroquinoline-1-oxide and CDDP, while all three polymerases play complementary roles in bypassing MMS-induced damage. Our findings indicate that the three Y-family polymerases play distinctly different roles in bypass replication, according to the type of DNA damage generated on the template strand.

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