Literature DB >> 24630996

Helicase and polymerase move together close to the fork junction and copy DNA in one-nucleotide steps.

Manjula Pandey1, Smita S Patel2.   

Abstract

By simultaneously measuring DNA synthesis and dNTP hydrolysis, we show that T7 DNA polymerase and T7 gp4 helicase move in sync during leading-strand synthesis, taking one-nucleotide steps and hydrolyzing one dNTP per base-pair unwound/copied. The cooperative catalysis enables the helicase and polymerase to move at a uniformly fast rate without guanine:cytosine (GC) dependency or idling with futile NTP hydrolysis. We show that the helicase and polymerase are located close to the replication fork junction. This architecture enables the polymerase to use its strand-displacement synthesis to increase the unwinding rate, whereas the helicase aids this process by translocating along single-stranded DNA and trapping the unwound bases. Thus, in contrast to the helicase-only unwinding model, our results suggest a model in which the helicase and polymerase are moving in one-nucleotide steps, DNA synthesis drives fork unwinding, and a role of the helicase is to trap the unwound bases and prevent DNA reannealing.
Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

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Year:  2014        PMID: 24630996      PMCID: PMC4010093          DOI: 10.1016/j.celrep.2014.02.025

Source DB:  PubMed          Journal:  Cell Rep            Impact factor:   9.423


  53 in total

1.  Properties of the human Cdc45/Mcm2-7/GINS helicase complex and its action with DNA polymerase epsilon in rolling circle DNA synthesis.

Authors:  Young-Hoon Kang; Wiebke Chemnitz Galal; Andrea Farina; Inger Tappin; Jerard Hurwitz
Journal:  Proc Natl Acad Sci U S A       Date:  2012-04-02       Impact factor: 11.205

2.  A257T linker region mutant of T7 helicase-primase protein is defective in DNA loading and rescued by T7 DNA polymerase.

Authors:  Gayatri Patel; Daniel S Johnson; Bo Sun; Manjula Pandey; Xiong Yu; Edward H Egelman; Michelle D Wang; Smita S Patel
Journal:  J Biol Chem       Date:  2011-04-22       Impact factor: 5.157

3.  Breathing fluctuations in position-specific DNA base pairs are involved in regulating helicase movement into the replication fork.

Authors:  Davis Jose; Steven E Weitzel; Peter H von Hippel
Journal:  Proc Natl Acad Sci U S A       Date:  2012-08-20       Impact factor: 11.205

Review 4.  Dynamic coupling between the motors of DNA replication: hexameric helicase, DNA polymerase, and primase.

Authors:  Smita S Patel; Manjula Pandey; Divya Nandakumar
Journal:  Curr Opin Chem Biol       Date:  2011-08-22       Impact factor: 8.822

5.  Helicase-DNA polymerase interaction is critical to initiate leading-strand DNA synthesis.

Authors:  Huidong Zhang; Seung-Joo Lee; Bin Zhu; Ngoc Q Tran; Stanley Tabor; Charles C Richardson
Journal:  Proc Natl Acad Sci U S A       Date:  2011-05-23       Impact factor: 11.205

6.  Experimental and computational analysis of DNA unwinding and polymerization kinetics.

Authors:  Manjula Pandey; Mikhail K Levin; Smita S Patel
Journal:  Methods Mol Biol       Date:  2010

7.  Coordinating DNA replication by means of priming loop and differential synthesis rate.

Authors:  Manjula Pandey; Salman Syed; Ilker Donmez; Gayatri Patel; Taekjip Ha; Smita S Patel
Journal:  Nature       Date:  2009-11-18       Impact factor: 49.962

8.  Mechanism of strand displacement synthesis by DNA replicative polymerases.

Authors:  Maria Manosas; Michelle M Spiering; Fangyuan Ding; David Bensimon; Jean-François Allemand; Stephen J Benkovic; Vincent Croquette
Journal:  Nucleic Acids Res       Date:  2012-03-20       Impact factor: 16.971

9.  Collaborative coupling between polymerase and helicase for leading-strand synthesis.

Authors:  Maria Manosas; Michelle M Spiering; Fangyuan Ding; Vincent Croquette; Stephen J Benkovic
Journal:  Nucleic Acids Res       Date:  2012-03-20       Impact factor: 16.971

10.  ATP-induced helicase slippage reveals highly coordinated subunits.

Authors:  Bo Sun; Daniel S Johnson; Gayatri Patel; Benjamin Y Smith; Manjula Pandey; Smita S Patel; Michelle D Wang
Journal:  Nature       Date:  2011-09-18       Impact factor: 49.962

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  20 in total

1.  Replicative DNA polymerases promote active displacement of SSB proteins during lagging strand synthesis.

Authors:  Fernando Cerrón; Sara de Lorenzo; Kateryna M Lemishko; Grzegorz L Ciesielski; Laurie S Kaguni; Francisco J Cao; Borja Ibarra
Journal:  Nucleic Acids Res       Date:  2019-06-20       Impact factor: 16.971

2.  Mechanism of substrate translocation by a ring-shaped ATPase motor at millisecond resolution.

Authors:  Wen Ma; Klaus Schulten
Journal:  J Am Chem Soc       Date:  2015-02-19       Impact factor: 15.419

3.  Two mechanisms coordinate replication termination by the Escherichia coli Tus-Ter complex.

Authors:  Manjula Pandey; Mohamed M Elshenawy; Slobodan Jergic; Masateru Takahashi; Nicholas E Dixon; Samir M Hamdan; Smita S Patel
Journal:  Nucleic Acids Res       Date:  2015-05-24       Impact factor: 16.971

Review 4.  A mechanistic study of helicases with magnetic traps.

Authors:  Samar Hodeib; Saurabh Raj; Maria Manosas; Weiting Zhang; Debjani Bagchi; Bertrand Ducos; Francesca Fiorini; Joanne Kanaan; Hervé Le Hir; Jean-François Allemand; David Bensimon; Vincent Croquette
Journal:  Protein Sci       Date:  2017-06-13       Impact factor: 6.725

5.  Cryo-EM structure of the replisome reveals multiple interactions coordinating DNA synthesis.

Authors:  Arkadiusz W Kulczyk; Arne Moeller; Peter Meyer; Piotr Sliz; Charles C Richardson
Journal:  Proc Natl Acad Sci U S A       Date:  2017-02-21       Impact factor: 11.205

Review 6.  Methods to study the coupling between replicative helicase and leading-strand DNA polymerase at the replication fork.

Authors:  Divya Nandakumar; Smita S Patel
Journal:  Methods       Date:  2016-05-09       Impact factor: 3.608

7.  Mechano-chemical kinetics of DNA replication: identification of the translocation step of a replicative DNA polymerase.

Authors:  José A Morin; Francisco J Cao; José M Lázaro; J Ricardo Arias-Gonzalez; José M Valpuesta; José L Carrascosa; Margarita Salas; Borja Ibarra
Journal:  Nucleic Acids Res       Date:  2015-03-23       Impact factor: 16.971

8.  Hexameric helicase G40P unwinds DNA in single base pair steps.

Authors:  Michael Schlierf; Ganggang Wang; Xiaojiang S Chen; Taekjip Ha
Journal:  Elife       Date:  2019-01-28       Impact factor: 8.140

9.  DNA sequences proximal to human mitochondrial DNA deletion breakpoints prevalent in human disease form G-quadruplexes, a class of DNA structures inefficiently unwound by the mitochondrial replicative Twinkle helicase.

Authors:  Sanjay Kumar Bharti; Joshua A Sommers; Jun Zhou; Daniel L Kaplan; Johannes N Spelbrink; Jean-Louis Mergny; Robert M Brosh
Journal:  J Biol Chem       Date:  2014-09-05       Impact factor: 5.157

Review 10.  The role of ATP-dependent machines in regulating genome topology.

Authors:  Glenn Hauk; James M Berger
Journal:  Curr Opin Struct Biol       Date:  2016-01-29       Impact factor: 6.809

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