Literature DB >> 30767010

Recycling of single-stranded DNA-binding protein by the bacterial replisome.

Lisanne M Spenkelink1,2,3, Jacob S Lewis1,2, Slobodan Jergic1,2, Zhi-Qiang Xu1,2, Andrew Robinson1,2, Nicholas E Dixon1,2, Antoine M van Oijen1,2.   

Abstract

Single-stranded DNA-binding proteins (SSBs) support DNA replication by protecting single-stranded DNA from nucleolytic attack, preventing intra-strand pairing events and playing many other regulatory roles within the replisome. Recent developments in single-molecule approaches have led to a revised picture of the replisome that is much more complex in how it retains or recycles protein components. Here, we visualize how an in vitro reconstituted Escherichia coli replisome recruits SSB by relying on two different molecular mechanisms. Not only does it recruit new SSB molecules from solution to coat newly formed single-stranded DNA on the lagging strand, but it also internally recycles SSB from one Okazaki fragment to the next. We show that this internal transfer mechanism is balanced against recruitment from solution in a manner that is concentration dependent. By visualizing SSB dynamics in live cells, we show that both internal transfer and external exchange mechanisms are physiologically relevant.
© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Year:  2019        PMID: 30767010      PMCID: PMC6486552          DOI: 10.1093/nar/gkz090

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  74 in total

1.  A general priming system employing only dnaB protein and primase for DNA replication.

Authors:  K Arai; A Kornberg
Journal:  Proc Natl Acad Sci U S A       Date:  1979-09       Impact factor: 11.205

2.  Single-molecule analysis reveals that the lagging strand increases replisome processivity but slows replication fork progression.

Authors:  Nina Y Yao; Roxana E Georgescu; Jeff Finkelstein; Michael E O'Donnell
Journal:  Proc Natl Acad Sci U S A       Date:  2009-08-03       Impact factor: 11.205

Review 3.  Single-molecule analysis of the Escherichia coli replisome and use of clamps to bypass replication barriers.

Authors:  Roxana E Georgescu; Nina Y Yao; Mike O'Donnell
Journal:  FEBS Lett       Date:  2010-04-11       Impact factor: 4.124

4.  Molecular Mechanism of Facilitated Dissociation of Fis Protein from DNA.

Authors:  Min-Yeh Tsai; Bin Zhang; Weihua Zheng; Peter G Wolynes
Journal:  J Am Chem Soc       Date:  2016-10-05       Impact factor: 15.419

5.  Binding mode transitions of Escherichia coli single strand binding protein-single-stranded DNA complexes. Cation, anion, pH, and binding density effects.

Authors:  W Bujalowski; L B Overman; T M Lohman
Journal:  J Biol Chem       Date:  1988-04-05       Impact factor: 5.157

Review 6.  Understanding DNA replication by the bacteriophage T4 replisome.

Authors:  Stephen J Benkovic; Michelle M Spiering
Journal:  J Biol Chem       Date:  2017-09-25       Impact factor: 5.157

Review 7.  Noise in the Machine: Alternative Pathway Sampling is the Rule During DNA Replication.

Authors:  Matthias J Scherr; Barbara Safaric; Karl E Duderstadt
Journal:  Bioessays       Date:  2017-12-28       Impact factor: 4.345

8.  The chi psi subunits of DNA polymerase III holoenzyme bind to single-stranded DNA-binding protein (SSB) and facilitate replication of an SSB-coated template.

Authors:  B P Glover; C S McHenry
Journal:  J Biol Chem       Date:  1998-09-04       Impact factor: 5.157

Review 9.  Escherichia coli single-stranded DNA-binding protein: multiple DNA-binding modes and cooperativities.

Authors:  T M Lohman; M E Ferrari
Journal:  Annu Rev Biochem       Date:  1994       Impact factor: 23.643

Review 10.  Single-molecule fluorescence microscopy review: shedding new light on old problems.

Authors:  Sviatlana Shashkova; Mark C Leake
Journal:  Biosci Rep       Date:  2017-07-21       Impact factor: 3.840

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  18 in total

Review 1.  When proteins play tag: the dynamic nature of the replisome.

Authors:  Stefan H Mueller; Lisanne M Spenkelink; Antoine M van Oijen
Journal:  Biophys Rev       Date:  2019-07-04

2.  Force-Dependent Facilitated Dissociation Can Generate Protein-DNA Catch Bonds.

Authors:  Katelyn Dahlke; Jing Zhao; Charles E Sing; Edward J Banigan
Journal:  Biophys J       Date:  2019-08-02       Impact factor: 4.033

3.  Single-Molecule Fluorescence Methods to Study Protein Exchange Kinetics in Supramolecular Complexes.

Authors:  Richard R Spinks; Lisanne M Spenkelink; Antoine M van Oijen
Journal:  Methods Mol Biol       Date:  2021

4.  Regulation of Nearest-Neighbor Cooperative Binding of E. coli SSB Protein to DNA.

Authors:  Alexander G Kozlov; Min Kyung Shinn; Timothy M Lohman
Journal:  Biophys J       Date:  2019-10-28       Impact factor: 4.033

5.  Tunability of DNA Polymerase Stability during Eukaryotic DNA Replication.

Authors:  Jacob S Lewis; Lisanne M Spenkelink; Grant D Schauer; Olga Yurieva; Stefan H Mueller; Varsha Natarajan; Gurleen Kaur; Claire Maher; Callum Kay; Michael E O'Donnell; Antoine M van Oijen
Journal:  Mol Cell       Date:  2019-11-05       Impact factor: 17.970

6.  Two components of DNA replication-dependent LexA cleavage.

Authors:  Kamila K Myka; Kenneth J Marians
Journal:  J Biol Chem       Date:  2020-06-08       Impact factor: 5.157

7.  ssDNA diffuses along replication protein A via a reptation mechanism.

Authors:  Garima Mishra; Lavi S Bigman; Yaakov Levy
Journal:  Nucleic Acids Res       Date:  2020-02-28       Impact factor: 16.971

8.  A comparative study of protein-ssDNA interactions.

Authors:  Maoxuan Lin; Fareeha K Malik; Jun-Tao Guo
Journal:  NAR Genom Bioinform       Date:  2021-02-23

9.  Development of a single-stranded DNA-binding protein fluorescent fusion toolbox.

Authors:  Katarzyna Dubiel; Camille Henry; Lisanne M Spenkelink; Alexander G Kozlov; Elizabeth A Wood; Slobodan Jergic; Nicholas E Dixon; Antoine M van Oijen; Michael M Cox; Timothy M Lohman; Steven J Sandler; James L Keck
Journal:  Nucleic Acids Res       Date:  2020-06-19       Impact factor: 16.971

10.  Probing E. coli SSB protein-DNA topology by reversing DNA backbone polarity.

Authors:  Alexander G Kozlov; Timothy M Lohman
Journal:  Biophys J       Date:  2021-02-23       Impact factor: 4.033

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