MutS homolog sliding clamps shield the DNA from binding proteins

Sliding clamps on DNA consist of evolutionarily conserved enzymes that coordinate DNA replication, repair, and the cellular DNA damage response. MutS homolog (MSH) proteins initiate mismatch repair (MMR) by recognizing mispaired nucleotides and in the presence of ATP form stable sliding clamps that randomly diffuse along the DNA. The MSH sliding clamps subsequently load MutL homolog (MLH/PMS) proteins that form a second extremely stable sliding clamp, which together coordinate downstream MMR components with the excision-initiation site that may be hundreds to thousands of nucleotides distant from the mismatch. Specific or nonspecific binding of other proteins to the DNA between the mismatch and the distant excision-initiation site could conceivably obstruct the free diffusion of these MMR sliding clamps, inhibiting their ability to initiate repair. Here, we employed bulk biochemical analysis, single-molecule fluorescence imaging, and mathematical modeling to determine how sliding clamps might overcome such hindrances along the DNA. Using both bacterial and human MSH proteins, we found that increasing the number of MSH sliding clamps on a DNA decreased the association of the Escherichia coli transcriptional repressor LacI to its cognate promoter LacO. Our results suggest a simple mechanism whereby thermal diffusion of MSH sliding clamps along the DNA alters the association kinetics of other DNA-binding proteins over extended distances. These observations appear generally applicable to any stable sliding clamp that forms on DNA.

• Publication year

  2018

• Venue

  Journal of Biological Chemistry

• Publication date

  2018-08-02

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1074/jbc.RA118.002264PMID 30072380PMCID PMC6139549
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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• An Efficient Site-Specific Method for Irreversible Covalent Labeling of Proteins with a Fluorophore

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  2015cited by this paper
• Mismatch repair protein hMSH2–hMSH6 recognizes mismatches and forms sliding clamps within a D-loop recombination intermediate

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• Single-molecule views of MutS on mismatched DNA.

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• Replication clamps and clamp loaders.

  2013cited by this paper
• Hydrazino-Pictet-Spengler ligation as a biocompatible method for the generation of stable protein conjugates.

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• From the Cover: PNAS Plus: Single-molecule imaging reveals target-search mechanisms during DNA mismatch repair

  2012cited by this paper
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  2012influential reference
• Single-molecule analysis of DNA replication in Xenopus egg extracts.

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  2011influential reference
• Protein induced fluorescence enhancement as a single molecule assay with short distance sensitivity

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  2010influential reference
• Statistical Mechanics of Nucleosomes Constrained by Higher-Order Chromatin Structure

  2010cited by this paper
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  2010cited by this paper
• Sequence context effect for hMSH2-hMSH6 mismatch-dependent activation

  2009cited by this paper
• Nucleosome remodeling by hMSH2-hMSH6.

  2009influential reference
• Crystal structure of the rad9-rad1-hus1 DNA damage checkpoint complex--implications for clamp loading and regulation.

  2009cited by this paper
• Structure of the human MutSalpha DNA lesion recognition complex.

  2007cited by this paper
• Inhibition of Msh6 ATPase activity by mispaired DNA induces a Msh2(ATP)-Msh6(ATP) state capable of hydrolysis-independent movement along DNA.

  2006cited by this paper
• Analysis of the Interaction between the Saccharomyces cerevisiae MSH2-MSH6 and MLH1-PMS1 Complexes with DNA Using a Reversible DNA End-blocking System*

  2005cited by this paper
• hMSH4-hMSH5 recognizes Holliday Junctions and forms a meiosis-specific sliding clamp that embraces homologous chromosomes.

  2004cited by this paper
• The coordinated functions of the E. coli MutS and MutL proteins in mismatch repair.

  2003cited by this paper
• HNPCC mutations in hMSH2 result in reduced hMSH2-hMSH6 molecular switch functions.

  2002cited by this paper
• Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA

  2000cited by this paper
• The crystal structure of DNA mismatch repair protein MutS binding to a G·T mismatch

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• hMSH2-hMSH6 forms a hydrolysis-independent sliding clamp on mismatched DNA.

  1999cited by this paper
• Dissociation of Mismatch Recognition and ATPase Activity by hMSH2-hMSH3*

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• The human mismatch recognition complex hMSH2-hMSH6 functions as a novel molecular switch.

  1997cited by this paper
• Identification and Characterization of a Thermostable MutS Homolog from Thermus aquaticus(*)

  1996cited by this paper
• The purification of a human mismatch-binding protein and identification of its associated ATPase and helicase activities.

  1992cited by this paper
• Altering the conserved nucleotide binding motif in the Salmonella typhimurium MutS mismatch repair protein affects both its ATPase and mismatch binding activities.

  1991cited by this paper
• The nucleotide sequence of the lac operator.

  1973cited by this paper
• ISOLATION OF THE LAC REPRESSOR

  1966cited by this paper
• Genetic regulatory mechanisms in the synthesis of proteins.

  1961cited by this paper
• The Complete Equation of State of One, Two and Three-Dimensional Gases of Hard Elastic Spheres

  1936cited by this paper

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