MutL traps MutS at a DNA mismatch

Qiu, Ruoyi; Sakato, Miho; Sacho, Elizabeth J.; Wilkins, Hunter; Zhang, Xingdong; Modrich, Paul; Hingorani, Manju; Erie, Dorothy A.; Weninger, Keith

doi:10.1073/pnas.1505655112

Cited by 60 publications

(81 citation statements)

References 43 publications

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“…Taken together, these studies strongly support a dynamic model for MMR (1,30) and effectively eliminate static or singlecomplex models (13,34). A surprising observation was that even in the absence of a mismatch, HsEXOI efficiently converts a 5′-strand scission into a gap bound by HsRPA before its exonuclease activity is fully inhibited (Fig.…”

Section: Discussionsupporting

confidence: 59%

Dynamic control of strand excision during human DNA mismatch repair

Jeon

Kim

Martín-López

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Mismatch repair (MMR) is activated by evolutionarily conserved MutS homologs (MSH) and MutL homologs (MLH/PMS). MSH recognizes mismatched nucleotides and form extremely stable sliding clamps that may be bound by MLH/PMS to ultimately authorize strand-specific excision starting at a distant 3′-or 5′-DNA scission. The mechanical processes associated with a complete MMR reaction remain enigmatic. The purified human (Homo sapien or Hs) 5′-MMR excision reaction requires the HsMSH2-HsMSH6 heterodimer, the 5′ → 3′ exonuclease HsEXOI, and the single-stranded binding heterotrimer HsRPA. The HsMLH1-HsPMS2 heterodimer substantially influences 5′-MMR excision in cell extracts but is not required in the purified system. Using real-time single-molecule imaging, we show that HsRPA or Escherichia coli EcSSB restricts HsEXOI excision activity on nicked or gapped DNA. HsMSH2-HsMSH6 activates HsEXOI by overcoming HsRPA/EcSSB inhibition and exploits multiple dynamic sliding clamps to increase tract length. Conversely, HsMLH1-HsPMS2 regulates tract length by controlling the number of excision complexes, providing a link to 5′ MMR.is a highly conserved strand-specific excision-resynthesis process that corrects nucleotide misincorporation errors during replication and nucleotide mismatches arising from recombination between heteroallelic parents or physical damage to the DNA (for review see ref. 1). Mutation of core MMR components results in elevated mutation rates and susceptibility to a variety of cancers (2).MMR has been reconstituted with purified Escherichia coli, Saccharomyces cerevisae, and human proteins (3-6). The core MutS homologs (MSH) and MutL homologs (MLH/PMS) components direct a strand-specific excision reaction, whereas resynthesis appears to be uniquely performed by the replicative polymerase complex (1). In all organisms the excision process is initiated at a single-strand DNA scission (ssDNA/S) that may be located either 3′ or 5′ and hundreds to thousands of base pairs distant from the mismatch (4, 7). An ssDNA/S positioned on the newly replicated strand ensures accurate correction of replication misincorporation errors (1).Excision directionality in γ-proteobacteria (E. coli) is linked to the choice of 3′ or 5′ exonucleases that specifically degrade ssDNA generated by the EcUvrD helicase in concert with EcMutS and EcMutL (1). The lack of a helicase distinguishes yeast and human MMR from γ-proteobacteria. Moreover, the eukaryotic 3′-and 5′-excision reactions require different core MMR components and likely occur by different mechanisms (1). For example, the 3′-MMR excision requires the replicative processivity factor PCNA to activate a cryptic MLH/PMS endonuclease activity (8), whereas 5′ MMR uses the only known MMR exonuclease EXOI (3, 5, 6). Unlike the E. coli ssDNA exonucleases, EXOI will initiate 5′ excision from a ssDNA/S in the absence of a helicase (9). Whereas the purified 5′-MMR reaction does not require MLH/PMS or PCNA, complementation studies with cellular extracts displayed a substantial requirement for...

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Section: Discussionsupporting

confidence: 59%

Dynamic control of strand excision during human DNA mismatch repair

Jeon

Kim

Martín-López

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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“…The transition involves multiple steps (coupled with ADP release and ATP binding), particularly disengagement of domains I from the mismatch and unbending of DNA, which in turn allow MutS to move away from the site (2 s −1 and 0.3 s −1 , respectively at 40 °C for Taq MutS; Fig. 3, 4c) [23,58]. In addition to domains I moving away from the mismatch [58], new structural data indicate that domains IV cross each other (keeping the clamp closed) and the connector domains II move outward [53]; hence, ATP-bound MutS can slide on DNA [41,59] without rotating along the helical contour, as confirmed recently by sm-tracking experiments with Taq and yeast MutS proteins [18-21,60].…”

Section: Muts Actions In Mmrmentioning

confidence: 99%

“…3, 4c) [23,58]. In addition to domains I moving away from the mismatch [58], new structural data indicate that domains IV cross each other (keeping the clamp closed) and the connector domains II move outward [53]; hence, ATP-bound MutS can slide on DNA [41,59] without rotating along the helical contour, as confirmed recently by sm-tracking experiments with Taq and yeast MutS proteins [18-21,60]. It is surprising that after the effort of finding and marking a rare mismatch on DNA (akin to finding a needle in a haystack), MutS adopts a mobile state that can diffuse freely away from the MMR target site.…”

Section: Muts Actions In Mmrmentioning

confidence: 99%

“…It is surprising that after the effort of finding and marking a rare mismatch on DNA (akin to finding a needle in a haystack), MutS adopts a mobile state that can diffuse freely away from the MMR target site. Recently published studies on MutS-MutL interactions following mismatch recognition provide new insights into the next stage of MMR, as described further in section 2.2 [53,58]. …”

Section: Muts Actions In Mmrmentioning

confidence: 99%

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Mismatch binding, ADP–ATP exchange and intramolecular signaling during mismatch repair

Hingorani

2016

DNA Repair

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The focus of this article is on the DNA binding and ATPase activities of the mismatch repair (MMR) protein, MutS—our current understanding of how this protein uses ATP to fuel its actions on DNA and initiate repair via interactions with MutL, the next protein in the pathway. Structure-function and kinetic studies have yielded detailed views of the MutS mechanism of action in MMR. How MutS and MutL work together after mismatch recognition to enable strand-specific nicking, which leads to strand excision and synthesis, is less clear and remains an active area of investigation.

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“…DNA complexes with the NER protein human XPA have been studied with scanning confocal fluorescence microscopy, (Segers-Nolten et al, 2002) capable of characterizing interaction dynamics on a time scale of 10 µs. We have employed TIRF-based single-molecule FRET as a complement to AFM studies to achieve simultaneous structural and dynamic characterization of DNA repair complexes (DeRocco et al, 2014; Gauer et al, 2016; Qiu et al, 2012, 2015; Sass et al, 2010). By fluorescently labeling protein domains or DNA, dynamic conformations of MMR proteins and DNA can be investigated.…”

Section: Complementary Techniquesmentioning

confidence: 99%

Using Atomic Force Microscopy to Characterize the Conformational Properties of Proteins and Protein–DNA Complexes That Carry Out DNA Repair

LeBlanc

Wilkins

et al. 2017

Methods in Enzymology

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Atomic force microscopy (AFM) is a scanning probe technique that allows visualization of single biomolecules and complexes deposited on a surface with nanometer resolution. AFM is a powerful tool for characterizing protein–protein and protein–DNA interactions. It can be used to capture snapshots of protein–DNA solution dynamics, which in turn, enables the characterization of the conformational properties of transient protein–protein and protein–DNA interactions. With AFM, it is possible to determine the stoichiometries and binding affinities of protein–protein and protein–DNA associations, the specificity of proteins binding to specific sites on DNA, and the conformations of the complexes. We describe methods to prepare and deposit samples, including surface treatments for optimal depositions, and how to quantitatively analyze images. We also discuss a new electrostatic force imaging technique called DREEM, which allows the visualization of the path of DNA within proteins in protein–DNA complexes. Collectively, these methods facilitate the development of comprehensive models of DNA repair and provide a broader understanding of all protein–protein and protein–nucleic acid interactions. The structural details gleaned from analysis of AFM images coupled with biochemistry provide vital information toward establishing the structure–function relationships that govern DNA repair processes.

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MutL traps MutS at a DNA mismatch

Cited by 60 publications

References 43 publications

Dynamic control of strand excision during human DNA mismatch repair

Dynamic control of strand excision during human DNA mismatch repair

Mismatch binding, ADP–ATP exchange and intramolecular signaling during mismatch repair

Using Atomic Force Microscopy to Characterize the Conformational Properties of Proteins and Protein–DNA Complexes That Carry Out DNA Repair

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