Large conformational changes in MutS during DNA scanning, mismatch recognition and repair signalling

Qiu, Ruoyi; DeRocco, Vanessa; Harris, C.; Sharma, Anil; Hingorani, Manju; Erie, Dorothy A.; Weninger, Keith

doi:10.1038/emboj.2012.95

Cited by 79 publications

(162 citation statements)

References 66 publications

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“…Despite the available crystal structures of MutS and MutS homologs bound to mispair-containing DNAs (2, 4, 18, 30), biochemical and genetic evidence suggests that crucial aspects of the function of MutS involve conformational states that have yet to be characterized at an atomic level (21,22,24,42,43). Here, we demonstrate the compatibility of PEG-coated gold labels on DNA with proteins and follow the effects of MutS conformational states and MutS/MutL association on DNA conformations.…”

Section: Discussionmentioning

confidence: 71%

DNA conformations in mismatch repair probed in solution by X-ray scattering from gold nanocrystals

Hura

Tsai

Claridge

et al. 2013

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

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DNA metabolism and processing frequently require transient or metastable DNA conformations that are biologically important but challenging to characterize. We use gold nanocrystal labels combined with small angle X-ray scattering to develop, test, and apply a method to follow DNA conformations acting in the Escherichia coli mismatch repair (MMR) system in solution. We developed a neutral PEG linker that allowed gold-labeled DNAs to be flashcooled and stored without degradation in sample quality. The 1,000-fold increased gold nanocrystal scattering vs. DNA enabled investigations at much lower concentrations than otherwise possible to avoid concentration-dependent tetramerization of the MMR initiation enzyme MutS. We analyzed the correlation scattering functions for the nanocrystals to provide higher resolution interparticle distributions not convoluted by the intraparticle distribution. We determined that mispair-containing DNAs were bent more by MutS than complementary sequence DNA (csDNA), did not promote tetramer formation, and allowed MutS conversion to a sliding clamp conformation that eliminated the DNA bends. Addition of second protein responder MutL did not stabilize the MutS-bent forms of DNA. Thus, DNA distortion is only involved at the earliest mispair recognition steps of MMR: MutL does not trap bent DNA conformations, suggesting migrating MutL or MutS/MutL complexes as a conserved feature of MMR. The results promote a mechanism of mismatch DNA bending followed by straightening in initial MutS and MutL responses in MMR. We demonstrate that small angle X-ray scattering with gold labels is an enabling method to examine protein-induced DNA distortions key to the DNA repair, replication, transcription, and packaging. D NA is frequently considered a passive component in interactions with proteins involved in DNA metabolism. Despite this view, many proteins use DNA structural features to mediate catalysis and identify damaged DNA through the effects of damage on DNA rigidity and conformation (1-6). The view of DNA as a passive element is therefore at least in part due to a paucity of robust tools to examine dynamic DNA conformational states during multistep reactions. Gold-labeled DNA enables measurement over length scales sufficient to accommodate several proteins to identify cooperative effects on DNA. Because X-rays scatter predominantly from electrons, using heavy atom labels (7-11) provides high contrast relative to organic molecules. By using labels of moderate size (∼5 nm), the scattering from gold nanocrystals dominates all other scattering signals by three orders of magnitude, thereby reducing analysis complexity while minimizing nanocrystal influence on biological macromolecules. Importantly, small angle X-ray scattering (SAXS) provides global information on conformations adopted by a population of macromolecules in almost any solution condition (12)(13)(14).Mismatch repair (MMR) is an evolutionarily conserved process that corrects mismatches generated during DNA replication (15,16). Despite the i...

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Section: Discussionmentioning

confidence: 71%

DNA conformations in mismatch repair probed in solution by X-ray scattering from gold nanocrystals

Hura

Tsai

Claridge

et al. 2013

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

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“…2) (Acharya et al 2003;Kolodner et al 2007). The mechanism that is most consistent with the data and the Brownian nature of molecular biology appears to be the molecular switch model (Gradia et al 1997(Gradia et al , 1999Fishel 1998Acharya et al 2003;Jeong et al 2011;Cho et al 2012;Gorman et al 2012;Qiu et al 2012;Spies 2013). Most, if not all, biochemical discrepancy can be traced to differences in the experimental conditions, an issue that persists today (Hall et al 2001;Drotschmann et al 2002;Tessmer et al 2008;Sass et al 2010;Tham et al 2013).…”

Section: Biochemical Activities Of the Mmr Proteinsmentioning

confidence: 63%

“…ATP exchange is a central function of all MSH proteins examined to date (Gradia et al 1997;Wilson et al 1999;Acharya et al 2003;Snowden et al 2004). ATP binding by the MSH dimer/heterodimer instigates a significant conformational transition (Gradia et al 1999;Wilson et al 1999;Acharya et al 2003;Qiu et al 2012), which results in an extremely stable (5-to 10-min lifetime) sliding clamp that freely diffuses along the DNA without ATP hydrolysis and in the absence of any stable backbone interactions ( Fig. 2A) (Cho et al 2012).…”

Section: Biochemical Activities Of the Mmr Proteinsmentioning

confidence: 99%

Mismatch Repair during Homologous and Homeologous Recombination

Spies

Fishel

2015

Cold Spring Harb Perspect Biol

148

150

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Homologous recombination (HR) and mismatch repair (MMR) are inextricably linked. HR pairs homologous chromosomes before meiosis I and is ultimately responsible for generating genetic diversity during sexual reproduction. HR is initiated in meiosis by numerous programmed DNA double-strand breaks (DSBs; several hundred in mammals). A characteristic feature of HR is the exchange of DNA strands, which results in the formation of heteroduplex DNA. Mismatched nucleotides arise in heteroduplex DNA because the participating parental chromosomes contain nonidentical sequences. These mismatched nucleotides may be processed by MMR, resulting in nonreciprocal exchange of genetic information (gene conversion). MMR and HR also play prominent roles in mitotic cells during genome duplication; MMR rectifies polymerase misincorporation errors, whereas HR contributes to replication fork maintenance, as well as the repair of spontaneous DSBs and genotoxic lesions that affect both DNA strands. MMR suppresses HR when the heteroduplex DNA contains excessive mismatched nucleotides, termed homeologous recombination. The regulation of homeologous recombination by MMR ensures the accuracy of DSB repair and significantly contributes to species barriers during sexual reproduction. This review discusses the history, genetics, biochemistry, biophysics, and the current state of studies on the role of MMR in homologous and homeologous recombination from bacteria to humans.

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“…The structure of an ATP-bound MSH dimer has yet to be solved. However, numerous biochemical and single-molecule studies have demonstrated that mismatch recognition triggers ADP→ATP nucleotide exchange, which results in a conformational transition that converts the MSH dimer into an ATP-bound stable sliding clamp that disengages from the mismatch and freely diffuses on the adjacent dsDNA for 8-10 min (14)(15)(16)(17)(18)(19)(20)(21). The formation of an ATP-bound MSH sliding clamp is followed by recruitment of MutL homologs (MLH/PMS) (22,23).…”

mentioning

confidence: 99%

Mismatch repair protein hMSH2–hMSH6 recognizes mismatches and forms sliding clamps within a D-loop recombination intermediate

Honda

Okuno

Hengel

et al. 2014

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

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High fidelity homologous DNA recombination depends on mismatch repair (MMR), which antagonizes recombination between divergent sequences by rejecting heteroduplex DNA containing excessive nucleotide mismatches. The hMSH2-hMSH6 heterodimer is the first responder in postreplicative MMR and also plays a prominent role in heteroduplex rejection. Whether a similar molecular mechanism underlies its function in these two processes remains enigmatic. We have determined that hMSH2-hMSH6 efficiently recognizes mismatches within a D-loop recombination initiation intermediate. Mismatch recognition by hMSH2-hMSH6 is not abrogated by human replication protein A (HsRPA) bound to the displaced single-stranded DNA (ssDNA) or by HsRAD51. In addition, ATP-bound hMSH2-hMSH6 sliding clamps that are essential for downstream MMR processes are formed and constrained within the heteroduplex region of the D-loop. Moreover, the hMSH2-hMSH6 sliding clamps are stabilized on the Dloop by HsRPA bound to the displaced ssDNA. Our findings reveal similarities and differences in hMSH2-hMSH6 mismatch recognition and sliding-clamp formation between a D-loop recombination intermediate and linear duplex DNA.

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Large conformational changes in MutS during DNA scanning, mismatch recognition and repair signalling

Cited by 79 publications

References 66 publications

DNA conformations in mismatch repair probed in solution by X-ray scattering from gold nanocrystals

DNA conformations in mismatch repair probed in solution by X-ray scattering from gold nanocrystals

Mismatch Repair during Homologous and Homeologous Recombination

Mismatch repair protein hMSH2–hMSH6 recognizes mismatches and forms sliding clamps within a D-loop recombination intermediate

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