Regulation of Homologous Recombination between Divergent DNA Sequences by Mismatch Repair Proteins

__Abstract__ Genomes of living organisms, from unicellular bacteria to multicellular human, are threatened by a plethora of DNA lesions. It is estimated that there are ~100,000 DNA lesions inflicted in a single cell on a daily basis (Lindahl, 1993). Both endogenous and exogenous agents induce the formation of these lesions in the genome. Internally, other than replication errors that generate DNA mismatches, reactive oxygen species, alkylating agents and spontaneous hydrolysis damage DNA. These structural alterations include oxidation, methylation, deamination, depurination and depyrimidation of DNA bases. External agents such as ultraviolet radiation, high-frequency radiations like X-rays and γ-rays, natural and synthetic toxins, can all damage DNA by changing its structure. These agents mediate the formation of intra- and interstrand crosslinks, of bulky adducts as well as of single- and double-strand breaks (DSBs) in the DNA. To ensure proper operation of DNA transactions, which are important for cellular survival, a variety of DNA-repair pathways act on these DNA lesions to preserve the integrity of the genome (Hoeijmakers 2001, 2009; Friedberg 2003; Garinis et al., 2008). These DNArepair pathways include DNA mismatch repair (MMR; Jiricny 2013), base excision repair (BER; Goosen and Moolenaar, 2008), nucleotide excision repair (NER; Goosen and Moolenaar, 2008), non-homologous end joining (NHEJ; Shuman and Glickman,

Mismatch repair inhibits homeologous recombination via coordinated directional unwinding of trapped DNA structures

Homeologous recombination between divergent DNA sequences is inhibited by DNA mismatch repair. In Escherichia coli, MutS and MutL respond to DNA mismatches within recombination intermediates and prevent strand exchange via an unknown mechanism. Here, using purified proteins and DNA substrates, we find that in addition to mismatches within the heteroduplex region, secondary structures within the displaced single-stranded DNA formed during branch migration within the recombination intermediate are involved in the inhibition. We present a model that explains how higher-order complex formation of MutS, MutL, and DNA blocks branch migration by preventing rotation of the DNA strands within the recombination intermediate. Furthermore, we find that the helicase UvrD is recruited to directionally resolve these trapped intermediates toward DNA substrates. Thus, our results explain on a mechanistic level how the coordinated action between MutS, MutL, and UvrD prevents homeologous recombination and maintains genome stability