DNA tandem repeat instability in the Escherichia coli chromosome is stimulated by mismatch repair at an adjacent CAG·CTG trinucleotide repeat

Abstract

Approximately half the human genome is composed of repetitive DNA sequences classified into microsatellites, minisatellites, tandem repeats, and dispersed repeats. These repetitive sequences have coevolved within the genome but little is known about their potential interactions. Trinucleotide repeats (TNRs) are a subclass of microsatellites that are implicated in human disease. Expansion of CAG·CTG TNRs is responsible for Huntington disease, myotonic dystrophy, and a number of spinocerebellar ataxias. In yeast DNA double-strand break (DSB) formation has been proposed to be associated with instability and chromosome fragility at these sites and replication fork reversal (RFR) to be involved either in promoting or in preventing instability. However, the molecular basis for chromosome fragility of repetitive DNA remains poorly understood. Here we show that a CAG·CTG TNR array stimulates instability at a 275-bp tandem repeat located 6.3 kb away on the Escherichia coli chromosome. Remarkably, this stimulation is independent of both DNA double-strand break repair (DSBR) and RFR but is dependent on a functional mismatch repair (MMR) system. Our results provide a demonstration, in a simple model system, that MMR at one type of repetitive DNA has the potential to influence the stability of another. Furthermore, the mechanism of this stimulation places a limit on the universality of DSBR or RFR models of instability and chromosome fragility at CAG·CTG TNR sequences. Instead, our data suggest that explanations of chromosome fragility should encompass the possibility of chromosome gaps formed during MMR.DNA repair | DNA replication | fragile site

Bacterial Genome Instability

“…Tandem-repeat instability varies as a function of the DNA sequence and the number of repeats (for example, CAG repeats are more instable than CTG repeats, and longer repeats are more instable [364]), their distance (365), their location in the genome (instability between repeats on the same molecules or on different molecules will result in different outcomes), and the cellular pathway leading to their instability (366). Additionally, the rate of tandem-repeat instability increases following DNA damage (367). Misalignment of repeated sequences might occur during DNA replication between the nascent strand and a second site on its template, on the nascent strand itself, or on the other sister chromosome.…”

“…The rates of microsatellite instability can be modulated by different cellular processes using DNA synthesis, such as DNA replication, recombination, and repair. Furthermore, it has been shown recently that mismatch repair at these sequences can stimulate strand slippage at a longer directly repeated sequence located several kilobases away (367). Microsatellites occur naturally in numerous bacteria, and their expansions and contractions can regulate specific gene expression or alter coding sequences, resulting in phase or antigenic variation (see "Phase and Antigenic Variation in Bacteria," below).…”

Chromosomal directionality of DNA mismatch repair in Escherichia coli

“…Blackwood and collaborators found that MMR at the site of an unstable trinucleotide repeat (TNR) array caused a stimulation of recombination at a nearby 275-bp tandem repeat. This stimulation occurred only when the tandem repeat was placed on the origin-proximal side the TNR that had generated a high frequency substrate for MMR (24). This Significance DNA mismatch repair (MMR) is critical to avoid mutations that can lead to genetic disease, cancer, and death.…”

“…Length instability at the level of a single trinucleotide unit in a CTG·CAG repeat array that is inserted in the chromosome of E. coli is elevated in MMR deficient cells (24). This elevation of mutation occurs to an equal extent in mutS, mutL, and mutH mutants indicating that correction of the 3-base IDL, precursor to a single trinucleotide repeat unit change, occurs by a normal MMR reaction involving recognition by MutS and strand cleavage by MutH (24).…”

“…Length instability at the level of a single trinucleotide unit in a CTG·CAG repeat array that is inserted in the chromosome of E. coli is elevated in MMR deficient cells (24). This elevation of mutation occurs to an equal extent in mutS, mutL, and mutH mutants indicating that correction of the 3-base IDL, precursor to a single trinucleotide repeat unit change, occurs by a normal MMR reaction involving recognition by MutS and strand cleavage by MutH (24). This is as expected for a 3-base IDL, which has been shown to be corrected with an efficiency close to that of a G·T mismatch (the best recognized single base mismatch) (6) and contrasts with changes of two or more CTG·CAG trinucleotide units, which are not elevated in MMR deficient cells (24), as predicted by the inability of the MMR system to recognize an IDL of 5 bases (6).…”