Rearrangements of repeated DNA sequences in Escherichia coli

Repeated DNA sequences of a variety of types are found in genomes of many organisms. Repeated DNA sequences are known to be unstable, and are prone to rearrangements causing loss or gain of the repeated sequence and any intervening DNA. The study of repeated DNA sequences provides insight not only to a number of diseases that are caused by DNA repeat instability, but also to the understanding of basic cellular processes (like recombination, replication and repair) and their role in processing non-repeated DNA sequences. Several models are proposed to explain the molecular mechanisms of repeat rearrangement in Escherichia coli. These models are divided into two major groups: RecA-dependent and RecA-independent recombination pathways.; We have investigated the effects of recombination and replication genes and inverted repeat sequences on expansion of nearby direct repeats (787 bp). We show that overall rate, dependence on RecA and stimulation by replication mutations, expansion of direct repeats resembles deletion of direct repeats of the same length. In contrast, we did not observe an inverted repeat stimulation on expansion of nearby direct repeats as was observed for to deletion of flanking direct repeats. We also studied the effects of inverted repeat stimulation on deletion of large direct repeats (787 bp), and the effects of trinucleotide repeat stimulation on deletion of flanking 101 bp. We show that inverted repeats that are predicted to form secondary structures, stimulate deletion of flanking 101 by and 787 by direct repeats similarly, but the latter to a lesser extent. In addition, our data clearly shows that inverted repeat secondary structures are processed differently than the putative secondary structures formed by trinucleotide repeats. Our data supports a model in which (CAG)_n and (CTG)_n form a secondary structure that has a weak enhancing effect of the deletion rate of flanking 101 by direct repeat. Lastly, we investigated the role of dnaK, a member of the highly conserved hsp70 class of proteins, in recombination and repair. We provide data that supports a new role for DnaK as mediating the RecA-independent replication slipped misalignments of low homologies.