Abstract
Strand mispairing interactions between repeated DNA sequences provoke a host of mutations and genetic rearrangements in bacteria. Repeated DNA sequences in either direct or inverted orientation can promote misalignment‐mediated mutations and rearrangements by very similar mechanisms. This chapter catalogs several types of misalignment‐mediated genetic changes in bacteria, with an emphasis on the mechanisms by which they occur. Systematic study of misalignment‐mediated mutation and genetic rearrangements has revealed many elements of the mechanisms of these processes, including the integral role for DNA replication. The impact of these misalignment processes on bacterial physiology and genomic evolution is also discussed in this chapter. Sister chromosome exchange (SCE)‐associated misalignment has been studied only on plasmid replicons. When recA‐independent deletions or expansions between tandem repeats are selected on plasmids, concomitant replicon dimerization is often seen. Single‐strand annealing (SSA) contributes as a major pathway to rearrangements in eukaryotes and in bacteriophage‐infected Escherichia coli but may occur efficiently only under restricted circumstances in normal bacterial growth. Short spurious repeats can be sites for deletion, duplication, or inversion; these processes create larger repeats that can lead to even higher rates of rearrangements. These rearrangements can occur independently of the bacterial homologous recombination pathways and are dependent on the length and perfection of the repeats, as well as their proximity.