Characterization of a novel class of mutation (Short Patch Illegitimate Recombination) in Acinetobacter baylyi

In prokaryotes, genetic variability contributes to the adaptation to novel environmental conditions, to resistance against threats such as antimicrobial agents and viruses, and ultimately to bacterial evolution through selection and drift. Genetic variability is mainly generated through mutations, e.g. point mutations, deletions, insertions, inversions, and duplications/amplifications. In addition, horizontal gene transfer (HGT) can contribute to variability by enabling a cell to acquire genetic material from closely (or more rarely, from distantly) related organisms. DNA taken up by HGT can be recombined with the chromosome of the recipient cell by either homologous recombination or illegitimate recombination. In this study a novel type of illegitimate recombination where small patches of DNA are recombined at microhomologous DNA segments, termed short patch illegitimate recombination (SPIR) is described in Acinetobacter baylyi. The results suggests that SPIR events typically lead to a substitution of 2-8 base pairs alone or together with a 3-9 base pair deletion, or a larger deletion up to 168 base pairs. It was also shown that SPIR occurs both in transformable and non-transformable strains, and that SPIR frequency is decreased by presence of the 3’-5’ single strand specific exonuclease ExoX. It is conceivable that SPIR enables greater changes in a genome over the course of a single generation than earlier described mutation mechanisms, and can thus play a role in adaptive evolution.