Evolution of Chi motifs in Proteobacteria

Abstract

Homologous recombination is a key pathway found in nearly all bacterial taxa. The recombination complex not only allows bacteria to repair DNA double-strand breaks but also promotes adaption through the exchange of DNA between cells. In Proteobacteria, this process is mediated by the RecBCD complex, which relies on the recognition of a DNA motif named Chi to initiate recombination. The Chi motif has been characterized in Escherichia coli and analogous sequences have been found in several other species from diverse families, suggesting that this mode of action is widespread across bacteria. However, the sequences of Chi-like motifs are known for only five bacterial species: E. coli, Haemophilus influenzae, Bacillus subtilis, Lactococcus lactis, and Staphylococcus aureus. In this study, we detected putative Chi motifs in a large dataset of Proteobacteria and identified four additional motifs sharing high sequence similarity and similar properties to the Chi motif of E. coli in 85 species of Proteobacteria. Most Chi motifs were detected in Enterobacteriaceae and this motif appears well conserved in this family. However, we did not detect Chi motifs for the majority of Proteobacteria, suggesting that different motifs are used in these species. Altogether these results substantially expand our knowledge on the evolution of Chi motifs and on the recombination process in bacteria.

Keywords: DNA motifs; bacteria; genome evolution; homologous recombination.

Figure 1

Frequencies and sequences of candidate Chi motifs identified in Proteobacteria. Five main Chi motifs have been detected in a total of 87 species of Proteobacteria based on our criteria.

Figure 2

Phylogenetic tree of Proteobacteria and distribution of species with inferred Chi motifs. The tree was inferred using a set of 43 universal proteins and with RaxML (see Materials and methods) using the LG substitution model and rooted using three Firmicutes species.

Figure 3

Distribution of candidate Chi motifs in Enterobacteriacaea. The subtree was extracted from the tree of Proteobacteria presented in Figure 2 and rooted with non-Enterobacteriacaea species.