Global LexA1 binding sites assessment in Leptospira interrogans serivar Copenhageni using ChIP-seq

The pathogen L. interrogans serovar Copenhageni can be shed in the urine of carrier mammals, and infect humans after weeks on water or mud. This wide range of possible niches implies the bacterium can be exposed to several different genotoxic stresses during its lifecycle. We assessed the impact of DNA damage in this leptospire, integrating high throughput data from ChIP-seq and DNA microarrays to determine the role of the SOS regulator LexA1. We observed 24 LexA1 binding sites located throughout the chromosome 1 and one in chromosome 2. Analyses of LexA1 ChIP-seq peak sequences revealed the SOS box is an imperfect asymmetric palindrome of 16bp, CTAA[A/T/G]CANNTG[T/A]TTAG. DNA damage caused significant changes of several aspects of bacterial physiology, decreasing expression of genes involved in energy metabolism and translation, in addition to genes related to virulence and motility. On the other hand, post replicative and recombination repair, but not the canonical DNA repair genes, were up regulated. The most striking feature of this response was the massive up-regulation of two prophages. Our findings point to an expression profile shift from cell growth and virulence to mutagenesis and recombination, emphasizing the fundamental role of DNA damage response as a highway for adaptation and evolution. Two pairs of samples were used: two "total" samples from lysates from exponential growing cells, crosslinked with 2% final concentration of formaldehyde and the corresponding immunoprecipitated sample. One lysate was crosslinked for 40min, and the other for 60min. The immunoprecipitation was carried with anti-LexA1 mice sera in 1:100 final concentration, and protein G Sepharose resin. The DNA from total and immunoprecipitated samples were isolated, size-selected for 200-400bp and sequenced by HiSeq. Aligment of reads to the reference genome was performed by Bowtie2 and peak-calling with CisGenome, using the total samples as background.