Analysis of the transcriptional response to DNA damage and replication arrest

Our results indicate that the transcriptional responses to HPUra, MMC, and UV are only partially overlapping. recA is the major transcriptional regulator under all of the tested conditions and LexA appears to directly repress expression of 63 genes in 26 operons, including the 18 operons previously identified as LexA targets. MMC and HPUra treatments caused induction of an integrative and conjugative element (ICEBs1) and resident prophages (PBSX and SPß), which affected expression of many host genes. Consistent with previous results, induction of these mobile elements required recA. Induction of the phage appeared to require inactivation of LexA. Unrepaired UV damage and treatment with MMC also affected expression of some of the genes that are controlled by DnaA. Furthermore, MMC treatment caused an increase in origin proximal gene dosage Keywords: time dependent DNA damage response Exponentially growing cultures (in S750 defined minimal medium at 37C) were split into two and one half was treated with UV,MMC, or HPUra. Comparisons were made between the mock treated and untreated samples. All experiments were performed with three biological replicates. Data are presented for 60min after treatment. For each experiment we compared treated sample vs reference on one array and untreated sample vs same reference RNA on another array. We then obtained ratio of the separate microarray Cy5/Cy3 ratios.