42) and TreC), and YeaG. Similar to proteome profiles of MMS-treated wild-type cells, one isoform of elongation factor Ts (Tsf) was detected on 2-D gels of MMS-treated ada cells. Interestingly, the MMS treatment of the ada Selleck GANT61 mutant cells resulted in the significant repression of the FliC involved in flagellar biosynthesis, which is

consistent with down-regulated expression of this gene in transcriptome data (Additional file 1: Table S1). In general, E. coli responds to alkylation stress by activating sets of co-regulated genes that help the cell to maintain homeostasis. However, the ada mutant cells would require a more rapid increase in the expression levels of specific genes for DNA repair in response to methylating agents, due to the lack of the Ada-dependent response mechanism. It can be seen from the 0.5 h profiles that the Blebbistatin concentration adaptive response mediates the induction of 23 genes involved in DNA replication, recombination,

modification and repair, such as b1360, dinD, lar, modF, mutH, ogt, phrB, pinO, polB, priA, recANT, rnb, rnpA, ruvB, tpr, umuCD, uvrA, yeeS, yfbL and yfjY. MMS treatment also caused a strong induction of the drug or antibiotic resistance genes, most of which are located ABT-888 ic50 in cell membrane (Figure 4, Additional file 2). Proteome profiles also showed that RcsB was increased in MMS-treated ada mutant cells. Taken together, the profiles for the ada mutant strain defective in adaptive response showed a far more rapid transcriptional response following MMS treatment when compared to the wild-type. From these results, we reasoned that the responses observed at earlier time point might allow identification of direct targets of the adaptive response, while the long-exposure time profiles would reflect

more complex regulation in cellular networks, including both stationary phase responses by the rpoS gene product [23, 24] and adaptive response by alkylating agents. Thus, the transcriptional and translational profiles of SDHB the wild-type and the ada mutant strain at 0.5 h were analyzed in more detail. Differences in expression levels between wild-type and ada mutant strains under normal growth condition In order to examine the intracellular changes that are induced by the ada gene deletion in the MMS-untreated, normal growth condition, the expression levels of genes and proteins of ada mutant cells were first compared with those of wild-type cells at the mid-log growth phase (at 0.5 h sampling point). The number of genes differentially expressed at greater than 2-fold levels was small. Only 69 and 10 genes were up- and down-regulated, respectively, in the ada mutant strain compared to the wild-type strain (Additional file 2). Interestingly, the expression levels of the genes involved in flagellar biosynthesis (flgCEG and fliAC) and chemotaxis (tar and cheW) were higher in the ada mutant strain than in the wild-type.