Bioinformatic prediction reveals posttranscriptional regulation of the chromosomal replication initiator gene <i>dnaA</i> by the attenuator sRNA rnTrpL in <i>Escherichia coli</i>

DnaA is the initiator protein of chromosome replication, but the regulation of its homoeostasis in enterobacteria is not well understood. The DnaA level remains stable at different growth rates, suggesting a link between metabolism and <i>dnaA</i> expression. In a bioinformatic prediction, which we made to unravel targets of the sRNA rnTrpL in <i>Enterobacteriaceae</i>, the <i>dnaA</i> mRNA was the most conserved target candidate. The sRNA rnTrpL is derived from the transcription attenuator of the tryptophan biosynthesis operon. In <i>Escherichia coli</i>, its level is higher in minimal than in rich medium due to derepressed transcription without external tryptophan supply. Overexpression and deletion of the rnTrpL gene decreased and increased, respectively, the levels of <i>dnaA</i> mRNA. The decrease of the <i>dnaA</i> mRNA level upon rnTrpL overproduction was dependent on <i>hfq</i> and <i>rne</i>. Base pairing between rnTrpL and <i>dnaA</i> mRNA <i>in vivo</i> was validated. In minimal medium, the <i>oriC</i> level was increased in the <i>ΔtrpL</i> mutant, in line with the expected DnaA overproduction and increased initiation of chromosome replication. In line with this, chromosomal rnTrpL mutation abolishing the interaction with <i>dnaA</i> increased both the <i>dnaA</i> mRNA and the <i>oriC</i> level. Moreover, upon addition of tryptophan to minimal medium cultures, the <i>oriC</i> level in the wild type was increased. Thus, rnTrpL is a base-pairing sRNA that posttranscriptionally regulates <i>dnaA</i> in <i>E. coli</i>. Furthermore, our data suggest that rnTrpL contributes to the DnaA homoeostasis in dependence on the nutrient availability, which is represented by the tryptophan level in the cell.