A. A schematic representation of the three VcdRP and VcdR/P variants used for the transcriptome analysis. Left to right: first, the native VcdRP variant which harbors both the small protein as well as the base-pairing region. Next, a STOP codon was introduced in the 3rd codon of vcdP ORF as a readout for VcdR devoid of VcdP. Finally, the sequence of the VcdP codons was scrambled such that the correct small protein is translated but the nucleotide sequence of the scrambled vcdP variant is significantly altered when compared to native vcdRP. This variant also carries an artificial 5'UTR and a terminator. The arrows indicate the TSS. 