Multiple transcription-activating sequences regulate the RsmZ regulatory small RNA of Pseudomonas brassicacearum

The mutS-rpoS region is known to be a highly polymorphic segment of the chromosome owing to horizontal gene transfer and evolutionary processes. In Pseudomonas, mutS-fdxA-rsmZ-rpoS organization is highly conserved, as well as the promoter region of the RsmZ small RNA (sRNA)-encoding gene. One exception to this conservation is in Pseudomonas brassicacearum, where a 308-nucleotide (nt) sequence, predicted to form a hairpin structure in single-stranded DNA (ssDNA), is inserted between the rpoS and rsmZ genes. Using MEME software, we identified nine consensus motifs in the rsmZ promoter region of 16 sequenced Pseudomonas genomes. We observed that an upstream activation sequence (UAS) and an M1 motif (located between the -10 promoter element and the UAS) are shared among examined Pseudomonas genomes. A third motif, the M2 motif, is localized within the coding sequence of the rpoS gene. Constructs fusing the different identified motifs to the lacZ reporter were produced. Our in vivo analysis of the rsmZ-activating elements indicates that the palindromic UAS located 180 bp upstream of the rsmZ transcriptional start in P. brassicacearum NFM 421 is essential, but not sufficient, for full rsmZ expression. Here, we demonstrate a role for the three motifs in the activation of the rsmZ gene, and we hypothesize the role of additional transcriptional factors, along with the DNA structuring role of the hairpin in the complex network controlling the expression of rsmZ.