Multiple Transcription-Activating Sequences Regulate the RsmZ Regulatory Small RNA of Pseudomonas brassicacearum
ABSTRACTThemutS-rpoSregion is known to be a highly polymorphic segment of the chromosome owing to horizontal gene transfer and evolutionary processes. InPseudomonas,mutS-fdxA-rsmZ-rpoSorganization is highly conserved, as well as the promoter region of the RsmZ small RNA (sRNA)-encoding gene. One exception to this conservation is inPseudomonas brassicacearum, where a 308-nucleotide (nt) sequence, predicted to form a hairpin structure in single-stranded DNA (ssDNA), is inserted between therpoSandrsmZgenes. Using MEME software, we identified nine consensus motifs in thersmZpromoter region of 16 sequencedPseudomonasgenomes. We observed that an upstream activation sequence (UAS) and an M1 motif (located between the −10 promoter element and the UAS) are shared among examinedPseudomonasgenomes. A third motif, the M2 motif, is localized within the coding sequence of therpoSgene. Constructs fusing the different identified motifs to thelacZreporter were produced. Ourin vivoanalysis of thersmZ-activating elements indicates that the palindromic UAS located 180 bp upstream of thersmZtranscriptional start inP. brassicacearumNFM 421 is essential, but not sufficient, for fullrsmZexpression. Here, we demonstrate a role for the three motifs in the activation of thersmZgene, 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 ofrsmZ.