No abstract

DsrA is an 87-nt untranslated RNA that regulates both the global transcriptional silencer and nucleoid protein H-NS and the stationary phase and stress response sigma factor RpoS ( s ). We demonstrate that DsrA acts via specific RNA:RNA base pairing interactions at the hns locus to antagonize H-NS translation. We also give evidence that supports a role for RNA:RNA interactions at the rpoS locus to enhance RpoS translation. Negative regulation of hns by DsrA is achieved by the RNA:RNA interaction blocking translation of hns RNA. In contrast, results suggest that positive regulation of rpoS by DsrA occurs by formation of an RNA structure that activates a cis-acting translational operator. Sequences within DsrA complementary to three additional genes, argR, ilvIH, and rbsD, suggest that DsrA is a riboregulator of gene expression that acts coordinately via RNA:RNA interactions at multiple loci.

DsrA is an 87-nucleotide regulatory RNA of Escherichia coli that acts in trans by RNA-RNA interactions with two different mRNAs, hns and rpoS. DsrA has opposite effects on these transcriptional regulators. H-NS levels decrease, whereas RpoS ( s ) levels increase. Here we show that DsrA enhances hns mRNA turnover yet stabilizes rpoS mRNA, either directly or via effects on translation. Computational and RNA footprinting approaches led to a refined structure for DsrA, and a model in which DsrA interacts with the hns mRNA start and stop codon regions to form a coaxial stack. Analogous bipartite interactions exist in eukaryotes, albeit with different regulatory consequences. In contrast, DsrA base pairs in discrete fashion with the rpoS RNA translational operator. Thus, different structural configurations for DsrA lead to opposite regulatory consequences for target RNAs.natural antisense ͉ RNA turnover ͉ RNA-RNA interactions ͉ structural dynamics ͉ translation R NA plays a variety of regulatory roles in the cell, in addition to its central function in translation processes. These activities are collectively termed riboregulation (1). RNA-RNA interactions provide a basis for sequence-specific RNA regulation of other RNAs in both prokaryotes and eukaryotes (2, 3). DsrA, an 87-nt untranslated RNA in Escherichia coli, is one such regulatory RNA. DsrA contains regions of sequence complementarity to at least five different genes, hns, argR, ilvIH, rpoS, and rbsD (4), and it has been demonstrated to regulate two of these genes, hns and rpoS, by RNA-RNA interactions (4, 5).H-NS is an abundant nucleoid-structuring protein with global transcriptional repressor functions (6, 7). DsrA antagonizes H-NS function by decreasing the levels of H-NS protein in the cell (4). In contrast, the translation of RpoS, the stationary phase and stress-response sigma factor (8), is enhanced by DsrA, especially at low temperatures (9). Thus, DsrA has opposite effects on these two targets, both mediated by RNA-RNA interactions, with global regulatory consequences for the transcriptional state of the cell. Whereas the mechanism of DsrA action at hns is not known, DsrA binds the translational operator of rpoS (4,5) to open a stable stem-loop of rpoS RNA (10), enabling access to the Shine-Dalgarno sequence and thus enhancing translation.Structure predictions based on thermodynamic criteria suggest that DsrA consists of three stem-loops, the third of which is the transcription terminator of DsrA ( Fig. 1A; ref. 11). The hns complementary region, in the center of the molecule, resides within the predicted second stem-loop, whereas the rpoS complementary region occupies the predicted first stemloop and the base of the second stem (4, 5). However, no additional structural data are currently available for DsrA. Mapping of the different regions of complementarity on the structure of DsrA is important for understanding how such a small RNA molecule interacts with multiple targets, and how such interactions might be regulated.Here we show that the basis of D...