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Genomic regions of the identified S. meliloti sRNA genes. The schematics (drawn to scale) summarize the bioinformatic predictions and the results of the experimental mapping. The smr genes are represented by red arrows and the flanking ORFs by blue arrows. Numbers indicate co-ordinates in the S. meliloti 1021 genome database. Experimentally determined 5'- and 3'-ends of the Smr transcripts are indicated with numbers. 3'-ends of the differentially expressed sRNAs were assigned to the last U in the consecutive stretch after extended stem-loops of Rho-independent terminators, which are denoted by green dots above the horizontal lines. The grey arrowhead indicates the processing site for Smr7C.
Sinorhizobium meliloti is an agronomically relevant α-proteobacterium able to induce the formation of new specialized organs, the so-called nodules, in the roots of its cognate legume hosts (i.e. some Medicago species). Within the nodule cells bacteria undergo a morphology differentiation to bacteroid, their endosymbiotic nitrogen-fixing competent form.Rhizobial adaptations to soil and plant cell environments require the coordinate expression of complex gene networks in which sRNAs are expected to participate.
Two complementary computational screens, eQRNA and RNAz, were used to search for novel sRNA-encoding genes in the intergenic regions IGRs of S. meliloti. Verification of eQRNA/RNAz predictions by Northern hybridization and RACE mapping led to the identification of eight previously unknown genes, with recognizable promoter and termination signatures, expressing small transcripts. These new genomic loci were referred to as smr, for S. meliloti RNA. Seven of the Smr transcripts, which conservation is restricted to phylogenetically related α-proteobacteria, accumulated differentially in free-living and endosymbiotic bacteria. These findings anticipate a function for these sRNAs as trans-acting antisense riboregulators of α-proteobacteria-eukaryote interactions.