The Yfr2 ncRNA family, a group of abundant RNA molecules widely conserved in cyanobacteria

Sequence signatures, predicted secondary structures and experimental data suggest the Yfr2 family of non-coding RNAs (ncRNAs) to be present in nearly all cyanobacteria sequenced to date. The common features of the family members include a central consensus element (CCE), 5'-RKT SGA AAC WHG GHM ASA M-3', predicted to form a 12 nt single stranded region plus a short helical region consisting of three base pairs and one unpaired nucleotide that is either bulging or the begin of a short internal loop. Yfr2 family members are 63 to 100 nucleotides in size and they share a conserved region at the 5' end, starting with 5'-GUGAGGA-3' or a closely related motif. The genes for ncRNAs of this family are suggested to exist in highly variable copy numbers in the individual genomes, with up to nine copies in some marine Synechococcus.