User:Michelle Meyer BC/L1

The L1-binding autogenous regulatory RNA consists of a 6-12 base-pair stem with an internal bulge. This bulge contains a potential non-canonical ‘G-A’ pair followed by an unpaired adenosine. These nucleotides and the base pairs immediately on either side of the bulge form a hydrogen bond network that is critical for protein binding. For many phyla only a few organisms were identified, but the small size and minimal sequence conservation of this RNA makes it difficult to find via computational methods. Thus, its presence in other organisms is likely. L1-binding RNAs have been identified in many bacterial phyla and archaea , and much work has been done to determine its function. This RNA is located on the E. coli operon containing rplK (L11) and rplA (L1), which are transcribed together in both E. coli and Firmicutes. In E. coli, the L1-binding RNA precedes rplK, and binding of L1 prevents translation of both L1 and L11. In the archaea Methanococcus vannielii, rplK and rplA are not co-localized in the geonome. The RNA structure directly precedes rplA, which is cotranscribed with rplJ and rplL. However, since the E. coli and M. vannielii L1-binding sites are similar, cross-species interaction studies between their proteins and RNAs show functionality. The L1-binding RNA exhibits an inconsistent genomic locus, where it can precede either rplK or rplA in most eubacteria. In Firmicutes, both binding sites have been identified in >40% of completed genomes, and the interaction between L1 ribosomal protein and the two RNA structures originating from Geobacillus kaustophilus was confirmed using filter-binding assays. Point-mutations to the consensus-binding site abolishes these interactions. This indicates that both sites are biologically relevant and play a role in L1 regulation in Firmicutes.