RNA structures regulating ribosomal protein biosynthesis in bacilli

Abstract

In Bacilli, there are three experimentally validated ribosomal-protein autogenous regulatory RNAs that are not shared with E. coli. Each of these RNAs forms a unique secondary structure that interacts with a ribosomal protein encoded by a downstream gene, namely S4, S15, and L20. Only one of these RNAs that interacts with L20 is currently found in the RNA Families Database. We created, or modified, existing structural alignments for these three RNAs and used them to perform homology searches. We have determined that each structure exhibits a narrow phylogenetic distribution, mostly relegated to the Firmicute class Bacilli. This work, in conjunction with other similar work, demonstrates that there are most likely many non-homologous RNA regulatory elements regulating ribosomal protein biosynthesis that still await discovery and characterization in other bacterial species.

Keywords: Bacillus subtilis; Geobacillus stearothermophilus; Infernal; Rfam; gram-positive; ribosomal leader sequence; ribosomal protein.

Figure 1. Consensus sequence and secondary structures of Bacilli ribosomal regulatory elements. Start codons (AUG) are depicted inside a black box when occurring within the RNA structure. Gray boxes indicate areas of high conservation and possible binding. Dotted boxes surround areas proposed to be important for binding. Co-varying base pairs are shaded red or green only when Watson-Crick base pairing is in > 95% of the aligned sequences. Helix numbering is consistent with previously published data for each RNA.

Figure 2. Phylogenetic distribution of Bacilli autogenous ribosomal regulators. (A) Distribution of autogenous regulators of ribosomal protein synthesis in eubacterial phyla. (B) Distribution of autogenous regulators of ribosomal protein synthesis for classes within the phylum Firmicutes.