RNA structures regulating ribosomal protein biosynthesis

Abstract

Most commonly known for being the blueprint for proteins, RNA also plays vital roles in gene regulation. Non-coding RNAs, functional RNA molecules that are not translated into proteins, are potential regulatory agents in bacteria. Ribosomal autogenous regulatory elements are short transcribed sequences between the promoter and a protein coding region that regulate expression of their associated gene(s), though they are not themselves translated. These sequences form RNA secondary structures that can regulate at either the transcriptional or translational level. These riboregulators have been well characterized in gram-negative bacteria such as Escherichia coli, but in gram-positive bacteria far less is known regarding how r-proteins are regulated. My main goal has been to find riboregulators of r-protein synthesis in Bacilli and determine their consensus structures and phylogenetic distributions. I have utilized the RNA homology search program Infernal, coupled with our high-capacity genomic context visualization tool, to identify homologues of ribosomal-protein autogenous regulatory RNAs found in Bacilli. The alignments produced from this work determine consensus secondary structures and phylogenetic distribution of these regulator RNAs that provide new insight into the structure and function of these RNAs.