Abstract
BackgroundAutogenous cis-regulators of ribosomal protein synthesis play a critical role in maintaining the stoichiometry of ribosome components. Structured portions within an mRNA transcript typically interact with specific ribosomal proteins to prevent expression of the entire operon, thus balancing levels of ribosomal proteins across transcriptional units. Three distinct RNA structures from different bacterial phyla have demonstrated interactions with S15 to regulate gene expression; however, these RNAs are distributed across a small fraction of bacterial diversity.ResultsWe used comparative genomics in combination with analysis of existing transcriptomic data to identify three novel putative RNA structures associated with the S15 coding region in microbial genomes. These structures are completely distinct from those previously published and encompass potential regulatory regions including ribosome-binding sites. To validate the biological relevance of our findings, we demonstrate that an example of the Alphaproteobacterial RNA from Rhizobium radiobacter specifically interacts with S15 in vitro, and allows in vivo regulation of gene expression in an E. coli reporter system. In addition, structural probing and nuclease protection assays confirm the predicted secondary structure and indicate nucleotides required for protein interaction.ConclusionsThis work illustrates the importance of integrating comparative genomic and transcriptomic approaches during de novo ncRNA identification and reveals a diversity of distinct natural RNA regulators that support analogous biological functions. Furthermore, this work indicates that many additional uncharacterized RNA regulators likely exist within bacterial genomes and that the plasticity of RNA structure allows unique, and likely independently derived, solutions to the same biological problem.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-657) contains supplementary material, which is available to authorized users.
Highlights
Autogenous cis-regulators of ribosomal protein synthesis play a critical role in maintaining the stoichiometry of ribosome components
Comparative genomics identifies several putative RNA structures associated with rpsO To identify putative RNA structures associated with the coding region for ribosomal protein S15, we implemented a computational pipeline, GAISR (Genomic Analysis for Illuminating Structured RNA, Figure 2) for de novo ncRNA discovery and candidate refinement
We used GAISR to examine the genomic region corresponding to the 5′-untranslated region of the gene encoding S15, rpsO, in fully sequenced bacterial genomes
Summary
Autogenous cis-regulators of ribosomal protein synthesis play a critical role in maintaining the stoichiometry of ribosome components. Over the last two decades numerous RNA regulators have been discovered that range in function from directing development in eukaryotes [1], to controlling bacterial virulence [2] and metabolism [3] These RNA regulators vary considerably in their sizes (from less than 20 to greater than 200 nucleotides), required processing proteins (e.g. Argonaut, Dicer, RNase P), and mechanisms of action (inhibition of transcription or translation; utilization of Watson-Crick base-pairing to recognize the transcript of interest, or the formation of complex tertiary structure to enable specific protein-binding or metabolite-sensing) [4,5,6,7]. These include methionine biosynthesis, which is regulated by at least three completely distinct S-adenosyl methionine (SAM)-binding riboswitch architectures [8,9,10,11], and glucosamine metabolism where both a glucosamine-6-phosphate responsive ribozyme [12] and a series of small RNAs [13] regulate the same pathway in different bacterial species
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