Characterization of small RNAs as ribosomal regulators during gene expression in bacteria

Abstract

Ribosome-associated non-coding RNAs (rancRNAs) are a recently discovered class of small RNA (sRNA) that regulate translation via direct interactions with the ribosome. rancRNA-dependent mechanisms have been confirmed in all domains of life but are poorly understood in bacteria. Since the ribosome is highly conserved among the three domains of life, common rancRNA mechanisms likely exist. To identify such potential regulatory rancRNAs, the sRNA pools of Escherichia coli ribosomes isolated under different stress conditions were analyzed using next-generation sequencing. Bioinformatic analysis detected 67 sRNAs, including eight novel sRNAs. In parallel, rancRNA candidates were identified using previously published RNAseq datasets. One candidate, rttR, was confirmed to preferentially bind to the 70S ribosome in vitro. However, rttR does not influence protein production in vitro or in vivo. Structural in silico analysis predicts that rttR interacts with 16S ribosomal RNA helix 17, suggesting a function for rttR during ribosome biogenesis, which requires further investigation.