T box riboswitches in Actinobacteria: Translational regulation via novel tRNA interactions

Abstract

The T box riboswitch regulates many amino acid-related genes in Gram-positive bacteria. T box riboswitch-mediated gene regulation was shown previously to occur at the level of transcription attenuation via structural rearrangements in the 5′ untranslated (leader) region of the mRNA in response to binding of a specific uncharged tRNA. In this study, a novel group of isoleucyl-tRNA synthetase gene (ileS) T box leader sequences found in organisms of the phylum Actinobacteria was investigated. The Stem I domains of these RNAs lack several highly conserved elements that are essential for interaction with the tRNA ligand in other T box RNAs. Many of these RNAs were predicted to regulate gene expression at the level of translation initiation through tRNAdependent stabilization of a helix that sequesters a sequence complementary to the Shine-Dalgarno (SD) sequence, thus freeing the SD sequence for ribosome binding and translation initiation. We demonstrated specific binding to the cognate tRNA Ile and tRNA Ile -dependent structural rearrangements consistent with regulation at the level of translation initiation, providing the first biochemical demonstration, to our knowledge, of translational regulation in a T box riboswitch.

A ribonucleopeptide world at the origin of life

“…One example supporting the RNPep world hypothesis is the existence of the T box riboswitch that reflects the expanding function of RNA beyond its sequence when it communicates through structural specificity with its cognate tRNA (Yousef et al, 2003;Saad et al, 2012). Interestingly, the T box riboswitch is a leader RNA that harbors a codon sequence by which it specifically recognizes its cognate tRNA to regulate gene expression through transcription attenuation (Henkin, 2014) and translation initiation inhibition (Sherwood et al, 2015). Therefore, during the RNPep world, one might assume that the T box riboswitch could be a relic of the first RNPep ribozymes capable of aminoacylating bound tRNAs.…”

A glyS T-box riboswitch with species-specific structural features responding to both proteinogenic and nonproteinogenic tRNAGly isoacceptors

“…Although previous bioinformatics analyses predicted the existence of such a T-box, they were based only on the recognition of the highly conserved T-box bulge sequence (Vitreschak et al 2008;Wels et al 2008;Sherwood et al 2015). In the case of the S. aureus glyS T-box, it was evident that stem I with the exception of the SL GGC codon did not exhibit the same conservation with other characterized T-boxes based on comparison with glyQS T-boxes from B. subtilis, O. iheyensis, and G. kaustophilus that have been structurally characterized (Fig.…”

“…They control transcription of downstream genes that either encode proteins involved in biosynthesis and transport of aa or aminoacyl-tRNA synthetases (aaRSs) which supply ribosomal protein synthesis with the aminoacylated tRNAs (aa-tRNAs) substrates (Henkin 2008(Henkin , 2014. Although their main regulatory mechanism is transcriptional attenuation, recently it was shown that the ileS T-box in Actinobacteria acts via sequestration of the Shine-Dalgarno sequence, thus modulating ribosome binding and translation initiation (Sherwood et al 2015).…”

“…Using this elegant system, bacteria (mainly gram positive) can control their metabolic rate under various environmental conditions (i.e., under amino acid starvation). On the other hand, stimulation of transcription of the gene under control is achieved only upon binding of cognate uncharged tRNAs to the specifier loop of the T-box, or via conformational changes which affect translational initiation (Sherwood et al 2015). By using the actual carriers of amino acids as ligands, bacteria can modulate the levels of their growth depending on the availability of amino acids as essential growth ingredients (Smith et al 2010;Raina and Ibba 2014).…”

A Tyrosine-Dependent Riboswitch Controls the Expression of a Tyrosyl-tRNA Synthetase from Acidithiobacillus ferrooxidans

“…Almost all T-box riboswitches studied to date regulate the expression of the corresponding gene at the level of transcription attenuation, with the exception of a T-box in Actinobacteria recently described, whose target is regulated at the translational level by blocking / deblocking the accessibility of the Shine-Dalgarno (SD) sequence in the mRNA to the ribosome. [7] The T-box mechanism is mostly present in Gram-positive bacteria and, although less common, by comparative genomic analysis it has been identified also in Gram-negative microorganisms. [8,9] Acidithiobacillus ferrooxidans is an acidophilic, Gram-negative, autotrophic, chemolithotrophic, facultative aerobic bacterium that participate in either natural or human-made bioleaching processes.…”