The T box riboswitch: A novel regulatory RNA that utilizes tRNA as its ligand

Henkin, Tina M.

doi:10.1016/j.bbagrm.2014.04.022

Cited by 45 publications

(65 citation statements)

References 46 publications

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“…In addition, tRNAs and tRNA-derived fragments also serve regulatory roles in E. coli 1,2 and other bacteria (recently reviewed in refs. 3,4 ). For example, in E. coli , uncharged tRNA at the ribosomal A-site is the signal that stimulates RelA to produce guanosine tetraphosphate (ppGpp), which initiates the stress response to amino acid starvation.…”

Section: Introductionmentioning

confidence: 99%

Transfer RNA instability as a stress response inEscherichia coli: Rapid dynamics of the tRNA pool as a function of demand

2018

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Production of the translation apparatus of E. coli is carefully matched to the demand for protein synthesis posed by a given growth condition. For example, the fraction of RNA polymerases that transcribe rRNA and tRNA drops from 80% during rapid growth to 24% within minutes of a sudden amino acid starvation. We recently reported in Nucleic Acids Research that the tRNA pool is more dynamically regulated than previously thought. In addition to the regulation at the level of synthesis, we found that tRNAs are subject to demand-based regulation at the level of their degradation. In this point-of-view article we address the question of why this phenomenon has not previously been described. We also present data that expands on the mechanism of tRNA degradation, and we discuss the possible implications of tRNA instability for the ability of E. coli to cope with stresses that affect the translation process.

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Section: Introductionmentioning

confidence: 99%

Transfer RNA instability as a stress response inEscherichia coli: Rapid dynamics of the tRNA pool as a function of demand

2018

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“…The apical region of Stem I contains the conserved AG bulge and terminal loop (6), which interdigitate to create a platform that interacts with the tRNA elbow in the glycyl-tRNA synthetase gene (glyQS) T box RNA (18,21). However, it is unclear whether glyQS structural information is generally applicable to other T box RNAs because of the absence of the Stem II and IIA/B conserved domains (15) and an unusual arrangement of sequences in the apical portion of Stem I that differs from the consensus T box arrangement (22).…”

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confidence: 99%

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

Sherwood¹,

Grundy

Henkin

2015

Proc. Natl. Acad. Sci. U.S.A.

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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.

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“…The SL codon is followed by the conserved purine which is a guanosine (instead of adenosine in B. subtilis and G. kaustophilus). As has been described for the B. subtilis glyQS T-box, the characteristic stem II and pseudoknot stem IIA/B are also absent from S. aureus glyS T-box (Henkin 2014). It has been proposed that the absence of stem II and pseudoknot stem IIA/B indicates that no additional trans-acting factors mediate the binding of the T-box with the tRNA Gly (Grundy and Henkin 2004;Vitreschak et al 2008).…”

Section: Identification Of the Glys Leader Sequence And Transcriptionmentioning

confidence: 80%

“…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).…”

Section: Introductionmentioning

confidence: 99%

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

Apostolidi

Saad

Drainas

et al. 2015

RNA

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In Staphylococcus aureus, a T-box riboswitch exists upstream of the glyS gene to regulate transcription of the sole glycyl-tRNA synthetase, which aminoacylates five tRNA Gly isoacceptors bearing GCC or UCC anticodons. Subsequently, the glycylated tRNAs serve as substrates for decoding glycine codons during translation, and also as glycine donors for exoribosomal synthesis of pentaglycine peptides during cell wall formation. Probing of the predicted T-box structure revealed a long stem I, lacking features previously described for similar T-boxes. Moreover, the antiterminator stem includes a 42-nt long intervening sequence, which is staphylococci-specific. Finally, the terminator conformation adopts a rigid two-stem structure, where the intervening sequence forms the first stem followed by the second stem, which includes the more conserved residues. Interestingly, all five tRNA Gly isoacceptors interact with S. aureus glyS T-box with different binding affinities and they all induce transcription readthrough at different levels. The ability of both GCC and UCC anticodons to interact with the specifier loop indicates ambiguity during the specifier triplet reading, similar to the unconventional reading of glycine codons during protein synthesis. The S. aureus glyS T-box structure is consistent with the recent crystallographic and NMR studies, despite apparent differences, and highlights the phylogenetic variability of T-boxes when studied in a genome-dependent context. Our data suggest that the S. aureus glyS T-box exhibits differential tRNA selectivity, which possibly contributes toward the regulation and synchronization of ribosomal and exoribosomal peptide synthesis, two essential but metabolically unrelated pathways.

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The T box riboswitch: A novel regulatory RNA that utilizes tRNA as its ligand

Cited by 45 publications

References 46 publications

Transfer RNA instability as a stress response inEscherichia coli: Rapid dynamics of the tRNA pool as a function of demand

Transfer RNA instability as a stress response inEscherichia coli: Rapid dynamics of the tRNA pool as a function of demand

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

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

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The T box riboswitch: A novel regulatory RNA that utilizes tRNA as its ligand

Cited by 45 publications

References 46 publications

Transfer RNA instability as a stress response inEscherichia coli: Rapid dynamics of the tRNA pool as a function of demand

Transfer RNA instability as a stress response inEscherichia coli: Rapid dynamics of the tRNA pool as a function of demand

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

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

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