T box RNA decodes both the information content and geometry of tRNA to affect gene expression

Abstract

The T box leader sequence is an RNA element that controls gene expression by binding directly to a specific tRNA and sensing its aminoacylation state. This interaction controls expression of amino acid-related genes in a negative feedback loop. The T box RNA structure is highly conserved, but its tRNA binding mechanism is only partially understood. Known sequence elements are the specifier sequence, which recognizes the tRNA anticodon, and the antiterminator bulge, which base pairs with the tRNA acceptor end. Here, we reveal the crucial function of the highly conserved stem I distal region in tRNA recognition and report its 2.65-Å crystal structure. The apex of this region contains an intricately woven looploop interaction between two conserved motifs, the Adenine-guanine (AG) bulge and the distal loop. This loop-loop structure presents a base triple on its surface that is optimally positioned for basestacking interactions. Mutagenesis, cross-linking, and small-angle X-ray scattering data demonstrate that the apical base triple serves as a binding platform to dock the tRNA D-and T-loops. Strikingly, the binding platform strongly resembles the D-and T-loop binding elements from RNase P and the ribosome exit site, suggesting that this loop-loop structure may represent a widespread tRNA recognition platform. We propose a two-checkpoint molecular ruler model for tRNA decoding in which the information content of tRNA is first examined through specifier sequence-anticodon interaction, and the length of the tRNA anticodon arm is then measured by the distal loop-loop platform. When both conditions are met, tRNA is secured, and its aminoacylation state is sensed.riboswitch | RNA-RNA complex C ells must maintain appropriate intracellular pools of aminoacylated transfer RNA (aa-tRNA) to survive. This is usually accomplished by tight regulation of many cellular factors, including amino acid biosynthesis and transporter genes, and tRNA synthetases (1). Most Gram-positive bacteria use the T box regulatory system to control their aa-tRNA levels (2). T box elements are a special family of regulatory RNAs located in the 5′-untranslated region of the mRNA for a regulated gene or operon. Unlike small molecule-sensing riboswitches, T box RNAs recognize tRNAs containing the cognate anticodon and discriminate between uncharged tRNA and aa-tRNA. They usually control gene expression via premature transcription termination, although there are rare examples that are predicted to regulate at the level of translation initiation (2-4). The T box motif was initially identified in the Bacillus subtilis (Bsub) tyrosyl-tRNA synthetase gene (tyrS) and was shown to respond to the aminoacylation state of tyrosine tRNA (5, 6). More than 1,000 T box elements have since been identified (3, 4).Selective tRNA recognition is achieved through a collective effort from several conserved domains in the T box RNA [Geobacillus kaustophilus (Gkau) glyQS T box sequence is shown in Fig. 1]. Stem I is the largest element. It is an ∼100-nucleotide (nt) stem-loop s...

Two-codon T-box riboswitch binding two tRNAs

“…As expected from previous in vivo experiments (14), removal of the UGG sequence in NT-box Δ(UGG) resulted in an inability to bind Cac tRNA Asn (Fig. S2C).…”

“…A recent study showed that binding of tRNA to the T-box can also involve interactions between specific nucleotides of the stem I apical loop with the D-and T-loop nucleotides of the tRNA (14). These interactions were proposed to serve as a specific molecular ruler that ensures effective binding of the correct tRNA.…”

“…T-boxes bind specific, cognate tRNA molecules mainly at two conserved sites: the anticodon sequence, which forms base pairs with the codon sequence of the specifier loop (SL); and the tRNA's NCCA 3′ accepting end, which pairs with the UGGN sequence found in the antiterminator bulge (12,13). Recently, a two-checkpoint mechanism has been proposed to serve as a molecular ruler, ensuring appropriate tRNA accommodation through interaction of the apical loop with the D and T loop of the tRNA during the progress of transcription (14).…”

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

“…The first domain of a T-box (stem I) contains the specifier loop (SL) that varies in size and contains a codon-like nucleotide triplet. The SL is responsible for recognition of the bound tRNA through "scanning" of its anticodon sequence by Watson-Crick base-pairing with the tRNA anticodon (Grigg et al 2013;Zhang and Ferré-D'Amaré 2013). At the beginning of the stem I duplex, a kink turn (or K-turn) is formed.…”

Induced Transcriptional Expression of <i>Bacillus subtilis</i> Amino Acid Permease <i>yvbW</i> in Response to Leucine Limitation

“…The leader mRNA contains a codon designated the "specifier sequence" which base-pairs with the anticodon of the cognate tRNA [3] [5]. Additionally, the conserved acceptor end sequence of tRNA, NCCA where N is referred to as the discriminator base, base-pairs with a bulged region of the antiterminator (UGGN) with covariance observed between the two variable bases (N) of these sequences [4].…”