The T box mechanism: tRNA as a regulatory molecule

Abstract

The T box mechanism is widely used in Gram-positive bacteria to regulate expression of aminoacyl-tRNA synthetase genes and genes involved in amino acid biosynthesis and uptake. Binding of a specific uncharged tRNA to a riboswitch element in the nascent transcript causes a structural change in the transcript that promotes expression of the downstream coding sequence. In most cases, this occurs by stabilization of an antiterminator element that competes with formation of a terminator helix. Specific tRNA recognition by the nascent transcript results in increased expression of genes important for tRNA aminoacylation in response to decreased pools of charged tRNA.

Figure 1

Structural model of the B. subtilis tyrS leader RNA. The sequence is shown (and numbered) from the transcription start-point through the end of the leader region transcriptional terminator (U274); the coding sequence for TyrRS is further downstream. The structural model of the terminator conformation is shown; the alternate antiterminator conformation is shown above the terminator element. Structural domains (Stem I, Stem II, Stem IIA/B pseudoknot, Stem III) and conserved sequence and structural elements (GA motif, S-turns, AG bulge, Specifier Loop, T box) are labeled. Residues that are highly conserved are marked with asterisks (*). The pseudoknot pairing is shown in purple. Sequences on the 5′ side of the terminator (blue) also participate in pairing with a portion of the T box sequence (red) to form the antiterminator helix. The Specifier sequence residues (UAC tyrosine codon) are boxed. Residues that participate in pairing with the tRNA (UACA in the Specifier Loop, UGGU in the antiterminator bulge) are shown in green.

Figure 2

The T box mechanism. Expression of genes in the T box family is regulated by the ratio of charged to uncharged tRNA in the cell. A. Aminoacylated tRNA binds only to the Specifier Loop; the presence of the amino acid prevents interaction of the acceptor end of the tRNA with the antiterminator. The more stable terminator helix (blue-black) forms and transcription terminates. B. Uncharged tRNA interacts at both the Specifier Loop and the antiterminator; this stabilizes the antiterminator (red-blue) which sequesters sequences (blue) that otherwise participate in formation of the terminator helix, and transcription reads through the termination site and into the downstream coding sequence. Binding of uncharged tRNA results in structural changes throughout the leader RNA. The tRNA is shown in cyan; the amino acid (aa) is shown as a yellow circle attached to the 3′ end of the charged tRNA. Positions of base-pairing between the leader RNA and the tRNA (Specifier Loop-tRNA anticodon, antiterminator bulge-tRNA acceptor end) are shown as green lines.