The T-Box Riboswitch: tRNA as an Effector to Modulate Gene Regulation

Kiel D. Kreuzer; Tina M. Henkin

doi:10.1128/microbiolspec.RWR-0028-2018

Chapter 6 : The T-Box Riboswitch: tRNA as an Effector to Modulate Gene Regulation

Authors: Kiel D. Kreuzer¹, Tina M. Henkin³

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Affiliations: 1: Department of Microbiology and Center for RNA Biology; 2: Molecular, Cellular and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH 43210; 3: Department of Microbiology and Center for RNA Biology

Content Type: Monograph

Publication Year: 2019

Category: Microbial Genetics and Molecular Biology

Book DOI: 10.1128/9781683670247

Chapter DOI: 10.1128/microbiolspec.RWR-0028-2018

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Abstract:

Bacteria have evolved a wide array of mechanisms to control gene expression in response to environmental changes. These regulatory mechanisms ensure that specific genes are expressed under the appropriate physiological conditions, and they regulate every step of expression from transcription initiation to posttranslational modification and protein stability. The discovery of the T-box mechanism revealed that an uncharged tRNA can interact with an mRNA to regulate expression of the downstream coding region ( 1 ) ( Fig. 1 ). This mechanism was the first of many regulatory systems to be discovered in which cis-encoded RNA responds directly to a physiological signal to control gene expression through structural rearrangements. Regulatory RNAs of this type, termed riboswitches, have become an intense focus of research, and to date dozens of riboswitch classes that respond to various signals have been identified and characterized, including those that respond to temperature, pH, and metabolites such as enzyme cofactors, amino acids, and nucleotides ( 2 ).

Citation: Kreuzer K, Henkin T. 2019. The T-Box Riboswitch: tRNA as an Effector to Modulate Gene Regulation, p 89-100. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0028-2018

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The T-Box Riboswitch: tRNA as an Effector to Modulate Gene Regulation

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Figure 1

The T-box mechanism. (A) tRNA interacts with Stem I of the T-box leader RNA at two locations. The tRNA anticodon base-pairs with the Specifier Sequence (green), and the tRNA elbow stacks with the Stem I platform (orange), which is formed by interactions between conserved sequence motifs. The presence of an amino acid (AA) at the 3′ end of a charged tRNA blocks the base-pairing interaction with a bulge in the antiterminator helix. The terminator helix forms and transcription terminates, which turns gene expression off. (B) Uncharged tRNA also interacts with the Specifier Sequence and Stem I platform, and the acceptor arm base-pairs with a bulge in the antiterminator helix (cyan). The stabilization of the antiterminator prevents formation of the competing terminator helix, and RNA polymerase continues to transcribe the downstream coding sequence.

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Figure 1

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Figure 2

B. subtilis tyrS leader RNA and tRNATyr secondary structure. (A) The tyrS sequence is numbered from the transcriptional start site to the end of the transcriptional terminator element. Conserved structural domains are labeled, including Stems I, II, IIA/B, and III and mutually exclusive terminator and antiterminator helices. The Stem IIB pseudoknot interaction is shown in magenta. The Specifier Sequence in the Specifier Loop and residues in the antiterminator bulge that base-pair with tRNA are shown in green and cyan, respectively. The orange sequences in the AG bulge and Stem I terminal loop interact to form the Stem I platform, which contacts the tRNA elbow. The red- and blue-labeled sequences interact to form the antiterminator element shown above the terminator conformation. The antiterminator is composed of helices A1 and A2. (B) Cloverleaf structure of tRNATyr. The anticodon sequence is shown in green, and the nucleotides in the acceptor arm that base-pair with the tyrS antiterminator bulge are shown in cyan. The orange residues in the D-loop and T-loop (G19 and C56) interact to form the outermost tertiary interaction of the elbow and stack with the Stem I platform.

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Figure 2

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Figure 3

Cocrystal structure of the glyQS Stem I-tRNA complex. The G. kaustophilus glyQS Stem I (gray) is bound to tRNAGly (purple). The Specifier Sequence-anticodon interaction is shown in green, and the Stem I platform that stacks with the tRNA elbow is shown in orange. Data from reference 11 (PDB ID: 4MGN).

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Figure 3

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