An evolving tale of two interacting RNAs—themes and variations of the T‐box riboswitch mechanism

Abstract

T‐box riboswitches are a widespread class of structured noncoding RNAs in Gram‐positive bacteria that regulate the expression of amino acid‐related genes. They form negative feedback loops to maintain steady supplies of aminoacyl‐transfer RNAs (tRNAs) to the translating ribosomes. T‐box riboswitches are located in the 5′ leader regions of mRNAs that they regulate and directly bind to their cognate tRNA ligands. T‐boxes further sense the aminoacylation state of the bound tRNAs and, based on this readout, regulate gene expression at the level of transcription or translation. T‐box riboswitches consist of two conserved domains—a 5′ Stem I domain that is involved in specific tRNA recognition and a 3′ antiterminator/antisequestrator (or discriminator) domain that senses the amino acid on the 3′ end of the bound tRNA. Interaction of the 3′ end of an uncharged but not charged tRNA with a thermodynamically weak discriminator domain stabilizes it to promote transcription readthrough or translation initiation. Recent biochemical, biophysical, and structural studies have provided high‐resolution insights into the mechanism of tRNA recognition by Stem I, several structural models of full‐length T‐box‐tRNA complexes, mechanism of amino acid sensing by the antiterminator domain, as well as kinetic details of tRNA binding to the T‐box riboswitches. In addition, translation‐regulating T‐box riboswitches have been recently characterized, which presented key differences from the canonical transcriptional T‐boxes. Here, we review the recent developments in understanding the T‐box riboswitch mechanism that have employed various complementary approaches. Further, the regulation of multiple essential genes by T‐boxes makes them very attractive drug targets to combat drug resistance. The recent progress in understanding the biochemical, structural, and dynamic aspects of the T‐box riboswitch mechanism will enable more precise and effective targeting with small molecules. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1167–1180, 2019

Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions

“…Riboswitches are cis -acting noncoding elements found in the 5′-UTR of some mRNAs (mostly in prokaryotes) [ 128 , 129 , 130 ]. They regulate the transcription, translation or splicing of downstream genes through direct binding of small-molecule metabolites [ 131 ] or tRNAs [ 132 , 133 ] to an aptamer domain, which in turn controls a conformational switch in the expression platform. Most riboswitches function with a single aptamer but some are organized into a tandem arrangement of two to three aptamers that bind the same or even different metabolites, thus linking two or more metabolic pathways [ 134 ].…”

Unboxing the T‐box riboswitches—A glimpse into multivalent and multimodal RNA–RNA interactions

“…The T-box riboswitches are modular RNA devices that consist of an obligate 5 0 Stem I domain which decodes the tRNA identity (Grigg & Ke, 2013;Lehmann, Jossinet, & Gautheret, 2013;Zhang & Ferré-D'Amaré, 2013), an optional intervening Stem II domain which reinforces Stem I-tRNA interactions (Battaglia, Grigg, & Ke, 2019;Suddala & Zhang, 2019a), and an essential 3 0 discriminator domain which senses tRNA aminoacylation and executes genetic switching ( Figure 1) (Battaglia et al, 2019;Li et al, 2019;Zhang & Ferré-D'Amaré, 2014). While the 3 0 -most discriminator domain employs a core architecture that is essentially identical among all known T-boxes, the Stem I and II domains are variable and exhibit interchangeability and characteristics of plug-and-play ( Figure 2; Gutierrez-Preciado et al, 2009;Vitreschak et al, 2008).…”

Another layer of complexity inStaphylococcus aureusmethionine biosynthesis control: unusual RNase III-driven T-box riboswitch cleavage determinesmetoperon mRNA stability and decay

“…Terminator stem presence in read-through transcripts might be explained by the high thermodynamic stability of the terminator stem (free energy Δ G = –32.60 kcal/mol) which is associated with its length and GC-richness (Figure 2B ). Formation of the antiterminator is likely to be transient as it is the thermodynamically much weaker structure which is only required to allow the RNA polymerase to pass the distal expression platform of the T-box riboswitch to accomplish downstream gene transcription ( 8 ). At the same time, immediate terminator stem formation in read-through transcripts will release uncharged tRNAs from the T-box riboswitch which will then be available for amino acid charging, once sufficient amounts of the cognate amino acid is synthesized ( 8 ).…”

“…Formation of the antiterminator is likely to be transient as it is the thermodynamically much weaker structure which is only required to allow the RNA polymerase to pass the distal expression platform of the T-box riboswitch to accomplish downstream gene transcription ( 8 ). At the same time, immediate terminator stem formation in read-through transcripts will release uncharged tRNAs from the T-box riboswitch which will then be available for amino acid charging, once sufficient amounts of the cognate amino acid is synthesized ( 8 ). In this respect, terminator stem formation in met leader/ met operon read-through transcripts makes sense.…”

“…The crucial checkpoint in this hierarchical string of regulatory events, however, is the T-box riboswitch, which acts in a highly selective and strictly methionine-dependent manner to control met operon transcription. T-box riboswitches represent unique RNA-based bacterial transcription control platforms that interact with tRNAs as ligands to regulate downstream gene expression (see references ( 8 , 9 ) for recent reviews). In brief, T-box riboswitches are located in 5′ untranslated regions (UTRs) of genes where they (usually) control transcription by forming either a transcription terminator (system OFF: premature transcription termination) or an antiterminator (system ON: read-through into downstream genes).…”