Tandem Riboswitch Architectures Exhibit Complex Gene Control Functions

Abstract

Riboswitches are structured RNAs typically located in the 5' untranslated regions of bacterial mRNAs that bind metabolites and control gene expression. Most riboswitches sense one metabolite and function as simple genetic switches. However, we found that the 5' region of the Bacillus clausii metE messenger RNA includes two riboswitches that respond to S-adenosylmethionine and coenzyme B12. This tandem arrangement yields a composite gene control system that functions as a two-input Boolean NOR logic gate. These findings and the discovery of additional tandem riboswitch architectures reveal how simple RNA elements can be assembled to make sophisticated genetic decisions without involving protein factors.

Design criteria for synthetic riboswitches acting on transcription

“…Hence, these elements obviously do not show cooperative binding effects, similar to their natural tandem counterparts consisting of complete riboswitch repeats. 33,36 The simple repeat of identical or nearly identical riboswitch elements leads to a considerable improvement of the functionality of our synthetic regulators. The serial arrangement of individual terminators causes a drastically reduced read-through during transcription, and, consequently, a very low reporter gene activity in the absence of theophylline.…”

“…The same phenomenon is discussed for natural arrangements consisting of complete riboswitches responding to the same ligand, as in the case of tandem TPP riboswitches. 33 Compared to single riboswitch elements, these combinations can sense various ligand concentrations with a correlating signal output.…”

“…[35][36][37] A third naturally occurring tandem arrangement is represented by a TPP riboswitch repeat. 38,33 Surprisingly, while the tandems consisting of complete riboswitch repeats show an independent function of each unit, the glycine riboswitches with 2 neighboring aptamer domains exhibit a In order to obtain functional riboswitches that act in a ligand-dependent manner, 2 parameters have to be considered. The stability of the terminator hairpin has to be adjusted to the stability of the competing structure of the ligand-bound aptamer.…”

“…The 5 0 -located element binds S-adenosylmethionine, while the second riboswitch recognizes coenzyme B12. 33 The independent gene regulation by these 2 elements represents a Boolean NOR gate, inhibiting the synthesis of metE in the presence of one of the ligands. 34 The second type of tandem arrangement is found in glycine riboswitches, where only the aptamer domain is present in 2 copies, followed by a single regulatory domain (containing a terminator or a ribosomal binding site).…”

Identification of a tertiary interaction important for cooperative ligand binding by the glycine riboswitch

“…The search found a widespread motif termed gcvT, upstream of bacterial genes expressing enzymes involved in the metabolism of glycine ). The motif is represented by two similar structural types (I and II) often found in a tandem arrangement, which have a common core flanked by different termini Sudarsan et al 2006;Welz and Breaker 2007;Tripp et al 2009). The secondary structure of the glycine riboswitch typically comprises two glycine-binding aptamers, followed by a single expression platform (Fig.…”