Tandem riboswitches form a natural Boolean logic gate to control purine metabolism in bacteria

Abstract

Gene control systems sometimes interpret multiple signals to set the expression levels of the genes they regulate. In rare instances, ligand-binding riboswitch aptamers form tandem arrangements to approximate the function of specific two-input Boolean logic gates. Here, we report the discovery of riboswitch aptamers for phosphoribosyl pyrophosphate (PRPP) that naturally exist either in singlet arrangements, or occur in tandem with guanine aptamers. Tandem guanine-PRPP aptamers can bind the target ligands, either independently or in combination, to approximate the function expected for an IMPLY Boolean logic gate to regulate transcription of messenger RNAs for de novo purine biosynthesis in bacteria. The existence of sophisticated all-RNA regulatory systems that sense two ancient ribonucleotide derivatives to control synthesis of RNA molecules supports the hypothesis that RNA World organisms could have managed a complex metabolic state without the assistance of protein regulatory factors.

Former orphan riboswitches reveal unexplored areas of bacterial metabolism, signaling, and gene control processes

“…For example, numerous representatives of eight novel RNA motifs were identified by comparing all intergenic regions from Bacillus subtilis with those from 90 additional bacterial species ). Seven of these eight motifs have since proven to represent distinct riboswitch classes (McCown et al 2017;Sherlock et al 2018a, Sherlock et al 2018b, Sherlock et al 2019).…”

“…Each of these riboswitch candidate classes, termed subtypes 2a through 2d, has distinct differences in the nucleotide positions corresponding to the binding pocket of guanidine-I aptamers that were predicted to alter ligand specificity. At this time, the ligands for subtypes 2a (Sherlock et al 2018a), 2b (Sherlock et al 2018b), and 2c (Sherlock et al 2019) have been established as noted below. The ligand for 2d has yet to be experimentally determined.…”

“…Subtype 2b ykkC RNAs regulate the expression of de novo purine biosynthesis genes in response to phosphoribosyl pyrophosphate (PRPP), a molecule necessary for the synthesis of all nucleotide monomers (Sherlock et al 2018b). High levels of PRPP, the activated ribose precursor for purine biosynthesis, trigger this riboswitch class to turn on all of the genes necessary to produce inosine monophosphate, which is at the branch point of AMP and GMP biosynthesis.…”

“…High levels of PRPP, the activated ribose precursor for purine biosynthesis, trigger this riboswitch class to turn on all of the genes necessary to produce inosine monophosphate, which is at the branch point of AMP and GMP biosynthesis. Frequently, a PRPP aptamer is located directly adjacent to a guanine aptamer (Mandal et al 2003), and the two aptamers share a single expression platform (terminator stem) to create a complex tandem riboswitch system that regulates purine metabolism according to the relative abundance of both the guanine and PRPP ligands (Sherlock et al 2018b).…”

“…For example, the initial consensus models for c-di-GMP (Weinberg et al 2007), SAM-VI (Mirihana Arachchilage et al 2018), and ykkC subtype 2 riboswitches were missing important structural features. In these cases, either the RNA constructs tested by in-line probing were fortuitously long enough to encompass the entire aptamer (Sudarsan et al 2008;Mirihana Arachchilage et al 2018), or additional conservation was found by comparative sequence analysis at a later time and the RNA constructs used for evaluation were adjusted accordingly (Sherlock et al 2018a(Sherlock et al , 2018b(Sherlock et al , 2019.…”