An expanded collection and refined consensus model of glmS ribozymes

Abstract

Self-cleaving glmS ribozymes selectively bind glucosamine-6-phosphate (GlcN6P) and use this metabolite as a cofactor to promote self-cleavage by internal phosphoester transfer. Representatives of the glmS ribozyme class are found in Gram-positive bacteria where they reside in the 59 untranslated regions (UTRs) of glmS messenger RNAs that code for the essential enzyme L-glutamine:D-fructose-6-phosphate aminotransferase. By using comparative sequence analyses, we have expanded the number of glmS ribozyme representatives from 160 to 463. All but two glmS ribozymes are present in glmS mRNAs and most exhibit striking uniformity in sequence and structure, which are features that make representatives attractive targets for antibacterial drug development. However, our discovery of rare variants broadens the consensus sequence and structure model. For example, in the Deinococcus-Thermus phylum, several structural variants exist that carry additional stems within the catalytic core and changes to the architecture of core-supporting substructures. These findings reveal that glmS ribozymes have a broader phylogenetic distribution than previously known and suggest that additional rare structural variants may remain to be discovered.

Riboswitch diversity and distribution

“…For example, an E-value threshold of one could be expected by random chance to yield a single false positive in the data set examined. By increasing the E-value threshold and permitting a higher number of false positives, careful examination of the results may yield new functional members of a riboswitch class that were missed initially due to variation of a putative conserved sequence or substructure represented in the previous consensus model (McCown et al 2011). By iteratively searching for new representatives and adjusting the consensus model accordingly, distinct variants that were previously missed in searches based on an earlier model can be identified.…”

“…However, the riboswitch classes that sense these compounds all have noteworthy characteristics. The first such riboswitch detects the modified sugar compound glucosamine-6-phosphate (GlcN6P), which is selectively bound by RNA to regulate the expression of the glmS gene in many Gram-positive bacteria McCown et al 2011). Importantly, members of this riboswitch class are called glmS ribozymes because they also function as selfcleaving RNAs ) that use the sugar ligand as a cofactor to promote RNA strand scission (Klein and Ferré-D'Amaré 2006;Cochrane et al 2007; Ferré-D'Amaré 2010; Bingaman et al 2017).…”

“…Bioinformatics updates of the consensus models and phylogenetic distributions for all riboswitch classes began with homology searches as previously described (McCown et al 2011(McCown et al , 2014Ruff et al 2016). Homology searches were conducted with INFERNAL 1.1 using the National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) Database release 56 (Pruitt et al 2009;O'Leary et al 2016) augmented with multiple environmental DNA sequence data sets (Nawrocki and Eddy 2013;Nelson et al 2013;McCown et al 2014).…”

Structural determinants for ligand capture by a class II preQ 1 riboswitch

“…Interestingly, the glmS ribozyme P4 hairpin is held rigidly in place in a markedly different orientation than the preQ 1 -II riboswitch, stabilized by tertiary interactions. The analogous J2-4 linker is limited to 1-4 nt, unlike the preQ 1 -II riboswitch, which has a longer linker (6-12 nt) (64). Finally, an in vitro evolved aptamer that binds the nerve growth factor protein also has a predicted secondary structure that is highly similar to that of preQ 1 -II, complete with adenines flanking P4 (65).…”

Prevalence of syn nucleobases in the active sites of functional RNAs

“…4A), which occurs in the 59 UTR of the gene that codes for the glucosamine synthetase enzyme (Barrick et al 2004;McCown et al 2011). High concentrations of glucosamine-6-phosphate (GlcN6P) bind the 59 UTR and induce the RNA to self-cleave, which silences gene expression.…”