Mechanism and distribution of glmS ribozymes

Abstract

Among the nine classes of ribozymes that have been experimentally validated to date is the metabolite-responsive self-cleaving ribozyme called glmS. This RNA is almost exclusively located in the 5'-untranslated region of bacterial mRNAs that code for the production of GlmS proteins, which catalyze the synthesis of the aminosugar glucosamine-6-phosphate (GlcN6P). Each glmS ribozyme forms a conserved catalytic core that selectively binds GlcN6P and uses this metabolite as a cofactor to promote ribozyme self-cleavage. Metabolite-induced self-cleavage results in down-regulation of glmS gene expression, and thus the ribozyme functions as a key riboswitch component to permit feedback regulation of GlcN6P levels. Representatives of glmS ribozymes also serve as excellent experimental models to elucidate how RNAs fold to recognize small molecule ligands and promote chemical transformations.

FIGURE 1

Key sequence and structural features of glmS ribozymes., its relation to an atomic-resolution structural model, and RNA contacts to GlcN6P. (A) Consensus sequence and secondary structure model for glmS ribozymes. The asterisk designates the site of self-cleavage. Optional hairpins (i) or optional hairpins and conserved nucleotides (ii) are present in some glmS ribozymes. When provided, numbered nucleotides correspond to positions from a previously reported glmS ribozyme structure (Klein and Ferré-D’Amaré 2006) as depicted in B. (B) Atomic-resolution structural model of a glmS ribozyme from T. tengcongensis (Klein et al. 2007; Protein Databank 3B4C). Nucleotides that are shaded in red are conserved in at least 97% of glmS ribozymes. Arrows depict the locations of optional sub-structures (i) and (ii) when present. (C) Model of the nucleotides forming the coenzyme-binding active site of the T. tengcongensis glmS ribozyme (Klein et al. 2007; Protein Databank 3B4C). Nucleotides are labeled and numbered according to the consensus model in A. Parts A and B are adapted from a previous publication (McCown et al. 2011).

FIGURE 2

Comparison of a canonical glmS ribozyme with an extreme variant. (A) The ribozyme from Thermoanaerobacter tengcongensis corresponds well to the consensus glmS ribozyme architecture typical of the vast majority of representatives. The asterisk identifies the site of self-cleavage and arrows denote zero-length connections. (B) A variant glmS ribozyme present in Truepera radiovictrix. Shaded regions identify sequences and structures that are substantially different from the typical glmS ribozyme consensus architecture.

FIGURE 3

Possible mechanism of cleavage for glmS ribozymes. Left: the reaction is initiated by deprotonation of the 2′ hydroxyl group of nucleotide A(-1). This creates a strong nucleophile for attack on the adjoining phosphorus center. The reaction is completed by protonation of the 5′ oxygen leaving group by the amine of GlcN6P. Right: Products of cofactor-mediated RNA chain cleavage. Dashed lines indicate continuation of the RNA chain.