An allosteric self-splicing ribozyme triggered by a bacterial second messenger

Abstract

Group I self-splicing ribozymes commonly function as components of selfish mobile genetic elements. We identified an allosteric group I ribozyme, wherein self-splicing is regulated by a distinct riboswitch class that senses the bacterial second messenger c-di-GMP. The tandem RNA sensory system resides in the 5' untranslated region of the messenger RNA for a putative virulence gene in the pathogenic bacterium Clostridium difficile. c-di-GMP binding by the riboswitch induces folding changes at atypical splice site junctions to modulate alternative RNA processing. Our findings indicate that some self-splicing ribozymes are not selfish elements but are harnessed by cells as metabolite sensors and genetic regulators.

Fig. 1

c-di-GMP-II riboswitches. (A) Consensus sequence and secondary structure model for c-di-GMP-II riboswitch aptamers. Nucleotides in red are conserved in >97% of the representatives. Other annotations are described in fig. S2. (B) Wild-type (WT) 84 Cd RNA encompassing the motif upstream of a possible virulence gene. Disruptive (M2) and restorative (M3) mutations are depicted, and sites of spontaneous cleavage are derived from C. Asterisks identify nucleotides added to facilitate in vitro transcription. (C) Denaturing polyacrylamide gel electrophoresis (PAGE) of WT 84 Cd RNA in-line probing cleavage products. Notations: no reaction (NR); partial digestion with RNase T1 (T1, cleaves after G residues); alkali (⁻ OH, cleaves at all linkages); incubation in the absence (− ) or presence (+) of 10 μM c-di-GMP. Selected RNase T1 digestion product bands are identified. (D) Plot of the fraction of RNA remaining unbound versus the logarithm of the concentration of c-di-GMP present during in-line probing (fig. S3). (E) K_D values for 84 Cd binding to c-di-GMP and various analogs.

Fig. 2

Architecture, mechanism and activity of a tandem riboswitch-ribozyme. (A) Tandem c-di-GMP-II aptamer and group I ribozyme arrangement. (B) Key features of the aptamer-ribozyme system including validated splice and GTP attack sites (fig. S8). Alternative base pair interactions guiding allosteric function are shaded blue and green. (C) PAGE separation of products generated by self-splicing assays. NR indicates no reaction; C-IVS and L-IVS designate circular and linear intervening sequences, respectively; Pre designates the 864-nt precursor RNA (fig. S5); 5′E-3′E designates spliced exons; 3′E* designates a 3′ fragment generated by GTP attack at an alternative site; Fragments designate additional RNA products presumably created by IVS circularization. Data for some mutants is presented elsewhere (fig. S11).

Fig. 3

Rate constant modulation by c-di-GMP. (A) Time course of [α-³²P]GTP attack at sites GTP₁ or GTP₂ in the absence or presence of c-di-GMP. (B) Plot of the natural logarithm of the fraction of unprocessed or differently processed RNA (“pre-dp RNA”) versus time for the reaction in A. Values for fraction processed were corrected for ~50% of the precursor remaining after exhaustive incubation. (C) Time course of the production of spliced exons (5′E-3′E) or alternative GTP₂ site fragment (3′E*) in the absence or presence of c-di-GMP. Annotations are as described for Fig. 2C. (D) Plot of the natural logarithm of the fraction of unprocessed or differently processed RNA versus time for the reaction in C, corrected as described in B. (E) Changes in splice product yields on introduction of c-di-GMP. Left: ratio of the number of 3′E* molecules versus the number of 5′E-3′E spliced exon molecules in the absence or presence of c-di-GMP, respectively. Right: ratio of the numbers of 3′E* molecules and the ratio of the numbers of 5′E-3′E spliced exon molecules in the absence or presence of c-di-GMP, respectively.

Fig. 4

Proposed mechanism for allosteric ribozyme-mediated gene control. (A) Precursor mRNA with the start codon sequestered by the ribozyme P10 stem. (B) RNA processed in the presence of GTP and c-di-GMP unmasks the start codon and creates a perfect ribosome binding site. (C) RNA processed in the presence of GTP alone lacks a ribosome binding site.