Table 1. Comparison of natural features exhibited by ligand-activated riboswitches and trans-encoded sRNAs.
| Differences | Ligand-binding riboswitches | Small RNAs (trans-encoded) |
|---|---|---|
| Functional role | • Regulate single gene transcript | • Regulate multiple gene transcripts |
| • When in tandem, exhibit complex gene control response | • Can be arranged in regulatory networks of high complexity | |
| • Triggered by a ligand | • Differentially expressed under certain stress conditions | |
| Structural mechanism | • Do not need chaperones | • Trans-encoded could require Hfq |
| • Undergo structural reconfigurations upon binding | • A diversity of mechanisms has been elucidated including target mRNA structural changes upon binding and indirect inhibition/enhancement of transcription; translation; and/or degradation | |
| • Direct triggering | • Indirect triggering: differentially expressed upon certain stress conditions (54) | |
| • Immediate response upon binding | • Potentially, concentration increase of Hfq upon environmental stress might increase sRNA activity | |
| • Single interaction between aptamer-metabolite activates response | • Multiple interactions: sRNA-Hfq, Hfq-mRNA and sRNA-mRNA base-pairing used to activate regulation | |
| • Highly specific pocket-like interaction with a small molecule | • High specificity for target mRNAs through reduced complementarity1 | |
| Structural | • One RNA motif: aptamer | • At least 2 RNA motifs: Hfq binding site and mRNA binding site. |
| • Usually one hairpin-like structure | • Usually more than one hairpin-like motif | |
| • Attached to mRNA | • Independent, stable RNAs (could be co-transcribed with non-target mRNAs) |
1 Reduced complementarity: few nucleotides (8–9) used for base-pairing with target43 in contrast with the eukaryotic counterpart. Also, often base-pairing is not perfect either, since it could include bulges. Note: sRNAs referred hereby are mRNA-binding molecules. Protein-binding class of sRNAs is not included here.