Table 1.
Major classes and distribution of ribozymes and RNA switches
| Class | Group | Members | Main functions | Natural ligand | Size (nucleotides) | Distribution |
|---|---|---|---|---|---|---|
| Cleaving ribozymes | ||||||
| Self-cleaving | Satellite RNAs | Hammerhead | Gene control (?); processing of multimeric transcripts during rolling-circle replication | 65 | Viroids, plant viral satellite RNA, eukaryotes (plants, crickets, amphibians, schistosomes) | |
| Hairpin | 75 | Plant viral satellite RNA | ||||
| VS | 155 | Satellite RNA of Neurospora spp. mitochondria | ||||
| HDV | 85 | Human satellite virus | ||||
| mRNAs | CoTC | Transcription termination (?) | GTP | 190 | Primates | |
| CPEB3 | Splicing regulation (?) | 70 | Mammals | |||
| glmS | Gene control | GlcN6P | 170 | Gram+ bacteria | ||
| Trans-cleaving | RNase P | tRNA processing | 140–500 | Prokaryotes, eukaryotes | ||
| Splicing ribozymes | ||||||
| Group I | Self-splicing | Guanosine | 200–1500 | Organelles (fungi, plants, protists), bacteria, bacteriophages, mitochondria (animals) | ||
| Group II | Self-splicing | 300–3000 | Organelles (fungi, plants, protists), bacteria, archaea | |||
| RNA switches | ||||||
| Thermosensors | Gene control | Variable | Phages, bacteria, eukaryotes | |||
| sRNAs | Gene control | Hfq | >85 | Bacteria | ||
| T-boxes | Gene control | tRNA | 190 | Mostly Gram+ bacteria | ||
| Metabolites | Coenzymes | TPP | Gene control | TPP | 100 | Bacteria, archaea, eukaryotes (fungi, plants) |
| FMN | Gene control | FMN | 120 | Bacteria | ||
| AdoCbl | Gene control | AdoCbl | 200 | Bacteria | ||
| SAM-I | Gene control | SAM | 105 | Mostly Gram+ bacteria | ||
| SAM-II | Gene control | SAM | 60 | α- and β-proteobacteria | ||
| SAM-III (SMK) | Gene control | SAM | 80 | Gram– bacteria | ||
| Amino acids | Lysine | Gene control | Lysine | 175 | γ-proteobacteria, Thermotogales, Firmicutes | |
| Glycine (I+II) | Gene control | Glycine | 110 | Bacteria | ||
| Nucleobases | Guanine | Gene control | Guanine, hypoxanthine | 70 | Gram+ bacteria | |
| Adenine | Gene control | Adenine | 70 | Bacteria | ||
| preQ1 | Gene control | preQ1 | 35 | Bacteria | ||
| Magnesium | mgtA | Gene control | Mg2+ | 70 | Gram– bacteria | |
AdoCbl, adenosylcobalamin; CoTC, co-transcriptional cleavage; FMN, flavin mononucleotide; GlcN6P, glucosamine-6-phosphate; Gram−, Gram-negative; Gram+, Gram-positive; HDV, hepatitus δ virus; Hfq, host factor Q, interacting with some sRNAs; preQ1, pre-quenosine-1; SAM, S-adenosylmethionine; sRNA, small RNA; TPP, thiamine pyrophosphate; VS,Varkud satellite. ? indicates an unconfirmed function.