Table 1.
The natural occurrence of ribozymes and riboswitches
| Type | Species* | Rfam accession number† | |
| Ribozyme | Group I intron | Thermus thermophila [1] | RF00028 |
| More than 20,000 sequences from all three kingdoms‡ | |||
| Didymium iridis (branching enzyme, group I intron derivative) [46] | |||
| Group II intron | Saccharomyces cerevisiae mitochondria [17,18] | RF00029 | |
| More than 8,000 sequences from all three kingdoms‡ | |||
| Hammerhead | Tobacco ringspot virus satellite RNA (sTRSV) [3] | RF00008 | |
| Several additional satellite RNAs of plant viruses§ | RF00163 | ||
| Viroids of the Avsunviroidae family [99,100] | |||
| Carnation small viroid-like RNA (CarSV RNA) [101] | |||
| Satellite DNAs of various amphibian species [102,103], Schistosoma mansoni [30] and Dolichopoda cave crickets [31] | |||
| Arabidopsis thaliana genome [33] | |||
| Hairpin | Tobacco ringspot virus satellite RNA (sTRSV) [4] | RF00173 | |
| Two additional satellite RNAs of plant viruses: sCYMV and sARMV [104] | |||
| HDV | Human hepatitis delta virus RNA [6] | RF00094 | |
| Homo sapiens genome (intronic) [29] | |||
| RNase P | Escherichia coli [2] | RF00010 | |
| More than 1,000 sequences from various Bacterial phyla¶ | RF00011 | ||
| Archeal phyla: Crenarchaeota, Euryarchaeota [105] | RF00373 | ||
| VS | Neurospora crassa Varkud satellite [8] | NL | |
| Catalytic riboswitch | Glms riboswitch | Bacillus subtilis [14] | RF00234 |
| Bacterial phyla: Actinobacteria, Firmicutes | |||
| Riboswitch | Adenine¥ | B. subtilis [106] | RF00167 |
| Bacterial phyla: Proteobacteria, Firmicutes | |||
| Coenzyme B12 | E. coli and Salmonella typhimurium btuB mRNAs [107] | RF00174 | |
| Bacterial phyla: Actinobacteria, Proteobacteria, Deinococcus-thermus, Bacteroidetes, Spirochaetes, Chloroflexi, Firmicutes, Fusobacteria, Cyanobacteria, Thermogales | |||
| Flavin mononucleotide (FMN) | 20 Gram-positive and Gram-negative bacteria [23,24,108] | RF00050 | |
| Bacterial phyla: Actinobacteria, Deinococcus-thermus, Thermus/deinococcus group, Proteobacteria, Firmicutes, Thermotogae, Fusobacteria, Thermogales | |||
| Guanine¥ | B. subtilis [25] | RF00167 | |
| Bacterial phyla: Proteobacteria, Firmicutes | |||
| Glycine | B. subtilis [109] | RF00154 | |
| Bacterial phyla: Actinobacteria, Proteobacteria, Fusobacteria, Firmicutes | |||
| Lysine | B. subtilis [25,110-112] | RF00168 | |
| Bacterial phyla: Proteobacteria, Thermogales, Firmicutes | |||
| Intracellular magnesium | S. enterica [113] | NL | |
| S-adenosylmethionine (SAM) | B. subtilis [114-116] | RF00162 | |
| Bacterial phyla: Cyanobacteria, Actinobacteria, Proteobacteria, Firmicutes | |||
| Thiamine pyrophosphate (TPP) | Rhizobium etli [117] | RF00059 | |
| Bacterial phyla: Actinobacteria, Deinococcus-thermus, Bacteroidetes, Proteobacteria, Thermus/deinococcus group, Spirochaetes, Chloroflexi, Firmicutes, Fusobacteria, Cyanobacteria, Thermogales | |||
| Eukaryal phyla: Metazoa, Cercozoa, Fungi, Viridiplantae | |||
| Archeal phyla: Euryarchaeota |
*For each type, the first entry represents the species in which the ribozyme or riboswitch was originally discovered. †Rfam accession numbers for detailed sequence listings [118]; NL, not listed in Rfam. ‡Detailed sequence listings also at [119]. §Detailed sequence listings also at [120]. ¶Detailed sequence listings also at [121]. ¥Adenine and guanine riboswitches are listed together as purine riboswitch in Rfam.