Table 1 |
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The natural occurrence of ribozymes and riboswitches |
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Type |
Species* |
Rfam accession number† |
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Ribozyme |
Group I intron |
Thermus thermophila [1] |
RF00028 |
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More than 20,000 sequences from all three kingdoms‡ |
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Didymium iridis (branching enzyme, group I intron derivative) [46] |
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Group II intron |
Saccharomyces cerevisiae mitochondria [17,18] |
RF00029 |
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More than 8,000 sequences from all three kingdoms‡ |
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Hammerhead |
Tobacco ringspot virus satellite RNA (sTRSV) [3] |
RF00008 |
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Several additional satellite RNAs of plant viruses§ |
RF00163 |
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Viroids of the Avsunviroidae family [99,100] |
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Carnation small viroid-like RNA (CarSV RNA) [101] |
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Satellite DNAs of various amphibian species [102,103], Schistosoma mansoni [30] and Dolichopoda cave crickets [31] |
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Arabidopsis thaliana genome [33] |
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Hairpin |
Tobacco ringspot virus satellite RNA (sTRSV) [4] |
RF00173 |
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Two additional satellite RNAs of plant viruses: sCYMV and sARMV [104] |
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HDV |
Human hepatitis delta virus RNA [6] |
RF00094 |
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Homo sapiens genome (intronic) [29] |
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RNase P |
Escherichia coli [2] |
RF00010 |
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More than 1,000 sequences from various Bacterial phyla¶ |
RF00011 |
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Archeal phyla: Crenarchaeota, Euryarchaeota [105] |
RF00373 |
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VS |
Neurospora crassa Varkud satellite [8] |
NL |
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Catalytic riboswitch |
Glms riboswitch |
Bacillus subtilis [14] |
RF00234 |
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Bacterial phyla: Actinobacteria, Firmicutes |
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Riboswitch |
Adenine¥ |
B. subtilis [106] |
RF00167 |
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Bacterial phyla: Proteobacteria, Firmicutes |
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Coenzyme B12 |
E. coli and Salmonella typhimurium btuB mRNAs [107] |
RF00174 |
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Bacterial phyla: Actinobacteria, Proteobacteria, Deinococcus-thermus, Bacteroidetes, Spirochaetes, Chloroflexi, Firmicutes, Fusobacteria, Cyanobacteria, Thermogales |
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Flavin mononucleotide (FMN) |
20 Gram-positive and Gram-negative bacteria [23,24,108] |
RF00050 |
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Bacterial phyla: Actinobacteria, Deinococcus-thermus, Thermus/deinococcus group, Proteobacteria, Firmicutes, Thermotogae, Fusobacteria, Thermogales |
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Guanine¥ |
B. subtilis [25] |
RF00167 |
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Bacterial phyla: Proteobacteria, Firmicutes |
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Glycine |
B. subtilis [109] |
RF00154 |
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Bacterial phyla: Actinobacteria, Proteobacteria, Fusobacteria, Firmicutes |
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Lysine |
B. subtilis [25,110-112] |
RF00168 |
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Bacterial phyla: Proteobacteria, Thermogales, Firmicutes |
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Intracellular magnesium |
S. enterica [113] |
NL |
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S-adenosylmethionine (SAM) |
B. subtilis [114-116] |
RF00162 |
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Bacterial phyla: Cyanobacteria, Actinobacteria, Proteobacteria, Firmicutes |
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Thiamine pyrophosphate (TPP) |
Rhizobium etli [117] |
RF00059 |
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Bacterial phyla: Actinobacteria, Deinococcus-thermus, Bacteroidetes, Proteobacteria, Thermus/deinococcus group, Spirochaetes, Chloroflexi, Firmicutes, Fusobacteria, Cyanobacteria, Thermogales |
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Eukaryal phyla: Metazoa, Cercozoa, Fungi, Viridiplantae |
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Archeal phyla: Euryarchaeota |
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*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. |
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Hammann and Westhof Genome Biology 2007 8:210 doi:10.1186/gb-2007-8-4-210 |
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