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Table 1 The natural occurrence of ribozymes and riboswitches

From: Searching genomes for 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

 
  1. *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.