Table 1.
Functional overview and distribution of riboswitches and riboswitch-like elements.
| Rfam ID | Name | Effector | Length1 | Total number2 | Representative lineages and riboswitch numbers2 | Functional categories of riboswitch regulons | References3 |
|---|---|---|---|---|---|---|---|
| RF00230 | T-box | uncharged tRNA | 564 | 1134 | Deinococcales (10), Bacillales (313), Lactobacillales (434), Clostridia (337), Actinomycetales (15), Chloroflexi (25) | Amino acid (AA) biosynthesis, AA transporters, Amino acyl-tRNA synthetases | [28] (b), [31] (e), [36] (a/b) |
| RF00059 | TPP (THI element) | thiamin pyrophosphate | 318 | 564 | Proteobacteria: α (64), β (24), γ (128), δ (21), ε; Deinococcales (10), Bacillales (77), Lactobacillales (59), Clostridia (62), Actinomycetales (45), Cyanobacteria (14), Chlorobiales (11), Bacteroidales (19), Thermotogales (16), Chloroflexi (14), Fusobacterales, Spirochaetales, Archaea, Eukaryotes | Thiamin biosynthesis, Thiamin & precursor transporters | [23] (a/b), [52] (g) |
| RF00174 | Cobalamin (B12 element) | adenosylcobalamin | 441 | 536 | Proteobacteria: α (112), β (45), γ (96), δ (23), ε; Deinococcales (12), Bacillales (18), Lactobacillales (1), Clostridia (50), Actinomycetales (27), Cyanobacteria (20), Chlorobiales (34), Bacteroidales (65), Thermotogales (20), Chloroflexi (13), Acidobacteria, Chlamydia, Fusobacterales, Spirochaetales | B12 biosynthesis, B12 & precursor transporters, Cobalt transporters, Isozymes of B12-dependent enzymes | [19] (d), [27], [35] (e/g/h), [37] (a/b) |
| RF00504 | Glycine | glycine | 220 | 324 | Proteobacteria: α (78), β (42), γ (69), δ (6), ε; Bacillales (30), Lactobacillales (18), Clostridiales (52), Actinomycetales (23), Chloroflexi (6), Fusobacterales | Glycine metabolism, Serine metabolism, Glycine transporters | [17], [52] (g), [108] |
| RF00050 | FMN (RFN element) | flavin mononucleotide | 221 | 233 | Proteobacteria: α (20), β (15), γ (52), δ (10), ε; Deinococcales (5), Bacillales (34), Lactobacillales (38), Clostridia (38), Actinomycetales (3), Chlorobiales (2), Thermotogales (8), Chloroflexi (8), Fusobacterales | Riboflavin biosynthesis, Riboflavin transporters | [26] (a/b), [52] (g) |
| RF00080 | yybP-ykoY | ? | 221 | 232 | Proteobacteria: α (8), β (20), γ (73), δ (7); Deinococcales (5), Bacillales (23), Lactobacillales (28), Clostridiales (35), Actinomycetales (23), Cyanobacteria (4), Thermotogales (1), Chloroflexi (5) | Miscellaneous | [52] (g), [101] (a) |
| RF00162 | SAM (S-box) | S-adenosylmethionine | 231 | 257 | Proteobacteria: α, γ, δ (4), ε; Deinococcales (9), Bacillales (138), Lactobacillales (2), Clostridia (72), Actinomycetales (1), Cyanobacteria (2), Chlorobiales (14), Bacteroidales. Thermotogales (1), Chloroflexi (14), Acidobacteria, Fusobacterales | Methionine biosynthesis, Methionine & SAM recycling, Cysteine biosynthesis, Methionine transporters | [35] (e/g/h), [36] (a/b) |
| RF00168 | Lysine (L-box) | lysine | 274 | 186 | Proteobacteria: γ (72); Bacillales (38), Lactobacillales (29), Clostridia (38), Thermotogales (9), Acidobacteria, Fusobacterales | Lysine biosynthesis, Lysine transporters | [24] (a/b), [52] (g) |
| RF00167 | Purine (G-box) | guanine, adenine | 113 | 141 | Proteobacteria: γ (13), δ, ε; Bacillales (56), Lactobacillales (29), Clostridia (41), Thermotogales (2), Fusobacterales | Purine metabolism, Purine & precursor transporters | [52] (g), [102] (d) |
| RF01051 | GEMM | cyclic di-GMP | 136 | 89 | Proteobacteria: β (1), γ (36), δ (5); Deinococcales (3), Bacillales (9), Clostridia (29), Cyanobacteria (6) | Polysaccharide degradation | [33] (a/d/e/h) |
| RF00522 | PreQ1 | pre-queuosine1 | 70 | 72 | Proteobacteria: α (1), β, γ (9), δ, ε; Bacillales (28), Lactobacillales (11), Clostridia (23), Fusobacterales | Queuosine biosynthesis, Queuosine & precursor transporters | [103] (d) |
| RF01068 | mini-ykkC | ? | 56 | 67 | Proteobacteria: α (26), β (11), γ (28), δ (1); Cyanobacteria (1) | Urea and agmatine utilization, Multidrug resistance transporter | [33] (a/d/e/h) |
| RF01055 | MOCO | molybdenum or tungsten cofactor? | 255 | 62 | Proteobacteria: α (2), γ (50); Deinococcales (1), Clostridia (6), Chlorobiales (1), Thermotogales (2) | Molybdenum cofactor biosynthesis, Molybdenum & tungsten transporters | [33] (a/d/e/h) |
| RF00379 | ydaO-yuaA | ATP | 335 | 59 | Proteobacteria: δ (1); Bacillales (18), Clostridia (18), Actinomycetales (14), Cyanobacteria (8) | Potassium transporters | [16], [52] (g) |
| RF00442 | ykkC-yxkD | ? | 181 | 58 | Proteobacteria: α (10), β (7), γ (7); Bacillales (12), Lactobacillales (2), Clostridia (11), Actinomycetales (3), Cyanobacteria (6) | Urea and agmatine utilization, Multidrug resistance transporter | [16], [33] (a/d/e/h), [35] (e/g/h) |
| RF00380 | ykoK (M-box) | magnesium | 278 | 48 | Proteobacteria: γ (6); Bacillales (7), Lactobacillales (15), Clostridia (10), Actinomycetales (10) | Magnesium transporters, | [16] |
| RF00234 | glmS | glucosamine-6-phosphate | 236 | 44 | Deinococcales (3), Bacillales (18), Lactobacillales (1), Clostridiales (17), Actinomycetales, Chloroflexi (5), Fusobacterales | Aminosugar biosynthesis | [18], [52] (g), [79] |
| RF01057 | SAH | S-adenosylhomocysteine | 172 | 27 | Proteobacteria: β (14), γ (7); Actinomycetales (6) | Methionine biosynthesis, Methionine & SAM recycling, | [33] (a/d/e/h) |
| RF00521 | SAM-Alpha (SAM-II) | S-adenosylmethionine | 85 | 39 | Proteobacteria: α (39), β, γ; Bacteroidales | Methionine biosynthesis | [34], [35] (e/g/h) |
| RF00517 | serC | ? | 55 | 32 | Proteobacteria: α (32) | Serine metabolism | [34] |
| RF01831 | THF | tetrahydrofolate | 179 | 23 | Lactobacillales (12), Clostridia (11) | Folate biosynthesis, Folate transporters | [35] (e/g/h), [104] (a/d/h) |
| RF01054 | PreQ1-II | pre-queuosine1 | 132 | 17 | Lactobacillales (17) | Queuosine & precursor transporters | [33] (a/d/e/h) |
| RF01070 | sucA | ? | 102 | 14 | Proteobacteria: β (14) | Citric acid cycle | [33] (a/d/e/h) |
| RF01739 | glnA | glutamine | 274 | 13 | Cyanobacteria (13) | Nitrogen metabolism | [17], [35] (e/g/h) |
| RF00634 | SAM-IV | S-adenosylmethionine | 152 | 13 | Actinomycetales (13) | Methionine biosynthesis, | [33] (a/d/e/h), [105] (a/d/e/h) |
| RF01767 | Smk-box (SAM-III) | S-adenosylmethionine | 148 | 13 | Lactobacillales (13) | Methionine & SAM recycling | [106] |
| RF01727 | SAM-SAH | S-adenosylmethionine, S-adenosylhomocysteine | 54 | 13 | Proteobacteria: α (13) | Methionine & SAM recycling | [35] (e/g/h) |
| RF00518 | speF | ? | 426 | 12 | Proteobacteria: α (12) | Ornithine degradation | [34] |
| RF01724 | SAM-Chlorobi | S-adenosylmethionine | 113 | 11 | Chlorobiales (11) | Methionine & SAM recycling | [35] (e/g/h) |
| RF00516 | ylbH | ? | 139 | 10 | Bacillales (10) | Miscellaneous | [16] |
| RF00520 | ybhL | ? | 92 | 8 | Proteobacteria: α (8) | Miscellaneous | [34] |
| RF01056 | Mg sensor | magnesium | 119 | 5 | Proteobacteria: γ (5) | Miscellaneous | [82] (a) |
The majority of the table is adopted from the previous comparative genomic analysis of riboswitches by Sun et al. [71].
1
Nucleotide length of riboswitches is based on the ‘seed’ alignments in the Rfam database [67].
2
Total number of riboswitch sites and numbers riboswitches detected in each lineage (given in parenthesis) are according to Sun et al. [71]. Representative lineages” incorporates data from Winkler & Breaker (2005) [107] and Barrick & Breaker (2007) [19].
3
References are given for papers that have used the following computational tools and databases for riboswitch identification: (a) Mfold, RNAfold and/or RNAalifold; (b) RNA-PATTERN; (c) RNAMotif; (d) Infernal; (e) Rfam; (f) Riboswitch Finder; (g) RibEx; (h) CMfinder.