Table 4 Mutagenesis
From: Secondary structural entropy in RNA switch (Riboswitch) identification
Wild-type | Riboswitch (Length) | Organism | Sensitivity % | Specificity % | ||
|---|---|---|---|---|---|---|
ID49 | TPP (158) | B. subtilis | 56.9 | 51.8 | ||
Mutants [26] | Function | Disruption of only one structure | ΔRND % | ΔBJK % | ΔBJKbp % | ΔSil % |
+30 | Disrupts anti-antiterminator | Yes | 0.7 | -2.6 | -3.9 | -55.2 |
+118 | Disrupts anti-terminator | Yes | -0.4 | 5.3 | -0.7 | -50.3 |
+80 | Disrupts thi-box | No | 0.8 | 3.3 | 0.8 | -38.2 |
+97 | Disrupts thi-box | No | -0.8 | 1.9 | 1.6 | -63.2 |
Wild-type | Riboswitch (Length) | Organism | Sensitivity % | Specificity % | ||
ID13 | FMN (236) | B. subtilis | 81.8 [1] | 64.3 | ||
Mutants [26] | Function | Disruption of only one structure | ΔRND % | ΔBJK % | ΔBJKbp % | ΔSil % |
G34C/G35C | Disrupts anti-terminator | Yes | -1.6 | -5.5 | -2.4 | 15.4 |
C86T | Disrupts rfn-box | No | 0.2 | -0.1 | 0.6 | 11.8 |
C49T | Disrupts rfn-box | No | 0.3 | 0.5 | 0 | -14.3 |
G157A/G160A | Disrupts anti-antiterminator | Yes | 0 | -0.7 | -0.9 | 66.7 |
Wild-type | Riboswitch (Length) | Organism | Sensitivity % | Specificity % | ||
ID36.1 [2] | SAM-I (159) | B. subtilis | 94 | 88.7 | ||
Mutants [134] | Function | Disruption of only one structure | ΔRND % | ΔBJK % | ΔBJKbp % | ΔSil % |
Ma | Disturbs both structures | No | 2.3 | 15.8 | 10.7 | -48.8 |
Mab | Disrupts anti-terminator | Yes | -2.3 | -0.29 | -0.4 | 4.1 |
Mc | Disrupts anti-terminator | Yes | 0.3 | -0.31 | -0.8 | -0.3 |
Mabc | Compensates mutations to wild type | No | -1.1 | -0.32 | -0.7 | -3.2 |
Wild-type | Riboswitch (Length) | Organism | Reference | Sensitivity % | Specificity % | |
ID18 | Magnesium (172) | Salmonella enterica | 64.5 [3] | 43.5 | ||
Mutant [20] | Function | Disruption of only one structure | ΔRND % | ΔBJK % | ΔBJKbp % | ΔSil % |
C145G | Favors high Mg2+ conformation | Yes | 1.7 | -1.8 | -4.7 | -10.1 |
Mutants [20] | Function | Disruption of only one structure | ΔRND % | ΔBJK % | ΔBJKbp % | ΔSil % |
M1 | Favors +FMN conformation | Yes | 0.4 | -3.8 | -5.8 | -43 |
M2 | Favors -FMN conformation | Yes | -1.4 | -1.9 | -1.2 | -5.7 |
Wild-type | Riboswitch (Length) | Organism | Sensitivity % | Specificity % | ||
ID20 | Magnesium (204) | B. subtilis | 78 | 65 | ||
Mutants [19] | Function | Disruption of only one structure | ΔRND % | ΔBJK % | ΔBJKbp % | ΔSil % |
M5 | Disrupts termination | Yes | 2.7 | 0.9 | 0.7 | -12.3 |
M6 | Distrupts anti-terminator | Yes | 3.9 | 12.4 | 8 | -14.8 |
Wild-type | Riboswitch (Length) | Organism | Sensitivity % | Specificity % | ||
ID33 | ROSE-P2 (135) | Bradyrhizobium | 22.7 [4] | 22.2 | ||
Mutant [22] | Function | Disruption of only one structure | ΔRND % | ΔBJK % | ΔBJKbp % | ΔSil % |
ΔG83[5] | Deletion of a critical nucleotide | Yes | -2.6 | -8.1 | -4.7 | 8.6 |