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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
  1. Percentage of change in entropy values of mutants compared to wild type. Mutation names are according to the literature. Type of disruption to wild type activity/conformation is denoted in column function (please see references for more detail on mutation information). Mutants have same length as the wild type, except for the ROSE-P2 thermosensor. Wild-type segments are the same as gathered data, except for the SAM-I riboswitch where a homologue has been used. ΔRND% and ΔBJK%, refer to structural entropy values for the RND and BJK models, respectively. ΔBJKbp% refers to the base-pairing entropy of the BJK model as defined by [54]. ΔSil% refers to the two-cluster average silhouette index of the energy landscape of the RNA as calculated by [46]. Sensitivity% and specificity% refer to BJK model accuracy to the secondary structural conformation, with disregard to pseudoknots.
  2. [1]Table 4: Two out of the 55 base-pairings of the B. subtilis FMN sequence are G-A pairs.
  3. [2]Table 4: ID36.1 is the metI SAM-I riboswitch in B. subtilis and has sequence identity of 76% with ID36 yitJ B. subtilis SAM-I riboswitch using BLAST. Sequence location on Location on the B. subtilis str. 168 strain embAL009126.3 (1258304-1258462), forward strand.
  4. [3]Table 4: CYK structural prediction under the BJK model and that of the MFE model via viennadetect different alteration of the Magnesium riboswitch in Salmonella enterica serovar Typhimurium. Structural distance of the MFE prediction to the high Mg2+ and low Mg2+ structures are 28 and 120, respectively while they are 114 and 74, under CYK-based structural prediction of the BJK model. Sensitivity and specificity values for the BJK model prediction of the low Mg2+ conformation are 22% and 22%.
  5. [4]Table 4: One out of the 44 base-pairings of the Bradyrhizobium ROSE-P2 sequence is a G-G pair.
  6. [5]Table 4: The ΔG83 mutant is one nucleotide shorter than the ROSE-P2 135nt-long wild type.
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