TABLE 2

Characteristics of evolved Rifr E. coli K12 (rif-1, rif-2, rif-8, rif-9)

MutantRelative fitness:
% growth/generation
(vs. mutant parent)
(±SEM)
MIC
(μg/ml rif)
Original rpoB
substitutiona
Mutation
clusterc
Secondary
rpoB substitutiona
Mutation
cluster
Transcription
efficiencyd
(±SEM)
K12(MG1655)0-120.058 (0.008)
rif-1100100-200I572L (ATC to CTC)II0.029 (0.004)
E-rif-1A119.9 (61.5)100-200I572L (ATC to CTC)IIG556G (GGT to GGG)II0.058 (0.014)
E-rif-1B114.1 (61.3)100-200I572L (ATC to CTC)IINone identified0.042 (0.009)
E-rif-1C112.1 (60.7)100-200I572L (ATC to CTC)IINone identifiedND
E-rif-1D114.2 (60.8)100-200I572L (ATC to CTC)IINone identifiedND
ER-rif-1Ab117.1 (61.1)400-800I572L (ATC to CTC)IID516G (GAC to GGC)II0.051 (0.018)
rif-210025-50L511Q (CTG to CAG)II0.021 (0.001)
E-rif-2A110.7 (61.5)25-50L511Q (CTG to CAG)IINone identified0.067 (0.014)
E-rif-2B110.8 (61.2)25-50L511Q (CTG to CAG)IINone identifiedND
E-rif-2C105.9 (61.4)25-50L511Q (CTG to CAG)IINone identified0.029 (0.002)
E-rif-2D107.7 (61.9)25-50L511Q (CTG to CAG)IINone identifiedND
ER-rif-2Ab111.0 (60.7)800-1000L511Q (CTG to CAG)IID516G (GAC to GGC)II0.060 (0.014)
ER-rif-2Bb113.2 (61.9)800-1000L511Q (CTG to CAG)IID516G (GAC to GGC)II0.059 (0.009)
rif-81003000-4000P564L (CCT to CTT)II0.019 (0.003)
E-rif-8A109.6 (60.6)3000-4000P564L (CCT to CTT)IIR211P (CGC to CCG)X0.040 (0.001)
E-rif-8B113.5 (61.0)3000-4000P564L (CCT to CTT)IINone identified0.027 (0.009)
E-rif-8C114.1 (60.7)5000-6000P564L (CCT to CTT)IINone identifiedND
E-rif-8D115.6 (60.6)5000-6000P564L (CCT to CTT)IIS574F (TCT to TTT)II0.031 (0.009)
ER-rif-8Ab114.9 (63.0)3000-4000P564L (CCT to CTT)IIL194R (CTG to CGG)X0.039 (0.019)
ER-rif-8Bb115.9 (68.7)5000-6000P564L (CCT to TTT)IIS574F (TCT to TTT)II0.044 (0.005)
rif-9100100-200D516G (GAC to GGC)II0.059 (0.009)
ER-rif-9Ab97.5 (60.7)400-800D516G (GAC to GGC)IIS574Y (TCT to TAT)II0.038 (0.003)
ER-rif-9Bb98.7 (60.7)400-800D516G (GAC to GGC)IIH554Y (CAC to TAC)II0.047 (0.007)
ER-rif-9Cb98.6 (60.5)400-800D516G (GAC to GGC)IIS574Y (TCT to TAT)IIND
  • a All evolved strains retained their original (parental) mutation. Secondary mutations are additional substitutions identified in evolved strains. All evolved strains were subjected to sequence analysis across the first 2226 nucleotides of the rpoB gene.

  • b E strains were passaged without drug. ER strains were evolved under drug selection pressure (25 μg/ml rifampin).

  • c See Figure 2 for description of mutation clusters I and II. X refers to positions outside defined mutation clusters.

  • d See Figure 3 legend for details regarding empirical determination of transcription efficiency. Values here represent the average of two to four independent efficiency determinations. Standard error is shown in parentheses. ND, not determined.