Table 1. Strains used in this study.
| Strain Abbreviation* | Ancestor (source)† | Genotype | # UAG Codons‡ | RF1 Status§ | Ribosomal rescue gene deletion | ssrA tag Status# | Investigated in |
|---|---|---|---|---|---|---|---|
| GRO.DD.prfA+ | GRO.AA (this study) | ΔmutS:zeo.Δ(ybhB-bioAB):[λcI857.Δ(cro-ea59):tetR-bla] | 0 | +RF1 | n/a | DD | GFP expression for mass spectrometry (Figure 2) |
| GRO.DD | GRO.AA (this study) | ΔmutS:zeo.Δ(ybhB-bioAB):[λcI857.Δ(cro-ea59):tetR-bla], ΔprfA, ΔtolC | 0 | ∆RF1 | n/a | DD | GFP expression for mass spectrometry (Figure 2) |
| ECNR2.AA | E. coli MG1655 (Wang et al., 2009) | MG1655 ΔmutS:zeo.Δ(ybhB-bioAB):[λcI857.Δ(cro-ea59):tetR-bla] | 321 | +RF1 | n/a | AA | Fitness, conjugation, and viral infection (Figures 3 and 4) |
| GRO.AA | ECNR2.AA (Lajoie et al., 2013b) | ΔmutS:zeo.Δ(ybhB-bioAB):[λcI857.Δ(cro-ea59):tetR-bla], ΔprfA, ΔtolC | 0 | ∆RF1 | n/a | AA | Fitness, conjugation, and viral infection (Figures 3 and 4) |
| GRO.AA.∆ssrA | GRO.AA (this study) | ΔmutS:zeo.Δ(ybhB-bioAB):[λcI857.Δ(cro-ea59):tetR-bla], ΔprfA, ΔtolC | 0 | ∆RF1 | ∆ssrA | AA | Fitness, conjugation, and viral infection (Figures 3 and 4) |
| GRO.AA.∆arfA | GRO.AA (this study) | ΔmutS:zeo.Δ(ybhB-bioAB):[λcI857.Δ(cro-ea59):tetR-bla], ΔprfA, ΔtolC | 0 | ∆RF1 | ∆arfA | AA | Fitness, conjugation, and viral infection (Figures 3 and 4) |
| GRO.AA.∆arfB | GRO.AA (this study) | ΔmutS:zeo.Δ(ybhB-bioAB):[λcI857.Δ(cro-ea59):tetR-bla], ΔprfA, ΔtolC | 0 | ∆RF1 | ∆arfB | AA | Fitness, conjugation, and viral infection (Figures 3 and 4) |
| GRO.AA.∆ssrA.∆arfB | GRO.AA (this study) | ΔmutS:zeo.Δ(ybhB-bioAB):[λcI857.Δ(cro-ea59):tetR-bla], ΔprfA, ΔtolC | 0 | ∆RF1 | ∆ssrA, ∆arfB | AA | Fitness, conjugation, and viral infection (Figures 3 and 4) |
| GRO.AA.∆arfA. ∆arfB | GRO.AA (this study) | ΔmutS:zeo.Δ(ybhB-bioAB):[λcI857.Δ(cro-ea59):tetR-bla], ΔprfA, ΔtolC | 0 | ∆RF1 | ∆arfA, ∆arfB | AA | Fitness, conjugation, and viral infection (Figures 3 and 4) |
*All strains derived from ECNR2, as described in Wang et al. (2009).
†See Key Resources Table for additional information on strains and sources. The GenBank accession number for E. coli MG1655 is U00096, and the GenBank accession number for GRO.AA is CP006698.
‡ Out of a total of 321 in the original ECNR2 strain.
§RF1 terminates translation at UAG and UAA. Deletion of RF1 eliminates recognition of UAG during translation; translational termination continues through RF2, which recognizes UAA and UGA.
#The ssrA gene encodes the tmRNA, which appends the ssrA degradation tag to stalled ribosomes. The wild-type sequence is AANDENYALAA; mutation of the C-terminus to AANDENYALDD slows degradation of peptides to enable detection by mass spectrometry.