ΔRF3 reduces expression of biosynthetic genes controlled by leader peptide attenuation.

(A and B) Scatter plots of ribosome footprint density in RPKM for K-12 RF2^K-12 and K-12 RF2^K-12ΔRF3 strains for all genes above minimum read threshold, with biosynthetic genes under the control of leader peptide attenuation in red are all others in grey. (A) Rich media samples of K-12 RF2^K-12 and K-12 RF2^K-12ΔRF3 grown in MOPS-complete glucose medium are averaged data across multiple replicates. (B) Minimal medium ribosome footprint densities between K-12 RF2^K-12 and K-12 RF2^K-12ΔRF3 in MOPS minimal glucose medium are plotted for a single replicate. (C) Schematic of the chromosomally integrated reporter constructs measuring expression of the leader peptide (reporter #1) or downstream gene expression (reporter #2), both under control of their native promoter. (D) Operon expression in K-12 RF2^K-12 and K-12 RF2^K-12ΔRF3 strains was calculated by dividing the β-galactosidase activity of reporter #2 by activity of reporter #1 and normalizing to the K-12 RF2^K-12 strain in in MOPS complete-glucose rich media. (E) Increased attenuation in K-12 RF2^K-12ΔRF3 strain may result from increased occupancy over the stop codon and post-ORF region. This mechanism would stabilize the formation of the downstream terminator loop over the anti-terminator loop.