Extended Data Fig. 4: Species- and codon-specific ribosome pauses in response to stress or antibiotic treatment.

Line plots showing amino acid-specific ribosome pauses as measured by fivepseq. A, Isoleucine (Ile) pause (-14 nt) comparing NT and MUP treatment in L. plantarum, L. reuteri and B. subtilis. B, The relative context-specific Alanine (Ala) and Serine (Ser) ribosome pauses (-8 nt) as measured by fivepseq for multiple species in response to CAM. Only in E. coli, which lacks RNase J, the 5´P degradome profile does not provide single-nucleotide resolution information of the ribosome stall. C-D, Principal component analysis plots based on 5P counts 14 nt upstream from each codon for L. plantarum and B. subtilis in stress conditions. The NT control samples of B. subtilis have been collected at different growths phases (OD₆₀₀ 0.2-0.3 and 0.6-0.8 respectively). The contribution of each codon is shown with gray loading vectors. The features with the longest loadings corresponding to those with highest absolute weight in the PC1 and PC2 are highlighted. The up arrows in labels indicate that the 5P counts increase in stress conditions for the codon. Codons of common amino acids between L. plantarum and B. subtilis are highlighted with stress-specific colours. E-F, relative Arg and Gln pauses (-14 nt) in stationary phase growth for L. plantarum (27 hours) and B. subtilis (8 days).