Figure 2.

Ribosome binding sites for representative small protein-coding genes. The sequence logo for E. coli ribosome binding sites is reproduced from reference 93. Sequences of 12 small protein genes of unknown function are listed below. Red type corresponds to the predicted start codon, while the blue type indicates stretches of four or more G and A residues. Gibbs free energies (ΔG° in kcal/mol) for the interaction between the sequence shown and the 16S RNA were calculated using IntaRNA (http://rna.informatik.uni-freiburg.de/IntaRNA/Input.jsp) (94). No value is given for the three sequences for which no significant interaction was detected. Rpm (reads per million mapped) values for ribosome profiling carried out in the presence of the inhibitor Onc112 are taken from reference 6.