(A) The percent of G, C, A, T nucleotides in each group of signal sequences. Symbols: percentage in individual fusion mRNAs. The box and whiskers represents the 50% and 95% quartiles, respectively. The individual panels correspond to native encodings of the SRP signal peptides (red), the SecB signal peptides (blue), and the cytoplasmic control peptides (cyan). The underrepresentation of nucleotide A in SRP signal peptide sequences is consistent with the previous finding of the underrepresentation of A in sequences encoding hydrophobic residues (Prilusky and Bibi, 2009), which are enriched in transmembrane domains. Identical skews were observed for the synthetic encodings of these signal peptides. (B) Average half-lives for beta lactamase (bla) fusions to all native (top) and synthetic (bottom) encodings of the SRP signal peptides (red), SecB signal peptides (blue), and cytoplasmic controls (cyan), measured as a function of the number of each type of nucleotide in the signal sequences (G, C, A, and T from left to right). Only results for bla fusions are shown but similar behaviors are observed for all five of the test genes (bla, neo, mMaple3, phoA, and lacZ). (C) The average ratio of SecB-fusion half-lives to SRP-fusion half-lives (blue) and the average ratio of the cytoplasmic control fusion half-lives to the SRP fusion half-lives (cyan) as a function of the number of each type of nucleotide in the signal sequences. The dashed lines represent a ratio of 1. The average is performed across all five test genes. Data in (B) and (C) have been binned in 3 nucleotide increments, and error bars represent the standard error of the mean. The mRNA half-life appears to depend on the nucleotide compositions, in particular the A and G content, in the signal sequences. However, for a fixed number of each nucleotide, SRP fusions have smaller average half-lives than the SecB and cytosolic control groups in most cases. Thus, SRP fusions destabilize the mRNAs relative to either the SecB or cytoplasmic control fusions even after controlling for nucleotide usage. See Figure 5—source data 1 for all abundance data versus time and the fit decay rates used to derive half-lives.