Background: Escherichia coli (E. coli) mazEF, a stress-induced toxin-antitoxin (TA) system,
has been studied extensively. The MazF toxin is an endoribonuclease that cleaves RNAs at ACA
sites. Thereby, under stress, the induced MazF generates a Stress-induced Translation Machinery
(STM), composed of MazF processed mRNAs and selective ribosomes that specifically translate the
Materials and Methods: Based on the data from the EcoCyc website of the National Center for Biotechnology
Information (NCBI), the sequence of all E. coli MG1655 genes were scanned for ACA
sites upstream from the initiation codons. Among these sequences, the fuzznuc program of the "European
Molecular Biology Open Software Suite" (EMBOSS) was used to find the "ACA" pattern. The
distribution of the ACA threonine codon, both in-frame and out-of-frame, was determined by using
the HTML Script Program (Supplementary Material).
Results: Here it is reported that for most of the E. coli proteins mediated by stress-induced MazF, the
ACA threonine codon in their mRNAs is not in-frame but rather out-of-frame; in these same RNAs,
the three synonymous threonine codons, ACG, ACU, and ACC, are in-frame. In contrast, for proteins
translated by the canonical translation system, in the majority of mRNAs, the ACA codon is located
Conclusion: The described bias in the genetic code is a characteristic of E. coli genes specifying for
stress-induced MazF-mediated proteins.