title: Whole genome analysis reveals a high incidence of non-optimal codons in secretory signal sequences of Escherichia coli.
abstract: Translational pausing may occur due to a number of mechanisms, including the presence of non-optimal codons, and it is thought to play a role in the folding of specific polypeptide domains during translation and in the facilitation of signal peptide recognition during sec-dependent protein targeting. In this whole genome analysis of Escherichia coli we have found that non-optimal codons in the signal peptide-encoding sequences of secretory genes are overrepresented relative to the "mature" portions of these genes; this is in addition to their overrepresentation in the 5'-regions of genes encoding non-secretory proteins. We also find increased non-optimal codon usage at the 3' ends of most E. coli genes, in both non-secretory and secretory sequences. Whereas presumptive translational pausing at the 5' and 3' ends of E. coli messenger RNAs may clearly have a general role in translation, we suggest that it also has a specific role in sec-dependent protein export, possibly in facilitating signal peptide recognition. This finding may have important implications for our understanding of how the majority of non-cytoplasmic proteins are targeted, a process that is essential to all biological cells.
authors.affiliation: School of Molecular and Microbial Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia.
authors.forename: Peter M
authors.initials: PM
authors.lastname: Power
authors.forename: Robert A
authors.initials: RA
authors.lastname: Jones
authors.forename: Ifor R
authors.initials: IR
authors.lastname: Beacham
authors.forename: Carolyn
authors.initials: C
authors.lastname: Bucholtz
authors.forename: Michael P
authors.initials: MP
authors.lastname: Jennings
mesh_terms: D003062:Codon / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics* / Q000502:physiology; D005821:Genetic Techniques; D016680:Genome, Bacterial; D016366:Open Reading Frames; D014176:Protein Biosynthesis / Q000235:genetics; D015398:Signal Transduction / Q000235:genetics*
chemical_list: D003062:Codon; D004269:DNA, Bacterial