Whole genome analysis reveals a high incidence of non-optimal codons in secretory signal sequences of Escherichia coli

Biochemical and Biophysical Research Communications
Peter M PowerMichael P Jennings

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.

References

May 20, 1989·Journal of Molecular Biology·M A SørensenS Pedersen
Sep 5, 1989·Journal of Molecular Biology·J F Curran, M Yarus
Jul 8, 1988·Journal of Theoretical Biology·M Bulmer
Sep 11, 1984·Nucleic Acids Research·M RobinsonG Humphreys
Jan 11, 1984·Nucleic Acids Research·J DevereuxO Smithies
Sep 25, 1993·Nucleic Acids Research·A Eyre-Walker, M Bulmer
Oct 1, 1996·Protein Science : a Publication of the Protein Society·T A Thanaraj, P Argos
Sep 5, 1997·Science·F R BlattnerY Shao
Aug 4, 1999·Trends in Microbiology·A Economou

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Citations

Feb 15, 2013·Genome Biology and Evolution·Yuanhui MaoShiheng Tao
Apr 7, 2010·PLoS Computational Biology·Vaughn S CooperPhilip J Hatcher
Nov 8, 2008·PLoS Genetics·Tobias WarneckeLaurence D Hurst
Jan 1, 2008·Bioinformation·Surajit BasakSantasabuj Das
Dec 23, 2011·Applied Microbiology and Biotechnology·David Matthias EkkersJan Dirk van Elsas
Sep 13, 2014·Journal of Industrial Microbiology & Biotechnology·Zhen KangJian Chen
Mar 25, 2009·Trends in Microbiology·Yaramah M ZaluckiMichael P Jennings
Feb 13, 2007·Biochemical and Biophysical Research Communications·Yaramah M Zalucki, Michael P Jennings
May 14, 2011·Biotechnology Journal·Yaramah M ZaluckiMichael P Jennings
Jun 28, 2011·Biochimica Et Biophysica Acta·Yaramah M ZaluckiMichael P Jennings
Jul 15, 2015·BMC Genomics·Daniel López, Florencio Pazos
Mar 17, 2010·Biochimica Et Biophysica Acta·Yaramah M ZaluckiMichael P Jennings
Dec 7, 2007·Biochemical and Biophysical Research Communications·Yaramah M ZaluckiMichael P Jennings
Nov 29, 2016·Nature Reviews. Microbiology·Alexandra TsirigotakiSpyridoula Karamanou
Oct 4, 2017·The Journal of Biological Chemistry·Ligia Acosta-SampsonJamie H D Cate
Sep 19, 2019·Microbial Cell Factories·Antti KulmalaUrpo Lamminmäki
Apr 28, 2017·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Juan C VilladaWendel Batista da Silveira
Apr 14, 2018·Engineering in Life Sciences·Gabriele R M Kleiner-GroteKarl Friehs
Oct 4, 2018·Biochimica Et Biophysica Acta. Biomembranes·Alexander L CopeMichael A Gilchrist
May 5, 2021·Genome Biology and Evolution·Martijn CallensStéphanie Bedhomme

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