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About the Authors:
Fei Qi
Roles Formal analysis, Investigation, Methodology, Visualization, Writing - original draft, Writing - review & editing
Affiliation: Department of Bioinformatics, Wissenschaftzentrum Weihenstephan, Technische Universität München, Freising, Germany
ORCID http://orcid.org/0000-0003-4578-0146
Magdalena Motz
Roles Methodology, Writing - original draft, Writing - review & editing
Affiliations Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
Kirsten Jung
Roles Conceptualization, Methodology, Project administration, Supervision, Writing - original draft, Writing - review & editing
Affiliations Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
ORCID http://orcid.org/0000-0003-0779-6841
Jürgen Lassak
Roles Conceptualization, Methodology, Project administration, Supervision, Writing - original draft, Writing - review & editing
Affiliations Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
ORCID http://orcid.org/0000-0003-3936-3389
Dmitrij Frishman
Roles Conceptualization, Methodology, Project administration, Supervision, Writing - original draft, Writing - review & editing
* E-mail: [email protected]
Affiliations Department of Bioinformatics, Wissenschaftzentrum Weihenstephan, Technische Universität München, Freising, Germany, St Petersburg State Polytechnic University, St Petersburg, RussiaAbstract
Translation of consecutive prolines causes ribosome stalling, which is alleviated but cannot be fully compensated by the elongation factor P. However, the presence of polyproline motifs in about one third of the E. coli proteins underlines their potential functional importance, which remains largely unexplored. We conducted an evolutionary analysis of polyproline motifs in the proteomes of 43 E. coli strains and found evidence of evolutionary selection against translational stalling, which is especially pronounced in proteins with high translational efficiency. Against the overall trend of polyproline motif loss in evolution, we observed their enrichment in the vicinity of translational start sites, in the inter-domain regions of multi-domain proteins, and downstream of transmembrane helices. Our analysis demonstrates that the time gain caused by ribosome pausing at polyproline motifs might be advantageous in protein regions bracketing domains and transmembrane helices. Polyproline motifs might therefore be crucial for co-translational folding and membrane insertion.
Author summary
Polyproline motifs induce ribosome stalling during translation, but the functional significance of this effect remains unclear. Our evolutionary analysis of polyproline motifs reveals that they are disfavored in E. coli proteomes as a consequence of the reduced translation efficiency, supporting the...