title: Translational stalling at polyproline stretches is modulated by the sequence context upstream of the stall site.
abstract: The polymerization of amino acids into proteins occurs on ribosomes, with the rate influenced by the amino acids being polymerized. The imino acid proline is a poor donor and acceptor for peptide-bond formation, such that translational stalling occurs when three or more consecutive prolines (PPP) are encountered by the ribosome. In bacteria, stalling at PPP motifs is rescued by the elongation factor P (EF-P). Using SILAC mass spectrometry of Escherichia coli strains, we identified a subset of PPP-containing proteins for which the expression patterns remained unchanged or even appeared up-regulated in the absence of EF-P. Subsequent analysis using in vitro and in vivo reporter assays revealed that stalling at PPP motifs is influenced by the sequence context upstream of the stall site. Specifically, the presence of amino acids such as Cys and Thr preceding the stall site suppressed stalling at PPP motifs, whereas amino acids like Arg and His promoted stalling. In addition to providing fundamental insight into the mechanism of peptide-bond formation, our findings suggest how the sequence context of polyproline-containing proteins can be modulated to maximize the efficiency and yield of protein production.
authors.affiliation: Gene Center and Department for Biochemistry, University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany.
authors.forename: Agata L
authors.initials: AL
authors.lastname: Starosta
authors.affiliation: Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany.
authors.forename: Jürgen
authors.initials: J
authors.lastname: Lassak
authors.affiliation: Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK Institute of Technology, University of Tartu, Tartu, Estonia.
authors.forename: Lauri
authors.initials: L
authors.lastname: Peil
authors.affiliation: Institute of Technology, University of Tartu, Tartu, Estonia Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden.
authors.forename: Gemma C
authors.initials: GC
authors.lastname: Atkinson
authors.affiliation: Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
authors.forename: Kai
authors.initials: K
authors.lastname: Virumäe
authors.affiliation: Institute of Technology, University of Tartu, Tartu, Estonia.
authors.forename: Tanel
authors.initials: T
authors.lastname: Tenson
authors.affiliation: Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
authors.forename: Jaanus
authors.initials: J
authors.lastname: Remme
authors.affiliation: Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany Center for integrated Protein Science Munich (CiPSM) at the University of Munich, Munich, Germany.
authors.forename: Kirsten
authors.initials: K
authors.lastname: Jung
authors.affiliation: Gene Center and Department for Biochemistry, University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany Center for integrated Protein Science Munich (CiPSM) at the University of Munich, Munich, Germany wilson@genzentrum.lmu.de.
authors.forename: Daniel N
authors.initials: DN
authors.lastname: Wilson
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000032:analysis; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000096:biosynthesis / Q000737:chemistry* / Q000235:genetics; D010455:Peptides / Q000032:analysis; D014176:Protein Biosynthesis; D012270:Ribosomes / Q000378:metabolism; D015854:Up-Regulation
chemical_list: D000596:Amino Acids; D029968:Escherichia coli Proteins; D010455:Peptides; C011083:polyproline