title: Determinants of the rate of mRNA translocation in bacterial protein synthesis.
abstract: Studying the kinetics of translocation of mRNA and tRNAs on the translating ribosome is technically difficult since the rate-limiting steps involve large conformational changes without covalent bond formation or disruption. Here, we have developed a unique assay system for precise estimation of the full translocation cycle time at any position in any type of open reading frame (ORF). Using a buffer system optimized for high accuracy of tRNA selection together with high concentration of elongation factor G, we obtained in vivo compatible translocation rates. We found that translocation was comparatively slow early in the ORF and faster further downstream of the initiation codon. The maximal translocation rate decreased from the in vivo compatible value of 30 s(-1) at 1 mM free Mg2+ concentration to the detrimentally low value of 1 s(-1) at 6 mM free Mg2+ concentration. Thus, high and in vivo compatible accuracy of codon translation, as well as high and in vivo compatible translocation rate, required a remarkably low Mg2+ concentration. Finally, we found that the rate of translocation deep inside an ORF was not significantly affected upon variation of the standard free energy of interaction between a 6-nt upstream Shine-Dalgarno (SD)-like sequence and the anti-SD sequence of 16S rRNA in a range of 0-6 kcal/mol. Based on these experiments, we discuss the optimal choice of Mg2+ concentration for maximal fitness of the living cell by taking its effects on the accuracy of translation, the peptide bond formation rate and the translocation rate into account.
authors.affiliation: Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, 751 24 Uppsala, Sweden; 3H Biomedical AB, Dag Hammarskjölds väg 34A, Uppsala Science Park, 751 83 Uppsala, Sweden. Electronic address: anneli.borg@icm.uu.se.
authors.forename: Anneli
authors.initials: A
authors.lastname: Borg
authors.affiliation: Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, 751 24 Uppsala, Sweden. Electronic address: ehrenberg@xray.bmc.uu.se.
authors.forename: Måns
authors.initials: M
authors.lastname: Ehrenberg
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism*; D018387:Codon, Initiator / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D016366:Open Reading Frames / Q000235:genetics*; D020653:Peptide Elongation Factor G / Q000235:genetics / Q000378:metabolism; D014176:Protein Biosynthesis / Q000502:physiology*; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism*; D012336:RNA, Ribosomal, 16S / Q000235:genetics / Q000378:metabolism; D012343:RNA, Transfer / Q000235:genetics / Q000378:metabolism; D012270:Ribosomes / Q000235:genetics / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D018387:Codon, Initiator; D020653:Peptide Elongation Factor G; D012333:RNA, Messenger; D012336:RNA, Ribosomal, 16S; D012343:RNA, Transfer
keywords: accuracy monitoring bases; fitness maximization; mRNA translocation; magnesium ions; speed accuracy trade-off