The kinetic mechanism of bacterial ribosome recycling.

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Nucleic acids research, ISSN: 1362-4962, Vol: 45, Issue: 17, Page: 10168-10177

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Chen, Yuanwei; Kaji, Akira; Kaji, Hideko; Cooperman, Barry S.
Oxford University Press (OUP); Oxford University Press
Biochemistry, Genetics and Molecular Biology; anisotropy; bacterial cell; controlled study; hydrolysis; light scattering; nonhuman; priority journal; protein binding; protein secretion; ribosome; sequence analysis; stoichiometry; stop codon; Medical Biochemistry; Medicine and Health Sciences
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Bacterial ribosome recycling requires breakdown of the post-termination complex (PoTC), comprising a messenger RNA (mRNA) and an uncharged transfer RNA (tRNA) cognate to the terminal mRNA codon bound to the 70S ribosome. The translation factors, elongation factor G and ribosome recycling factor, are known to be required for recycling, but there is controversy concerning whether these factors act primarily to effect the release of mRNA and tRNA from the ribosome, with the splitting of the ribosome into subunits being somewhat dispensable, or whether their main function is to catalyze the splitting reaction, which necessarily precedes mRNA and tRNA release. Here, we utilize three assays directly measuring the rates of mRNA and tRNA release and of ribosome splitting in several model PoTCs. Our results largely reconcile these previously held views. We demonstrate that, in the absence of an upstream Shine-Dalgarno (SD) sequence, PoTC breakdown proceeds in the order: mRNA release followed by tRNA release and then by 70S splitting. By contrast, in the presence of an SD sequence all three processes proceed with identical apparent rates, with the splitting step likely being rate-determining. Our results are consistent with ribosome profiling results demonstrating the influence of upstream SD-like sequences on ribosome occupancy at or just before the mRNA stop codon.