The kinetic mechanism of bacterial ribosome recycling.

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

Sharp estimates on minimum travelling wave speed of reaction diffusion systems modelling autocatalysis

This article studies propagating wave fronts in an isothermal chemical reaction A + 2B - \u3e 3B involving two chemical species, a reactant A and an autocatalyst B, whose diffusion coefficients, D-A and D-B, are unequal due to different molecular weights and/or sizes. Explicit bounds v(*) and v* that depend on D-B/D-A are derived such that there is a unique travelling wave of every speed v \u3e = v* and there does not exist any travelling wave of speed v \u3c v*. New to the literature, it is shown that v(*) proportional to v* proportional to D-B/D-A when D-B = v(min). Estimates on v(min) significantly improve those of early works. The framework is built upon general isothermal autocatalytic chemical reactions A + nB - \u3e (n + 1)B of arbitrary order n \u3e = 1