How Does a 30S Ribosome Find Its Target on an mRNA?

Abstract

To initiate translation in prokaryotes, the 30S ribosome must bind to the Ribosomal Binding Site (RBS) on the mRNA. The rate at which this process occurs affects the overall efficiency of the translation process and thus impacts the speed at which prokaryotes can grow and divide. Experimental evidence that 80% of ribosomes are actively translating suggests the search process may represent a significant biophysical challenge for the cell, and further places a rough upper limit of 4s on the time the search process may take. This bound is significantly exceeded by a search that only utilizes the free 3D diffusion of the 30S and mRNA, suggesting that the 30S may perform local searches on each mRNA to which it nonspecifically binds. Here, we employ a simple theoretical framework to examine several possibilities for these local searches. The 30S may: 1) diff use along the mRNA in 1D; 2) simultaneously bind to two sites along the mRNA chain and perform an Intersegmental Transfer (IT) between them; 3) diffuse within the mRNA coil; or 4) utilize a combination of these strategies. We demonstrate that nearly all these search strategies may be fast enough to be biologically viable; however, in comparing our results to recent in vitro experiments measuring the dissociation rate of the 30S from the mRNA (Mil on et al., 2012), we find that the most likely candidates for the search process are searches using ITs that do not include diffusion within the mRNA coil. Finally, we suggest future in vitro experiments, based on the predicted scaling behavior of the search time and dissociation rate with mRNA length and concentration, whose results may indicate which search strategy is used by the 30S.