Translation Initiation is Controlled by RNA Folding Kinetics via a Ribosome Drafting Mechanism

RNA
folding plays an important role in controlling protein synthesis
as well as other cellular processes. Existing models have focused
on how RNA folding energetics control translation initiation rate
under equilibrium conditions but have largely ignored the effects
of nonequilibrium RNA folding. We introduce a new mechanism, called
“ribosome drafting”, that explains how a mRNA’s
folding kinetics and the ribosome’s binding rate collectively
control its translation initiation rate. During cycles of translation,
ribosome drafting emerges whenever successive ribosomes bind to a
mRNA faster than the mRNA can refold, maintaining it in a nonequilibrium
state with an acceleration of protein synthesis. Using computational
design, time-correlated single photon counting, and expression measurements,
we demonstrate that slow-folding and fast-folding RNA structures with
equivalent folding energetics can vary protein synthesis rates by
1000-fold. We determine the necessary conditions for ribosome drafting
by characterizing mRNAs with rationally designed ribosome binding
rates, folding kinetics, and folding energetics, confirming the predictions
of a nonequilibrium Markov model of translation. Our results have
widespread implications, illustrating how competitive folding and
assembly kinetics can shape the gene expression machinery’s
sequence–structure–function relationship inside cells.