Chaperone saturation mediates translation and protein folding efficiency

Whether the emergence of a nascent protein from the ribosome and the formation of structural elements are synchronized has been a longstanding question. Paradoxically, kinetically efficient translation can induce mis-folding and aggregation despite the presence of molecular chaperones, which in Escherichia coli are induced by unfolded protein via s32. The molecular mechanisms mediating translation efficiency and protein folding efficiency remain poorly understood. Using ribosome profiling and protein quantitation, we show that synonymous changes to Firefly Luciferase (Luc) mRNA have a direct effect on its translation efficiency. These changes alone cause up to a 70-fold difference in Luc protein levels. However, increased Luc protein is met with at most a ~2-fold increase in chaperone levels, revealing that the s32 transcriptional response has saturable properties. This response is found to be poised near its midpoint (where it is most sensitive to perturbation) when Luc mRNA has an intermediate translation efficiency. These results suggest not only that chaperone saturation limits the ability of cells to maintain protein folding homeostasis when challenged with highly efficient translation, but that translation efficiency and protein folding efficiency evolved for mutual sensitivity. Overall design: Cells containing pACYC177 plasmid serve as the control samples expressing no Firefly Luciferase. All experiments were performed in duplicate or triplicate. Some samples were processed at the same time and sequenced together (5 total series): C_1, S_1, W_1, H_1, F_1 C_2, S_2, W_2, H_2, F_2 C_3, S_3, W_3, H_3, F_3 SF_1, SF_2, SF_3, FS_1, FS_2, FS_3 SinF_1, SinF_2, FinS_1, FinS_2 mRNA sequencing experiments were performed once. C_mRNA,S_mRNA,W_mRNA,H_mRNA,F_mRNA