Translational control through differential ribosome pausing during amino acid limitation in mammalian cells

Abstract

Limitation for amino acids is thought to regulate translation in mammalian cells primarily by signaling through the kinases mTORC1 and GCN2. We find that limitation for the amino acid arginine causes a selective loss of isoacceptor tRNA charging, which regulates translation through selective ribosome pausing at two of six arginine codons. Interestingly, limitation for leucine, an essential and abundant amino acid in proteins, resulted in little or no ribosome pausing. Chemical and genetic perturbation of mTORC1 and GCN2 signaling revealed that their robust response to leucine limitation prevented ribosome pausing, while an insufficient response to arginine limitation led to loss of arginine tRNA charging and ribosome pausing. Codon-specific ribosome pausing decreased protein production specifically during arginine limitation without significantly reducing mRNA levels. Together, our results suggest an evolutionarily conserved role for synonymous codon usage in elongation rate control of protein synthesis during limitation for single amino acids.