Codon usage and protein length-dependent feedback from translation elongation to translation initiation and kinetics

In yeast and mammals, activated GCN2 can phosphorylate its substrate eIF2a, which is a part of the eIF2-GTP-Met-tRNAiMet ternary complex. The eIF2a phosphorylation blocks the ternary complex formation and therefore inhibits translation initiation. Meanwhile, GCN2 activation associates with ribosomes and some translation elongation factors such as eEF1A. In Neurospora crassa, the homolog of GCN2 is CPC-3. Ribosome profiling and accompanying RNA-seq experiments in this project were used to explore the effects of CPC-3 on translation kinetics. Here we show that poor codon usage of mRNAs with long CDS preferentially causes CPC-3 activation, which in turn suppresses the translation initiation and elongation in both codon usage and CDS length dependent manner. Overall design: The ribosome protected fragment (RPF) profiles and transcription profiles of ?cpc-3 and wild-type strains of Neurospora crassa were generated by high-throughput sequencing