GCN sensitive protein translation in yeast

PLoS One. 2020 Sep 18;15(9):e0233197. doi: 10.1371/journal.pone.0233197. eCollection 2020.

Abstract

Levels of protein translation by ribosomes are governed both by features of the translation machinery as well as sequence properties of the mRNAs themselves. We focus here on a striking three-nucleotide periodicity, characterized by overrepresentation of GCN codons and underrepresentation of G at the second position of codons, that is observed in Open Reading Frames (ORFs) of mRNAs. Our examination of mRNA sequences in Saccharomyces cerevisiae revealed that this periodicity is particularly pronounced in the initial codons-the ramp region-of ORFs of genes with high protein expression. It is also found in mRNA sequences immediately following non-standard AUG start sites, located upstream or downstream of the standard annotated start sites of genes. To explore the possible influences of the ramp GCN periodicity on translation efficiency, we tested edited ramps with accentuated or depressed periodicity in two test genes, SKN7 and HMT1. Greater conformance to (GCN)n was found to significantly depress translation, whereas disrupting conformance had neutral or positive effects on translation. Our recent Molecular Dynamics analysis of a subsystem of translocating ribosomes in yeast revealed an interaction surface that H-bonds to the +1 codon that is about to enter the ribosome decoding center A site. The surface, comprised of 16S/18S rRNA C1054 and A1196 (E. coli numbering) and R146 of ribosomal protein Rps3, preferentially interacts with GCN codons, and we hypothesize that modulation of this mRNA-ribosome interaction may underlie GCN-mediated regulation of protein translation. Integration of our expression studies with large-scale reporter studies of ramp sequence variants suggests a model in which the C1054-A1196-R146 (CAR) interaction surface can act as both an accelerator and braking system for ribosome translation.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Base Composition / genetics
  • Codon, Initiator / genetics*
  • Codon, Initiator / metabolism
  • DNA-Binding Proteins / biosynthesis
  • DNA-Binding Proteins / genetics
  • Molecular Dynamics Simulation
  • Open Reading Frames / genetics
  • Protein Biosynthesis / genetics*
  • Protein-Arginine N-Methyltransferases / biosynthesis
  • Protein-Arginine N-Methyltransferases / genetics
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Repressor Proteins / biosynthesis
  • Repressor Proteins / genetics
  • Ribosomes / metabolism*
  • Saccharomyces cerevisiae / cytology
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / biosynthesis
  • Saccharomyces cerevisiae Proteins / genetics
  • Transcription Factors / biosynthesis
  • Transcription Factors / genetics

Substances

  • Codon, Initiator
  • DNA-Binding Proteins
  • RNA, Messenger
  • Repressor Proteins
  • SKN7 protein, S cerevisiae
  • Saccharomyces cerevisiae Proteins
  • Transcription Factors
  • HMT1 protein, S cerevisiae
  • Protein-Arginine N-Methyltransferases