Lyu et al. 2021 (PRJNA708348)

General Details

Title Codon usage and protein length-dependent feedback from translation elongation to translation initiation and kinetics
Organism
Number of Samples 25
Release Date 2021/03/09 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP310013
ENA SRP310013
GEO GSE168595
BioProject PRJNA708348

Publication

Title
Authors Lyu X,Yang Q,Zhao F,Liu Y
Journal Nucleic acids research
Publication Date 2021 Sep 20
Abstract Essential cellular functions require efficient production of many large proteins but synthesis of large proteins encounters many obstacles in cells. Translational control is mostly known to be regulated at the initiation step. Whether translation elongation process can feedback to regulate initiation efficiency is unclear. Codon usage bias, a universal feature of all genomes, plays an important role in determining gene expression levels. Here, we discovered that there is a conserved but codon usage-dependent genome-wide negative correlation between protein abundance and CDS length. The codon usage effects on protein expression and ribosome flux on mRNAs are influenced by CDS length; optimal codon usage preferentially promotes production of large proteins. Translation of mRNAs with long CDS and non-optimal codon usage preferentially induces phosphorylation of initiation factor eIF2α, which inhibits translation initiation efficiency. Deletion of the eIF2α kinase CPC-3 (GCN2 homolog) in Neurospora preferentially up-regulates large proteins encoded by non-optimal codons. Surprisingly, CPC-3 also inhibits translation elongation rate in a codon usage and CDS length-dependent manner, resulting in slow elongation rates for long CDS mRNAs. Together, these results revealed a codon usage and CDS length-dependent feedback mechanism from translation elongation to regulate both translation initiation and elongation kinetics. © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.
PMC PMC8450115
PMID 34417614
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR13919657 PRJNA708348 Neurospora crassa Ribo-Seq
SRR13919658 PRJNA708348 Neurospora crassa Ribo-Seq
SRR13919659 PRJNA708348 Neurospora crassa Ribo-Seq Cycloheximide
SRR13919660 PRJNA708348 Neurospora crassa Ribo-Seq
SRR13919661 PRJNA708348 Neurospora crassa Ribo-Seq
SRR13919662 PRJNA708348 Neurospora crassa Ribo-Seq Cycloheximide
SRR13919663 PRJNA708348 Neurospora crassa Ribo-Seq
SRR13919664 PRJNA708348 Neurospora crassa Ribo-Seq
SRR13919665 PRJNA708348 Neurospora crassa Ribo-Seq Cycloheximide
SRR13919666 PRJNA708348 Neurospora crassa Ribo-Seq
SRR13919667 PRJNA708348 Neurospora crassa Ribo-Seq
SRR13919668 PRJNA708348 Neurospora crassa Ribo-Seq Cycloheximide
SRR13919669 PRJNA708348 Neurospora crassa Ribo-Seq
SRR13919670 PRJNA708348 Neurospora crassa Ribo-Seq
SRR13919671 PRJNA708348 Neurospora crassa Ribo-Seq
SRR13919672 PRJNA708348 Neurospora crassa Ribo-Seq
SRR13919673 PRJNA708348 Neurospora crassa Ribo-Seq
SRR13919674 PRJNA708348 Neurospora crassa Ribo-Seq
SRR13919675 PRJNA708348 Neurospora crassa Ribo-Seq
SRR13919676 PRJNA708348 Neurospora crassa Ribo-Seq
SRR13919677 PRJNA708348 Neurospora crassa Ribo-Seq
SRR13919678 PRJNA708348 Neurospora crassa Ribo-Seq
SRR13919679 PRJNA708348 Neurospora crassa Ribo-Seq
SRR13919680 PRJNA708348 Neurospora crassa Ribo-Seq
SRR13919681 PRJNA708348 Neurospora crassa Ribo-Seq
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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