Lyu et al. 2020 (PRJNA534111)

General Details

Title Effect of adat2 silencing in Neurospora crassa on translation kinetics and transcriptome
Organism
Number of Samples 4
Release Date 2019/04/22 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP193378
ENA SRP193378
GEO GSE130155
BioProject PRJNA534111

Publication

Title
Authors Lyu X, Yang Q, Li L, Dang Y, Zhou Z, Chen S, Liu Y
Journal PLoS genetics
Publication Date 2020 Jun
Abstract Codon usage bias is a universal feature of all genomes and plays an important role in regulating protein expression levels. Modification of adenosine to inosine at the tRNA anticodon wobble position (I34) by adenosine deaminases (ADATs) is observed in all eukaryotes and has been proposed to explain the correlation between codon usage and tRNA pool. However, how the tRNA pool is affected by I34 modification to influence codon usage-dependent gene expression is unclear. Using Neurospora crassa as a model system, by combining molecular, biochemical and bioinformatics analyses, we show that silencing of adat2 expression severely impaired the I34 modification levels for the ADAT-related tRNAs, resulting in major ADAT-related tRNA profile changes and reprogramming of translation elongation kinetics on ADAT-related codons. adat2 silencing also caused genome-wide codon usage-biased ribosome pausing on mRNAs and proteome landscape changes, leading to selective translational repression or induction of different mRNAs. The induced expression of CPC-1, the Neurospora ortholog of yeast GCN4p, mediates the transcriptional response after adat2 silencing and amino acid starvation. Together, our results demonstrate that the tRNA I34 modification by ADAT plays a major role in driving codon usage-biased translation to shape proteome landscape.
PMC PMC7289440
PMID 32479508
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR9002961 PRJNA534111 Neurospora crassa 0.0 Ribo-Seq Cycloheximide
SRR9002962 PRJNA534111 Neurospora crassa 0.0 Ribo-Seq Cycloheximide
SRR9601985 PRJNA534111 Neurospora crassa 0.0 Ribo-Seq Cycloheximide
SRR9601986 PRJNA534111 Neurospora crassa 0.0 Ribo-Seq Cycloheximide
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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