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Translation in amino acid-poor environments is limited by tRNAGln charging

UID: 10823

Author(s): Pavlova, Natalya N.*, King, Bryan C.*, Thompson, Craig B.* * MSK affiliated

Description
Summary from the GEO: "An inadequate supply of amino acids leads to accumulation of uncharged tRNAs, which can bind and activate GCN2 kinase to reduce translation. Here, we show that glutamine-specific tRNAs selectively become uncharged when extracellular amino acid availability is compromised. In contrast, all other tRNAs retain charging of their cognate amino acids in a manner that is dependent upon intact lysosomal function. In addition to GCN2 activation and reduced total translation, the reduced charging of tRNAGln in amino acid-deprived cells also leads to specific depletion of proteins containing polyglutamine tracts including core binding factor α1, mediator subunit 12, transcriptional coactivator CBP and TATA-box binding protein. Treating amino acid-deprived cells with exogenous glutamine or glutaminase inhibitors restores tRNAGln charging and the levels of polyglutamine-containing proteins. Together, these results demonstrate that the activation of GCN2 and the translation of polyglutamine-encoding transcripts serve as the key sensors of glutamine availability in mammalian cells."

Overall design from the GEO: "Mouse embryonic fibroblasts were cultured for 6h with or without amino acids in the presence of glutaminase inhibitor (CB-839) or vehicle (DMSO). RNA was extracted from cells and treated with either 10mM sodium periodite ("oxidized") or sodium chloride ("non-oxidized) prior to sequencing library preparation to calculate tRNA charging ratios."
Subject of Study
Mus musculus
Subject(s)
Amino Acids
Glutamine
Peptides
RNA, Transfer, Gln
Access via GEO

Plain Text file with processed data from the experiment
Accession #: GSE157276

Access via SRA

Transcriptome sequencing of 16 samples
Accession #: SRP279607

Access via BioProject

Additional information about the overall inititative.
Accession #: PRJNA660742

Access Restrictions
Free to All
Access Instructions
The NCBI Gene Expression Omnibus, SRA, and BioProject databases provide open access to these files. The SRA Run Selector link at the bottom of the page is a processing tool for raw data.
Associated Publications
Pavlova N, King B, Josselsohn R, et al. Translation in amino-acid-poor environments is limited by tRNA(Gln) charging. eLife. 2020; 9:e62307.
Data Type
Genomic
Equipment Used
Illumina MiSeq

The MiSeq is an integrated instrument that performs clonal amplification, genomic DNA sequencing, and data analysis with base calling, alignment, variant calling, and reporting in a single run.

Software Used
SRA Toolkit

The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.

Dataset Format(s)
Plain Text, SRA
Data Tool(s)
RNA Seq
Dataset Size
5.3 KB (TXT), 20 Gb (SRA)
Data Catalog Record Updated
2023-12-07