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Translatome and transcriptome analysis of TMA20 (MCT-1) and TMA64 (eIF2D) knockout yeast strains

ABSTRACT: We report ribosome profiling and RNA-Seq data of S.cerevisiae strains with TMA20, TMA64 single- and TMA20/TMA64 double-gene knockouts, grown in the rich YPD or minimal SD medium.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE122039 | GEO | 2018/11/01

REPOSITORIES: GEO

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Translatome and transcriptome analysis of TMA20 (MCT-1) and TMA64 (eIF2D) knockout yeast strains

Project description:Translatome and transcriptome analysis of TMA20 (MCT-1) and TMA64 (eIF2D) knockout yeast strains

| PRJNA503203 | ENA

Tma64 (eIF2D), Tma20 (MCT-1), and Tma22 (DENR) recycle post-termination 40S subunits in vivo

Project description:The recycling of ribosomal subunits after translation termination is critical for efficient gene expression. Tma64 (eIF2D), Tma20 (MCT-1), and Tma22 (DENR) function as 40S recycling factors in vitro, but it is unknown whether they perform this function in vivo or serve as alternative initiation factors. Ribosome profiling of strains missing these factors revealed 80S ribosomes queued behind the stop codon, consistent with a block in 40S recycling. We found that unrecycled ribosomes could reinitiate translation at AUG codons in the 3’UTR, as evidenced by peaks in the footprint data and 3’UTR reporter analysis. In vitro translation experiments using reporter mRNAs containing upstream ORFs (uORFs) further established that reinitiation increased in the absence of these proteins. In some cases, 40S ribosomes appeared to rejoin with 60S subunits and undergo an alternative 80S reinitiation process in 3’UTRs. These results support a crucial role for Tma64, Tma20, and Tma22 in the recycling of 40S ribosomal subunits at stop codons and translation reinitiation.

2018-08-30 | GSE108942 | GEO

40S ribosome profiling reveals distinct roles for Tma20/Tma22 (MCT-1/DENR) and Tma64 (eIF2D) in 40S subunit recycling

Project description:The recycling of ribosomes at stop codons for use in further rounds of translation is critical for efficient protein synthesis. Removal of the 60S subunit is catalyzed by the ATPase Rli1 (ABCE1) while removal of the 40S is thought to require Tma64 (eIF2D), Tma20 (MCT-1), and Tma22 (DENR). However, it remains unclear how these Tma proteins cause 40S removal and control reinitiation of downstream translation. Here we developed an enhanced 40S ribosome footprinting strategy to directly observe intermediate steps of ribosome recycling in cells. Deletion of the genes encoding these Tma proteins resulted in broad accumulation of unrecycled 40S subunits at stop codons, directly establishing their role in 40S recycling. Furthermore, the Tma20/Tma22 heterodimer was responsible for a majority of 40S recycling events while Tma64 played a minor role. Introduction of an autism-associated mutation into TMA22 resulted in a loss of 40S recycling activity, linking ribosome recycling and neurological disease.

2021-03-01 | GSE145904 | GEO

Translatome and transcriptome analysis of TMA20 (MCT-1) and TMA64 (eIF2D) knockout yeast strains.

Project description: Not available

| S-EPMC6378902 | biostudies-literature

Reprogramming of translation in yeast cells impaired for ribosome recycling favors short, efficiently translated mRNAs

Project description:Yeast strains lacking orthologs of mammalian eIF2D (Tma64), and either MCT-1 (Tma20) or DENR (Tma22) are broadly impaired for 40S recycling; however, it was unknown whether this defect leads to reduced 43S PIC levels with an impact on translation of particular mRNAs. To test this, we by combined ribosome footprint profiling with RNA-seq analysis of mRNA abundance.

2021-03-31 | GSE166987 | GEO

Tma64 (eIF2D), Tma20 (MCT-1), and Tma22 (DENR) recycle post-termination 40S subunits in vivo

Project description:Tma64 (eIF2D), Tma20 (MCT-1), and Tma22 (DENR) recycle post-termination 40S subunits in vivo

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Spatial reorganization of telomeres in long-lived quiescent cells

2015-08-27 | GSE71273 | GEO

40S ribosome profiling reveals distinct roles for Tma20/Tma22 (MCT-1/DENR) and Tma64 (eIF2D) in 40S subunit recycling

Project description:40S ribosome profiling reveals distinct roles for Tma20/Tma22 (MCT-1/DENR) and Tma64 (eIF2D) in 40S subunit recycling

| PRJNA608705 | ENA

Spatial reorganization of telomeres in long-lived quiescent cells

Project description:Two conditions experiment, ChIP-chip anti-Sir3 comparing Sir3 occupancy in exponentially growing S.cerevisiae cells to Sir3 occupancy in the dense fraction of 7 days YPD culture of S.cerevisiae Two conditions experiment with biological duplicates. Both conditions were processed on the same array, duplicates have been carried separately

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The expression profile under cooper sulfate treatment

Project description:The expression profile of natural isolate of S. cerevisiae carrying different copy of CUP2 were compared under cooper sulfate stress The gene expression profiles of natural isolate of S.cerevisiae(EC9-7), EC9-7 cup2∆ and Ec9-7 cup2∆cup2∆ strains under YPD with 1mM copper sulfate for 1h and rich medium(YPD) were compared.

2011-08-25 | E-GEOD-31661 | biostudies-arrayexpress

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