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Yeast poly(A)-binding protein (Pab1) controls translation initiation in vivo primarily by blocking mRNA decapping and decay

ABSTRACT: Yeast poly(A)-binding protein (Pab1) controls translation initiation in vivo primarily by blocking mRNA decapping and decay

PROVIDER: PRJNA1111749 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29031400_subreads.fastq.gz	Fastqsanger.gz
	SRR29031401_subreads.fastq.gz	Fastqsanger.gz
	SRR29031402.fastq.gz	Fastqsanger.gz
	SRR29031403.fastq.gz	Fastqsanger.gz
	SRR29031404.fastq.gz	Fastqsanger.gz

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Similar Datasets

Yeast poly(A)-binding protein (Pab1) controls translation initiation in vivo primarily by blocking mRNA decapping and decay

Project description:Poly(A)-binding protein (Pab1 in yeast) is involved in mRNA decay and translation initiation, but its molecular functions are incompletely understood. In this study, we employed a comprehensive multiomics strategy encompassing Ribosome profiling, spike-in normalized RNA-seq, SMPAT-seq, and CAGE-seq to gain mechanistic insight into Pab1's role in Saccharomyces cerevisiae. We found that auxin-induced degradation of Pab1 reduced bulk mRNA and polysome abundance in a manner suppressed by deleting the catalytic subunit of decapping enzyme (dcp2Δ), demonstrating that enhanced decapping/degradation is the major driver of reduced mRNA abundance and protein synthesis at limiting Pab1 levels. An increased median poly(A) tail length conferred by Pab1 depletion was also nullified by dcp2Δ, suggesting that mRNA isoforms with shorter tails are preferentially decapped/degraded at limiting Pab1. In contrast to findings on mammalian cells, the translational efficiencies (TEs) of many mRNAs were altered by Pab1 depletion; however, these changes were broadly diminished by dcp2∆, suggesting that reduced mRNA abundance is a major driver of translational reprogramming at limiting Pab1. Thus, assembly of the closed-loop mRNP via PABP-eIF4G interaction appears to be dispensable for normal translation of most yeast mRNAs in vivo at normal mRNA levels. Interestingly, histone mRNAs and proteins are preferentially diminished on Pab1 depletion dependent on Dcp2, accompanied by activation of internal cryptic promoters in the manner expected for reduced nucleosome occupancies, revealing a new layer of post-transcriptional control of histone gene expression.

2025-03-19 | GSE267513 | GEO

Yeast poly(A)-binding protein (Pab1) controls translation initiation in vivo primarily by blocking mRNA decapping and decay.

Project description:Poly(A)-binding protein (Pab1 in yeast) is involved in mRNA decay and translation initiation, but its molecular functions are incompletely understood. We found that auxin-induced degradation of Pab1 reduced bulk mRNA and polysome abundance in a manner suppressed by deleting the catalytic subunit of decapping enzyme (dcp2Δ), demonstrating that enhanced decapping/degradation is the major driver of reduced mRNA abundance and protein synthesis at limiting Pab1 levels. An increased median poly(A) tail length conferred by Pab1 depletion was also nullified by dcp2Δ, suggesting that mRNA isoforms with shorter tails are preferentially decapped/degraded at limiting Pab1. In contrast to findings on mammalian cells, the translational efficiencies (TEs) of many mRNAs were altered by Pab1 depletion; however, these changes were broadly diminished by dcp2∆, suggesting that reduced mRNA abundance is a major driver of translational reprogramming at limiting Pab1. Thus, assembly of the closed-loop mRNP via PABP-eIF4G interaction appears to be dispensable for normal translation of most yeast mRNAs in vivo. Interestingly, histone mRNAs and proteins are preferentially diminished on Pab1 depletion dependent on Dcp2, accompanied by activation of internal cryptic promoters in the manner expected for reduced nucleosome occupancies, revealing a new layer of post-transcriptional control of histone gene expression.

| S-EPMC11188147 | biostudies-literature

Direct and indirect consequences of PAB1 deletion in the regulation of translation initiation, translation termination, and mRNA decay [Ribo-seq]

Project description:Cytoplasmic poly(A)-binding protein (PABPC, yeast Pab1) is involved in various stages of mRNA post-transcriptional control, including translation initiation, translation termination, and mRNA decay regulation. Due to the multi-functional properties of PABPC, attempts to define a specific role for PABPC in vivo by deleting, depleting, overexpressing, or mutating the protein has led to conflicting models of PABPC's function. To specifically assess direct and indirect consequences of deleting PABPC, we generated and analyzed RNA-Seq, ribosome profiling, and mass spectrometry data from yeast cells lacking Pab1.

2023-05-31 | GSE229692 | GEO

Direct and indirect consequences of PAB1 deletion in the regulation of translation initiation, translation termination, and mRNA decay [RNA-seq]

2023-05-31 | GSE229691 | GEO

Primarily cultured neurospheres

Project description:Primarily cultured neurospheres

| PRJNA599138 | ENA

Direct and indirect consequences of PAB1 deletion in the regulation of translation initiation, translation termination, and mRNA decay

2023-06-09 | PXD041495 | Pride

0549_2 Fission yeast Pab1 interactome

Project description:We performed mass-spectrometry analysis of proteins co-purifying with the Pab1, the B55 regulatory subunit of the PP2A protein phosphatase complex. Pab1 was tagged with YFP at the C-terminus and expressed from its endogenous promoter at its chromosomal locus. After one hour of nitrogen starvation, Pab1-YFP was pulled down and co-purifying proteins were analysed by mass-spectrometry. Our results revealed the presence of all components of PP2A protein complexes including Paa1, the catalytic subunits Ppa1, Ppa2, and Ppa3.

2024-12-02 | PXD047697 | Pride

Nonsense-mediated mRNA decay in yeast does not require PAB1 or a poly(A) tail.

Project description:Eukaryotic mRNAs harboring premature translation termination codons are recognized and rapidly degraded by the nonsense-mediated mRNA decay (NMD) pathway. The mechanism for discriminating between mRNAs that terminate translation prematurely and those subject to termination at natural stop codons remains unclear. Studies in multiple organisms indicate that proximity of the termination codon to the 3' poly(A) tail and the poly(A) RNA-binding protein, PAB1, constitute the critical determinant in NMD substrate recognition. We demonstrate that mRNA in yeast lacking a poly(A) tail can be destabilized by introduction of a premature termination codon and, importantly, that this mRNA is a substrate of the NMD machinery. We further show that, in cells lacking Pab1p, mRNA substrate recognition and destabilization by NMD are intact. These results establish that neither the poly(A) tail nor PAB1 is required in yeast for discrimination of nonsense-codon-containing mRNA from normal by NMD.

| S-EPMC2241659 | biostudies-literature

GFP:Pab1 interactome in EMM2-N 1hour

Project description:To look for Pab1 interacting proteins, GFP-Pab1 was purified from S. pombe cell under nitrogen depletion (cultureed in EMM2-N for 1hour) and subjected to LC-MS/MS analysis.

2024-12-02 | PXD047579 | Pride

Pumilio-Homology Domain protein APUM9 regulates seed dormancy via decapping-dependent mRNA decay

Project description:APUM9 is a conserved PUF RNA-binding protein (RBP) and the expression of this protein is under complex epigenetic regulation. A transposable element (TE)-mediates this epigenetic regulation and thereby restricts its expression in Arabidopsis. Currently, little is known about the molecular function of the APUM protein family and the biological relevance of the TE-mediated epigenetic control of APUM9 in plant development and stress responses. By combining a range of transient assays, we show here that APUM9 binding to target transcripts can trigger their rapid decay via its conserved C-terminal RNA-binding domain. APUM9 directly interacts with DCP2, the catalytic subunits of the decapping complex suggesting that APUM9-mediated mRNA decay predominantly occurs via the decapping-dependent exonucleolytic pathway. APUM9 negatively regulates the expression of ABA signaling genes during seed imbibition, and thereby might contribute to the switch from dormant stage to seed germination. By contrast, strong TE-mediated repression of APUM9 is important for normal plant growth in the later developmental stages. Finally, APUM9 overexpression plants show slightly enhanced heat tolerance suggesting that TE-mediated epigenetic control of plant APUM9, might have a role not only in embryonic development, but also in plant adaptation to heat stress conditions.

2019-10-11 | GSE104860 | GEO

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