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Pbp1 associates with Puf3 and promotes translation of its target mRNAs involved in mitochondrial biogenesis

ABSTRACT: Pbp1 associates with Puf3 and promotes translation of its target mRNAs involved in mitochondrial biogenesis

PROVIDER: PRJNA944698 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23865834_1.fastq.gz	Fastqsanger.gz
	SRR23865834_2.fastq.gz	Fastqsanger.gz
	SRR23865835_1.fastq.gz	Fastqsanger.gz
	SRR23865835_2.fastq.gz	Fastqsanger.gz
	SRR23865836_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Pbp1 associates with Puf3 and promotes translation of its target mRNAs involved in mitochondrial biogenesis

Project description:Pbp1 (polyA-binding protein - binding protein 1) is a stress granule marker and polyglutamine expansions in its mammalian ortholog ataxin-2 have been linked to neurodegenerative conditions. Pbp1 was recently shown to form intracellular assemblies that function in the negative regulation of TORC1 signaling under respiratory conditions. Furthermore, it was observed that loss of Pbp1 leads to mitochondrial dysfunction. Here, we show that loss of Pbp1 leads to a specific decrease in mitochondrial proteins whose encoding mRNAs are targets of the RNA-binding protein Puf3, suggesting a functional relationship between Pbp1 and Puf3. We found that Pbp1 stabilizes and promotes the translation of Puf3-target mRNAs in respiratory conditions, such as those involved in the assembly of cytochrome c oxidase. We further show that Pbp1 and Puf3 associate through their respective low complexity domains, which is required for target mRNA stabilization and translation. Our findings reveal a key role for Pbp1-containing assemblies in enabling the translation of mRNAs critical for mitochondrial biogenesis and respiration under metabolically challenging conditions. They may further explain prior associations of Pbp1/ataxin-2 with stress granule biology and RNA metabolism.

2023-05-08 | GSE227356 | GEO

Puf3 participates in ribosomal biogenesis in malaria parasites

Project description:Puf3 participates in ribosomal biogenesis in malaria parasites

| PRJNA414782 | ENA

Rpb4 and Puf3 imprint and post-transcriptionally control stability of a common set of mRNAs in yeast

Project description:Gene expression involving RNA polymerase II is regulated by the concerted interplay between mRNA synthesis and degradation, a crosstalk where mRNA decay machinery impacts transcription and transcription machinery influences mRNA stability. Rpb4, and likely the dimer Rpb4/7 seem to be the central components of the RNA pol II governing these processes. In this work we unravel more precisely the molecular mechanisms participated by Rpb4 that mediates the posttranscriptional events regulating mRNA imprinting and stability. We analysed genome-wide, by RIP-seq, the association of Rpb4 with mRNAs and demonstrated that it targets a broad population of about 1400 transcripts. A group of mRNAs are also targets of the RPB, Puf3. We demonstrated that Rpb4 and Puf3, physically, genetically and functionally interact and cooperate to imprint and regulate stability of this group of mRNA. We also demonstrated, by the first time, that Puf3 associates with the chromatin, in an Rpb4-dependent manner. Our data also point to Rpb4 as the key element of the RNA pol II that interplay mRNA synthesis, imprinting and stability, in cooperation with RBPs.

2022-11-09 | GSE152094 | GEO

Puf3 participates in ribosomal biogenesis in malaria parasites

Project description:Recent studies of the Puf family of RNA-binding proteins revealed that besides their traditional roles in translational regulation of mRNAs, some Puf proteins are also involved in ribosome biogenesis by binding rRNA. In this study, we report the role of a Puf-like protein in Plasmodium falciparum (name as PfPuf3) and its ortholog PyPuf3 in Plasmodium yoelii in ribosome biogenesis. Secondary structure prediction suggested that the RNA-binding domain of Puf3 consists of 11 pumilio repeats, similar to human Puf-A/yeast Puf6, which involved in ribosome biogenesis. Neither pfpuf3 nor pypuf3 could be genetically disrupted, suggesting they may be essential for the intraerythrocytic developmental cycle (IDC). A time-course study of PfPuf3 protein indicated that PfPuf3 was expressed during the entire IDC, with peak expression in early trophozoites. Cellular fractionation of PfPuf3 revealed that it is preferentially partitioned to the nuclear than the cytoplasmic fractions, which is consistent with a nuclear localization of PfPuf3::GFP and PyPuf3::GFP as seen by immunofluorescence. Further, we found PfPuf3 co-localized with a well-known nucleolus maker, PfNop1, demonstrating that PfPuf3 is a nucleolar protein. This localization is in contrast to the cytoplasmic localization of PfPuf1 and PfPuf2, but matches the localization of human Puf-A and yeast Puf6. Affinity purification of an N-terminal PTP-tagged variant of PfPuf3 revealed an association with 32 proteins associated with the 60S ribosome, and an enrichment of 28S rRNA and ITS2. Taken together, these results demonstrate a nucleolar localization of PfPuf3 and suggest an essential function of PfPuf3 in ribosomal biogenesis.

2018-03-11 | GSE105126 | GEO

Rpb4 and Puf3

Project description:Rpb4 and Puf3

| PRJNA638290 | ENA

Schizosaccharomyces pombe Puf3 interactome

Project description:Puf3 is a RNA-binding protein, a member of the conserved Puf-protein family. Combining different functional genomics data, we have analyzed the role of Puf3 in post-transcriptional gene regulation in S. pombe. We present data on Puf3 interacting proteins and regulatory mRNA targets.

2022-03-23 | PXD006318 | Pride

Expression data from wild-type, ccr4∆, and ccr4∆ pbp1∆ yeast cells.

Project description:Wild type, ccr4∆, ccr4∆ pbp1∆ cells were grown in YPD medium from log phase to stationary phase. Total RNAs ere extracted and subjected to microarray analysis.

2022-03-18 | GSE198743 | GEO

Identification of RNAs associated with S. cerevisiae or N. crassa Puf3

Project description:Affinity purification of S. cerevisiae or N. crassa Puf3 from S. cerevisiae cells and identification of associated RNAs by microarray

2015-03-16 | GSE50996 | GEO

Quantitative global proteomics of yeast PBP1 deletion mutants and their stress responses reveals glucose metabolism, translation and stress granule changes

Project description:The yeast protein PBP1 has been implicated in diverse pathways such as polyadenylation, translation, RNA-DNA hybrid formation, stress granule homeostasis, mitochondrial dysfunction, and TORC1 sequestration. Intriguingly, its deletion mitigates the toxicity of human neurodegeneration factors, but the molecular mechanisms of these effects are poorly understood. Here we performed label-free quantitative global proteomics to identify crucial downstream factors, comparing two PBP1 deletion strains (DB and SM) and two cell stress conditions (heat and NaN3). In all four analyses, downregulations of key bioenergetics enzymes (CIT1, SDH1, MLS1), cell wall mannoproteins (HSP150, PST1) and the prion protein RNQ1 as well as upregulations of the leucine biosynthesis enzyme LEU1 and the transcription factor TAF6 were documented. Consistently for both unstressed PBP1-deleted strains, over 2-fold dysregulations were documented for potential PBP1 interactors such as MKT1 or RPL39 and the stress granule component NRP1. Upregulation of the ribosomal biogenesis factor NOP10 was observed as in the mouse mutant. Consistently for both PBP1 deletion strains, heat stress triggered changes of the stress granule component GIS2 and several of its interactors.

2016-12-23 | PXD003868 | Pride

PUF3 RNAi in bloodstream-form trypanosomes

Project description:PUF3 was depleted by RNAi for 24h in bloodstream-form trypanosomes (Trypanosoma brucei). No effect was seen on the transcriptome.

2019-06-30 | E-MTAB-8062 | biostudies-arrayexpress

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