Schizosaccharomyces pombe Puf3 interactome
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Schizosaccharomyces Pombe 972h-
SUBMITTER: 
James Wright
LAB HEAD: Jyoti Choudhary
PROVIDER: PXD006318 | Pride | 2022-03-23
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| FTPuf303T-0A.RAW | Raw | |||
| FTPuf303T-0B.RAW | Raw | |||
| FTPuf303T-1.RAW | Raw | |||
| FTPuf303T-10.RAW | Raw | |||
| FTPuf303T-10A.RAW | Raw |
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Project description:The Puf family of RNA-binding proteins regulate the expression of genes by controlling protein synthesis or stimulating RNA decay. Puf3p is one of six Puf-family members in Saccharomyces cerevisiae. Puf3p has been characterised previously as regulating mRNA decay of nuclear mRNAs that encode for mitochondrial proteins. We undertook a series of genome wide approaches to identify an expanded set of Puf3p target mRNAs and to quantitatively assess the impact of loss of PUF3 on the expression control in actively growing wild type and puf3Δ strains. Here we report our quantifications of relative protein levels. The data suggest that loss of Puf3p only impacts on a small proportion of the proteins encoded by its mRNA targets.
2016-04-13 | PXD001903 | Pride
Project description:The Puf family of RNA-binding proteins regulate gene expression by controlling protein synthesis or stimulating RNA decay. Puf3p is one of six related proteins in Saccharomyces cerevisiae characterised as targeting and regulating decay of nuclear-encoded mRNAs specifying mitochondrial proteins. Much prior work has examined how Puf3p regulates COX17 mRNA. We undertook a genome-wide approach to quantitatively assess the impact of loss of PUF3 on gene expression. Comparing transcript levels in wild-type and puf3∆ cells revealed that that only a small fraction of mRNA levels alter, suggesting Puf3p determines mRNA stability for only some target mRNAs.
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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.
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Project description:The Puf family of RNA-binding proteins regulates gene expression by controlling protein synthesis or stimulating RNA decay. Puf3p is one of six related proteins in Saccharomyces cerevisiae characterised as targeting and regulating decay of nuclear-encoded mRNAs specifying mitochondrial proteins. Much prior work has examined how Puf3p regulates COX17 mRNA. We undertook a genome-wide approach to quantitatively assess the impact of loss of PUF3 on gene expression using polysome profiling. Our translatomic study suggests that loss of Puf3p has widespread, but modest, impact on mRNA translation.
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Project description:Investigation of the proteins associated with Puf3, an RNA-binding protein, in Saccharomyces cerevisiae. The goal is to compare the Puf3 interactome in a wild-type strain and in a Not4-deleted strain (Δnot4), in order to assess the potential role of Not4 in modulating Puf3-associated complexes. Puf3 carries a TAP tag at its C-terminus. A non-tagged strain was included as a negative control and to know if unspecific bindings are occurring in vitro that would be due to specific backgrounds, samples were mixed with a strain that does not contain any tag before breaking the cells. Additionally, the user is also interested in exploring post-translational modifications, including phosphorylation and ubiquitination. The objective of this analysis is to identify potential Puf3 interactors in wild-type versus Δnot4 strains using a mass spectrometry-based (LC-ESI-MSMS) label-free quantitative proteomics approach.
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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 (Puf3) in ribosome biogenesis in Plasmodium falciparum and Plasmodium yoelii. Secondary structure prediction suggested that the RNA-binding domain of Puf3 consists of 11 pumilio repeats, similar to human Puf-A/yeast Puf6, which is 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 rather 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 a C-terminal PTP-tagged variant of PfPuf3 revealed an association with 32 proteins associated with the 60S ribosome, and an enrichment of 28S rRNA and internal transcribed spacer 2. Taken together, these results demonstrate a nucleolar localization of PfPuf3 and suggest an essential function of PfPuf3 in ribosomal biogenesis.
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Project description:Affinity purification of S. cerevisiae or N. crassa Puf3 from S. cerevisiae cells and identification of associated RNAs by microarray
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