Puf3 participates in ribosomal biogenesis in malaria parasites
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PXD007978
PROVIDER: PRJNA414782 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6187451.fastq.gz | Fastqsanger.gz | |||
| SRR6187452.fastq.gz | Fastqsanger.gz | |||
| SRR6187453.fastq.gz | Fastqsanger.gz | |||
| SRR6187454.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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
Project description:In this study, we characterized the Puf family gene member Puf3 in the malaria parasites Plasmodium falciparum and Plasmodium yoelii Secondary structure prediction suggested that the RNA-binding domains of the Puf3 proteins consisted of 11 pumilio repeats that were similar to those in the human Puf-A (also known as PUM3) and Saccharomyces cerevisiae Puf6 proteins, which are involved in ribosome biogenesis. Neither P. falciparum (Pf)Puf3 nor P. yoelii (Py)Puf3 could be genetically disrupted, suggesting they may be essential for the intraerythrocytic developmental cycle. Cellular fractionation of PfPuf3 in the asexual stages revealed preferential partitioning to the nuclear fraction, consistent with nuclear localization of PfPuf3::GFP and PyPuf3::GFP as detected by immunofluorescence. Furthermore, PfPuf3 colocalized with the nucleolar marker PfNop1, demonstrating that PfPuf3 is a nucleolar protein in the asexual stages. We found, however, that PyPuf3 changed its localization from being nucleolar to being present in cytosolic puncta in the mosquito and liver stages, which may reflect alternative functions in these stages. Affinity purification of molecules that associated with a PTP-tagged variant of PfPuf3 revealed 31 proteins associated with the 60S ribosome, and an enrichment of 28S rRNA and internal transcribed spacer 2 sequences. Taken together, these results suggest an essential function for PfPuf3 in ribosomal biogenesis.
| S-EPMC5897713 | biostudies-literature
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
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
Project description:Pbp1 associates with Puf3 and promotes translation of its target mRNAs involved in mitochondrial biogenesis
| PRJNA944698 | ENA
Project description:Single-cell RNA-sequencing is revolutionising our understanding of seemingly homogeneous cell populations but has not yet been widely applied to single-celled organisms. Transcriptional variation in unicellular malaria parasites from the Plasmodium genus is associated with critical phenotypes including red blood cell invasion and immune evasion, yet transcriptional variation at an individual parasite level has not been examined in depth. Here, we describe the adaptation of a single-cell RNA-sequencing (scRNA-seq) protocol to deconvolute transcriptional variation for more than 500 individual parasites of both rodent and human malaria comprising asexual and sexual life-cycle stages. We uncover previously hidden discrete transcriptional signatures during the pathogenic part of the life cycle, suggesting that expression over development is not as continuous as commonly thought. In transmission stages, we find novel, sex-specific roles for differential expression of contingency gene families that are usually associated with immune evasion and pathogenesis.
2017-02-08 | E-ERAD-611 | biostudies-arrayexpress
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
Project description:To introduce a non-canonical RNA interference pathway into Plasmodium berghei (P. berghei), we generated a P. berghei line constitutively expressing the human protein Argonaute 2 (Ago2) and episomally expressed Ago2-dependent short hairpin RNAs (AgoshRNAs) against GFP. Using RNA sequencing (RNA-Seq), we analyzed transcriptomes of wild type parasites (PbGFPcon), Ago2-expressing parasites (PbAgo2) and PbAgo2 parasites expressing a scrambled AgoshRNA (scr) or anti-GFP-AgoshRNA (aGFP). We compared PbAgo2 to wildtype PbGFPcon parasites and find that Ago2 expression interferes with the expression of development-of-zygote-inhibited (DOZI)-dependent transcripts. When comparing PbAgo2 plus scr with PbAgo2 expressing aGFP, we find a clear knockdown of GFP; Other than that, we do not observe a significant off-targeting in these samples besides differential expression of genes belonging to multi-gene families.
2019-02-22 | GSE95534 | GEO
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