Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Developmental mRNA clearance by PIWI-bound endo-siRNAs in Paramecium

ABSTRACT: The clearance of untranslated mRNAs by Argonaute proteins is essential for embryonic development in metazoans. However, it is currently unknown whether a similar process exists in unicellular eukaryotes. The ciliate Paramecium tetraurelia harbors a vast array of Argonaute proteins of the Piwi-clade involved in various small RNA pathways, many of which have not yet been investigated. In this work, we investigated the function of a Piwi protein, Ptiwi08, whose expression is limited to a narrow time window during development, concomitant with the start of zygotic transcription. We show that Ptiwi08 acts in an endo-siRNA pathway involved in the clearance of a set of mRNAs at the post-transcriptional level. Based on their features, we hypothesized that these mRNAs may be untranslated. In this dataset, we used mass spectrometry to determine whether any protein products of these mRNAs can be found.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Paramecium Tetraurelia

SUBMITTER: Manfred Heller

LAB HEAD: Mariusz Nowacki

PROVIDER: PXD038984 | Pride | 2023-05-10

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Developmental mRNA clearance by PIWI-bound endo-siRNAs in Paramecium.

Solberg Therese T Mason Victor V Wang Chundi C Nowacki Mariusz M

Cell reports 20230303 3

The clearance of untranslated mRNAs by Argonaute proteins is essential for embryonic development in metazoans. However, it is currently unknown whether similar processes exist in unicellular eukaryotes. The ciliate Paramecium tetraurelia harbors a vast array of PIWI-clade Argonautes involved in various small RNA (sRNA) pathways, many of which have not yet been investigated. Here, we investigate the function of a PIWI protein, Ptiwi08, whose expression is limited to a narrow time window during de ...[more]

PMID: 36870062

Similar Datasets

Identification of regenerating island-derived protein 3E in dogs

Project description:Our aim was to identify Regenerating islet-derived (REG proteins in dogs. We annotated REG-family members in the canine genome and proteome, and identified one member of the REG3 subfamily, consequently termed REG3E by the Vertebrate Gene Nomenclature Committee. We verified REG3E gene expression using publicly available RNA-seq data (www.barkbase.org). We investigated the presence of REG3E protein in canine pancreatic tissue and plasma with Western blot and immunohistochemistry, using anti-human REG3A antibodies. Protein identity was subsequently confirmed with mass spectrometry on canine pancreas homogenates and plasma.

2022-10-17 | PXD035694 | Pride

Metaproteome plasticity sheds light on the ecology of the rumen microbiome and its connection to host traits

Project description:The arsenal of genes that microbes express reflect the way in which they sense their environment. We have previously reported that the rumen microbiome composition and its coding capacity are different in animals having distinct feed efficiency states, even when fed an identical diet. Here, we reveal that many microbial populations show divergent proteome production in function of the feed efficiency state. Thus, proteomic data serve as a strong indicator of host feed efficiency state phenotype, overpowering predictions based on genomic and taxonomic information. We highlight protein production of specific phylogenies associated with each of the feed efficiency states. We also find remarkable plasticity of the proteome both in the individual population and at the community level, driven by niche partitioning and competition. These mechanisms result in protein production patterns which exhibit functional redundancy and checkerboard distribution that are tightly linked to the host feed efficiency phenotype. By linking microbial protein production and the ecological mechanisms that act within the microbiome feed efficiency states, our present work reveals a layer of complexity that bears immense importance to the current global of food security and sustainability.

2022-08-25 | PXD033418 | Pride

Characterisation of the Semliki Forest Virus-host cell interactome reveals the viral capsid protein as an inhibitor of nonsense-mediated mRNA decay

Project description:Understanding the complex interactions between the viral and the host cell proteins is crucial for elucidating the mechanisms underlying successful virus replication strategies and for developing specific antiviral interventions. This project presents the first comprehensive protein-protein interaction map between the proteins of Semliki Forest Virus (SFV), a mosquito-borne member of the alphaviruses, and host cell proteins. We additionally overlay an SFV siRNA screen to assign pro- or antiviral functions to the interactors. Among the many identified cellular interactors of SFV proteins, there was an enrichment of factors involved in translation and nonsense-mediated mRNA decay (NMD). Validating these findings, we observed a general inhibition of NMD during SFV infection and demonstrated that transient expression of the SFV capsid protein was sufficient to inhibit NMD in cells.

2021-05-07 | PXD022036 | Pride

The dual prey-inactivation strategy of spiders - In-depth venomic analysis of Cupiennius salei

Project description:Most knowledge on spider venoms concerns neurotoxins acting on ion channels, whereas proteins and their significance for the envenomation process are neglected. The comprehensive analysis presented here of the venom gland transcriptome and proteome of Cupiennius salei with a focus on proteins and cysteine-containing peptides offers new insight into the structure and function of spider venom, presented here as dual prey-inactivation strategy. After venom injection, many enzymes and proteins, dominated by α-amylase, angiotensin-converting enzyme, and cysteine-rich secretory proteins, interact with main metabolic pathways, leading to major disturbance of the cellular homeostasis. Hyaluronidase and cytolytic peptides destroy tissue and membranes, thus supporting the spread of other venom compounds. We detected 81 transcripts of neurotoxins from 13 peptide families, whereof two families comprise 93.7% of all cysteine-containing peptides. This raises the question of the importance of the other low-expressed peptide families. The identification of a venom gland-specific defensin-like peptide and an aga-toxin-like peptide in the hemocytes offers an important clue on the recruitment and neofunctionalization of body proteins and peptides as the origin of toxins.

2019-03-25 | PXD012881 | Pride

MGA interactome in 293T cells using affinity purification and mass spectrometry

Project description:Tandem affinity purification of MGA-interacting proteins and mass spectrometry

2021-07-06 | PXD025930 | Pride

40S hnRNP particles are a novel class of nuclear biomolecular condensates

Project description:Heterogenous nuclear ribonucleoproteins (hnRNPs) are abundant proteins implicated in various steps of RNA processing that assemble on nuclear RNA into larger complexes termed 40S hnRNP particles. Despite their initial discovery 55 years ago, our understanding of these intriguing macromolecular assemblies remains limited. We biochemically purified native 40S hnRNP particles and determined their complete protein composition by label-free quantitative mass spectrometry, identifying A-group and C-group hnRNPs as the major protein constituents.

2022-05-30 | PXD031677 | Pride

Clients of membrane-bound PDI family members

Project description:The client-specificity of TMX3, TMX4 and TMX5 in cellula, was assessed by expressing mutant forms of the enzymes, where the last cysteine residue of the TMX’s CXXC catalytic sites has been mutated to alanine, which stabilizes the mixed disulfide that oxidoreductases establish with clients. Clients remain disulfide-bonded to the oxidoreductase and are identified upon co-immunoprecipitation and mass spectrometry analyses.

2023-06-12 | PXD041156 | Pride

Shotgun protemoics of lobules 1-4 and crus 2

Project description:Data used to produce Figure 2D from "A multifaceted gradient in human cerebellum of structural and functional development." Shotgun proteomic analysis from tissue samples taken from lobules 1-4 and crus 2 of the human cerebellum. Single subject, 3yo female.

2023-03-08 | PXD034848 | Pride

Differential modifications of the C-terminal tails of alpha-tubulin isoforms and their importance for kinesin-based microtubule transport in vivo

Project description:Microtubules (MTs) are built from alpha/beta-tubulin dimers and used as tracks by kinesin and dynein motors to transport a variety of cargos, such as mRNAs, proteins, and organelles, within the cell. Tubulins are subjected to several post-translational modifications (PTMs). Glutamylation is one of them, and it is responsible for adding one or more glutamic acid residues as branched peptide chains to the C-terminal tails of both alpha- and beta-tubulin. However, very little is known about the specific modifications found on the different tubulin isoforms in vivo and the role of these PTMs in cargo transport along MTs in vivo. In this study, we found that in Drosophila, glutamylation of the alpha-tubulin isoforms occurs specifically on the C-terminal ends of TBA1 and TBA3 in the ovaries. In contrast, the ovarian isoform TBA4 is not glutamylated. The C-terminal ends of TBA1 and TBA3 are glutamylated at several glutamyl side chains in various combinations. Drosophila TTLL5 is required for the mono- and polyglutamylation of ovarian TBA1 and 3. Furthermore, glutamylation of the alpha-tubulin is essential for the efficient localization of Staufen/osk mRNA and to give directionality to the fast ooplasmic streaming, two processes known to depend on kinesin mediated processes during oogenesis. In the nervous system, the kinesin-dependent neuronal transport of mitochondria also depends on TTLL5. Additionally, alpha-tubulin glutamylation affects the pausing of the transport of individual mitochondria in the axons. Our results demonstrate the in vivo role of TTLL5 in differential glutamylation of alpha-tubulin isoforms and point to the in vivo importance of alpha-tubulin glutamylation for kinesin-dependent processes.

2023-07-11 | PXD035270 | Pride

CDC14B interactome - The proteomic approach aimed at the identification of interaction partners for the human dual phosphatase and tumor suppressor CDC14B by Co-inmunoprecipitation (Co-IP) experiments. In this approach, CDC14B interactomes from unsynchronized and G2/M enriched cells were compared semi-quantitatively based on spectral counting. This approach yielded the deubiquitylase USP9X as a G2/M-specific CDC14B interactor which has been confirmed by Western-blot (WB).

Project description:The proteomic approach aimed at the identification of interaction partners for the human dual phosphatase and tumor suppressor CDC14B by Co-inmunoprecipitation (Co-IP) experiments. In this approach, CDC14B interactomes from unsynchronized and G2/M enriched cells were compared semi-quantitatively based on spectral counting. This approach yielded the deubiquitylase USP9X as a G2/M-specific CDC14B interactor which has been confirmed by Western-blot (WB).

2020-03-25 | PXD012732 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data