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Nuclear pore complexes interactome dissection

ABSTRACT: We purified the different types of NPCs in yeast using a differential affinity purification strategy and analyzed their respective compositions and interactomes by mass spectrometry. Therefore, we compared the relative abundancies of specific nuclear factors and NPCs associated factor between all pores, basket-less pores, basket-containing pores, and pores upon MLP1/2 deletion

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Marlene Oeffinger

LAB HEAD: Marlene Oeffinger

PROVIDER: PXD027872 | Pride | 2022-10-13

REPOSITORIES: Pride

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			Action	DRS
	OF_20200910_OEF_01.mzid.gz	Mzid
	OF_20200910_OEF_01.raw	Raw
	OF_20200910_OEF_01___E1.mzid_OF_20200910_OEF_01___E1.MGF	Mzid
	OF_20200910_OEF_02.mzid.gz	Mzid
	OF_20200910_OEF_02.raw	Raw

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Publications

Nuclear mRNA metabolism drives selective basket assembly on a subset of nuclear pore complexes in budding yeast.

Bensidoun Pierre P Reiter Taylor T Montpetit Ben B Zenklusen Daniel D Oeffinger Marlene M

Molecular cell 20221010 20

To determine which transcripts should reach the cytoplasm for translation, eukaryotic cells have established mechanisms to regulate selective mRNA export through the nuclear pore complex (NPC). The nuclear basket, a substructure of the NPC protruding into the nucleoplasm, is thought to function as a stable platform where mRNA-protein complexes (mRNPs) are rearranged and undergo quality control prior to export, ensuring that only mature mRNAs reach the cytoplasm. Here, we use proteomic, genetic, ...[more]

PMID: 36220102

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NPC transcriptome disection

Project description:We report the ananlysis of polyAdenylated transcripts copurified with nuclear pore complexes in yeast S.cerevisae. We purified all NPCs and the 2 different types of pores (basket-containing and basket-less pores) and co-isolated their interactomes. The transcripts co-purified were polyA enriched and sequenced with Novaseq6000, and identified over 300X10^6 reads

2021-09-15 | GSE181199 | GEO

SUMO protease and proteasome recruitment at the nuclear periphery differently affect replication dynamics at arrested forks.

Project description:Nuclear pores complexes (NPCs) are genome organizers, defining a particular nuclear compartment enriched for SUMO protease and proteasome activities, and act as docking sites for DNA repair. In fission yeast, the anchorage of perturbed replication forks to NPCs is an integral part of the recombination-dependent replication restart mechanism (RDR) that resumes DNA synthesis at terminally dysfunctional forks. By mapping DNA polymerase usage, we report that SUMO protease Ulp1-associated NPCs ensure efficient initiation of restarted DNA synthesis, whereas proteasome-associated NPCs sustain the speed of restarted DNA polymerase. In contrast to Ulp1, this last function occurs independently of SUMO chains formation. By analyzing the role of the nuclear basket, the nucleoplasmic extension of the NPC, we reveal that the activities of Ulp1 and the proteasome cannot compensate for each other and affect the dynamics of RDR in distinct ways. Our work probes the mechanisms by which the NPC environment ensures optimal RDR.

2023-11-13 | GSE247371 | GEO

Docking a flexible basket onto the core of the nuclear pore complex

Project description:The nuclear basket attaches to the nucleoplasmic side of the nuclear pore complex (NPC), coupling transcription to mRNA quality control and export. The basket expands the functional repertoire of a subset of NPCs in S. cerevisiae by drawing a unique RNA/protein interactome. Yet, how the basket docks onto the NPC core remains unknown. By integrating AlphaFold-powered interaction screens, electron microscopy and membrane-templated reconstitution, we uncovered a membrane-anchored tripartite junction between basket and NPC core. The basket subunit Nup60 harbours three adjacent short linear motifs (SLiMs) which connect Mlp1, a parallel homodimer consisting of coiled-coil segments interrupted by flexible hinges, and the Nup85 subunit of the Y-complex. We reconstituted the Y-complex•Nup60•Mlp1 assembly on a synthetic membrane and validated the protein interfaces in vivo. Our study explains how a SLiM-based protein junction can substantially reshape NPC structure and function, advancing our understanding of compositional and conformational NPC heterogeneity.

2024-07-11 | PXD052015 | Pride

Meiotic Nuclear Pore Complex Modularity Provides Key Insights into Nuclear Basket Organization

Project description:Using phosphoproteomics and time-lapse fluorescence microscopy, we report that NPCs nuclear pore complexes (NPCs) undergo two distinct modularity events for the nucleoporins Nup60 and Nup2 during budding yeast meiosis: partial and full nuclear basket detachment.

2022-12-08 | PXD033245 | Pride

Nuclear pore complexes mediate subtelomeric gene silencing by regulating PCNA levels on chro atin

Project description:The nuclear pore complex (NPC) physically interacts with chromatin and regulates gene expression. The Saccharomyces cerevisiae inner ring nucleoporin Nup170 has been implicated in chromatin organization and the maintenance of gene silencing in subtelomeric regions. To gain insight into how Nup170 regulates this process, we used protein-protein interactions, genetic interactions, and transcriptome correlation analyses to identify the Ctf18-RFC complex, an alternative proliferating cell nuclear antigen (PCNA) loader, as a facilitator of the gene regulatory functions of Nup170. The Ctf18-RFC complex is recruited to a subpopulation of NPCs that lack the nuclear basket proteins Mlp1 and Mlp2. In the absence of Nup170, PCNA levels on DNA are reduced, resulting in the loss of silencing of subtelomeric genes. Increasing PCNA levels on DNA by removing Elg1, which is required for PCNA unloading, rescues subtelomeric silencing defects in nup170Δ. The NPC therefore mediates subtelomeric gene silencing by regulating PCNA levels on DNA.

2023-06-13 | PXD041496 | Pride

Distinct Basket Nucleoporins roles in Nuclear Pore Function and Gene Expression

Project description:Nuclear pore complexes (NPCs) are important for cellular functions beyond nucleocytoplasmic trafficking, including genome organization and gene expression. This multi-faceted nature and the slow turnover of NPC components complicates investigations of how individual nucleoporins act in these diverse processes. To address this question, we used an Auxin-Induced Degron (AID) system to distinguish roles of basket nucleoporins Nup153, Nup50 and Tpr. Here, we provide MS data for the Nuclear Pore-enriched fraction of human DLD-1 cells, expressing CRISPR-engeneered degron, fused with the endogenous locus of corresponding basket NUPs, in the absence or presence of Auxin.

2020-06-30 | PXD020075 | Pride

The interactomes of GlPXD1, 3 and 6 PIP-binding proteins in Giardia lamblia

Project description:We investigated the composition of the interactomes of 7 proteins in the parasitic protist Giardia lamblia, some of which were found to be associated to clathrin assemblies. This accession refers to the first three namely GlPXD1, 3 and 6.

2019-05-20 | PXD013890 | Pride

The interactomes of GlNECAP PIP-binding proteins in Giardia lamblia

2019-05-20 | PXD013896 | Pride

The interactomes of GlFYVE PIP-binding protein in Giardia lamblia

2019-05-20 | PXD013897 | Pride

The interactomes of GlPXD2 and 4 PIP-binding proteins in Giardia lamblia

Project description:We investigated the composition of the interactomes of overall 7 proteins in the parasitic protist Giardia lamblia, some of which were found to be associated to clathrin assemblies. This accession refers to proteins GlPXD2 and 4

2019-05-20 | PXD013899 | Pride

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