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BoDV-1 phosphoprotein BioID in HEK293

ABSTRACT: Here we have identified human proteins in spatial proximity (proximal interaction network) of BoDV-1 Phosphoprotein fused to BirA* (E.Coli biotin ligase R118G abortive mutant) at the N-ter and C-ter ends in human cells by proximity-dependent biotinylation (BioID)-based approach. We report 301 high-confidence virus-host PPI involving 207 unique cellular targets.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Etienne Coyaud

LAB HEAD: Etienne COYAUD

PROVIDER: PXD036750 | Pride | 2026-01-27

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	FB_P_A.raw	Raw
	FB_P_B.raw	Raw
	FB_P_C.raw	Raw
	P-BF_A.raw	Raw
	P-BF_B.raw	Raw

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1 - 5 of 27

Publications

Borna Disease Virus 1 Phosphoprotein Forms a Tetramer and Interacts with Host Factors Involved in DNA Double-Strand Break Repair and mRNA Processing.

Tarbouriech Nicolas N Chenavier Florian F Kawasaki Junna J Bachiri Kamel K Bourhis Jean-Marie JM Legrand Pierre P Freslon Lily L LL Laurent Estelle M N EMN Suberbielle Elsa E Ruigrok Rob W H RWH Tomonaga Keizo K Gonzalez-Dunia Daniel D Horie Masayuki M Coyaud Etienne E Crépin Thibaut T

Viruses 20221026 11

Determining the structural organisation of viral replication complexes and unravelling the impact of infection on cellular homeostasis represent important challenges in virology. This may prove particularly useful when confronted with viruses that pose a significant threat to human health, that appear unique within their family, or for which knowledge is scarce. Among <i>Mononegavirales</i>, bornaviruses (family <i>Bornaviridae</i>) stand out due to their compact genomes and their nuclear locali ...[more]

PMID: 36366462

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HPV16 and HPV42 E6 and E7 proximal interactomics

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2022-10-15 | PXD031438 | Pride

SARS-CoV-2 proteins BioID in HEK293

Project description:SARS-CoV-2 proteins orchestrate complex mechanisms that underlie SARS-CoV-2 infection and COVID-19 causing pathogenic processes. Here we have exhaustively defined human proteins in spatial proximity (proximal interaction network) of 27/28 SARS-CoV-2 proteins in human cells by proximity-dependent biotinylation (BioID)-based approach. We report 10,185 high-confidence virus-host PPI involving 2,592 unique cellular targets.

2025-03-07 | PXD033452 | Pride

GFI1 tethers the NuRD complex to open and transcriptionally active chromatin in myeloid progenitors

Project description:GFI is a DNA binding transcriptional repressor that regulates myeloid differentiation. Here, we show that GFI1 interacts with the chromodomain helicase CHD4 and other components of the nucleosome remodeling and deacetylase (NuRD) complex. Our data demonstrated that GFI1 and GFI1/CHD4 complexes occupy sites of open chromatin enriched for histone marks associated with active transcription or different sets of genes that are either enriched for IRF1 or SPI-1 consensus binding sites. In addition, our study provided evidence that GFI1 affects the chromatin remodeling activity of the NuRD complex. Overall, our results indicate that GFI1/CHD4 complexes control chromatin openness and histone modifications differentially to regulate target genes, which govern the immune response, nucleosome organization, or metabolic processes.

2021-11-02 | PXD028945 | Pride

Differential roles of Sall4 isoforms in ES cell pluripotency

Project description:This SuperSeries is composed of the following subset Series: GSE21054: Differential roles of Sall4 isoforms in ES cell pluripotency: expression GSE21055: Differential Role of Sall4 isoforms in ES cell pluripotency: ChIP-chip Refer to individual Series

2010-09-13 | E-GEOD-21056 | biostudies-arrayexpress

Toxoplasma gondii MOB1 interactome

Project description:MOB1 is a conserved protein that regulates cellular proliferation versus apoptosis, centrosome duplication and cellular differentiation in multicellular eukaryotes and also cytokinesis and division axis orientation in unicellular and multicellular eukaryotes. Toxoplasma gondii, an obligate intracellular parasite of veterinary and medical importance, presents one MOB1 protein. T. gondii interconverts between several cellular stages during its life cycle, namely between fast replicating tachyzoite and slow replicating bradyzoite stages during its asexual cycle, a key ability for its success as a parasite. Bradyzoites produce tissue cysts, establishing a chronic infection that enables recrudescence. Conversion is dependent on cell cycle regulation and involves cell differentiation and regulation of replication. This led us to select MOB1 as a strong candidate to be involved in the Toxoplasma replication process. To elucidate how MOB1 acts in T. gondii, we employed a proximity biotinylation method and identified the MOB1 interactome. Toxoplasma gondii RH tachyzoites were transfected with BirA containing plasmid vectors for random integration and two strains were isolated. The control strain expresses a FLAG-BirA recombinant protein while the test strain expresses a FLAG-BirA-MOB1 recombinant protein. Biotinylated proteins were purified using streptavidin-agarose beads. The purified proteins were trypsinized and analyzed by nanoLC-MS/MS.

2022-02-16 | PXD028781 | Pride

MCM8IP activates the MCM8-9 helicase to promote DNA synthesis and homologous recombination upon DNA damage

Project description:Homologous recombination (HR) mediates the error-free repair of DNA double-strand breaks to maintain genomic stability. Here we characterize C17orf53/MCM8IP, an OB-fold containing protein that binds ssDNA, as a DNA repair factor involved in HR. MCM8IP-deficient cells exhibit HR defects, especially in long-tract gene conversion, occurring downstream of RAD51 loading, consistent with a role for MCM8IP in HR-dependent DNA synthesis. Moreover, loss of MCM8IP confers cellular sensitivity to crosslinking agents and PARP inhibition. Importantly, we report that MCM8IP directly associates with MCM8-9, a helicase complex mutated in primary ovarian insufficiency, and RPA1. We additionally show that the interactions of MCM8IP with MCM8-9 and RPA facilitate HR and promote replication fork progression and cellular viability in response to treatment with crosslinking agents. Mechanistically, MCM8IP stimulates the helicase activity of MCM8-9. Collectively, our work identifies MCM8IP as a key regulator of DNA damage-associated DNA synthesis during DNA recombination and replication.

2020-06-15 | PXD019156 | Pride

A Proximity dependent labeling approach to define flotillin-2 interacting proteins within Membrane Domains of HeLa cells

Project description:The formation of plasma membrane microdomains, known as lipid rafts, is driven by specific interactions among cholesterol, sphingolipids, and certain proteins such as flotillins. Flotillins are known to oligomerize and associate with defined lipid assemblies, thereby promoting the coalescence and stabilization of these membrane rafts. Acting as scaffolding molecules, flotillins play critical roles in various cellular processes, including the spatial organization of signaling complexes and membrane compartmentalization. To identify flotillin-associated proteins within membrane rafts in vivo, we employed the BioID proximity labeling technique to analyze the flotillin-2 interactome in living HeLa cells. Flotillin-2 was fused to the promiscuous biotin ligase BirA* at either the N- or C-terminus and expressed in HeLa cells, enabling biotinylation of proximal proteins. Biotinylated proteins were enriched on streptavidin affinity beads and subsequently identified via LC-MS analysis. This investigation of the flotillin-2 interactome provides new insights into the molecular composition of membrane rafts and offers a valuable framework for understanding the mechanisms underlying raft formation, regulation, and associated cellular functions in native membranes.

2025-08-22 | PXD065739 | Pride

Proximity-dependent biotinylation to elucidate the interactome of TNK2 non-receptor tyrosine kinase

Project description:Non-receptor tyrosine kinases represent an important class of signaling molecules which are involved in driving diverse cellular pathways. Although the large majority have been well-studied in terms of their protein binding partners, the interactomes of some important non-receptor tyrosine kinases such as TNK2 (also known as activated Cdc42-associated kinase 1 or ACK1) have not been systematically investigated. Aberrant expression and hyperphosphorylation of TNK2 have been implicated in a number of cancers, although the exact proteins and cellular events that mediate phenotypic changes downstream of TNK2 are unclear. Biological systems that employ proximity-dependent protein labeling methods, such as biotinylation identification (BioID), are being increasingly used to map protein-protein interactomes as they provide increased sensitivity in finding interaction partners. In the present study, we employ BioID coupled to a Biotinylation Site Identification Technology (BioSITe) method we recently developed to perform molecular mapping of intracellular protein interactors of TNK2. By performing a controlled comparative analysis between full-length TNK2 and its truncated counterpart, we were not only able to confidently identify site-level biotinylation of previously well-established TNK2 binders and substrates, but also several novel binders of TNK2 that may help explain its role in oncogenic signaling.

2021-08-25 | PXD010474 | Pride

Definition of the fibroblast adhesome using multiplexed proximity biotinylation

Project description:Integrin adhesion complexes (IACs) bridge the extracellular matrix to the actin cytoskeleton and transduce signals in response to both chemical and mechanical cues. The composition, interactions, stoichiometry and topological organisation of proteins within IACs are not fully understood. To address this gap, we used multiplexed proximity biotinylation (BioID) to generate an in situ, proximity-dependent adhesome. Integration of the interactomes of 16 IAC-associated baits revealed a network of 147 proteins with 361 proximity interactions. Candidates with underappreciated roles in adhesion were identified, in addition to established IAC components. Bioinformatic analysis revealed five clusters of IAC baits that link to common groups of prey, and which therefore may represent functional modules. The five clusters, and their spatial associations, are consistent with current models of IAC interaction networks and stratification. This study provides a resource to examine proximal relationships within IACs on a global level.

2020-06-01 | PXD017241 | Pride

RNF43 truncations trap CK1 to drive niche-independent self-renewal in cancer

Project description:Wnt/b-catenin signaling is a primary pathway for stem cell maintenance during tissue renewal and a frequent target for mutations in cancer. Impaired Wnt receptor endocytosis due to loss of the ubiquitin ligase RNF43 gives rise to Wnt-hypersensitive tumors that are susceptible to anti-Wnt-based therapy. Contrary to this paradigm, we identify a class of RNF43 truncating cancer mutations that induce b-catenin-mediated transcription, despite exhibiting retained Wnt receptor downregulation. These mutations interfere with an ubiquitin-independent suppressor role of the RNF43 cytosolic tail that involves casein kinase-1 (CK1) binding and phosphorylation. Mechanistically, truncated RNF43 variants trap CK1 at the plasma membrane, thereby preventing b-catenin turnover and propelling ligandindependent target gene transcription. Gene editing of human colon stem cells shows that RNF43 truncations cooperate with p53 loss to drive a niche-independent program for self-renewal and proliferation. Moreover, these RNF43 variants confer decreased sensitivity to anti-Wnt-based therapy. Our data demonstrate the relevance of studying patient-derived mutations for understanding disease mechanisms and improved applications of precision medicine.

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