Search results for "Interactome"

A reliable and unbiased human protein network with the disparity filter

2017

AbstractThe living cell operates thanks to an intricate network of protein interactions. Proteins activate, transport, degrade, stabilise and participate in the production of other proteins. As a result, a reliable and systematically generated protein wiring diagram is crucial for a deeper understanding of cellular functions. Unfortunately, current human protein networks are noisy and incomplete. Also, they suffer from both study and technical biases: heavily studied proteins (e.g. those of pharmaceutical interest) are known to be involved in more interactions than proteins described in only a few publications. Here, we use the experimental evidence supporting the interaction between protei…

Inhibitory activities of short linear motifs underlie Hox interactome specificity in vivo

2015

Hox proteins are well-established developmental regulators that coordinate cell fate and morphogenesis throughout embryogenesis. In contrast, our knowledge of their specific molecular modes of action is limited to the interaction with few cofactors. Here, we show that Hox proteins are able to interact with a wide range of transcription factors in the live Drosophila embryo. In this context, specificity relies on a versatile usage of conserved short linear motifs (SLiMs), which, surprisingly, often restrains the interaction potential of Hox proteins. This novel buffering activity of SLiMs was observed in different tissues and found in Hox proteins from cnidarian to mouse species. Although th…

Identification of novel interaction partners for Vlgr1b/GPR98 - a key component of the periciliary Usher syndrome protein network in photoreceptor ce…

2012

The human Usher syndrome (USH) is the most common form of combined hereditary deaf-blindness. Three clinical subtypes (USH1-3) are differentiated based on severity, age of onset and progression of the symptoms. Mutations in the GPR98 gene encoding the USH2C protein Vlgr1b or GPR98 cause USH2, the most common form of USH. The G-protein coupled receptor Vlgr1b was previously identified as a component of the periciliary USH protein network, crucial for ciliary cargo transport in photoreceptors. Nonetheless, the exact role of Vlgr1b in this and other cellular processes remains to be elucidated. To learn more about its involvement in cellular functions we searched for novel interaction partners …

Looking for pathways related to COVID-19 phenotypes: Confirmation of pathogenic mechanisms by SARS-CoV-2 - Host interactome

2020

AbstractIn the last months, many studies have clearly described several mechanisms of SARS-CoV-2 infection at cell and tissue level. Host conditions and comorbidities were identified as risk factors for severe and fatal disease courses, but the mechanisms of interaction between host and SARS-CoV-2 determining the grade of COVID- 19 severity, are still unknown.We provide a network analysis on protein–protein interactions (PPI) between viral and host proteins to better identify host biological responses, induced by both whole proteome of SARS-CoV-2 and specific viral proteins. A host-virus interactome was inferred on published PPI, using an explorative algorithm (Random Walk with Restart) tri…

Author response: Inhibitory activities of short linear motifs underlie Hox interactome specificity in vivo

2015

Global Functional Analyses of Cellular Responses to Pore-Forming Toxins

2011

Here we present the first global functional analysis of cellular responses to pore-forming toxins (PFTs). PFTs are uniquely important bacterial virulence factors, comprising the single largest class of bacterial protein toxins and being important for the pathogenesis in humans of many Gram positive and Gram negative bacteria. Their mode of action is deceptively simple, poking holes in the plasma membrane of cells. The scattered studies to date of PFT-host cell interactions indicate a handful of genes are involved in cellular defenses to PFTs. How many genes are involved in cellular defenses against PFTs and how cellular defenses are coordinated are unknown. To address these questions, we pe…

2015

High-throughput detection of protein interactions has had a major impact in our understanding of the intricate molecular machinery underlying the living cell, and has permitted the construction of very large protein interactomes. The protein networks that are currently available are incomplete and a significant percentage of their interactions are false positives. Fortunately, the structural properties observed in good quality social or technological networks are also present in biological systems. This has encouraged the development of tools, to improve the reliability of protein networks and predict new interactions based merely on the topological characteristics of their components. Sinc…

Proteome-Wide Characterization of the RNA-Binding Protein RALY-Interactome Using the in Vivo-Biotinylation-Pulldown-Quant (iBioPQ) Approach

2013

RALY is a member of the heterogeneous nuclear ribonucleoproteins, a family of RNA-binding proteins generally involved in many processes of mRNA metabolism. No quantitative proteomic analysis of RALY-containing ribonucleoparticles (RNPs) has been performed so far, and the biological role of RALY remains elusive. Here, we present a workflow for the characterization of RALY's interaction partners, termed iBioPQ, that involves in vivo biotinylation of biotin acceptor peptide (BAP)-fused protein in the presence of the prokaryotic biotin holoenzyme synthetase of BirA so that it can be purified using streptavidin-coated magnetic beads, circumventing the need for specific antibodies and providing e…

BAG3 Proteomic Signature under Proteostasis Stress

2020

The multifunctional HSP70 co-chaperone BAG3 (BCL-2-associated athanogene 3) represents a key player in the quality control of the cellular proteostasis network. In response to stress, BAG3 specifically targets aggregation-prone proteins to the perinuclear aggresome and promotes their degradation via BAG3-mediated selective macroautophagy. To adapt cellular homeostasis to stress, BAG3 modulates and functions in various cellular processes and signaling pathways. Noteworthy, dysfunction and deregulation of BAG3 and its pathway are pathophysiologically linked to myopathies, cancer, and neurodegenerative disorders. Here, we report a BAG3 proteomic signature under proteostasis stress. To elucidat…

Competing endogenous RNA and interactome bioinformatic analyses on human telomerase.

2014

We present a classic interactome bioinformatic analysis and a study on competing endogenous (ce) RNAs for hTERT. The hTERT gene codes for the catalytic subunit and limiting component of the human telomerase complex. Human telomerase reverse transcriptase (hTERT) is essential for the integrity of telomeres. Telomere dysfunctions have been widely reported to be involved in aging, cancer, and cellular senescence. The hTERT gene network has been analyzed using the BioGRID interaction database (http://thebiogrid.org/) and related analysis tools such as Osprey (http://biodata.mshri.on.ca/osprey/servlet/Index) and GeneMANIA (http://genemania.org/). The network of interaction of hTERT transcripts h…