Mapping the Proximity Interaction Network of STIM1 Reveals New Mechanisms of Cytoskeletal Regulation

Stromal interaction molecule 1 (STIM1) resides primarily in the sarco/endoplasmic reticulum, where it senses intraluminal Ca2+ levels and activates Orai channels on the plasma membrane to initiate Ca2+ influx. We have previously shown that STIM1 is involved in the dynamic remodeling of the actin cytoskeleton. However, the downstream effectors of STIM1 that lead to cytoskeletal remodeling are not known. The proximity-labeling technique (BioID) can capture weak and transient protein-protein interactions, including proteins that reside in the close vicinity of the bait, but that may not be direct binders. Hence, in the present study, we investigated the STIM1 interactome using the BioID technique. A promiscuous biotin ligase was fused to the cytoplasmic C-terminus of STIM1 and was stably expressed in a mouse embryonic fibroblast (MEF) cell line. Screening of biotinylated proteins identified several high confidence targets. Here, we report Gelsolin (GSN) as a new member of the STIM1 interactome. GSN is a Ca2+-dependent actin-severing protein that promotes actin filament assembly and disassembly. Results were validated using knockdown approaches and immunostaining. We tested our results in neonatal cardiomyocytes where STIM1 overexpression induced altered actin dynamics and cytoskeletal instability. This is the first time that BioID assay was used to investigate the STIM1 interactome. Our work highlights the role of STIM1/GSN in the structure and function of the cytoskeleton.

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The Cac1 subunit of histone chaperone CAF-1 organizes CAF-1-H3/H4 architecture and tetramerizes histones

eLife ◽

10.7554/elife.18023 ◽

2016 ◽

Vol 5 ◽

Cited By ~ 27

Author(s):

Wallace H Liu ◽

Sarah C Roemer ◽

Yeyun Zhou ◽

Zih-Jie Shen ◽

Briana K Dennehey ◽

...

Keyword(s):

Protein Interactions ◽

Histone Chaperone ◽

Protein Protein Interactions ◽

Rich Domain ◽

C Terminus ◽

Assembly Factor ◽

Hydrogen Deuterium ◽

And Function ◽

Minimal Region

The histone chaperone Chromatin Assembly Factor 1 (CAF-1) deposits tetrameric (H3/H4)2 histones onto newly-synthesized DNA during DNA replication. To understand the mechanism of the tri-subunit CAF-1 complex in this process, we investigated the protein-protein interactions within the CAF-1-H3/H4 architecture using biophysical and biochemical approaches. Hydrogen/deuterium exchange and chemical cross-linking coupled to mass spectrometry reveal interactions that are essential for CAF-1 function in budding yeast, and importantly indicate that the Cac1 subunit functions as a scaffold within the CAF-1-H3/H4 complex. Cac1 alone not only binds H3/H4 with high affinity, but also promotes histone tetramerization independent of the other subunits. Moreover, we identify a minimal region in the C-terminus of Cac1, including the structured winged helix domain and glutamate/aspartate-rich domain, which is sufficient to induce (H3/H4)2 tetramerization. These findings reveal a key role of Cac1 in histone tetramerization, providing a new model for CAF-1-H3/H4 architecture and function during eukaryotic replication.

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E. coli primase and DNA polymerase III holoenzyme are able to bind concurrently to a primed template during DNA replication

Scientific Reports ◽

10.1038/s41598-019-51031-0 ◽

2019 ◽

Vol 9 (1) ◽

Author(s):

Andrea Bogutzki ◽

Natalie Naue ◽

Lidia Litz ◽

Andreas Pich ◽

Ute Curth

Keyword(s):

Dna Replication ◽

Dna Polymerase ◽

Protein Interactions ◽

Dna Polymerase Iii ◽

Protein Protein Interactions ◽

Single Stranded Dna ◽

E Coli ◽

Polymerase Iii ◽

C Terminus ◽

Pol Iii

Abstract During DNA replication in E. coli, a switch between DnaG primase and DNA polymerase III holoenzyme (pol III) activities has to occur every time when the synthesis of a new Okazaki fragment starts. As both primase and the χ subunit of pol III interact with the highly conserved C-terminus of single-stranded DNA-binding protein (SSB), it had been proposed that the binding of both proteins to SSB is mutually exclusive. Using a replication system containing the origin of replication of the single-stranded DNA phage G4 (G4ori) saturated with SSB, we tested whether DnaG and pol III can bind concurrently to the primed template. We found that the addition of pol III does not lead to a displacement of primase, but to the formation of higher complexes. Even pol III-mediated primer elongation by one or several DNA nucleotides does not result in the dissociation of DnaG. About 10 nucleotides have to be added in order to displace one of the two primase molecules bound to SSB-saturated G4ori. The concurrent binding of primase and pol III is highly plausible, since even the SSB tetramer situated directly next to the 3′-terminus of the primer provides four C-termini for protein-protein interactions.

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Short loop functional commonality identified in leukaemia proteome highlights crucial protein sub-networks

NAR Genomics and Bioinformatics ◽

10.1093/nargab/lqab010 ◽

2021 ◽

Vol 3 (1) ◽

Author(s):

Sun Sook Chung ◽

Joseph C F Ng ◽

Anna Laddach ◽

N Shaun B Thomas ◽

Franca Fraternali

Keyword(s):

Protein Interactions ◽

Large Scale ◽

Interaction Network ◽

Protein Protein Interactions ◽

Protein Protein Interaction ◽

Ppi Networks ◽

Short Loop ◽

New Strategy ◽

Loop Network ◽

Protein Protein Interaction Network

Abstract Direct drug targeting of mutated proteins in cancer is not always possible and efficacy can be nullified by compensating protein–protein interactions (PPIs). Here, we establish an in silico pipeline to identify specific PPI sub-networks containing mutated proteins as potential targets, which we apply to mutation data of four different leukaemias. Our method is based on extracting cyclic interactions of a small number of proteins topologically and functionally linked in the Protein–Protein Interaction Network (PPIN), which we call short loop network motifs (SLM). We uncover a new property of PPINs named ‘short loop commonality’ to measure indirect PPIs occurring via common SLM interactions. This detects ‘modules’ of PPI networks enriched with annotated biological functions of proteins containing mutation hotspots, exemplified by FLT3 and other receptor tyrosine kinase proteins. We further identify functional dependency or mutual exclusivity of short loop commonality pairs in large-scale cellular CRISPR–Cas9 knockout screening data. Our pipeline provides a new strategy for identifying new therapeutic targets for drug discovery.

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Frequent assembly of chimeric complexes in the protein interaction network of an interspecies yeast hybrid

Molecular Biology and Evolution ◽

10.1093/molbev/msaa298 ◽

2020 ◽

Author(s):

Rohan Dandage ◽

Caroline M Berger ◽

Isabelle Gagnon-Arsenault ◽

Kyung-Mee Moon ◽

Richard Greg Stacey ◽

...

Keyword(s):

Protein Interactions ◽

Molecular Level ◽

Yeast Species ◽

Protein Complexes ◽

Mitochondrial Protein ◽

Chimeric Protein ◽

Interaction Network ◽

Protein Protein Interactions ◽

Extreme Phenotypes ◽

Yeast Hybrid

Abstract Hybrids between species often show extreme phenotypes, including some that take place at the molecular level. In this study, we investigated the phenotypes of an interspecies diploid hybrid in terms of protein-protein interactions inferred from protein correlation profiling. We used two yeast species, Saccharomyces cerevisiae and Saccharomyces uvarum, which are interfertile, but yet have proteins diverged enough to be differentiated using mass spectrometry. Most of the protein-protein interactions are similar between hybrid and parents, and are consistent with the assembly of chimeric complexes, which we validated using an orthogonal approach for the prefoldin complex. We also identified instances of altered protein-protein interactions in the hybrid, for instance in complexes related to proteostasis and in mitochondrial protein complexes. Overall, this study uncovers the likely frequent occurrence of chimeric protein complexes with few exceptions, which may result from incompatibilities or imbalances between the parental proteins.

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Transactivation Functions of the N-Terminal Domains of Nuclear Hormone Receptors: Protein Folding and Coactivator Interactions

Molecular Endocrinology ◽

10.1210/me.2002-0258 ◽

2003 ◽

Vol 17 (1) ◽

pp. 1-10 ◽

Cited By ~ 125

Author(s):

Raj Kumar ◽

E. Brad Thompson

Keyword(s):

Dna Binding ◽

Protein Interactions ◽

Hormone Receptors ◽

Nuclear Hormone Receptor ◽

Binding Domain ◽

Dna Binding Domain ◽

Protein Protein Interactions ◽

Carboxy Terminal ◽

And Function ◽

Terminal Domains

Abstract The N-terminal domains (NTDs) of many members of the nuclear hormone receptor (NHR) family contain potent transcription-activating functions (AFs). Knowledge of the mechanisms of action of the NTD AFs has lagged, compared with that concerning other important domains of the NHRs. In part, this is because the NTD AFs appear to be unfolded when expressed as recombinant proteins. Recent studies have begun to shed light on the structure and function of the NTD AFs. Recombinant NTD AFs can be made to fold by application of certain osmolytes or when expressed in conjunction with a DNA-binding domain by binding that DNA-binding domain to a DNA response element. The sequence of the DNA binding site may affect the functional state of the AFs domain. If properly folded, NTD AFs can bind certain cofactors and primary transcription factors. Through these, and/or by direct interactions, the NTD AFs may interact with the AF2 domain in the ligand binding, carboxy-terminal portion of the NHRs. We propose models for the folding of the NTD AFs and their protein-protein interactions.

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PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data

BioMed Research International ◽

10.1155/2016/2891918 ◽

2016 ◽

Vol 2016 ◽

pp. 1-13

Author(s):

Stefan Kalkhof ◽

Stefan Schildbach ◽

Conny Blumert ◽

Friedemann Horn ◽

Martin von Bergen ◽

...

Keyword(s):

Mass Spectrometry ◽

Protein Interactions ◽

Isotope Labeling ◽

Affinity Purification ◽

Interaction Network ◽

Mass Spectrometry Data ◽

Protein Protein Interactions ◽

Protein Protein Interaction ◽

Binding Behavior ◽

Bona Fide

The functionality of most proteins is regulated by protein-protein interactions. Hence, the comprehensive characterization of the interactome is the next milestone on the path to understand the biochemistry of the cell. A powerful method to detect protein-protein interactions is a combination of coimmunoprecipitation or affinity purification with quantitative mass spectrometry. Nevertheless, both methods tend to precipitate a high number of background proteins due to nonspecific interactions. To address this challenge the software Protein-Protein-Interaction-Optimizer (PIPINO) was developed to perform an automated data analysis, to facilitate the selection of bona fide binding partners, and to compare the dynamic of interaction networks. In this study we investigated the STAT1 interaction network and its activation dependent dynamics. Stable isotope labeling by amino acids in cell culture (SILAC) was applied to analyze the STAT1 interactome after streptavidin pull-down of biotagged STAT1 from human embryonic kidney 293T cells with and without activation. Starting from more than 2,000 captured proteins 30 potential STAT1 interaction partners were extracted. Interestingly, more than 50% of these were already reported or predicted to bind STAT1. Furthermore, 16 proteins were found to affect the binding behavior depending on STAT1 phosphorylation such as STAT3 or the importin subunits alpha 1 and alpha 6.

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ArabidopsisImmunophilin-like TWD1 Functionally Interacts with Vacuolar ABC Transporters

Molecular Biology of the Cell ◽

10.1091/mbc.e03-11-0831 ◽

2004 ◽

Vol 15 (7) ◽

pp. 3393-3405 ◽

Cited By ~ 70

Author(s):

Markus Geisler ◽

Marjolaine Girin ◽

Sabine Brandt ◽

Vincent Vincenzetti ◽

Sonia Plaza ◽

...

Keyword(s):

Protein Interactions ◽

Abc Transporters ◽

Loss Of Function ◽

Protein Protein Interactions ◽

Binding Motifs ◽

Calmodulin Binding ◽

C Terminus ◽

Domain Mapping ◽

Tetratricopeptide Repeat Domain

Previously, the immunophilin-like protein TWD1 from Arabidopsis has been demonstrated to interact with the ABC transporters AtPGP1 and its closest homologue, AtPGP19. Physiological and biochemical investigation of pgp1/pgp19 and of twd1 plants suggested a regulatory role of TWD1 on AtPGP1/AtPGP19 transport activities. To further understand the dramatic pleiotropic phenotype that is caused by loss-of-function mutation of the TWD1 gene, we were interested in other TWD1 interacting proteins. AtMRP1, a multidrug resistance-associated (MRP/ABCC)-like ABC transporter, has been isolated in a yeast two-hybrid screen. We demonstrate molecular interaction between TWD1 and ABC transporters AtMRP1 and its closest homologue, AtMRP2. Unlike AtPGP1, AtMRP1 binds to the C-terminal tetratricopeptide repeat domain of TWD1, which is well known to mediate protein-protein interactions. Domain mapping proved that TWD1 binds to a motif of AtMRP1 that resembles calmodulin-binding motifs; and calmodulin binding to the C-terminus of MRP1 was verified. By membrane fractionation and GFP-tagging, we localized AtMRP1 to the central vacuolar membrane and the TWD1-AtMRP1 complex was verified in vivo by coimmunoprecipitation. We were able to demonstrate that TWD1 binds to isolated vacuoles and has a significant impact on the uptake of metolachlor-GS and estradiol-β-glucuronide, well-known substrates of vacuolar transporters AtMRP1 and AtMRP2.

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Multi-Omics Analysis Identifying Key Biomarkers in Ovarian Cancer

Cancer Control ◽

10.1177/1073274820976671 ◽

2020 ◽

Vol 27 (1) ◽

pp. 107327482097667

Author(s):

Ju-Yueh Li ◽

Chia-Jung Li ◽

Li-Te Lin ◽

Kuan-Hao Tsui

Keyword(s):

Ovarian Cancer ◽

Protein Interactions ◽

Malignant Tumors ◽

Single Gene ◽

Protein Protein Interactions ◽

Normal Tissues ◽

Human Protein Atlas ◽

Copy Number Changes ◽

And Function ◽

Cancer Tissues

Ovarian cancer is one of the most common malignant tumors. Here, we aimed to study the expression and function of the CREB1 gene in ovarian cancer via the bioinformatic analyses of multiple databases. Previously, the prognosis of ovarian cancer was based on single-factor or single-gene studies. In this study, different bioinformatics tools (such as TCGA, GEPIA, UALCAN, MEXPRESS, and Metascape) have been used to assess the expression and prognostic value of the CREB1 gene. We used the Reactome and cBioPortal databases to identify and analyze CREB1 mutations, copy number changes, expression changes, and protein–protein interactions. By analyzing data on the CREB1 differential expression in ovarian cancer tissues and normal tissues from 12 studies collected from the “Human Protein Atlas” database, we found a significantly higher expression of CREB1 in normal ovarian tissues. Using this database, we collected information on the expression of 25 different CREB-related proteins, including TP53, AKT1, and AKT3. The enrichment of these factors depended on tumor metabolism, invasion, proliferation, and survival. Individualized tumors based on gene therapy related to prognosis have become a new possibility. In summary, we established a new type of prognostic gene profile for ovarian cancer using the tools of bioinformatics.

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Aspartic Acid Isomerization Characterized by High Definition Mass Spectrometry Significantly Alters the Bioactivity of a Novel Toxin from Poecilotheria

Toxins ◽

10.3390/toxins12040207 ◽

2020 ◽

Vol 12 (4) ◽

pp. 207 ◽

Cited By ~ 1

Author(s):

Stephen R. Johnson ◽

Hillary G. Rikli

Keyword(s):

Mass Spectrometry ◽

Protein Interactions ◽

Ion Mobility ◽

Protein Protein Interactions ◽

High Definition ◽

Vast Number ◽

Post Translational Modifications ◽

C Terminus ◽

Acid Isomerization

Research in toxinology has created a pharmacological paradox. With an estimated 220,000 venomous animals worldwide, the study of peptidyl toxins provides a vast number of effector molecules. However, due to the complexity of the protein-protein interactions, there are fewer than ten venom-derived molecules on the market. Structural characterization and identification of post-translational modifications are essential to develop biological lead structures into pharmaceuticals. Utilizing advancements in mass spectrometry, we have created a high definition approach that fuses conventional high-resolution MS-MS with ion mobility spectrometry (HDMSE) to elucidate these primary structure characteristics. We investigated venom from ten species of “tiger” spider (Genus: Poecilotheria) and discovered they contain isobaric conformers originating from non-enzymatic Asp isomerization. One conformer pair conserved in five of ten species examined, denominated PcaTX-1a and PcaTX-1b, was found to be a 36-residue peptide with a cysteine knot, an amidated C-terminus, and isoAsp33Asp substitution. Although the isomerization of Asp has been implicated in many pathologies, this is the first characterization of Asp isomerization in a toxin and demonstrates the isomerized product’s diminished physiological effects. This study establishes the value of a HDMSE approach to toxin screening and characterization.

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Divisome under Construction: Distinct Domains of the Small Membrane Protein FtsB Are Necessary for Interaction with Multiple Cell Division Proteins

Journal of Bacteriology ◽

10.1128/jb.01597-08 ◽

2009 ◽

Vol 191 (8) ◽

pp. 2815-2825 ◽

Cited By ~ 40

Author(s):

Mark D. Gonzalez ◽

Jon Beckwith

Keyword(s):

Cell Division ◽

Membrane Proteins ◽

Protein Interactions ◽

Cell Envelope ◽

Coiled Coil ◽

Main Function ◽

Protein Protein Interactions ◽

Molecular Scaffold ◽

C Terminus ◽

Under Construction

ABSTRACT Cell division in bacteria requires the coordinated action of a set of proteins, the divisome, for proper constriction of the cell envelope. Multiple protein-protein interactions are required for assembly of a stable divisome. Within the Escherichia coli divisome is a conserved subcomplex of inner membrane proteins, the FtsB/FtsL/FtsQ complex, which is necessary for linking the upstream division proteins, which are predominantly cytoplasmic, with the downstream division proteins, which are predominantly periplasmic. FtsB and FtsL are small bitopic membrane proteins with predicted coiled-coil motifs, which themselves form a stable subcomplex that can recruit downstream division proteins independently of FtsQ; however, the details of how FtsB and FtsL interact together and with other proteins remain to be characterized. Despite the small size of FtsB, we identified separate interaction domains of FtsB that are required for interaction with FtsL and FtsQ. The N-terminal half of FtsB is necessary for interaction with FtsL and sufficient, when in complex with FtsL, for recruitment of downstream division proteins, while a portion of the FtsB C terminus is necessary for interaction with FtsQ. These properties of FtsB support the proposal that its main function is as part of a molecular scaffold to allow for proper formation of the divisome.

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