The BioGRID interaction database: 2013 update

The Biological General Repository for Interaction Datasets (BioGRID: http//thebiogrid.org) is an open access archive of genetic and protein interactions that are curated from the primary biomedical literature for all major model organism species. As of September 2012, BioGRID houses more than 500 000 manually annotated interactions from more than 30 model organisms. BioGRID maintains complete curation coverage of the literature for the budding yeast Saccharomyces cerevisiae, the fission yeast Schizosaccharomyces pombe and the model plant Arabidopsis thaliana. A number of themed curation projects in areas of biomedical importance are also supported. BioGRID has established collaborations and/or shares data records for the annotation of interactions and phenotypes with most major model organism databases, including Saccharomyces Genome Database, PomBase, WormBase, FlyBase and The Arabidopsis Information Resource. BioGRID also actively engages with the text-mining community to benchmark and deploy automated tools to expedite curation workflows. BioGRID data are freely accessible through both a user-defined interactive interface and in batch downloads in a wide variety of formats, including PSI-MI2.5 and tab-delimited files. BioGRID records can also be interrogated and analyzed with a series of new bioinformatics tools, which include a post-translational modification viewer, a graphical viewer, a REST service and a Cytoscape plugin

The BioGRID interaction database: 2015 update

The Biological General Repository for Interaction Datasets (BioGRID: http://thebiogrid.org) is an open access database that houses genetic and protein interactions curated from the primary biomedical literature for all major model organism species and humans. As of September 2014, the BioGRID contains 749 912 interactions as drawn from 43 149 publications that represent 30 model organisms. This interaction count represents a 50% increase compared to our previous 2013 BioGRID update. BioGRID data are freely distributed through partner model organism databases and meta-databases and are directly downloadable in a variety of formats. In addition to general curation of the published literature for the major model species, BioGRID undertakes themed curation projects in areas of particular relevance for biomedical sciences, such as the ubiquitin-proteasome system and various human disease-associated interaction networks. BioGRID curation is coordinated through an Interaction Management System (IMS) that facilitates the compilation interaction records through structured evidence codes, phenotype ontologies, and gene annotation. The BioGRID architecture has been improved in order to support a broader range of interaction and post-translational modification types, to allow the representation of more complex multi-gene/protein interactions, to account for cellular phenotypes through structured ontologies, to expedite curation through semi-automated text-mining approaches, and to enhance curation quality control

Phospho-regulation of gamma-tubulin in budding yeast

Chromosome segregation is the crucial step for cell division in most living organisms. In order to segregate the chromosomes equally into mother and daughter cells, the cell needs to build a spindle, which comprises three major components: chromosomes, microtubules and microtubule organizing center (centrosome in animal cells or spindle pole body in fungal cells). The building and normal execution of spindle function are tightly linked to cell cycle control system. gamma-Tubulin is an evolutionally conserved protein with its canonical function as a microtubule nucleator. Here we report that gamma-tubulin is phosphorylated at residue S360, a Cdk1/Cdc28 site. Phosphorylation of S360 in vivo was identified in a global analysis of the phosphoproteome of the spindle pole body (J. Keck and M. Jones, et al.). We confirmed Cdc28-Clb2 can phosphorylate S360 by in vitro kinase assay and peptide identification by mass spectrometry, and in vivo assay using two dimensional-polyacrylamide gel electrophoresis (2D-PAGE). A phospho-mimetic mutation (tub4-S360D) causes mitotic delay but does not inhibit recruitment of the gamma-tubulin complex (reported by GRIP Spc97-EGFP) to spindle poles. Analysis of synthetic genetic interactions and live cell imaging revealed that cytoplasmic microtubule function is normal in tub4-S360D cells but spindle microtubule function is perturbed. High-resolution analysis of spindle dynamics revealed fluctuations in length in metaphase and anaphase spindles. The velocities of spindle elongation in anaphase are similar in S360D and WT spindles, but the initial phase of rapid elongation in anaphase is prolonged in the S360D mutant, and spindle breakdown is delayed. Interpolar microtubules play a central role in spindle assembly and are actively responsible for spindle elongation with sliding forces generated from microtubule cross-linking proteins such as kinesin-5 (Cin8 in budding yeast). Genetic analysis indicates that mutations in proteins that act redundantly to Cin8 enhance the growth defect in S360D, and S360A can partially suppress deletion of Cin8. High-resolution tomography analysis of S360D mutant and WT cells reveals that the interpolar microtubules organization in S360D is completely perturbed, as almost none overlapping of interpolar microtubules were observed.Therefore, we conclude that S360 phosphorylation of gamma-tubulin/Tub4 by Cdk1/Cdc28 plays an important role in the control of spindle microtubule organization during spindle assembly, through docking and/or monitoring critical microtubule associated proteins, for example Cin8, at microtubule minus end hence regulating their functions on the plus end.La ségrégation des chromosomes est une étape cruciale pour la division des cellules de la plupart des être vivants. Pour que les chromosomes ségrégent également entre les cellules mère et fille, la cellule doit produire un fuseau comprenant trois composants : les chromosomes, les microtubules et un centre d'organisation des microtubules (le centrosomes chez les cellules animales ou le spindle pole body chez les cellules fongiques). La production et l'exécution normale de la fonction du fuseau sont étroitement couplées au système de contrôle du cycle cellulaire.La gamma-tubuline, une protéine très conservée dans l'évolution, a une fonction de nucléation des microtubules. Nous reportons ici que la gamma-tubuline est phosphorylée au résidu S360, un site pour Cdk1/Cdc28. Initialement identifiée in vivo lors d'une analyse globale du phosphoprotéome du spindle pole body (J. Keck and M. Jones, et al.), la phosphorylation de S360 par Cdc28-Clb2 est confirmée par nos travaux in vitro grâce à des essais kinase suivis d'identification de peptides par spectroscopie de masse et in vivo grâce à l'électrophorèse bidimensionnelle en gel de polyacrylamide (2D-PAGE). Une mutation phospho-mimétique (tub4-S360D) provoque un délai mitotique mais n'inhibe pas le recrutement du complexe de gamma-tubuline (détecté grâce à GRIP Spc97-EGFP) aux pôles du fuseau. Les études des interactions génétiques synthétiques et d'imagerie sur cellules vivantes révèlent que la fonction cytoplasmique des microtubules est normale chez le mutant tub4-S360D alors que la fonction des microtubules au niveau du fuseau est perturbée. Une analyse dynamique à haute résolution révèle des fluctuations de la longueur des fuseaux en métaphase et en anaphase. Bien que les vitesses d'élongation du fuseau durant l'anaphase soient similaires chez le mutant S360D et chez le sauvage, la phase initiale d'élongation rapide en anaphase est prolongée et la déconstruction du fuseau est retardée chez la mutant S360D.Les microtubules interpolaires jouent un rôle central dans l'assemblage du fuseau est sont activement responsables de l'élongation du fuseau grâce aux forces de glissement générées par les protéines liant les microtubules telle la kinesine-5 (Cin8 dans la levure de boulangerie). Une analyse génétique indique que des mutations de protéines redondantes avec Cin8 augmentent le défaut de croissance du mutant S360D alors que la mutation S360A supprime partiellement la délétion de Cin8. L'analyse tomographique à haute résolution de cellules du mutant S360D et de cellules sauvages révèle une perturbation extrême de l'organisation des microtubules interpolaires du mutant S360D avec très peu de microtubules interpolaires chevauchants observés.En conséquence, nous concluons que la phosphorylation du résidu S360 de la gamma-tubuline/Tub4 par Cdk1/Cdc28 joue un rôle important dans le contrôle de l'organisation des microtubules au cours de l'assemblage du fuseau, via l'arrimage et/ou le contrôle de protéines associées aux microtubules à l'extrémité (-) des microtubules, comme Cin8, et la régulation de leur fonction à l'extrémité (+) des microtubules

Additional file 1 of MCCC2 is a novel mediator between mitochondria and telomere and functions as an oncogene in colorectal cancer

Additional file 1. Fig. S1. MCCC2 promoted cell proliferation, invasion, and migration in vitro. A The MCCC2 expression level in human CRC cell line based on Expression Altas database from EMBL-EBL website. B The relative mRNA expression level of MCCC2 in human 8 CRC cell lines analyzed by qRT-PCR. C Proliferation assay using IncuCyte in both transient MCCC2 overexpression by cell transfection of MCCC2-FLAG plasmids and transient siRNA MCCC2 in DLD1 cells showed that MCCC2 selective expression could affect cell proliferation in DLD1 cells. Two‐way ANOVA was used to calculate p value. DRepresentative images and quantification of colony formation assay in both transient MCCC2 overexpression by cell transfection of MCCC2-FLAG plasmids and transient siRNA MCCC2 in DLD1 cells showed that MCCC2 selective expression could affect cell proliferation ability (n = 3). A paired two-tailed Student’s t-test was used to calculate p values. E Representative images and quantification of wound healing in both transient MCCC2 overexpression by cell transfection of MCCC2-FLAG plasmids and transient siRNA MCCC2 in DLD1 cells showed that MCCC2 selective expression could affect cell migration ability (n = 3). A paired two-tailed Student’s t-test was used to calculate p value. F Representative images and quantification of Transwell assay in both transient MCCC2 overexpression by cell transfection of MCCC2-FLAG plasmids and transient siRNA MCCC2 in DLD1 cells showed that MCCC2 selective expression could affect the invasion ability (n = 3). A paired two-tailed Student’s t-test was used to calculate p value. (All data are represented as the mean ± SEM. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001

A PDX model combined with CD-DST assay to evaluate the antitumor properties of KRpep-2d and oxaliplatin in KRAS (G12D) mutant colorectal cancer

Patient-derived xenograft (PDX) models are more faithful in maintaining the characteristics of human tumors than cell lines and are widely used in drug development, although they have some disadvantages, including their relative low success rate, long turn-around time, and high costs. The collagen gel droplet embedded culture drug sensitivity test (CD-DST) has been used as an in-vitro drug sensitivity test for patients with cancer because of its high success rate of primary cell culture, high sensitivity, and good clinical relevance, but it is based on an in-vitro cell culture and may not simulate the tumor microenvironment accurately. This study aims to combine a PDX model with CD-DST to evaluate the efficiency of antitumor agents. KRpep-2d, a small peptide targeting KRAS (G12D), and oxaliplatin were used to verify the feasibility of this approach. Whole-exome sequencing and Sanger sequencing were first applied to test and validate the KRAS mutation status of a panel of colorectal cancer PDX tissues. One PDX model was verified to carry KRAS (G12D) mutation and was used for in-vivo and the CD-DST drug tests. We then established the PDX mouse model from the patient with the KRAS (G12D) mutation and obtained viable cancer cells derived from the same PDX model. Next, the antitumor abilities of KRpep-2d and oxaliplatin were estimated in the PDX model and the CD-DST. We found that KRpep-2d showed no significant antitumor effect on the xenograft model or on cancer cells derived from the same PDX model. In contrast, oxaliplatin showed significant inhibitory effects in both tests. In conclusion, the PDX model in combination with the CD-DST assay is a comprehensive and feasible method of evaluating the antitumor properties of compounds and could be applied for new drug discovery

Use of the BioGRID Database for Analysis of Yeast Protein and Genetic Interactions

The BioGRID database is an extensive repository of curated genetic and protein interactions for the budding yeast Saccharomyces cerevisiae, the fission yeast Schizosaccharomyces pombe, and the yeast Candida albicans SC5314, as well as for several other model organisms and humans. This protocol describes how to use the BioGRID website to query genetic or protein interactions for any gene of interest, how to visualize the associated interactions using an embedded interactive network viewer, and how to download data files for either selected interactions or the entire BioGRID interaction data set

BioGRID: A Resource for Studying Biological Interactions in Yeast: Table 1.

The Biological General Repository for Interaction Datasets (BioGRID) is a freely available public database that provides the biological and biomedical research communities with curated protein and genetic interaction data. Structured experimental evidence codes, an intuitive search interface, and visualization tools enable the discovery of individual gene, protein, or biological network function. BioGRID houses interaction data for the major model organism species—including yeast, nematode, fly, zebrafish, mouse, and human—with particular emphasis on the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe as pioneer eukaryotic models for network biology. BioGRID has achieved comprehensive curation coverage of the entire literature for these two major yeast models, which is actively maintained through monthly curation updates. As of September 2015, BioGRID houses approximately 335,400 biological interactions for budding yeast and approximately 67,800 interactions for fission yeast. BioGRID also supports an integrated posttranslational modification (PTM) viewer that incorporates more than 20,100 yeast phosphorylation sites curated through its sister database, the PhosphoGRID