Drosophila melanogaster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA238018 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:RNAseq analysis of Malpighian tubules upon IMD activation
| PRJDB16488 | ENA
Project description:This project aims to define, by using a functional proteomic approach, the molecular partners associated with the canonical coupound of the IMD pathway. The Drosophila defense against pathogens largely relies on the activation of two major pathways, IMD and TOLL. The IMD pathway is activated mainly by Gram-negative bacteria, whereas the TOLL pathway responds predominantly to Gram-positive bacteria and fungi. The activation of this pathway leads to the rapid induction via NF-kB of numerous genes of the immune system, including various antimicrobial peptide genes. Recent evidence indicates that the IMD pathway is also involved in various other reactions in the absence of infection ("inflammatory-like" reactions). To gain a better understanding of the molecular machineries underlying the pleiotropic functions of this pathway, we have developed a proteomics analysis. Our first aim was to identify the proteins interacting with the 11 canonical members (PGRP-LC, PGRP-LE, IMD, BG4 (dFADD), DREDD, TAK1, TAB2, IAP2, IRD5 (DmIKKbeta), KEY (DmIKKgamma), and RELISH) previously shown to be involved in the activation of the IMD pathway. Each protein was fused N-terminally or C-terminally with a biotin tag and was stably expressed in S2 cells previously subjected to stable integration of the bacterial enzyme BirA to allow for biotinylation of the tags. In total, we established 22 stable transformant cell lines (11 genes x 2 tag locations), which were individually stimulated by heat-killed E.coli before harvest at 4 different time points (t=0 min, 10 min, 2 hour, and 8 hour). This procedure was followed by streptavidin-mediated affinity purification of 96 bait-protein complexes (22 transformants x 4 time points, plus 8 unstimulated controls without baits), on-bead trypsin digestions of the protein complexes and six LC-MS/MS analyses. We have identified 371 interactanting proteins in heat-killed E.coli stimulated Drosophila S2 cells, 90% of which have human orthologues. Comparative analysis of Gene Ontology (GO) annotation datasets from Human and Flies point to three significant common categories: (1) NuA4 Histone acetyltransferase complex, (2) SWI/SNF-type Chromatin remodeling complex, and (3) Transcription cofactor binding. Our Drosophila data point in particular to SUMOylation of the IkB-kinase homologue Ird5 in Drosophila, a level of regulation not described to date. Among numerous directions opened by our proteomics analysis, we have decided to first investigate this facet of the IMD pathway. We show nthat a highly conserved SUMOylation consensus site binds Drosophila SUMO (SMT3) in a challenge-dependent manner and that this process confers an increased level of activation of the antimicrobial peptide genes during bacterial challenge both in vitro and in flies. Our results demonstrate that SUMOylation of IKKbeta plays an important role in the induction of antimicrobial peptide genes. The MS analysis was performed on a FT ICR mass spectrometer (LTQ-FT Ultra, ThermoFisher Scientific, San Jose, CA) with the top 7 acquisition method: MS resolution 60,000, mass range 500-2000 Th, followed by 7 MS/MS (LTQ) on the 7 most intense peaks, with a dynamic exclusion for 90 s. The raw data were processed using Xcalibur 2.0.7 software. Each sample was first analyzed in triplicate then an exclusion list was added for three next runs. The database search was done on merged data using Mascot search engine (Matrix Science Mascot 2.3) on the 17D melanogaster databank (16535 sequences). Proteome Discoverer 1.3 (ThermoFisher Scientific) and Mascot were used to search the data and filter the results. The following parameters were used: up to 2 miss cleavages; MS tolerance 10 ppm; MSMS tolerance 1 Da; full tryptic peptides; partial modifications carbamidomethyla- tion (C), oxydation (M, H, W), Phosphorylation (Y).
2013-05-22 | PXD000129 | Pride
Project description:The response of drosophila to bacterial and fungal infections involves two signaling pathways, Toll and Imd, which both activate NF-kB family members. We have studied the global transcriptional response of flies to infection with drosophila C virus. Viral infection induced a set of genes distinct from those regulated by the Toll or Imd pathways, and triggered activation of a STAT binding activity. Genetic experiments showed that the JAK kinase Hopscotch was involved in the control of the viral load in infected flies, and was required, though not sufficient, for the induction of some virus-regulated genes. Our results indicate that in addition to Toll and Imd, a third evolutionary conserved innate immunity pathway operates in drosophila and counters viral infection.
2007-07-07 | E-GEOD-2828 | biostudies-arrayexpress
Project description:We have carried out ChIP-seq to study the distribution of Brahma in the genome of S2 cells and to identify the Brahma-bound genes. We have also knocked down Brahma by RNA interference and we have carried out RNA-seq to determine the changes induced by Brahma depletion in the transcriptome of S2 cells. Furthermore, we have carried out RNA-seq experiments to profile S2 cells in which we first deplete Brahma by RNA interference and then express recombinant Brahma (either wild-type or ATPase mutant). These datasets are being used in several projects aimed at gaining understanding on the roles of Brahma in transcription regulation and pre-mRNA processing.
2018-05-11 | GSE95236 | GEO
Project description:The distribution of Brahma in the genome of Drosophila melanogaster S2 cells and the roles of Brahma in transcription and pre-mRNA processing
| PRJNA376457 | ENA
Project description:Drosophila gut transcriptome in larvae and adult flies which experienced larval IMD activation
| PRJDB11191 | ENA
Project description:The response of drosophila to bacterial and fungal infections involves two signaling pathways, Toll and Imd, which both activate NF-kB family members. We have studied the global transcriptional response of flies to infection with drosophila C virus. Viral infection induced a set of genes distinct from those regulated by the Toll or Imd pathways, and triggered activation of a STAT binding activity. Genetic experiments showed that the JAK kinase Hopscotch was involved in the control of the viral load in infected flies, and was required, though not sufficient, for the induction of some virus-regulated genes. Our results indicate that in addition to Toll and Imd, a third evolutionary conserved innate immunity pathway operates in drosophila and counters viral infection. Keywords: JAK/STAT virus drosophila immunity
2005-08-08 | GSE2828 | GEO
Project description:Drosophila S2 cells Raw sequence reads
| PRJNA847178 | ENA
Project description:Expression in Aneuploid Drosophila S2 Cells
| PRJNA116335 | ENA