Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Dissecting the malaria interactome

ABSTRACT: To identify malaria protein interactions systematically we combined blue native polyacrylamide electrophoresis fractionation with quantitative mass spectrometry and machine learning. Our integrative approach identified over twenty thousand protein interactions in Plasmodium schizonts, organized into 600 complexes, the majority of which are novel, and generated a high-confidence Plasmodium protein interaction network.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Plasmodium Berghei

TISSUE(S): Schizont

DISEASE(S): Malaria

SUBMITTER: James Wright

LAB HEAD: Jyoti Choudhary

PROVIDER: PXD010117 | Pride | 2019-08-06

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Fusion_MP001_4R1.raw	Raw
	Fusion_MP001_4R1X.raw	Raw
	Fusion_MP001_7R1.raw	Raw
	Fusion_MP002_8.raw	Raw
	Fusion_MP002_8X.raw	Raw

Items per page:

1 - 5 of 7

Publications

Landscape of the Plasmodium Interactome Reveals Both Conserved and Species-Specific Functionality.

Hillier Charles C Pardo Mercedes M Yu Lu L Bushell Ellen E Sanderson Theo T Metcalf Tom T Herd Colin C Anar Burcu B Rayner Julian C JC Billker Oliver O Choudhary Jyoti S JS

Cell reports 20190801 6

Malaria represents a major global health issue, and the identification of new intervention targets remains an urgent priority. This search is hampered by more than one-third of the genes of malaria-causing Plasmodium parasites being uncharacterized. We report a large-scale protein interaction network in Plasmodium schizonts, generated by combining blue native-polyacrylamide electrophoresis with quantitative mass spectrometry and machine learning. This integrative approach, spanning 3 species, id ...[more]

PMID: 31390575

Similar Datasets

Dissecting the malaria interactome

Project description:To identify malaria protein interactions systematically we combined blue native polyacrylamide electrophoresis fractionation with quantitative mass spectrometry and machine learning. Our integrative approach identified over twenty thousand protein interactions in Plasmodium schizonts, organized into 600 complexes, the majority of which are novel, and generated a high-confidence Plasmodium protein interaction network.

2019-08-06 | PXD009039 | Pride

Plasmodium berghei SUN1 and allantoicase interaction proteomics

Project description:SUN1 was identified in a screen for fertility genes in Plasmodium berghei. To understand its role, SUN1 was tagged with an HA tag at the endogenous locus, and SUN1 interacting proteins were characterised by affinity purification followed by mass spectrometry. This led to the identification of allantoicase as a SUN1-associated protein. Subsequent affinity interaction proteomics of HA-tagged allantoicase confirmed the interaction between these two proteins.

2024-10-24 | PXD048341 | Pride

Interactome analysis of FAM50A via affinity purification coupled to mass spectrometry

Project description:FAM50A missense variants are present in Armfield XLID syndrome patients. Zebrafish lacking fam50a display related phenotypes and show dysregulation of the transcriptome, increased spliceosome mRNAs and a preponderance of 3’ alternative splicing events, suggesting a role for Fam50a in the spliceosome C complex. Fam50A protein-protein interaction studies show that in 293T cells FAM50A interacts with spliceosome components. In sum, aberrant mRNA processing caused by FAM50A mutation underpins Armfield XLID syndrome.

2020-05-08 | PXD017642 | Pride

PBANKA_0828000 interactome proteomics

Project description:PBANKA_0828000 was identified in a screen for sex determination genes in Plasmodium berghei. PBANKA_0828000 encodes a zinc finger protein of unknown function. To address its role, PBANKA_0828000 was tagged with an HA tag at the endogenous locus, and protein interactions were characterised by affinity purification followed by mass spectrometry.

2023-02-22 | PXD033827 | Pride

FYRN and FYRC domains of the histone demethylase, JMJ14, mediated chromatin binding and transgene silencing through a pair of NAC transcription factors

Project description:JmjC domain containing protein 14 (JMJ14) is an H3K4-specific histone demethylase that plays important roles in RNA-mediated gene silencing and flowering time regulation in Arabidopsis. However, how JMJ14 is recruited to their target genes remains unclear. Here, we show that the C-terminal FYRN and FYRC domains of JMJ14 are required for RNA silencing and flowering time regulation. Chromatin binding of JMJ14 is lost upon deletion of its FYRN and FYRC domains, along with increased H3K4me3. FYRN and FYRC domains interact with a pair of NAC domain containing transcription factors, NAC050 and NAC052. Genome-wide analysis revealed that JMJ14 and NAC050/052 share a set of common target genes with CTTGNNNNNCAAG consensus sequences. Mutations in either NAC052 or NAC050 impair RNA-mediated gene silencing. Thus, our findings demonstrate an important role of FYRN and FYRC in targeting JMJ14 through direct interaction with NAC050/052 transcription factors, which reveals a novel mechanism of recruiting a histone demethylases to its target loci in higher plants. anti-HA ChIP-seq were performed with six samples: Col, NAC050-HA, NAC052-HA, jmj14-1, JMJ14-HA and JMJ14-FYR-HA. Anti-H3K4me3 ChIP were performed with four samples: Col, jmj14-1, JMJ14-HA and JMJ14-FYR-HA. (NAC050-HA indicates PNAC050::NAC050-HA nac050-1, NAC052-HA indicates PNAC052::NAC052-HA nac052-2, JMJ14-HA indicates PJMJ14::JMJ14-HA jmj14-1, JMJ14-FYR-HA indicates PJMJ14::JMJ14-FYR-HA jmj14-1)

2015-08-28 | E-GEOD-60084 | biostudies-arrayexpress

Discovery of telomere repeat-binding factor in the malaria parasite Plasmodium falciparum

Project description:ChIP-seq experiments were performed for the putative telomere repeat-binding factor (PfTRF) in the malaria parasite Plasmodium falciparum strain 3D7. The gene encoding this factor (PF3D7_1209300) was endogenously tagged with either a GFP- or a 3xHA-tag and these transgenic parasite lines were used in ChIP-sequencing experiments. Sequencing of the ChIP and input libraries showed enrichment of PfTRF at all telomere-repeat containing chromosome ends (reference genome Plasmodium falciparum 3D7 from PlasmoDB version 6.1) as well as in all upsB var promoters.In addition,PfTRF was enriched at seven additional, intra-chromosomal sites and called in the PfTRF-HA ChIP-seq only. Plasmodium falciparum 3D7 parasites were generated with -GFP or -3xHA C-terminal tagged TRF (PF3D7_1209300). Nuclei were isolated from formaldehyde cross-linked schizont-stage transgenic parasites and used to prepare chromatin. Chromatin immunoprecipitations were performed using mouse anti-GFP (Roche Diagnostics, #11814460001) or rat anti-HA 3F10 (Roche Diagnostics, #12158167001). Sequencing libraries were prepared according to a Plasmodium-optimized library preparation procedure including KAPA polymerase-mediated PCR amplification.

2016-07-15 | E-GEOD-76537 | biostudies-arrayexpress

Genome-wide analysis of genes regulated by ARR22 overexpression.

Project description:The experiment was designed to enable comparison of Pro35S:ARR22:HA in the presence of DEX or absence of DEX.

2013-07-27 | E-MEXP-3685 | biostudies-arrayexpress

Effects of Plasmodium berghei infection on Anopheles gambiae during oocysts development

Project description:Plasmodium ssp. are pathogens in their vertebrate hosts and also cause deleterious effects to their insect vectors. We show here, however, that Plasmodium-infected mosquitoes more efficiently accumulate energy resources (glycogen) during oocyst development, and survive better when they are starved. Microarray analysis revealed that mosquito metabolism is altered by the presence of rapidly growing oocysts in the midgut. Plasmodium infection is associated with enhanced expression of several insulin-like peptides in mosquitoes and blocking insulin-like signaling results in diminished Plasmodium development. We conclude that Plasmodium infection dramatically changes mosquito metabolism pathways, epitomized by enhanced insulin-signaling, and thereby confer a survival advantage to the insects during periods of starvation. Manipulation of this pathway may provide new strategies to influence the ability of mosquitoes to transmit the protozoa that cause malaria. One-condition experiment: P. berghei infected vs uninfected mosquitoes; 10 mosquitoes per sample; 4 biological replicates for each group; two different time points, 10 and 17 days post infection; control mosquitoes were from same batch as infected mosquitoes that were fed on clean mice.

2011-12-31 | E-GEOD-32200 | biostudies-arrayexpress

RNA-seq characterization of Physarum macroplasmodia

Project description:We report a novel approach for studying the transcriptomic changes during cell differentiation, using Physarum as a model 3 samples examined: starved plasmodium, starved plasmodium collected 2 hours after photoinduction, and starved plasmodium collected 6 hours after induction

2011-12-01 | E-GEOD-33793 | biostudies-arrayexpress

RNA-seq analysis of anti-malarial drug chemotherapy of murine experimental Cerebral Malaria (ECM)

Project description:Cerebral Malaria (HCM) is a serious neurological complication caused by Plasmodium falciparum infection. Currently the only treatment for HCM is the provision of anti-malarial drugs; however, such treatment by itself often fails to prevent death or development of neurological sequelae. To identify new potential adjunct treatments for HCM, we performed a non-biased whole brain transcriptomic time-course analysis of anti-malarial drug chemotherapy of murine experimental CM (ECM).

2018-07-03 | E-MTAB-6474 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data