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MetabolomicsPROMIS, global analysis of PROtein-Metabolite Interactions using Size separation in Arabidopsis thaliana
Small molecules not only represent cellular building blocks and metabolic intermediates, but also regulatory ligands and signaling molecules that interact with proteins. Although these interactions affect cellular metabolism, growth, and development, they have been largely understudied. Herein, we d...
2018-07-19 | MTBLS94 | MetaboLights
MetabolomicsIntegrating two chromatographies in a co-fractionation mass spectrometry approach improved protein-metabolite interactions (PMIs) mapping capabilities and revealed novel protein-ligand pairings in Escherichia coli.
The protein-metabolite interactome remains understudied. We previously developed a co-fractionation mass-spectrometry-based approach called PROMIS to address this gap. PROMIS relies on size separation chromatography of protein-metabolite complexes from lysates, followed by proteomics and metabolomic...
2025-04-25 | MTBLS9098 | MetaboLights
MetabolomicsATAD3A has a scaffolding role regulating mitochondria inner membrane structure and protein assembly

The ATPase Family AAA Domain Containing 3A (ATAD3A), is a mitochondrial inner membrane protein conserved in metazoans. ATAD3A has been associated with several mitochondrial functions, including nucleoid organization, cholesterol metabolism, and mitochondrial translation. To address its primary ro...

2022-01-14 | MTBLS3786 | MetaboLights
MetabolomicsSystematic analyses of lipid mobilization by human lipid transfer proteins

Lipid transfer proteins (LTPs) maintain the specialised lipid compositions of biological membranes, and many are associated with disease. In eukaryotes, they support organellar functions by transporting lipids between compartmentalised metabolic pathways. However, for the majority of the hundreds...

2025-11-14 | MTBLS9567 | MetaboLights
GenomicsVirulence regulator EspR of Mycobacterium tuberculosis is a nucleoid-associated protein
The principal virulence determinant of Mycobacterium tuberculosis (Mtb), the ESX-1 protein secretion system, is positively controlled at the transcriptional level by EspR. Depletion of EspR reportedly affects a small number of genes, both positively or negatively, including a key ESX-1 component, th...
ORGANISM(S): Mycobacterium tuberculosis 
2012-04-02 | E-GEOD-35149 | biostudies-arrayexpress
TranscriptomicsAbsolute quantification of protein production reveals principles underlying protein synthesis rates
A quantitative view of cellular functions requires precise measures of the rates of biomolecule production, especially proteins-the direct effectors of biological processes. Here we present a genome-wide approach, based on ribosome profiling, for measuring absolute protein synthesis rates. The resul...
ORGANISM(S): Escherichia coli 
2014-04-24 | E-GEOD-53767 | biostudies-arrayexpress
TranscriptomicsRibosomal protein S3: a functional component of NF-kB p65 binding complexes
To explore the effects on the NF-kB transcriptome after knockdown of RPS3 in stimulated T cells, we performed microarray assays comparing RPS3-silenced versus NS-treated samples on the same chip. p65-silenced versus NS-treated samples were used as a control. Keywords: time series design Jurkat cells...
ORGANISM(S): Homo sapiens 
2010-05-26 | E-GEOD-7231 | biostudies-arrayexpress
TranscriptomicsA multiplexed assay to identify condition-dependent changes in protein-protein interactions
Testing the effect of 80 small molecules on the interaction between 250 protein pairs
ORGANISM(S): Saccharomyces cerevisiae 
2012-04-02 | E-MEXP-3467 | biostudies-arrayexpress
GenomicsInterconversion between active and inactive TATA-binding protein transcription complexes in the mouse genome.
The conserved core domain of the TATA binding protein (TBP) interacts with multiple partners forming the complexes required for transcription by RNA Polymerases I, II and III. We use genetically modified mouse embryonic fibroblasts to show that many TBP core domain mutants complement loss of endogen...
ORGANISM(S): Mus musculus 
2012-03-01 | E-GEOD-27908 | biostudies-arrayexpress
TranscriptomicsA Role for the RNA-Binding Protein MOS2 in MicroRNA Maturation in Arabidopsis
microRNAs (miRNAs) play important roles in the regulation of gene expression. In Arabidopsis, mature miRNAs are processed from primary miRNA transcripts (pri-miRNAs) by nuclear HYL1/SE/DCL1 complexes that form Dicing bodies (D-bodies). Here we report that a RNA-binding protein MOS2 bound to pri-miRN...
ORGANISM(S): Arabidopsis thaliana 
2012-10-27 | E-GEOD-41843 | biostudies-arrayexpress
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