sorry, we can't preview this file
S7 Supplementary Data 1.7z (56.79 MB)
Dataset for: The Hfq regulon of Neisseria meningitidis
dataset
posted on 2017-05-12, 08:44 authored by Robert Huis in 't Veld, Gertjan Kramer, Arie Van der Ende, Dave Speijer, Yvonne PannekoekThe conserved RNA-binding protein Hfq has multiple regulatory roles within the prokaryotic cell, including promoting stable duplex formation between small RNAs and mRNAs, and thus hfq deletion mutants have pleiotropic phenotypes. Previous proteome and transcriptome studies of Neisseria meningitidis have generated limited insight into differential gene expression due to Hfq loss. In this study, reversed-phase liquid chromatography combined with data-independent alternate scanning mass spectrometry (LC-MSE) was utilized for rapid high-resolution quantitative proteomic analysis to further elucidate the differentially expressed proteome of a meningococcal hfq deletion mutant. Whole cell lysates of N. meningitidis serogroup B H44/76 wild type (wt) and H44/76Δhfq (Δhfq) grown in liquid growth medium were subjected to tryptic digestion. The resulting peptide mixtures were separated by LC prior to analysis by MSE. Differential expression was analyzed by Student’s t-Test with control for false discovery rate (FDR). Reliable quantification of relative expression comparing wt and Δhfq was achieved with 506 proteins (20%). Upon FDR control at q ≤ 0.05, 48 up- and 59 downregulated proteins were identified. From these, 81 were identified as novel Hfq-regulated candidates, while 15 proteins were previously found by SDS-PAGE/MS and 24 with microarray analyses. Thus, using LC-MSE we have expanded the repertoire of Hfq regulated proteins. In conjunction with previous studies, a comprehensive network of Hfq regulated proteins was constructed and differentially expressed proteins were found to be involved in a large variety of cellular processes. The results and comparisons with other Gram-negative model systems, suggest still unidentified sRNA analogues in N. meningitidis.
History
collectionID
3777857Usage metrics
Categories
- Regenerative medicine (incl. stem cells)
- Synthetic biology
- Plant cell and molecular biology
- Animal cell and molecular biology
- Evolution of developmental systems
- Structural biology (incl. macromolecular modelling)
- Proteomics and intermolecular interactions (excl. medical proteomics)
- Evolutionary biology not elsewhere classified
- Signal transduction
- Cancer cell biology
- Systems biology
- Bioinformatics and computational biology not elsewhere classified
- Biostatistics
- Computational methods in fluid flow, heat and mass transfer (incl. computational fluid dynamics)
Keywords
sRNANeisseria meningitidisHfqproteomicsribo-regulationmass spectrometryStem CellsSynthetic BiologyMolecular BiologyDevelopmental BiologyStructural BiologyProteomics and Intermolecular Interactions (excl. Medical Proteomics)Evolutionary BiologySignal TransductionCancer Cell BiologySystems BiologyBioinformaticsBiostatisticsHeat and Mass Transfer Operations
Licence
Exports
RefWorks
BibTeX
Ref. manager
Endnote
DataCite
NLM
DC