Dataset for: The Hfq regulon of <i>Neisseria meningitidis</i>

The 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 <i>hfq</i> deletion mutants have pleiotropic phenotypes. Previous proteome and transcriptome studies of <i>Neisseria meningitidis</i> 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-MS^E) was utilized for rapid high-resolution quantitative proteomic analysis to further elucidate the differentially expressed proteome of a meningococcal <i>hfq</i> deletion mutant. Whole cell lysates of <i>N. meningitidis</i> serogroup B H44/76 wild type (wt) and H44/76Δ<i>hfq</i> (Δ<i>hfq</i>) grown in liquid growth medium were subjected to tryptic digestion. The resulting peptide mixtures were separated by LC prior to analysis by MS^E. Differential expression was analyzed by Student’s <i>t</i>-Test with control for false discovery rate (FDR). Reliable quantification of relative expression comparing wt and Δ<i>hfq</i> was achieved with 506 proteins (20%). Upon FDR control at <i>q</i> ≤ 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-MS^E 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 <i>N. meningitidis</i>.