Deep sequencing whole transcriptome exploration of the σE regulon in Neisseria meningitidis

• Published in: PloS one 2011-12, Vol.6 (12), p.e29002-e29002
• Main Authors: Huis in 't Veld, Robert Antonius Gerhardus, Willemsen, Antonius Marcellinus, van Kampen, Antonius Hubertus Cornelis, Bradley, Edward John, Baas, Frank, Pannekoek, Yvonne, van der Ende, Arie
• Format: Article
• Language: English
• Subjects: Bacteria; Base Sequence; Bioinformatics; Biology; Biosynthesis; DNA, Intergenic - genetics; E coli; Environmental changes; Epidemiology; Escherichia coli; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Genes; Genes, Bacterial - genetics; Genetic Loci - genetics; Genomes; Helicobacter pylori; High-Throughput Nucleotide Sequencing - methods; Humans; Infections; Laboratories; Ligands; Molecular Sequence Data; Neisseria meningitidis; Neisseria meningitidis - genetics; Nitrite reductase; Non-coding RNA; Nucleic Acid Conformation; Operon - genetics; Pathogens; Pharynx; Phenols; Protein A; Protein expression; Proteins; Regulon - genetics; Ribonucleic acid; RNA; RNA, Antisense - genetics; RNA, Bacterial - chemistry; RNA, Bacterial - genetics; Salmonella; Salmonella Typhimurium; Shigella; Sigma Factor - genetics; Stress response; Surface protein A; Transcription factors; Transcription, Genetic; Transcriptome - genetics; Up-Regulation - genetics
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0029002

Bacteria live in an ever-changing environment and must alter protein expression promptly to adapt to these changes and survive. Specific response genes that are regulated by a subset of alternative σ(70)-like transcription factors have evolved in order to respond to this changing environment. Recently, we have described the existence of a σ(E) regulon including the anti-σ-factor MseR in the obligate human bacterial pathogen Neisseria meningitidis. To unravel the complete σ(E) regulon in N. meningitidis, we sequenced total RNA transcriptional content of wild type meningococci and compared it with that of mseR mutant cells (ΔmseR) in which σ(E) is highly expressed. Eleven coding genes and one non-coding gene were found to be differentially expressed between H44/76 wildtype and H44/76ΔmseR cells. Five of the 6 genes of the σ(E) operon, msrA/msrB, and the gene encoding a pepSY-associated TM helix family protein showed enhanced transcription, whilst aniA encoding a nitrite reductase and nspA encoding the vaccine candidate Neisserial surface protein A showed decreased transcription. Analysis of differential expression in IGRs showed enhanced transcription of a non-coding RNA molecule, identifying a σ(E) dependent small non-coding RNA. Together this constitutes the first complete exploration of an alternative σ-factor regulon in N. meningitidis. The results direct to a relatively small regulon indicative for a strictly defined response consistent with a relatively stable niche, the human throat, where N. meningitidis resides.