Abstract
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 σ70-like transcription factors have evolved in order to respond to this changing environment. Recently, we have described the existence of a σE regulon including the anti-σ-factor MseR in the obligate human bacterial pathogen Neisseria meningitidis. To unravel the complete σE 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 σE 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 σE 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 σE 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.
Highlights
Bacteria live in an ever-changing environment and must alter protein expression promptly to adapt to these changes and survive
The name extracytoplasmic function (ECF) sigma factors or sE factors refer to the fact that most of the genes under control of these s factors encode proteins residing in the outer membrane or periplasmic space [2]
The proportion of mapped reads ranged from 50% to 68%, with the second less stringent mapping accounting for 4–6% of all mapped reads
Summary
Bacteria live in an ever-changing environment and must alter protein expression promptly to adapt to these changes and survive. The proteomic exploration of the sE regulon of meningococci and a microarray gene expression analysis for the closely related human pathogen Neisseria gonorrhoeae performed by others have revealed a surprisingly small regulon for the sE factor in Neisseria [6]. Both methods have several inherent and technical limitations. Reliability and reproducibility remains a concern [7,8,9] Both approaches are unsuitable to detect an important class of RNA regulators called small RNAs (sRNA) [10,11]. In order to unravel the complete sE regulon in N. meningitidis, we sequenced total RNA transcriptional content of wild type meningococci and compared it with that of mseR knock-out cells in which sE is highly expressed
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