The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq.
Neisseria meningitidis is a human commensal that can also cause life-threatening meningitis and septicemia. Despite growing evidence for RNA-based regulation in meningococci, their transcriptome structure and output of regulatory small RNAs (sRNAs) are incompletely understood. Using dRNA-seq, we have mapped at single-nucleotide resolution the primary transcriptome of N. meningitidis strain 8013. Annotation of 1625 transcriptional start sites defines transcription units for most protein-coding genes but also reveals a paucity of classical σ70-type promoters, suggesting the existence of activators that compensate for the lack of -35 consensus sequences in N. meningitidis. The transcriptome maps also reveal 65 candidate sRNAs, a third of which were validated by northern blot analysis. Immunoprecipitation with the RNA chaperone Hfq drafts an unexpectedly large post-transcriptional regulatory network in this organism, comprising 23 sRNAs and hundreds of potential mRNA targets. Based on this data, using a newly developed gfp reporter system we validate an Hfq-dependent mRNA repression of the putative colonization factor PrpB by the two trans-acting sRNAs RcoF1/2. Our genome-wide RNA compendium will allow for a better understanding of meningococcal transcriptome organization and riboregulation with implications for colonization of the human nasopharynx.
RNA Biology Group, Institute for Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany.
Nadja
N
Heidrich
Institute for Hygiene and Microbiology (IHM), University of Würzburg, D-97080 Würzburg, Germany.
Saskia
S
Bauriedl
RNA Biology Group, Institute for Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany.
Lars
L
Barquist
Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Lei
L
Li
Institute for Hygiene and Microbiology (IHM), University of Würzburg, D-97080 Würzburg, Germany.
Christoph
C
Schoen
RNA Biology Group, Institute for Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany.|Helmholtz Institute for RNA-based Infection Research (HIRI), D-97080 Würzburg, Germany.
Jörg
J
Vogel
D020413:3' Untranslated Regions / Q000235:genetics; D001426:Bacterial Proteins / Q000378:metabolism*; D001483:Base Sequence; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D035001:Host Factor 1 Protein / Q000378:metabolism*; D035683:MicroRNAs / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D018832:Molecular Chaperones / Q000378:metabolism*; D009345:Neisseria meningitidis / Q000235:genetics* / Q000472:pathogenicity; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D020871:RNA Stability; D012329:RNA, Bacterial / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D013045:Species Specificity; D059467:Transcriptome; D014774:Virulence
D020413:3' Untranslated Regions; D001426:Bacterial Proteins; D035001:Host Factor 1 Protein; D035683:MicroRNAs; D018832:Molecular Chaperones; D012329:RNA, Bacterial; D012333:RNA, Messenger