TY  - JOUR
A1  - Heidrich, Nadja
A1  - Bauriedl, Saskia
A1  - Barquist, Lars
A1  - Li, Lei
A1  - Schoen, Christoph
A1  - Vogel, Jörg
T1  - The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq
JF  - Nucleic Acids Research
N2  - 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.
KW  - RNA
KW  - Neisseria meningitidis
KW  - dRNA-seq
KW  - transcriptome
KW  - RNA chaperone Hfq
Y1  - 2017
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-170828
VL  - 45
IS  - 10
ER  - 
TY  - JOUR
A1  - Bauriedl, Saskia
A1  - Gerovac, Milan
A1  - Heidrich, Nadja
A1  - Bischler, Thorsten
A1  - Barquist, Lars
A1  - Vogel, Jörg
A1  - Schoen, Christoph
T1  - The minimal meningococcal ProQ protein has an intrinsic capacity for structure-based global RNA recognition
JF  - Nature Communications
N2  - FinO-domain proteins are a widespread family of bacterial RNA-binding proteins with regulatory functions. Their target spectrum ranges from a single RNA pair, in the case of plasmid-encoded FinO, to global RNA regulons, as with enterobacterial ProQ. To assess whether the FinO domain itself is intrinsically selective or promiscuous, we determine in vivo targets of Neisseria meningitidis, which consists of solely a FinO domain. UV-CLIP-seq identifies associations with 16 small non-coding sRNAs and 166 mRNAs. Meningococcal ProQ predominantly binds to highly structured regions and generally acts to stabilize its RNA targets. Loss of ProQ alters transcript levels of >250 genes, demonstrating that this minimal ProQ protein impacts gene expression globally. Phenotypic analyses indicate that ProQ promotes oxidative stress resistance and DNA damage repair. We conclude that FinO domain proteins recognize some abundant type of RNA shape and evolve RNA binding selectivity through acquisition of additional regions that constrain target recognition. FinO-domain proteins are bacterial RNA-binding proteins with a wide range of target specificities. Here, the authors employ UV CLIP-seq and show that minimal ProQ protein of Neisseria meningitidis binds to various small non-coding RNAs and mRNAs involved in virulence.
KW  - Neisseria meningitidis
KW  - natural transformation
KW  - dual function
KW  - FinO family
KW  - HFQ
KW  - chaperone
KW  - transcriptome
KW  - regulator
KW  - sequence
KW  - in vivo
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-230040
VL  - 11
ER  -