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  - 
TY  - JOUR
A1  - Michaux, Charlotte
A1  - Hansen, Elisabeth E.
A1  - Jenniches, Laura
A1  - Gerovac, Milan
A1  - Barquist, Lars
A1  - Vogel, Jörg
T1  - Single-Nucleotide RNA Maps for the Two Major Nosocomial Pathogens Enterococcus faecalis and Enterococcus faecium
JF  - Frontiers in Cellular and Infection Microbiology
N2  - Enterococcus faecalis and faecium are two major representative clinical strains of the Enterococcus genus and are sadly notorious to be part of the top agents responsible for nosocomial infections. Despite their critical implication in worldwide public healthcare, essential and available resources such as deep transcriptome annotations remain poor, which also limits our understanding of post-transcriptional control small regulatory RNA (sRNA) functions in these bacteria. Here, using the dRNA-seq technique in combination with ANNOgesic analysis, we successfully mapped and annotated transcription start sites (TSS) of both E. faecalis V583 and E. faecium AUS0004 at single nucleotide resolution. Analyzing bacteria in late exponential phase, we capture ~40% (E. faecalis) and 43% (E. faecium) of the annotated protein-coding genes, determine 5′ and 3′ UTR (untranslated region) length, and detect instances of leaderless mRNAs. The transcriptome maps revealed sRNA candidates in both bacteria, some found in previous studies and new ones. Expression of candidate sRNAs is being confirmed under biologically relevant environmental conditions. This comprehensive global TSS mapping atlas provides a valuable resource for RNA biology and gene expression analysis in the Enterococci. It can be accessed online at www.helmholtz-hiri.de/en/datasets/enterococcus through an instance of the genomic viewer JBrowse.
KW  - transcription start sites
KW  - RNA-seq
KW  - sRNA atlas
KW  - Gram-positive bacteria
KW  - post-transcriptional regulation
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-217947
SN  - 2235-2988
VL  - 10
ER  -