The minimal meningococcal ProQ protein has an intrinsic capacity for structure-based global RNA recognition

Saskia Bauriedl, Milan Gerovac, Nadja Heidrich, Thorsten Bischler, Lars Barquist, Jörg Vogel () and Christoph Schoen ()
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Saskia Bauriedl: University of Würzburg
Milan Gerovac: University of Würzburg
Nadja Heidrich: University of Würzburg
Thorsten Bischler: University of Würzburg
Lars Barquist: Helmholtz Centre for Infection Research (HZI)
Jörg Vogel: University of Würzburg
Christoph Schoen: University of Würzburg

Nature Communications, 2020, vol. 11, issue 1, 1-15

Abstract: Abstract 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.

Date: 2020
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DOI: 10.1038/s41467-020-16650-6

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