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J Bacteriol. 2019 Mar 18. pii: JB.00730-18. doi: 10.1128/JB.00730-18. [Epub ahead of print]

The RNase YbeY is vital for ribosome maturation, stress resistance and virulence of the natural genetic engineer Agrobacterium tumefaciens.

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Microbial Biology, Ruhr University Bochum, Bochum, Germany.
German National Library of Medicine, Information Center for Life Sciences, Cologne, Germany.
Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
Microbial Biology, Ruhr University Bochum, Bochum, Germany


Riboregulation involving regulatory RNAs, RNA chaperones and ribonucleases is fundamental for the rapid adaptation of gene expression to changing environmental conditions. The gene coding for the RNase YbeY belongs to the minimal prokaryotic genome set and has a profound impact on physiology in a wide range of bacteria. Here, we show that the Agrobacterium tumefaciens ybeY gene is not essential. Deletion of the gene in the plant pathogen reduced growth, motility and stress tolerance. Most interestingly, YbeY is crucial for A. tumefaciens-mediated T-DNA transfer and tumor formation. Comparative proteomics by using isobaric tags for relative and absolute quantitation (iTRAQ) revealed dysregulation of 59 proteins, many of which have previously been found to be dependent on the RNA chaperone Hfq. YbeY and Hfq have opposing effects on production of these proteins. Accumulation of a 16S rRNA precursor in the ybeY mutant suggests that A. tumefaciens YbeY is involved in rRNA processing. RIP (RNA co-immunoprecipitation)-Seq showed binding of YbeY to the region immediately upstream of the 16S rRNA. Purified YbeY is an oligomer with ribonuclease activity. It does not physically interact with Hfq and thus plays a partially overlapping but distinct role in the riboregulatory network of the plant pathogen.IMPORTANCE Although ybeY gene belongs to the universal bacterial core genome, its biological function is incompletely understood. Here show that YbeY is critical for fitness and host-microbe interaction in the plant pathogen Agrobacterium tumefaciens Consistent with the reported endoribonuclease activity of YbeY, A. tumefaciens YbeY acts as a ribonuclease involved in maturation of 16S rRNA. This report adds a worldwide plant pathogen and natural genetic engineer of plants to the growing list of bacteria that require the conserved YbeY protein for host-microbe interaction.


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