The RNase YbeY Is Vital for Ribosome Maturation, Stress Resistance, and Virulence of the Natural Genetic Engineer Agrobacterium tumefaciens

Abstract

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. RNA coimmunoprecipitation-sequencing (RIP-Seq) showed binding of YbeY to the region immediately upstream of the 16S rRNA. Purified YbeY is an oligomer with RNase 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, we 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 RNase 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.

YBEY is an essential biogenesis factor for mitochondrial ribosomes

“…Based on studies in various bacteria, YbeY has been implicated in ribosome maturation and quality control, with a particularly important role in small subunit (SSU) biogenesis (3-8), and post-transcriptional gene expression regulation (9-14). The deletion of ybeY is often lethal or associated with severe alterations of cellular metabolism and growth, indicating its indispensability for a wide variety of bacterial-type ribosomes (4,6,7,(13)(14)(15)(16)(17).…”

“…Based on studies in various bacteria, YbeY has been implicated in ribosome maturation and quality control, with a particularly important role in small subunit (SSU) biogenesis (3-8), and post-transcriptional gene expression regulation (9-14). The deletion of ybeY is often lethal or associated with severe alterations of cellular metabolism and growth, indicating its indispensability for a wide variety of bacterial-type ribosomes (4,6,7,(13)(14)(15)(16)(17).Mechanistically, YbeY has been described as a metal-dependent endoribonuclease (5,12), and in some bacteria, ybeY mutants accumulate 16S rRNA with an unprocessed 3' end (3,5,7,8). Therefore, YbeY was proposed to be the "missing" 3' endoribonuclease required for 16S rRNA maturation to obtain the correct anti-Shine-Dalgarno sequence, which is needed for translation initiation on most bacterial mRNAs.…”

Identification of flavonoids as regulators of YbeY activity in Liberibacter asiaticus

“…meliloti , and A . tumefaciens , YbeY homologues are involved in normal cellular growth as well as antibiotic resistance (β‐lactams) and resistance to environmental stress, including temperature, detergents and oxidative stress (Davies and Walker, ; Davies et al ., ; Budnick et al ., ; Möller et al ., ). YbeY homologues in Bacillus subtilis and Haemophilus influenzae serve a more critical role and are recognized as essential proteins (Akerley et al ., ; Kobayashi et al ., ; Baumgardt et al ., ).…”

“…In this study, we reported the characterization of YbeY from Liberibacter asiaticus and established the feasibility of using this protein as a target for the development of antimicrobials. In E. coli, B. abortus, S. meliloti, and A. tumefaciens, YbeY homologues are involved in normal cellular growth as well as antibiotic resistance (β-lactams) and resistance to environmental stress, including temperature, detergents and oxidative stress (Davies and Walker, 2008;Davies et al, 2010;Budnick et al, 2018;Möller et al, 2019). YbeY homologues in Bacillus subtilis and Haemophilus influenzae serve a more critical role and are recognized as essential proteins (Akerley et al, 2002;Kobayashi et al, 2003;Baumgardt et al, 2018).…”

“…In enterohemorrhagic Escherichia coli, YbeY was found to stabilize a type 3 secretion system required for virulence in humans (McAteer et al, 2018). A recent study also found that YbeY was crucial for T-DNA transfer and tumour formation in the plant pathogen Agrobacterium tumefaciens (Möller et al, 2019).…”