Role of Escherichia coli YbeY, a highly conserved protein, in rRNA processing

Abstract

SummaryThe UPF0054 protein family is highly conserved with homologues present in nearly every sequenced bacterium. In some bacteria, the respective gene is essential, while in others its loss results in a highly pleiotropic phenotype. Despite detailed structural studies, a cellular role for this protein family has remained unknown. We report here that deletion of the Escherichia coli homologue, YbeY, causes striking defects that affect ribosome activity, translational fidelity and ribosome assembly. Mapping of 16S, 23S and 5S rRNA termini reveals that YbeY influences the maturation of all three rRNAs, with a particularly strong effect on maturation at both the 5Ј-and 3Ј-ends of 16S rRNA as well as maturation of the 5Ј-termini of 23S and 5S rRNAs. Furthermore, we demonstrate strong genetic interactions between ybeY and rnc (encoding RNase III), ybeY and rnr (encoding RNase R), and ybeY and pnp (encoding PNPase), further suggesting a role for YbeY in rRNA maturation. Mutation of highly conserved amino acids in YbeY, allowed the identification of two residues (H114, R59) that were found to have a significant effect in vivo. We discuss the implications of these findings for rRNA maturation and ribosome assembly in bacteria.

RBF1, a Plant Homolog of the Bacterial Ribosome-Binding Factor RbfA, Acts in Processing of the Chloroplast 16S Ribosomal RNA

“…Work in bacteria has elucidated the sequence of events in ribosome assembly and established detailed assembly maps for both ribosomal subunits (Dabbs, 1991;Talkington et al, 2005;Kaczanowska and Rydén-Aulin, 2007;Woodson, 2008;Connolly and Culver, 2009;Fournier et al, 2010). It also identified a number of auxiliary factors acting in rRNA processing and/or ribosome maturation (Davies et al, 2010;Connolly and Culver, 2013;Jacob et al, 2013). For some of these factors, homologous genes have been identified in the nuclear genomes of plants and algae, but very few of these have been studied functionally (Bang et al, 2012), and for most of the encoded proteins, their site of action Figure 2.…”

Multiple Exoribonucleases Catalyze Maturation of the 3′ Terminus of 16S Ribosomal RNA (rRNA)

“…In a very recent study (23), one protein of previously unknown function, YbeY, known to participate in 3Ј processing of 16S rRNA (24), was shown to be an endoribonuclease. As a consequence, it was proposed that YbeY is responsible for removal of most of the 33 extra 3Ј-residues, although no direct evidence for this assertion was presented (23).…”

“…Based on our data, we believe it is unlikely that YbeY directly removes extra 3Ј-nucleotides inasmuch as all 33 residues remain when the exoribonucleases identified here are removed. Thus, although it is clear that YbeY is needed for 3Ј maturation of 16S rRNA (24), its actual role remains to be determined.…”

The small RNA SraG participates in PNPase homeostasis

“…We also tested the role of other RNases such as RNase BN (elaC or rbn), RNase P (rnpA), and YbeY (ybeY), which is a metal-dependent single-strand-specific endoribonuclease (Davies et al 2010;Pandey et al 2011). Their inactivation had no effect on the level or the balance between SraG and SraGp (Supplemental Fig.…”