ArticleBMC genomics2014
Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 53 citations in OpenAlex.
- Chromosomal and Plasmid-Based CRISPRi Platforms for Conditional Gene Silencing inInternational journal of molecular sciences · 2025Article
- Methodologies for bacterial ribonuclease characterization using RNA-seq.FEMS microbiology reviews · 2023Review
- Crystal Structure of the Metallo-Endoribonuclease YbeY fromJournal of microbiology and biotechnology · 2023Article
- Review
- The world of ribonucleases from pseudomonads: a short trip through the main features and singularities.Microbial biotechnology · 2021Review
- YbeY controls the type III and type VI secretion systems and biofilm formation through RetS inApplied and environmental microbiology · 2021Article
- YBEY is an essential biogenesis factor for mitochondrial ribosomes.Nucleic acids research · 2020Article
- Endoribonuclease YbeY Is Essential for RNA Processing and Virulence in Pseudomonas aeruginosa.mBio · 2020Article
- Article
- Sinorhizobium meliloti YbeY is a zinc-dependent single-strand specific endoribonuclease that plays an important role in 16S ribosomal RNA processing.Nucleic acids research · 2020Article
- AtxA-Controlled Small RNAs ofFrontiers in microbiology · 2020Article
- RNA-Binding Proteins Driving the Regulatory Activity of Small Non-coding RNAs in Bacteria.Frontiers in molecular biosciences · 2020Review
- Bacterial ribonucleases and their roles in RNA metabolism.Critical reviews in biochemistry and molecular biology · 2019Review
- Advances in engineered trans-acting regulatory RNAs and their application in bacterial genome engineering.Journal of industrial microbiology & biotechnology · 2019Review
- The RNase YbeY Is Vital for Ribosome Maturation, Stress Resistance, and Virulence of the Natural Genetic EngineerJournal of bacteriology · 2019Article
- RNA-binding proteins in bacteria.Nature reviews. Microbiology · 2018Review
- Elevated Levels of Era GTPase Improve Growth, 16S rRNA Processing, and 70S Ribosome Assembly of Escherichia coli Lacking Highly Conserved Multifunctional YbeY Endoribonuclease.Journal of bacteriology · 2018Article
- sRNA-dependent control of curli biosynthesis in Escherichia coli: McaS directs endonucleolytic cleavage of csgD mRNA.Nucleic acids research · 2018Article
- Endoribonuclease YbeY Is Linked to Proper Cellular Morphology and Virulence in Brucella abortus.Journal of bacteriology · 2018Article
- Ribosome maturation by the endoribonuclease YbeY stabilizes a type 3 secretion system transcript required for virulence of enterohemorrhagicThe Journal of biological chemistry · 2018Article
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Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundConceptual parallels exist between bacterial and eukaryotic small-RNA (sRNA) pathways, yet relatively little is known about which protein may recognize and recruit bacterial sRNAs to interact with targets. In eukaryotes, Argonaute (AGO) proteins discharge such functions. The highly conserved bacterial YbeY RNase has structural similarities to the MID domain of AGOs. A limited study had indicated that in Sinorhizobium meliloti the YbeY ortholog regulates the accumulation of sRNAs as well as the target mRNAs, raising the possibility that YbeY may play a previously unrecognized role in bacterial sRNA regulation.
resultsWe have applied a multipronged approach of loss-of-function studies, genome-wide mRNA and sRNA expression profiling, pathway analysis, target prediction, literature mining and network analysis to unravel YbeY-dependent molecular responses of E. coli exposed to hydroxyurea (HU). Loss of ybeY function, which results in a marked resistance to HU, had global affects on sRNA-mediated gene expression. Of 54 detectable E. coli sRNAs in our microarray analysis, 30 sRNAs showed a differential expression upon HU stress, of which 28 sRNAs displayed a YbeY-dependent change in expression. These included 12 Hfq-dependent and 16 Hfq-independent sRNAs. We successfully identified at least 57 experimentally inferred sRNA-mRNA relationships. Further applying a 'context likelihood of relatedness' algorithm, we reverse engineered the YbeY-dependent Hfq-dependent sRNA-mRNA network as well as YbeY-dependent Hfq-independent sRNA-mRNA network.
conclusionYbeY extensively modulates Hfq-dependent and independent sRNA-mRNA interactions. YbeY-dependent sRNAs have central roles in modulating cellular response to HU stress.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.