Regulating the regulators

Oeiras, 10.01.2017

Almost all bacteria have the gene ybeY that codes for a protein that is supposed to have catalytic and/or RNA-binding/chaperone functions in bacteria. Until now, protein YbeY was described to have a single stranded-specific ribonuclease activity. Now, researchers from Cecília Arraiano lab with collaborators from Grupo de Ecología Genética de la Rizosfera, Consejo Superior de Investigaciones Científicas (Spain) have studied this enzyme in Sinorhizobium meliloti, a symbiotic nitrogen fixing bacteria with agricultural, economic and environmental impact. It was demonstrated that YbeY indistinctly cleaved single and double-stranded RNA substrates, a unique ability among bacterial endoribonucleases. The results have just been published in Nucleic Acids Research.

In Sinorhizobium meliloti YbeY has a strong impact in the biology of the microbe, namely modulating ABC transporters and genes involved in nitrogen fixation. Moreover, its activity is modulated by divalent metal ions, with Ca²⁺ specifically blocking activity on double-stranded and some structured RNA molecules.

"We think that the ability of YbeY to cleave dsRNAs together with its involvement in the control of gene expression through regulatory RNAs resembles the RNAi phenomenon from eukaryotes", said Margarida Saramago, first author of this work.

“The different cleavage specificity of YbeY according to the metal cofactor used in the reactions can have an important biological significance”, mentioned Rute Matos, also author of the paper.  

"This endoribonuclease really has unprecedented catalytic features, we were surprised and very excited with these results." according to Cecília Arraiano, coordinator of the Control of Gene Expression Lab.

Researchers Margarida Saramago, Rute Matos and Cecília Arraiano

Original article

Nucleic Acids Research, 2016 1 doi: 10.1093/nar/gkw1234

Sinorhizobium meliloti YbeY is an endoribonuclease with unprecedented catalytic features, acting as silencing enzyme in riboregulation

Margarida Saramago, Alexandra Peregrina, Marta Robledo, Rute G. Matos, Rolf Hilker, Javier Serrania, Anke Becker, Cecilia M. Arraiano and José I. Jiménez-Zurdo

Previous highlights of Cecilia Arraiano Lab on ribonucleases

• "A global perspective of RNases - Next generation sequencing reveals effect of bacterial exoribonucleases" (2015)

• "A CRISPR revolution: How bacteria fight their own infections - Researchers uncover new system of bacterial adaptative immunity" (2014)

• "The end is important too - Bacterial 3’UTRs are important for mRNA stability" (2014)
• "The difference was in the tail - New RNA degrading enzyme targets polyU mRNAs" (2013)
• "Who killed the unprotected RNA molecule? - Researchers uncovered alternative pathway in degradation of small non-coding RNAs" (2012)
• "Silencing genes in bacteria - Researchers uncover target-dependent small RNA regulation pathway" (2011)
• "The Making of a “Super”-Enzyme - One single aminoacid change in RNase II drastically improves its catalysis" (2009)
• "A Swiss army knife for RNA degradation - Specialized regions within the exossome uncovered by researchers" (2008)
• "ITQB publishes 3D Structure of RNase II in Nature - How to kill the messenger" (2006)