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Nucleic Acids Research Advance Access published online on June 24, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp527
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Nucleic Acid Enzymes

Degradation of nanoRNA is performed by multiple redundant RNases in Bacillus subtilis

Ming Fang1, Wencke-Maria Zeisberg1, Ciaran Condon2, Vasily Ogryzko3, Antoine Danchin1 and Undine Mechold1,*

1Institut Pasteur, URA 2171, Unité de Génétique des Génomes Bactériens, 75724 Paris Cedex 15, 2Institut de Biologie Physico-Chimique, CNRS UPR 9073, 75005 Paris and 3Institut Gustave Roussy, UMR 8126, Unité d’ Interactions Moléculaires et Cancer, 94805 Villejuif, France

*To whom correspondence should be addressed. Tel: +33 14 0613870; Fax: +33 14 5688948; Email: undine.mechold{at}pasteur.fr

Received January 28, 2009. Revised April 30, 2009. Accepted June 3, 2009.

Escherichia coli possesses only one essential oligoribonuclease (Orn), an enzyme that can degrade oligoribonucleotides of five residues and shorter in length (nanoRNA). Firmicutes including Bacillus subtilis do not have an Orn homolog. We had previously identified YtqI (NrnA) as functional analog of Orn in B. subtilis. Screening a genomic library from B. subtilis for genes that can complement a conditional orn mutant, we identify here YngD (NrnB) as a second nanoRNase in B. subtilis. Like NrnA, NrnB is a member of the DHH/DHHA1 protein family of phosphoesterases. NrnB degrades nanoRNA 5-mers in vitro similarily to Orn. Low expression levels of NrnB are sufficient for orn complementation. YhaM, a known RNase present in B. subtilis, degrades nanoRNA efficiently in vitro but requires high levels of expression for only partial complementation of the orn– strain. A triple mutant (nrnA–, nrnB–, yhaM–) in B. subtilis is viable and shows almost no impairment in growth. Lastly, RNase J1 seems also to have some 5'-to-3' exoribonuclease activity on nanoRNA and thus can potentially finish degradation of RNA. We conclude that, unlike in E. coli, degradation of nanoRNA is performed in a redundant fashion in B. subtilis.


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