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Nucleic Acids Research 2005 33(13):4368-4376; doi:10.1093/nar/gki752
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Published online 2 August 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

The 5S rRNA maturase, ribonuclease M5, is a Toprim domain family member

Frédéric Allemand, Nathalie Mathy, Dominique Brechemier-Baey and Ciarán Condon*

UPR 9073 (affiliated with Université de Paris 7—Denis Diderot), Institut de Biologie Physico-Chimique 13 rue Pierre et Marie Curie, 75005 Paris, France

*To whom correspondence should be addressed. Tel: +33 1 58 41 51 23; Fax: +33 1 58 41 50 20; Email: condon{at}ibpc.fr

Received May 30, 2005. Revised July 8, 2005. Accepted July 19, 2005.

The maturation of 5S ribosomal RNA in low G+C Gram-positive bacteria is catalyzed by a highly conserved, ~190 residue, enzyme, called ribonuclease M5 (RNase M5). Sequence alignment had predicted that the N-terminal half of RNase M5 would consist of a Toprim domain, a protein fold found in type IA and type II topoisomerases, DnaG-like primases, OLD family nucleases and RecR proteins [L. Aravind, D. D. Leipe and E. V. Koonin (1998) Nucleic Acids Res., 26, 4205–4213]. Here, we present structural modelling data and a mutational analysis of RNase M5 that confirms this hypothesis. The N-terminal half of RNase M5 can be fitted to the Toprim domain of the DnaG catalytic core. Mutation of amino acid residues highly conserved among RNase M5 enzymes and members of the Toprim domain family showed that alteration of residues critical for topoisomerase and primase activity also had a dramatic effect on the cleavage of 5S rRNA precursor by RNase M5 both in vivo and in vitro. This suggests that the mechanisms of double-stranded RNA cleavage by RNase M5 and double-stranded DNA cleavage by members of the topoisomerase family are related.


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