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Nucleic Acids Research Advance Access originally published online on June 16, 2008
Nucleic Acids Research 2008 36(12):4172-4180; doi:10.1093/nar/gkn360
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Nucleic Acids Research, 2008, Vol. 36, No. 12 4172-4180
© 2008 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.

RNA

Studies on Methanocaldococcus jannaschii RNase P reveal insights into the roles of RNA and protein cofactors in RNase P catalysis

Dileep K. Pulukkunat and Venkat Gopalan*

Ohio State Biochemistry Program and Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA

*To whom correspondence should be addressed. Tel: +614 292 1332; Fax: +614 292 6773; Email: gopalan.5{at}osu.edu

Received April 20, 2008. Revised May 15, 2008. Accepted May 20, 2008.

Ribonuclease P (RNase P), a ribonucleoprotein (RNP) complex required for tRNA maturation, comprises one essential RNA (RPR) and protein subunits (RPPs) numbering one in bacteria, and at least four in archaea and nine in eukarya. While the bacterial RPR is catalytically active in vitro, only select euryarchaeal and eukaryal RPRs are weakly active despite secondary structure similarity and conservation of nucleotide identity in their putative catalytic core. Such a decreased archaeal/eukaryal RPR function might imply that their cognate RPPs provide the functional groups that make up the active site. However, substrate-binding defects might mask the ability of some of these RPRs, such as that from the archaeon Methanocaldococcus jannaschii (Mja), to catalyze precursor tRNA (ptRNA) processing. To test this hypothesis, we constructed a ptRNA-Mja RPR conjugate and found that indeed it self-cleaves efficiently (kobs, 0.15 min–1 at pH 5.5 and 55°C). Moreover, one pair of Mja RPPs (POP5-RPP30) enhanced kobs for the RPR-catalyzed self-processing by ~100-fold while the other pair (RPP21-RPP29) had no effect; both binary RPP complexes significantly reduced the monovalent and divalent ionic requirement. Our results suggest a common RNA-mediated catalytic mechanism in all RNase P and help uncover parallels in RNase P catalysis hidden by plurality in its subunit make-up.


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