Structural insights into the dual activity of RNase J

Abstract

The maturation and stability of RNA transcripts is controlled by a combination of endo- and exoRNases. RNase J is unique, as it combines an RNase E–like endoribonucleolytic and a 5′-to-3′ exoribonucleolytic activity in a single polypeptide. The structural basis for this dual activity is unknown. Here we report the crystal structures of Thermus thermophilus RNase J and its complex with uridine 5′-monophosphate. A binding pocket coordinating the phosphate and base moieties of the nucleotide in the vicinity of the catalytic center provide a rationale for the 5′-monophosphate–dependent 5′-to-3′ exoribonucleolytic activity. We show that this dependence is strict; an initial 5′-PPP transcript cannot be degraded exonucleolytically from the 5′-end. Our results suggest that RNase J might switch promptly from endo- to exonucleolytic mode on the same RNA, a property that has important implications for RNA metabolism in numerous prokaryotic organisms and plant organelles containing RNase J orthologs.

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Figure 1: Structure of RNase J and close up of the active site.
Figure 2: Comparison of the structures of T. thermophilus RNase J and E. coli RNase E (catalytic N-terminal domain).
Figure 3: In vitro activity of B. subtilis RNase J1 mutants and inhibition of the exonuclease activity by a 5′-PPP moiety.

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Acknowledgements

We thank J. Plumbridge, M. Dreyfus, C. Condon and D. Picot for discussions, and Véronique Norman for help with the crystallization assays. We acknowledge the European Synchrotron Radiation Facility for providing the synchrotron radiation facilities and would like to thank X. Thibault for assistance in using beamline ID14-4, D. Picot and L. Barucq for the collection of the RNase J–UMP data at beamline ID29, J.L. Popot for the use of crystallography facilities and X-ray generator at the Institut de Biologie Physico-Chimique, and V. Urlacher and J. Berenguer for their gift of T. thermophilus chromosomal DNA. This work was supported by the Université Paris 7-Denis Diderot, the CNRS (UPR9073), the Agence Nationale de la Recherche and the Conseil Régionale de l'Ile de France. A.J. was supported by a scholarship from the Iranian Ministry of Science.

Author information

Protein samples for structural studies were prepared by L.Z. Functional experiments and cloning were carried out by A.J. and L.Z., and analyzed by H.P. and A.J. Crystallization, structure calculation and refinement were carried out by I.L.d.l.S.-G. The manuscript was written by H.P. and I.L.d.l.S.-G.

Correspondence to Harald Putzer.

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de la Sierra-Gallay, I., Zig, L., Jamalli, A. et al. Structural insights into the dual activity of RNase J. Nat Struct Mol Biol 15, 206–212 (2008). https://doi.org/10.1038/nsmb.1376

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