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Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover

Abstract

The coordinated regulation of gene expression is required for homeostasis, growth and development in all organisms. Such coordination may be partly achieved at the level of messenger RNA stability1, in which the targeted destruction of subsets of transcripts generates the potential for cross-regulating metabolic pathways. In Escherichia coli, the balance and composition of the transcript population is affected by RNase E, an essential endoribonuclease that not only turns over RNA but also processes certain key RNA precursors2,3,4,5,6,7,8,9,10. RNase E cleaves RNA internally, but its catalytic power is determined by the 5′ terminus of the substrate, even if this lies at a distance from the cutting site11,12,13,14. Here we report crystal structures of the catalytic domain of RNase E as trapped allosteric intermediates with RNA substrates. Four subunits of RNase E catalytic domain associate into an interwoven quaternary structure, explaining why the subunit organization is required for catalytic activity. The subdomain encompassing the active site is structurally congruent to a deoxyribonuclease, making an unexpected link in the evolutionary history of RNA and DNA nucleases. The structure explains how the recognition of the 5′ terminus of the substrate may trigger catalysis and also sheds light on the question of how RNase E might selectively process, rather than destroy, specific RNA precursors.

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Acknowledgements

We thank the staff of the Daresbury Synchrotron Radiation Source, the European Synchrotron Radiation Facility and the Advanced Light Source synchrotrons for the use of facilities. We thank A. Murzin for pointing out the similarity with DNase I, and A. and T. Andreeva for helpful discussions about the structural deconvolution. We thank V. Chandran, K. Nagai, A. J. Carpousis and M. Symmons for advice. We thank C. Hill for synthesis of the protected RNA and L. Packman for protein and peptide analyses. This work was supported by the Wellcome Trust.

Author information

Correspondence to Ben F. Luisi.

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Competing interests

The coordinates and structure factors have been deposited in the Protein Data Bank (PDB ID 2BX2, R2BX2SF and 2COB). Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

Supplementary information

Supplementary Data

This file contains additional commentary on the structural features with references for all the supplementary subsections. (DOC 46 kb)

Supplementary Methods

Contains details of the crystallographic data collection, structure solution, refinement and analysis. (DOC 32 kb)

Supplementary Figure Legends

This contains the figure legends for Supplementary Figures S1–S3. (DOC 32 kb)

Supplementary Table 1

Contains the summary of the catalytic and RNA binding assays for RNase E catalytic domain mutants. (DOC 33 kb)

Supplementary Table 2

Crystallographic data (equivalent to the Nature formula Xray.doc) (DOC 85 kb)

Supplementary Table 3

A comprehensive list of mutagenic primers for RNase E catalytic domain mutants. (DOC 32 kb)

Supplementary Figure 1

Alignment of the RNase E catalytic domain homologues (PDF 298 kb)

Supplementary Figure 2

A figure showing the folds within the RNase E protomer. (PDF 810 kb)

Supplementary Figure 3

Showing the superposition of three RNase E/RNA complexes. (PDF 668 kb)

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Further reading

Figure 1: The structure of RNase E catalytic domain.
Figure 2: RNase E isolated protomer–RNA complex.
Figure 3: The RNA-binding channel.
Figure 4: RNA recognition by RNase E catalytic domain.

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