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The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities

Abstract

The eukaryotic exosome is a ten-subunit 3′ exoribonucleolytic complex responsible for many RNA-processing and RNA-degradation reactions. How the exosome accomplishes this is unknown. Rrp44 (also known as Dis3), a member of the RNase II family of enzymes, is the catalytic subunit of the exosome. We show that the PIN domain of Rrp44 has endoribonucleolytic activity. The PIN domain is preferentially active toward RNA with a 5′ phosphate, suggesting coordination of 5′ and 3′ processing. We also show that the endonuclease activity is important in vivo. Furthermore, the essential exosome subunit Csl4 does not contain any domains that are required for viability, but its zinc-ribbon domain is required for exosome-mediated mRNA decay. These results suggest that specific exosome domains contribute to specific functions, and that different RNAs probably interact with the exosome differently. The combination of an endoRNase and an exoRNase activity seems to be a widespread feature of RNA-degrading machines.

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Figure 1: The N-terminal region of Rrp44 has RNase activity.
Figure 2: The PIN active site is important for exosome function.
Figure 3: The RNB domain of Rrp44 is required for both RNA-processing and RNA-degradation activities of the exosome.
Figure 4: The essential Csl4 does not contain any essential domains, but its zinc-ribbon domain is required for cytoplasmic exosome-mediated mRNA decay.
Figure 5

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Acknowledgements

We are grateful to T. Link and R. Brennan for help with calculating the buried surfaces between the different domains of the cap proteins and the PH ring, and A. Klauer for technical assistance. GAL::rrp44, GAL::csl4, GAL::rrp4 and GAL::rrp40 strains were kindly provided by P. Mitchell (University of Sheffield) and D. Tollervey (University of Edinburgh). R. Parker, M. Wilkinson, M. Steiger and members of the van Hoof and Arraiano laboratories gave insightful comments on the manuscript. This research was supported by the Pew Scholarship Program in the Biomedical Sciences and by the National Institutes of Health (GM069900) to A.v.H. E.G.D and M.S.-R. were supported by The University of Texas at Houston Medical School-Summer Research Program. The work at the Instituto de Tecnologia Química e Biológica was supported by Fundação para a Ciência e a Tecnologia (FCT), Portugal. A.B. was a recipient of a post-doctoral fellowship from FCT, Portugal.

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Schaeffer, D., Tsanova, B., Barbas, A. et al. The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities. Nat Struct Mol Biol 16, 56–62 (2009). https://doi.org/10.1038/nsmb.1528

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