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

Nature Structural & Molecular Biology volume 16, pages 5662 (2009) | Download Citation

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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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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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  1. Department of Microbiology and Molecular Genetics, University of Texas Health Science Center-Houston, 6431 Fannin Street, MSB 1.212 Houston, Texas 77030, USA.

    • Daneen Schaeffer
    • , Borislava Tsanova
    • , Eeshita Ghosh Dastidar
    • , Maya Sanchez-Rotunno
    •  & Ambro van Hoof
  2. Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal.

    • Ana Barbas
    • , Filipa Pereira Reis
    •  & Cecília Maria Arraiano

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Correspondence to Ambro van Hoof.

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https://doi.org/10.1038/nsmb.1528

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