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

Abstract

The exosome is a large complex with cellular functions including exoribonucleolytic mRNA degradation and processing of a number of RNAs including small nuclear RNAs, small nucleolar RNAs and ribosomal RNAs. The yeast exosome is now shown to possess an unexpected endoribonucleolytic activity, and the essential Csl4 subunit is shown to contain a domain involved in mRNA decay. This suggests that particular domains in the complex have specialized roles. 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.