Initially identified in yeast, the exosome has emerged as a central component of the RNA maturation and degradation machinery both in Archaea and eukaryotes. Here we describe a series of high-resolution structures of the RNase PH ring from the Pyrococcus abyssi exosome, one of them containing three 10-mer RNA strands within the exosome catalytic chamber, and report additional nucleotide interactions involving positions N5 and N7. Residues from all three Rrp41-Rrp42 heterodimers interact with a single RNA molecule, providing evidence for the functional relevance of exosome ring-like assembly in RNA processivity. Furthermore, an ADP-bound structure showed a rearrangement of nucleotide interactions at site N1, suggesting a rationale for the elimination of nucleoside diphosphate after catalysis. In combination with RNA degradation assays performed with mutants of key amino acid residues, the structural data presented here provide support for a model of exosome-mediated RNA degradation that integrates the events involving catalytic cleavage, product elimination, and RNA translocation. Finally, comparisons between the archaeal and human exosome structures provide a possible explanation for the eukaryotic exosome inability to catalyze phosphate-dependent RNA degradation. Initially identified in yeast, the exosome has emerged as a central component of the RNA maturation and degradation machinery both in Archaea and eukaryotes. Here we describe a series of high-resolution structures of the RNase PH ring from the Pyrococcus abyssi exosome, one of them containing three 10-mer RNA strands within the exosome catalytic chamber, and report additional nucleotide interactions involving positions N5 and N7. Residues from all three Rrp41-Rrp42 heterodimers interact with a single RNA molecule, providing evidence for the functional relevance of exosome ring-like assembly in RNA processivity. Furthermore, an ADP-bound structure showed a rearrangement of nucleotide interactions at site N1, suggesting a rationale for the elimination of nucleoside diphosphate after catalysis. In combination with RNA degradation assays performed with mutants of key amino acid residues, the structural data presented here provide support for a model of exosome-mediated RNA degradation that integrates the events involving catalytic cleavage, product elimination, and RNA translocation. Finally, comparisons between the archaeal and human exosome structures provide a possible explanation for the eukaryotic exosome inability to catalyze phosphate-dependent RNA degradation. Initially described as a multisubunit RNase complex required for maturation of 5.8 S rRNA in yeast (1Mitchell P. Petfalski E. Shevchenko A. Mann M. 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Chem. 2006; 281: 6751-6759Abstract Full Text Full Text PDF PubMed Scopus (31) Google Scholar). after by the was at for by at for The Rrp41-Rrp42 complex was by of the to acid by from the a with the hexameric RNase PH as by and in assembly of the subunits Rrp4 was in E. and by on described C.R.R. Oliveira C.L.P. Torriani I.L. Oliveira C.C. J. Biol. Chem. 2006; 281: 6751-6759Abstract Full Text Full Text PDF PubMed Scopus (31) Google Scholar). The RNase PH ring was with a of Rrp4 in for at the mixture was on a to Rrp4 from the which was as a single and of the Rrp41-Rrp42 complex by the at by of in with of of and as the at a at the of the and J. Scopus Google Scholar). data from two Rrp41-Rrp42 to of and of the P. abyssi exosome RNase PH ring into composed of containing or RNA 10-mer for and data of to a of and of data presented in and in for the of with in for the with J. Google Scholar). in a Structure Determination and structure of the P. abyssi exosome RNase PH ring was by molecular with the A. A. J. 1997; Scopus Google of the Biol. PubMed Scopus Google Scholar). of the A. fulgidus Rrp41-Rrp42 as the A. fulgidus and of and with P. abyssi and was to of into the and P. K. Biol. 2004; PubMed Scopus Google and was and in P. J.S. J. M. R.J. T. Biol. 1998; PubMed Scopus Google Scholar). of performed with Biol. 1997; PubMed Scopus Google Biol. 2001; PubMed Scopus Google for within the the in the in with nucleotide The and of the on the of and the The structures from into 10-mer RNA and the P. abyssi structure as the an of the structures to performed with as described for the The and in the structures and and 10-mer RNA in the into the all by the A. Biol. 1997; PubMed Scopus Google Scholar). of the shown in and and and a in and a was in The exosome the for the RNA degradation assays performed at in of and containing as complex to in the mixture for to complex The assays presented in and and performed with complex of The on data and structure have with and for the P. abyssi exosome RNase PH ring to 10-mer and The subunits and of the P. abyssi exosome in E. and the complex was in the The structure was by molecular the of the A. fulgidus Rrp41-Rrp42 as the model The structure was at to an of with The one Rrp41-Rrp42 and of the the exosome RNase PH which composed of a hexameric ring of alternating subunits E. Walter P. Fribourg S. Evguenieva-Hackenberg E. Klug G. Conti E. Nat. Struct. Mol. Biol. 2005; 12: 575-581Crossref PubMed Scopus (175) Google The structure of the P. abyssi exosome RNase PH ring to its archaeal from A. fulgidus and S. solfataricus (19Büttner K. Wenig K. Hopfner K.P. Mol. 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Cell. 2005; 20: Full Text Full Text PDF PubMed Scopus Google Scholar), was in the P. abyssi all the structures in showed a between the of and the from the which of the the of the RNA the nucleotide N5 in the P. abyssi RNase PH structure the of for the 3′ end the RNA to the exosome central the of N5 with and of the from the the relevance of the and and to RNA degradation assays with and These amino acid as as performed in the RNase PH ring assembly and the exosome the for the complex and and The of and from by RNA degradation to of catalytic in the complex with the exosome a catalytic with and with assays with the complex presented to the hexameric ring to the central archaeal from both heterodimers from and from and in of the RNA and for RNA degradation. These provide the evidence of the role of archaeal exosome structure in RNA at the P. abyssi exosome RNA the of the structure of two additional which to positions and the from the exosome site the of the RNase PH ring and in a and in the structure formed at the of the ring the at formed by from the and subunits at the of two the at formed in the of the three subunits by the containing the of a structure for exosome on RNA degradation, from heterodimers in nucleotide and interact with the exosome in with the interactions between the and the exosome RNA the of the that and by and interactions that to a on the of and was possible to model the 10-mer RNA within the exosome catalytic the central at the and the the model that the catalytic of the archaeal exosome three RNA strands the of the RNA strands the that for a to and to interact with the which to them a the of in the and A. E. J. A. Conti E. M. EMBO Rep. 2007; 8: PubMed Scopus Google showed that the archaeal RNase PH ring three RNA its with the Rrp4 subunits the to the structure described in that the formed by the Rrp4 the RNase PH ring as the structural that to one RNA at a in the exosome catalytic Furthermore, the of between the three RNA strands the of RNA by the PH ring with the complex A. E. J. A. Conti E. M. EMBO Rep. 2007; 8: PubMed Scopus Google Scholar). In the presented in showed that the 3′ end of the RNA the exosome catalytic the of the RNase PH which three 10-mer in with evidence from RNase assays E. Conti E. Mol. Cell. 2005; 20: Full Text Full Text PDF PubMed Scopus Google and from structural data on the S. solfataricus exosome with a RNA containing a 3′ E. Dziembowski A. Lindner D. Seraphin B. Conti E. EMBO Rep. 2007; 8: 470-476Crossref PubMed Scopus (89) Google Scholar). The of and studies (19Büttner K. Wenig K. Hopfner K.P. Mol. 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EMBO Rep. 2007; 8: 470-476Crossref PubMed Scopus (89) Google have shown the relevance of the archaeal RNase PH ring in the RNA to the exosome catalytic the of a and nucleotide within the exosome central a the role of and in the RNA processing between the and structures revealed a in the of the the and structures to the exosome the of the structure by and for the and nucleotide to the for structure to for in Furthermore, the a structural rearrangement to the RNA which in the of and of the in archaeal exosome structures and the that the be to of These with the data presented in that the and nucleotide in the central of the archaeal exosome structures that structural RNA evidence on the RNA by the exosome, RNA degradation assays performed with the exosome the to the site and with nucleotide the of its by a to a functional role for the and in RNA degradation. The the complex with and with the degradation presented by of RNA and which for the exosome and a the to nucleotide fragments and the degradation to the to the RNA the by the with from the to the The structural and data a model for exosome-mediated RNA degradation in which the and be with the to the RNA within the exosome catalytic in a that RNA degradation. the site and RNA degradation and from a to a for of the the in the of the exosome, we performed the with the to the degradation for the RNase PH the to of These that the model for RNA and processing involving and be to the The structure in cleavage, the formed nucleoside diphosphate within the exosome site to In with the nucleotide in the 10-mer structural a of interactions with the exosome and structural of the product with the elimination of the 3′ end nucleotide by one into the of archaeal exosomes RNA degradation. the of the P. abyssi exosome structure in showed a nucleoside diphosphate to the site as an with two possible the suggesting a nucleoside diphosphate structural rearrangement to In to the of the product after as shown by and Conti E. 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The of conservation of nucleotide within the eukaryotic that by the RNA suggesting that the complex has the of for the exosome Structure of eukaryotic exosomes to or to R. R. for providing the containing the P. abyssi and C. C. and G. for and J. for of the with
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