title: The oligomeric architecture of the archaeal exosome is important for processive and efficient RNA degradation.
abstract: The exosome plays an important role in RNA degradation and processing. In archaea, three Rrp41:Rrp42 heterodimers assemble into a barrel like structure that contains a narrow RNA entrance pore and a lumen that contains three active sites. Here, we demonstrate that this quaternary structure of the exosome is important for efficient RNA degradation. We find that the entrance pore of the barrel is required for nM substrate affinity. This strong interaction is crucial for processive substrate degradation and prevents premature release of the RNA from the enzyme. Using methyl TROSY NMR techniques, we establish that the 3' end of the substrate remains highly flexible inside the lumen. As a result, the RNA jumps between the three active sites that all equally participate in substrate degradation. The RNA jumping rate is, however, much faster than the cleavage rate, indicating that not all active site:substrate encounters result in catalysis. Enzymatic turnover therefore benefits from the confinement of the active sites and substrate in the lumen, which ensures that the RNA is at all times bound to one of the active sites. The evolution of the exosome into a hexameric complex and the optimization of its catalytic efficiency were thus likely co-occurring events.
authors.affiliation: Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
authors.forename: Maxime J C
authors.initials: MJ
authors.lastname: Audin
authors.affiliation: Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
authors.forename: Jan Philip
authors.initials: JP
authors.lastname: Wurm
authors.affiliation: Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
authors.forename: Milos A
authors.initials: MA
authors.lastname: Cvetkovic
authors.affiliation: Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany remco.sprangers@tuebingen.mpg.de.
authors.forename: Remco
authors.initials: R
authors.lastname: Sprangers
mesh_terms: D000595:Amino Acid Sequence; D019843:Archaeal Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D055162:Biocatalysis; D020134:Catalytic Domain; D003001:Cloning, Molecular; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D063326:Exosome Multienzyme Ribonuclease Complex / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D055354:Exosomes / Q000737:chemistry* / Q000201:enzymology; D015870:Gene Expression; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011485:Protein Binding; D055503:Protein Multimerization; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D020871:RNA Stability; D019642:RNA, Archaeal / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D048229:Sulfolobus solfataricus / Q000737:chemistry / Q000201:enzymology* / Q000235:genetics
chemical_list: D019843:Archaeal Proteins; D019642:RNA, Archaeal; D016601:RNA-Binding Proteins; D063326:Exosome Multienzyme Ribonuclease Complex
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