RESUMO
BACKGROUND: The archaeal exosome is formed by a hexameric RNase PH ring and three RNA binding subunits and has been shown to bind and degrade RNA in vitro. Despite extensive studies on the eukaryotic exosome and on the proteins interacting with this complex, little information is yet available on the identification and function of archaeal exosome regulatory factors. RESULTS: Here, we show that the proteins PaSBDS and PaNip7, which bind preferentially to poly-A and AU-rich RNAs, respectively, affect the Pyrococcus abyssi exosome activity in vitro. PaSBDS inhibits slightly degradation of a poly-rA substrate, while PaNip7 strongly inhibits the degradation of poly-A and poly-AU by the exosome. The exosome inhibition by PaNip7 appears to depend at least partially on its interaction with RNA, since mutants of PaNip7 that no longer bind RNA, inhibit the exosome less strongly. We also show that FITC-labeled PaNip7 associates with the exosome in the absence of substrate RNA. CONCLUSIONS: Given the high structural homology between the archaeal and eukaryotic proteins, the effect of archaeal Nip7 and SBDS on the exosome provides a model for an evolutionarily conserved exosome control mechanism.
Assuntos
Proteínas Arqueais/metabolismo , Exorribonucleases/metabolismo , Proteínas Arqueais/química , Exorribonucleases/química , Poli A/química , Poli A/metabolismo , Poli A-U/química , Poli A-U/metabolismo , Ligação Proteica , Pyrococcus abyssi/metabolismo , Estabilidade de RNA , RNA Arqueal/metabolismoRESUMO
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.
Assuntos
Archaea/metabolismo , Proteínas Arqueais/química , Estabilidade de RNA , RNA/química , Catálise , Dimerização , Humanos , Modelos Biológicos , Conformação Molecular , Mutagênese , Nucleotídeos/química , Fosfatos/química , Pyrococcus abyssi/metabolismo , RNA/metabolismo , Processamento Pós-Transcricional do RNA , Sulfolobus solfataricus/metabolismoRESUMO
Saccharomyces cerevisiae Nip7p is a nucleolar protein required for accurate processing of the 27S precursor of the 25S and 5.8S ribosomal RNAs. Nip7p homologues are found in eukaryotes and archaea. The Pyrococcus abyssi homologue of Nip7p (PaNip7) was cloned, expressed in Escherichia coli and purified for crystallization. X-ray diffraction data were collected from native crystals and an iodide derivative using synchrotron radiation. PaNip7 native crystals diffract to 1.8 A and belong to space group C2, with unit-cell parameters a = 88.49, b = 90.28, c = 63.35 A, beta = 134.29 degrees. The PaNip7 structure was solved using the SIRAS method.