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Identification of archaeal proteins that affect the exosome function in vitro

Juliana S Luz1, Celso RR Ramos14, Márcia CT Santos1, Patricia P Coltri25, Fernando L Palhano3, Debora Foguel3, Nilson IT Zanchin2 and Carla C Oliveira1*

Author Affiliations

1 Department of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-000, São Paulo, SP, Brazil

2 Center for Structural Molecular Biology, Brazilian Synchrotron Light Laboratory, LNLS, 13083-970, Campinas, SP, Brazil

3 Institute of Medical Biochemistry, CCS, Federal University of Rio de Janeiro, 21941-590, Rio de Janeiro, RJ, Brazil

4 Department of Helminthology, Fiocruz, 21045-900, Rio de Janeiro, RJ, Brazil

5 Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA

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BMC Biochemistry 2010, 11:22  doi:10.1186/1471-2091-11-22

Published: 27 May 2010



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.


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.


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.