Identification of archaeal proteins that affect the exosome function in vitro.
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.
Luz
Juliana S
JS
Department of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-000, São Paulo, SP, Brazil.
Ramos
Celso R R
CR
Santos
Márcia C T
MC
Coltri
Patricia P
PP
Palhano
Fernando L
FL
Foguel
Debora
D
Zanchin
Nilson I T
NI
Oliveira
Carla C
CC
D019843:Archaeal Proteins / Q000737:chemistry / Q000378:metabolism*; D005095:Exoribonucleases / Q000737:chemistry / Q000378:metabolism*; D011061:Poly A / Q000737:chemistry / Q000378:metabolism; D011063:Poly A-U / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D043903:Pyrococcus abyssi / Q000378:metabolism; D020871:RNA Stability; D019642:RNA, Archaeal / Q000378:metabolism
D019843:Archaeal Proteins; D019642:RNA, Archaeal; D011063:Poly A-U; D011061:Poly A; D005095:Exoribonucleases