title: The PMC2NT domain of the catalytic exosome subunit Rrp6p provides the interface for binding with its cofactor Rrp47p, a nucleic acid-binding protein.
abstract: The exosome complex is a key component of the cellular RNA surveillance machinery and is required for normal 3' end processing of many stable RNAs. Exosome activity requires additional factors such as the Ski or TRAMP complexes to activate the complex or facilitate substrate binding. Rrp47p promotes the catalytic activity of the exosome component Rrp6p, but its precise function is unknown. Here we show that recombinant Rrp47p is expressed as an apparently hexameric complex that specifically binds structured nucleic acids. Furthermore, pull-down assays demonstrated that Rrp47p interacts directly with the N-terminal region of Rrp6p that contains the functionally uncharacterized PMC2NT domain. Strains expressing a mutant form of Rrp6p lacking the N-terminal region failed to accumulate Rrp47p at normal levels, exhibited a slow growth phenotype characteristic of rrp47-Delta mutants and showed RNA processing defects consistent with loss of Rrp47p function. These findings suggest Rrp47p promotes Rrp6p activity by facilitating binding via the PMC2NT domain to structural elements within RNA. Notably, characterized Rrp6p substrates such as the 5.8S+30 species are predicted to contain helices at their 3' termini, while others such as intergenic or antisense cryptic unstable transcripts could potentially form extensive double-stranded molecules with overlapping mRNAs.
authors: Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.
authors: Jonathan A
authors: JA
authors: Stead
authors: Joe L
authors: JL
authors: Costello
authors: Michaela J
authors: MJ
authors: Livingstone
authors: Phil
authors: P
authors: Mitchell
mesh_terms: D004247:DNA / Q000378:metabolism; D004268:DNA-Binding Proteins; D005095:Exoribonucleases / Q000737:chemistry* / Q000378:metabolism*; D063326:Exosome Multienzyme Ribonuclease Complex; D009687:Nuclear Proteins / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D012313:RNA / Q000378:metabolism; D026721:RNA 3' End Processing; D012340:RNA, Ribosomal, 5.8S / Q000378:metabolism; D020537:RNA, Small Nucleolar / Q000378:metabolism; D016601:RNA-Binding Proteins; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; C494789:LRP1 protein, S cerevisiae; D009687:Nuclear Proteins; D012340:RNA, Ribosomal, 5.8S; D020537:RNA, Small Nucleolar; D016601:RNA-Binding Proteins; D029701:Saccharomyces cerevisiae Proteins; D012313:RNA; D004247:DNA; D005095:Exoribonucleases; D063326:Exosome Multienzyme Ribonuclease Complex; C112610:RRP6 protein, S cerevisiae
references: Cell. 2001 Nov 16;107(4):451-64
references: 11719186
references: Genome Res. 2001 Feb;11(2):240-52
references: 11157787
references: Biochem Soc Trans. 2002 Apr;30(2):150-5
references: 12035760
references: Mol Microbiol. 2002 Nov;46(4):947-57
references: 12421302
references: Nat Biotechnol. 2003 Apr;21(4):379-86
references: 12640466
references: FASEB J. 2003 Jun;17(9):961-83
references: 12773480
references: Curr Opin Cell Biol. 2003 Jun;15(3):332-7
references: 12787776
references: Cell. 2003 Jun 27;113(7):919-33
references: 12837249
references: RNA. 2003 Sep;9(9):1049-57
references: 12923254
references: RNA. 2003 Sep;9(9):1098-107
references: 12923258
references: Mol Cell Biol. 2003 Oct;23(19):6982-92
references: 12972615
references: Nature. 2003 Oct 16;425(6959):737-41
references: 14562106
references: Bioinformatics. 2004 Feb 12;20(3):426-7
references: 14960472
references: Bioessays. 2004 May;26(5):567-81
references: 15112237
references: Proc Natl Acad Sci U S A. 2004 Jun 8;101(23):8658-63
references: 15161972
references: Proc Natl Acad Sci U S A. 2004 Jun 8;101(23):8581-6
references: 15173578
references: J Mol Biol. 1990 Feb 20;211(4):699-712
references: 2179564
references: EMBO J. 1991 Jan;10(1):25-33
references: 1989886
references: Nucleic Acids Res. 1993 Jul 11;21(14):3329-30
references: 8341614
references: Yeast. 1993 Jul;9(7):715-22
references: 8368005
references: Genes Dev. 1996 Feb 15;10(4):502-13
references: 8600032
references: Cell. 1997 Nov 14;91(4):457-66
references: 9390555
references: Trends Biochem Sci. 1997 Nov;22(11):417-8
references: 9397680
references: Nucleic Acids Res. 1997 Dec 15;25(24):5110-8
references: 9396823
references: EMBO J. 1998 Feb 16;17(4):1128-40
references: 9463390
references: Nucleic Acids Res. 1998 Mar 1;26(5):1160-6
references: 9469821
references: EMBO J. 1998 Mar 2;17(5):1497-506
references: 9482746
references: J Biol Chem. 1998 May 22;273(21):13255-63
references: 9582370
references: Nucleic Acids Res. 1998 Aug 1;26(15):3460-7
references: 9671805
references: Genes Dev. 1999 Aug 15;13(16):2148-58
references: 10465791
references: EMBO J. 1999 Oct 1;18(19):5399-410
references: 10508172
references: Genes Dev. 2004 Nov 1;18(21):2652-62
references: 15489286
references: Cell. 2005 Jun 3;121(5):713-24
references: 15935758
references: Cell. 2005 Jun 3;121(5):725-37
references: 15935759
references: PLoS Biol. 2005 Jun;3(6):e189
references: 15828860
references: Science. 2005 Sep 2;309(5740):1564-6
references: 16141073
references: Mol Cell. 2005 Nov 11;20(3):461-71
references: 16285927
references: Mol Cell. 2005 Nov 11;20(3):473-81
references: 16285928
references: RNA. 2006 Jan;12(1):26-32
references: 16373491
references: EMBO Rep. 2006 Feb;7(2):205-11
references: 16374505
references: Proc Natl Acad Sci U S A. 2006 Apr 4;103(14):5320-5
references: 16569694
references: Nat Rev Mol Cell Biol. 2006 Jul;7(7):529-39
references: 16829983
references: Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):11898-903
references: 16882719
references: Mol Cell. 2006 Sep 15;23(6):841-51
references: 16973436
references: Cell. 2006 Dec 15;127(6):1223-37
references: 17174896
references: Nat Struct Mol Biol. 2007 Jan;14(1):15-22
references: 17173052
references: Curr Opin Struct Biol. 2007 Apr;17(2):209-14
references: 17395456
references: Nucleic Acids Res. 2007;35(8):2564-72
references: 17412707
references: Mol Cell Biol. 2000 Jan;20(2):441-52
references: 10611222
references: Mol Cell Biol. 2000 Jan;20(2):604-16
references: 10611239
references: Structure. 1999 Dec 15;7(12):1557-66
references: 10647186
references: Mol Cell Biol. 2000 Feb;20(4):1311-20
references: 10648617
references: Annu Rev Biochem. 2000;69:651-97
references: 10966472
references: Structure. 2000 Nov 15;8(11):1215-26
references: 11080643
references: Science. 2002 Mar 22;295(5563):2262-4
references: 11910110