title: Quantitative analysis of processive RNA degradation by the archaeal RNA exosome.
abstract: RNA exosomes are large multisubunit assemblies involved in controlled RNA processing. The archaeal exosome possesses a heterohexameric processing chamber with three RNase-PH-like active sites, capped by Rrp4- or Csl4-type subunits containing RNA-binding domains. RNA degradation by RNA exosomes has not been studied in a quantitative manner because of the complex kinetics involved, and exosome features contributing to efficient RNA degradation remain unclear. Here we derive a quantitative kinetic model for degradation of a model substrate by the archaeal exosome. Markov Chain Monte Carlo methods for parameter estimation allow for the comparison of reaction kinetics between different exosome variants and substrates. We show that long substrates are degraded in a processive and short RNA in a more distributive manner and that the cap proteins influence degradation speed. Our results, supported by small angle X-ray scattering, suggest that the Rrp4-type cap efficiently recruits RNA but prevents fast RNA degradation of longer RNAs by molecular friction, likely by RNA contacts to its unique KH-domain. We also show that formation of the RNase-PH like ring with entrapped RNA is not required for high catalytic efficiency, suggesting that the exosome chamber evolved for controlled processivity, rather than for catalytic chemistry in RNA decay.
authors.affiliation: Center for Integrated Protein Sciences, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany.
authors.forename: Sophia
authors.initials: S
authors.lastname: Hartung
authors.forename: Theresa
authors.initials: T
authors.lastname: Niederberger
authors.forename: Marianne
authors.initials: M
authors.lastname: Hartung
authors.forename: Achim
authors.initials: A
authors.lastname: Tresch
authors.forename: Karl-Peter
authors.initials: KP
authors.lastname: Hopfner
mesh_terms: D019843:Archaeal Proteins / Q000737:chemistry* / Q000378:metabolism; D019611:Archaeoglobus fulgidus / Q000201:enzymology; D005095:Exoribonucleases / Q000737:chemistry* / Q000378:metabolism; D007700:Kinetics; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D012329:RNA, Bacterial / Q000737:chemistry / Q000378:metabolism; D053838:Scattering, Small Angle; D014961:X-Ray Diffraction
chemical_list: D019843:Archaeal Proteins; D012329:RNA, Bacterial; D012313:RNA; D005095:Exoribonucleases
references.citation: Cell. 2006 Dec 15;127(6):1223-37
references.pmid: 17174896
references.citation: Genome Res. 2001 Feb;11(2):240-52
references.pmid: 11157787
references.citation: Mol Cell. 2005 Nov 11;20(3):473-81
references.pmid: 16285928
references.citation: J Biol Chem. 2006 Mar 10;281(10):6751-9
references.pmid: 16407194
references.citation: Nat Rev Mol Cell Biol. 2006 Jul;7(7):529-39
references.pmid: 16829983
references.citation: Nat Struct Mol Biol. 2007 Jan;14(1):15-22
references.pmid: 17173052
references.citation: Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):850-5
references.pmid: 15983406
references.citation: Proc Natl Acad Sci U S A. 2007 Oct 23;104(43):16844-9
references.pmid: 17942686
references.citation: EMBO Rep. 2005 Dec;6(12):1188-93
references.pmid: 16282984
references.citation: Nat Struct Mol Biol. 2005 Jul;12(7):575-81
references.pmid: 15951817
references.citation: Trends Biochem Sci. 2008 Oct;33(10):501-10
references.pmid: 18786828
references.citation: Mol Cell. 2008 Mar 28;29(6):717-28
references.pmid: 18374646
references.citation: Nat Methods. 2009 Aug;6(8):606-12
references.pmid: 19620974
references.citation: J Comput Biol. 2001;8(6):557-69
references.pmid: 11747612
references.citation: EMBO J. 1998 Mar 2;17(5):1497-506
references.pmid: 9482746
references.citation: J Appl Crystallogr. 2009 Apr 1;42(Pt 2):342-346
references.pmid: 27630371
references.citation: EMBO J. 1999 Oct 1;18(19):5399-410
references.pmid: 10508172
references.citation: Bioessays. 2002 Sep;24(9):785-8
references.pmid: 12210514
references.citation: Acta Crystallogr D Biol Crystallogr. 1994 Sep 1;50(Pt 5):760-3
references.pmid: 15299374
references.citation: Mol Cell. 2005 Nov 11;20(3):461-71
references.pmid: 16285927
references.citation: Mol Microbiol. 2006 Nov;62(4):1076-89
references.pmid: 17078816
references.citation: Cell. 2009 Oct 30;139(3):547-59
references.pmid: 19879841
references.citation: Nature. 2008 Dec 18;456(7224):993-6
references.pmid: 19060886
references.citation: EMBO Rep. 2007 May;8(5):470-6
references.pmid: 17380186
references.citation: Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):905-21
references.pmid: 9757107
references.citation: EMBO Rep. 2003 Sep;4(9):889-93
references.pmid: 12947419
references.citation: Cell. 1997 Nov 14;91(4):457-66
references.pmid: 9390555
references.citation: Mol Cell. 2007 Jul 20;27(2):324-331
references.pmid: 17643380
references.citation: Mol Cell. 2003 May;11(5):1405-13
references.pmid: 12769863
references.citation: Genes Dev. 2007 Aug 1;21(15):1833-56
references.pmid: 17671086
references.citation: Genes Dev. 1999 Aug 15;13(16):2148-58
references.pmid: 10465791
references.citation: Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
references.pmid: 15572765
references.citation: Biophys J. 2001 Jun;80(6):2946-53
references.pmid: 11371467
references.citation: Mol Cell Biol. 2007 Jan;27(1):92-101
references.pmid: 17074811
references.citation: J Biol Chem. 2008 May 16;283(20):14120-31
references.pmid: 18353775
references.citation: Mol Microbiol. 2006 Sep;61(6):1372-9
references.pmid: 16968219
references.citation: Nat Struct Mol Biol. 2009 Jan;16(1):56-62
references.pmid: 19060898