title: Cleavage mediated by the P15 domain of bacterial RNase P RNA.
abstract: Independently folded domains in RNAs frequently adopt identical tertiary structures regardless of whether they are in isolation or are part of larger RNA molecules. This is exemplified by the P15 domain in the RNA subunit (RPR) of the universally conserved endoribonuclease P, which is involved in the processing of tRNA precursors. One of its domains, encompassing the P15 loop, binds to the 3'-end of tRNA precursors resulting in the formation of the RCCA-RNase P RNA interaction (interacting residues underlined) in the bacterial RPR-substrate complex. The function of this interaction was hypothesized to anchor the substrate, expose the cleavage site and result in re-coordination of Mg(2+) at the cleavage site. Here we show that small model-RNA molecules (~30 nt) carrying the P15-loop mediated cleavage at the canonical RNase P cleavage site with significantly reduced rates compared to cleavage with full-size RPR. These data provide further experimental evidence for our model that the P15 domain contributes to both substrate binding and catalysis. Our data raises intriguing evolutionary possibilities for 'RNA-mediated' cleavage of RNA.
authors.affiliation: Department of Cell and Molecular Biology, Box 596, Biomedical Centre, SE-751 24 Uppsala, Sweden.
authors.forename: Ema
authors.initials: E
authors.lastname: Kikovska
authors.forename: Shiying
authors.initials: S
authors.lastname: Wu
authors.forename: Guanzhong
authors.initials: G
authors.lastname: Mao
authors.forename: Leif A
authors.initials: LA
authors.lastname: Kirsebom
mesh_terms: D001483:Base Sequence; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry* / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry / Q000378:metabolism; D043262:Ribonuclease P / Q000737:chemistry* / Q000378:metabolism
chemical_list: D012329:RNA, Bacterial; D012343:RNA, Transfer; D043262:Ribonuclease P
references.citation: EMBO J. 1983;2(11):2047-52
references.pmid: 6357781
references.citation: Nat Struct Biol. 1994 May;1(5):273-80
references.pmid: 7545072
references.citation: Proc Natl Acad Sci U S A. 1994 Jul 19;91(15):6729-34
references.pmid: 8041690
references.citation: Biochimie. 1982 Oct;64(10):867-81
references.pmid: 6817818
references.citation: J Biol Chem. 1965 Feb;240:863-9
references.pmid: 14275146
references.citation: RNA. 1996 Jun;2(6):551-63
references.pmid: 8718684
references.citation: Nucleic Acids Res. 1996 Apr 15;24(8):1497-503
references.pmid: 8628683
references.citation: Nucleic Acids Res. 2010 Dec;38(22):8316-27
references.pmid: 20705647
references.citation: Mol Cell. 2006 Nov 3;24(3):445-56
references.pmid: 17081993
references.citation: Trends Biochem Sci. 2007 Mar;32(3):138-45
references.pmid: 17289393
references.citation: Curr Opin Struct Biol. 2006 Jun;16(3):279-87
references.pmid: 16713707
references.citation: J Mol Biol. 2005 Aug 12;351(2):251-7
references.pmid: 16005891
references.citation: Proc Natl Acad Sci U S A. 2010 Dec 28;107(52):22493-8
references.pmid: 21135215
references.citation: Nucleic Acids Res. 2004 Oct 11;32(18):5418-29
references.pmid: 15477392
references.citation: Nat Rev Microbiol. 2006 Oct;4(10):729-40
references.pmid: 16980936
references.citation: J Mol Biol. 1990 Dec 5;216(3):585-610
references.pmid: 2258934
references.citation: Biochemistry. 1996 Aug 13;35(32):10493-505
references.pmid: 8756706
references.citation: Proc Natl Acad Sci U S A. 1992 Feb 15;89(4):1266-70
references.pmid: 1741379
references.citation: Nucleic Acids Res. 1998 Sep 15;26(18):4093-9
references.pmid: 9722626
references.citation: Nucleic Acids Res. 1996 Jun 1;24(11):2022-35
references.pmid: 8668532
references.citation: Nature. 2010 Dec 9;468(7325):784-9
references.pmid: 21076397
references.citation: Q Rev Biophys. 2005 Aug;38(3):221-43
references.pmid: 16817983
references.citation: EMBO J. 1983;2(1):33-8
references.pmid: 11894905
references.citation: Mol Microbiol. 1994 Mar;11(5):849-59
references.pmid: 7517485
references.citation: Biochimie. 2007 Oct;89(10):1183-94
references.pmid: 17624654
references.citation: J Mol Biol. 2003 Jan 24;325(4):697-709
references.pmid: 12507473
references.citation: Biochemistry. 1995 Jan 24;34(3):902-9
references.pmid: 7827048
references.citation: Biochemistry. 1999 Jul 6;38(27):8612-20
references.pmid: 10393536
references.citation: EMBO J. 1994 Oct 17;13(20):4870-6
references.pmid: 7525271
references.citation: IUBMB Life. 2009 Mar;61(3):189-200
references.pmid: 19243011
references.citation: J Mol Evol. 2008 Jan;66(1):21-35
references.pmid: 18058157
references.citation: Biochemistry. 1993 May 25;32(20):5291-300
references.pmid: 7684607
references.citation: Mol Cell. 2006 Aug;23(4):447-50
references.pmid: 16916633
references.citation: EMBO J. 2000 Sep 15;19(18):5007-18
references.pmid: 10990464
references.citation: RNA. 2003 Aug;9(8):907-18
references.pmid: 12869701
references.citation: RNA. 1995 Jun;1(4):391-406
references.pmid: 7493317
references.citation: BMC Bioinformatics. 2010 Mar 24;11:153
references.pmid: 20334683
references.citation: Cell. 2006 Jul 28;126(2):309-20
references.pmid: 16859740
references.citation: Proc Natl Acad Sci U S A. 2007 Feb 13;104(7):2062-7
references.pmid: 17284611
references.citation: J Mol Biol. 2011 Aug 12;411(2):384-96
references.pmid: 21689663
references.citation: RNA. 1998 Aug;4(8):875-89
references.pmid: 9701280
references.citation: RNA. 1998 Jul;4(7):777-88
references.pmid: 9671051
references.citation: Cell. 1988 Apr 22;53(2):267-72
references.pmid: 3359488
references.citation: Nucleic Acids Res. 1982 Nov 11;10(21):6797-808
references.pmid: 6294615
references.citation: J Mol Biol. 1998 Jun 19;279(4):773-93
references.pmid: 9642060
references.citation: J Mol Biol. 2007 Oct 5;372(5):1149-64
references.pmid: 17719605
references.citation: Nucleic Acids Res. 2005 Dec 06;33(21):6920-30
references.pmid: 16332695
references.citation: Crit Rev Biochem Mol Biol. 2010 Jun;45(3):215-32
references.pmid: 20446804
references.citation: Science. 1952 Sep 26;116(3013):329-31
references.pmid: 12984118
references.citation: Proc Natl Acad Sci U S A. 2001 Nov 6;98(23):12943-7
references.pmid: 11606743
references.citation: RNA. 1996 May;2(5):463-72
references.pmid: 8665413
references.citation: J Biol Chem. 1972 Aug 25;247(16):5243-51
references.pmid: 4560501
references.citation: FEBS Lett. 2010 Jan 21;584(2):287-96
references.pmid: 19931535
references.citation: J Mol Biol. 1998 Jun 12;279(3):621-31
references.pmid: 9641982
references.citation: Nucleic Acids Res. 2011 Feb;39(3):1105-16
references.pmid: 20935047