title: How a CCA sequence protects mature tRNAs and tRNA precursors from action of the processing enzyme RNase BN/RNase Z.
abstract: In many organisms, 3' maturation of tRNAs is catalyzed by the endoribonuclease, RNase BN/RNase Z, which cleaves after the discriminator nucleotide to generate a substrate for addition of the universal CCA sequence. However, tRNAs or tRNA precursors that already contain a CCA sequence are not cleaved, thereby avoiding a futile cycle of removal and readdition of these essential residues. We show here that the adjacent C residues of the CCA sequence and an Arg residue within a highly conserved sequence motif in the channel leading to the RNase catalytic site are both required for the protective effect of the CCA sequence. When both of these determinants are present, CCA-containing RNAs in the channel are unable to move into the catalytic site; however, substitution of either of the C residues by A or U or mutation of Arg(274) to Ala allows RNA movement and catalysis to proceed. These data define a novel mechanism for how tRNAs are protected against the promiscuous action of a processing enzyme.
authors.affiliation: From the Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida 33136.
authors.forename: Tanmay
authors.initials: T
authors.lastname: Dutta
authors.affiliation: From the Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida 33136.
authors.forename: Arun
authors.initials: A
authors.lastname: Malhotra
authors.affiliation: From the Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida 33136. Electronic address: mdeutsch@med.miami.edu.
authors.forename: Murray P
authors.initials: MP
authors.lastname: Deutscher
mesh_terms: D001120:Arginine; D001483:Base Sequence; D020134:Catalytic Domain; D004722:Endoribonucleases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D005095:Exoribonucleases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012322:RNA Precursors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012323:RNA Processing, Post-Transcriptional / Q000502:physiology*; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D029968:Escherichia coli Proteins; D012322:RNA Precursors; D012329:RNA, Bacterial; D012343:RNA, Transfer; D001120:Arginine; D004722:Endoribonucleases; D005095:Exoribonucleases; C110250:RNase Z; C038206:ribonuclease BN
keywords: Enzyme Structure; Nucleic Acid Chemistry; Nucleic Acid Enzymology; Phosphodiesterases; Protein-Nucleic Acid Interaction; RNA Catalysis; RNA Processing; RNA-Protein Interaction; Structural Biology; Transfer RNA (tRNA)
references.citation: Nature. 2005 Feb 10;433(7026):657-61
references.pmid: 15654328
references.citation: J Biol Chem. 2003 Nov 14;278(46):45041-4
references.pmid: 12941949
references.citation: Nat Rev Microbiol. 2007 Apr;5(4):278-86
references.pmid: 17363966
references.citation: J Biol Chem. 2009 Jun 5;284(23):15425-31
references.pmid: 19366704
references.citation: Nucleic Acids Res. 2006 Feb 01;34(2):659-66
references.pmid: 16452296
references.citation: J Mol Biol. 2000 Sep 8;302(1):205-17
references.pmid: 10964570
references.citation: Nat Struct Mol Biol. 2006 Apr;13(4):376-7
references.pmid: 16518398
references.citation: J Biol Chem. 2012 Oct 12;287(42):35747-35755
references.pmid: 22893707
references.citation: Proc Natl Acad Sci U S A. 1983 Jun;80(11):3301-4
references.pmid: 6344080
references.citation: RNA. 1999 Feb;5(2):245-56
references.pmid: 10024176
references.citation: Science. 2010 Nov 12;330(6006):937-40
references.pmid: 21071662
references.citation: J Biol Chem. 2004 Apr 9;279(15):15688-97
references.pmid: 14749326
references.citation: J Biol Chem. 2005 Apr 29;280(17):16542-5
references.pmid: 15764599
references.citation: Prog Mol Biol Transl Sci. 2009;85:187-229
references.pmid: 19215773
references.citation: Nucleic Acids Res. 2011 Jul;39(Web Server issue):W13-7
references.pmid: 21558174
references.citation: J Biol Chem. 2010 Jul 23;285(30):22874-81
references.pmid: 20489203
references.citation: Nucleic Acids Res. 2001 Jul 1;29(13):2860-74
references.pmid: 11433033
references.citation: Bioinformatics. 1999 Apr;15(4):305-8
references.pmid: 10320398
references.citation: Trends Biochem Sci. 1988 Apr;13(4):136-9
references.pmid: 2472685
references.citation: Nat Chem Biol. 2011 May 15;7(7):425-7
references.pmid: 21572425
references.citation: J Bacteriol. 2006 Feb;188(4):1607-14
references.pmid: 16452444
references.citation: J Biol Chem. 2011 Jul 29;286(30):26732-42
references.pmid: 21653694
references.citation: J Biol Chem. 2002 Aug 16;277(33):29654-61
references.pmid: 12050169
references.citation: J Biol Chem. 1994 Feb 25;269(8):6064-71
references.pmid: 7509797
references.citation: EMBO J. 2003 Sep 1;22(17):4534-43
references.pmid: 12941704
references.citation: Curr Opin Struct Biol. 2006 Feb;16(1):12-7
references.pmid: 16364630
references.citation: Structure. 2012 Oct 10;20(10):1769-77
references.pmid: 22940585
references.citation: Nat Rev Microbiol. 2013 Jan;11(1):45-57
references.pmid: 23241849
references.citation: FASEB J. 1993 Jan;7(1):143-8
references.pmid: 8422961
references.citation: FEMS Microbiol Rev. 2010 Sep;34(5):883-923
references.pmid: 20659169
references.citation: Nat Chem Biol. 2011 Apr;7(4):236-43
references.pmid: 21317904
references.citation: Cell. 1996 Aug 9;86(3):503-12
references.pmid: 8756732
references.citation: Proc Natl Acad Sci U S A. 1985 Oct;82(19):6427-30
references.pmid: 2413440