title: Comparative sequence and structure analysis reveals the conservation and diversity of nucleotide positions and their associated tertiary interactions in the riboswitches.
abstract: The tertiary motifs in complex RNA molecules play vital roles to either stabilize the formation of RNA 3D structure or to provide important biological functionality to the molecule. In order to better understand the roles of these tertiary motifs in riboswitches, we examined 11 representative riboswitch PDB structures for potential agreement of both motif occurrences and conservations. A total of 61 unique tertiary interactions were found in the reference structures. In addition to the expected common A-minor motifs and base-triples mainly involved in linking distant regions the riboswitch structures three highly conserved variants of A-minor interactions called G-minors were found in the SAM-I and FMN riboswitches where they appear to be involved in the recognition of the respective ligand's functional groups. From our structural survey as well as corresponding structure and sequence alignments, the agreement between motif occurrences and conservations are very prominent across the representative riboswitches. Our analysis provide evidence that some of these tertiary interactions are essential components to form the structure where their sequence positions are conserved despite a high degree of diversity in other parts of the respective riboswitches sequences. This is indicative of a vital role for these tertiary interactions in determining the specific biological function of riboswitch.
authors.affiliation: School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia.
authors.forename: Sri D
authors.initials: SD
authors.lastname: Appasamy
authors.forename: Effirul Ikhwan
authors.initials: EI
authors.lastname: Ramlan
authors.forename: Mohd
authors.initials: M
authors.lastname: Firdaus-Raih
mesh_terms: D001483:Base Sequence; D017124:Conserved Sequence; D030561:Databases, Nucleic Acid; D014644:Genetic Variation; D008958:Models, Molecular; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D012333:RNA, Messenger / Q000737:chemistry*; D058928:Riboswitch / Q000502:physiology*; D016415:Sequence Alignment
chemical_list: D012333:RNA, Messenger; D058928:Riboswitch
references.citation: Nucleic Acids Res. 2007;35(16):5568-80
references.pmid: 17704135
references.citation: J Comput Chem. 2004 Oct;25(13):1605-12
references.pmid: 15264254
references.citation: RNA. 2002 Sep;8(9):1112-9
references.pmid: 12358430
references.citation: Nature. 2004 Nov 18;432(7015):411-5
references.pmid: 15549109
references.citation: Nature. 2008 Oct 30;455(7217):1263-7
references.pmid: 18784651
references.citation: J Mol Biol. 1996 May 10;258(3):480-500
references.pmid: 8642604
references.citation: Nature. 2009 Mar 12;458(7235):233-7
references.pmid: 19169240
references.citation: Nature. 2006 Jun 29;441(7097):1167-71
references.pmid: 16728979
references.citation: RNA. 2008 Dec;14(12):2465-77
references.pmid: 18957492
references.citation: Science. 2004 Oct 8;306(5694):275-9
references.pmid: 15472076
references.citation: Nat Struct Mol Biol. 2008 Feb;15(2):177-82
references.pmid: 18204466
references.citation: Biochemistry. 2010 Aug 31;49(34):7351-9
references.pmid: 20690679
references.citation: Chem Biol. 1995 Dec;2(12):827-40
references.pmid: 8807816
references.citation: Nature. 2006 Jun 29;441(7097):1172-5
references.pmid: 16810258
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3450-60
references.pmid: 12824344
references.citation: Chembiochem. 2004 Jan 3;5(1):62-72
references.pmid: 14695514
references.citation: Nat Struct Biol. 1997 Aug;4(8):644-9
references.pmid: 9253414
references.citation: RNA. 2003 Jun;9(6):640-3
references.pmid: 12756321
references.citation: Biochem Cell Biol. 2008 Apr;86(2):157-68
references.pmid: 18443629
references.citation: Genome Biol. 2007;8(11):R239
references.pmid: 17997835
references.citation: Chem Biol. 2006 Aug;13(8):805-7
references.pmid: 16931328
references.citation: Nat Struct Mol Biol. 2009 Mar;16(3):343-4
references.pmid: 19234468
references.citation: Nucleic Acids Res. 1985 Mar 11;13(5):1717-31
references.pmid: 4000943
references.citation: Curr Opin Struct Biol. 2009 Jun;19(3):251-9
references.pmid: 19303767
references.citation: Nucleic Acids Res. 2008 Mar;36(4):1138-52
references.pmid: 18158305
references.citation: Nature. 2004 Mar 18;428(6980):281-6
references.pmid: 15029187
references.citation: Nucleic Acids Res. 2011 Apr;39(8):3373-87
references.pmid: 21169337
references.citation: Chem Biol. 2004 Dec;11(12):1729-41
references.pmid: 15610857
references.citation: Nucleic Acids Res. 2012 Jul;40(Web Server issue):W35-41
references.pmid: 22661578
references.citation: J Virol. 2005 Jan;79(1):380-92
references.pmid: 15596831
references.citation: Nucleic Acids Res. 2000 Jan 1;28(1):235-42
references.pmid: 10592235
references.citation: Nat Rev Mol Cell Biol. 2004 Jun;5(6):451-63
references.pmid: 15173824
references.citation: Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6421-6
references.pmid: 15096624
references.citation: J Mol Biol. 1997 Apr 4;267(3):624-39
references.pmid: 9126842
references.citation: Nat Struct Mol Biol. 2007 Apr;14(4):308-17
references.pmid: 17384645
references.citation: Genome Biol. 2005;6(8):R70
references.pmid: 16086852
references.citation: Science. 1996 Sep 20;273(5282):1696-9
references.pmid: 8781229
references.citation: Acta Crystallogr D Biol Crystallogr. 2004 May;60(Pt 5):829-35
references.pmid: 15103128
references.citation: Trends Biochem Sci. 2007 Sep;32(9):415-24
references.pmid: 17764952
references.citation: Science. 1991 May 24;252(5009):1167-71
references.pmid: 1709522
references.citation: Cell. 2007 Sep 7;130(5):878-92
references.pmid: 17803910
references.citation: RNA. 2008 Jan;14(1):25-34
references.pmid: 18042658
references.citation: Structure. 2004 May;12(5):807-18
references.pmid: 15130473
references.citation: PLoS Biol. 2005 Jun;3(6):e213
references.pmid: 15941360
references.citation: Science. 2006 May 26;312(5777):1208-11
references.pmid: 16675665
references.citation: Mol Microbiol. 2005 Aug;57(4):1008-21
references.pmid: 16091040
references.citation: Curr Opin Struct Biol. 2005 Jun;15(3):342-8
references.pmid: 15919195
references.citation: BMC Bioinformatics. 2011;12 Suppl 13:S2
references.pmid: 22373013
references.citation: Nat Struct Biol. 1996 Dec;3(12):1026-33
references.pmid: 8946856
references.citation: Biochemistry. 2007 Nov 20;46(46):13297-309
references.pmid: 17960911
references.citation: EMBO J. 2001 Aug 1;20(15):4214-21
references.pmid: 11483524
references.citation: Mol Cell. 2004 Nov 5;16(3):351-62
references.pmid: 15525509
references.citation: Bioinformatics. 2009 May 1;25(9):1189-91
references.pmid: 19151095
references.citation: RNA. 2007 Aug;13(8):1256-67
references.pmid: 17585050
references.citation: Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):4899-903
references.pmid: 11296253
references.citation: J Biol Chem. 2009 Apr 24;284(17):11012-6
references.pmid: 19261617
references.citation: EMBO J. 1995 Mar 15;14(6):1276-85
references.pmid: 7720718
references.citation: Annu Rev Microbiol. 2005;59:487-517
references.pmid: 16153177
references.citation: J Mol Biol. 2008 Nov 14;383(3):475-81
references.pmid: 18773908
references.citation: Nat Struct Mol Biol. 2008 Oct;15(10):1076-83
references.pmid: 18806797
references.citation: Biochim Biophys Acta. 2009 Sep-Oct;1789(9-10):584-91
references.pmid: 19595806
references.citation: Genes Dev. 2008 Dec 15;22(24):3383-90
references.pmid: 19141470
references.citation: Cell. 2003 May 30;113(5):577-86
references.pmid: 12787499
references.citation: Acc Chem Res. 2011 Dec 20;44(12):1302-11
references.pmid: 21899297
references.citation: J Mol Biol. 2002 Jul 12;320(3):455-74
references.pmid: 12096903
references.citation: J Mol Biol. 2011 Apr 8;407(4):556-70
references.pmid: 21315082
references.citation: Plant Cell. 2007 Nov;19(11):3437-50
references.pmid: 17993623
references.citation: Structure. 2007 Mar;15(3):259-65
references.pmid: 17355861
references.citation: Proc Natl Acad Sci U S A. 1994 Aug 30;91(18):8705-9
references.pmid: 8078946
references.citation: Bioinformatics. 2009 May 15;25(10):1335-7
references.pmid: 19307242
references.citation: Nucleic Acids Res. 2012 Feb;40(4):1407-23
references.pmid: 22053086
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D136-40
references.pmid: 18953034