title: Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA.
abstract: In Gram-positive bacteria, T-box riboswitches regulate the expression of aminoacyl-tRNA synthetases and other proteins in response to fluctuating transfer RNA aminoacylation levels under various nutritional states. T-boxes reside in the 5'-untranslated regions of the messenger RNAs they regulate, and consist of two conserved domains. Stem I contains the specifier trinucleotide that base pairs with the anticodon of cognate tRNA. 3' to stem I is the antiterminator domain, which base pairs with the tRNA acceptor end and evaluates its aminoacylation state. Despite high phylogenetic conservation and widespread occurrence in pathogens, the structural basis of tRNA recognition by this riboswitch remains ill defined. Here we demonstrate that the ~100-nucleotide T-box stem I is necessary and sufficient for specific, high-affinity (dissociation constant (Kd) ~150 nM) tRNA binding, and report the structure of Oceanobacillus iheyensis glyQ stem I in complex with its cognate tRNA at 3.2 Å resolution. Stem I recognizes the overall architecture of tRNA in addition to its anticodon, something accomplished by large ribonucleoproteins such as the ribosome, or proteins such as aminoacyl-tRNA synthetases, but is unprecedented for a compact mRNA domain. The C-shaped stem I cradles the L-shaped tRNA, forming an extended (1,604 Å(2)) intermolecular interface. In addition to the specifier-anticodon interaction, two interdigitated T-loops near the apex of stem I stack on the tRNA elbow in a manner analogous to those of the J11/12-J12/11 motif of RNase P and the L1 stalk of the ribosomal E-site. Because these ribonucleoproteins and T-boxes are unrelated, this strategy to recognize a universal tRNA feature probably evolved convergently. Mutually induced fit of stem I and the tRNA exploiting the intrinsic flexibility of tRNA and its conserved post-transcriptional modifications results in high shape complementarity, which in addition to providing specificity and affinity, globally organizes the T-box to orchestrate tRNA-dependent transcription regulation.
authors.affiliation: National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, Maryland 20892-8012, USA.
authors.forename: Jinwei
authors.initials: J
authors.lastname: Zhang
authors.forename: Adrian R
authors.initials: AR
authors.lastname: Ferré-D'Amaré
mesh_terms: D001406:Bacillaceae / Q000737:chemistry*; D001426:Bacterial Proteins / Q000737:chemistry*; D008958:Models, Molecular; D011485:Protein Binding; D020836:Protein Structure, Quaternary; D012343:RNA, Transfer / Q000737:chemistry*; D058928:Riboswitch; D020825:T-Box Domain Proteins / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D058928:Riboswitch; D020825:T-Box Domain Proteins; D012343:RNA, Transfer
references.citation: Wiley Interdiscip Rev RNA. 2013 Sep-Oct;4(5):507-22
references.pmid: 23754657
references.citation: Cell. 1997 Nov 28;91(5):705-12
references.pmid: 9393863
references.citation: Cell. 2006 Sep 22;126(6):1065-77
references.pmid: 16962654
references.citation: Methods Enzymol. 1997;276:307-26
references.pmid: 27754618
references.citation: RNA. 2001 Aug;7(8):1165-72
references.pmid: 11497434
references.citation: RNA. 2012 Apr;18(4):759-70
references.pmid: 22355167
references.citation: Science. 2011 May 20;332(6032):981-4
references.pmid: 21596992
references.citation: J Mol Biol. 2011 Apr 22;408(1):99-117
references.pmid: 21333656
references.citation: Cell. 1993 Aug 13;74(3):475-82
references.pmid: 8348614
references.citation: Nature. 2003 Feb 13;421(6924):760-4
references.pmid: 12610630
references.citation: Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):125-32
references.pmid: 20124692
references.citation: RNA. 2003 Sep;9(9):1148-56
references.pmid: 12923262
references.citation: FEBS Lett. 2010 Jan 21;584(2):318-24
references.pmid: 19932103
references.citation: Biophys J. 2000 Mar;78(3):1606-19
references.pmid: 10692345
references.citation: Nature. 2008 Jul 17;454(7202):358-61
references.pmid: 18548004
references.citation: Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):72-82
references.pmid: 16369096
references.citation: Science. 2006 Sep 29;313(5795):1935-42
references.pmid: 16959973
references.citation: Nucleic Acids Res. 2010 Jul;38(12):4154-62
references.pmid: 20203084
references.citation: Nat Struct Biol. 2003 Feb;10(2):104-8
references.pmid: 12514741
references.citation: Science. 2007 Jun 22;316(5832):1759-61
references.pmid: 17588934
references.citation: Nature. 2010 Dec 9;468(7325):784-9
references.pmid: 21076397
references.citation: Science. 2009 Oct 30;326(5953):688-694
references.pmid: 19833920
references.citation: Acta Crystallogr D Biol Crystallogr. 2000 Aug;56(Pt 8):965-72
references.pmid: 10944333
references.citation: Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501
references.pmid: 20383002
references.citation: Microbiol Mol Biol Rev. 2009 Mar;73(1):36-61
references.pmid: 19258532
references.citation: RNA. 2010 Mar;16(3):598-609
references.pmid: 20106958
references.citation: EMBO J. 2001 Aug 1;20(15):4214-21
references.pmid: 11483524
references.citation: RNA. 2000 Aug;6(8):1091-105
references.pmid: 10943889
references.citation: Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):352-67
references.pmid: 22505256
references.citation: Chem Biol. 2008 Oct 20;15(10):1125-37
references.pmid: 18940672
references.citation: Nucleic Acids Res. 1996 Mar 15;24(6):1073-9
references.pmid: 8604341
references.citation: J Mol Biol. 2005 Jun 3;349(2):273-87
references.pmid: 15890195
references.citation: Biochemistry. 2012 Nov 6;51(44):8705-29
references.pmid: 23075299
references.citation: Anal Chem. 2012 Jun 5;84(11):5066-73
references.pmid: 22530732
references.citation: Biochemistry. 2012 May 1;51(17):3662-74
references.pmid: 22468768
references.citation: Proc Natl Acad Sci U S A. 2013 Apr 30;110(18):7240-5
references.pmid: 23589841
references.citation: Nucleic Acids Res. 2013 May 1;41(10):5494-502
references.pmid: 23580544
references.citation: Cell. 2000 Nov 22;103(5):793-803
references.pmid: 11114335
references.citation: RNA. 2001 Apr;7(4):499-512
references.pmid: 11345429
references.citation: Nucleic Acids Res. 2005 Apr 28;33(8):2395-409
references.pmid: 15860776
references.citation: J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674
references.pmid: 19461840
references.citation: RNA. 2008 Apr;14(4):717-35
references.pmid: 18359782
references.citation: RNA. 2013 Feb;19(2):167-76
references.pmid: 23249744
references.citation: RNA. 1998 Sep;4(9):1134-53
references.pmid: 9740131
references.citation: Acta Crystallogr A. 2008 Jan;64(Pt 1):112-22
references.pmid: 18156677
references.citation: Nat Struct Biol. 2003 Nov;10(11):899-906
references.pmid: 14566331
references.citation: Curr Opin Struct Biol. 2007 Jun;17(3):273-9
references.pmid: 17574837
references.citation: RNA. 2010 Jan;16(1):186-96
references.pmid: 19948769