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Volumn 19, Issue 10, 2011, Pages 1413-1423

The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer

Author keywords

[No Author keywords available]

Indexed keywords

7 DEAZAGUANINE; APTAMER; FOLINIC ACID; GUANINE DERIVATIVE; PTERIN; TETRAHYDROFOLIC ACID; UNCLASSIFIED DRUG;

EID: 80054074740     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2011.06.019     Document Type: Article
Times cited : (109)

References (56)
  • 2
    • 85011940614 scopus 로고    scopus 로고
    • Bacterial aptamers that selectively bind glutamine
    • T.D. Ames, and R.R. Breaker Bacterial aptamers that selectively bind glutamine RNA Biol. 8 2011 82 89
    • (2011) RNA Biol. , vol.8 , pp. 82-89
    • Ames, T.D.1    Breaker, R.R.2
  • 3
    • 77955437093 scopus 로고    scopus 로고
    • A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate
    • T.D. Ames, D.A. Rodionov, Z. Weinberg, and R.R. Breaker A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate Chem. Biol. 17 2010 681 685
    • (2010) Chem. Biol. , vol.17 , pp. 681-685
    • Ames, T.D.1    Rodionov, D.A.2    Weinberg, Z.3    Breaker, R.R.4
  • 4
    • 57349085197 scopus 로고    scopus 로고
    • In vitro approaches to analysis of transcription termination
    • I. Artsimovitch, and T.M. Henkin In vitro approaches to analysis of transcription termination Methods 47 2009 37 43
    • (2009) Methods , vol.47 , pp. 37-43
    • Artsimovitch, I.1    Henkin, T.M.2
  • 6
    • 9244225713 scopus 로고    scopus 로고
    • Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine
    • DOI 10.1038/nature03037
    • R.T. Batey, S.D. Gilbert, and R.K. Montange Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine Nature 432 2004 411 415 (Pubitemid 39551677)
    • (2004) Nature , vol.432 , Issue.7015 , pp. 411-415
    • Batey, R.T.1    Gilbert, S.D.2    Montange, R.K.3
  • 9
    • 0035996799 scopus 로고    scopus 로고
    • The folic acid biosynthesis pathway in bacteria: Evaluation of potential for antibacterial drug discovery
    • DOI 10.1002/bies.10114
    • A. Bermingham, and J.P. Derrick The folic acid biosynthesis pathway in bacteria: evaluation of potential for antibacterial drug discovery Bioessays 24 2002 637 648 (Pubitemid 34780351)
    • (2002) BioEssays , vol.24 , Issue.7 , pp. 637-648
    • Bermingham, A.1    Derrick, J.P.2
  • 10
    • 33845700514 scopus 로고    scopus 로고
    • Riboswitches as antibacterial drug targets
    • DOI 10.1038/nbt1268, PII NBT1268
    • K.F. Blount, and R.R. Breaker Riboswitches as antibacterial drug targets Nat. Biotechnol. 24 2006 1558 1564 (Pubitemid 44967480)
    • (2006) Nature Biotechnology , vol.24 , Issue.12 , pp. 1558-1564
    • Blount, K.F.1    Breaker, R.R.2
  • 11
    • 79953052076 scopus 로고    scopus 로고
    • Structural basis of cooperative ligand binding by the glycine riboswitch
    • E.B. Butler, Y. Xiong, J. Wang, and S.A. Strobel Structural basis of cooperative ligand binding by the glycine riboswitch Chem. Biol. 18 2011 293 298
    • (2011) Chem. Biol. , vol.18 , pp. 293-298
    • Butler, E.B.1    Xiong, Y.2    Wang, J.3    Strobel, S.A.4
  • 12
    • 34548253368 scopus 로고    scopus 로고
    • Structure and Mechanism of a Metal-Sensing Regulatory RNA
    • DOI 10.1016/j.cell.2007.06.051, PII S0092867407009014
    • C.E. Dann III, C.A. Wakeman, C.L. Sieling, S.C. Baker, I. Irnov, and W.C. Winkler Structure and mechanism of a metal-sensing regulatory RNA Cell 130 2007 878 892 (Pubitemid 47332567)
    • (2007) Cell , vol.130 , Issue.5 , pp. 878-892
    • Dann III, C.E.1    Wakeman, C.A.2    Sieling, C.L.3    Baker, S.C.4    Irnov, I.5    Winkler, W.C.6
  • 13
    • 13944278373 scopus 로고    scopus 로고
    • SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments
    • DOI 10.1261/rna.7214405
    • R. Das, A. Laederach, S.M. Pearlman, D. Herschlag, and R.B. Altman SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments RNA 11 2005 344 354 (Pubitemid 40270826)
    • (2005) RNA , vol.11 , Issue.3 , pp. 344-354
    • Das, R.1    Laederach, A.2    Pearlman, S.M.3    Herschlag, D.4    Altman, R.B.5
  • 14
    • 70350107533 scopus 로고    scopus 로고
    • Three-way RNA junctions with remote tertiary contacts: A recurrent and highly versatile fold
    • M. de la Peña, D. Dufour, and J. Gallego Three-way RNA junctions with remote tertiary contacts: a recurrent and highly versatile fold RNA 15 2009 1949 1964
    • (2009) RNA , vol.15 , pp. 1949-1964
    • De La Peña, M.1    Dufour, D.2    Gallego, J.3
  • 15
    • 58149138753 scopus 로고    scopus 로고
    • A structural basis for the recognition of 2′-deoxyguanosine by the purine riboswitch
    • A.L. Edwards, and R.T. Batey A structural basis for the recognition of 2′-deoxyguanosine by the purine riboswitch J. Mol. Biol. 385 2009 938 948
    • (2009) J. Mol. Biol. , vol.385 , pp. 938-948
    • Edwards, A.L.1    Batey, R.T.2
  • 17
    • 65649133549 scopus 로고    scopus 로고
    • Monitoring RNA-ligand interactions using isothermal titration calorimetry
    • S.D. Gilbert, and R.T. Batey Monitoring RNA-ligand interactions using isothermal titration calorimetry Methods Mol. Biol. 540 2009 97 114
    • (2009) Methods Mol. Biol. , vol.540 , pp. 97-114
    • Gilbert, S.D.1    Batey, R.T.2
  • 18
    • 36248982074 scopus 로고    scopus 로고
    • Mutational analysis of the purine riboswitch aptamer domain
    • DOI 10.1021/bi700410g
    • S.D. Gilbert, C.E. Love, A.L. Edwards, and R.T. Batey Mutational analysis of the purine riboswitch aptamer domain Biochemistry 46 2007 13297 13309 (Pubitemid 350136370)
    • (2007) Biochemistry , vol.46 , Issue.46 , pp. 13297-13309
    • Gilbert, S.D.1    Love, C.E.2    Edwards, A.L.3    Batey, R.T.4
  • 19
    • 38849204944 scopus 로고    scopus 로고
    • Direct observation of hierarchical folding in single riboswitch aptamers
    • DOI 10.1126/science.1151298
    • W.J. Greenleaf, K.L. Frieda, D.A. Foster, M.T. Woodside, and S.M. Block Direct observation of hierarchical folding in single riboswitch aptamers Science 319 2008 630 633 (Pubitemid 351197067)
    • (2008) Science , vol.319 , Issue.5863 , pp. 630-633
    • Greenleaf, W.J.1    Frieda, K.L.2    Foster, D.A.N.3    Woodside, M.T.4    Block, S.M.5
  • 20
    • 0041620358 scopus 로고    scopus 로고
    • PSEUDOVIEWER2: Visualization of RNA pseudoknots of any type
    • DOI 10.1093/nar/gkg539
    • K. Han, and Y. Byun PSEUDOVIEWER2: visualization of RNA pseudoknots of any type Nucleic Acids Res. 31 2003 3432 3440 (Pubitemid 37442173)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3432-3440
    • Han, K.1    Byun, Y.2
  • 21
    • 62549154008 scopus 로고    scopus 로고
    • Structural insights into riboswitch control of the biosynthesis of queuosine, a modified nucleotide found in the anticodon of tRNA
    • M. Kang, R. Peterson, and J. Feigon Structural insights into riboswitch control of the biosynthesis of queuosine, a modified nucleotide found in the anticodon of tRNA Mol. Cell 33 2009 784 790
    • (2009) Mol. Cell , vol.33 , pp. 784-790
    • Kang, M.1    Peterson, R.2    Feigon, J.3
  • 22
    • 34447260753 scopus 로고    scopus 로고
    • A General Strategy to Solve the Phase Problem in RNA Crystallography
    • DOI 10.1016/j.str.2007.06.003, PII S0969212607002080
    • A.Y. Keel, R.P. Rambo, R.T. Batey, and J.S. Kieft A general strategy to solve the phase problem in RNA crystallography Structure 15 2007 761 772 (Pubitemid 47042432)
    • (2007) Structure , vol.15 , Issue.7 , pp. 761-772
    • Keel, A.Y.1    Rambo, R.P.2    Batey, R.T.3    Kieft, J.S.4
  • 23
    • 62049086072 scopus 로고    scopus 로고
    • Cocrystal structure of a class i preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase
    • D.J. Klein, T.E. Edwards, and A.R. Ferré-D'Amaré Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase Nat. Struct. Mol. Biol. 16 2009 343 344
    • (2009) Nat. Struct. Mol. Biol. , vol.16 , pp. 343-344
    • Klein, D.J.1    Edwards, T.E.2    Ferré-D'Amaré, A.R.3
  • 24
    • 71449123530 scopus 로고    scopus 로고
    • Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch
    • N. Kulshina, N.J. Baird, and A.R. Ferré-D'Amaré Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch Nat. Struct. Mol. Biol. 16 2009 1212 1217
    • (2009) Nat. Struct. Mol. Biol. , vol.16 , pp. 1212-1217
    • Kulshina, N.1    Baird, N.J.2    Ferré-D'Amaré, A.R.3
  • 26
    • 0035010211 scopus 로고    scopus 로고
    • Geometric nomenclature and classification of RNA base pairs
    • DOI 10.1017/S1355838201002515
    • N.B. Leontis, and E. Westhof Geometric nomenclature and classification of RNA base pairs RNA 7 2001 499 512 (Pubitemid 32416808)
    • (2001) RNA , vol.7 , Issue.4 , pp. 499-512
    • Leontis, N.B.1    Westhof, E.2
  • 27
    • 29844453234 scopus 로고    scopus 로고
    • Topology of three-way junctions in folded RNAs
    • DOI 10.1261/rna.2208106
    • A. Lescoute, and E. Westhof Topology of three-way junctions in folded RNAs RNA 12 2006 83 93 (Pubitemid 43037456)
    • (2006) RNA , vol.12 , Issue.1 , pp. 83-93
    • Lescoute, A.1    Westhof, E.2
  • 28
    • 5044234799 scopus 로고    scopus 로고
    • A glycine-dependent riboswitch that uses cooperative binding to control gene expression
    • DOI 10.1126/science.1100829
    • M. Mandal, M. Lee, J.E. Barrick, Z. Weinberg, G.M. Emilsson, W.L. Ruzzo, and R.R. Breaker A glycine-dependent riboswitch that uses cooperative binding to control gene expression Science 306 2004 275 279 (Pubitemid 39336872)
    • (2004) Science , vol.306 , Issue.5694 , pp. 275-279
    • Mandal, M.1    Lee, M.2    Barrick, J.E.3    Weinberg, Z.4    Emilsson, G.M.5    Ruzzo, W.L.6    Breaker, R.R.7
  • 29
    • 34247162792 scopus 로고    scopus 로고
    • A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry
    • DOI 10.1021/ja0704028
    • S.A. Mortimer, and K.M. Weeks A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry J. Am. Chem. Soc. 129 2007 4144 4145 (Pubitemid 46595421)
    • (2007) Journal of the American Chemical Society , vol.129 , Issue.14 , pp. 4144-4145
    • Mortimer, S.A.1    Weeks, K.M.2
  • 31
    • 78650532236 scopus 로고    scopus 로고
    • Evidence for an autonomous 5′ target recognition domain in an Hfq-associated small RNA
    • K. Papenfort, M. Bouvier, F. Mika, C.M. Sharma, and J. Vogel Evidence for an autonomous 5′ target recognition domain in an Hfq-associated small RNA Proc. Natl. Acad. Sci. USA 107 2010 20435 20440
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 20435-20440
    • Papenfort, K.1    Bouvier, M.2    Mika, F.3    Sharma, C.M.4    Vogel, J.5
  • 33
    • 67650713931 scopus 로고    scopus 로고
    • The structural and functional diversity of metabolite-binding riboswitches
    • A. Roth, and R.R. Breaker The structural and functional diversity of metabolite-binding riboswitches Annu. Rev. Biochem. 78 2009 305 334
    • (2009) Annu. Rev. Biochem. , vol.78 , pp. 305-334
    • Roth, A.1    Breaker, R.R.2
  • 34
    • 0021881054 scopus 로고
    • Serine hydroxymethyltransferase from Escherichia coli: Purification and properties
    • V. Schirch, S. Hopkins, E. Villar, and S. Angelaccio Serine hydroxymethyltransferase from Escherichia coli: purification and properties J. Bacteriol. 163 1985 1 7 (Pubitemid 15011709)
    • (1985) Journal of Bacteriology , vol.163 , Issue.1 , pp. 1-7
    • Schirch, V.1    Hopkins, S.2    Villar, E.3    Angelaccio, S.4
  • 36
    • 33745635350 scopus 로고    scopus 로고
    • Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch
    • DOI 10.1038/nature04740, PII N04740
    • A. Serganov, A. Polonskaia, A.T. Phan, R.R. Breaker, and D.J. Patel Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch Nature 441 2006 1167 1171 (Pubitemid 43990739)
    • (2006) Nature , vol.441 , Issue.7097 , pp. 1167-1171
    • Serganov, A.1    Polonskaia, A.2    Phan, A.T.3    Breaker, R.R.4    Patel, D.J.5
  • 37
    • 0024808080 scopus 로고
    • Folylpolyglutamate synthesis and role in the regulation of one-carbon metabolism
    • B. Shane Folylpolyglutamate synthesis and role in the regulation of one-carbon metabolism Vitam. Horm. 45 1989 263 335
    • (1989) Vitam. Horm. , vol.45 , pp. 263-335
    • Shane, B.1
  • 39
    • 66449089224 scopus 로고    scopus 로고
    • The structural basis for recognition of the preQ0 metabolite by an unusually small riboswitch aptamer domain
    • R.C. Spitale, A.T. Torelli, J. Krucinska, V. Bandarian, and J.E. Wedekind The structural basis for recognition of the preQ0 metabolite by an unusually small riboswitch aptamer domain J. Biol. Chem. 284 2009 11012 11016
    • (2009) J. Biol. Chem. , vol.284 , pp. 11012-11016
    • Spitale, R.C.1    Torelli, A.T.2    Krucinska, J.3    Bandarian, V.4    Wedekind, J.E.5
  • 40
    • 0027025261 scopus 로고
    • The PurR binding site in the glyA promoter region of Escherichia coli
    • J.G. Steiert, C. Kubu, and G.V. Stauffer The PurR binding site in the glyA promoter region of Escherichia coli FEMS Microbiol. Lett. 78 1992 299 304 (Pubitemid 23000272)
    • (1992) FEMS Microbiology Letters , vol.99 , Issue.2-3 , pp. 299-304
    • Steiert, J.G.1    Kubu, C.2    Stauffer, G.V.3
  • 42
    • 41649108293 scopus 로고    scopus 로고
    • Ligand-dependent folding of the three-way junction in the purine riboswitch
    • DOI 10.1261/rna.736908
    • C.D. Stoddard, S.D. Gilbert, and R.T. Batey Ligand-dependent folding of the three-way junction in the purine riboswitch RNA 14 2008 675 684 (Pubitemid 351480880)
    • (2008) RNA , vol.14 , Issue.4 , pp. 675-684
    • Stoddard, C.D.1    Gilbert, S.D.2    Batey, R.T.3
  • 44
    • 0242298623 scopus 로고    scopus 로고
    • An mRNA structure in bacteria that controls gene expression by binding lysine
    • DOI 10.1101/gad.1140003
    • N. Sudarsan, J.K. Wickiser, S. Nakamura, M.S. Ebert, and R.R. Breaker An mRNA structure in bacteria that controls gene expression by binding lysine Genes Dev. 17 2003 2688 2697 (Pubitemid 37363073)
    • (2003) Genes and Development , vol.17 , Issue.21 , pp. 2688-2697
    • Sudarsan, N.1    Wickiser, J.K.2    Nakamura, S.3    Ebert, M.S.4    Breaker, R.R.5
  • 45
    • 0034928775 scopus 로고    scopus 로고
    • New perspectives on folate catabolism
    • DOI 10.1146/annurev.nutr.21.1.255
    • J.R. Suh, A.K. Herbig, and P.J. Stover New perspectives on folate catabolism Annu. Rev. Nutr. 21 2001 255 282 (Pubitemid 32695272)
    • (2001) Annual Review of Nutrition , vol.21 , pp. 255-282
    • Suh, J.R.1    Herbig, A.K.2    Stover, P.J.3
  • 47
    • 2342594534 scopus 로고    scopus 로고
    • Multivitamin production in Lactococcus lactis using metabolic engineering
    • DOI 10.1016/j.ymben.2003.11.002
    • W. Sybesma, C. Burgess, M. Starrenburg, D. van Sinderen, and J. Hugenholtz Multivitamin production in Lactococcus lactis using metabolic engineering Metab. Eng. 6 2004 109 115 (Pubitemid 38601065)
    • (2004) Metabolic Engineering , vol.6 , Issue.2 , pp. 109-115
    • Sybesma, W.1    Burgess, C.2    Starrenburg, M.3    Van Sinderen, D.4    Hugenholtz, J.5
  • 48
    • 33744469562 scopus 로고    scopus 로고
    • Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand
    • DOI 10.1126/science.1128451
    • S. Thore, M. Leibundgut, and N. Ban Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand Science 312 2006 1208 1211 (Pubitemid 43801145)
    • (2006) Science , vol.312 , Issue.5777 , pp. 1208-1211
    • Thore, S.1    Leibundgut, M.2    Ban, N.3
  • 49
    • 79953324324 scopus 로고    scopus 로고
    • Construction of a thiamine pyrophosphate high-producing strain of Aspergillus oryzae by overexpression of three genes involved in thiamine biosynthesis
    • M. Tokui, T. Kubodera, K. Gomi, N. Yamashita, and A. Nishimura Construction of a thiamine pyrophosphate high-producing strain of Aspergillus oryzae by overexpression of three genes involved in thiamine biosynthesis J. Biosci. Bioeng. 111 2011 388 390
    • (2011) J. Biosci. Bioeng. , vol.111 , pp. 388-390
    • Tokui, M.1    Kubodera, T.2    Gomi, K.3    Yamashita, N.4    Nishimura, A.5
  • 50
    • 0030768931 scopus 로고    scopus 로고
    • The Hill equation revisited: Uses and misuses
    • J.N. Weiss The Hill equation revisited: uses and misuses FASEB J. 11 1997 835 841 (Pubitemid 27371892)
    • (1997) FASEB Journal , vol.11 , Issue.11 , pp. 835-841
    • Weiss, J.N.1
  • 51
    • 26444620938 scopus 로고    scopus 로고
    • The kinetics of ligand binding by an adenine-sensing riboswitch
    • DOI 10.1021/bi051008u
    • J.K. Wickiser, M.T. Cheah, R.R. Breaker, and D.M. Crothers The kinetics of ligand binding by an adenine-sensing riboswitch Biochemistry 44 2005 13404 13414 (Pubitemid 41429463)
    • (2005) Biochemistry , vol.44 , Issue.40 , pp. 13404-13414
    • Wickiser, J.K.1    Cheah, M.T.2    Breaker, R.R.3    Crothers, D.M.4
  • 52
    • 15944382675 scopus 로고    scopus 로고
    • The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch
    • DOI 10.1016/j.molcel.2005.02.032
    • J.K. Wickiser, W.C. Winkler, R.R. Breaker, and D.M. Crothers The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch Mol. Cell 18 2005 49 60 (Pubitemid 40444647)
    • (2005) Molecular Cell , vol.18 , Issue.1 , pp. 49-60
    • Wickiser, J.K.1    Winkler, W.C.2    Breaker, R.R.3    Crothers, D.M.4
  • 53
    • 33947720028 scopus 로고    scopus 로고
    • Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): Quantitative RNA structure analysis at single nucleotide resolution
    • K.A. Wilkinson, E.J. Merino, and K.M. Weeks Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution Nat. Protoc. 1 2006 1610 1616
    • (2006) Nat. Protoc. , vol.1 , pp. 1610-1616
    • Wilkinson, K.A.1    Merino, E.J.2    Weeks, K.M.3
  • 54
    • 75649151032 scopus 로고    scopus 로고
    • Xia2: An expert system for macromolecular crystallography data reduction
    • G. Winter xia2: an expert system for macromolecular crystallography data reduction J. Appl. Crystallogr. 43 2010 186 190
    • (2010) J. Appl. Crystallogr. , vol.43 , pp. 186-190
    • Winter, G.1
  • 56
    • 0030752211 scopus 로고    scopus 로고
    • Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA
    • DOI 10.1038/nsb0897-644
    • G.R. Zimmermann, R.D. Jenison, C.L. Wick, J.P. Simorre, and A. Pardi Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA Nat. Struct. Biol. 4 1997 644 649 (Pubitemid 27323447)
    • (1997) Nature Structural Biology , vol.4 , Issue.8 , pp. 644-649
    • Zimmermann, G.R.1    Jenison, R.D.2    Wick, C.L.3    Simorre, J.-P.4    Pardi, A.5


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