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Volumn 407, Issue 4, 2011, Pages 556-570

Insights into Metalloregulation by M-box Riboswitch RNAs via Structural Analysis of Manganese-Bound Complexes

Author keywords

analytical ultracentrifugation; AUC; N methylisatoic anhydride; NMIA; PDB; Protein Data Bank; selective 2 hydroxyl acylation analyzed by primer extension; SHAPE

Indexed keywords

APTAMER; CATION; MAGNESIUM; MANGANESE; METAL COMPLEX; RNA;

EID: 79952444960     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2011.01.049     Document Type: Article
Times cited : (42)

References (50)
  • 1
    • 34547229278 scopus 로고    scopus 로고
    • Metal sensor proteins: Nature's metalloregulated allosteric switches
    • DOI 10.1039/b706769k
    • Giedroc D.P., and Arunkumar A.I. Metal sensor proteins: nature's metalloregulated allosteric switches Dalton Trans. 2007 3107 3120 (Pubitemid 47117766)
    • (2007) Dalton Transactions , Issue.29 , pp. 3107-3120
    • Giedroc, D.P.1    Arunkumar, A.I.2
  • 2
    • 0027183546 scopus 로고
    • Transition metals in control of gene expression
    • O'Halloran T.V. Transition metals in control of gene expression Science 261 1993 715 725 (Pubitemid 23278386)
    • (1993) Science , vol.261 , Issue.5122 , pp. 715-725
    • O'Halloran, T.V.1
  • 3
    • 70350637580 scopus 로고    scopus 로고
    • Coordination chemistry of bacterial metal transport and sensing
    • Ma Z., Jacobsen F.E., and Giedroc D.P. Coordination chemistry of bacterial metal transport and sensing Chem. Rev. 109 2009 4644 4681
    • (2009) Chem. Rev. , vol.109 , pp. 4644-4681
    • Ma, Z.1    Jacobsen, F.E.2    Giedroc, D.P.3
  • 4
    • 0026409841 scopus 로고
    • Characterization of the cytoplasm of Escherichia coli K-12 as a function of external osmolarity: Implications for protein-DNA interactions in vivo
    • Cayley S., Lewis B.A., Guttman H.J., and Record M.T. Jr Characterization of the cytoplasm of Escherichia coli K-12 as a function of external osmolarity. Implications for protein-DNA interactions in vivo J. Mol. Biol. 222 1991 281 300 (Pubitemid 121004007)
    • (1991) Journal of Molecular Biology , vol.222 , Issue.2 , pp. 281-300
    • Cayley, S.1    Lewis, B.A.2    Guttman, H.J.3    Record Jr., M.T.4
  • 6
    • 33744489098 scopus 로고    scopus 로고
    • Magnesium transporters: Properties, regulation and structure
    • DOI 10.2741/2039
    • Maguire M.E. Magnesium transporters: properties, regulation and structure Front. Biosci. 11 2006 3149 3163 (Pubitemid 43800403)
    • (2006) Frontiers in Bioscience , vol.11 , Issue.SUPPL. 3 , pp. 3149-3163
    • Maguire, M.E.1
  • 9
    • 34548253368 scopus 로고    scopus 로고
    • Structure and Mechanism of a Metal-Sensing Regulatory RNA
    • DOI 10.1016/j.cell.2007.06.051, PII S0092867407009014
    • Dann C.E. III, Wakeman C.A., Sieling C.L., Baker S.C., Irnov I., and Winkler W.C. 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
  • 11
    • 16244363320 scopus 로고    scopus 로고
    • Metal ions and RNA folding: A highly charged topic with a dynamic future
    • DOI 10.1016/j.cbpa.2005.02.004, Bioorganic Chemistry / Biocatalysis and Biotransformation
    • Woodson S.A. Metal ions and RNA folding: a highly charged topic with a dynamic future Curr. Opin. Chem. Biol. 9 2005 104 109 (Pubitemid 40462481)
    • (2005) Current Opinion in Chemical Biology , vol.9 , Issue.2 , pp. 104-109
    • Woodson, S.A.1
  • 12
    • 33846478681 scopus 로고    scopus 로고
    • Intimate relationships between metal ions and nucleic acids
    • DOI 10.1002/anie.200605065
    • Sigel R.K. Intimate relationships between metal ions and nucleic acids Angew. Chem., Int. Ed. Engl. 46 2007 654 656 (Pubitemid 46155388)
    • (2007) Angewandte Chemie - International Edition , vol.46 , Issue.5 , pp. 654-656
    • Sigel, R.K.O.1
  • 13
    • 58749105663 scopus 로고    scopus 로고
    • RNA folding: Thermodynamic and molecular descriptions of the roles of ions
    • Draper D.E. RNA folding: thermodynamic and molecular descriptions of the roles of ions Biophys. J. 95 2008 5489 5495
    • (2008) Biophys. J. , vol.95 , pp. 5489-5495
    • Draper, D.E.1
  • 14
    • 0036940303 scopus 로고    scopus 로고
    • Metal ions in the structure and function of RNA
    • DOI 10.1007/s00775-002-0387-6
    • Pyle A.M. Metal ions in the structure and function of RNA J. Biol. Inorg. Chem. 7 2002 679 690 (Pubitemid 36056354)
    • (2002) Journal of Biological Inorganic Chemistry , vol.7 , Issue.7-8 , pp. 679-690
    • Pyle, A.M.1
  • 15
    • 34247242053 scopus 로고    scopus 로고
    • Structures of RNA switches: Insight into molecular recognition and tertiary structure
    • DOI 10.1002/anie.200604163
    • Schwalbe H., Buck J., Furtig B., Noeske J., and Wohnert J. Structures of RNA switches: insight into molecular recognition and tertiary structure Angew. Chem., Int. Ed. Engl. 46 2007 1212 1219 (Pubitemid 46981366)
    • (2007) Angewandte Chemie - International Edition , vol.46 , Issue.8 , pp. 1212-1219
    • Schwalbe, H.1    Buck, J.2    Furtig, B.3    Noeske, J.4    Wohnert, J.5
  • 16
    • 48249104039 scopus 로고    scopus 로고
    • Riboswitches: Emerging themes in RNA structure and function
    • Montange R.K., and Batey R.T. Riboswitches: emerging themes in RNA structure and function Annu. Rev. Biophys. 37 2008 117 133
    • (2008) Annu. Rev. Biophys. , vol.37 , pp. 117-133
    • Montange, R.K.1    Batey, R.T.2
  • 17
    • 63749126957 scopus 로고    scopus 로고
    • Expanding roles for metabolite-sensing regulatory RNAs
    • Dambach M.D., and Winkler W.C. Expanding roles for metabolite-sensing regulatory RNAs Curr. Opin. Microbiol. 12 2009 161 169
    • (2009) Curr. Opin. Microbiol. , vol.12 , pp. 161-169
    • Dambach, M.D.1    Winkler, W.C.2
  • 18
    • 67650713931 scopus 로고    scopus 로고
    • The structural and functional diversity of metabolite-binding riboswitches
    • Roth A., and Breaker R.R. 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
  • 19
    • 0346687595 scopus 로고    scopus 로고
    • The riboswitch control of bacterial metabolism
    • DOI 10.1016/j.tibs.2003.11.004
    • Nudler E., and Mironov A.S. The riboswitch control of bacterial metabolism Trends Biochem. Sci. 29 2004 11 17 (Pubitemid 38068475)
    • (2004) Trends in Biochemical Sciences , vol.29 , Issue.1 , pp. 11-17
    • Nudler, E.1    Mironov, A.S.2
  • 20
    • 37249040135 scopus 로고    scopus 로고
    • Mechanism of mRNA destabilization by the glmS ribozyme
    • DOI 10.1101/gad.1605307
    • Collins J.A., Irnov I., Baker S., and Winkler W.C. Mechanism of mRNA destabilization by the glmS ribozyme Genes Dev. 21 2007 3356 3368 (Pubitemid 350277761)
    • (2007) Genes and Development , vol.21 , Issue.24 , pp. 3356-3368
    • Collins, J.A.1    Irnov, I.2    Baker, S.3    Winkler, W.C.4
  • 22
    • 85011941301 scopus 로고    scopus 로고
    • Magnesium-sensing riboswitches in bacteria
    • Ramesh A., and Winkler W.C. Magnesium-sensing riboswitches in bacteria RNA Biol. 7 2010 77 83
    • (2010) RNA Biol. , vol.7 , pp. 77-83
    • Ramesh, A.1    Winkler, W.C.2
  • 23
    • 33845971464 scopus 로고    scopus 로고
    • Structural Transitions and Thermodynamics of a Glycine-Dependent Riboswitch from Vibrio cholerae
    • DOI 10.1016/j.jmb.2006.10.022, PII S002228360601360X
    • Lipfert J., Das R., Chu V.B., Kudaravalli M., Boyd N., Herschlag D., and Doniach S. Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae J. Mol. Biol. 365 2007 1393 1406 (Pubitemid 46048825)
    • (2007) Journal of Molecular Biology , vol.365 , Issue.5 , pp. 1393-1406
    • Lipfert, J.1    Das, R.2    Chu, V.B.3    Kudaravalli, M.4    Boyd, N.5    Herschlag, D.6    Doniach, S.7
  • 24
    • 77149165421 scopus 로고    scopus 로고
    • Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis
    • Baird N.J., and Ferre-D'Amare A.R. Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis RNA 16 2010 598 609
    • (2010) RNA , vol.16 , pp. 598-609
    • Baird, N.J.1    Ferre-D'Amare, A.R.2
  • 25
    • 71449123530 scopus 로고    scopus 로고
    • Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch
    • Kulshina N., Baird N.J., and Ferre-D'Amare A.R. 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    Ferre-D'Amare, A.R.3
  • 26
    • 0035105303 scopus 로고    scopus 로고
    • The pleiotropic two-component regulatory system PhoP-PhoQ
    • DOI 10.1128/JB.183.6.1835-1842.2001
    • Groisman E.A. The pleiotropic two-component regulatory system PhoP-PhoQ J. Bacteriol. 183 2001 1835 1842 (Pubitemid 32225978)
    • (2001) Journal of Bacteriology , vol.183 , Issue.6 , pp. 1835-1842
    • Groisman, E.A.1
  • 27
    • 34249817554 scopus 로고    scopus 로고
    • MgtC: A key player in intramacrophage survival
    • DOI 10.1016/j.tim.2007.03.007, PII S0966842X07000650
    • Alix E., and Blanc-Potard A.B. MgtC: a key player in intramacrophage survival Trends Microbiol. 15 2007 252 256 (Pubitemid 46856161)
    • (2007) Trends in Microbiology , vol.15 , Issue.6 , pp. 252-256
    • Alix, E.1    Blanc-Potard, A.-B.2
  • 28
    • 4344569647 scopus 로고    scopus 로고
    • The contribution of metal ions to the structural stability of the large ribosomal subunit
    • DOI 10.1261/rna.7390804
    • Klein D.J., Moore P.B., and Steitz T.A. The contribution of metal ions to the structural stability of the large ribosomal subunit RNA 10 2004 1366 1379 (Pubitemid 39122107)
    • (2004) RNA , vol.10 , Issue.9 , pp. 1366-1379
    • Klein, D.J.1    Moore, P.B.2    Steitz, T.A.3
  • 29
    • 0027247579 scopus 로고
    • Metal coordination sites that contribute to structure and catalysis in the group I intron from Tetrahymena
    • Christian E.L., and Yarus M. Metal coordination sites that contribute to structure and catalysis in the group I intron from Tetrahymena Biochemistry 32 1993 4475 4480 (Pubitemid 23143233)
    • (1993) Biochemistry , vol.32 , Issue.17 , pp. 4475-4480
    • Christian, E.L.1    Yarus, M.2
  • 31
    • 0021769550 scopus 로고
    • 2+ complexes of adenine nucleotides and thionucleotides and rate constants for formation and dissociation of MgATP and MgADP
    • 2+ complexes of adenine nucleotides and thionucleotides and rate constants for formation and dissociation of MgATP and MgADP Biochemistry 23 1984 5262 5271
    • (1984) Biochemistry , vol.23 , pp. 5262-5271
    • Pecoraro, V.L.1    Hermes, J.D.2    Cleland, W.W.3
  • 32
    • 69349104590 scopus 로고    scopus 로고
    • Multiple metal-binding cores are required for metalloregulation by M-box riboswitch RNAs
    • Wakeman C.A., Ramesh A., and Winkler W.C. Multiple metal-binding cores are required for metalloregulation by M-box riboswitch RNAs J. Mol. Biol. 392 2009 723 735
    • (2009) J. Mol. Biol. , vol.392 , pp. 723-735
    • Wakeman, C.A.1    Ramesh, A.2    Winkler, W.C.3
  • 33
    • 62249156218 scopus 로고    scopus 로고
    • Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch
    • Serganov A., Huang L., and Patel D.J. Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch Nature 458 2009 233 237
    • (2009) Nature , vol.458 , pp. 233-237
    • Serganov, A.1    Huang, L.2    Patel, D.J.3
  • 34
    • 0035085466 scopus 로고    scopus 로고
    • Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA-solvent interactions
    • DOI 10.1016/S0969-2126(01)00579-2, PII S0969212601005792
    • Juneau K., Podell E., Harrington D.J., and Cech T.R. Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA-solvent interactions Structure 9 2001 221 231 (Pubitemid 32245873)
    • (2001) Structure , vol.9 , Issue.3 , pp. 221-231
    • Juneau, K.1    Podell, E.2    Harrington, D.J.3    Cech, T.R.4
  • 35
    • 0030929889 scopus 로고    scopus 로고
    • A magnesium ion core at the heart of a ribozyme domain
    • DOI 10.1038/nsb0797-553
    • Cate J.H., Hanna R.L., and Doudna J.A. A magnesium ion core at the heart of a ribozyme domain Nat. Struct. Biol. 4 1997 553 558 (Pubitemid 27282151)
    • (1997) Nature Structural Biology , vol.4 , Issue.7 , pp. 553-558
    • Gate, J.H.1    Hanna, R.L.2    Doudna, J.A.3
  • 36
    • 0038719800 scopus 로고    scopus 로고
    • A crystallographic study of the binding of 13 metal ions of two related RNA duplexes
    • DOI 10.1093/nar/gkg350
    • Ennifar E., Walter P., and Dumas P. A crystallographic study of the binding of 13 metal ions to two related RNA duplexes Nucleic Acids Res. 31 2003 2671 2682 (Pubitemid 37441752)
    • (2003) Nucleic Acids Research , vol.31 , Issue.10 , pp. 2671-2682
    • Ennifar, E.1    Walter, P.2    Dumas, P.3
  • 37
    • 16244412610 scopus 로고    scopus 로고
    • RNA structure analysis at single nucleotide resolution by Selective 2′-Hydroxyl Acylation and Primer Extension (SHAPE)
    • DOI 10.1021/ja043822v
    • Merino E.J., Wilkinson K.A., Coughlan J.L., and Weeks K.M. RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE) J. Am. Chem. Soc. 127 2005 4223 4231 (Pubitemid 40463047)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.12 , pp. 4223-4231
    • Merino, E.J.1    Wilkinson, K.A.2    Coughlan, J.L.3    Weeks, K.M.4
  • 38
    • 53049094260 scopus 로고    scopus 로고
    • Crystal structure of the lysine riboswitch regulatory mRNA element
    • Garst A.D., Heroux A., Rambo R.P., and Batey R.T. Crystal structure of the lysine riboswitch regulatory mRNA element J. Biol. Chem. 283 2008 22347 22351
    • (2008) J. Biol. Chem. , vol.283 , pp. 22347-22351
    • Garst, A.D.1    Heroux, A.2    Rambo, R.P.3    Batey, R.T.4
  • 39
    • 74649084566 scopus 로고    scopus 로고
    • The ligand-free state of the TPP riboswitch: A partially folded RNA structure
    • Ali M., Lipfert J., Seifert S., Herschlag D., and Doniach S. The ligand-free state of the TPP riboswitch: a partially folded RNA structure J. Mol. Biol. 396 2010 153 165
    • (2010) J. Mol. Biol. , vol.396 , pp. 153-165
    • Ali, M.1    Lipfert, J.2    Seifert, S.3    Herschlag, D.4    Doniach, S.5
  • 40
    • 34547654293 scopus 로고    scopus 로고
    • Structural Metals in the Group I Intron: A Ribozyme with a Multiple Metal Ion Core
    • DOI 10.1016/j.jmb.2007.06.026, PII S0022283607008212
    • Stahley M.R., Adams P.L., Wang J., and Strobel S.A. Structural metals in the group I intron: a ribozyme with a multiple metal ion core J. Mol. Biol. 372 2007 89 102 (Pubitemid 47223219)
    • (2007) Journal of Molecular Biology , vol.372 , Issue.1 , pp. 89-102
    • Stahley, M.R.1    Adams, P.L.2    Wang, J.3    Strobel, S.A.4
  • 41
    • 41949138497 scopus 로고    scopus 로고
    • Solvent Structure and Hammerhead Ribozyme Catalysis
    • DOI 10.1016/j.chembiol.2008.03.010, PII S1074552108001221
    • Martick M., Lee T.S., York D.M., and Scott W.G. Solvent structure and hammerhead ribozyme catalysis Chem. Biol. 15 2008 332 342 (Pubitemid 351508433)
    • (2008) Chemistry and Biology , vol.15 , Issue.4 , pp. 332-342
    • Martick, M.1    Lee, T.-S.2    York, D.M.3    Scott, W.G.4
  • 42
    • 0034101184 scopus 로고    scopus 로고
    • Solving large RNA structures by X-ray crystallography
    • Cate J.H., and Doudna J.A. Solving large RNA structures by X-ray crystallography Methods Enzymol. 317 2000 169 180 (Pubitemid 30418085)
    • (2000) Methods in Enzymology , vol.317 , pp. 169-180
    • Cate, J.H.1    Doudna, J.A.2
  • 43
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • DOI 10.1016/S0076-6879(97)76066-X
    • Otwinowsky Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1997 307 326 (Pubitemid 27085611)
    • (1997) Methods in Enzymology , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 45
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • Collaborative Computational Project, Number 4
    • Collaborative Computational Project, Number 4 The CCP4 suite: programs for protein crystallography Acta Crystallogr., Sect. D: Biol. Crystallogr. 50 1994 760 763
    • (1994) Acta Crystallogr., Sect. D: Biol. Crystallogr. , vol.50 , pp. 760-763
  • 48
    • 3242886771 scopus 로고    scopus 로고
    • PDB2PQR: An automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
    • Dolinsky T.J., Nielsen J.E., McCammon J.A., and Baker N.A. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations Nucleic Acids Res. 32 2004 W665 W667
    • (2004) Nucleic Acids Res. , vol.32
    • Dolinsky, T.J.1    Nielsen, J.E.2    McCammon, J.A.3    Baker, N.A.4


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