메뉴 건너뛰기




Volumn 57, Issue 6, 2015, Pages 1110-1123

Mn2+-Sensing Mechanisms of yybP-ykoY Orphan Riboswitches

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE; MANGANESE; RNA POLYMERASE; ADENOSINE TRIPHOSPHATASE; BACTERIAL RNA; MAGNESIUM; REGULATORY RNA SEQUENCE; RIBOSWITCH;

EID: 84925067690     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2015.02.016     Document Type: Article
Times cited : (99)

References (54)
  • 2
    • 0021248136 scopus 로고
    • Manganese acquisition by Lactobacillus plantarum
    • Archibald F.S., Duong M.N. Manganese acquisition by Lactobacillus plantarum. J.Bacteriol. 1984, 158:1-8.
    • (1984) J.Bacteriol. , vol.158 , pp. 1-8
    • Archibald, F.S.1    Duong, M.N.2
  • 5
    • 34447528960 scopus 로고    scopus 로고
    • A loop loop interaction and a K-turn motif located in the lysine aptamer domain are important for the riboswitch gene regulation control
    • Blouin S., Lafontaine D.A. A loop loop interaction and a K-turn motif located in the lysine aptamer domain are important for the riboswitch gene regulation control. RNA 2007, 13:1256-1267.
    • (2007) RNA , vol.13 , pp. 1256-1267
    • Blouin, S.1    Lafontaine, D.A.2
  • 6
    • 80052973462 scopus 로고    scopus 로고
    • Prospects for riboswitch discovery and analysis
    • Breaker R.R. Prospects for riboswitch discovery and analysis. Mol. Cell 2011, 43:867-879.
    • (2011) Mol. Cell , vol.43 , pp. 867-879
    • Breaker, R.R.1
  • 8
    • 0031027138 scopus 로고    scopus 로고
    • Ribonuclease P catalysis requires Mg2+ coordinated to the pro-RP oxygen of the scissile bond
    • Chen Y., Li X., Gegenheimer P. Ribonuclease P catalysis requires Mg2+ coordinated to the pro-RP oxygen of the scissile bond. Biochemistry 1997, 36:2425-2438.
    • (1997) Biochemistry , vol.36 , pp. 2425-2438
    • Chen, Y.1    Li, X.2    Gegenheimer, P.3
  • 12
    • 0034708334 scopus 로고    scopus 로고
    • Structure and function of the hairpin ribozyme
    • Fedor M.J. Structure and function of the hairpin ribozyme. J.Mol. Biol. 2000, 297:269-291.
    • (2000) J.Mol. Biol. , vol.297 , pp. 269-291
    • Fedor, M.J.1
  • 13
    • 84913570361 scopus 로고    scopus 로고
    • Broccoli: rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution
    • Filonov G.S., Moon J.D., Svensen N., Jaffrey S.R. Broccoli: rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution. J.Am. Chem. Soc. 2014, 136:16299-16308.
    • (2014) J.Am. Chem. Soc. , vol.136 , pp. 16299-16308
    • Filonov, G.S.1    Moon, J.D.2    Svensen, N.3    Jaffrey, S.R.4
  • 15
    • 84876907659 scopus 로고    scopus 로고
    • T box RNA decodes both the information content and geometry of tRNA to affect gene expression
    • Grigg J.C., Chen Y., Grundy F.J., Henkin T.M., Pollack L., Ke A. T box RNA decodes both the information content and geometry of tRNA to affect gene expression. Proc. Natl. Acad. Sci. USA 2013, 110:7240-7245.
    • (2013) Proc. Natl. Acad. Sci. USA , vol.110 , pp. 7240-7245
    • Grigg, J.C.1    Chen, Y.2    Grundy, F.J.3    Henkin, T.M.4    Pollack, L.5    Ke, A.6
  • 16
    • 0036315896 scopus 로고    scopus 로고
    • Intracellular magnesium and magnesium buffering
    • Grubbs R.D. Intracellular magnesium and magnesium buffering. Biometals 2002, 15:251-259.
    • (2002) Biometals , vol.15 , pp. 251-259
    • Grubbs, R.D.1
  • 17
    • 0042952817 scopus 로고    scopus 로고
    • The global transcriptional response of Bacillus subtilis to manganese involves the MntR, Fur, TnrA and sigmaB regulons
    • Guedon E., Moore C.M., Que Q., Wang T., Ye R.W., Helmann J.D. The global transcriptional response of Bacillus subtilis to manganese involves the MntR, Fur, TnrA and sigmaB regulons. Mol. Microbiol. 2003, 49:1477-1491.
    • (2003) Mol. Microbiol. , vol.49 , pp. 1477-1491
    • Guedon, E.1    Moore, C.M.2    Que, Q.3    Wang, T.4    Ye, R.W.5    Helmann, J.D.6
  • 18
    • 0030597337 scopus 로고    scopus 로고
    • Plasmids for ectopic integration in Bacillus subtilis
    • Guérout-Fleury A.M., Frandsen N., Stragier P. Plasmids for ectopic integration in Bacillus subtilis. Gene 1996, 180:57-61.
    • (1996) Gene , vol.180 , pp. 57-61
    • Guérout-Fleury, A.M.1    Frandsen, N.2    Stragier, P.3
  • 19
    • 80052982281 scopus 로고    scopus 로고
    • The dynamic nature of RNA askey to understanding riboswitch mechanisms
    • Haller A., Soulière M.F., Micura R. The dynamic nature of RNA askey to understanding riboswitch mechanisms. Acc. Chem. Res. 2011, 44:1339-1348.
    • (2011) Acc. Chem. Res. , vol.44 , pp. 1339-1348
    • Haller, A.1    Soulière, M.F.2    Micura, R.3
  • 20
    • 84934434394 scopus 로고    scopus 로고
    • Mespeus-a database of metal interactions with proteins
    • Harding M.M., Hsin K.Y. Mespeus-a database of metal interactions with proteins. Methods Mol. Biol. 2014, 1091:333-342.
    • (2014) Methods Mol. Biol. , vol.1091 , pp. 333-342
    • Harding, M.M.1    Hsin, K.Y.2
  • 21
    • 84907833692 scopus 로고    scopus 로고
    • Specificity of metal sensing: iron and manganese homeostasis in Bacillus subtilis
    • Helmann J.D. Specificity of metal sensing: iron and manganese homeostasis in Bacillus subtilis. J.Biol. Chem. 2014, 289:28112-28120.
    • (2014) J.Biol. Chem. , vol.289 , pp. 28112-28120
    • Helmann, J.D.1
  • 22
    • 84873632585 scopus 로고    scopus 로고
    • The expression platform and the aptamer: cooperativity between Mg2+ and ligand in the SAM-I riboswitch
    • Hennelly S.P., Novikova I.V., Sanbonmatsu K.Y. The expression platform and the aptamer: cooperativity between Mg2+ and ligand in the SAM-I riboswitch. Nucleic Acids Res. 2013, 41:1922-1935.
    • (2013) Nucleic Acids Res. , vol.41 , pp. 1922-1935
    • Hennelly, S.P.1    Novikova, I.V.2    Sanbonmatsu, K.Y.3
  • 23
    • 84915749862 scopus 로고    scopus 로고
    • Single-molecule conformational dynamics of a biologically functional hydroxocobalamin riboswitch
    • Holmstrom E.D., Polaski J.T., Batey R.T., Nesbitt D.J. Single-molecule conformational dynamics of a biologically functional hydroxocobalamin riboswitch. J.Am. Chem. Soc. 2014, 136:16832-16843.
    • (2014) J.Am. Chem. Soc. , vol.136 , pp. 16832-16843
    • Holmstrom, E.D.1    Polaski, J.T.2    Batey, R.T.3    Nesbitt, D.J.4
  • 24
    • 84907820812 scopus 로고    scopus 로고
    • The mismetallation of enzymes during oxidative stress
    • Imlay J.A. The mismetallation of enzymes during oxidative stress. J.Biol. Chem. 2014, 289:28121-28128.
    • (2014) J.Biol. Chem. , vol.289 , pp. 28121-28128
    • Imlay, J.A.1
  • 26
    • 4344596976 scopus 로고    scopus 로고
    • Crystallization of RNA and RNA-protein complexes
    • Ke A., Doudna J.A. Crystallization of RNA and RNA-protein complexes. Methods 2004, 34:408-414.
    • (2004) Methods , vol.34 , pp. 408-414
    • Ke, A.1    Doudna, J.A.2
  • 28
    • 34248669001 scopus 로고    scopus 로고
    • Functional specialization within the Fur family of metalloregulators
    • Lee J.W., Helmann J.D. Functional specialization within the Fur family of metalloregulators. Biometals 2007, 20:485-499.
    • (2007) Biometals , vol.20 , pp. 485-499
    • Lee, J.W.1    Helmann, J.D.2
  • 29
    • 84876034308 scopus 로고    scopus 로고
    • Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing
    • Li S., Breaker R.R. Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing. Nucleic Acids Res. 2013, 41:3022-3031.
    • (2013) Nucleic Acids Res. , vol.41 , pp. 3022-3031
    • Li, S.1    Breaker, R.R.2
  • 30
    • 84870236230 scopus 로고    scopus 로고
    • Origins of specificity and cross-talk in metal ion sensing by Bacillus subtilis Fur
    • Ma Z., Faulkner M.J., Helmann J.D. Origins of specificity and cross-talk in metal ion sensing by Bacillus subtilis Fur. Mol. Microbiol. 2012, 86:1144-1155.
    • (2012) Mol. Microbiol. , vol.86 , pp. 1144-1155
    • Ma, Z.1    Faulkner, M.J.2    Helmann, J.D.3
  • 32
    • 0003785155 scopus 로고
    • Cold Spring Harbor Laborator, Cold Spring Harbor, New York
    • Miller J.H. Experiments in Molecular Genetics 1972, Cold Spring Harbor Laborator, Cold Spring Harbor, New York.
    • (1972) Experiments in Molecular Genetics
    • Miller, J.H.1
  • 33
    • 34247162792 scopus 로고    scopus 로고
    • A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry
    • Mortimer S.A., Weeks K.M. A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry. J.Am. Chem. Soc. 2007, 129:4144-4145.
    • (2007) J.Am. Chem. Soc. , vol.129 , pp. 4144-4145
    • Mortimer, S.A.1    Weeks, K.M.2
  • 35
    • 84891776041 scopus 로고    scopus 로고
    • Changes in transcriptional pausing modify the folding dynamics of the pH-responsive RNA element
    • Nechooshtan G., Elgrably-Weiss M., Altuvia S. Changes in transcriptional pausing modify the folding dynamics of the pH-responsive RNA element. Nucleic Acids Res. 2014, 42:622-630.
    • (2014) Nucleic Acids Res. , vol.42 , pp. 622-630
    • Nechooshtan, G.1    Elgrably-Weiss, M.2    Altuvia, S.3
  • 36
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Academic Press, C. Carter, R. Sweet (Eds.)
    • Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods in Enzymology 1997, 307-326. Academic Press. C. Carter, R. Sweet (Eds.).
    • (1997) Methods in Enzymology , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 37
    • 4644366388 scopus 로고    scopus 로고
    • HKL2MAP: a graphical user interface for phasing with SHELX programs
    • Pape T., Schneider T.R. HKL2MAP: a graphical user interface for phasing with SHELX programs. J.Appl. Cryst. 2004, 37:843-844.
    • (2004) J.Appl. Cryst. , vol.37 , pp. 843-844
    • Pape, T.1    Schneider, T.R.2
  • 38
    • 84908063090 scopus 로고    scopus 로고
    • Themes and variations in riboswitch structure and function
    • Peselis A., Serganov A. Themes and variations in riboswitch structure and function. Biochim. Biophys. Acta 2014, 1839:908-918.
    • (2014) Biochim. Biophys. Acta , vol.1839 , pp. 908-918
    • Peselis, A.1    Serganov, A.2
  • 39
    • 84908077361 scopus 로고    scopus 로고
    • Common themes and differences inSAM recognition among SAM riboswitches
    • Price I.R., Grigg J.C., Ke A. Common themes and differences inSAM recognition among SAM riboswitches. Biochim. Biophys. Acta 2014, 1839:931-938.
    • (2014) Biochim. Biophys. Acta , vol.1839 , pp. 931-938
    • Price, I.R.1    Grigg, J.C.2    Ke, A.3
  • 40
    • 84861152754 scopus 로고    scopus 로고
    • Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function
    • Quarta G., Sin K., Schlick T. Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function. PLoS Comput. Biol. 2012, 8:e1002368.
    • (2012) PLoS Comput. Biol. , vol.8 , pp. e1002368
    • Quarta, G.1    Sin, K.2    Schlick, T.3
  • 41
    • 0033624818 scopus 로고    scopus 로고
    • Manganese homeostasis in Bacillus subtilis is regulated by MntR, a bifunctional regulator related to the diphtheria toxin repressor family of proteins
    • Que Q., Helmann J.D. Manganese homeostasis in Bacillus subtilis is regulated by MntR, a bifunctional regulator related to the diphtheria toxin repressor family of proteins. Mol. Microbiol. 2000, 35:1454-1468.
    • (2000) Mol. Microbiol. , vol.35 , pp. 1454-1468
    • Que, Q.1    Helmann, J.D.2
  • 42
    • 0034750146 scopus 로고    scopus 로고
    • Invivo effects ofsporulation kinases on mutant Spo0A proteins in Bacillus subtilis
    • Quisel J.D., Burkholder W.F., Grossman A.D. Invivo effects ofsporulation kinases on mutant Spo0A proteins in Bacillus subtilis. J.Bacteriol. 2001, 183:6573-6578.
    • (2001) J.Bacteriol. , vol.183 , pp. 6573-6578
    • Quisel, J.D.1    Burkholder, W.F.2    Grossman, A.D.3
  • 43
    • 84861920270 scopus 로고    scopus 로고
    • Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch
    • Ren A., Rajashankar K.R., Patel D.J. Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch. Nature 2012, 486:85-89.
    • (2012) Nature , vol.486 , pp. 85-89
    • Ren, A.1    Rajashankar, K.R.2    Patel, D.J.3
  • 44
    • 84864185753 scopus 로고    scopus 로고
    • Pseudoknot preorganization of the preQ1 class I riboswitch
    • Santner T., Rieder U., Kreutz C., Micura R. Pseudoknot preorganization of the preQ1 class I riboswitch. J.Am. Chem. Soc. 2012, 134:11928-11931.
    • (2012) J.Am. Chem. Soc. , vol.134 , pp. 11928-11931
    • Santner, T.1    Rieder, U.2    Kreutz, C.3    Micura, R.4
  • 45
    • 84872543206 scopus 로고    scopus 로고
    • A decade of riboswitches
    • Serganov A., Nudler E. A decade of riboswitches. Cell 2013, 152:17-24.
    • (2013) Cell , vol.152 , pp. 17-24
    • Serganov, A.1    Nudler, E.2
  • 46
    • 77950793231 scopus 로고    scopus 로고
    • Experimental phasing with SHELXC/D/E: combining chain tracing with density modification
    • Sheldrick G.M. Experimental phasing with SHELXC/D/E: combining chain tracing with density modification. Acta Crystallogr. D Biol. Crystallogr. 2010, 66:479-485.
    • (2010) Acta Crystallogr. D Biol. Crystallogr. , vol.66 , pp. 479-485
    • Sheldrick, G.M.1
  • 47
    • 77958143617 scopus 로고    scopus 로고
    • The battle for iron between bacterial pathogens and their vertebrate hosts
    • Skaar E.P. The battle for iron between bacterial pathogens and their vertebrate hosts. PLoS Pathog. 2010, 6:e1000949.
    • (2010) PLoS Pathog. , vol.6 , pp. e1000949
    • Skaar, E.P.1
  • 48
    • 24644492337 scopus 로고    scopus 로고
    • Structural evidence for a two-metal-ion mechanism of group I intron splicing
    • Stahley M.R., Strobel S.A. Structural evidence for a two-metal-ion mechanism of group I intron splicing. Science 2005, 309:1587-1590.
    • (2005) Science , vol.309 , pp. 1587-1590
    • Stahley, M.R.1    Strobel, S.A.2
  • 49
    • 41749109563 scopus 로고    scopus 로고
    • Crystal structure of a self-spliced group II intron
    • Toor N., Keating K.S., Taylor S.D., Pyle A.M. Crystal structure of a self-spliced group II intron. Science 2008, 320:77-82.
    • (2008) Science , vol.320 , pp. 77-82
    • Toor, N.1    Keating, K.S.2    Taylor, S.D.3    Pyle, A.M.4
  • 50
    • 80053457231 scopus 로고    scopus 로고
    • A novel metal transporter mediating manganese export (MntX) regulates the Mn to Fe intracellular ratio and Neisseria meningitidis virulence
    • Veyrier F.J.B., Boneca I.G., Cellier M.F., Taha M.K. A novel metal transporter mediating manganese export (MntX) regulates the Mn to Fe intracellular ratio and Neisseria meningitidis virulence. PLoS Pathog. 2011, 7:e1002261.
    • (2011) PLoS Pathog. , vol.7 , pp. e1002261
    • Veyrier, F.J.B.1    Boneca, I.G.2    Cellier, M.F.3    Taha, M.K.4
  • 51
    • 80055048346 scopus 로고    scopus 로고
    • The Escherichia coli MntR miniregulon includes genes encoding a small protein and an efflux pump required for manganese homeostasis
    • Waters L.S.S., Sandoval M., Storz G. The Escherichia coli MntR miniregulon includes genes encoding a small protein and an efflux pump required for manganese homeostasis. J.Bacteriol. 2011, 193:5887-5897.
    • (2011) J.Bacteriol. , vol.193 , pp. 5887-5897
    • Waters, L.S.S.1    Sandoval, M.2    Storz, G.3
  • 52
    • 77951606278 scopus 로고    scopus 로고
    • Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes
    • Weinberg Z., Wang J.X., Bogue J., Yang J., Corbino K., Moy R.H., Breaker R.R. Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol. 2010, 11:R31. 10.1186/gb-2010-11-3-r31.
    • (2010) Genome Biol. , vol.11 , pp. R31
    • Weinberg, Z.1    Wang, J.X.2    Bogue, J.3    Yang, J.4    Corbino, K.5    Moy, R.H.6    Breaker, R.R.7
  • 53
    • 33947720028 scopus 로고    scopus 로고
    • Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution
    • Wilkinson K.A., Merino E.J., Weeks K.M. Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat. Protoc. 2006, 1:1610-1616.
    • (2006) Nat. Protoc. , vol.1 , pp. 1610-1616
    • Wilkinson, K.A.1    Merino, E.J.2    Weeks, K.M.3
  • 54
    • 0037165996 scopus 로고    scopus 로고
    • Correlating structural dynamics and function in single ribozyme molecules
    • Zhuang X., Kim H., Pereira M.J., Babcock H.P., Walter N.G., Chu S. Correlating structural dynamics and function in single ribozyme molecules. Science 2002, 296:1473-1476.
    • (2002) Science , vol.296 , pp. 1473-1476
    • Zhuang, X.1    Kim, H.2    Pereira, M.J.3    Babcock, H.P.4    Walter, N.G.5    Chu, S.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.