메뉴 건너뛰기




Volumn 17, Issue 4, 2010, Pages 504-512

Conformational dynamics of single pre-mRNA molecules during in vitro splicing

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; MESSENGER RNA PRECURSOR; UBIQUITIN CONJUGATING ENZYME; UBIQUITIN CONJUGATING ENZYME 4; UNCLASSIFIED DRUG;

EID: 77950516144     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.1767     Document Type: Article
Times cited : (81)

References (39)
  • 1
    • 0042671357 scopus 로고    scopus 로고
    • Pre-mRNA splicing: Awash in a sea of proteins
    • Jurica, M.S. & Moore, M.J. Pre-mRNA splicing: awash in a sea of proteins. Mol. Cell 12, 5-14 (2003).
    • (2003) Mol. Cell , vol.12 , pp. 5-14
    • Jurica, M.S.1    Moore, M.J.2
  • 2
    • 60349104299 scopus 로고    scopus 로고
    • The spliceosome: Design principles of a dynamic RNP machine
    • Wahl, M.C., Will, C.L. & Luhrmann, R. The spliceosome: design principles of a dynamic RNP machine. Cell 136, 701-718 (2009).
    • (2009) Cell , vol.136 , pp. 701-718
    • Wahl, M.C.1    Will, C.L.2    Luhrmann, R.3
  • 3
    • 0032489021 scopus 로고    scopus 로고
    • Mechanical devices of the spliceosome: Motors, clocks, springs, and things
    • Staley, J.P. & Guthrie, C. Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell 92, 315-326 (1998).
    • (1998) Cell , vol.92 , pp. 315-326
    • Staley, J.P.1    Guthrie, C.2
  • 4
    • 0027287852 scopus 로고
    • A mechanism to enhance mRNA splicing fidelity: The RNA-dependent ATPase Prp16 governs usage of a discard pathway for aberrant lariat intermediates
    • DOI 10.1016/0092-8674(93)90363-U
    • Burgess, S.M. & Guthrie, C. A mechanism to enhance mRNA splicing fdelity: the RNA-dependent ATPase Prp16 governs usage of a discard pathway for aberrant lariat intermediates. Cell 73, 1377-1391 (1993). (Pubitemid 23201150)
    • (1993) Cell , vol.73 , Issue.7 , pp. 1377-1391
    • Burgess, S.M.1    Guthrie, C.2
  • 5
    • 0023370562 scopus 로고
    • A trans-acting suppressor restores splicing of a yeast intron with a branch point mutation
    • Couto, J.R., Tamm, J., Parker, R. & Guthrie, C. A trans-acting suppressor restores splicing of a yeast intron with a branch point mutation. Genes Dev. 1, 445-455 (1987).
    • (1987) Genes Dev. , vol.1 , pp. 445-455
    • Couto, J.R.1    Tamm, J.2    Parker, R.3    Guthrie, C.4
  • 6
    • 33744937919 scopus 로고    scopus 로고
    • Exon ligation is proofread by the DExD/H-box ATPase Prp22p
    • Mayas, R.M., Maita, H. & Staley, J.P. Exon ligation is proofread by the DExD/H-box ATPase Prp22p. Nat. Struct. Mol. Biol. 13, 482-490 (2006).
    • (2006) Nat. Struct. Mol. Biol. , vol.13 , pp. 482-490
    • Mayas, R.M.1    Maita, H.2    Staley, J.P.3
  • 7
    • 36749080450 scopus 로고    scopus 로고
    • Competition between the ATPase Prp5 and branch region-U2 snRNA pairing modulates the fdelity of spliceosome assembly
    • Xu, Y.Z. & Query, C.C. Competition between the ATPase Prp5 and branch region-U2 snRNA pairing modulates the fdelity of spliceosome assembly. Mol. Cell 28, 838-849 (2007).
    • (2007) Mol. Cell , vol.28 , pp. 838-849
    • Xu, Y.Z.1    Query, C.C.2
  • 8
    • 44449097780 scopus 로고    scopus 로고
    • Do-it-yourself guide: How to use the modern single-molecule toolkit
    • Walter, N.G., Huang, C.Y., Manzo, A.J. & Sobhy, M.A. Do-it-yourself guide: how to use the modern single-molecule toolkit. Nat. Methods 5, 475-489 (2008).
    • (2008) Nat. Methods , vol.5 , pp. 475-489
    • Walter, N.G.1    Huang, C.Y.2    Manzo, A.J.3    Sobhy, M.A.4
  • 9
    • 0029012941 scopus 로고
    • Purifcation of the spliceosome A-complex and its visualization by electron microscopy
    • Furman, E. & Glitz, D.G. Purifcation of the spliceosome A-complex and its visualization by electron microscopy. J. Biol. Chem. 270, 15515-15522 (1995).
    • (1995) J. Biol. Chem. , vol.270 , pp. 15515-15522
    • Furman, E.1    Glitz, D.G.2
  • 10
    • 0036242097 scopus 로고    scopus 로고
    • And characterization of native spliceosomes suitable for three-dimensional structural analysis
    • Jurica, M.S., Licklider, L.J., Gygi, S.R., Grigorieff, N. & Moore, M.J. Purifcation and characterization of native spliceosomes suitable for three-dimensional structural analysis. RNA 8, 426-439 (2002).
    • (2002) RNA , vol.8 , pp. 426-439
    • Jurica, M.S.1    Licklider, L.J.2    Gygi, S.R.3    Grigorieff, N.4    Purifcation, J.M.M.5
  • 11
    • 0036315512 scopus 로고    scopus 로고
    • Early organization of pre-mRNA during spliceosome assembly
    • Kent, O.A. & MacMillan, A.M. Early organization of pre-mRNA during spliceosome assembly. Nat. Struct. Biol. 9, 576-581 (2002).
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 576-581
    • Kent, O.A.1    MacMillan, A.M.2
  • 12
    • 0029400769 scopus 로고
    • SnRNA interactions at 5′ and 3′ splice sites monitored by photoactivated crosslinking in yeast spliceosomes
    • Newman, A.J., Teigelkamp, S. & Beggs, J.D. snRNA interactions at 5′ and 3′ splice sites monitored by photoactivated crosslinking in yeast spliceosomes. RNA 1, 968-980 (1995).
    • (1995) RNA , vol.1 , pp. 968-980
    • Newman, A.J.1    Teigelkamp, S.2    Beggs., J.D.3
  • 14
    • 0024710729 scopus 로고
    • Isolation and characterization of pre-mRNA splicing mutants of Saccharomyces cerevisiae
    • Vijayraghavan, U., Company, M. & Abelson, J. Isolation and characterization of pre-mRNA splicing mutants of Saccharomyces cerevisiae. Genes Dev. 3, 1206-1216 (1989).
    • (1989) Genes Dev. , vol.3 , pp. 1206-1216
    • Vijayraghavan, U.1    Company, M.2    Abelson, J.3
  • 15
    • 0037012922 scopus 로고    scopus 로고
    • Genomewide analysis of mRNA processing in yeast using splicing-specifc microarrays
    • Clark, T.A., Sugnet, C.W. & Ares, M. Jr. Genomewide analysis of mRNA processing in yeast using splicing-specifc microarrays. Science 296, 907-910 (2002).
    • (2002) Science , vol.296 , pp. 907-910
    • Clark, T.A.1    Sugnet, C.W.2    Ares, M.3
  • 16
    • 34247255773 scopus 로고    scopus 로고
    • Transcript specifcity in yeast pre-mRNA splicing revealed by mutations in core spliceosomal components
    • Pleiss, J.A., Whitworth, G.B., Bergkessel, M. & Guthrie, C. Transcript specifcity in yeast pre-mRNA splicing revealed by mutations in core spliceosomal components. PLoS Biol. 5, e90 (2007).
    • (2007) PLoS Biol. , vol.5
    • Pleiss, J.A.1    Whitworth, G.B.2    Bergkessel, M.3    Guthrie, C.4
  • 17
    • 0022747370 scopus 로고
    • Mutations in conserved intron sequences affect multiple steps in the yeast splicing pathway, particularly assembly of the spliceosome
    • Vijayraghavan, U. et al. Mutations in conserved intron sequences affect multiple steps in the yeast splicing pathway, particularly assembly of the spliceosome. EMBO J. 5, 1683-1695 (1986).
    • (1986) EMBO J. , vol.5 , pp. 1683-1695
    • Vijayraghavan, U.1
  • 18
    • 3042709638 scopus 로고    scopus 로고
    • Single-molecule enzymology of RNA: Essential functional groups impact catalysis from a distance
    • Rueda, D. et al. Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance. Proc. Natl. Acad. Sci. USA 101, 10066-10071 (2004).
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 10066-10071
    • Rueda, D.1
  • 19
    • 58149083620 scopus 로고    scopus 로고
    • A rugged free energy landscape separates multiple functional RNA folds throughout denaturation
    • Ditzler, M.A., Rueda, D., Mo, J., Hakansson, K. & Walter, N.G. A rugged free energy landscape separates multiple functional RNA folds throughout denaturation. Nucleic Acids Res. 36, 7088-7099 (2008).
    • (2008) Nucleic Acids Res. , vol.36 , pp. 7088-7099
    • Ditzler, M.A.1    Rueda, D.2    Mo, J.3    Hakansson, K.4    Walter, N.G.5
  • 20
    • 50049086369 scopus 로고    scopus 로고
    • Single vs. ribozyme molecules reveal dynamic and hierarchical folding toward catalysis
    • Pereira, M.J. et al. Single vs. ribozyme molecules reveal dynamic and hierarchical folding toward catalysis. J. Mol. Biol. 382, 496-509 (2008).
    • (2008) J. Mol. Biol. , vol.382 , pp. 496-509
    • Pereira, M.J.1
  • 21
    • 58149085388 scopus 로고    scopus 로고
    • Leakage and slow allostery limit performance of single drug-sensing aptazyme molecules based on the hammerhead ribozyme
    • de Silva, C. & Walter, N.G. Leakage and slow allostery limit performance of single drug-sensing aptazyme molecules based on the hammerhead ribozyme. RNA 15, 76-84 (2009).
    • (2009) RNA , vol.15 , pp. 76-84
    • De Silva, C.1    Walter, N.G.2
  • 22
    • 0027488624 scopus 로고
    • Isolation of new ribozymes from a large pool of random sequences
    • Bartel, D.P. & Szostak, J.W. Isolation of new ribozymes from a large pool of random sequences. Science 261, 1411-1418 (1993).
    • (1993) Science , vol.261 , pp. 1411-1418
    • Bartel, D.P.1    Szostak, J.W.2
  • 23
    • 33847051154 scopus 로고    scopus 로고
    • Identifcation of two distinct hybrid state intermediates on the ribosome
    • Munro, J.B., Altman, R.B., O'Connor, N. & Blanchard, S.C. Identifcation of two distinct hybrid state intermediates on the ribosome. Mol. Cell 25, 505-517 (2007).
    • (2007) Mol. Cell , vol.25 , pp. 505-517
    • Munro, J.B.1    Altman, R.B.2    O'Connor, N.3    Blanchard, S.C.4
  • 24
    • 33746747438 scopus 로고    scopus 로고
    • Analysis of single-molecule FRET trajectories using hidden Markov modeling
    • McKinney, S.A., Joo, C. & Ha, T. Analysis of single-molecule FRET trajectories using hidden Markov modeling. Biophys. J. 91, 1941-1951 (2006).
    • (2006) Biophys. J. , vol.91 , pp. 1941-1951
    • McKinney, S.A.1    Joo, C.2    Ha, T.3
  • 25
    • 44949117567 scopus 로고    scopus 로고
    • A conformational rearrangement in the spliceosome sets the stage for Prp22-dependent mRNA release
    • Schwer, B. A conformational rearrangement in the spliceosome sets the stage for Prp22-dependent mRNA release. Mol. Cell 30, 743-754 (2008).
    • (2008) Mol. Cell , vol.30 , pp. 743-754
    • Schwer, B.1
  • 26
    • 38049077956 scopus 로고    scopus 로고
    • Visualizing the splicing of single pre-mRNA molecules in whole cell extract
    • Crawford, D.J., Hoskins, A.A., Friedman, L.J., Gelles, J. & Moore, M.J. Visualizing the splicing of single pre-mRNA molecules in whole cell extract. RNA 14, 170-179 (2008).
    • (2008) RNA , vol.14 , pp. 170-179
    • Crawford, D.J.1    Hoskins, A.A.2    Friedman, L.J.3    Gelles, J.4    Moore, M.J.5
  • 27
    • 0142215475 scopus 로고    scopus 로고
    • Global analysis of protein expression in yeast
    • Ghaemmaghami, S. et al. Global analysis of protein expression in yeast. Nature 425, 737-741 (2003).
    • (2003) Nature , vol.425 , pp. 737-741
    • Ghaemmaghami, S.1
  • 28
    • 0024325159 scopus 로고
    • Identifcation of functional U1 snRNA-pre-mRNA complexes committed to spliceosome assembly and splicing
    • Seraphin, B. & Rosbash, M. Identifcation of functional U1 snRNA-pre-mRNA complexes committed to spliceosome assembly and splicing. Cell 59, 349-358 (1989).
    • (1989) Cell , vol.59 , pp. 349-358
    • Seraphin, B.1    Rosbash, M.2
  • 29
    • 0036158942 scopus 로고    scopus 로고
    • Composition and functional characterization of the yeast spliceosomal penta-snRNP
    • Stevens, S.W. et al. Composition and functional characterization of the yeast spliceosomal penta-snRNP. Mol. Cell 9, 31-44 (2002).
    • (2002) Mol. Cell , vol.9 , pp. 31-44
    • Stevens, S.W.1
  • 30
    • 0033634673 scopus 로고    scopus 로고
    • Functional recognition of 5′ splice site by U4/U6.U5 tri-snRNP defnes a novel ATP-dependent step in early spliceosome assembly
    • Maroney, P.A., Romfo, C.M. & Nilsen, T.W. Functional recognition of 5′ splice site by U4/U6.U5 tri-snRNP defnes a novel ATP-dependent step in early spliceosome assembly. Mol. Cell 6, 317-328 (2000).
    • (2000) Mol. Cell , vol.6 , pp. 317-328
    • Maroney, P.A.1    Romfo, C.M.2    Nilsen, T.W.3
  • 31
    • 52949135935 scopus 로고    scopus 로고
    • Mechanistic insights from reversible splicing catalysis
    • Smith, D.J. & Konarska, M.M. Mechanistic insights from reversible splicing catalysis. RNA 14, 1975-1978 (2008).
    • (2008) RNA , vol.14 , pp. 1975-1978
    • Smith, D.J.1    Konarska, M.M.2
  • 32
    • 46449086933 scopus 로고    scopus 로고
    • Both catalytic steps of nuclear pre-mRNA splicing are reversible
    • Tseng, C.K. & Cheng, S.C. Both catalytic steps of nuclear pre-mRNA splicing are reversible. Science 320, 1782-1784 (2008).
    • (2008) Science , vol.320 , pp. 1782-1784
    • Tseng, C.K.1    Cheng, S.C.2
  • 33
    • 44449125068 scopus 로고    scopus 로고
    • Spontaneous intersubunit rotation in single ribosomes
    • Cornish, P.V., Ermolenko, D.N., Noller, H.F. & Ha, T. Spontaneous intersubunit rotation in single ribosomes. Mol. Cell 30, 578-588 (2008).
    • (2008) Mol. Cell , vol.30 , pp. 578-588
    • Cornish, P.V.1    Ermolenko, D.N.2    Noller, H.F.3    Ha, T.4
  • 34
    • 33751118289 scopus 로고    scopus 로고
    • An RNA ligase-mediated method for the effcient creation of large, synthetic RNAs
    • Stark, M.R., Pleiss, J.A., Deras, M., Scaringe, S.A. & Rader, S.D. An RNA ligase-mediated method for the effcient creation of large, synthetic RNAs. RNA 12, 2014-2019 (2006).
    • (2006) RNA , vol.12 , pp. 2014-2019
    • Stark, M.R.1    Pleiss, J.A.2    Deras, M.3    Scaringe, S.A.4    Rader, S.D.5
  • 35
    • 0036270848 scopus 로고    scopus 로고
    • Yeast pre-mRNA splicing: Methods, mechanisms, and machinery
    • Stevens, S.W. & Abelson, J. Yeast pre-mRNA splicing: methods, mechanisms, and machinery. Methods Enzymol. 351, 200-220 (2002).
    • (2002) Methods Enzymol. , vol.351 , pp. 200-220
    • Stevens, S.W.1    Abelson, J.2
  • 36
    • 0037057630 scopus 로고    scopus 로고
    • Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase
    • Ha, T. et al. Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase. Nature 419, 638-641 (2002).
    • (2002) Nature , vol.419 , pp. 638-641
    • Ha, T.1
  • 37
    • 0041821716 scopus 로고    scopus 로고
    • Single-molecule kinetics of lambda exonuclease reveal base dependence and dynamic disorder
    • van Oijen, A.M. et al. Single-molecule kinetics of lambda exonuclease reveal base dependence and dynamic disorder. Science 301, 1235-1238 (2003).
    • (2003) Science , vol.301 , pp. 1235-1238
    • Van Oijen, A.M.1
  • 38
    • 0037165996 scopus 로고    scopus 로고
    • Correlating structural dynamics and function in single ribozyme molecules
    • Zhuang, X. et al. Correlating structural dynamics and function in single ribozyme molecules. Science 296, 1473-1476 (2002).
    • (2002) Science , vol.296 , pp. 1473-1476
    • Zhuang, X.1
  • 39
    • 33750295496 scopus 로고    scopus 로고
    • Nonblinking and long-lasting single-molecule fuorescence imaging
    • Rasnik, I., McKinney, S.A. & Ha, T. Nonblinking and long-lasting single-molecule fuorescence imaging. Nat. Methods 3, 891-893 (2006).
    • (2006) Nat. Methods , vol.3 , pp. 891-893
    • Rasnik, I.1    McKinney, S.A.2    Ha, T.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.