New insights into the spliceosome by single molecule fluorescence microscopy

Current Opinion in Chemical Biology - Tập 15 - Trang 864-870 - 2011
Aaron A Hoskins1,2, Jeff Gelles3, Melissa J Moore1,2
1Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St., Worcester, MA 01605, USA
2Howard Hughes Medical Institute USA
3Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02453, USA

Tài liệu tham khảo

Fabrizio, 2009, The evolutionarily conserved core design of the catalytic activation step of the yeast spliceosome, Mol Cell, 36, 593, 10.1016/j.molcel.2009.09.040 Jurica, 2003, Pre-mRNA splicing: awash in a sea of proteins, Mol Cell, 12, 5, 10.1016/S1097-2765(03)00270-3 Smith, 2008, Nought may endure but mutability: spliceosome dynamics and the regulation of splicing, Mol Cell, 30, 657, 10.1016/j.molcel.2008.04.013 Horowitz, 2011, The splice is right: guarantors of fidelity in pre-mRNA splicing, RNA, 17, 551, 10.1261/rna.2577511 Wahl, 2009, The spliceosome: design principles of a dynamic RNP machine, Cell, 136, 701, 10.1016/j.cell.2009.02.009 Matlin, 2007, Spliceosome assembly and composition, Adv Exp Med Biol, 623, 14, 10.1007/978-0-387-77374-2_2 Warkocki, 2009, Reconstitution of both steps of Saccharomyces cerevisiae splicing with purified spliceosomal components, Nat Struct Mol Biol, 16, 1237, 10.1038/nsmb.1729 Bessonov, 2008, Isolation of an active step I spliceosome and composition of its RNP core, Nature, 452, 846, 10.1038/nature06842 Walter, 2008, Do-it-yourself guide: how to use the modern single-molecule toolkit, Nat Meth, 5, 475, 10.1038/nmeth.1215 Kapanidis, 2009, Biology, one molecule at a time, Trends Biochem Sci, 34, 234, 10.1016/j.tibs.2009.01.008 Crawford, 2008, Visualizing the splicing of single pre-mRNA molecules in whole cell extract, RNA, 14, 170, 10.1261/rna.794808 Abelson, 2010, Conformational dynamics of single pre-mRNA molecules during in vitro splicing, Nat Struct Mol Biol, 17, 504, 10.1038/nsmb.1767 Ishihama, 2005, Single molecule imaging of mRNA splicing, Nucl Acids Symp Series, 10.1093/nass/49.1.209 Abelson, 2010, Preparation of fluorescent pre-mRNA substrates for an smFRET study of pre-mRNA splicing in yeast, Meth Enzymol, 472, 31, 10.1016/S0076-6879(10)72017-6 Robertson, 2006, Fluorescent PNA probes as hybridization labels for biological RNA, Biochemistry, 45, 6066, 10.1021/bi052050s Konarska, 2006, Repositioning of the reaction intermediate within the catalytic center of the spliceosome, Mol Cell, 21, 543, 10.1016/j.molcel.2006.01.017 Liu, 2007, Opposing classes of prp8 alleles modulate the transition between the catalytic steps of pre-mRNA splicing, Nat Struct Mol Biol, 14, 519, 10.1038/nsmb1240 Query, 2004, Suppression of multiple substrate mutations by spliceosomal prp8 alleles suggests functional correlations with ribosomal ambiguity mutants, Mol Cell, 14, 343, 10.1016/S1097-2765(04)00217-5 Mayas, 2010, Spliceosome discards intermediates via the DEAH box ATPase Prp43p, Proc Natl Acad Sci USA, 107, 10020, 10.1073/pnas.0906022107 Koodathingal, 2010, The DEAH box ATPases Prp16 and Prp43 cooperate to proofread 5′ splice site cleavage during pre-mRNA splicing, Mol Cell, 39, 385, 10.1016/j.molcel.2010.07.014 Guo, 2009, Single-molecule analysis of protein-free U2-U6 snRNAs, Nat Struct Mol Biol, 16, 1154, 10.1038/nsmb.1672 Sashital, 2004, U2-U6 RNA folding reveals a group II intron-like domain and a four-helix junction, Nat Struct Mol Biol, 11, 1237, 10.1038/nsmb863 Sun, 1995, A novel U2-U6 snRNA structure is necessary for mammalian mRNA splicing, Genes Dev, 9, 843, 10.1101/gad.9.7.843 Madhani, 1992, A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome, Cell, 71, 803, 10.1016/0092-8674(92)90556-R Hilliker, 2004, Multiple functions for the invariant AGC triad of U6 snRNA, RNA, 10, 921, 10.1261/rna.7310704 Tardiff, 2006, Arrested yeast splicing complexes indicate stepwise snRNP recruitment during in vivo spliceosome assembly, RNA, 12, 968, 10.1261/rna.50506 Huranová, 2010, The differential interaction of snRNPs with pre-mRNA reveals splicing kinetics in living cells, J Cell Biol, 191, 75, 10.1083/jcb.201004030 Cheng, 1987, Spliceosome assembly in yeast, Genes Dev, 1, 1014, 10.1101/gad.1.9.1014 Stevens, 2002, Composition and functional characterization of the yeast spliceosomal penta-snRNP, Mol Cell, 9, 31, 10.1016/S1097-2765(02)00436-7 Hoskins, 2011, Ordered and dynamic assembly of single spliceosomes, Science, 331, 1289, 10.1126/science.1198830 Miller, 2005, In vivo protein labeling with trimethoprim conjugates: a flexible chemical tag, Nat Meth, 2, 255, 10.1038/nmeth749 Keppler, 2004, Labeling of fusion proteins with synthetic fluorophores in live cells, Proc Natl Acad Sci USA, 101, 9955, 10.1073/pnas.0401923101 Birdsall, 1980, Binding of coenzyme analogues to Lactobacillus casei dihydrofolate reductase: binary and ternary complexes, Biochemistry, 19, 3723, 10.1021/bi00557a013 Friedman, 2006, Viewing dynamic assembly of molecular complexes by multi-wavelength single-molecule fluorescence, Biophys J, 91, 1023, 10.1529/biophysj.106.084004 Seraphin, 1989, Identification of functional U1 snRNA-pre-mRNA complexes committed to spliceosome assembly and splicing, Cell, 59, 349, 10.1016/0092-8674(89)90296-1 Legrain, 1988, Early commitment of yeast pre-mRNA to the spliceosome pathway, Mol Cell Biol, 8, 3755, 10.1128/MCB.8.9.3755 Marshall, 2009, GTP hydrolysis by IF2 guides progression of the ribosome into elongation, Mol Cell, 35, 37, 10.1016/j.molcel.2009.06.008 Blosser, 2009, Dynamics of nucleosome remodelling by individual ACF complexes, Nature, 462, 1022, 10.1038/nature08627 Zhao, 2010, Laser-assisted single-molecule refolding (LASR), Biophys J, 99, 1925, 10.1016/j.bpj.2010.07.019 Wang, 2011, A microfluidic approach for investigating the temperature dependence of biomolecular activity with single-molecule resolution, Lab Chip, 11, 274, 10.1039/C0LC00157K Pleiss, 2007, Transcript specificity in yeast pre-mRNA splicing revealed by mutations in core spliceosomal components, PLoS Biol, 5, e90, 10.1371/journal.pbio.0050090 Matlin, 2005, Understanding alternative splicing: towards a cellular code, Nat Rev Mol Cell Biol, 6, 386, 10.1038/nrm1645 Cherny, 2010, Stoichiometry of a regulatory splicing complex revealed by single-molecule analyses, EMBO J, 29, 2161, 10.1038/emboj.2010.103 Lamichhane, 2010, RNA looping by PTB: evidence using FRET and NMR spectroscopy for a role in splicing repression, Proc Natl Acad Sci USA, 107, 4105, 10.1073/pnas.0907072107 Larson, 2011, Real-time observation of transcription initiation and elongation on an endogenous yeast gene, Science, 332, 475, 10.1126/science.1202142 Yu Y-T, Scharl EC, Smith CM, Steitz JA: The Growing World of Small Nuclear Ribonucleoproteins. In The RNA World, edn 2. Edited by Gesteland, R. et al., Cold Spring Harbor Laboratory Press 2000, pp. 487–524 Rino, 2007, A stochastic view of spliceosome assembly and recycling in the nucleus, PLoS Comput Biol, 3, 2019, 10.1371/journal.pcbi.0030201 Manley, 2008, High-density mapping of single-molecule trajectories with photoactivated localization microscopy, Nat Meth, 5, 155, 10.1038/nmeth.1176