RNA induces conformational changes in the SF1/U2AF65 splicing factor complex

Journal of Molecular Biology

Volumn 405, Issue 5, 2011, Pages 1128-1138

  Gupta, Ankit ^a   Jenkins, Jermaine L ^a   Kielkopf, Clara L ^a  

^a UNIVERSITY OF ROCHESTER SCHOOL OF MEDICINE AND DENTISTRY   (United States)

Author keywords

pre mRNA splicing; protein RNA interactions; small angle X ray scattering; splicing factor 1; U2 snRNP auxiliary factor

Indexed keywords

GLUTATHIONE TRANSFERASE; LIGAND; RNA; RNA BINDING PROTEIN; RNA SPLICING FACTOR 1; U2 AUXILIARY FACTOR 65; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; ADENOVIRUS; AMINO TERMINAL SEQUENCE; ANISOTROPY; ARTICLE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; PROTEIN STRUCTURE; RNA SPLICING; X RAY CRYSTALLOGRAPHY;

ADENOVIRIDAE;

EID: 78751578931     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2010.11.054     Document Type: Article

References (53)

1. Wang E.T., Sandberg R., Luo S., Khrebtukova I., Zhang L., and Mayr C. Alternative isoform regulation in human tissue transcriptomes Nature 456 2008 470 476
2. Garcia-Blanco M.A., Baraniak A.P., and Lasda E.L. Alternative splicing in disease and therapy Nat. Biotechnol. 22 2004 535 546
3. Golling G., Amsterdam A., Sun Z., Antonelli M., Maldonado E., and Chen W. Insertional mutagenesis in zebrafish rapidly identifies genes essential for early vertebrate development Nat. Genet. 31 2002 135 140
4. Zuccato E., Buratti E., Stuani C., Baralle F.E., and Pagani F. An intronic polypyrimidine-rich element downstream of the donor site modulates cystic fibrosis transmembrane conductance regulator exon 9 alternative splicing J. Biol. Chem. 279 2004 16980 16988
5. Tiscornia G., and Mahadevan M.S. Myotonic dystrophy: the role of the CUG triplet repeats in splicing of a novel DMPK exon and altered cytoplasmic DMPK mRNA isoform ratios Mol. Cell 5 2000 959 967
6. 65 in an isoform-dependent manner and can be incorporated into spliceosomes Genes Dev. 12 1998 3217 3225
7. Maeda T., and Furukawa S. Transformation-associated changes in gene expression of alternative splicing regulatory factors in mouse fibroblast cells Oncol. Rep. 8 2001 563 566
8. Tanackovic G., and Kramer A. Human splicing factor SF3a, but not SF1, is essential for pre-mRNA splicing in vivo Mol. Biol. Cell 16 2005 1366 1377
9. +/- mice to azoxymethane-induced colon tumorigenesis Cancer Sci. 98 2007 1862 1867
10. Shitashige M., Naishiro Y., Idogawa M., Honda K., Ono M., Hirohashi S., and Yamada T. Involvement of splicing factor-1 in β-catenin/T-cell factor-4-mediated gene transactivation and pre-mRNA splicing Gastroenterology 132 2007 1039 1054
11. Cattaruzza M., Schafer K., and Hecker M. Cytokine-induced down-regulation of zfm1/splicing factor-1 promotes smooth muscle cell proliferation J. Biol. Chem. 277 2002 6582 6589
12. 65 J. Biol. Chem. 2008
13. Berglund J.A., Chua K., Abovich N., Reed R., and Rosbash M. The splicing factor BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC Cell 89 1997 781 787
14. 65 and mBBP/SF1 facilitates branchpoint region recognition Genes Dev. 12 1998 858 867
15. Zamore P.D., Patton J.G., and Green M.R. Cloning and domain structure of the mammalian splicing factor U2AF Nature 355 1992 609 614
16. Wahl M.C., Will C.L., and Luhrmann R. The spliceosome: design principles of a dynamic RNP machine Cell 136 2009 701 718
17. Kielkopf C.L., Lucke S., and Green M.R. U2AF homology motifs: protein recognition in the RRM world Genes Dev. 18 2004 1513 1526
18. Rain J.C., Rafi Z., Rhani Z., Legrain P., and Kramer A. Conservation of functional domains involved in RNA binding and protein-protein interactions in human and Saccharomyces cerevisiae pre-mRNA splicing factor SF1 RNA 4 1998 551 565
19. 65 and SF1/mBBP Mol. Cell 11 2003 965 976
20. Rudner D.Z., Kanaar R., Breger K.S., and Rio D.C. Interaction between subunits of heterodimeric splicing factor U2AF is essential in vivo Mol. Cell. Biol. 18 1998 1765 1773
21. Zorio D.A., and Blumenthal T. Both subunits of U2AF recognize the 3′ splice site in Caenorhabditis elegans Nature 402 1999 835 838
22. 35 Nature 402 1999 832 835
23. 35 and the 3′ splice site AG Nature 402 1999 838 841
24. 65 RS region with pre-mRNA branch point and promotion of base pairing with U2 snRNA Science 273 1996 1706 1709
25. Liu Z., Luyten I., Bottomley M.J., Messias A.C., Houngninou-Molango S., and Sprangers R. Structural basis for recognition of the intron branch site RNA by splicing factor 1 Science 294 2001 1098 1102
26. 65 FEBS J. 273 2006 577 587
27. 65 Mol. Cell 23 2006 49 59
28. 65 heterodimer Cell 106 2001 595 605
29. Michaud S., and Reed R. A functional association between the 5′ and 3′ splice site is established in the earliest prespliceosome complex (E) in mammals Genes Dev. 7 1993 1008 1020
30. Barabino S.M., Blencowe B.J., Ryder U., Sproat B.S., and Lamond A.I. Targeted snRNP depletion reveals an additional role for mammalian U1 snRNP in spliceosome assembly Cell 63 1990 293 302
31. Kent O.A., and MacMillan A.M. Early organization of pre-mRNA during spliceosome assembly Nat. Struct. Biol. 9 2002 576 581
32. 65 J. Biol. Chem. 278 2003 50572 50577
33. Lee C.G., Zamore P.D., Green M.R., and Hurwitz J. RNA annealing activity is intrinsically associated with U2AF J. Biol. Chem. 268 1993 13472 13478
34. Shen H., and Green M.R. A pathway of sequential arginine-serine-rich domain-splicing signal interactions during mammalian spliceosome assembly Mol. Cell 16 2004 363 373
35. Putnam C.D., Hammel M., Hura G.L., and Tainer J.A. X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution Q. Rev. Biophys. 40 2007 191 285
36. Vachette P., Koch M.H., and Svergun D.I. Looking behind the beamstop: X-ray solution scattering studies of structure and conformational changes of biological macromolecules Methods Enzymol. 374 2003 584 615
37. Yue B.G., Ajuh P., Akusjarvi G., Lamond A.I., and Kreivi J.P. Functional coexpression of serine protein kinase SRPK1 and its substrate ASF/SF2 in Escherichia coli Nucleic Acids Res. 28 2000 E14
38. Caceres J.F., and Krainer A.R. Functional analysis of pre-mRNA splicing factor SF2/ASF structural domains EMBO J. 12 1993 4715 4726
39. Arning S., Gruter P., Bilbe G., and Kramer A. Mammalian splicing factor SF1 is encoded by variant cDNAs and binds to RNA RNA 2 1996 794 810
40. 65 binding sites within SF3b155: thermodynamic and spectroscopic characterization of protein-protein interactions among pre-mRNA splicing factors J. Mol. Biol. 356 2006 664 683
41. Guinier A., and Fournet G. Small-Angle Scattering of X-rays 1955 Wiley Interscience New York
42. Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D., and Bairoch A. Protein identification and analysis tools on the ExPASy server J.M. Walker, The Proteomics Protocols Handbook 2005 Humana Press Totowa, NJ 571 607
43. Svergun D.I. Determination of regularization parameters in indirect-transform methods using perceptual criteria J. Appl. Crystallogr. 25 1992 495 503
44. Mertens H.D., and Svergun D.I. Structural characterization of proteins and complexes using small-angle X-ray solution scattering J. Struct. Biol. 172 2010 128 141
45. Feigin L.A., and Svergun D.I. Structure Analysis by Small-Angle X-Ray and Neutron Scattering 1987 Springer New York.
46. Svergun D.I. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing Biophys. J. 76 1999 2879 2886
47. Svergun D.I., Petoukhov M.V., and Koch M.H. Determination of domain structure of proteins from X-ray solution scattering Biophys. J. 80 2001 2946 2953
48. Kozin M.B., and Svergun D.I. Automated matching of high and low resolution structural models J. Appl. Crystallogr. 34 2001 33 41
49. Volkov V., and Svergun D.I. Uniqueness of ab initio shape determination in small angle scattering J. Appl. Crystallogr. 36 2003 860 864
50. Petoukhov M.V., and Svergun D.I. Global rigid body modeling of macromolecular complexes against small-angle scattering data Biophys. J. 89 2005 1237 1250
51. 65) recognize polypyrimidine tracts using multiple modes of binding RNA 9 2003 88 99
52. Abovich N., and Rosbash M. Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals Cell 89 1997 403 412
53. Bernado P., Perez Y., Blobel J., Fernandez-Recio J., Svergun D.I., and Pons M. Structural characterization of unphosphorylated STAT5a oligomerization equilibrium in solution by small-angle X-ray scattering Protein Sci. 18 2009 716 726