Structure-function analysis and genetic interactions of the yeast branchpoint binding protein Msl5

Nucleic Acids Research

Volumn 40, Issue 10, 2012, Pages 4539-4552

  Chang, Jonathan ^a   Schwer, Beate ^b   Shuman, Stewart ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b WEILL CORNELL MEDICAL COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; FUNGAL ENZYME; FUNGAL PROTEIN; POLYPEPTIDE; PROTEIN MSL5; PROTEIN MUD2; PROTEIN NAM8; PROTEIN PRP40; PROTEIN TGS1; SMALL NUCLEAR RIBONUCLEOPROTEIN; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; FUNGUS GROWTH; GENE INTERACTION; GENE MAPPING; GENE MUTATION; IN VIVO STUDY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROLINE RICH PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; RNA SPLICING; SACCHAROMYCES CEREVISIAE; STRUCTURE ACTIVITY RELATION;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; GUANOSINE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; PROTEIN STRUCTURE, TERTIARY; RIBONUCLEOPROTEIN, U1 SMALL NUCLEAR; RIBONUCLEOPROTEINS; RIBONUCLEOPROTEINS, SMALL NUCLEAR; RNA-BINDING PROTEINS; SACCHAROMYCES CEREVISIAE PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP;

SACCHAROMYCES CEREVISIAE;

EID: 84861563099     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks049     Document Type: Article

References (38)

1. Nilsen, T.W. and Graveley, B.R. (2010) Expansion of the eukaryotic proteome by alternative splicing. Nature, 463, 457-463.
2. Tazi, J., Bakkour, N. and Stamm, S. (2009) Alternative splicing and disease. Biochim. Biophys. Acta, 1792, 14-26.
3. Fabrizio, P., Dannenberg, J., Dube, P., Kastner, B., Stark, H., Urlaub, H. and Lührmann, R. (2009) The evolutionarily conserved core design of the catalytic activation step of the yeast spliceosome. Mol. Cell, 36, 593-608.
4. Warkocki, Z., Odenwälder, P., Schmitzovä, J., Platzmann, F., Stark, H., Urlaub, H., Ficner, R., Fabrizio, P. and Lührmann, R. (2009) Reconstitution of both steps of Saccharomyces cerevisiae splicing with purified spliceosomal components. Nat. Struct. Mol. Biol., 16, 1237-1243.
5. Hoskins, A.A., Friedman, L.J., Gallagher, S.S., Crawford, D.J., Anderson, E.G., Wombacher, R., Ramirez, N., Cornish, V.W., Gelles, J. and Moore, M.J. (2011) Ordered and dynamic assembly of single spliceosomes. Science, 331, 1289-1295.
6. Tang, J., Abovich, N. and Rosbash, M. (1996) Identification and characterization of a yeast gene encoding the U2 small nuclear ribonucleoprotein particle B" protein. Mol. Cell. Biol., 16, 2787-2795.
7. Fortes, P., Kufel, J., Fornerod, M., Polycarpou-Schwarz, M., Lafontaine, D., Tollervey, D. and Mattaj, I.W. (1999) Genetic and physical interactions involving the yeast nuclear cap-binding complex. Mol. Cell. Biol., 19, 6543-6553.
8. Tong, A.H., Evangelista, M., Parsons, A.B., Xu, H., Bader, G.D., PageN., Robinson, M., Raghibizadeh, S., Hogue, C.W., Bussey, H. et al. (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science, 294, 2364-2368.
9. Wilmes, G.M., Bergkessel, M., Bandyopadhyay, S., Shales, M., Braberg, H., Cagney, G., Collins, S.R., Whitworth, G.B., Kress, T.L., Weissman, J.S. et al. (2008) A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Mol. Cell, 32, 735-746.
10. Hausmann, S., Zheng, S., Costanzo, M., Brost, R.L., Garcin, D., Boone, C., Shuman, S. and Schwer, B. (2008) Genetic and biochemical analysis of yeast and human cap trimethylguanosine synthase: functional overlap of TMG caps, snRNP components, pre-mRNA splicing factors, and RNA decay pathways. J. Biol. Chem., 283, 31706-31718.
11. Khanna, M., Van Bakel, H., Tang, X., Calarco, J.A., Babak, T., Guo, G., Emili, A., Greenblatt, J.F., Hughes, T.R., Krogan, N.J. et al. (2009) A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300. RNA, 15, 2174-2185.
12. Costanzo, M., Baryshnikova, A., Bellay, J., Kim, Y., Spear, E.D., Sevier, C.S., Ding, H., Koh, J.L., Toufighi, K., Mostafavi, S. et al. (2010) The genetic landscape of a cell. Science, 327, 425-431.
13. Mouaikel, J., Verheggen, C., Bertrand, E., Tazi, J. and BordonneR. (2002) Hypermethylation of the cap structure of both yeast snRNAs and snoRNAs requires a conserved methyltransferase that is localized to the nucleolus. Mol. Cell, 9, 891-901.
14. Hausmann, S. and Shuman, S. (2005) Specificity and mechanism of RNA cap guanine-N2 methyltransferase (Tgs1). J. Biol. Chem., 280, 4021-4024.
15. Benarroch, D., Jankowska-Anyszka, M., Stepinski, J., Darzynkiewicz, E. and Shuman, S. (2010) Cap analog substrates reveal three clades of cap guanine-N2 methyltransferases with distinct methyl acceptor specificities. RNA, 16, 211-220.
16. Chang, J., Schwer, B. and Shuman, S. (2010) Mutational analyses of trimethylguanosine synthase (Tgs1) and Mud2: proteins implicated in pre-mRNA splicing. RNA, 16, 1018-1031.
17. Hausmann, S., Ramirez, A., Schneider, S., Schwer, B. and Shuman, S. (2007) Biochemical and genetic analysis of RNA cap guanine-N2 methyltransferases from Giardia lamblia and Schizosaccharomyces pombe. Nucleic Acids Res., 35, 1411-1420.
18. Schwer, B., Erdjument-Bromage, H. and Shuman, S. (2011) Composition of yeast snRNPs and snoRNPs in the absence of trimethylguanosine caps reveals nuclear cap binding protein as a gained U1 component implicated in the cold-sensitivity of tgs1-cells. Nucleic Acids Res., 39, 6715-6728.
19. Abovich, N., Liao, X.C. and Rosbash, M. (1994) The yeast MUD2 protein: an interaction with PRP11 defines a bridge between commitment complexes and U2 snRNP addition. Genes Dev., 8, 843-854.
20. Wang, Q., Zhang, L., Lynn, B. and Rymond, B.C. (2008) A BBP-Mud2p heterodimer mediates branchpoint recognition and influences splicing substrate abundance in budding yeast. Nucleic Acids Res., 36, 2787-2798.
21. Abovich, N. and Rosbash, M. (1997) Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals. Cell, 89, 403-412.
22. Rain, J.C., Rafi, Z., Legrain, P. and Krämer, A. (1998) Conservation of functional domains involved in RNA binding and protein-protein interactions in human and Saccharomyces cerevisiae pre-mRNA splicing factor SF1. RNA, 4, 551-565.
23. Rutz, B. and Seraphin, B. (1999) Transient interaction of BBP/ScSF1 and Mud2 with the splicing machinery affects the kinetics of spliceosome assembly. RNA, 5, 819-831.
24. Qiu, Z.R., Schwer, B. and Shuman, S. (2011) Determinants of Nam8-dependent splicing of meiotic pre-mRNAs. Nucleic Acids Res., 39, 3427-3445.
25. Garrey, S.M., Voelker, R. and Berglund, J.A. (2006) An extended RNA binding site for the yeast branch point-binding protein and the role of its zinc knuckle domains in RNA binding. J. Biol. Chem., 281, 27443-27453.
26. Garrey, S.M., Cass, D.M., Wandler, A.M., Scanlan, M.S. and Berglund, J.A. (2008) Transposition of two amino acids changes a promiscuous RNA binding protein into a sequence-specific RNA binding protein. RNA, 14, 78-88.
27. Wiesner, S., Stier, G., Sattler, M. and Macias, M.J. (2002) Solution structure and ligand recognition of the WW domain pair of the yeast splicing factor Prp40. J. Mol. Biol., 324, 807-822.
28. Rigaut, G., Shevchenko, A., Rutz, B., Wilm, M., Mann, M. and Seaphin, B. (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol., 17, 1030-1032.
29. Berglund, J.A., Abovich, N. and Rosbash, M. (1998) A cooperative interaction between U2AF65 and mBBP/SF1 facilitates branchpoint region recognition. Genes Dev., 12, 858-867.
30. Selenko, P., Gregorovic, G., Sprangers, R., Stier, G., Rhani, Z., Krämer, A. and Sattler, M. (2003) Structural basis for the molecular recognition between human splicing factors U2AF65 and SF1/mBBP. Mol. Cell, 11, 965-976.
31. Kielkopf, C.L., Lücke, S. and Green, M.R. (2004) U2AF homology motifs: protein recognition in the RRM world. Genes Dev., 18, 1513-1526.
32. Sickmier, E.A., Frato, K.E., Shen, H., Paranawithana, S.R., Green, M.R. and Kielkopf, C.L. (2006) Structural basis for polypyrimidine tract recognition by the essential pre-mRNA splicing factor U2AF65. Mol. Cell, 23, 49-59.
33. Ash, M.R., Faelber, K., Kosslick, D., Albert, G.I., Roske, Y., Kofler, M., Schuemann, M., Krause, E. and Freund, C. (2010) Conserved b-hairpin recognition by the GYF domains of Smy2 and GIGYF2 in mRNA surveillance and vesicular transport complexes. Structure, 18, 944-954.
34. Rymond, B.C. (2010) The branchpoint binding protein: in and out of the spliceosome cycle. Adv. Exp. Med. Biol., 693, 123-141.
35. Liu, Z., Luyten, I., Bottomley, M.J., Messias, A.C., Houngninou-Molango, S., Sprangers, R., Zanier, K., Krämer, A. and Sattler, M. (2001) Structural basis for recognition of the intron branch site RNA by splicing factor 1. Science, 294, 1098-1102.
36. Görnemann, J., Barrandon, C., Hujer, K., Rutz, B., Rigaut, G., Kotovic, K.M., Faux, C., Neugebauer, K.M. and Seaphin, B. (2011) Cotranscriptional spliceosome assembly and splicing are independent of the Prp40p WW domain. RNA, 17, 2119-2129.
37. Rutz, B. and Seaphin, B. (2000) A dual role for BBP/ScSF1 in nuclear pre-mRNA retention and splicing. EMBO J., 19, 1873-1886.
38. Balzer, R.J. and Henry, M.F. (2008) Snu56p is required for Mer1p-activated meiotic splicing. Mol. Cell. Biol., 28, 2497-2508.