782
Views
17
CrossRef citations to date
0
Altmetric
Research Paper

Multiple RNA binding domains of Bruno confer recognition of diverse binding sites for translational repression

Pages 1047-1060 | Received 23 May 2011, Accepted 04 Jul 2011, Published online: 01 Nov 2011

References

  • Dreyfuss G, Kim VN, Kataoka N. Messenger-RNA-binding proteins and the messages they carry. Nat Rev Mol Cell Biol 2002; 3:195 - 205
  • Singh R, Valcárcel J, Green MR. Distinct binding specificities and functions of higher eukaryotic polypyrimidine tract-binding proteins. Science 1995; 268:1173 - 1176
  • Pérez I, Lin CH, McAfee JG, Patton JG. Mutation of PTB binding sites causes misregulation of alternative 3′ splice site selection in vivo. RNA 1997; 3:764 - 778
  • Blanchette M, Green RE, MacArthur S, Brooks AN, Brenner SE, Eisen MB, Rio DC. Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members. Mol Cell 2009; 33:438 - 449
  • Chen Y, Varani G. Protein families and RNA recognition. FEBS J 2005; 272:2088 - 2097
  • Lunde BM, Moore C, Varani G. RNA-binding proteins: modular design for efficient function. Nat Rev Mol Cell Biol 2007; 8:479 - 490
  • Varani G, Nagai K. RNA recognition by RNP proteins during RNA processing. Annu Rev Biophys Biomol Struct 1998; 27:407 - 445
  • Maris C, Dominguez C, Allain FH. The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression. FEBS J 2005; 272:2118 - 2131
  • Cléry A, Blatter M, Allain FH. RNA recognition motifs: boring? Not quite. Curr Opin Struct Biol 2008; 18:290 - 298
  • Handa N, Nureki O, Kurimoto K, Kim I, Sakamoto H, Shimura Y, et al. Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein. Nature 1999; 398:579 - 585
  • Wang X, Tanaka Hall TM. Structural basis for recognition of AU-rich element RNA by the HuD protein. Nat Struct Biol 2001; 8:141 - 145
  • Allain FH, Bouvet P, Dieckmann T, Feigon J. Molecular basis of sequence-specific recognition of pre-ribosomal RNA by nucleolin. EMBO J 2000; 19:6870 - 6881
  • Deo RC, Bonanno JB, Sonenberg N, Burley SK. Recognition of polyadenylate RNA by the poly(A)-binding protein. Cell 1999; 98:835 - 845
  • Oberstrass FC, Auweter SD, Erat M, Hargous Y, Henning A, Wenter P, et al. Structure of PTB bound to RNA: specific binding and implications for splicing regulation. Science 2005; 309:2054 - 2057
  • Webster PJ, Liang L, Berg CA, Lasko P, Macdonald PM. Translational repressor bruno plays multiple roles in development and is widely conserved. Genes Dev 1997; 11:2510 - 2521
  • Kim-Ha J, Kerr K, Macdonald PM. Translational regulation of oskar mRNA by bruno, an ovarian RNA-binding protein, is essential. Cell 1995; 81:403 - 412
  • Reveal B, Yan N, Snee MJ, Pai C, Gim Y, Macdonald PM. BREs Mediate Both Repression and Activation of oskar mRNA Translation and Act In trans. Dev Cell 2010; 18:496 - 502
  • Lie Y, Macdonald PM. Translational regulation of oskar mRNA occurs independent of the cap and poly(A) tail in Drosophila ovarian extracts. Development 1999; 126:4989 - 4996
  • Castagnetti S, Hentze MW, Ephrussi A, Gebauer F. Control of oskar mRNA translation by Bruno in a novel cell-free system from Drosophila ovaries. Development 2000; 127:1063 - 1068
  • Snee M, Benz D, Jen J, Macdonald PM. Two distinct domains of Bruno bind specifically to the oskar mRNA. RNA Biol 2008; 5
  • Lyon A, Reveal B, Macdonald PM, Hoffman D. Bruno protein contains an expanded RNA recognition motif. Biochemistry 2009; 48:12202 - 12212
  • Sugimura I, Lilly MA. Bruno inhibits the expression of mitotic cyclins during the prophase I meiotic arrest of Drosophila oocytes. Dev Cell 2006; 10:127 - 135
  • Filardo P, Ephrussi A. Bruno regulates gurken during Drosophila oogenesis. Mech Dev 2003; 120:289 - 297
  • Yan N, Macdonald PM. Genetic interactions of Drosophila melanogaster arrest reveal roles for translational repressor Bruno in accumulation of Gurken and activity of Delta. Genetics 2004; 168:1433 - 1442
  • Wang Z, Lin H. Sex-lethal is a target of Brunomediated translational repression in promoting the differentiation of stem cell progeny during Drosophila oogenesis. Dev Biol 2007; 302:160 - 168
  • Moore J, Han H, Lasko P. Bruno negatively regulates germ cell-less expression in a BRE-independent manner. Mech Dev 2009; 126:503 - 516
  • Tuerk C, Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 1990; 249:505 - 510
  • Bailey TL, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 1994; 2:28 - 36
  • Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003; 31:3406 - 3415
  • Mathews DH, Sabina J, Zuker M, Turner DH. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 1999; 288:911 - 940
  • Auweter SD, Oberstrass FC, Allain FH. Sequencespecific binding of single-stranded RNA: is there a code for recognition?. Nucleic Acids Res 2006; 34:4943 - 4959
  • Oubridge C, Ito N, Evans PR, Teo CH, Nagai K. Crystal structure at 1.92 A resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature 1994; 372:432 - 438
  • Faustino NA, Cooper TA. Identification of putative new splicing targets for ETR-3 using sequences identified by systematic evolution of ligands by exponential enrichment. Mol Cell Biol 2005; 25:879 - 887
  • Marquis J, Paillard L, Audic Y, Cosson B, Danos O, Le Bec C, Osborne HB. CUG-BP1/CELF1 requires UGU-rich sequences for high-affinity binding. Biochem J 2006; 400:291 - 301
  • Rorth P. Gal4 in the Drosophila female germline. Mech Dev 1998; 78:113 - 118
  • Timchenko LT, Timchenko NA, Caskey CT, Roberts R. Novel proteins with binding specificity for DNA CTG repeats and RNA CUG repeats: implications for myotonic dystrophy. Hum Mol Genet 1996; 5:115 - 121
  • Timchenko LT, Miller JW, Timchenko NA, DeVore DR, Datar KV, Lin L, et al. Identification of a (CUG) n triplet repeat RNA-binding protein and its expression in myotonic dystrophy. Nucleic Acids Res 1996; 24:4407 - 4414
  • Tsuda K, Kuwasako K, Takahashi M, Someya T, Inoue M, Terada T, et al. Structural basis for the sequence-specific RNA-recognition mechanism of human CUGBP1 RRM3. Nucleic Acids Res 2009; 37:5151 - 5166
  • Teplova M, Song J, Gaw HY, Teplov A, Patel DJ. Structural insights into RNA recognition by the alternate-splicing regulator CUG-binding protein 1. Structure 2010; 18:1364 - 1377
  • Zhang L, Lee JE, Wilusz J, Wilusz CJ. The RNA-binding protein CUGBP1 regulates stability of tumor necrosis factor mRNA in muscle cells: implications for myotonic dystrophy. J Biol Chem 2008; 283:22457 - 22463
  • Chekulaeva M, Hentze MW, Ephrussi A. Bruno acts as a dual repressor of oskar translation, promoting mRNA oligomerization and formation of silencing particles. Cell 2006; 124:521 - 533
  • Besse F, Lopez de Quinto S, Marchand V, Trucco A, Ephrussi A. Drosophila PTB promotes formation of high-order RNP particles and represses oskar translation. Genes Dev 2009; 23:195 - 207
  • Abe R, Sakashita E, Yamamoto K, Sakamoto H. Two different RNA binding activities for the AU-rich element and the poly(A) sequence of the mouse neuronal protein mHuC. Nucleic Acids Res 1996; 24:4895 - 901
  • Sickmier EA, Frato KE, Shen H, Paranawithana SR, Green MR, Kielkopf CL. Structural basis for polypyrimidine tract recognition by the essential pre-mRNA splicing factor U2AF65. Mol Cell 2006; 23:49 - 59
  • Thickman KR, Sickmier EA, Kielkopf CL. Alternative conformations at the RNA-binding surface of the N-terminal U2AF(65) RNA recognition motif. J Mol Biol 2007; 366:703 - 710
  • Rao JN, Schweimer K, Wenzel S, Wöhrl BM, Rösch P. NELF-E RRM undergoes major structural changes in flexible protein regions on target RNA binding. Biochemistry 2008; 47:3756 - 3761
  • Banerjee H, Rahn A, Davis W, Singh R. Sex lethal and U2 small nuclear ribonucleoprotein auxiliary factor (U2AF65) recognize polypyrimidine tracts using multiple modes of binding. RNA 2003; 9:88 - 99
  • Munro TP, Kwon S, Schnapp BJ, St Johnston D. A repeated IMP-binding motif controls oskar mRNA translation and anchoring independently of Drosophila melanogaster IMP. J Cell Biol 2006; 172:577 - 588
  • Reich J, Snee MJ, Macdonald PM. miRNA-dependent translational repression in the Drosophila ovary. PLoS ONE 2009; 4:4669
  • Van Doren M, Williamson AL, Lehmann R. Regulation of zygotic gene expression in Drosophila primordial germ cells. Curr Biol 1998; 8:243 - 246
  • Martin SG, St. Johnston D. A role for Drosophila LKB1 in anterior-posterior axis formation and epithelial polarity. Nature 2003; 421:379 - 384
  • Schüpbach T, Wieschaus E. Female sterile mutations on the second chromosome of Drosophila melanogaster. II. Mutations blocking oogenesis or altering egg morphology. Genetics 1991; 129:1119 - 1136
  • Wong I, Lohman TM. A double-filter method for nitrocellulose-filter binding: application to proteinnucleic acid interactions. Proc Natl Acad Sci USA 1993; 90:5428 - 5432

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.