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A novel family of plant splicing factors with a Zn knuckle motif: examination of RNA binding and splicing activities

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Abstract

An important group of splicing factors involved in constitutive and alternative splicing contain an arginine/serine (RS)-rich domain. We have previously demonstrated the existence of such factors in plants and report now on a new family of splicing factors (termed the RSZ family) from Arabidopsis thaliana which additionally harbor a Zn knuckle motif similar to the human splicing factor 9G8. Although only around 20 kDa in size, members of this family possess a multi-domain structure. In addition to the N-terminal RNA recognition motif (RRM), a Zn finger motif of the CCHC-type is inserted in an RGG-rich region; all three motifs are known to contribute to RNA binding. The C-terminal domain has a characteristic repeated structure which is very arginine-rich and centered around an SP dipeptide. One member of this family, atRSZp22, has been shown to be a phosphoprotein with properties similar to SR proteins. Furthermore, atRSZp22 was able to complement efficiently splicing deficient mammalian S100 as well as h9G8-depleted extracts. RNA binding assays to selected RNA sequences indicate an RNA binding specificity similar to the human splicing factors 9G8 and SRp20. Taken together, these result show that atRSZp22 is a true plant splicing factor which combines structural and functional features of both h9G8 and hSRp20.

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References

  1. Aris JP, Blobel G: cDNA cloning and sequencing of human fibrillarin, a conserved nucleolar protein recognized by autoimmune antisera. Proc Natl Acad Sci USA 88: 931–935 (1991).

    PubMed  Google Scholar 

  2. Arning S, Gruter P, Bilbe G, Kramer A: Mammalian splicing factor SF1 is encoded by variant cDNAs and binds to RNA. RNA 2: 794–810(1996).

    PubMed  Google Scholar 

  3. Barta A, Sommergruber K, Thompson D, Hartmuth K, Matzke MA, Matzke AJM: The expression of a nopaline synthase-human growth hormone chimaeric gene in transformed tobacco and sunflower callus tissue. PlantMol Biol 6: 347–357(1986).

    Google Scholar 

  4. Berget SM: Exon recognition in vertebrate splicing. J Biol Chem 270: 2411–2414(1995).

    PubMed  Google Scholar 

  5. Biamonti G, Ruggiu M, Saccone S, Della Valle G, Riva S: Two homologous genes, originated by duplication, encode the human hnRNP proteins A2 and A1. Nucl Acids Res 22: 1996–2002 (1994).

    PubMed  Google Scholar 

  6. Birney E, Kumar S, Krainer AR: Analysis of the RNArecognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors. Nucl Acids Res 21: 5803–5816(1993).

    PubMed  Google Scholar 

  7. Burd CG, Dreyfuss G: RNA binding specificity of hnRNP A1: significance of hnRNP A1 high-affinity binding sites in premRNA splicing. EMBO J 13: 1197–1204(1994).

    PubMed  Google Scholar 

  8. Buvoli M, Biamonti G, Tsoulfas P, Bassi MT, Ghetti A, Riva S, Morandi C: cDNA cloning of human hnRnp protein A1 reveals the existence of multiple mRNA isoforms. Nucl Acids Res 16: 3751–3770(1988).

    PubMed  Google Scholar 

  9. Caizergues Ferrer M, Mariottini P, Curie C, Lapeyre B, Gas N, Amalric F, Amaldi F: Nucleolin from Xenopus laevis: cDNA cloning and expression during development. Genes Dev 3: 324–333(1989).

    PubMed  Google Scholar 

  10. Calnan BJ, Tidor B, Biancalana S, Hudson D, Frankel AD: Arginine-mediated RNA recognition: the arginine fork [published erratum in Science 255 (1992) [665]. Science 252: 1167–1171(1991).

    PubMed  Google Scholar 

  11. Cao W, Jamison SF, Garcia-Blanco MA: Both phosphorylation and dephosphorylation of ASF/SF2 are required for pre-mRNA splicing in vitro. RNA 3: 1456–1467(1997).

    PubMed  Google Scholar 

  12. Carroll SB, Stollar BD: Antibodies to calf thymus RNA polymerase II from egg yolks of immunized hens. J Biol Chem 258: 24–26(1983).

    PubMed  Google Scholar 

  13. Cavaloc Y, Popielarz M, Fuchs JP, Gattoni R, Stevenin J: Characterization and cloning of the human splicing factor 9G8: a novel 35 kDa factor of the serine/arginine protein family. EMBO J 13: 2639–2649(1994).

    PubMed  Google Scholar 

  14. Colwill K, Feng LL, Yeakley JM, Gish GD, Caceres JF, Pawson T, Fu XD: SRPK1 and Clk/Sty protein kinases show distinct substrate specificities for serine/arginine-rich splicing factors. J Biol Chem 271: 24569–24575(1996).

    PubMed  Google Scholar 

  15. Colwill K, Pawson T, Andrews B, Prasad J, Manley JL, Bell JC, Duncan PI: The Clk/Sty protein kinase phosphorylates SR splicing factors and regulates their intracellular distribution. EMBO J 15: 265–275(1996).

    PubMed  Google Scholar 

  16. Darlix JL, Lapadat Tapolsky M, de Rocquigny H, Roques BP: First glimpses at structure-function relationships of the nucleocapsid protein of retroviruses. J Mol Biol 254: 523–537 (1995).

    PubMed  Google Scholar 

  17. de Oliveira DE, Seurinck J, Inzé D, Van Montagu M, Botterman J: Differential expression of five Arabidopsis genes encoding glycine-rich proteins. Plant Cell 2: 427–436(1990).

    Article  PubMed  Google Scholar 

  18. Dorer DR, Christensen AC, Johnson DH: A novel RNA helicase gene tightly linked to the Triplo-lethal locus of Drosophila. Nucl Acids Res 18: 5489–5494(1990).

    PubMed  Google Scholar 

  19. Filipowicz W, Gniadkowski M, Klahre U, Liu H-X: PremRNA splicing in plants. In: Lamond A )(ed) Pre-mRNA Processing, pp. 66–77. R.G. Landes, Georgetown, TX (1995).

    Google Scholar 

  20. Franck A, Guilley H, Jonard G, Richards K, Hirth L: Nucleotide sequence of cauliflower mosaic virus DNA. Cell 21: 285–294(1980).

    Article  PubMed  Google Scholar 

  21. Frank D, Guthrie C: An essential splicing factor, SLU7, mediates 30 splice site choice in yeast. Genes Dev 6: 2112–2124 (1992).

    PubMed  Google Scholar 

  22. Fu X-D: The superfamily of arginine/serine-rich splicing factors. RNA 1: 663–680(1995).

    PubMed  Google Scholar 

  23. Fu XD: Specific commitment of different pre-mRNAs to splicing by single SR proteins. Nature 365: 82–85(1993).

    PubMed  Google Scholar 

  24. Golovkin M, Reddy AS: Structure and expression of a plant U1 snRNP 70K gene: alternative splicing of U1 snRNP 70K pre-mRNAs produces two different transcripts. Plant Cell 8: 1421–1435(1996).

    Article  PubMed  Google Scholar 

  25. Gorlach M, Burd CG, Dreyfuss G: The determinants of RNAbinding specificity of the heterogeneous nuclear ribonucleoprotein C proteins. J Biol Chem 269: 23074–23078(1994).

    PubMed  Google Scholar 

  26. Grandbastien MA, Spielmann A, Caboche M: Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature 337: 376–380(1989).

    PubMed  Google Scholar 

  27. Gui JF, Lane WS, Fu XD: A serine kinase regulates intracellular localization of splicing factors in the cell cycle [see comments]. Nature 369: 678–682(1994).

    PubMed  Google Scholar 

  28. Gui JF, Tronchere H, Chandler SD, Fu XD: Purification and characterization of a kinase specific for the serine-and arginine-rich pre-mRNA splicing factors. Proc Natl Acad Sci USA 91: 10824–10828(1994).

    PubMed  Google Scholar 

  29. Hanano S, Sugita M, Sugiura M: Isolation of a novel RNAbinding protein and its association with a large ribonucleoprotein particle present in the nucleoplasm of tobacco cells. Plant Mol Biol 31: 57–68(1996).

    PubMed  Google Scholar 

  30. Heinrichs V, Baker BS: The Drosophila SR protein RBP1 contributes to the regulation of doublesex alternative splicing by recognizing RBP1 RNA target sequences. EMBO J 14: 3987–4000(1995).

    PubMed  Google Scholar 

  31. Jonak C, Kiegerl S, Ligterink W, Barker PJ, Huskisson NS, Hirt H: Stress signaling in plants: a mitogen-activated protein kinase pathway is activated by cold and drought. Proc Natl Acad Sci USA 93: 11274–11279(1996).

    Article  PubMed  Google Scholar 

  32. Jumaa H, Guenet JL, Nielsen PJ: Regulated expression and RNA processing of transcripts from the Srp20 splicing factor gene during the cell cycle. Mol Cell Biol 17: 3116–3124 (1997).

    PubMed  Google Scholar 

  33. Jumaa H, Nielsen PJ: The splicing factor SRp20 modifies splicing of its own mRNA and ASF/SF2 antagonizes this regulation. EMBO J 16: 5077–5085(1997).

    PubMed  Google Scholar 

  34. Kanopka A, Muhlemann O, Akusjarvi G: Inhibition by SR proteins of splicing of a regulated adenovirus pre-mRNA. Nature 381: 535–538(1996).

    PubMed  Google Scholar 

  35. Kiledjian M, Dreyfuss G: Primary structure and binding activity of the hnRNP U protein: binding RNA through RGG box. EMBO J 11: 2655–2664(1992).

    Google Scholar 

  36. Kramer A: Mammalian protein factors involved in nuclear premRNA splicing. RNA 1: 260–272(1995).

    PubMed  Google Scholar 

  37. Lavigueur A, La Branche H, Kornblihtt AR, Chabot B: A splicing enhancer in the human fibronectin alternate ED1 exon interacts with SR proteins and stimulates U2 snRNP binding. Genes Dev 7: 2405–2417(1993).

    PubMed  Google Scholar 

  38. Lazar G, Schaal T, Maniatis T, Goodman HM: Identification of a plant serine-arginine-rich protein similar to the mammalian splicing factor SF2/ASF. Proc Natl Acad Sci USA 92: 7672–7676 (1995).

    PubMed  Google Scholar 

  39. Lazinski D, Grzadzielska E, Das A: Sequence-specific recognition of RNA hairpins by bacteriophage antiterminators requires a conserved arginine-rich motif. Cell 59: 207–218 (1989).

    PubMed  Google Scholar 

  40. Lopato S, Mayeda A, Krainer A, Barta A: Pre-mRNA splicing in plants: Characterization of SR splicing factors. Proc Natl Acad Sci USA 93: 3074–3079(1996).

    PubMed  Google Scholar 

  41. Lopato S, Waigmann E, Barta A: Characterization of a novel arginine/serine-rich splicing factor in Arabidopsis. Plant Cell 8: 2255–2264(1996).

    PubMed  Google Scholar 

  42. Luehrsen KR, Taha S, Walbot V: Nuclear pre-mRNA processing in higher plants. Prog Nucl Acid Res Mol Biol 47: 149–193(1994).

    Google Scholar 

  43. Macknight R, Bancroft I, Page T, Lister C, Schmidt R, Love K, Westphal L, Murphy G, Sherson S, Cobbett C, Dean C: FCA, a gene controlling flowering time in Arabidopsis, encodes a protein containing RNA-binding domains. Cell 89: 737–745 (1997).

    PubMed  Google Scholar 

  44. Manley JL, Tacke R: SR proteins and splicing control. Genes Dev 10: 1569–1579(1996).

    PubMed  Google Scholar 

  45. McNally LM, McNally MT: SR protein splicing factors interact with the Rous sarcoma virus negative regulator of splicing element. J Virol 70: 1163–1172(1996).

    PubMed  Google Scholar 

  46. Mermoud JE, Cohen PT, Lamond AI: Regulation of mammalian spliceosome assembly by a protein phosphorylation mechanism. EMBO J 13: 5679–5688(1994).

    PubMed  Google Scholar 

  47. Misteli T, Spector DL: Serine/threonine phosphatase 1 modulates the subnuclear distribution of pre-mRNA splicing factors. Mol Biol Cell 7: 1559–1572(1996).

    PubMed  Google Scholar 

  48. Misteli T, Spector DL: Protein phosphorylation and the nuclear organization of pre-mRNA splicing. Trends Cell Biol 7: 135–138(1997).

    Google Scholar 

  49. Obokata J, Ohme M, Hayashida N: Nucleotide sequence of a cDNA clone encoding a putative glycine-rich protein of 19.7 kDa in Nicotiana sylvestris. Plant Mol Biol 17: 953–955 (1991).

    PubMed  Google Scholar 

  50. Pearson WR, Lipman DJ: Impoved tools for biological sequence comparison. Proc Natl Acad Sci USA 85: 2444–2448 (1988).

    PubMed  Google Scholar 

  51. Popielarz M, Cavaloc Y, Mattei MG, Gattoni R, Stevenin J: The gene encoding human splicing factor 9G8. Structure, chromosomal localization, and expression of alternatively processed transcripts. J Biol Chem 270: 17830–17835(1995).

    PubMed  Google Scholar 

  52. Rajavashisth TB, Taylor AK, Andalibi A, Svenson KL, Lusis AJ: Identification of a zinc finger protein that binds to the sterol regulatory element. Science 245: 640–643(1989).

    PubMed  Google Scholar 

  53. Ramchatesingh J, Zahler AM, Neugebauer KM, Roth MB, Cooper TA: A subset of SR proteins activates splicing of the cardiac troponin T alternative exon by direct interactions with an exonic enhancer. Mol Cell Biol 15: 4898–4907(1995).

    PubMed  Google Scholar 

  54. Roth MB, Zahler AM, Stolk JA: A conserved family of nuclear phosphoproteins localized to sites of polymerase II transcription. J Cell Biol 115: 587–596(1991).

    PubMed  Google Scholar 

  55. Scherly D, Boelens W, Dathan NA, Kambach C, van Venrooij WJ, Mattaj IW: Binding specificity determinants of U1A and U2B00 proteins. Mol Biol Rep 14: 181–182(1990).

    PubMed  Google Scholar 

  56. Schmitt P, Gattoni R, Keohavong P, Stevenin J: Alternative splicing of E1A transcripts of adenovirus requires appropriate ionic conditions in vitro. Cell 50: 31–39(1987).

    PubMed  Google Scholar 

  57. Screaton GR, Caceres JF, Mayeda A, Bell MV, Plebanski M, Jackson DG, Bell JI, Krainer AR: Identification and characterization of three members of the human SR family of pre-mRNA splicing factors. EMBO J 14: 4336–4349(1995).

    PubMed  Google Scholar 

  58. Sessa G, Raz V, Savaldi S, Fluhr R: PK12, a plant dualspecificity protein kinase of the LAMMER family, is regulated by the hormone ethylene. Plant Cell 8: 2223–2234(1996).

    Article  PubMed  Google Scholar 

  59. Songyang Z, Blechner S, Hoagland N, Hoekstra MF, Piwnica Worms H, Cantley LC: Use of an oriented peptide library to determine the optimal substrates of protein kinases. Curr Biol 4: 973–982(1994).

    PubMed  Google Scholar 

  60. Songyang Z, Lu KP, Kwon YT, Tsai LH, Filhol O, Cochet C, Brickey DA, Soderling TR, Bartleson C, Graves DJ, DeMaggio AJ, Hoekstra MF, Blenis J, Hunter T, Cantley LC: A structural basis for substrate specificities of protein Ser/Thr kinases: primary sequence preference of casein kinases I and II, NIMA, phosphorylase kinase, calmodulin-dependent kinase II, CDK5, and Erk1. Mol Cell Biol 16: 6486–6493(1996).

    PubMed  Google Scholar 

  61. Sun Q, Mayeda A, Hampson RK, Krainer AR, Rottman FM: General splicing factor SF2/ASF promotes alternative splicing by binding to an exonic splicing enhancer. Genes Dev 7: 2598–2608 (1993).

    PubMed  Google Scholar 

  62. Tacke R, Chen Y, Manley JL: Sequence-specific RNA binding by an SR protein requires RS domain phosphorylation: creation of an SRp40-specific splicing enhancer. Bioessays 19: 189–192(1997).

    PubMed  Google Scholar 

  63. Tacke R, Manley JL: The human splicing factors ASF/SF2 and SC35 possess distinct, functionally significant RNA binding specificities. EMBO J 14: 3540–3551(1995).

    PubMed  Google Scholar 

  64. Tian M, Maniatis T: A splicing enhancer complex controls alternative splicing of doublesex pre-mRNA. Cell 74: 105–114 (1993).

    PubMed  Google Scholar 

  65. Van Santen VL, Spritz RA: Splicing of plant pre-mRNAs in animal systems and vice versa. Gene 56: 253–265(1987).

    Article  PubMed  Google Scholar 

  66. Wu CI, Lyttle TW, Wu ML, Lin GF: Association between a satellite DNA sequence and the Responder of Segregation Distorter in D. melanogaster. Cell 54: 179–189(1988).

    PubMed  Google Scholar 

  67. Zahler AM, Lane WS, Stolk JA, Roth MB: SR proteins: a conserved family of pre-mRNA splicing factors. Genes Dev 6: 837–847(1992).

    PubMed  Google Scholar 

  68. Zahler AM, Neugebauer KM, Lane WS, Roth MB: Distinct functions of SR proteins in alternative pre-mRNA splicing. Science 260: 219–222(1993).

    PubMed  Google Scholar 

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Authors and Affiliations

  1. Institut für Biochemie, Universität Wien, Vienna Biocenter, Dr. Bohrgasse 9, 1030 , Vienna, Austria

    Sergiy Lopato, Gustav Fabini & Andrea Barta

  2. Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM, BP 163, 67404 , Illkirch Cédex, C.U. de Strasbourg, France

    Renata Gattoni & James Stevenin

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  1. Sergiy Lopato
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Lopato, S., Gattoni, R., Fabini, G. et al. A novel family of plant splicing factors with a Zn knuckle motif: examination of RNA binding and splicing activities. Plant Mol Biol 39, 761–773 (1999). https://doi.org/10.1023/A:1006129615846

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