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PMID: 16407443 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Molecular characterization and phylogeny of U2AF35 homologs in plants.

Plant physiology ·Vol. 140 ·No. 2 ·2006-02-00 ·Pages 624-36

Wang BB, Brendel V

Abstract

U2AF (U2 small nuclear ribonucleoprotein auxiliary factor) is an essential splicing factor with critical roles in recognition of the 3'-splice site. In animals, the U2AF small subunit (U2AF35) can bind to the 3'-AG intron border and promote U2 small nuclear RNP binding to the branch-point sequences of introns through interaction with the U2AF large subunit. Two copies of U2AF35-encoding genes were identified in Arabidopsis (Arabidopsis thaliana; atU2AF35a and atU2AF35b). Both are expressed in all tissues inspected, with atU2AF35a expressed at a higher level than atU2AF35b in most tissues. Differences in the expression patterns of atU2AF35a and atU2AF35b in roots were revealed by a promoter::beta-glucuronidase assay, with atU2AF35b expressed strongly in whole young roots and root tips and atU2AF35a limited to root vascular regions. Altered expression levels of atU2AF35a or atU2AF35b cause pleiotropic phenotypes (including flowering time, leaf morphology, and flower and silique shape). Novel slicing isoforms were generated from FCA pre-mRNA by splicing of noncanonical introns in plants with altered expression levels of atU2AF35. U2AF35 homologs were also identified from maize (Zea mays) and other plants with large-scale expressed sequence tag projects. A C-terminal motif (named SERE) is highly conserved in all seed plant protein homologs, suggesting it may have an important function specific to higher plants.

MeSH Terms
Alternative Splicing Amino Acid Motifs Amino Acid Sequence Arabidopsis/anatomy & histology,genetics,metabolism Arabidopsis Proteins/classification,genetics,metabolism Cell Nucleus/metabolism Genes, Reporter Molecular Sequence Data Nuclear Proteins/classification,genetics,metabolism Phenotype Phylogeny Plants, Genetically Modified/genetics,metabolism Ribonucleoproteins/classification,genetics,metabolism Sequence Alignment Sequence Analysis, DNA Sequence Homology, Nucleic Acid Splicing Factor U2AF
Chemicals
Arabidopsis Proteins Nuclear Proteins Ribonucleoproteins Splicing Factor U2AF
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Wang Bing-Bing
Department of Genetics, Development and Cell Biology , Iowa State University, Ames, Iowa 50010, USA.
Brendel Volker
References (58)
58 references, click to expand
  1. Evidence for substrate-specific requirement of the splicing factor U2AF(35) and for its function after polypyrimidine tract recognition by U2AF(65).
    Mol Cell Biol. 1999 Dec;19(12):8263-71 PMID: 10567551
  2. Multiple forms of the U2 small nuclear ribonucleoprotein auxiliary factor U2AF subunits expressed in higher plants.
    J Biol Chem. 1998 Dec 18;273(51):34603-10 PMID: 9852132
  3. Functional recognition of the 3' splice site AG by the splicing factor U2AF35.
    Nature. 1999 Dec 16;402(6763):832-5 PMID: 10617206
  4. Inhibition of msl-2 splicing by Sex-lethal reveals interaction between U2AF35 and the 3' splice site AG.
    Nature. 1999 Dec 16;402(6763):838-41 PMID: 10617208
  5. Expressing the human genome.
    Nature. 2001 Feb 15;409(6822):832-3 PMID: 11237001
  6. FPA, a gene involved in floral induction in Arabidopsis, encodes a protein containing RNA-recognition motifs.
    Plant Cell. 2001 Jun;13(6):1427-36 PMID: 11402170
  7. A novel peptide recognition mode revealed by the X-ray structure of a core U2AF35/U2AF65 heterodimer.
    Cell. 2001 Sep 7;106(5):595-605 PMID: 11551507
  8. Dual function for U2AF(35) in AG-dependent pre-mRNA splicing.
    Mol Cell Biol. 2001 Nov;21(22):7673-81 PMID: 11604503
  9. Characterization of U2AF(6), a splicing factor related to U2AF(35).
    Mol Cell Biol. 2002 Jan;22(1):221-30 PMID: 11739736
  10. Modulation of abscisic acid signal transduction and biosynthesis by an Sm-like protein in Arabidopsis.
    Dev Cell. 2001 Dec;1(6):771-81 PMID: 11740939
  11. MEGA2: molecular evolutionary genetics analysis software.
    Bioinformatics. 2001 Dec;17(12):1244-5 PMID: 11751241
  12. Genome analysis: RNA recognition motif (RRM) and K homology (KH) domain RNA-binding proteins from the flowering plant Arabidopsis thaliana.
    Nucleic Acids Res. 2002 Feb 1;30(3):623-35 PMID: 11809873
  13. Expression of Arabidopsis SR-like splicing proteins confers salt tolerance to yeast and transgenic plants.
    Plant J. 2002 Jun;30(5):511-9 PMID: 12047626
  14. Network of interactions of a novel plant-specific Arg/Ser-rich protein, atRSZ33, with atSC35-like splicing factors.
    J Biol Chem. 2002 Oct 18;277(42):39989-98 PMID: 12176998
  15. Alternative splicing modulation by a LAMMER kinase impinges on developmental and transcriptome expression.
    Plant Cell. 2003 Apr;15(4):926-38 PMID: 12671088
  16. A gateway cloning vector set for high-throughput functional analysis of genes in planta.
    Plant Physiol. 2003 Oct;133(2):462-9 PMID: 14555774
  17. Nuclear localization and in vivo dynamics of a plant-specific serine/arginine-rich protein.
    Plant J. 2003 Dec;36(6):883-93 PMID: 14675452
  18. An Arabidopsis RNA lariat debranching enzyme is essential for embryogenesis.
    J Biol Chem. 2004 Jan 9;279(2):1468-73 PMID: 14570879
  19. Nuclear bodies and compartmentalization of pre-mRNA splicing factors in higher plants.
    Chromosoma. 2004 Feb;112(5):255-66 PMID: 14740228
  20. The splicing factor U2AF small subunit is functionally conserved between fission yeast and humans.
    Mol Cell Biol. 2004 May;24(10):4229-40 PMID: 15121844
  21. Tissue-specific expression and dynamic organization of SR splicing factors in Arabidopsis.
    Mol Biol Cell. 2004 Jun;15(6):2664-73 PMID: 15034145
  22. Diversity of vertebrate splicing factor U2AF35: identification of alternatively spliced U2AF1 mRNAS.
    J Biol Chem. 2004 Jun 25;279(26):27039-49 PMID: 15096518
  23. Use of fluorescent protein tags to study nuclear organization of the spliceosomal machinery in transiently transformed living plant cells.
    Mol Biol Cell. 2004 Jul;15(7):3233-43 PMID: 15133128
  24. U2AF homology motifs: protein recognition in the RRM world.
    Genes Dev. 2004 Jul 1;18(13):1513-26 PMID: 15231733
  25. A plethora of plant serine/arginine-rich proteins: redundancy or evolution of novel gene functions?
    Biochem Soc Trans. 2004 Aug;32(Pt 4):561-4 PMID: 15270675
  26. Lesions in the mRNA cap-binding gene ABA HYPERSENSITIVE 1 suppress FRIGIDA-mediated delayed flowering in Arabidopsis.
    Plant J. 2004 Oct;40(1):112-9 PMID: 15361145
  27. Identification, purification, and biochemical characterization of U2 small nuclear ribonucleoprotein auxiliary factor.
    Proc Natl Acad Sci U S A. 1989 Dec;86(23):9243-7 PMID: 2531895
  28. The organization of 3' splice-site sequences in mammalian introns.
    Genes Dev. 1989 Dec;3(12B):2113-23 PMID: 2628164
  29. Cloning and domain structure of the mammalian splicing factor U2AF.
    Nature. 1992 Feb 13;355(6361):609-14 PMID: 1538748
  30. Cloning and intracellular localization of the U2 small nuclear ribonucleoprotein auxiliary factor small subunit.
    Proc Natl Acad Sci U S A. 1992 Sep 15;89(18):8769-73 PMID: 1388271
  31. A splicing enhancer complex controls alternative splicing of doublesex pre-mRNA.
    Cell. 1993 Jul 16;74(1):105-14 PMID: 8334698
  32. The yeast MUD2 protein: an interaction with PRP11 defines a bridge between commitment complexes and U2 snRNP addition.
    Genes Dev. 1994 Apr 1;8(7):843-54 PMID: 7926772
  33. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
    Nucleic Acids Res. 1994 Nov 11;22(22):4673-80 PMID: 7984417
  34. Identification of a plant serine-arginine-rich protein similar to the mammalian splicing factor SF2/ASF.
    Proc Natl Acad Sci U S A. 1995 Aug 15;92(17):7672-6 PMID: 7644475
  35. Structures, sequence characteristics, and synteny relationships of the transcription factor E4TF1, the splicing factor U2AF35 and the cystathionine beta synthetase genes from Fugu rubripes.
    Gene. 1999 Jan 21;226(2):211-23 PMID: 9931491
  36. The FLF MADS box gene: a repressor of flowering in Arabidopsis regulated by vernalization and methylation.
    Plant Cell. 1999 Mar;11(3):445-58 PMID: 10072403
  37. U2AF35 is encoded by an essential gene clustered in an operon with RRM/cyclophilin in Caenorhabditis elegans.
    RNA. 1999 Apr;5(4):487-94 PMID: 10199565
  38. atSRp30, one of two SF2/ASF-like proteins from Arabidopsis thaliana, regulates splicing of specific plant genes.
    Genes Dev. 1999 Apr 15;13(8):987-1001 PMID: 10215626
  39. A novel family of plant splicing factors with a Zn knuckle motif: examination of RNA binding and splicing activities.
    Plant Mol Biol. 1999 Mar;39(4):761-73 PMID: 10350090
  40. CAP3: A DNA sequence assembly program.
    Genome Res. 1999 Sep;9(9):868-77 PMID: 10508846
  41. Compartmentalization of the splicing machinery in plant cell nuclei.
    Trends Plant Sci. 2004 Dec;9(12):565-8 PMID: 15564119
  42. The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing.
    Genome Biol. 2004;5(12):R102 PMID: 15575968
  43. A mutation in the Cap Binding Protein 20 gene confers drought tolerance to Arabidopsis.
    Plant Mol Biol. 2004 Jul;55(5):679-86 PMID: 15604709
  44. A DEAD box RNA helicase is essential for mRNA export and important for development and stress responses in Arabidopsis.
    Plant Cell. 2005 Jan;17(1):256-67 PMID: 15598798
  45. Functional distribution and dynamics of Arabidopsis SR splicing factors in living plant cells.
    Plant J. 2005 Feb;41(4):567-82 PMID: 15686520
  46. Two novel arginine/serine (SR) proteins in maize are differentially spliced and utilize non-canonical splice sites.
    Biochim Biophys Acta. 2005 May 1;1728(3):105-14 PMID: 15780972
  47. Genome-wide insertional mutagenesis of Arabidopsis thaliana.
    Science. 2003 Aug 1;301(5633):653-7 PMID: 12893945
  48. Ectopic expression of atRSZ33 reveals its function in splicing and causes pleiotropic changes in development.
    Mol Biol Cell. 2003 Sep;14(9):3565-77 PMID: 12972547
  49. Isolation and mapping of human homologues of an imprinted mouse gene U2af1-rs1.
    Genomics. 1995 Nov 20;30(2):257-63 PMID: 8586425
  50. Pre-mRNA splicing in plants: characterization of Ser/Arg splicing factors.
    Proc Natl Acad Sci U S A. 1996 Apr 2;93(7):3074-9 PMID: 8610170
  51. The small subunit of the splicing factor U2AF is conserved in fission yeast.
    Nucleic Acids Res. 1996 May 15;24(10):1849-54 PMID: 8657565
  52. The splicing factor U2AF35 mediates critical protein-protein interactions in constitutive and enhancer-dependent splicing.
    Genes Dev. 1996 Jun 1;10(11):1356-68 PMID: 8647433
  53. Mutations in the small subunit of the Drosophila U2AF splicing factor cause lethality and developmental defects.
    Proc Natl Acad Sci U S A. 1996 Sep 17;93(19):10333-7 PMID: 8816800
  54. Characterization of a novel arginine/serine-rich splicing factor in Arabidopsis.
    Plant Cell. 1996 Dec;8(12):2255-64 PMID: 8989882
  55. FCA, a gene controlling flowering time in Arabidopsis, encodes a protein containing RNA-binding domains.
    Cell. 1997 May 30;89(5):737-45 PMID: 9182761
  56. Molecular genetic analysis of the heterodimeric splicing factor U2AF: the RS domain on either the large or small Drosophila subunit is dispensable in vivo.
    Genes Dev. 1998 Apr 1;12(7):1010-21 PMID: 9531538
  57. The plant U1 small nuclear ribonucleoprotein particle 70K protein interacts with two novel serine/arginine-rich proteins.
    Plant Cell. 1998 Oct;10(10):1637-48 PMID: 9761791
  58. An SC35-like protein and a novel serine/arginine-rich protein interact with Arabidopsis U1-70K protein.
    J Biol Chem. 1999 Dec 17;274(51):36428-38 PMID: 10593939
Article Info
Journal
Plant physiology
Abbr.
Plant Physiol
ISSN
0032-0889
DOI
10.1104/pp.105.073858
Published
2006-02-00
Epub
2006-00-11
Pages
624-36
Language
English
Region
United States
NLM ID
0401224
PMCID
PMC1361329
Subset
IM
Databases
GENBANK
AF409139, AF409140
External Links
PubMed source DOI: 10.1104/pp.105.073858 PMC Full Text View journal details
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