Protein & Cell

, Volume 2, Issue 5, pp 395–409

Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae

  • Bing Yu
  • Petra Fey
  • Karen E. Kestin-Pilcher
  • Alexei Fedorov
  • Ashwin Prakash
  • Rex L. Chisholm
  • Jane Y. Wu
Research Article

Abstract

Little is known about pre-mRNA splicing in Dictyostelium discoideum although its genome has been completely sequenced. Our analysis suggests that pre-mRNA splicing plays an important role in D. discoideum gene expression as two thirds of its genes contain at least one intron. Ongoing curation of the genome to date has revealed 40 genes in D. discoideum with clear evidence of alternative splicing, supporting the existence of alternative splicing in this unicellular organism. We identified 160 candidate U2-type spliceosomal proteins and related factors in D. discoideum based on 264 known human genes involved in splicing. Spliceosomal small ribonucleoproteins (snRNPs), PRP19 complex proteins and late-acting proteins are highly conserved in D. discoideum and throughout the metazoa. In non-snRNP and hnRNP families, D. discoideum orthologs are closer to those in A. thaliana, D. melanogaster and H. sapiens than to their counterparts in S. cerevisiae. Several splicing regulators, including SR proteins and CUG-binding proteins, were found in D. discoideum, but not in yeast. Our comprehensive catalog of spliceosomal proteins provides useful information for future studies of splicing in D. discoideum where the efficient genetic and biochemical manipulation will also further our general understanding of pre-mRNA splicing.

Keywords

pre-mRNA splicing spliceosomal genes Dictyostelium discoideum comparative genomics splicing regulators 

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Copyright information

© Higher Education Press and Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Bing Yu
    • 1
  • Petra Fey
    • 2
  • Karen E. Kestin-Pilcher
    • 2
  • Alexei Fedorov
    • 4
  • Ashwin Prakash
    • 4
  • Rex L. Chisholm
    • 2
  • Jane Y. Wu
    • 3
  1. 1.Department of Molecular and Clinical Genetics, Royal Prince Alfred Hospital and Sydney Medical School (Central)the University of SydneySydneyAustralia
  2. 2.dictyBase, Center for Genetic MedicineNorthwestern UniversityChicagoUSA
  3. 3.Department of Neurology and Lurie Comprehensive Cancer Center, Center for Genetic MedicineNorthwestern University Feinberg Medical SchoolChicagoUSA
  4. 4.Department of Medicine and Program in Bioinformatics and Proteomics/GenomicsThe University of ToledoToledoUSA

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