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

Bing Yu1, Petra Fey2, Karen E. Kestin-Pilcher2, Alexei Fedorov4, Ashwin Prakash4, Rex L. Chisholm2, Jane Y. Wu3()

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Protein Cell ›› 2011, Vol. 2 ›› Issue (5) : 395-409. DOI: 10.1007/s13238-011-1052-z
RESEARCH ARTICLE

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

  • Bing Yu1, Petra Fey2, Karen E. Kestin-Pilcher2, Alexei Fedorov4, Ashwin Prakash4, Rex L. Chisholm2, Jane Y. Wu3()
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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 Ddiscoideum 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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Bing Yu, Petra Fey, Karen E. Kestin-Pilcher, Alexei Fedorov, Ashwin Prakash, Rex L. Chisholm, Jane Y. Wu. Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae. Prot Cell, 2011, 2(5): 395‒409 https://doi.org/10.1007/s13238-011-1052-z

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