A role for SRp54 during intron bridging of small introns with pyrimidine tracts upstream of the branch point.
One of the earliest steps in pre-mRNA recognition involves binding of the splicing factor U2 snRNP auxiliary factor (U2AF or MUD2 in Saccharomyces cerevisiae) to the 3' splice site region. U2AF interacts with a number of other proteins, including members of the serine/arginine (SR) family of splicing factors as well as splicing factor 1 (SF1 or branch point bridging protein in S. cerevisiae), thereby participating in bridging either exons or introns. In vertebrates, the binding site for U2AF is the pyrimidine tract located between the branch point and 3' splice site. Many small introns, especially those in nonvertebrates, lack a classical 3' pyrimidine tract. Here we show that a 59-nucleotide Drosophila melanogaster intron contains C-rich pyrimidine tracts between the 5' splice site and branch point that are needed for maximal binding of both U1 snRNPs and U2 snRNPs to the 5' and 3' splice site, respectively, suggesting that the tracts are the binding site for an intron bridging factor. The tracts are shown to bind both U2AF and the SR protein SRp54 but not SF1. Addition of a strong 3' pyrimidine tract downstream of the branch point increases binding of SF1, but in this context, the upstream pyrimidine tracts are inhibitory. We suggest that U2AF- and/or SRp54-mediated intron bridging may be an alternative early recognition mode to SF1-directed bridging for small introns, suggesting gene-specific early spliceosome assembly.
Kennedy
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CF
Verna and Marrs McLean Department of Biochemistry, Program in Cell and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.
Krämer
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A
Berget
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SM
D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D004330:Drosophila; D005656:Fungal Proteins / Q000378:metabolism; D006801:Humans; D007438:Introns; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009838:Oligodeoxyribonucleotides; D017354:Point Mutation; D011743:Pyrimidines; D017413:Ribonucleoprotein, U2 Small Nuclear / Q000378:metabolism; D012261:Ribonucleoproteins / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D018271:Signal Recognition Particle / Q000096:biosynthesis / Q000737:chemistry* / Q000378:metabolism*; D000072668:Splicing Factor U2AF
D005656:Fungal Proteins; C089980:MUD2 protein, S cerevisiae; D009838:Oligodeoxyribonucleotides; D011743:Pyrimidines; D017413:Ribonucleoprotein, U2 Small Nuclear; D012261:Ribonucleoproteins; D029701:Saccharomyces cerevisiae Proteins; D018271:Signal Recognition Particle; D000072668:Splicing Factor U2AF; C097836:SrpA protein, Aspergillus niger