Nucleic Acids Research, 1989, Vol. 17, No. 6 2159-2180
© 1989
SURVEY AND SUMMARY |
The 5' splice site: phylogetic evalution and variable geometry of association with U1RNA
Laboratoire de Génétique Moléulaire des Eucaryotes du CNRS, Unité 184 de Biologie Moléculaire et de Génie Génétique de l'INSERM, Institut de Chimie Biologique 11 rue Humann, 67085 Strasbourg Cétlex, France
Received January 3, 1989. Accepted February 17, 1989.
The 5' splice site sequences of 3294 introns from various organisms (1–672) were analyzed in order to determine the rules governing evolution of this sequence, which may shed light on the mechanism of cleavage at the exonintron junction. The data indicate that, currently, in all organisms, a common sequence 
UAAG
and its derivatives are used as well as an additional sequence and its derivatives, which differ, in metazoa (G/UgAG), lower eucaryotes (UAxG) and higher plants (AG/U
). They all partly resemble the prototype sequence AG/UAAG whose 8 contigous nucleotides are complementary to the nucleotides 4–11 of U1RNA, which are perfectly conserved in the course of phylogenetic evolution. Detailed examination of the data shows that U1RNA can recognize different parts of 5' splice sites. As a rule, either prototype nucleotides at position –2 and –1 or at positions 4, 5 or 6 or at positions 3–4 are dispensable provided that the stability of the U1RNA-5' splice site hybrid is conserved. On the basis of frequency of sequences, the optimal size of the hybridizable region is 5–7 nucleotides. Thus, the cleavage at the exonintron junction seems to imply, first, that the 5' splice site is recognized by U1RKA according to a "variable geometry" program ; second, that the precise cleavage site 1s determined by the conserved sequence of U1RNA since it occurs exactly opposite to the junction between nucleotides C9 and CIO of U1RNA. The variable geometry of the U1RNA-5' splice site association provides flexibility to the system and allows diversification in the course of phylogenetic evolution.
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