U2 snRNA sequence conservation in eukaryotes

The sequences for Human (H. sapiens, K0323), Mouse (M. musculus, X07913), Fly (D. melanogaster, X04256), SC (S. cerevisiae, M14625), and SP (S. pombe, X55772) are taken from NCBI . The sequence for SK (S. kluyveri, AU0AA010F08T1) was extracted from the Génolevures RST libraries and the sequence for CA (C. albicans, Contig6_2470(r) ) from the Stanford's C. albicans sequence assembly 6 by using the SC U2 sequence as bait [Bon et al., 2003].

The RNA has been divided into three domains according to Guthrie & Patterson [Guthrie & Patterson, Annu. Rev. Genet., 1988, 22, 387-419]: 5' and 3' terminal and central. Functional sites are indicated : the IBP-box of the 5' terminal domain which is the region recognising the intron branch splice site by base pairing, and the SmBP-box which is the region of the 3' terminal domain that base pairs to the Sm proteins.

The size and general organisation of U2 is highly conserved in all organisms except in the hemiascomycetous yeasts where it is more or less divergent, having a large size in S. cerevisiae (1177 nt) and in S. servazzii (1100 nt), and a smaller one in the less related yeast species like C. albicans (234 nt) and Y. lipolytica (195 nt) which is close to the human size of 187 nt [Guthrie & Patterson, 1988; Roiha et al., 1989, Gene, 82, 137-144; Bon et al., 2003].

All of these differences can be accounted for by variability in the 3' terminal domain of the molecule. Thus, S. cerevisiae U2 exhibits a supplementary region of 956 nt (at 125-1080) in the 3' terminal domain [Guthrie & Patterson, 1988], as well as homology to vertebrate U4 (at 828-848), U5 (at 1086-1096) and U6 snRNAs [Ares M., 1986, Cell, 47, 49-59]. It was suggested that the ?extra? 956 nucleotides might correspond to a ?poly-snRNA?, in which the functional equivalents of U4, U5, and U6 were covalently joined to the U2 molecule [Ares M., 1986, Cell, 47, 49-59].

Unlike their U1 counterparts, these 'extra' residues seem to be phylogenetically hypervariable, being present in the most closely related S. cerevisiae related species and reduced in the most distant ones [Bon et al., 2003].

(r) Reverse and complement sequence

CLUSTALX multiple alignment of U2 snRNA sequences

Last modified: Tue Feb 10 11:16:32 CET 2004