U1 snRNA sequence conservation in eukaryotes

The sequences for Human (H. sapiens, V00591), Mouse (M. musculus, J00645), Fly (D. melanogaster, X04257), Nematode (C. elegans, X51371), Tomato (L. esculentum, X14412), SC (S. cerevisiae, M17205.1), SB (S. bayanus, U03476), KL (K. lactis, U03475) and SP (S. pombe, X55773) are taken from NCBI . The sequences for ZR (Z. rouxii, AR0AA014A08CP1), and KT (K. thermotolerans, AY0AA003C07DP1) were extracted from the Génolevures RST libraries by using the SC U1 sequence as bait [Bon et al., 2003]. Note that only partial sequences are available for ZR and KT.

The RNAs have been divided into three domains according to Guthrie & Patterson [Guthrie & Patterson, 1988, Annu.Rev.Genet., 22, 387-419]: 5' and 3', central. Functional sites like the IBP-box of the 5' terminal domain which is the region recognising the intron 5' 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, are indicated.

The size and general organization of U1 is highly conserved in all organisms except in S. cerevisiae [Guthrie & Patterson, 1988] and in the other hemiascomycetous yeasts. In general the length of each domain is conserved, the total size of U1 varying only between 148 (S. pombe) to 166 (D. melanogaster) nucleotides. The situation is a little bit different in the hemiascomycetous yeast species with U1 homologues exhibiting a variable size and a different structural organisation. Thus, U1 snRNA homologues have a larger size in the Saccharomyces-kluyveromyces related species (568 nt in S. cerevisiae and 470 nt in S. kluyveri), and a smaller one in the other yeast species like in Y.lipolytica (135 nt) which have a U1 size close to that observed in humans (164 nt) [Roiha et al., 1989, Gene, 82, 137-144]. The comparison of their sequences clearly show that such discordance is due to the presence of supplementary regions in the central domain of the U1 snRNAs as well as a shorter 3'end involving the lack of a 3' terminal stem/loop element. These 'extra' regions, in part functionally nonessential in S. cerevisiae [Guthrie & Patterson, 1988], seem to be phylogenetically conserved in the 'Saccharomyces kluyveromyces' related species like S. bayanus, Z. rouxii, K. thermotolerans, and K. lactis [Bon et al., 2003].

CLUSTALX multiple alignment of U1 snRNA sequences

Last modified: Tue Feb 10 11:15:27 CET 2004