Phylogenetic conservation of modified nucleotides in the terminal loop 1 of the spliceosomal U5 snRNA

In order to study the phylogenetic conservation of modified nucleotides in the spliceosomal U5 snRNA, we determined the nucleotide sequences of the U5 snRNAs from the slime mold Physarum polycephalum (EMBL data bank accession numbers: X74440 and X74441) and we identified the pseudouridine and 2′-O-methylated residues. From a comparison of all the U5 snRNAs studied at the level of nucleotide modifications, we concluded that the modified nucleotides in U5 snRNA can be divided into three classes according to their degree of conservation: i) the modified nucleotides of the 5′ terminal cap structure that display some variations from one species to the other; ii) the modified nucleotides located in the helical part of the stem/loop structure I that vary greatly in number, position and identity from one species to the other; and iii) the modified nucleotides of the terminal loop 1, that are almost identical in all the species studied. Taking into account the recent discovery of a crucial role played by this terminal loop of U5 snRNA in 5′ and 3′ splice site definition, we postulate that the numerous modified nucleotides it contains, five out of a total of 11, play an important role in spliceosome assembly and function. Their possible role is discussed.