The U6 snRNA (U6) is the most conserved small nuclear RNA (snRNA) and
apparently plays a central role in catalysis of the cis-splicing react
ion. In trans-splicing, U6 may have an additional function. In the nem
atode trans-splicing system, a direct interaction between the U6 and s
pliced leader (SL) RNAs has been demonstrated, suggesting that U6 may
serve as a bridge between the SL RNA and the acceptor pre-mRNA. To exa
mine possible phylogenetic conservation of trypanosomatid U6 sequences
that may interact with spliceosomal RNAs, we have cloned and sequence
d the U6 gene from the monogenetic trypanosomatid Leptomonas collosoma
(Lc). The Le U6 deviates from the Trypanosoma brucei (Tb) RNA only in
four positions located in the 5' stem-loop and the central domains. A
s in Tb, U6 is a single-copy gene and two tRNA genes, tRNA(Gln) and tR
NA(Ile), are found upstream to the gene. The tRNAs are differentially
expressed; tRNA(Gln) is transcribed in the opposite direction to U6, w
hereas tRNA(Ile) is not transcribed. Possible base-pairing between U6
and the U2 and SL RNAs, similar to the interactions that take place in
the nematode trans-splicing system, are proposed.