The U6 snRNA-encoding gene of the monogenetic trypanosomatid Leptomonas collosoma.

The U6 snRNA (U6) is the most conserved small nuclear RNA (snRNA) and apparently plays a central role in catalysis of the cis-splicing reaction. In trans-splicing, U6 may have an additional function. In the nematode trans-splicing system, a direct interaction between the U6 and spliced leader (SL) RNAs has been demonstrated, suggesting that U6 may serve as a bridge between the SL RNA and the acceptor pre-mRNA. To examine possible phylogenetic conservation of trypanosomatid U6 sequences that may interact with spliceosomal RNAs, we have cloned and sequenced the U6 gene from the monogenetic trypanosomatid Leptomonas collosoma (Lc). The Lc U6 deviates from the Trypanosoma brucei (Tb) RNA only in four positions located in the 5' stem-loop and the central domains. As in Tb, U6 is a single-copy gene and two tRNA genes, tRNAGln and tRNAIle, are found upstream to the gene. The tRNAs are differentially expressed; tRNAGln is transcribed in the opposite direction to U6, whereas tRNAIle 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.