Transcription termination and 3 '-end processing of the spliced leader RNAin kinetoplastids

Addition of a 39-nucleotide (nt) spliced leader (SL) by trans splicing is a basic requirement for all trypanosome nuclear mRNAs. The SL RNA in Leishma nia tarentolae is a 96-nt precursor transcript synthesized by a polymerase that resembles polymerase II most closely. To analyze SL RNA genesis, we mu tated SL RNA intron structures and sequence elements: stem-loops II and III , the Sm-binding site, and the downstream T tract. Using an exon-tagged SL RNA gene, we examined the phenotypes produced by a second-site 10-bp linker scan mutagenic series and directed mutagenesis. Here we report that transc ription is terminated by the T tract, which is common to the 3' end of all kinetoplastid SL RNA genes, and that more than six T's are required for eff icient termination in vivo. We describe mutants whose SL RNAs end in the T tract or appear to lack efficient termination but can generate wild-type 3' ends. Transcriptionally active nuclear extracts show staggered products in the T tract, directed by eight or more T's. The in vivo and in vitro data suggest that SL RNA transcription termination is staggered in the T tract a nd is followed by nucleolytic processing to generate the mature 3' end. We show that the Sm-binding site and stem-loop In structures are necessary for correct 3'-end formation. Thus, we have defined the transcription terminat ion element for the SL RNA gene. The termination mechanism differs from tha t of vertebrate small nuclear RNA genes and the SL RNA homologue in Ascaris .