Chimeric and truncated RNAs in Trypanosoma brucei suggest transesterifications at non-consecutive sites during RNA editing

RNA editing adds and removes uridines at specific sites in several mitochondrial transcripts in kinetoplastid parasites probably as specified by guide RNA5 (gRNAs) that are complementary to the final edited sequence. Editing has been postulated to involve trans esterification which predicts (1) chimeric molecules with a gRNA covalently attached by its non-encoded oligo U tail to an internal editing site in the mRNA and (2) the corresponding truncated 5′ portions of the mRNAs. We have characterized cDNAs representing a large number of both types of intermediates from Trypanosoma brucei. The lengths of both U tails and encoded gRNA sequences vary greatly in length. The majority of encoded gRNA sequences are shorter than predicted based on their minicircle coding sequences. Analysis of the predominant sites of gRNA attachment in chimeras suggests that the transesterifications that religate the truncated 5′ mRNAs may proceed more rapidly at editing sites at the 5′ end of an editing domain and at sites of U deletion. Partially edited sequences in the mRNA portion of chimeras and at the 3′ ends of truncated 5′ mRNAs also indicate a non-consecutive order of site selection during RNA editing.