Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes. Academic Article uri icon

abstract

  • Trypanosome U-insertion/deletion RNA editing in mitochondrial mRNAs involves guide RNAs (gRNAs) and the auxiliary RNA editing substrate binding complex (RESC) and RNA editing helicase 2 complex (REH2C). RESC and REH2C stably copurify with editing mRNAs but the functional interplay between these complexes remains unclear. Most steady-state mRNAs are partially edited and include misedited "junction" regions that match neither pre-mRNA nor fully edited transcripts. Editing specificity is central to mitochondrial RNA maturation and function, but its basic control mechanisms remain unclear. Here we applied a novel nucleotide-resolution RNA-seq approach to examine ribosomal protein subunit 12 (RPS12) and ATPase subunit 6 (A6) mRNA transcripts. We directly compared transcripts associated with RESC and REH2C to those found in total mitochondrial RNA. RESC-associated transcripts exhibited site-preferential enrichments in total and accurate edits. REH2C loss-of-function induced similar substrate-specific and site-specific editing effects in total and RESC-associated RNA. It decreased total editing primarily at RPS12 5' positions but increased total editing at examined A6 3' positions. REH2C loss-of-function caused site-preferential loss of accurate editing in both transcripts. However, changes in total or accurate edits did not necessarily involve common sites. A few 5' nucleotides of the initiating gRNA (gRNA-1) directed accurate editing in both transcripts. However, in RPS12, two conserved 3'-terminal adenines in gRNA-1 could direct a noncanonical 2U-insertion that causes major pausing in 3'-5' progression. In A6, a noncanonical sequence element that depends on REH2C in a region normally targeted by the 3' half of gRNA-1 may hinder early editing progression. Overall, we defined transcript-specific effects of REH2C loss.

author list (cited authors)

  • Kumar, V., Ivens, A., Goodall, Z., Meehan, J., Doharey, P. K., Hillhouse, A., ... Cruz-Reyes, J.

complete list of authors

  • Kumar, Vikas||Ivens, Alasdair||Goodall, Zachary||Meehan, Joshua||Doharey, Pawan Kumar||Hillhouse, Andrew||Hurtado, Daniel Osorio||Cai, James J||Zhang, Xiuren||Schnaufer, Achim||Cruz-Reyes, Jorge

publication date

  • January 1, 2020 11:11 AM

published in

  • RNA  Journal