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Kumar V, Ivens A, Goodall Z, Meehan J, Doharey PK, Hillhouse A, Hurtado DO, Cai JJ, Zhang X, Schnaufer A, Cruz-Reyes J. Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes. RNA 2020; 26:1862-1881. [PMID: 32873716 PMCID: PMC7668249 DOI: 10.1261/rna.076513.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 08/22/2020] [Indexed: 05/21/2023]
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.
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Affiliation(s)
- Vikas Kumar
- Department of Biochemistry, Texas A&M University, College Station, Texas 77843, USA
| | - Alasdair Ivens
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh EH9 3FL, Scotland, United Kingdom
| | - Zachary Goodall
- Department of Biochemistry, Texas A&M University, College Station, Texas 77843, USA
| | - Joshua Meehan
- Department of Biochemistry, Texas A&M University, College Station, Texas 77843, USA
| | - Pawan Kumar Doharey
- Department of Biochemistry, Texas A&M University, College Station, Texas 77843, USA
| | - Andrew Hillhouse
- Texas A&M Institute for Genome Sciences and Society, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA
| | - Daniel Osorio Hurtado
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA
| | - James J Cai
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA
| | - Xiuren Zhang
- Department of Biochemistry, Texas A&M University, College Station, Texas 77843, USA
| | - Achim Schnaufer
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh EH9 3FL, Scotland, United Kingdom
| | - Jorge Cruz-Reyes
- Department of Biochemistry, Texas A&M University, College Station, Texas 77843, USA
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