Cargando…
Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes
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 comp...
Autores principales: | , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory Press
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7668249/ https://www.ncbi.nlm.nih.gov/pubmed/32873716 http://dx.doi.org/10.1261/rna.076513.120 |
_version_ | 1783610454041427968 |
---|---|
author | 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 |
author_facet | 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 |
author_sort | Kumar, Vikas |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-7668249 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-76682492021-12-01 Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes 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 RNA Article 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. Cold Spring Harbor Laboratory Press 2020-12 /pmc/articles/PMC7668249/ /pubmed/32873716 http://dx.doi.org/10.1261/rna.076513.120 Text en © 2020 Kumar et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/. |
spellingShingle | Article 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 Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes |
title | Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes |
title_full | Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes |
title_fullStr | Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes |
title_full_unstemmed | Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes |
title_short | Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes |
title_sort | site-specific and substrate-specific control of accurate mrna editing by a helicase complex in trypanosomes |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7668249/ https://www.ncbi.nlm.nih.gov/pubmed/32873716 http://dx.doi.org/10.1261/rna.076513.120 |
work_keys_str_mv | AT kumarvikas sitespecificandsubstratespecificcontrolofaccuratemrnaeditingbyahelicasecomplexintrypanosomes AT ivensalasdair sitespecificandsubstratespecificcontrolofaccuratemrnaeditingbyahelicasecomplexintrypanosomes AT goodallzachary sitespecificandsubstratespecificcontrolofaccuratemrnaeditingbyahelicasecomplexintrypanosomes AT meehanjoshua sitespecificandsubstratespecificcontrolofaccuratemrnaeditingbyahelicasecomplexintrypanosomes AT dohareypawankumar sitespecificandsubstratespecificcontrolofaccuratemrnaeditingbyahelicasecomplexintrypanosomes AT hillhouseandrew sitespecificandsubstratespecificcontrolofaccuratemrnaeditingbyahelicasecomplexintrypanosomes AT hurtadodanielosorio sitespecificandsubstratespecificcontrolofaccuratemrnaeditingbyahelicasecomplexintrypanosomes AT caijamesj sitespecificandsubstratespecificcontrolofaccuratemrnaeditingbyahelicasecomplexintrypanosomes AT zhangxiuren sitespecificandsubstratespecificcontrolofaccuratemrnaeditingbyahelicasecomplexintrypanosomes AT schnauferachim sitespecificandsubstratespecificcontrolofaccuratemrnaeditingbyahelicasecomplexintrypanosomes AT cruzreyesjorge sitespecificandsubstratespecificcontrolofaccuratemrnaeditingbyahelicasecomplexintrypanosomes |