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McDermott SM, Pham V, Oliver B, Carnes J, Sather DN, Stuart KD. Deep mutational scanning of the RNase III-like domain in Trypanosoma brucei RNA editing protein KREPB4. Front Cell Infect Microbiol 2024; 14:1381155. [PMID: 38650737 PMCID: PMC11033214 DOI: 10.3389/fcimb.2024.1381155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/14/2024] [Indexed: 04/25/2024] Open
Abstract
Kinetoplastid pathogens including Trypanosoma brucei, T. cruzi, and Leishmania species, are early diverged, eukaryotic, unicellular parasites. Functional understanding of many proteins from these pathogens has been hampered by limited sequence homology to proteins from other model organisms. Here we describe the development of a high-throughput deep mutational scanning approach in T. brucei that facilitates rapid and unbiased assessment of the impacts of many possible amino acid substitutions within a protein on cell fitness, as measured by relative cell growth. The approach leverages several molecular technologies: cells with conditional expression of a wild-type gene of interest and constitutive expression of a library of mutant variants, degron-controlled stabilization of I-SceI meganuclease to mediate highly efficient transfection of a mutant allele library, and a high-throughput sequencing readout for cell growth upon conditional knockdown of wild-type gene expression and exclusive expression of mutant variants. Using this method, we queried the effects of amino acid substitutions in the apparently non-catalytic RNase III-like domain of KREPB4 (B4), which is an essential component of the RNA Editing Catalytic Complexes (RECCs) that carry out mitochondrial RNA editing in T. brucei. We measured the impacts of thousands of B4 variants on bloodstream form cell growth and validated the most deleterious variants containing single amino acid substitutions. Crucially, there was no correlation between phenotypes and amino acid conservation, demonstrating the greater power of this method over traditional sequence homology searching to identify functional residues. The bloodstream form cell growth phenotypes were combined with structural modeling, RECC protein proximity data, and analysis of selected substitutions in procyclic form T. brucei. These analyses revealed that the B4 RNaseIII-like domain is essential for maintenance of RECC integrity and RECC protein abundances and is also involved in changes in RECCs that occur between bloodstream and procyclic form life cycle stages.
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Affiliation(s)
- Suzanne M. McDermott
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, United States
| | - Vy Pham
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
| | - Brian Oliver
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
| | - Jason Carnes
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
| | - D. Noah Sather
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, United States
| | - Kenneth D. Stuart
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, United States
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Carnes J, McDermott SM, Stuart K. RNA editing catalytic complexes edit multiple mRNA sites non-processively in Trypanosoma brucei. Mol Biochem Parasitol 2023; 256:111596. [PMID: 37742784 DOI: 10.1016/j.molbiopara.2023.111596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/25/2023] [Accepted: 09/20/2023] [Indexed: 09/26/2023]
Abstract
RNA editing generates mature mitochondrial mRNAs in T. brucei by extensive uridine insertion and deletion at numerous editing sites (ESs) as specified by guide RNAs (gRNAs). The editing is performed by three RNA Editing Catalytic Complexes (RECCs) which each have a different endonuclease in addition to 12 proteins in common resulting in RECC1 that is specific for deletion ESs and RECC2 and RECC3 that are specific for insertion ESs. Thus, different RECCs are required for editing of mRNA sequence regions where single gRNAs specify a combination of insertion and deletion ESs. We investigated how the three different RECCs might edit combinations of insertion and deletion ESs that are specified by single gRNAs by testing whether their endonuclease compositions are stable or dynamic during editing. We analyzed in vivo BirA* proximity labeling and found that the endonucleases remain associated with their set of common RECC proteins during editing when expressed at normal physiological levels. We also found that overexpression of endonuclease components resulted in minor effects on RECCs but did not affect growth. Thus, the protein stoichiometries that exist within each RECC can be altered by perturbations of RECC expression levels. These results indicate that editing of consecutive insertion and deletion ESs occurs by successive engagement and disengagement of RECCs, i.e., is non-processive, which is likely the case for consecutive pairs of insertion or deletion ESs. This clarifies the nature of the complex patterns of partially edited mRNAs that occur in vivo.
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Affiliation(s)
- Jason Carnes
- Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Suzanne M McDermott
- Seattle Children's Research Institute, Seattle, WA 98109, USA; Departments of Pediatrics and Global Health, University of Washington, Seattle, WA 98195, USA
| | - Kenneth Stuart
- Seattle Children's Research Institute, Seattle, WA 98109, USA; Departments of Pediatrics and Global Health, University of Washington, Seattle, WA 98195, USA.
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3
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Davidge B, McDermott SM, Carnes J, Lewis I, Tracy M, Stuart KD. Multiple domains of the integral KREPA3 protein are critical for the structure and precise functions of RNA editing catalytic complexes in Trypanosoma brucei. RNA (NEW YORK, N.Y.) 2023; 29:1591-1609. [PMID: 37474258 PMCID: PMC10578492 DOI: 10.1261/rna.079691.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/30/2023] [Indexed: 07/22/2023]
Abstract
The gRNA directed U-insertion and deletion editing of mitochondrial mRNAs that is essential in different life-cycle stages for the protozoan parasite Trypanosoma brucei is performed by three similar multiprotein catalytic complexes (CCs) that contain the requisite enzymes. These CCs also contain a common set of eight proteins that have no apparent direct catalytic function, including six that have an OB-fold domain. We show here that one of these OB-fold proteins, KREPA3 (A3), has structural homology to other editing proteins, is essential for editing, and is multifunctional. We investigated A3 function by analyzing the effects of single amino acid loss of function mutations, most of which were identified by screening bloodstream form (BF) parasites for loss of growth following random mutagenesis. Mutations in the zinc fingers (ZFs), an intrinsically disordered region (IDR), and several within or near the carboxy-terminal OB-fold domain variably impacted CC structural integrity and editing. Some mutations resulted in almost complete loss of CCs and its proteins and editing, whereas others retained CCs but had aberrant editing. All but a mutation which is near the OB-fold affected growth and editing in BF but not procyclic form (PF) parasites. These data indicate that multiple positions within A3 have essential functions that contribute to the structural integrity of CCs, the precision of editing and the developmental differences in editing between BF and PF stages.
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Affiliation(s)
- Brittney Davidge
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
| | - Suzanne M McDermott
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
- Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
| | - Jason Carnes
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
| | - Isaac Lewis
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
| | - Maxwell Tracy
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
| | - Kenneth D Stuart
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
- Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
- Department of Global Health, University of Washington, Seattle, Washington 98195, USA
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4
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Davidge B, McDermott SM, Carnes J, Lewis I, Tracy M, Stuart KD. Multiple domains of the integral KREPA3 protein are critical for the structure and precise functions of RNA Editing Catalytic Complexes in Trypanosoma brucei. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.537538. [PMID: 37131796 PMCID: PMC10153193 DOI: 10.1101/2023.04.19.537538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The gRNA directed U-insertion and deletion editing of mitochondrial mRNAs that is essential in different life cycle stages for the protozoan parasite Trypanosoma brucei is performed by three similar multi-protein catalytic complexes (CCs) that contain the requisite enzymes. These CCs also contain a common set of eight proteins that have no apparent direct catalytic function, including six that have an OB-fold domain. We show here that one of these OB-fold proteins, KREPA3 (A3), has structural homology to other editing proteins, is essential for editing and is multifunctional. We investigated A3 function by analyzing the effects of single amino acid loss of function mutations most of which were identified by screening bloodstream form (BF) parasites for loss of growth following random mutagenesis. Mutations in the ZFs, an intrinsically disordered region (IDR) and several within or near the C-terminal OB-fold domain variably impacted CC structural integrity and editing. Some mutations resulted in almost complete loss of CCs and its proteins and editing whereas others retained CCs but had aberrant editing. All but a mutation which is near the OB-fold affected growth and editing in BF but not procyclic form (PF) parasites. These data indicate that multiple positions within A3 have essential functions that contribute to the structural integrity of CCs, the precision of editing and the developmental differences in editing between BF and PF stages.
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Affiliation(s)
- Brittney Davidge
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, WA 98109
| | - Suzanne M McDermott
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, WA 98109
- Department of Pediatrics, University of Washington, Seattle, WA
| | - Jason Carnes
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, WA 98109
| | - Isaac Lewis
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, WA 98109
| | - Maxwell Tracy
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, WA 98109
| | - Kenneth D Stuart
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, WA 98109
- Department of Pediatrics, University of Washington, Seattle, WA
- Department of Global Health, University of Washington, Seattle, WA
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5
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Carnes J, McDermott SM, Lewis I, Tracy M, Stuart K. Domain function and predicted structure of three heterodimeric endonuclease subunits of RNA editing catalytic complexes in Trypanosoma brucei. Nucleic Acids Res 2022; 50:10123-10139. [PMID: 36095119 PMCID: PMC9508840 DOI: 10.1093/nar/gkac753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 08/18/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
Each of the three similar RNA Editing Catalytic Complexes (RECCs) that perform gRNA-directed uridine insertion and deletion during Trypanosoma brucei mitochondrial (mt) mRNA editing has a distinct endonuclease activity that requires two related RNase III proteins, with only one competent for catalysis. We identified multiple loss-of-function mutations in the RNase III and other motifs of the non-catalytic KREPB6, KREPB7, and KREPB8 components by random mutagenesis and screening. These mutations had various effects on growth, editing, and both the abundances and RECC associations of these RNase III protein pairs in bloodstream form (BF) and procyclic form (PF) cells. Protein structure modelling predicted that the Zinc Finger (ZnF) of each paired RNase III protein contacts RNA positioned at the heterodimeric active site which is flanked by helices of a novel RNase III-Associated Motif (RAM). The results indicate that the protein domains of the non-catalytic subunits function together in RECC integrity, substrate binding, and editing site recognition during the multistep RNA editing process. Additionally, several mutants display distinct functional consequences in different life cycle stages. These results highlight the complementary roles of protein pairs and three RECCs within the complicated T. brucei mRNA editing machinery that matures mt mRNAs differentially between developmental stages.
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Affiliation(s)
- Jason Carnes
- Seattle Children's Research Institute, Seattle, WA, USA
| | - Suzanne M McDermott
- Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Isaac Lewis
- Seattle Children's Research Institute, Seattle, WA, USA
| | - Maxwell Tracy
- Seattle Children's Research Institute, Seattle, WA, USA
| | - Kenneth Stuart
- Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
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How RNases Shape Mitochondrial Transcriptomes. Int J Mol Sci 2022; 23:ijms23116141. [PMID: 35682820 PMCID: PMC9181182 DOI: 10.3390/ijms23116141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022] Open
Abstract
Mitochondria are the power houses of eukaryote cells. These endosymbiotic organelles of prokaryote origin are considered as semi-autonomous since they have retained a genome and fully functional gene expression mechanisms. These pathways are particularly interesting because they combine features inherited from the bacterial ancestor of mitochondria with characteristics that appeared during eukaryote evolution. RNA biology is thus particularly diverse in mitochondria. It involves an unexpectedly vast array of factors, some of which being universal to all mitochondria and others being specific from specific eukaryote clades. Among them, ribonucleases are particularly prominent. They play pivotal functions such as the maturation of transcript ends, RNA degradation and surveillance functions that are required to attain the pool of mature RNAs required to synthesize essential mitochondrial proteins such as respiratory chain proteins. Beyond these functions, mitochondrial ribonucleases are also involved in the maintenance and replication of mitochondrial DNA, and even possibly in the biogenesis of mitochondrial ribosomes. The diversity of mitochondrial RNases is reviewed here, showing for instance how in some cases a bacterial-type enzyme was kept in some eukaryotes, while in other clades, eukaryote specific enzymes were recruited for the same function.
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Aphasizheva I, Alfonzo J, Carnes J, Cestari I, Cruz-Reyes J, Göringer HU, Hajduk S, Lukeš J, Madison-Antenucci S, Maslov DA, McDermott SM, Ochsenreiter T, Read LK, Salavati R, Schnaufer A, Schneider A, Simpson L, Stuart K, Yurchenko V, Zhou ZH, Zíková A, Zhang L, Zimmer S, Aphasizhev R. Lexis and Grammar of Mitochondrial RNA Processing in Trypanosomes. Trends Parasitol 2020; 36:337-355. [PMID: 32191849 PMCID: PMC7083771 DOI: 10.1016/j.pt.2020.01.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/19/2020] [Accepted: 01/22/2020] [Indexed: 12/15/2022]
Abstract
Trypanosoma brucei spp. cause African human and animal trypanosomiasis, a burden on health and economy in Africa. These hemoflagellates are distinguished by a kinetoplast nucleoid containing mitochondrial DNAs of two kinds: maxicircles encoding ribosomal RNAs (rRNAs) and proteins and minicircles bearing guide RNAs (gRNAs) for mRNA editing. All RNAs are produced by a phage-type RNA polymerase as 3' extended precursors, which undergo exonucleolytic trimming. Most pre-mRNAs proceed through 3' adenylation, uridine insertion/deletion editing, and 3' A/U-tailing. The rRNAs and gRNAs are 3' uridylated. Historically, RNA editing has attracted major research effort, and recently essential pre- and postediting processing events have been discovered. Here, we classify the key players that transform primary transcripts into mature molecules and regulate their function and turnover.
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Affiliation(s)
- Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA 02118, USA.
| | - Juan Alfonzo
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Jason Carnes
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Igor Cestari
- Institute of Parasitology, McGill University, 21,111 Lakeshore Road, Ste-Anne-de-Bellevue, H9X3V9, Québec, Canada
| | - Jorge Cruz-Reyes
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - H Ulrich Göringer
- Department of Molecular Genetics, Darmstadt University of Technology, 64287 Darmstadt, Germany
| | - Stephen Hajduk
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Susan Madison-Antenucci
- Parasitology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
| | - Dmitri A Maslov
- Department of Molecular, Cell, and Systems Biology, University of California - Riverside, Riverside, CA 92521, USA
| | - Suzanne M McDermott
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Torsten Ochsenreiter
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, Bern CH-3012, Switzerland
| | - Laurie K Read
- Department of Microbiology and Immunology, University at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Reza Salavati
- Institute of Parasitology, McGill University, 21,111 Lakeshore Road, Ste-Anne-de-Bellevue, H9X3V9, Québec, Canada
| | - Achim Schnaufer
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - André Schneider
- Department of Chemistry and Biochemistry, University of Bern, Bern CH-3012, Switzerland
| | - Larry Simpson
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095, USA
| | - Kenneth Stuart
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic; Martsinovsky Institute of Medical Parasitology, Sechenov University, Moscow, Russia
| | - Z Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095, USA
| | - Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Liye Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Sara Zimmer
- University of Minnesota Medical School, Duluth campus, Duluth, MN 55812, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA 02118, USA
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McDermott SM, Carnes J, Stuart K. Editosome RNase III domain interactions are essential for editing and differ between life cycle stages in Trypanosoma brucei. RNA (NEW YORK, N.Y.) 2019; 25:1150-1163. [PMID: 31171708 PMCID: PMC6800513 DOI: 10.1261/rna.071258.119] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/05/2019] [Indexed: 06/04/2023]
Abstract
Multiprotein editosomes catalyze gRNA-specified insertion and deletion of uridines to create functional mitochondrial mRNAs in Trypanosoma brucei Three functionally distinct editosomes are distinguished by their single KREN1, KREN2, or KREN3 RNase III endonuclease and, respectively, KREPB8, KREPB7, and KREPB6 partner proteins. These endonucleases perform the first catalytic step of editing, cleaving mRNA in diverse mRNA/gRNA heteroduplex substrates. We identified divergent and likely noncatalytic RNase III domains in KREPB4, KREPB5, KREPB6, KREPB7, KREPB8, KREPB9, and KREPB10 editosome proteins. Because known RNase III endonuclease functional domains are dimeric, the editing endonucleases may form heterodimers with one or more of these divergent RNase III proteins. We show here using conditional null cell lines that KREPB6, KREPB7, and KREPB8 are essential in both procyclic form (PF) and bloodstream (BF) cells. Loss of these proteins results in growth defects and loss of editing in vivo, as does mutation of their RNase III domain that is predicted to prevent dimerization. Loss of KREPB6, KREPB7, or KREPB8 also dramatically reduces cognate endonuclease abundance, as does the RNase III mutation, indicating that RNase III interactions with their partner proteins stabilize the endonucleases. The phenotypic consequences of repression are more severe in BF than in PF, indicating differences in endonuclease function between developmental stages that could impact regulation of editing. These results suggest that KREPB6, KREPB7, and KREPB8 form heterodimers with their respective endonucleases to perform mRNA cleavage. We also present a model wherein editosome proteins with divergent RNase III domains function in substrate selection via enzyme-pseudoenzyme interactions.
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Affiliation(s)
- Suzanne M McDermott
- Seattle Children's Research Institute (formerly Center for Infectious Disease Research), Seattle, Washington 98109, USA
| | - Jason Carnes
- Seattle Children's Research Institute (formerly Center for Infectious Disease Research), Seattle, Washington 98109, USA
| | - Kenneth Stuart
- Seattle Children's Research Institute (formerly Center for Infectious Disease Research), Seattle, Washington 98109, USA
- Department of Global Health, University of Washington, Seattle, Washington 98195, USA
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9
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Cruz-Reyes J, Mooers BHM, Doharey PK, Meehan J, Gulati S. Dynamic RNA holo-editosomes with subcomplex variants: Insights into the control of trypanosome editing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1502. [PMID: 30101566 DOI: 10.1002/wrna.1502] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 07/03/2018] [Accepted: 07/09/2018] [Indexed: 12/14/2022]
Abstract
RNA editing causes massive remodeling of the mitochondrial mRNA transcriptome in trypanosomes and related kinetoplastid protozoa. This type of editing involves the specific insertion or deletion of uridylates (U) directed by small noncoding guide RNAs (gRNAs). Because U-insertion exceeds U-deletion by a factor of 10, editing increases the nascent mRNA size by up to 55%. In Trypanosoma brucei, the editing apparatus uses ~40 proteins and >1,200 gRNAs to create the functional open reading frame in 12 mRNAs. Thousands of sites are specifically recognized in the pre-edited mRNAs and a myriad of partially edited transcript intermediates accumulates in mitochondria. The control of editing is poorly understood, but past work suggests that it occurs during substrate recognition, the initiation and progression of editing, and during the life-cycle in different hosts. The growing understanding of the editing proteins offers clues about editing control. Most editing proteins reside in the "RNA-free" RNA editing core complex (RECC) and in the accessory RNA editing substrate complex (RESC) that contains gRNA. Two accessory RNA helicases are known, including one in the RNA editing helicase 2 complex (REH2C). Both the RESC and the REH2C associate with mRNA, providing a rationale for the assembly of mRNA or its mRNPs, RESC, and the RECC enzyme. Identified variants of the canonical editing complexes further complicate the model of RNA editing. We examine specific examples of complex variants, differential effects of editing proteins on the mRNAs within and between T. brucei life stages, and possible control points in RNA holo-editosomes. This article is categorized under: RNA Processing > RNA Editing and Modification RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Jorge Cruz-Reyes
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Blaine H M Mooers
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Pawan K Doharey
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Joshua Meehan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Shelly Gulati
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
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