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Wackowski K, Zhu X, Shen S, Zhang M, Qu J, Read LK. RESC14 and RESC8 cooperate to mediate RESC function and dynamics during trypanosome RNA editing. Nucleic Acids Res 2024:gkae561. [PMID: 38967000 DOI: 10.1093/nar/gkae561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 05/16/2024] [Accepted: 06/18/2024] [Indexed: 07/06/2024] Open
Abstract
Mitochondrial transcripts in Trypanosoma brucei require extensive uridine insertion/deletion RNA editing to generate translatable open reading frames. The RNA editing substrate binding complex (RESC) serves as the scaffold that coordinates the protein-protein and protein-RNA interactions during editing. RESC broadly contains two modules termed the guide RNA binding complex (GRBC) and the RNA editing mediator complex (REMC), as well as organizer proteins. How the protein and RNA components of RESC dynamically interact to facilitate editing is not well understood. Here, we examine the roles of organizer proteins, RESC8 and RESC14, in facilitating RESC dynamics. High-throughput sequencing of editing intermediates reveals an overlapping RESC8 and RESC14 function during editing progression across multiple transcripts. Blue native PAGE analysis demonstrates that RESC14 is essential for incorporation of RESC8 into a large RNA-containing complex, while RESC8 is important in recruiting a smaller ribonucleoprotein complex (RNP) to this large complex. Proximity labeling shows that RESC14 is important for stable RESC protein-protein interactions, as well as RESC-RECC associations. Together, our data support a model in which RESC14 is necessary for assembly of editing competent RESC through recruitment of an RNP containing RESC8, GRBC and gRNA to REMC and mRNA.
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Affiliation(s)
- Katherine Wackowski
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Xiaoyu Zhu
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA and NYS Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Shichen Shen
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA and NYS Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Ming Zhang
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA and NYS Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA and NYS Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Laurie K Read
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
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2
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Poorinmohammad N, Salavati R. Prioritization of Trypanosoma brucei editosome protein interactions interfaces at residue resolution through proteome-scale network analysis. BMC Mol Cell Biol 2024; 25:3. [PMID: 38279116 PMCID: PMC10811811 DOI: 10.1186/s12860-024-00499-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/19/2024] [Indexed: 01/28/2024] Open
Abstract
BACKGROUND Trypanosoma brucei is the causative agent for trypanosomiasis in humans and livestock, which presents a growing challenge due to drug resistance. While identifying novel drug targets is vital, the process is delayed due to a lack of functional information on many of the pathogen's proteins. Accordingly, this paper presents a computational framework for prioritizing drug targets within the editosome, a vital molecular machinery responsible for mitochondrial RNA processing in T. brucei. Importantly, this framework may eliminate the need for prior gene or protein characterization, potentially accelerating drug discovery efforts. RESULTS By integrating protein-protein interaction (PPI) network analysis, PPI structural modeling, and residue interaction network (RIN) analysis, we quantitatively ranked and identified top hub editosome proteins, their key interaction interfaces, and hotspot residues. Our findings were cross-validated and further prioritized by incorporating them into gene set analysis and differential expression analysis of existing quantitative proteomics data across various life stages of T. brucei. In doing so, we highlighted PPIs such as KREL2-KREPA1, RESC2-RESC1, RESC12A-RESC13, and RESC10-RESC6 as top candidates for further investigation. This includes examining their interfaces and hotspot residues, which could guide drug candidate selection and functional studies. CONCLUSION RNA editing offers promise for target-based drug discovery, particularly with proteins and interfaces that play central roles in the pathogen's life cycle. This study introduces an integrative drug target identification workflow combining information from the PPI network, PPI 3D structure, and reside-level information of their interface which can be applicable to diverse pathogens. In the case of T. brucei, via this pipeline, the present study suggested potential drug targets with residue-resolution from RNA editing machinery. However, experimental validation is needed to fully realize its potential in advancing urgently needed antiparasitic drug development.
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Affiliation(s)
- Naghmeh Poorinmohammad
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Montreal, Quebec, H9X 3V9, Canada
| | - Reza Salavati
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Montreal, Quebec, H9X 3V9, Canada.
- Department of Biochemistry, McGill University, Montreal, Quebec, H3G 1Y6, Canada.
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3
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Ehlert C, Poorinmohammad N, Mohammaei S, Zhang L, Salavati R. Structure-Function Analysis of RBP7910: An Editosome Z-Binding Protein in Trypanosomatids. Molecules 2023; 28:6963. [PMID: 37836806 PMCID: PMC10574248 DOI: 10.3390/molecules28196963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/01/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023] Open
Abstract
RNA editing, a unique post-transcriptional modification, is observed in trypanosomatid parasites as a crucial procedure for the maturation of mitochondrial mRNAs. The editosome protein complex, involving multiple protein components, plays a key role in this process. In Trypanosoma brucei, a putative Z-DNA binding protein known as RBP7910 is associated with the editosome. However, the specific Z-DNA/Z-RNA binding activity and the interacting interface of RBP7910 have yet to be determined. In this study, we conducted a comparative analysis of the binding behavior of RBP7910 with different potential ligands using microscale thermophoresis (MST). Additionally, we generated a 3D model of the protein, revealing potential Z-α and Z-β nucleic acid-binding domains of RBP7910. RBP7910 belongs to the winged-helix-turn-helix (HTH) superfamily of proteins with an α1α2α3β1β2 topology. Finally, using docking techniques, potential interacting surface regions of RBP7910 with notable oligonucleotide ligands were identified. Our findings indicate that RBP7910 exhibits a notable affinity for (CG)n Z-DNA, both in single-stranded and double-stranded forms. Moreover, we observed a broader interacting interface across its Z-α domain when bound to Z-DNA/Z-RNA compared to when bound to non-Z-form nucleic acid ligands.
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Affiliation(s)
- Curtis Ehlert
- Institute of Parasitology, McGill University, Montreal, QC H9X 3V9, Canada; (C.E.); (N.P.); (S.M.); (L.Z.)
| | - Naghmeh Poorinmohammad
- Institute of Parasitology, McGill University, Montreal, QC H9X 3V9, Canada; (C.E.); (N.P.); (S.M.); (L.Z.)
| | - Saba Mohammaei
- Institute of Parasitology, McGill University, Montreal, QC H9X 3V9, Canada; (C.E.); (N.P.); (S.M.); (L.Z.)
| | - Linhua Zhang
- Institute of Parasitology, McGill University, Montreal, QC H9X 3V9, Canada; (C.E.); (N.P.); (S.M.); (L.Z.)
| | - Reza Salavati
- Institute of Parasitology, McGill University, Montreal, QC H9X 3V9, Canada; (C.E.); (N.P.); (S.M.); (L.Z.)
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada
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4
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Liu S, Wang H, Li X, Zhang F, Lee JKJ, Li Z, Yu C, Hu JJ, Zhao X, Suematsu T, Alvarez-Cabrera AL, Liu Q, Zhang L, Huang L, Aphasizheva I, Aphasizhev R, Zhou ZH. Structural basis of gRNA stabilization and mRNA recognition in trypanosomal RNA editing. Science 2023; 381:eadg4725. [PMID: 37410820 DOI: 10.1126/science.adg4725] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/17/2023] [Indexed: 07/08/2023]
Abstract
In Trypanosoma brucei, the editosome, composed of RNA-editing substrate-binding complex (RESC) and RNA-editing catalytic complex (RECC), orchestrates guide RNA (gRNA)-programmed editing to recode cryptic mitochondrial transcripts into messenger RNAs (mRNAs). The mechanism of information transfer from gRNA to mRNA is unclear owing to a lack of high-resolution structures for these complexes. With cryo-electron microscopy and functional studies, we have captured gRNA-stabilizing RESC-A and gRNA-mRNA-binding RESC-B and RESC-C particles. RESC-A sequesters gRNA termini, thus promoting hairpin formation and blocking mRNA access. The conversion of RESC-A into RESC-B or -C unfolds gRNA and allows mRNA selection. The ensuing gRNA-mRNA duplex protrudes from RESC-B, likely exposing editing sites to RECC-catalyzed cleavage, uridine insertion or deletion, and ligation. Our work reveals a remodeling event facilitating gRNA-mRNA hybridization and assembly of a macromolecular substrate for the editosome's catalytic modality.
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Affiliation(s)
- Shiheng Liu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Hong Wang
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA, USA
| | - Xiaorun Li
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Fan Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jane K J Lee
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Zihang Li
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California, Irvine, CA, USA
| | - Jason J Hu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Xiaojing Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Takuma Suematsu
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA, USA
| | - Ana L Alvarez-Cabrera
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Qiushi Liu
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA, USA
| | - Liye Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, CA, USA
| | - Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA, USA
- Department of Biochemistry, Boston University Medical Campus, Boston, MA, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
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5
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Dubey AP, Tylec BL, Mishra A, Sortino K, Chen R, Sun Y, Read LK. KREH1 RNA helicase activity promotes utilization of initiator gRNAs across multiple mRNAs in trypanosome RNA editing. Nucleic Acids Res 2023; 51:5791-5809. [PMID: 37140035 PMCID: PMC10287954 DOI: 10.1093/nar/gkad292] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/04/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023] Open
Abstract
Mitochondrial U-indel RNA editing in kinetoplastid protozoa is directed by trans-acting gRNAs and mediated by a holoenzyme with associated factors. Here, we examine the function of the holoenzyme-associated KREH1 RNA helicase in U-indel editing. We show that KREH1 knockout (KO) impairs editing of a small subset of mRNAs. Overexpression of helicase-dead mutants results in expanded impairment of editing across multiple transcripts, suggesting the existence of enzymes that can compensate for KREH1 in KO cells. In depth analysis of editing defects using quantitative RT-PCR and high-throughput sequencing reveals compromised editing initiation and progression in both KREH1-KO and mutant-expressing cells. In addition, these cells exhibit a distinct defect in the earliest stages of editing in which the initiator gRNA is bypassed, and a small number of editing events takes place just outside this region. Wild type KREH1 and a helicase-dead KREH1 mutant interact similarly with RNA and holoenzyme, and overexpression of both similarly disorders holoenzyme homeostasis. Thus, our data support a model in which KREH1 RNA helicase activity facilitates remodeling of initiator gRNA-mRNA duplexes to permit accurate utilization of initiating gRNAs on multiple transcripts.
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Affiliation(s)
- Ashutosh P Dubey
- Dept. of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Brianna L Tylec
- Dept. of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Amartya Mishra
- Dept. of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Katherine Sortino
- Dept. of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Runpu Chen
- Dept. of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Yijun Sun
- Dept. of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Laurie K Read
- Dept. of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
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6
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Sortino K, Tylec BL, Chen R, Sun Y, Read LK. Conserved and transcript-specific functions of the RESC factors, RESC13 and RESC14, in kinetoplastid RNA editing. RNA (NEW YORK, N.Y.) 2022; 28:1496-1508. [PMID: 36096641 PMCID: PMC9745829 DOI: 10.1261/rna.079389.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/28/2022] [Indexed: 05/21/2023]
Abstract
Uridine insertion/deletion RNA editing is an extensive post-transcriptional modification of mitochondrial mRNAs in kinetoplastid organisms, including Trypanosoma brucei This process is carried out using trans-acting gRNAs and complex protein machinery. The essential RNA editing substrate binding complex (RESC) serves as the scaffold that modulates protein and RNA interactions during editing, and contains the guide RNA binding complex (GRBC), the RNA editing mediator complexes (REMCs), and organizer proteins. Despite the importance of RESC in editing, the functions of each protein comprising this complex are not completely understood. Here, we further define the roles of a REMC protein, RESC13, and a RESC organizer, RESC14, using high-throughput sequencing on two large pan-edited mRNAs, A6 and COIII. When comparing our analyses to that of a previously published small pan-edited mRNA, RPS12, we find that RESC13 has conserved functions across the three transcripts with regard to editing initiation, gRNA utilization, gRNA exchange, and restricting the formation of long misedited junctions that likely arise from its ability to modulate RNA structure. However, RESC13 does have transcript-specific effects on the types of long junctions whose formation it restricts. RESC14 has a conserved effect on gRNA utilization across the three transcripts analyzed, but has transcript-specific effects on editing initiation, gRNA exchange, and junction formation. Our data suggest that transcript-specific effects of both proteins are due to differences in transcript length and sequences as well as transcript-specific protein interactions. These findings highlight the importance of studying multiple transcripts to determine the function of editing factors.
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Affiliation(s)
- Katherine Sortino
- Department of Microbiology and Immunology, University at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York 14203, USA
| | - Brianna L Tylec
- Department of Microbiology and Immunology, University at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York 14203, USA
| | - Runpu Chen
- Department of Microbiology and Immunology, University at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York 14203, USA
| | - Yijun Sun
- Department of Microbiology and Immunology, University at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York 14203, USA
| | - Laurie K Read
- Department of Microbiology and Immunology, University at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York 14203, USA
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7
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Dubey AP, Tylec BL, McAdams NM, Sortino K, Read L. Trypanosome RNAEditing Substrate Binding Complex integrity and function depends on the upstream action of RESC10. Nucleic Acids Res 2021; 49:3557-3572. [PMID: 33677542 PMCID: PMC8034615 DOI: 10.1093/nar/gkab129] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/11/2021] [Accepted: 02/17/2021] [Indexed: 01/17/2023] Open
Abstract
Uridine insertion/deletion editing of mitochondrial mRNAs is a characteristic feature of kinetoplastids, including Trypanosoma brucei. Editing is directed by trans-acting gRNAs and catalyzed by related RNA Editing Core Complexes (RECCs). The non-catalytic RNA Editing Substrate Binding Complex (RESC) coordinates interactions between RECC, gRNA and mRNA. RESC is a dynamic complex comprising GRBC (Guide RNA Binding Complex) and heterogeneous REMCs (RNA Editing Mediator Complexes). Here, we show that RESC10 is an essential, low abundance, RNA binding protein that exhibits RNase-sensitive and RNase-insensitive interactions with RESC proteins, albeit its minimal in vivo interaction with RESC13. RESC10 RNAi causes extensive RESC disorganization, including disruption of intra-GRBC protein-protein interactions, as well as mRNA depletion from GRBC and accumulation on REMCs. Analysis of mitochondrial RNAs at single nucleotide resolution reveals transcript-specific effects: RESC10 dramatically impacts editing progression in pan-edited RPS12 mRNA, but is critical for editing initiation in mRNAs with internally initiating gRNAs, pointing to distinct initiation mechanisms for these RNA classes. Correlations between sites at which editing pauses in RESC10 depleted cells and those in knockdowns of previously studied RESC proteins suggest that RESC10 acts upstream of these factors and that RESC is particularly important in promoting transitions between uridine insertion and deletion RECCs.
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Affiliation(s)
- Ashutosh P Dubey
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Brianna L Tylec
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Natalie M McAdams
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Katherine Sortino
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Laurie K Read
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
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8
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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 (NEW YORK, N.Y.) 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] [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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9
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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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McAdams NM, Harrison GL, Tylec BL, Ammerman ML, Chen R, Sun Y, Read LK. MRB10130 is a RESC assembly factor that promotes kinetoplastid RNA editing initiation and progression. RNA (NEW YORK, N.Y.) 2019; 25:1177-1191. [PMID: 31221726 PMCID: PMC6800514 DOI: 10.1261/rna.071902.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/18/2019] [Indexed: 05/03/2023]
Abstract
Uridine insertion deletion editing in kinetoplastid protozoa requires a complex machinery, a primary component of which is the RNA editing substrate binding complex (RESC). RESC contains two modules termed GRBC (guide RNA binding complex) and REMC (RNA editing mediator complex), although how interactions between these modules and their mRNA and gRNA binding partners are controlled is not well understood. Here, we demonstrate that the ARM/HEAT repeat containing RESC protein, MRB10130, controls REMC association with mRNA- and gRNA-loaded GRBC. High-throughput sequencing analyses show that MRB10130 functions in both initiation and 3' to 5' progression of editing through gRNA-defined domains. Editing intermediates that accumulate upon MRB10130 depletion significantly intersect those in cells depleted of another RESC organizer, MRB7260, but are distinct from those in cells depleted of specific REMC proteins. We present a model in which MRB10130 coordinates numerous protein-protein and protein-RNA interactions during editing progression.
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Affiliation(s)
- Natalie M McAdams
- Department of Microbiology and Immunology, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York 14203, USA
| | - Gregory L Harrison
- Department of Microbiology and Immunology, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York 14203, USA
| | - Brianna L Tylec
- Department of Microbiology and Immunology, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York 14203, USA
| | - Michelle L Ammerman
- Department of Chemistry and Biochemistry, Kettering University, Flint, Michigan 48504, USA
| | - Runpu Chen
- Department of Computer Science and Engineering, University at Buffalo, Buffalo, New York 14260, USA
| | - Yijun Sun
- Department of Microbiology and Immunology, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York 14203, USA
| | - Laurie K Read
- Department of Microbiology and Immunology, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York 14203, USA
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11
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Kumar V, Doharey PK, Gulati S, Meehan J, Martinez MG, Hughes K, Mooers BHM, Cruz-Reyes J. Protein features for assembly of the RNA editing helicase 2 subcomplex (REH2C) in Trypanosome holo-editosomes. PLoS One 2019; 14:e0211525. [PMID: 31034523 PMCID: PMC6488192 DOI: 10.1371/journal.pone.0211525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 04/11/2019] [Indexed: 02/06/2023] Open
Abstract
Uridylate insertion/deletion RNA editing in Trypanosoma brucei is a complex system that is not found in humans, so there is interest in targeting this system for drug development. This system uses hundreds of small non-coding guide RNAs (gRNAs) to modify the mitochondrial mRNA transcriptome. This process occurs in holo-editosomes that assemble several macromolecular trans factors around mRNA including the RNA-free RNA editing core complex (RECC) and auxiliary ribonucleoprotein (RNP) complexes. Yet, the regulatory mechanisms of editing remain obscure. The enzymatic accessory RNP complex, termed the REH2C, includes mRNA substrates and products, the multi-domain 240 kDa RNA Editing Helicase 2 (REH2) and an intriguing 8-zinc finger protein termed REH2-Associated Factor 1 (H2F1). Both of these proteins are essential in editing. REH2 is a member of the DExH/RHA subfamily of RNA helicases with a conserved C-terminus that includes a regulatory OB-fold domain. In trypanosomes, H2F1 recruits REH2 to the editing apparatus, and H2F1 downregulation causes REH2 fragmentation. Our systematic mutagenesis dissected determinants in REH2 and H2F1 for the assembly of REH2C, the stability of REH2, and the RNA-mediated association of REH2C with other editing trans factors. We identified functional OB-fold amino acids in eukaryotic DExH/RHA helicases that are conserved in REH2 and that impact the assembly and interactions of REH2C. H2F1 upregulation stabilized REH2 in vivo. Mutation of the core cysteines or basic amino acids in individual zinc fingers affected the stabilizing property of H2F1 but not its interactions with other examined editing components. This result suggests that most, if not all, fingers may contribute to REH2 stabilization. Finally, a recombinant REH2 (240 kDa) established that the full-length protein is a bona fide RNA helicase with ATP-dependent unwinding activity. REH2 is the only DExH/RHA-type helicase in kinetoplastid holo-editosomes.
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Affiliation(s)
- Vikas Kumar
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Pawan K. Doharey
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Shelly Gulati
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Joshua Meehan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Mary G. Martinez
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Karrisa Hughes
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Blaine H. M. Mooers
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
- * E-mail: (JC); (BM)
| | - Jorge Cruz-Reyes
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
- * E-mail: (JC); (BM)
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12
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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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13
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Zimmer SL, Simpson RM, Read LK. High throughput sequencing revolution reveals conserved fundamentals of U-indel editing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1487. [PMID: 29888550 DOI: 10.1002/wrna.1487] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/26/2018] [Accepted: 04/30/2018] [Indexed: 01/18/2023]
Abstract
Among Euglenozoans, mitochondrial RNA editing occurs in the diplonemids and in the kinetoplastids that include parasitic trypanosomes. Yet U-indel editing, in which open reading frames (ORFs) on mRNAs are generated by insertion and deletion of uridylates in locations dictated by guide RNAs, appears confined to kinetoplastids. The nature of guide RNA and edited mRNA populations has been cursorily explored in a surprisingly extensive number of species over the years, although complete sets of fully edited mRNAs for most kinetoplast genomes are largely missing. Now, however, high throughput sequencing technologies have had an enormous impact on what we know and will learn about the mechanisms, benefits, and final edited products of U-indel editing. Tools including PARERS, TREAT, and T-Aligner function to organize and make sense of U-indel mRNA transcriptomes, which are comprised of mRNAs harboring uridylate indels both consistent and inconsistent with translatable products. From high throughput sequencing data come arguments that partially edited mRNAs containing "junction regions" of noncanonical editing are editing intermediates, and conversely, arguments that they are dead-end products. These data have also revealed that the percent of a given transcript population that is fully or partially edited varies dramatically between transcripts and organisms. Outstanding questions that are being addressed include the prevalence of sequences that apparently encode alternative ORFs, diversity of editing events in ORF termini and 5' and 3' untranslated regions, and the differences that exist in this byzantine process between species. High throughput sequencing technologies will also undoubtedly be harnessed to probe U-indel editing's evolutionary origins. This article is categorized under: RNA Processing > RNA Editing and Modification RNA Evolution and Genomics > Computational Analyses of RNA.
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Affiliation(s)
- Sara L Zimmer
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, Minnesota
| | - Rachel M Simpson
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Laurie K Read
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
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14
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McAdams NM, Simpson RM, Chen R, Sun Y, Read LK. MRB7260 is essential for productive protein-RNA interactions within the RNA editing substrate binding complex during trypanosome RNA editing. RNA (NEW YORK, N.Y.) 2018; 24:540-556. [PMID: 29330168 PMCID: PMC5855954 DOI: 10.1261/rna.065169.117] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 01/08/2018] [Indexed: 05/20/2023]
Abstract
The trypanosome RNA editing substrate binding complex (RESC) acts as the platform for mitochondrial uridine insertion/deletion RNA editing and facilitates the protein-protein and protein-RNA interactions required for the editing process. RESC is broadly comprised of two subcomplexes: GRBC (guide RNA binding complex) and REMC (RNA editing mediator complex). Here, we characterize the function and position in RESC organization of a previously unstudied RESC protein, MRB7260. We show that MRB7260 forms numerous RESC-related complexes, including a novel, small complex with the guide RNA binding protein, GAP1, which is a canonical GRBC component, and REMC components MRB8170 and TbRGG2. RNA immunoprecipitations in MRB7260-depleted cells show that MRB7260 is critical for normal RNA trafficking between REMC and GRBC. Analysis of protein-protein interactions also reveals an important role for MRB7260 in promoting stable association of the two subcomplexes. High-throughput sequencing analysis of RPS12 mRNAs from MRB7260 replete and depleted cells demonstrates that MRB7260 is critical for gRNA exchange and early gRNA utilization, with the exception of the initiating gRNA. Together, these data demonstrate that MRB7260 is essential for productive protein-RNA interactions with RESC during RNA editing.
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Affiliation(s)
- Natalie M McAdams
- Department of Microbiology and Immunology, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York 14203, USA
| | - Rachel M Simpson
- Department of Microbiology and Immunology, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York 14203, USA
| | - Runpu Chen
- Department of Computer Science and Engineering, University at Buffalo, Buffalo, New York 14260, USA
| | - Yijun Sun
- Department of Microbiology and Immunology, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York 14203, USA
| | - Laurie K Read
- Department of Microbiology and Immunology, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York 14203, USA
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15
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16
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Simpson RM, Bruno AE, Chen R, Lott K, Tylec BL, Bard JE, Sun Y, Buck MJ, Read LK. Trypanosome RNA Editing Mediator Complex proteins have distinct functions in gRNA utilization. Nucleic Acids Res 2017; 45:7965-7983. [PMID: 28535252 PMCID: PMC5737529 DOI: 10.1093/nar/gkx458] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 05/01/2017] [Accepted: 05/10/2017] [Indexed: 11/13/2022] Open
Abstract
Uridine insertion/deletion RNA editing is an essential process in kinetoplastid parasites whereby mitochondrial mRNAs are modified through the specific insertion and deletion of uridines to generate functional open reading frames, many of which encode components of the mitochondrial respiratory chain. The roles of numerous non-enzymatic editing factors have remained opaque given the limitations of conventional methods to interrogate the order and mechanism by which editing progresses and thus roles of individual proteins. Here, we examined whole populations of partially edited sequences using high throughput sequencing and a novel bioinformatic platform, the Trypanosome RNA Editing Alignment Tool (TREAT), to elucidate the roles of three proteins in the RNA Editing Mediator Complex (REMC). We determined that the factors examined function in the progression of editing through a gRNA; however, they have distinct roles and REMC is likely heterogeneous in composition. We provide the first evidence that editing can proceed through numerous paths within a single gRNA and that non-linear modifications are essential, generating commonly observed junction regions. Our data support a model in which RNA editing is executed via multiple paths that necessitate successive re-modification of junction regions facilitated, in part, by the REMC variant containing TbRGG2 and MRB8180.
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Affiliation(s)
- Rachel M. Simpson
- Department of Microbiology and Immunology, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, 3435 Main Street, Buffalo, NY 14214, USA
| | - Andrew E. Bruno
- Center for Computational Research, University at Buffalo, 701 Ellicott St., Buffalo, NY 14203, USA
| | - Runpu Chen
- Department of Computer Science and Engineering, New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott St., Buffalo, NY 14203, USA
| | - Kaylen Lott
- Department of Microbiology and Immunology, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, 3435 Main Street, Buffalo, NY 14214, USA
| | - Brianna L. Tylec
- Department of Microbiology and Immunology, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, 3435 Main Street, Buffalo, NY 14214, USA
| | - Jonathan E. Bard
- Genomics and Bioinformatics Core, University at Buffalo, 701 Ellicott St., Buffalo, NY 14203, USA
| | - Yijun Sun
- Department of Microbiology and Immunology, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, 3435 Main Street, Buffalo, NY 14214, USA
- Center for Computational Research, University at Buffalo, 701 Ellicott St., Buffalo, NY 14203, USA
| | - Michael J. Buck
- Department of Biochemistry, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, 701 Ellicott St., Buffalo, NY 14203, USA
| | - Laurie K. Read
- Department of Microbiology and Immunology, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, 3435 Main Street, Buffalo, NY 14214, USA
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Differential Binding of Mitochondrial Transcripts by MRB8170 and MRB4160 Regulates Distinct Editing Fates of Mitochondrial mRNA in Trypanosomes. mBio 2017; 8:mBio.02288-16. [PMID: 28143982 PMCID: PMC5285507 DOI: 10.1128/mbio.02288-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A dozen mRNAs are edited by multiple insertions and/or deletions of uridine residues in the mitochondrion of Trypanosoma brucei Several protein complexes have been implicated in performing this type of RNA editing, including the mitochondrial RNA-binding complex 1 (MRB1). Two paralogous novel RNA-binding proteins, MRB8170 and MRB4160, are loosely associated with the core MRB1 complex. Their roles in RNA editing and effects on target mRNAs are so far not well understood. In this study, individual-nucleotide-resolution UV-cross-linking and affinity purification (iCLAP) revealed a preferential binding of both proteins to mitochondrial mRNAs, which was positively correlated with their extent of editing. Integrating additional in vivo and in vitro data, we propose that binding of MRB8170 and/or MRB4160 onto pre-mRNA marks it for the initiation of editing and that initial binding of both proteins may facilitate the recruitment of other components of the RNA editing/processing machinery to ensure efficient editing. Surprisingly, MRB8170 also binds never-edited mRNAs, suggesting that at least this paralog has an additional role outside RNA editing to shape the mitochondrial transcriptome. IMPORTANCE Trypanosoma brucei mitochondrial mRNAs undergo maturation by RNA editing, a unique process involving decrypting open reading frames by the precise deletion and/or insertion of uridine (U) residues at specific positions on an mRNA. This process is catalyzed by multiprotein complexes, such as the RNA editing core complex, which provides the enzymatic activities needed for U insertion/deletion at a single editing site. Less well understood is how RNA editing occurs throughout an mRNA bearing multiple sites. To address this question, we mapped at single-nucleotide resolution the RNA interactions of two unique RNA-binding proteins (RBPs). These RBPs are part of the mitochondrial RNA-binding complex 1, hypothesized to mediate multiple rounds of RNA editing. Both RBPs were shown to mark mRNAs for the process in correlation with the number of editing sites on the transcript. Surprisingly, one also binds mRNAs that bypass RNA editing, indicating that it may have an additional role outside RNA editing.
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Cruz-Reyes J, Mooers BHM, Abu-Adas Z, Kumar V, Gulati S. DEAH-RHA helicase•Znf cofactor systems in kinetoplastid RNA editing and evolutionarily distant RNA processes. RNA & DISEASE 2016; 3. [PMID: 27540585 PMCID: PMC4987287 DOI: 10.14800/rd.1336] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Multi-zinc finger proteins are an emerging class of cofactors in DEAH-RHA RNA helicases across highly divergent eukaryotic lineages. DEAH-RHA helicase•zinc finger cofactor partnerships predate the split of kinetoplastid protozoa, which include several human pathogens, from other eukaryotic lineages 100-400 Ma. Despite a long evolutionary history, the prototypical DEAH-RHA domains remain highly conserved. This short review focuses on a recently identified DEAH-RHA helicase•zinc finger cofactor system in kinetoplastid RNA editing, and its potential functional parallels with analogous systems in embryogenesis control in nematodes and antivirus protection in humans.
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Affiliation(s)
- Jorge Cruz-Reyes
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Blaine H M Mooers
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Zakaria Abu-Adas
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Vikas Kumar
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Shelly Gulati
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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