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Meehan J, Ivens A, Grote S, Rodshagen T, Chen Z, Goode C, Sharma SK, Kumar V, Frese A, Goodall Z, McCleskey L, Sechrist R, Zeng L, Savill NJ, Rouskin S, Schnaufer A, McDermott SM, Cruz-Reyes J. KREH2 helicase represses ND7 mRNA editing in procyclic-stage Trypanosoma brucei by opposite modulation of canonical and 'moonlighting' gRNA utilization creating a proposed mRNA structure. Nucleic Acids Res 2024:gkae699. [PMID: 39149912 DOI: 10.1093/nar/gkae699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 07/17/2024] [Accepted: 08/01/2024] [Indexed: 08/17/2024] Open
Abstract
Unknown factors regulate mitochondrial U-insertion/deletion (U-indel) RNA editing in procyclic-form (PCF) and bloodstream-form (BSF) T. brucei. This editing, directed by anti-sense gRNAs, creates canonical protein-encoding mRNAs and may developmentally control respiration. Canonical editing by gRNAs that specify protein-encoding mRNA sequences occurs amid massive non-canonical editing of unclear sources and biological significance. We found PCF-specific repression at a major early checkpoint in mRNA ND7, involving helicase KREH2-dependent opposite modulation of canonical and non-canonical 'terminator' gRNA utilization. Terminator-programmed editing derails canonical editing and installs proposed repressive structure in 30% of the ND7 transcriptome. BSF-to-PCF differentiation in vitro recreated this negative control. Remarkably, KREH2-RNAi knockdown relieved repression and increased editing progression by reverting canonical/terminator gRNA utilization. ND7 transcripts lacking early terminator-directed editing in PCF exhibited similar negative editing control along the mRNA sequence, suggesting global modulation of gRNA utilization fidelity. The terminator is a 'moonlighting' gRNA also associated with mRNA COX3 canonical editing, so the gRNA transcriptome seems multifunctional. Thus, KREH2 is the first identified repressor in developmental editing control. This and our prior work support a model whereby KREH2 activates or represses editing in a stage and substrate-specific manner. KREH2's novel dual role tunes mitochondrial gene expression in either direction during development.
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Affiliation(s)
- Joshua Meehan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Alasdair Ivens
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Scott Grote
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Tyler Rodshagen
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Zihao Chen
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Cody Goode
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Sunil K Sharma
- 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
| | - Addison Frese
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Zachary Goodall
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Laura McCleskey
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Rebecca Sechrist
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Nicholas J Savill
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Silvi Rouskin
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Achim Schnaufer
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Suzanne M McDermott
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Jorge Cruz-Reyes
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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2
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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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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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Smith JT, Tylec B, Naguleswaran A, Roditi I, Read LK. Developmental dynamics of mitochondrial mRNA abundance and editing reveal roles for temperature and the differentiation-repressive kinase RDK1 in cytochrome oxidase subunit II mRNA editing. mBio 2023; 14:e0185423. [PMID: 37795988 PMCID: PMC10653865 DOI: 10.1128/mbio.01854-23] [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: 07/13/2023] [Accepted: 08/15/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE Trypanosoma brucei is the unicellular parasite that causes African sleeping sickness and nagana disease in livestock. The parasite has a complex life cycle consisting of several developmental forms in the human and tsetse fly insect vector. Both the mammalian and insect hosts provide different nutritional environments, so T. brucei must adapt its metabolism to promote its survival and to complete its life cycle. As T. brucei is transmitted from the human host to the fly, the parasite must regulate its mitochondrial gene expression through a process called uridine insertion/deletion editing to achieve mRNAs capable of being translated into functional respiratory chain proteins required for energy production in the insect host. Therefore, it is essential to understand the mechanisms by which T. brucei regulates mitochondrial gene expression during transmission from the mammalian host to the insect vector.
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Affiliation(s)
- Joseph T. Smith
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - Brianna Tylec
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | | | - Isabel Roditi
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Laurie K. Read
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
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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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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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Callejas-Hernández F, Herreros-Cabello A, Del Moral-Salmoral J, Fresno M, Gironès N. The Complete Mitochondrial DNA of Trypanosoma cruzi: Maxicircles and Minicircles. Front Cell Infect Microbiol 2021; 11:672448. [PMID: 34268138 PMCID: PMC8277381 DOI: 10.3389/fcimb.2021.672448] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/04/2021] [Indexed: 11/13/2022] Open
Abstract
The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA or kDNA or mtDNA, consists of a few maxicircles and thousands of minicircles concatenated together into a huge complex network. These structures present species-specific sizes, from 20 to 40 Kb in maxicircles and from 0.5 to 10 Kb in minicircles. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles contain coding guide RNAs involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. The knowledge about this mitochondrial genome is especially relevant since the expression of nuclear and mitochondrial genes involved in oxidative phosphorylation must be coordinated. In Trypanosoma cruzi (T. cruzi), the mtDNA has a dual relevance; the production of energy, and its use as a phylogenetic marker due to its high conservation among strains. Therefore, this study aimed to assemble, annotate, and analyze the complete repertoire of maxicircle and minicircle sequences of different T. cruzi strains by using DNA sequencing. We assembled and annotated the complete maxicircle sequence of the Y and Bug2148 strains. For Bug2148, our results confirm that the maxicircle sequence is the longest assembled to date, and is composed of 21 genes, most of them conserved among Trypanosomatid species. In agreement with previous results, T. cruzi minicircles show a conserved structure around 1.4 Kb, with four highly conserved regions and other four hypervariable regions interspersed between them. However, our results suggest that the parasite minicircles display several sizes and numbers of conserved and hypervariable regions, contrary to those previous studies. Besides, this heterogeneity is also reflected in the three conserved sequence blocks of the conserved regions that play a key role in the minicircle replication. Our results using sequencing technologies of second and third-generation indicate that the different consensus sequences of the maxicircles and minicircles seem to be more complex than previously described indicating at least four different groups in T. cruzi minicircles.
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Affiliation(s)
- Francisco Callejas-Hernández
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
| | - Alfonso Herreros-Cabello
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
| | - Javier Del Moral-Salmoral
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
| | - Manuel Fresno
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain.,Instituto Sanitario de Investigación de la Princesa, Group 12, Madrid, Spain
| | - Núria Gironès
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain.,Instituto Sanitario de Investigación de la Princesa, Group 12, Madrid, Spain
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