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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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Simpson RM, Bruno AE, Bard JE, Buck MJ, Read LK. High-throughput sequencing of partially edited trypanosome mRNAs reveals barriers to editing progression and evidence for alternative editing. RNA (NEW YORK, N.Y.) 2016; 22:677-95. [PMID: 26908922 PMCID: PMC4836643 DOI: 10.1261/rna.055160.115] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/28/2016] [Indexed: 05/20/2023]
Abstract
Uridine insertion/deletion RNA editing in kinetoplastids entails the addition and deletion of uridine residues throughout the length of mitochondrial transcripts to generate translatable mRNAs. This complex process requires the coordinated use of several multiprotein complexes as well as the sequential use of noncoding template RNAs called guide RNAs. The majority of steady-state mitochondrial mRNAs are partially edited and often contain regions of mis-editing, termed junctions, whose role is unclear. Here, we report a novel method for sequencing entire populations of pre-edited partially edited, and fully edited RNAs and analyzing editing characteristics across populations using a new bioinformatics tool, the Trypanosome RNA Editing Alignment Tool (TREAT). Using TREAT, we examined populations of two transcripts, RPS12 and ND7-5', in wild-typeTrypanosoma brucei We provide evidence that the majority of partially edited sequences contain junctions, that intrinsic pause sites arise during the progression of editing, and that the mechanisms that mediate pausing in the generation of canonical fully edited sequences are distinct from those that mediate the ends of junction regions. Furthermore, we identify alternatively edited sequences that constitute plausible alternative open reading frames and identify substantial variability in the 5' UTRs of both canonical and alternatively edited sequences. This work is the first to use high-throughput sequencing to examine full-length sequences of whole populations of partially edited transcripts. Our method is highly applicable to current questions in the RNA editing field, including defining mechanisms of action for editing factors and identifying potential alternatively edited sequences.
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Affiliation(s)
- Rachel M Simpson
- Department of Microbiology and Immunology, University at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York 14214, USA
| | - Andrew E Bruno
- Center for Computational Research, University at Buffalo, Buffalo, New York 14203, USA
| | - Jonathan E Bard
- University at Buffalo Genomics and Bioinformatics Core, Buffalo, New York 14222, USA
| | - Michael J Buck
- Deparment of Biochemistry, University at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York 14214, USA
| | - Laurie K Read
- Department of Microbiology and Immunology, University at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York 14214, USA
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Madina BR, Kumar V, Mooers BHM, Cruz-Reyes J. Native Variants of the MRB1 Complex Exhibit Specialized Functions in Kinetoplastid RNA Editing. PLoS One 2015; 10:e0123441. [PMID: 25928631 PMCID: PMC4415780 DOI: 10.1371/journal.pone.0123441] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 03/04/2015] [Indexed: 12/20/2022] Open
Abstract
Adaptation and survival of Trypanosoma brucei requires editing of mitochondrial mRNA by uridylate (U) insertion and deletion. Hundreds of small guide RNAs (gRNAs) direct the mRNA editing at over 3,000 sites. RNA editing is controlled during the life cycle but the regulation of substrate and stage specificity remains unknown. Editing progresses in the 3' to 5' direction along the pre-mRNA in blocks, each targeted by a unique gRNA. A critical editing factor is the mitochondrial RNA binding complex 1 (MRB1) that binds gRNA and transiently interacts with the catalytic RNA editing core complex (RECC). MRB1 is a large and dynamic complex that appears to be comprised of distinct but related subcomplexes (termed here MRBs). MRBs seem to share a 'core' complex of proteins but differ in the composition of the 'variable' proteins. Since some proteins associate transiently the MRBs remain imprecisely defined. MRB1 controls editing by unknown mechanisms, and the functional relevance of the different MRBs is unclear. We previously identified two distinct MRBs, and showed that they carry mRNAs that undergo editing. We proposed that editing takes place in the MRBs because MRBs stably associate with mRNA and gRNA but only transiently interact with RECC, which is RNA free. Here, we identify the first specialized functions in MRBs: 1) 3010-MRB is a major scaffold for RNA editing, and 2) REH2-MRB contains a critical trans-acting RNA helicase (REH2) that affects multiple steps of editing function in 3010-MRB. These trans effects of the REH2 include loading of unedited mRNA and editing in the first block and in subsequent blocks as editing progresses. REH2 binds its own MRB via RNA, and conserved domains in REH2 were critical for REH2 to associate with the RNA and protein components of its MRB. Importantly, REH2 associates with a ~30 kDa RNA-binding protein in a novel ~15S subcomplex in RNA-depleted mitochondria. We use these new results to update our model of MRB function and organization.
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Affiliation(s)
- Bhaskara R. Madina
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States of America
| | - Vikas Kumar
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States of America
| | - Blaine H. M. Mooers
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, United States of America
| | - Jorge Cruz-Reyes
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States of America
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Madina BR, Kumar V, Metz R, Mooers BH, Bundschuh R, Cruz-Reyes J. Native mitochondrial RNA-binding complexes in kinetoplastid RNA editing differ in guide RNA composition. RNA (NEW YORK, N.Y.) 2014; 20:1142-52. [PMID: 24865612 PMCID: PMC4114691 DOI: 10.1261/rna.044495.114] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 04/25/2014] [Indexed: 05/20/2023]
Abstract
Mitochondrial mRNAs in kinetoplastids require extensive U-insertion/deletion editing that progresses 3'-to-5' in small blocks, each directed by a guide RNA (gRNA), and exhibits substrate and developmental stage-specificity by unsolved mechanisms. Here, we address compositionally related factors, collectively known as the mitochondrial RNA-binding complex 1 (MRB1) or gRNA-binding complex (GRBC), that contain gRNA, have a dynamic protein composition, and transiently associate with several mitochondrial factors including RNA editing core complexes (RECC) and ribosomes. MRB1 controls editing by still unknown mechanisms. We performed the first next-generation sequencing study of native subcomplexes of MRB1, immunoselected via either RNA helicase 2 (REH2), that binds RNA and associates with unwinding activity, or MRB3010, that affects an early editing step. The particles contain either REH2 or MRB3010 but share the core GAP1 and other proteins detected by RNA photo-crosslinking. Analyses of the first editing blocks indicate an enrichment of several initiating gRNAs in the MRB3010-purified complex. Our data also indicate fast evolution of mRNA 3' ends and strain-specific alternative 3' editing within 3' UTR or C-terminal protein-coding sequence that could impact mitochondrial physiology. Moreover, we found robust specific copurification of edited and pre-edited mRNAs, suggesting that these particles may bind both mRNA and gRNA editing substrates. We propose that multiple subcomplexes of MRB1 with different RNA/protein composition serve as a scaffold for specific assembly of editing substrates and RECC, thereby forming the editing holoenzyme. The MRB3010-subcomplex may promote early editing through its preferential recruitment of initiating gRNAs.
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MESH Headings
- Amino Acid Sequence
- Base Composition
- Base Sequence
- Cells, Cultured
- Kinetoplastida/genetics
- Kinetoplastida/metabolism
- Molecular Sequence Data
- Protozoan Proteins/genetics
- Protozoan Proteins/metabolism
- RNA/chemistry
- RNA/metabolism
- RNA Editing
- RNA, Guide, Kinetoplastida/chemistry
- RNA, Guide, Kinetoplastida/genetics
- RNA, Guide, Kinetoplastida/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- RNA, Mitochondrial
- RNA, Protozoan/chemistry
- RNA, Protozoan/metabolism
- Trypanosoma brucei brucei/genetics
- Trypanosoma brucei brucei/metabolism
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Affiliation(s)
- Bhaskara R. Madina
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
| | - Vikas Kumar
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
| | - Richard Metz
- Texas AgriLife Genomics and Bioinformatics Service, Texas A&M University, College Station, Texas 77845, USA
| | - Blaine H.M. Mooers
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA
| | - Ralf Bundschuh
- Department of Physics, Department of Chemistry & Biochemistry, Division of Hematology, Center of RNA Biology, The Ohio State University, Columbus, Ohio 43210-1117, USA
| | - Jorge Cruz-Reyes
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
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Hernandez A, Madina BR, Ro K, Wohlschlegel JA, Willard B, Kinter MT, Cruz-Reyes J. REH2 RNA helicase in kinetoplastid mitochondria: ribonucleoprotein complexes and essential motifs for unwinding and guide RNA (gRNA) binding. J Biol Chem 2010; 285:1220-8. [PMID: 19850921 PMCID: PMC2801250 DOI: 10.1074/jbc.m109.051862] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Revised: 09/25/2009] [Indexed: 01/01/2023] Open
Abstract
Regulation of gene expression in kinetoplastid mitochondria is largely post-transcriptional and involves the orchestration of polycistronic RNA processing, 3'-terminal maturation, RNA editing, turnover, and translation; however, these processes remain poorly studied. Core editing complexes and their U-insertion/deletion activities are relatively well characterized, and a battery of ancillary factors has recently emerged. This study characterized a novel DExH-box RNA helicase, termed here REH2 (RNA editing associated helicase 2), in unique ribonucleoprotein complexes that exhibit unwinding and guide RNA binding activities, both of which required a double-stranded RNA-binding domain (dsRBD) and a functional helicase motif I of REH2. REH2 complexes and recently identified related particles share a multiprotein core but are distinguished by several differential polypeptides. Finally, REH2 associates transiently, via RNA, with editing complexes, mitochondrial ribosomes, and several ancillary factors that control editing and RNA stability. We propose that these putative higher order structures coordinate mitochondrial gene expression.
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Affiliation(s)
- Alfredo Hernandez
- From the Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Bhaskara Reddy Madina
- From the Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Kevin Ro
- the Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095-1737, and
| | - James A. Wohlschlegel
- the Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095-1737, and
| | - Belinda Willard
- the Department of Cell Biology, Cleveland Clinic Foundation, Cleveland, Ohio 44195
| | - Mike T. Kinter
- the Department of Cell Biology, Cleveland Clinic Foundation, Cleveland, Ohio 44195
| | - Jorge Cruz-Reyes
- From the Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
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Reifur L, Koslowsky DJ. Trypanosoma brucei ATPase subunit 6 mRNA bound to gA6-14 forms a conserved three-helical structure. RNA (NEW YORK, N.Y.) 2008; 14:2195-211. [PMID: 18772247 PMCID: PMC2553734 DOI: 10.1261/rna.1144508] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Accepted: 07/17/2008] [Indexed: 05/26/2023]
Abstract
T. brucei survival relies on the expression of mitochondrial genes, most of which require RNA editing to become translatable. In trypanosomes, RNA editing involves the insertion and deletion of uridylates, a developmentally regulated process directed by guide RNAs (gRNAs) and catalyzed by the editosome, a complex of proteins. The pathway for mRNA/gRNA complex formation and assembly with the editosome is still unknown. Work from our laboratory has suggested that distinct mRNA/gRNA complexes anneal to form a conserved core structure that may be important for editosome assembly. The secondary structure for the apocytochrome b (CYb) pair has been previously determined and is consistent with our model of a three-helical structure. Here, we used cross-linking and solution structure probing experiments to determine the structure of the ATPase subunit 6 (A6) mRNA hybridized to its cognate gA6-14 gRNA in different stages of editing. Our results indicate that both unedited and partially edited A6/gA6-14 pairs fold into a three-helical structure similar to the previously characterized CYb/gCYb-558 pair. These results lead us to conclude that at least two mRNA/gRNA pairs with distinct editing sites and distinct primary sequences fold to a three-helical secondary configuration that persists through the first few editing events.
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Affiliation(s)
- Larissa Reifur
- Comparative Medicine and Integrative Biology, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan 48824, USA
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Hernandez A, Panigrahi A, Cifuentes-Rojas C, Sacharidou A, Stuart K, Cruz-Reyes J. Determinants for association and guide RNA-directed endonuclease cleavage by purified RNA editing complexes from Trypanosoma brucei. J Mol Biol 2008; 381:35-48. [PMID: 18572190 PMCID: PMC2596986 DOI: 10.1016/j.jmb.2008.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Revised: 04/29/2008] [Accepted: 05/02/2008] [Indexed: 11/18/2022]
Abstract
U-insertion/deletion RNA editing in the single mitochondrion of kinetoplastids, an ancient lineage of eukaryotes, is a unique mRNA maturation process needed for translation. Multisubunit editing complexes recognize many pre-edited mRNA sites and modify them via cycles of three catalytic steps: guide RNA (gRNA)-directed cleavage, insertion or deletion of uridylates at the 3'-terminus of the upstream cleaved piece, and ligation of the two mRNA pieces. While catalytic and many structural protein subunits of these complexes have been identified, the mechanisms and basic determinants of substrate recognition are still poorly understood. This study defined relatively simple single- and double-stranded determinants for association and gRNA-directed cleavage. To this end, we used an electrophoretic mobility shift assay to directly score the association of purified editing complexes with RNA ligands, in parallel with UV photocrosslinking and functional studies. The cleaved strand required a minimal 5' overhang of 12 nt and an approximately 15-bp duplex with gRNA to direct the cleavage site. A second protruding element in either the cleaved or the guide strand was required unless longer duplexes were used. Importantly, the single-stranded RNA requirement for association can be upstream or downstream of the duplex, and the binding and cleavage activities of purified editing complexes could be uncoupled. The current observations together with our previous reports in the context of purified native editing complexes show that the determinants for association, cleavage and full-round editing gradually increase in complexity as these stages progress. The native complexes in these studies contained most, if not all, known core subunits in addition to components of the MRP complex. Finally, we found that the endonuclease KREN1 in purified complexes photocrosslinks with a targeted editing site. A model is proposed whereby one or more RNase III-type endonucleases mediate the initial binding and scrutiny of potential ligands and subsequent catalytic selectivity triggers either insertion or deletion editing enzymes.
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Affiliation(s)
- Alfredo Hernandez
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843
| | - Aswini Panigrahi
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, Washington 98109
| | - Catherine Cifuentes-Rojas
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843
| | - Anastasia Sacharidou
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843
| | - Kenneth Stuart
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, Washington 98109
| | - Jorge Cruz-Reyes
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843
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Homann M. Editing Reactions from the Perspective of RNA Structure. NUCLEIC ACIDS AND MOLECULAR BIOLOGY 2008. [DOI: 10.1007/978-3-540-73787-2_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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10
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Abstract
Trypanosoma brucei has three distinct approximately 20S editosomes that catalyze RNA editing by the insertion and deletion of uridylates. Editosomes with the KREN1 or KREN2 RNase III type endonucleases specifically cleave deletion and insertion editing site substrates, respectively. We report here that editosomes with KREPB2, which also has an RNase III motif, specifically cleave cytochrome oxidase II (COII) pre-mRNA insertion editing site substrates in vitro. Conditional repression and mutation studies also show that KREPB2 is an editing endonuclease specifically required for COII mRNA editing in vivo. Furthermore, KREPB2 expression is essential for the growth and survival of bloodstream forms. Thus, editing in T. brucei requires at least three compositionally and functionally distinct approximately 20S editosomes, two of which distinguish between different insertion editing sites. This unexpected finding reveals an additional level of complexity in the RNA editing process and suggests a mechanism for how the selection of sites for editing in vivo is controlled.
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Abstract
Multisubunit RNA editing complexes recognize thousands of pre-mRNA sites in the single mitochondrion of trypanosomes. Specific determinants at each editing site must trigger the complexes to catalyze a complete cycle of either uridylate insertion or deletion. While a wealth of information on the protein composition and catalytic activities of these complexes is currently available, the precise mechanisms that govern substrate recognition and editing site specificity remain unknown. This chapter describes basic assays to visualize direct photocrosslinking interactions between purified editing complexes and targeted deletion and insertion sites in model substrates for full-round editing. It also illustrates how variations of these assays can be applied to examine the specificity of the editing enzyme/substrate association, and to dissect structural or biochemical requirements of both the substrates and enzyme complex.
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Affiliation(s)
- Jorge Cruz-Reyes
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, USA
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12
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Cifuentes-Rojas C, Pavia P, Hernandez A, Osterwisch D, Puerta C, Cruz-Reyes J. Substrate determinants for RNA editing and editing complex interactions at a site for full-round U insertion. J Biol Chem 2007; 282:4265-4276. [PMID: 17158098 DOI: 10.1074/jbc.m605554200] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Multisubunit RNA editing complexes catalyze uridylate insertion/deletion RNA editing directed by complementary guide RNAs (gRNAs). Editing in trypanosome mitochondria is transcript-specific and developmentally controlled, but the molecular mechanisms of substrate specificity remain unknown. Here we used a minimal A6 pre-mRNA/gRNA substrate to define functional determinants for full-round insertion and editing complex interactions at the editing site 2 (ES2). Editing begins with pre-mRNA cleavage within an internal loop flanked by upstream and downstream duplexes with gRNA. We found that substrate recognition around the internal loop is sequence-independent and that completely artificial duplexes spanning a single helical turn are functional. Furthermore, after our report of cross-linking interactions at the deletion ES1 (35), we show for the first time editing complex contacts at an insertion ES. Our studies using site-specific ribose 2' substitutions defined 2'-hydroxyls within the (a) gRNA loop region and (b) flanking helixes that markedly stimulate both pre-mRNA cleavage and editing complex interactions at ES2. Modification of the downstream helix affected scissile bond specificity. Notably, a single 2'-hydroxyl at ES2 is essential for cleavage but dispensable for editing complex cross-linking. This study provides new insights on substrate recognition during full-round editing, including the relevance of secondary structure and the first functional association of specific (pre-mRNA and gRNA) riboses with both endonuclease cleavage and cross-linking activities of editing complexes at an ES. Importantly, most observed cross-linking interactions are both conserved and relatively stable at ES2 and ES1 in hybrid substrates. However, they were also detected as transient low-stability contacts in a non-edited transcript.
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Affiliation(s)
| | - Paula Pavia
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843 and
| | - Alfredo Hernandez
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843 and
| | - Daniel Osterwisch
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843 and
| | - Concepcion Puerta
- Laboratorio of Parasitologia Molecular, Pontificia Universidad Javeriana, Carrera 7a No. 43-82, Ed. 50, Lab 113, Bogota´, Colombia
| | - Jorge Cruz-Reyes
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843 and.
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Abstract
The uridine nucleotide insertion and deletion editing of trypanosomatid mitochondrial mRNAs is catalyzed by a macromolecular complex, the editosome. Many investigations of RNA editing involve some assessment of editosome activity either in vitro or in vivo. Assays to detect insertion or deletion editing activity on RNAs in vitro have been particularly useful, and can include the initial endonucleolytic step (full-round) or bypass it (precleaved). Additional assays to examine individual catalytic steps have also proved useful to dissect particular steps in editing. Detection of RNA editing activity in vivo has been significantly advanced by the application of real-time PCR technology, which can simultaneously assay several edited and pre-edited targets. Here we describe these assays to assess editing both in vitro (full-round insertion and deletion; precleaved insertion and deletion; individual TUTase, ligase, or helicase activity) and in vivo (real-time PCR).
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Affiliation(s)
- Jason Carnes
- Seattle Biomedical Research Institute, Seattle, Washington, USA
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14
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Kang X, Gao G, Rogers K, Falick AM, Zhou S, Simpson L. Reconstitution of full-round uridine-deletion RNA editing with three recombinant proteins. Proc Natl Acad Sci U S A 2006; 103:13944-9. [PMID: 16963561 PMCID: PMC1599893 DOI: 10.1073/pnas.0604476103] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Uridine (U)-insertion/deletion RNA editing in trypanosome mitochondria involves an initial cleavage of the preedited mRNA at specific sites determined by the annealing of partially complementary guide RNAs. An involvement of two RNase III-containing core editing complex (L-complex) proteins, MP90 (KREPB1) and MP61 (KREPB3) in, respectively, U-deletion and U-insertion editing, has been suggested, but these putative enzymes have not been characterized or expressed in active form. Recombinant MP90 proteins from Trypanosoma brucei and Leishmania major were expressed in insect cells and cytosol of Leishmania tarentolae, respectively. These proteins were active in specifically cleaving a model U-deletion site and not a U-insertion site. Deletion or mutation of the RNase III motif abolished this activity. Full-round guide RNA (gRNA)-mediated in vitro U-deletion editing was reconstituted by a mixture of recombinant MP90 and recombinant RNA editing exonuclease I from L. major, and recombinant RNA editing RNA ligase 1 from L. tarentolae. MP90 is designated REN1, for RNA-editing nuclease 1.
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Affiliation(s)
- Xuedong Kang
- *Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095; and
| | - Guanghan Gao
- *Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095; and
| | - Kestrel Rogers
- *Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095; and
| | - Arnold M. Falick
- Department of Molecular and Cell Biology
- Howard Hughes Medical Institute Mass Spectrometry Laboratory, University of California, Berkeley, CA 94720
| | - Sharleen Zhou
- Department of Molecular and Cell Biology
- Howard Hughes Medical Institute Mass Spectrometry Laboratory, University of California, Berkeley, CA 94720
| | - Larry Simpson
- *Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095; and
- To whom correspondence should be addressed at:
Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, 1602 Molecular Science Building, Box 951489, Los Angeles, CA 90095-1489. E-mail:
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