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Davidge B, McDermott SM, Carnes J, Lewis I, Tracy M, Stuart KD. Multiple domains of the integral KREPA3 protein are critical for the structure and precise functions of RNA editing catalytic complexes in Trypanosoma brucei. RNA (NEW YORK, N.Y.) 2023; 29:1591-1609. [PMID: 37474258 PMCID: PMC10578492 DOI: 10.1261/rna.079691.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/30/2023] [Indexed: 07/22/2023]
Abstract
The gRNA directed U-insertion and deletion editing of mitochondrial mRNAs that is essential in different life-cycle stages for the protozoan parasite Trypanosoma brucei is performed by three similar multiprotein catalytic complexes (CCs) that contain the requisite enzymes. These CCs also contain a common set of eight proteins that have no apparent direct catalytic function, including six that have an OB-fold domain. We show here that one of these OB-fold proteins, KREPA3 (A3), has structural homology to other editing proteins, is essential for editing, and is multifunctional. We investigated A3 function by analyzing the effects of single amino acid loss of function mutations, most of which were identified by screening bloodstream form (BF) parasites for loss of growth following random mutagenesis. Mutations in the zinc fingers (ZFs), an intrinsically disordered region (IDR), and several within or near the carboxy-terminal OB-fold domain variably impacted CC structural integrity and editing. Some mutations resulted in almost complete loss of CCs and its proteins and editing, whereas others retained CCs but had aberrant editing. All but a mutation which is near the OB-fold affected growth and editing in BF but not procyclic form (PF) parasites. These data indicate that multiple positions within A3 have essential functions that contribute to the structural integrity of CCs, the precision of editing and the developmental differences in editing between BF and PF stages.
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Affiliation(s)
- Brittney Davidge
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
| | - Suzanne M McDermott
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
- Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
| | - Jason Carnes
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
| | - Isaac Lewis
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
| | - Maxwell Tracy
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
| | - Kenneth D Stuart
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
- Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
- Department of Global Health, University of Washington, Seattle, Washington 98195, USA
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2
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Smith Jr. JT, Doleželová E, Tylec B, Bard JE, Chen R, Sun Y, Zíková A, Read LK. Developmental regulation of edited CYb and COIII mitochondrial mRNAs is achieved by distinct mechanisms in Trypanosoma brucei. Nucleic Acids Res 2020; 48:8704-8723. [PMID: 32738044 PMCID: PMC7470970 DOI: 10.1093/nar/gkaa641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 01/01/2023] Open
Abstract
Trypanosoma brucei is a parasitic protozoan that undergoes a complex life cycle involving insect and mammalian hosts that present dramatically different nutritional environments. Mitochondrial metabolism and gene expression are highly regulated to accommodate these environmental changes, including regulation of mRNAs that require extensive uridine insertion/deletion (U-indel) editing for their maturation. Here, we use high throughput sequencing and a method for promoting life cycle changes in vitro to assess the mechanisms and timing of developmentally regulated edited mRNA expression. We show that edited CYb mRNA is downregulated in mammalian bloodstream forms (BSF) at the level of editing initiation and/or edited mRNA stability. In contrast, edited COIII mRNAs are depleted in BSF by inhibition of editing progression. We identify cell line-specific differences in the mechanisms abrogating COIII mRNA editing, including the possible utilization of terminator gRNAs that preclude the 3' to 5' progression of editing. By examining the developmental timing of altered mitochondrial mRNA levels, we also reveal transcript-specific developmental checkpoints in epimastigote (EMF), metacyclic (MCF), and BSF. These studies represent the first analysis of the mechanisms governing edited mRNA levels during T. brucei development and the first to interrogate U-indel editing in EMF and MCF life cycle stages.
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Affiliation(s)
- Joseph T Smith Jr.
- Department of Microbiology and Immunology, University at Buffalo – Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Eva Doleželová
- Institute of Parasitology, Biology Centre Czech Academy of Science, České Budejovice, Czech Republic
| | - Brianna Tylec
- Department of Microbiology and Immunology, University at Buffalo – Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Jonathan E Bard
- Genomics and Bioinformatics Core, University at Buffalo, Buffalo, NY 14203, USA
| | - Runpu Chen
- Department of Computer Science and Engineering, University at Buffalo, Buffalo, NY 14260, USA
| | - Yijun Sun
- Department of Microbiology and Immunology, University at Buffalo – Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Alena Zíková
- Institute of Parasitology, Biology Centre Czech Academy of Science, České Budejovice, Czech Republic
| | - Laurie K Read
- Department of Microbiology and Immunology, University at Buffalo – Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
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3
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McDermott SM, Stuart K. The essential functions of KREPB4 are developmentally distinct and required for endonuclease association with editosomes. RNA (NEW YORK, N.Y.) 2017; 23:1672-1684. [PMID: 28802260 PMCID: PMC5648035 DOI: 10.1261/rna.062786.117] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 08/07/2017] [Indexed: 05/20/2023]
Abstract
Uridine insertion and deletion RNA editing generates functional mitochondrial mRNAs in Trypanosoma brucei, and several transcripts are differentially edited in bloodstream (BF) and procyclic form (PF) cells correlating with changes in mitochondrial function. Editing is catalyzed by three ∼20S editosomes that have a common set of 12 proteins, but are typified by mutually exclusive RNase III KREN1, N2, and N3 endonucleases with distinct cleavage specificities. KREPB4 is a common editosome protein that has a degenerate RNase III domain lacking conserved catalytic residues, in addition to zinc-finger and Pumilio/fem-3 mRNA binding factor (PUF) motifs. Here we show that KREPB4 is essential for BF and PF growth, in vivo RNA editing, and editosome integrity, but that loss of KREPB4 has differential effects on editosome components and complexes between BF and PF cells. We used targeted mutagenesis to investigate the functions of the conserved PUF and RNase III domains in both life-cycle stages and show that the PUF motif is not essential for function in BF or PF. In contrast, specific mutations in the RNase III domain severely inhibit BF and PF growth and editing, and disrupt ∼20S editosomes, while others indicate that the RNase III domain is noncatalytic. We further show that KREPB4, specifically the noncatalytic RNase III domain, is required for the association of KREN1, N2, and N3 with PF editosomes. These results, combined with previous studies, support a model in which KREPB4 acts as a pseudoenzyme to form the noncatalytic half of an RNase III heterodimer with the editing endonucleases.
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Affiliation(s)
- Suzanne M McDermott
- Center for Infectious Disease Research (formerly Seattle BioMed), Seattle, Washington 98109, USA
| | - Kenneth Stuart
- Center for Infectious Disease Research (formerly Seattle BioMed), Seattle, Washington 98109, USA
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4
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Abstract
Uridine insertion and deletion RNA editing generates functional mitochondrial mRNAs in Trypanosoma brucei Editing is catalyzed by three distinct ∼20S editosomes that have a common set of 12 proteins, but are typified by mutually exclusive RNase III endonucleases with distinct cleavage specificities and unique partner proteins. Previous studies identified a network of protein-protein interactions among a subset of common editosome proteins, but interactions among the endonucleases and their partner proteins, and their interactions with common subunits were not identified. Here, chemical cross-linking and mass spectrometry, comparative structural modeling, and genetic and biochemical analyses were used to define the molecular architecture and subunit organization of purified editosomes. We identified intra- and interprotein cross-links for all editosome subunits that are fully consistent with editosome protein structures and previously identified interactions, which we validated by genetic and biochemical studies. The results were used to create a highly detailed map of editosome protein domain proximities, leading to identification of molecular interactions between subunits, insights into the functions of noncatalytic editosome proteins, and a global understanding of editosome architecture.
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5
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Identification by Random Mutagenesis of Functional Domains in KREPB5 That Differentially Affect RNA Editing between Life Cycle Stages of Trypanosoma brucei. Mol Cell Biol 2015; 35:3945-61. [PMID: 26370513 DOI: 10.1128/mcb.00790-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 09/08/2015] [Indexed: 11/20/2022] Open
Abstract
KREPB5 is an essential component of ∼ 20S editosomes in Trypanosoma brucei which contains a degenerate, noncatalytic RNase III domain. To explore the function of this protein, we used a novel approach to make and screen numerous conditional null T. brucei bloodstream form cell lines that express randomly mutagenized KREPB5 alleles. We identified nine single amino acid substitutions that could not complement the conditional loss of wild-type KREPB5. Seven of these were within the RNase III domain, and two were in the C-terminal region that has no homology to known motifs. Exclusive expression of these mutated KREPB5 alleles in the absence of wild-type allele expression resulted in growth inhibition, the loss of ∼ 20S editosomes, and inhibition of RNA editing in BF cells. Eight of these mutations were lethal in bloodstream form parasites but not in procyclic-form parasites, showing that multiple domains function in a life cycle-dependent manner. Amino acid changes at a substantial number of positions, including up to 7 per allele, allowed complementation and thus did not block KREPB5 function. Hence, the degenerate RNase III domain and a newly identified domain are critical for KREPB5 function and have differential effects between the life cycle stages of T. brucei that differentially edit mRNAs.
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6
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McDermott SM, Guo X, Carnes J, Stuart K. Differential Editosome Protein Function between Life Cycle Stages of Trypanosoma brucei. J Biol Chem 2015; 290:24914-31. [PMID: 26304125 DOI: 10.1074/jbc.m115.669432] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Indexed: 11/06/2022] Open
Abstract
Uridine insertion and deletion RNA editing generates functional mitochondrial mRNAs in Trypanosoma brucei. The mRNAs are differentially edited in bloodstream form (BF) and procyclic form (PF) life cycle stages, and this correlates with the differential utilization of glycolysis and oxidative phosphorylation between the stages. The mechanism that controls this differential editing is unknown. Editing is catalyzed by multiprotein ∼20S editosomes that contain endonuclease, 3'-terminal uridylyltransferase, exonuclease, and ligase activities. These editosomes also contain KREPB5 and KREPA3 proteins, which have no functional catalytic motifs, but they are essential for parasite viability, editing, and editosome integrity in BF cells. We show here that repression of KREPB5 or KREPA3 is also lethal in PF, but the effects on editosome structure differ from those in BF. In addition, we found that point mutations in KREPB5 or KREPA3 differentially affect cell growth, editosome integrity, and RNA editing between BF and PF stages. These results indicate that the functions of KREPB5 and KREPA3 editosome proteins are adjusted between the life cycle stages. This implies that these proteins are involved in the processes that control differential editing and that the 20S editosomes differ between the life cycle stages.
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Affiliation(s)
- Suzanne M McDermott
- From the Center for Infectious Disease Research, formerly known as Seattle Biomedical Research Institute, Seattle, Washington 98109
| | - Xuemin Guo
- From the Center for Infectious Disease Research, formerly known as Seattle Biomedical Research Institute, Seattle, Washington 98109
| | - Jason Carnes
- From the Center for Infectious Disease Research, formerly known as Seattle Biomedical Research Institute, Seattle, Washington 98109
| | - Kenneth Stuart
- From the Center for Infectious Disease Research, formerly known as Seattle Biomedical Research Institute, Seattle, Washington 98109
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7
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Additive and transcript-specific effects of KPAP1 and TbRND activities on 3' non-encoded tail characteristics and mRNA stability in Trypanosoma brucei. PLoS One 2012; 7:e37639. [PMID: 22629436 PMCID: PMC3357391 DOI: 10.1371/journal.pone.0037639] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 04/26/2012] [Indexed: 01/09/2023] Open
Abstract
Short, non-encoded oligo(A), oligo(U), or A/U tails can impact mRNA stability in kinetoplastid mitochondria. However, a comprehensive picture of the relative effects of these modifications in RNA stability is lacking. Furthermore, while the U-preferring exoribonuclease TbRND acts on U-tailed gRNAs, its role in decay of uridylated mRNAs has only been cursorily investigated. Here, we analyzed the roles of mRNA 3′ tail composition and TbRND in RNA decay using cells harbouring single or double knockdown of TbRND and the KPAP1 poly(A) polymerase. Analysis of mRNA abundance and tail composition reveals dramatic and transcript-specific effects of adenylation and uridylation on mitochondrial RNAs. Oligo(A) and A-rich tails can stabilize a proportion of edited and never-edited RNAs. However, non-tailed RNAs are not inherently unstable, implicating additional stability determinants and/or spatial segregation of sub-populations of a given RNA in regulation of RNA decay. Oligo(U) tails, which have been shown to contribute to decay of some never-edited RNAs, are not universally destabilizing. We also show that RNAs display very different susceptibility to uridylation in the absence of KPAP1, a factor that may contribute to regulation of decay. Finally, 3′ tail composition apparently impacts the ability of an RNA to be edited.
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8
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Ochsenreiter T, Cipriano M, Hajduk SL. Alternative mRNA editing in trypanosomes is extensive and may contribute to mitochondrial protein diversity. PLoS One 2008; 3:e1566. [PMID: 18270563 PMCID: PMC2215773 DOI: 10.1371/journal.pone.0001566] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2007] [Accepted: 01/02/2008] [Indexed: 11/18/2022] Open
Abstract
The editing of trypanosome mitochondrial mRNAs produces transcripts necessary for mitochondrial functions including electron transport and oxidative phosphorylation. Precursor-mRNAs are often extensively edited by specific uridine insertion or deletion that is directed by small guide RNAs (gRNAs). Recently, it has been shown that cytochrome c oxidase subunit III (COXIII) mRNAs can be alternatively edited to encode a novel mitochondrial membrane protein composed of a unique hydrophilic N-terminal sequence of unknown function and the C-terminal hydrophobic segment of COXIII. To extend the analysis of alternative editing in Trypanosoma brucei we have constructed libraries with over 1100 full-length mitochondrial cDNAs and the sequences of over 1200 gRNA genes. Using this data, we show that alternative editing of COXIII, ATPase subunit 6 (A6), and NADH dehydrogenase subunits 7, 8 and 9 (ND7, 8, 9) mRNAs can produce novel open reading frames (ORFs). Several gRNAs potentially responsible for the alternative editing of these mRNAs were also identified. These findings show that alternative editing of mitochondrial mRNAs is common in T. brucei and expands the diversity of mitochondrial proteins in these organisms.
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Affiliation(s)
- Torsten Ochsenreiter
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Michael Cipriano
- Department of Medical Microbiology, University of California Davis, Davis, California, United States of America
| | - Stephen L. Hajduk
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
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9
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10
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Lukes J, Hashimi H, Zíková A. Unexplained complexity of the mitochondrial genome and transcriptome in kinetoplastid flagellates. Curr Genet 2005; 48:277-99. [PMID: 16215758 DOI: 10.1007/s00294-005-0027-0] [Citation(s) in RCA: 145] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2005] [Revised: 09/03/2005] [Accepted: 09/07/2005] [Indexed: 10/25/2022]
Abstract
Kinetoplastids are flagellated protozoans, whose members include the pathogens Trypanosoma brucei, T. cruzi and Leishmania species, that are considered among the earliest diverging eukaryotes with a mitochondrion. This organelle has become famous because of its many unusual properties, which are unique to the order Kinetoplastida, including an extensive kinetoplast DNA network and U-insertion/deletion type RNA editing of its mitochondrial transcripts. In the last decade, considerable progress has been made in elucidating the complex machinery of RNA editing. Moreover, our understanding of the structure and replication of kinetoplast DNA has also dramatically improved. Much less however, is known, about the developmental regulation of RNA editing, its integration with other RNA maturation processes, stability of mitochondrial mRNAs, or evolution of the editing process itself. Yet the profusion of genomic data recently made available by sequencing consortia, in combination with methods of reverse genetics, hold promise in understanding the complexity of this exciting organelle, knowledge of which may enable us to fight these often medically important protozoans.
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Affiliation(s)
- Julius Lukes
- Institute of Parasitology, Czech Academy of Sciences, Faculty of Biology, University of South Bohemia, Branisovská 31, 37005, Ceské Budejovice, Czech Republic.
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11
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Schnaufer A, Domingo GJ, Stuart K. Natural and induced dyskinetoplastic trypanosomatids: how to live without mitochondrial DNA. Int J Parasitol 2002; 32:1071-84. [PMID: 12117490 DOI: 10.1016/s0020-7519(02)00020-6] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Salivarian trypanosomes are the causative agents of several diseases of major social and economic impact. The most infamous parasites of this group are the African subspecies of the Trypanosoma brucei group, which cause sleeping sickness in humans and nagana in cattle. In terms of geographical distribution, however, Trypanosoma equiperdum and Trypanosoma evansi have been far more successful, causing disease in livestock in Africa, Asia, and South America. In these latter forms the mitochondrial DNA network, the kinetoplast, is altered or even completely lost. These natural dyskinetoplastic forms can be mimicked in bloodstream form T. brucei by inducing the loss of kinetoplast DNA (kDNA) with intercalating dyes. Dyskinetoplastic T. brucei are incapable of completing their usual developmental cycle in the insect vector, due to their inability to perform oxidative phosphorylation. Nevertheless, they are usually as virulent for their mammalian hosts as parasites with intact kDNA, thus questioning the therapeutic value of attempts to target mitochondrial gene expression with specific drugs. Recent experiments, however, have challenged this view. This review summarises the data available on dyskinetoplasty in trypanosomes and revisits the roles the mitochondrion and its genome play during the life cycle of T. brucei.
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Affiliation(s)
- Achim Schnaufer
- Seattle Biomedical Research Institute, 4 Nickerson Street, Suite 200, Seattle, WA 98109, USA.
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12
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Tan THP, Pach R, Crausaz A, Ivens A, Schneider A. tRNAs in Trypanosoma brucei: genomic organization, expression, and mitochondrial import. Mol Cell Biol 2002; 22:3707-17. [PMID: 11997507 PMCID: PMC133840 DOI: 10.1128/mcb.22.11.3707-3716.2002] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The mitochondrial genome of Trypanosoma brucei does not encode tRNAs. Consequently, all mitochondrial tRNAs are imported from the cytosol and originate from nucleus-encoded genes. Analysis of all currently available T. brucei sequences revealed that its genome carries 50 tRNA genes representing 40 different isoacceptors. The identified set is expected to be nearly complete since all but four codons are accounted for. The number of tRNA genes in T. brucei is very low for a eukaryote and lower than those of many prokaryotes. Using quantitative Northern analysis we have determined the absolute abundance in the cell and the mitochondrion of a group of 15 tRNAs specific for 12 amino acids. Except for the initiator type tRNA(Met), which is cytosol specific, the cytosolic and the mitochondrial sets of tRNAs were qualitatively identical. However, the extent of mitochondrial localization was variable for the different tRNAs, ranging from 1 to 7.5% per cell. Finally, by using transgenic cell lines in combination with quantitative Northern analysis it was shown that import of tRNA(Leu)(CAA) is independent of its 5'-genomic context, suggesting that the in vivo import substrate corresponds to the mature, fully processed tRNA.
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Affiliation(s)
- Timothy H P Tan
- Department of Biology/Zoology, University of Fribourg, CH-1700 Fribourg, Switzerland
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13
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Hayman ML, Miller MM, Chandler DM, Goulah CC, Read LK. The trypanosome homolog of human p32 interacts with RBP16 and stimulates its gRNA binding activity. Nucleic Acids Res 2001; 29:5216-25. [PMID: 11812855 PMCID: PMC97595 DOI: 10.1093/nar/29.24.5216] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2001] [Revised: 10/12/2001] [Accepted: 10/22/2001] [Indexed: 11/13/2022] Open
Abstract
RBP16 is a guide RNA (gRNA)-binding protein that was shown through immunoprecipitation experiments to interact with approximately 30% of total gRNAs in Trypanosoma brucei mitochondria. To gain insight into the biochemical function of RBP16, we used affinity chromatography and immunoprecipitation to identify RBP16 protein binding partners. By these methods, RBP16 does not appear to stably interact with the core editing machinery. However, fractionation of mitochondrial extracts on MBP-RBP16 affinity columns consistently isolated proteins of 12, 16, 18 and 22 kDa that were absent from MBP control columns. We describe here our analysis of one RBP16-associated protein, p22. The predicted p22 protein has significant sequence similarity to a family of multimeric, acidic proteins that includes human p32 and Saccharomyces cerevisiae mam33p. Glutaraldehyde crosslinking of recombinant p22 identified homo-multimeric forms of the protein, further substantiating its homology to p32. We confirmed the p22-RBP16 interaction and demonstrated that the two proteins bind each other directly by ELISA utilizing recombinant p22 and RBP16. p32 family members have been reported to modulate viral and cellular pre-mRNA splicing, in some cases by perturbing interaction of their binding partners with RNA. To determine whether p22 similarly affects the gRNA binding properties of RBP16, we titrated recombinant p22 into UV crosslinking assays. These experiments revealed that p22 significantly stimulates the gRNA binding capacity of RBP16. Thus, p22 has the potential to be a regulatory factor in T.brucei mitochondrial gene expression by modulating the RNA binding properties of RBP16.
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Affiliation(s)
- M L Hayman
- Department of Microbiology and Witebsky Center for Microbial Pathogenesis and Immunology, SUNY Buffalo School of Medicine, 138 Farber Hall, Buffalo, NY 14214, USA
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14
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Carrillo R, Thiemann OH, Alfonzo JD, Simpson L. Uridine insertion/deletion RNA editing in Leishmania tarentolae mitochondria shows cell cycle dependence. Mol Biochem Parasitol 2001; 113:175-81. [PMID: 11254966 DOI: 10.1016/s0166-6851(00)00385-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- R Carrillo
- Howard Hughes Medical Institute, UCLA School of Medicine, Los Angles, CA 90095-1662, USA
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15
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Oppegard LM, Kabb AL, Connell GJ. Activation of guide RNA-directed editing of a cytochrome b mRNA. J Biol Chem 2000; 275:33911-9. [PMID: 10940300 DOI: 10.1074/jbc.m003002200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The coding sequence of several mitochondrial mRNAs of the kinetoplastid protozoa is created only after the addition or deletion of specific uridines. Although in vitro systems have been valuable in characterizing the editing mechanism, only a limited number of mRNAs are accurately edited in vitro. We demonstrate here that in vitro editing of cytochrome b mRNA is inhibited by an A-U sequence present on both the 5'-untranslated sequence and on a cytochrome b guide RNA. Mutation of the sequence on the guide RNA stimulates directed editing and results in the loss of binding to at least one component within the editing extract. Mutation of the sequence on the mRNA increases the accuracy of the editing. Evidence is provided that suggests the A-U sequence interacts with the editing machinery both in vitro and in vivo.
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Affiliation(s)
- L M Oppegard
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455-0347, USA
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16
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Abstract
The uridine insertion/deletion RNA editing in trypanosome mitochondria is a unique posttranscriptional RNA maturation process that involves the addition or removal of uridine residues at precise sites usually within the coding regions of mitochondrial transcripts. This process creates initiation and termination codons, corrects frameshifts and even builds entire open-reading frames from nonsense sequences. The development of several in-vitro editing assays has provided much insight into the molecular mechanism of RNA editing, which appears to involve cleavage, U addition, exonuclease trimming and ligation, essentially as proposed in the original 'enzyme cascade' model (Blum, B., Bakalara, N., Simpson, L., 1990. A model for RNA editing in kinetoplastid mitochondria: 'Guide' RNA molecules transcribed from maxicircle DNA provide the edited information. Cell 60, 189-198). However, little is known about the biochemical properties of the proteins involved and the significance and role of this process. This article is a review of recent findings on uridine-insertion/deletion editing in trypanosome mitochondria, with an emphasis on the proteins isolated and characterized that may have a role in this process.
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Affiliation(s)
- A M Estévez
- Howard Hughes Medical Institute, UCLA School of Medicine, 6780 MacDonald Building, Los Angeles, CA, USA
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17
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Hayman ML, Read LK. Trypanosoma brucei RBP16 is a mitochondrial Y-box family protein with guide RNA binding activity. J Biol Chem 1999; 274:12067-74. [PMID: 10207031 DOI: 10.1074/jbc.274.17.12067] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Trypanosoma brucei mitochondria possess a unique mechanism of mRNA maturation called RNA editing. In this process, uridylate residues are inserted and deleted posttranscriptionally into pre-mRNA to create translatable messages. The genetic information for RNA editing resides in small RNA molecules called guide RNAs (gRNAs). Thus, proteins in direct contact with gRNA are likely to catalyze or influence RNA editing. Herein we characterize an abundant gRNA-binding protein from T. brucei mitochondria. This protein, which we term RBP16 (for RNA-binding protein of 16 kDa), binds to different gRNA molecules. The major determinant of this interaction is the oligo(U) tail, present on the 3'-ends of gRNAs. RBP16 forms multiple, stable complexes with gRNA in vitro, and immunoprecipitation experiments provide evidence for an association between RBP16 and gRNA within T. brucei mitochondria. Mature RBP16 contains a cold shock domain at the N terminus and a C-terminal region rich in arginine and glycine. The presence of the cold shock domain places RBP16 as the first organellar member of the highly conserved Y-box protein family. The arginine and glycine rich C terminus in combination with the cold shock domain predicts that RBP16 will be involved in the regulation of gene expression at the posttranscriptional level.
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Affiliation(s)
- M L Hayman
- Department of Microbiology and Center for Microbial Pathogenesis, State University of New York at Buffalo School of Medicine, Buffalo, New York 14214, USA
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18
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Brown LM, Burbach BJ, McKenzie BA, Connell GJ. A cis-acting A-U sequence element induces kinetoplastid U-insertions. J Biol Chem 1999; 274:6295-304. [PMID: 10037718 DOI: 10.1074/jbc.274.10.6295] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A 34-nucleotide A-U sequence located immediately upstream of the editing sites of the Leishmania tarentolae cytochrome b mRNA induces a mitochondrial extract to insert U nucleotides independent of guide RNA. Insertions are localized to positions immediately 5' and 3' of the A-U sequence. When placed within an unedited mammalian transcript, the A-U sequence is sufficient to induce U-insertions. The sequence has a high degree of similarity with the templating nucleotides of a cytochrome b guide RNA and with a sequence adjacent to the editing sites in ND7 mRNA, the other characterized kinetoplastid mRNA supporting guide RNA-independent U-insertions. At least one protein specifically interacts with the A-U sequence. The reaction is consistent with a mechanism proposed for guide RNA-directed editing.
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Affiliation(s)
- L M Brown
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455-0347, USA
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Allen TE, Heidmann S, Reed R, Myler PJ, Göringer HU, Stuart KD. Association of guide RNA binding protein gBP21 with active RNA editing complexes in Trypanosoma brucei. Mol Cell Biol 1998; 18:6014-22. [PMID: 9742118 PMCID: PMC109187 DOI: 10.1128/mcb.18.10.6014] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/1998] [Accepted: 06/19/1998] [Indexed: 11/20/2022] Open
Abstract
RNA editing in Trypanosoma brucei mitochondria produces mature mRNAs by a series of enzyme-catalyzed reactions that specifically insert or delete uridylates in association with a macromolecular complex. Using a mitochondrial fraction enriched for in vitro RNA editing activity, we produced several monoclonal antibodies that are specific for a 21-kDa guide RNA (gRNA) binding protein initially identified by UV cross-linking. Immunofluorescence studies localize the protein to the mitochondrion, with a preference for the kinetoplast. The antibodies cause a supershift of previously identified gRNA-specific ribonucleoprotein complexes and immunoprecipitate in vitro RNA editing activities that insert and delete uridylates. The immunoprecipitated material also contains gRNA-specific endoribonuclease, terminal uridylyltransferase, and RNA ligase activities as well as gRNA and both edited and unedited mRNA. The immunoprecipitate contains numerous proteins, of which the 21-kDa protein, a 90-kDa protein, and novel 55- and 16-kDa proteins can be UV cross-linked to gRNA. These studies indicate that the 21-kDa protein associates with the ribonucleoprotein complex (or complexes) that catalyze RNA editing.
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Affiliation(s)
- T E Allen
- Seattle Biomedical Research Institute, Seattle, Washington, 98109-1651, USA
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20
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Abstract
RNA editing in trypanosomes produces mature mRNAs by posttranscriptional guide RNA (gRNA)-directed uridylate insertion and deletion. This article describes methods for the study of RNA editing with an emphasis on an in vitro editing system that was used to explore the general mechanism of editing and that can be adapted for more in-depth studies of this intriguing and important process. Methods used to investigate the macromolecular complex that catalyzes RNA editing are also described. This complex is composed of multiple proteins and contains several catalytic activities. It is in the early stages of characterization. The methods described here are intended to assist in its further analysis.
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Affiliation(s)
- K Stuart
- Seattle Biomedical Research Institute, Washington 98109-1651, USA.
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Blom D, de Haan A, van den Berg M, Sloof P, Jirku M, Lukes J, Benne R. RNA editing in the free-living bodonid Bodo saltans. Nucleic Acids Res 1998; 26:1205-13. [PMID: 9469817 PMCID: PMC147379 DOI: 10.1093/nar/26.5.1205] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In parasitic kinetoplastid protozoa, mitochondrial (mt) mRNAs are post-transcriptionally edited by insertion and deletion of uridylate residues, the information being provided by guide (g) RNAs. In order to further explore the role and evolutionary history of this process, we searched for editing in mt RNAs of the free-living bodonid Bodo saltans. We found extensive editing in the transcript for NADH dehydrogenase (ND) subunit 5, which is unedited in trypanosomatids. In contrast, B.saltans cytochrome c oxidase (cox) subunit 2 and maxicircle unidentified reading frame (MURF) 2 RNAs display limited editing in the same regions as their trypanosomatid counterparts. A putative intramolecular cox2 gRNA and the gene for gMURF2-I directing the insertion of only one U in the 5' editing domain of MURF2 RNA, are conserved in B.saltans. This lends (further) evolutionary support to the proposed role of these sequences as gRNAs. Phylogenetic analysis showed that B.saltans is more closely related to trypanosomatids than the cryptobiids Trypanoplasma borreli and Cryptobia helicis, in line with the trypanosomatid-like cox2 and MURF2 RNA editing patterns. Nevertheless, other features like the apparent absence of a catenated mtDNA network, are shared with bodonid and cryptobiid species. ND5 RNA editing may represent yet another example of editing 'on the way out' during kinetoplastid evolution, but in view of the fact that cox2 RNA is unedited in T. borreli and C.helicis, we infer that the editing of this RNA may have arisen relatively recently. Our results provide the first examples of RNA editing in a free-living kinetoplastid, indicating that there is no direct link between U-insertion/deletion editing and a parasitic lifestyle.
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Affiliation(s)
- D Blom
- Department of Biochemistry/AMC, University of Amsterdam, Academic Medical Centre, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
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22
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Abstract
RNA editing in kinetoplastids involves post-transcriptional insertion and deletion of uridylates (Us) to produce mature mitochondrial mRNAs with sequences specified by trans acting small guide RNAs. In vitro studies indicate the reaction pathway involves endonucleolytic cleavage of the precursor mRNA at the editing site, uridylate addition or removal at the 3' end of the 5' cleavage product, followed by ligation to the 3' cleavage product. This editing is catalyzed by a macromolecular complex that is in the early stages of characterization. Recent studies have resolved the general mechanism of editing, and show that editing occurs in association with a macromolecular complex.
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Affiliation(s)
- K Stuart
- Seattle Biomedical Research Institute, 4 Nickerson Street, WA 98109-1651, USA.
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23
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Speijer D, Breek CK, Muijsers AO, Hartog AF, Berden JA, Albracht SP, Samyn B, Van Beeumen J, Benne R. Characterization of the respiratory chain from cultured Crithidia fasciculata. Mol Biochem Parasitol 1997; 85:171-86. [PMID: 9106191 DOI: 10.1016/s0166-6851(96)02823-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Mitochondrial mRNAs encoding subunits of respiratory-chain complexes in kinetoplastids are post-transcriptionally edited by uridine insertion and deletion. In order to identify the proteins encoded by these mRNAs, we have analyzed respiratory-chain complexes from cultured cells of Crithidia fasciculata with the aid of 2D polyacrylamide gel electrophoresis (PAGE). The subunit composition of F0F1-ATPase (complex V), identified on the basis of its activity as an oligomycin-sensitive ATPase, is similar to that of bovine mitochondrial F0F1-ATPase. Amino acid sequence analysis, combined with binding studies using dicyclohexyldiimide and azido ATP allowed the identification of two F0 subunits (b and c) and all of the F1 subunits. The F0 b subunit has a low degree of similarity to subunit b from other organisms. The F1 alpha subunit is extremely small making the beta subunit the largest F1 subunit. Other respiratory-chain complexes were also analyzed. Interestingly, an NADH: ubiquinone oxidoreductase (complex I) appeared to be absent, as judged by electron paramagnetic resonance (EPR), enzyme activity and 2D PAGE analysis. Cytochrome c oxidase (complex IV) displayed a subunit pattern identical to that reported for the purified enzyme, whereas cytochrome c reductase (complex III) appeared to contain two extra subunits. A putative complex II was also identified. The amino acid sequences of the subunits of these complexes also show a very low degree of similarity (if any) to the corresponding sequences in other organisms. Remarkably, peptide sequences derived from mitochondrially encoded subunits were not found in spite of the fact that sequences were obtained of virtually all subunits of complex III, IV and V.
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Affiliation(s)
- D Speijer
- Department of Biochemistry, University of Amsterdam, Netherlands
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24
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Abstract
Mitochondrial transcripts in kinetoplastids undergo remarkable posttranscriptional editing by uridylate insertion and deletion. The often dramatic remodeling of pre-mRNA sequences is directed by small guide RNAs (gRNAs) to produce mature mRNAs. In vitro analyses of editing have been used to determine the mechanism of editing and show that editing occurs by a series of enzyme-catalyzed steps. They also show that chimeric gRNA/mRNA molecules are not editing intermediates as proposed but are aberrant end products of editing. The complexes and molecules that catalyze editing are now being identified and characterized. The origin of editing, its developmental regulation which helps control the switching between terminal respiratory systems during the life cycle of trypanosomes, and other areas for future study are discussed.
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Affiliation(s)
- K Stuart
- Seattle Biomedical Research Institute, Washington 98109-1651, USA.
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Schmid B, Read LK, Stuart K, Göringer HU. Experimental verification of the secondary structures of guide RNA-pre-mRNA chimaeric molecules in Trypanosoma brucei. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 240:721-31. [PMID: 8856076 DOI: 10.1111/j.1432-1033.1996.0721h.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
RNA editing in kinetoplastid organisms is an RNA-processing reaction that adds and deletes U nucleotides at specific sites in mitochondrial pre-mRNAs. The edited sequence is specified by guide RNAs and the processing presumably occurs within a high-molecular-mass ribonucleoprotein complex containing several enzymatic activities. Although the mechanism is not currently known, potential intermediates or by-products of the editing process are chimaeric RNAs where guide (g) RNAs are covalently attached, via their non-encoded U-tail, to their cognate pre-mRNAs. We determined the secondary structures of three different ATPase 6 chimaeras of Trypanosoma brucei using a set of structure-sensitive chemical and enzymatic probes. The experiments revealed a bipartite domain structure consisting of a gRNA/pre-mRNA interaction hairpin and an independently folding mRNA stem/loop in all three RNAs. The connecting U-tail was a determinant for the length of the interaction stems with the oligo(U) nucleotides base pairing to internal gRNA sequences. The probed structures have calculated delta G27o values of -92 kJ/ mol to -134 kJ/mol, somewhat less stable than the predicted minimal free energy structures and support previously proposed models for the interaction between gRNAs and pre-mRNAs. Optical melting studies indicated additional, higher order structural features for all three molecules with four defined melting transition between 10 degrees C and 90 degrees C. A comparison of CD spectra in the absence and presence of mitochondrial protein extracts demonstrated no gross structural changes of the RNA structures induced by the association with polypeptides.
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Affiliation(s)
- B Schmid
- Laboratorium für molekulare Biologie - Genzentrum, Universität München am Max-Planck-Institut für Biochemie, Martinsried, Germany
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Arts GJ, Benne R. Mechanism and evolution of RNA editing in kinetoplastida. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1307:39-54. [PMID: 8652667 DOI: 10.1016/0167-4781(96)00021-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- G J Arts
- E.C. Slater Institute, University of Amsterdam, Academic Medical Centre, The Netherlands
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27
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Abstract
Considerable progress has been made in unraveling the mechanistic features of RNA editing processes in a number of genetic systems. Recent highlights include the identification of the catalytic subunit of the mammalian apolipoprotein B mRNA editing enzyme as a zinc-dependent cytidine deaminase that binds to RNA, the demonstration that adenosines in brain glutamate receptor pre-mRNAs are converted into inosines and that double-stranded RNA A deaminase (dsRAD), the candidate enzyme, is another zinc-dependent RNA nucleotide deaminase, and a mounting body of evidence for a cleavage-ligation mechanism for U insertion/deletion editing in kinetoplastid protozoa.
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Affiliation(s)
- R Benne
- Department of Biochemistry, Faculty of Medicine, University of Amsterdam, Academic Medical Centre, The Netherlands.
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Seiwert SD, Heidmann S, Stuart K. Direct visualization of uridylate deletion in vitro suggests a mechanism for kinetoplastid RNA editing. Cell 1996; 84:831-41. [PMID: 8601307 DOI: 10.1016/s0092-8674(00)81062-4] [Citation(s) in RCA: 172] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Deletion of uridylates from the 3'-most editing site of synthetic ATPase 6 pre-mRNA can be visualized directly by coincubation of a radiolabeled substrate RNA and a synthetic gRNA in 20S fractions of T.brucie mitochondrial lysates. Substrate RNA cleavage is gRNA directed and occurs 3' to the uridylates to be deleted. U residues appear to be sequentially removed from the 3' end of the 5' cleavage product prior to religation of the two pre-mRNA halves. gRNA/mRNA chimeric molecules are also produced. Time course experiments indicate that chimeras appear after cleavage intermediates and edited product. Furthermore, a mutant gRNA promotes formation of edited product but not detectable chimeras. Our results suggest a model for kinetoplastid RNA editing in which chimeric molecules are nonproductive end products of editing and not intermediates that serve as a repository for deleted U's.
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Affiliation(s)
- S D Seiwert
- Seattle Biomedical Research Institute, Washington, 98109, USA
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29
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Abstract
Over 30 million people in tropical regions suffer from Chagas disease, African sleeping sickness or leishmaniasis. The causative agents of these diseases, flagellated protozoa collectively known as kinetoplastids, represent an ancient lineage of eukaryotes. These unusual organisms carry out a large number of unique biochemical processes, one striking example being the sequence editing of mitochondrial messenger RNAs. In this review, Scott Seiwert focuses on recent studies that examine the reaction mechanism, molecular machinery and evolutionary history of this unusual RNA processing reaction.
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Affiliation(s)
- S D Seiwert
- Seattle Biomedical Research Institute, WA 98109, USA.
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