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Nascimento JF, Souza ROO, Alencar MB, Marsiccobetre S, Murillo AM, Damasceno FS, Girard RBMM, Marchese L, Luévano-Martinez LA, Achjian RW, Haanstra JR, Michels PAM, Silber AM. How much (ATP) does it cost to build a trypanosome? A theoretical study on the quantity of ATP needed to maintain and duplicate a bloodstream-form Trypanosoma brucei cell. PLoS Pathog 2023; 19:e1011522. [PMID: 37498954 PMCID: PMC10409291 DOI: 10.1371/journal.ppat.1011522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/08/2023] [Accepted: 06/29/2023] [Indexed: 07/29/2023] Open
Abstract
ATP hydrolysis is required for the synthesis, transport and polymerization of monomers for macromolecules as well as for the assembly of the latter into cellular structures. Other cellular processes not directly related to synthesis of biomass, such as maintenance of membrane potential and cellular shape, also require ATP. The unicellular flagellated parasite Trypanosoma brucei has a complex digenetic life cycle. The primary energy source for this parasite in its bloodstream form (BSF) is glucose, which is abundant in the host's bloodstream. Here, we made a detailed estimation of the energy budget during the BSF cell cycle. As glycolysis is the source of most produced ATP, we calculated that a single parasite produces 6.0 x 1011 molecules of ATP/cell cycle. Total biomass production (which involves biomass maintenance and duplication) accounts for ~63% of the total energy budget, while the total biomass duplication accounts for the remaining ~37% of the ATP consumption, with in both cases translation being the most expensive process. These values allowed us to estimate a theoretical YATP of 10.1 (g biomass)/mole ATP and a theoretical [Formula: see text] of 28.6 (g biomass)/mole ATP. Flagellar motility, variant surface glycoprotein recycling, transport and maintenance of transmembrane potential account for less than 30% of the consumed ATP. Finally, there is still ~5.5% available in the budget that is being used for other cellular processes of as yet unknown cost. These data put a new perspective on the assumptions about the relative energetic weight of the processes a BSF trypanosome undergoes during its cell cycle.
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Affiliation(s)
- Janaina F. Nascimento
- Laboratory of Biochemistry of Tryps–LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo–São Paulo, Brazil
| | - Rodolpho O. O. Souza
- Laboratory of Biochemistry of Tryps–LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo–São Paulo, Brazil
| | - Mayke B. Alencar
- Laboratory of Biochemistry of Tryps–LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo–São Paulo, Brazil
| | - Sabrina Marsiccobetre
- Laboratory of Biochemistry of Tryps–LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo–São Paulo, Brazil
| | - Ana M. Murillo
- Laboratory of Biochemistry of Tryps–LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo–São Paulo, Brazil
| | - Flávia S. Damasceno
- Laboratory of Biochemistry of Tryps–LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo–São Paulo, Brazil
| | - Richard B. M. M. Girard
- Laboratory of Biochemistry of Tryps–LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo–São Paulo, Brazil
| | - Letícia Marchese
- Laboratory of Biochemistry of Tryps–LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo–São Paulo, Brazil
| | - Luis A. Luévano-Martinez
- Laboratory of Biochemistry of Tryps–LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo–São Paulo, Brazil
| | - Renan W. Achjian
- Laboratory of Biochemistry of Tryps–LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo–São Paulo, Brazil
| | - Jurgen R. Haanstra
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Paul A. M. Michels
- School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Ariel M. Silber
- Laboratory of Biochemistry of Tryps–LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo–São Paulo, Brazil
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2
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Aphasizheva I, Aphasizhev R. Mitochondrial RNA quality control in trypanosomes. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1638. [PMID: 33331073 PMCID: PMC9805618 DOI: 10.1002/wrna.1638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 01/04/2023]
Abstract
Unicellular parasites Trypanosoma brucei spp. cause African human and animal trypanosomiasis, a spectrum of diseases that jeopardize public health and afflict the economy in sub-Saharan Africa. These hemoflagellates are distinguished by a single mitochondrion, which contains a kinetoplast nucleoid composed of DNA and histone-like proteins. Kinetoplast DNA (kDNA) represents a densely packed network of interlinked relaxed circular molecules: a few ~23-kb maxicircles encoding ribosomal RNAs (rRNAs) and proteins, and approximately 5,000 1-kb minicircles bearing guide RNA (gRNA) genes. The transcription start site defines the mRNA's 5' terminus while the primary RNA is remodeled into a monocistronic messenger by 3'-5' exonucleolytic trimming, 5' and 3' end modifications, and, in most cases, by internal U-insertion/deletion editing. Ribosomal and guide RNA precursors are also trimmed, and the processed molecules are uridylated. For 35 years, mRNA editing has attracted a major effort, but more recently the essential pre- and postediting processing and turnover events have been discovered and the key effectors have been identified. Among these, pentatricopeptide repeat (PPR) RNA binding proteins emerged as conduits coupling modifications of mRNA termini with internal sequence changes introduced by editing. Among 39 annotated PPRs, 20 belong to ribosomal subunits or assembly intermediates, four function as polyadenylation factors, a single factor directs 5' mRNA modification, and one protein is found in F1-ATPase. Nuclear and mitochondrial RNases P consist of a single PPR polypeptide, PRORP1 and PROP2, respectively. Here, we review PPR-mediated mitochondrial processes and discuss their potential roles in mRNA maturation, quality control, translational activation, and decay. This article is categorized under: RNA Processing > Capping and 5' End Modifications RNA Processing > 3' End Processing RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, Massachusetts
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, Massachusetts,Department of Biochemistry, Boston University Medical Campus, Boston, Massachusetts
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3
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Gao Y, Liu H, Zhang C, Su S, Chen Y, Chen X, Li Y, Shao Z, Zhang Y, Shao Q, Li J, Huang Z, Ma J, Gan J. Structural basis for guide RNA trimming by RNase D ribonuclease in Trypanosoma brucei. Nucleic Acids Res 2021; 49:568-583. [PMID: 33332555 PMCID: PMC7797062 DOI: 10.1093/nar/gkaa1197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/24/2020] [Indexed: 11/18/2022] Open
Abstract
Infection with kinetoplastid parasites, including Trypanosoma brucei (T. brucei), Trypanosoma cruzi (T. cruzi) and Leishmania can cause serious disease in humans. Like other kinetoplastid species, mRNAs of these disease-causing parasites must undergo posttranscriptional editing in order to be functional. mRNA editing is directed by gRNAs, a large group of small RNAs. Similar to mRNAs, gRNAs are also precisely regulated. In T. brucei, overexpression of RNase D ribonuclease (TbRND) leads to substantial reduction in the total gRNA population and subsequent inhibition of mRNA editing. However, the mechanisms regulating gRNA binding and cleavage by TbRND are not well defined. Here, we report a thorough structural study of TbRND. Besides Apo- and NMP-bound structures, we also solved one TbRND structure in complexed with single-stranded RNA. In combination with mutagenesis and in vitro cleavage assays, our structures indicated that TbRND follows the conserved two-cation-assisted mechanism in catalysis. TbRND is a unique RND member, as it contains a ZFD domain at its C-terminus. In addition to T. brucei, our studies also advanced our understanding on the potential gRNA degradation pathway in T. cruzi, Leishmania, as well for as other disease-associated parasites expressing ZFD-containing RNDs.
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Affiliation(s)
- Yanqing Gao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Hehua Liu
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Chong Zhang
- College of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Shichen Su
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yiqing Chen
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xi Chen
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yangyang Li
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhiwei Shao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yixi Zhang
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qiyuan Shao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jixi Li
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhen Huang
- College of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jianhua Gan
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
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4
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Aphasizheva I, Alfonzo J, Carnes J, Cestari I, Cruz-Reyes J, Göringer HU, Hajduk S, Lukeš J, Madison-Antenucci S, Maslov DA, McDermott SM, Ochsenreiter T, Read LK, Salavati R, Schnaufer A, Schneider A, Simpson L, Stuart K, Yurchenko V, Zhou ZH, Zíková A, Zhang L, Zimmer S, Aphasizhev R. Lexis and Grammar of Mitochondrial RNA Processing in Trypanosomes. Trends Parasitol 2020; 36:337-355. [PMID: 32191849 PMCID: PMC7083771 DOI: 10.1016/j.pt.2020.01.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/19/2020] [Accepted: 01/22/2020] [Indexed: 12/15/2022]
Abstract
Trypanosoma brucei spp. cause African human and animal trypanosomiasis, a burden on health and economy in Africa. These hemoflagellates are distinguished by a kinetoplast nucleoid containing mitochondrial DNAs of two kinds: maxicircles encoding ribosomal RNAs (rRNAs) and proteins and minicircles bearing guide RNAs (gRNAs) for mRNA editing. All RNAs are produced by a phage-type RNA polymerase as 3' extended precursors, which undergo exonucleolytic trimming. Most pre-mRNAs proceed through 3' adenylation, uridine insertion/deletion editing, and 3' A/U-tailing. The rRNAs and gRNAs are 3' uridylated. Historically, RNA editing has attracted major research effort, and recently essential pre- and postediting processing events have been discovered. Here, we classify the key players that transform primary transcripts into mature molecules and regulate their function and turnover.
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Affiliation(s)
- Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA 02118, USA.
| | - Juan Alfonzo
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Jason Carnes
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Igor Cestari
- Institute of Parasitology, McGill University, 21,111 Lakeshore Road, Ste-Anne-de-Bellevue, H9X3V9, Québec, Canada
| | - Jorge Cruz-Reyes
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - H Ulrich Göringer
- Department of Molecular Genetics, Darmstadt University of Technology, 64287 Darmstadt, Germany
| | - Stephen Hajduk
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Susan Madison-Antenucci
- Parasitology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
| | - Dmitri A Maslov
- Department of Molecular, Cell, and Systems Biology, University of California - Riverside, Riverside, CA 92521, USA
| | - Suzanne M McDermott
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Torsten Ochsenreiter
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, Bern CH-3012, Switzerland
| | - Laurie K Read
- Department of Microbiology and Immunology, University at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Reza Salavati
- Institute of Parasitology, McGill University, 21,111 Lakeshore Road, Ste-Anne-de-Bellevue, H9X3V9, Québec, Canada
| | - Achim Schnaufer
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - André Schneider
- Department of Chemistry and Biochemistry, University of Bern, Bern CH-3012, Switzerland
| | - Larry Simpson
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095, USA
| | - Kenneth Stuart
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic; Martsinovsky Institute of Medical Parasitology, Sechenov University, Moscow, Russia
| | - Z Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095, USA
| | - Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Liye Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Sara Zimmer
- University of Minnesota Medical School, Duluth campus, Duluth, MN 55812, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA 02118, USA
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5
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Abstract
Mitochondrial genomes are often transcribed into polycistronic RNAs punctuated by tRNAs whose excision defines mature RNA boundaries. Although kinetoplast DNA lacks tRNA genes, it is commonly held that in Trypanosoma brucei the monophosphorylated 5' ends of functional molecules typify precursor partitioning by an unknown endonuclease. On the contrary, we demonstrate that individual mRNAs and rRNAs are independently synthesized as 3'-extended precursors. The transcription-defined 5' terminus is converted into a monophosphorylated state by the pyrophosphohydrolase complex, termed the "PPsome." Composed of the MERS1 NUDIX enzyme, the MERS2 pentatricopeptide repeat RNA-binding subunit, and MERS3 polypeptide, the PPsome binds to specific sequences near mRNA 5' termini. Most guide RNAs lack PPsome-recognition sites and remain triphosphorylated. The RNA-editing substrate-binding complex stimulates MERS1 pyrophosphohydrolase activity and enables an interaction between the PPsome and the polyadenylation machinery. We provide evidence that both 5' pyrophosphate removal and 3' adenylation are essential for mRNA stabilization. Furthermore, we uncover a mechanism by which antisense RNA-controlled 3'-5' exonucleolytic trimming defines the mRNA 3' end before adenylation. We conclude that mitochondrial mRNAs and rRNAs are transcribed and processed as insulated units irrespective of their genomic location.
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Differential Binding of Mitochondrial Transcripts by MRB8170 and MRB4160 Regulates Distinct Editing Fates of Mitochondrial mRNA in Trypanosomes. mBio 2017; 8:mBio.02288-16. [PMID: 28143982 PMCID: PMC5285507 DOI: 10.1128/mbio.02288-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A dozen mRNAs are edited by multiple insertions and/or deletions of uridine residues in the mitochondrion of Trypanosoma brucei Several protein complexes have been implicated in performing this type of RNA editing, including the mitochondrial RNA-binding complex 1 (MRB1). Two paralogous novel RNA-binding proteins, MRB8170 and MRB4160, are loosely associated with the core MRB1 complex. Their roles in RNA editing and effects on target mRNAs are so far not well understood. In this study, individual-nucleotide-resolution UV-cross-linking and affinity purification (iCLAP) revealed a preferential binding of both proteins to mitochondrial mRNAs, which was positively correlated with their extent of editing. Integrating additional in vivo and in vitro data, we propose that binding of MRB8170 and/or MRB4160 onto pre-mRNA marks it for the initiation of editing and that initial binding of both proteins may facilitate the recruitment of other components of the RNA editing/processing machinery to ensure efficient editing. Surprisingly, MRB8170 also binds never-edited mRNAs, suggesting that at least this paralog has an additional role outside RNA editing to shape the mitochondrial transcriptome. IMPORTANCE Trypanosoma brucei mitochondrial mRNAs undergo maturation by RNA editing, a unique process involving decrypting open reading frames by the precise deletion and/or insertion of uridine (U) residues at specific positions on an mRNA. This process is catalyzed by multiprotein complexes, such as the RNA editing core complex, which provides the enzymatic activities needed for U insertion/deletion at a single editing site. Less well understood is how RNA editing occurs throughout an mRNA bearing multiple sites. To address this question, we mapped at single-nucleotide resolution the RNA interactions of two unique RNA-binding proteins (RBPs). These RBPs are part of the mitochondrial RNA-binding complex 1, hypothesized to mediate multiple rounds of RNA editing. Both RBPs were shown to mark mRNAs for the process in correlation with the number of editing sites on the transcript. Surprisingly, one also binds mRNAs that bypass RNA editing, indicating that it may have an additional role outside RNA editing.
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Aphasizhev R, Suematsu T, Zhang L, Aphasizheva I. Constructive edge of uridylation-induced RNA degradation. RNA Biol 2016; 13:1078-1083. [PMID: 27715485 PMCID: PMC5100348 DOI: 10.1080/15476286.2016.1229736] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/06/2016] [Accepted: 08/24/2016] [Indexed: 12/18/2022] Open
Abstract
RNA uridylation is a significant transcriptome-shaping factor in protists, fungi, metazoans, and plants. The 3' U-additions are catalyzed by terminal uridyltransferases (TUTases), a diverse group of enzymes that along with non-canonical poly(A) polymerases form a distinct group in the superfamily of DNA polymerase β-like nucleotidyl transferases. Within and across studied organisms and subcellular compartments, TUTases differ in nucleotide triphosphate selectivity, interacting partners, and RNA targets. A general premise linking RNA uridylation to 3'-5' degradation received support from several studies of small RNAs and mRNA turnover. However, recent work on kinetoplastid protists typified by Trypanosoma brucei provides evidence that RNA uridylation may play a more nuanced role in generating functional small RNAs. In this pathogen's mitochondrion, most mRNAs are internally edited by U-insertions and deletions, and subjected to 3' adenylation/uridylation; guide RNAs (gRNAs) required for editing are U-tailed. The prominent role of uridylation in mitochondrial RNA metabolism stimulated identification of the first TUTase, RNA editing TUTase 1 (RET1). Here we discuss functional studies of mitochondrial uridylation in trypanosomes that have revealed an unorthodox pathway of small RNA biogenesis. The current model accentuates physical coupling of RET1 and 3'-5' RNase II/RNB-type exonuclease DSS1 within a stable complex termed the mitochondrial 3' processome (MPsome). In the confines of this complex, RET1 initially uridylates a long precursor to activate its 3'-5' degradation by DSS1, and then uridylates trimmed guide RNA to disengage the processing complex from the mature molecule. We also discuss a potential role of antisense transcription in the MPsome pausing at a fixed distance from gRNA's 5' end. This step likely defines the mature 3' end by enabling kinetic competition between TUTase and exonuclease activities.
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Affiliation(s)
- Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA, USA
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Takuma Suematsu
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA, USA
| | - Liye Zhang
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA, USA
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Simpson L, Douglass SM, Lake JA, Pellegrini M, Li F. Comparison of the Mitochondrial Genomes and Steady State Transcriptomes of Two Strains of the Trypanosomatid Parasite, Leishmania tarentolae. PLoS Negl Trop Dis 2015. [PMID: 26204118 PMCID: PMC4512693 DOI: 10.1371/journal.pntd.0003841] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
U-insertion/deletion RNA editing is a post-transcriptional mitochondrial RNA modification phenomenon required for viability of trypanosomatid parasites. Small guide RNAs encoded mainly by the thousands of catenated minicircles contain the information for this editing. We analyzed by NGS technology the mitochondrial genomes and transcriptomes of two strains, the old lab UC strain and the recently isolated LEM125 strain. PacBio sequencing provided complete minicircle sequences which avoided the assembly problem of short reads caused by the conserved regions. Minicircles were identified by a characteristic size, the presence of three short conserved sequences, a region of inherently bent DNA and the presence of single gRNA genes at a fairly defined location. The LEM125 strain contained over 114 minicircles encoding different gRNAs and the UC strain only ~24 minicircles. Some LEM125 minicircles contained no identifiable gRNAs. Approximate copy numbers of the different minicircle classes in the network were determined by the number of PacBio CCS reads that assembled to each class. Mitochondrial RNA libraries from both strains were mapped against the minicircle and maxicircle sequences. Small RNA reads mapped to the putative gRNA genes but also to multiple regions outside the genes on both strands and large RNA reads mapped in many cases over almost the entire minicircle on both strands. These data suggest that minicircle transcription is complete and bidirectional, with 3’ processing yielding the mature gRNAs. Steady state RNAs in varying abundances are derived from all maxicircle genes, including portions of the repetitive divergent region. The relative extents of editing in both strains correlated with the presence of a cascade of cognate gRNAs. These data should provide the foundation for a deeper understanding of this dynamic genetic system as well as the evolutionary variation of editing in different strains. U-insertion/deletion RNA editing is a unique post-transcriptional mRNA modification process that occurs in trypanosomatid parasites and is required for viability. The participation of guide RNAs which are transcribed from the thousands of catenated minicircles in determining the precise sites and number of U’s inserted and deleted to create translatable mRNAs is novel and significant in terms of the recently realized importance of small RNAs in biology. This study contributes the necessary bioinformatics foundation for a deeper understanding of this important genetic system in molecular detail using a model trypanosomatid, Leishmania tarentolae. We used Next Generation Sequencing methods to determine the complete maxicircle and minicircle genomes and to map maxicircle pre-edited and edited transcripts and minicircle transcripts. The transcription of minicircle-encoded guide RNAs was confirmed and novel information about minicircle gene expression was obtained. The biological context involved a comparison of two strains of the parasites, one recently isolated and having an intact mitochondrial genetic system and the other an old lab strain that has developed a partially defective mitochondrial genome. The data are important for an understanding of the mitochondrial genomic complexity and expression of this dynamic genetic system.
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Affiliation(s)
- Larry Simpson
- Department of Microbiology, Immunology and Molecular Genetics, Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail:
| | - Stephen M. Douglass
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - James A. Lake
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Matteo Pellegrini
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Feng Li
- Dental Research Institute, School of Dentistry, University of California, Los Angeles, Los Angeles, California, United States of America
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9
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Verner Z, Basu S, Benz C, Dixit S, Dobáková E, Faktorová D, Hashimi H, Horáková E, Huang Z, Paris Z, Peña-Diaz P, Ridlon L, Týč J, Wildridge D, Zíková A, Lukeš J. Malleable mitochondrion of Trypanosoma brucei. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 315:73-151. [PMID: 25708462 DOI: 10.1016/bs.ircmb.2014.11.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The importance of mitochondria for a typical aerobic eukaryotic cell is undeniable, as the list of necessary mitochondrial processes is steadily growing. Here, we summarize the current knowledge of mitochondrial biology of an early-branching parasitic protist, Trypanosoma brucei, a causative agent of serious human and cattle diseases. We present a comprehensive survey of its mitochondrial pathways including kinetoplast DNA replication and maintenance, gene expression, protein and metabolite import, major metabolic pathways, Fe-S cluster synthesis, ion homeostasis, organellar dynamics, and other processes. As we describe in this chapter, the single mitochondrion of T. brucei is everything but simple and as such rivals mitochondria of multicellular organisms.
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Affiliation(s)
- Zdeněk Verner
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Present address: Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Present address: Faculty of Sciences, Charles University, Prague, Czech Republic
| | - Somsuvro Basu
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic; Present address: Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Germany
| | - Corinna Benz
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Sameer Dixit
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Eva Dobáková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Present address: Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Drahomíra Faktorová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Hassan Hashimi
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Eva Horáková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic
| | - Zhenqiu Huang
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Zdeněk Paris
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic
| | - Priscila Peña-Diaz
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic
| | - Lucie Ridlon
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic; Present address: Salk Institute, La Jolla, San Diego, USA
| | - Jiří Týč
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - David Wildridge
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic
| | - Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
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10
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Trypanosoma brucei Tb927.2.6100 is an essential protein associated with kinetoplast DNA. EUKARYOTIC CELL 2013; 12:970-8. [PMID: 23650088 DOI: 10.1128/ec.00352-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The mitochondrial DNA of trypanosomatid protozoa consists of a complex, intercatenated network of tens of maxicircles and thousands of minicircles. This structure, called kinetoplast DNA (kDNA), requires numerous proteins and multiprotein complexes for replication, segregation, and transcription. In this study, we used a proteomic approach to identify proteins that are associated with the kDNA network. We identified a novel protein encoded by Tb927.2.6100 that was present in a fraction enriched for kDNA and colocalized the protein with kDNA by fluorescence microscopy. RNA interference (RNAi) knockdown of its expression resulted in a growth defect and changes in the proportion of kinetoplasts and nuclei in the cell population. RNAi also resulted in shrinkage and loss of the kinetoplasts, loss of maxicircle and minicircle components of kDNA at similar rates, and (perhaps secondarily) loss of edited and pre-edited mRNA. These results indicate that the Tb927.2.6100 protein is essential for the maintenance of kDNA.
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11
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Hashimi H, Zimmer SL, Ammerman ML, Read LK, Lukeš J. Dual core processing: MRB1 is an emerging kinetoplast RNA editing complex. Trends Parasitol 2013; 29:91-9. [PMID: 23305619 PMCID: PMC3558622 DOI: 10.1016/j.pt.2012.11.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 11/28/2012] [Accepted: 11/28/2012] [Indexed: 12/17/2022]
Abstract
Our understanding of kinetoplastid RNA (kRNA) editing has centered on this paradigm: guide RNAs (gRNAs) provide a blueprint for uridine insertion/deletion into mitochondrial mRNAs by the RNA editing core complex (RECC). The characterization of constituent subunits of the mitochondrial RNA-binding complex 1 (MRB1) implies that it too is vital to the editing process. The recently elucidated MRB1 architecture will be instrumental in putting functional data from individual subunits into context. Our model depicts two functions for MRB1: mediating multi-round kRNA editing by coordinating the exchange of multiple gRNAs required by RECC to edit lengthy regions of mRNAs, and then linking kRNA editing with other RNA processing events.
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Affiliation(s)
- Hassan Hashimi
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, and Faculty of Science, University of South Bohemia, České Budějovice (Budweis) 370 05, Czech Republic
| | - Sara L. Zimmer
- Department of Microbiology and Immunology, School of Medicine, State University of New York at Buffalo, NY 14214, USA
| | - Michelle L. Ammerman
- Department of Microbiology and Immunology, School of Medicine, State University of New York at Buffalo, NY 14214, USA
| | - Laurie K. Read
- Department of Microbiology and Immunology, School of Medicine, State University of New York at Buffalo, NY 14214, USA
| | - Julius Lukeš
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, and Faculty of Science, University of South Bohemia, České Budějovice (Budweis) 370 05, Czech Republic
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12
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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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13
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Editosome accessory factors KREPB9 and KREPB10 in Trypanosoma brucei. EUKARYOTIC CELL 2012; 11:832-43. [PMID: 22562468 DOI: 10.1128/ec.00046-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Multiprotein complexes, called editosomes, catalyze the uridine insertion and deletion RNA editing that forms translatable mitochondrial mRNAs in kinetoplastid parasites. We have identified here two new U1-like zinc finger proteins that associate with editosomes and have shown that they are related to KREPB6, KREPB7, and KREPB8, and thus we have named them Kinetoplastid RNA Editing Proteins, KREPB9 and KREPB10. They are conserved and syntenic in trypanosomatids although KREPB10 is absent in Trypanosoma vivax and both are absent in Leishmania. Tandem affinity purification (TAP)-tagged KREPB9 and KREPB10 incorporate into ~20S editosomes and/or subcomplexes thereof and preferentially associate with deletion subcomplexes, as do KREPB6, KREPB7, and KREPB8. KREPB10 also associates with editosomes that are isolated via a chimeric endonuclease, KREN1 in KREPB8 RNA interference (RNAi) cells, or MEAT1. The purified complexes have precleaved editing activities and endonuclease cleavage activity that appears to leave a 5' OH on the 3' product. RNAi knockdowns did not affect growth but resulted in relative reductions of both edited and unedited mitochondrial mRNAs. The similarity of KREPB9 and KREPB10 to KREPB6, KREPB7, and KREPB8 suggests they may be accessory factors that affect editing endonuclease activity and as a consequence may affect mitochondrial mRNA stability. KREPB9 and KREPB10, along with KREPB6, KREPB7, and KREPB8, may enable the endonucleases to discriminate among and accurately cleave hundreds of different editing sites and may be involved in the control of differential editing during the life cycle of T. brucei.
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14
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Aphasizhev R, Aphasizheva I. Uridine insertion/deletion editing in trypanosomes: a playground for RNA-guided information transfer. WILEY INTERDISCIPLINARY REVIEWS. RNA 2011; 2:669-85. [PMID: 21823228 PMCID: PMC3154072 DOI: 10.1002/wrna.82] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
RNA editing is a collective term referring to enzymatic processes that change RNA sequence apart from splicing, 5' capping or 3' extension. In this article, we focus on uridine insertion/deletion mRNA editing found exclusively in mitochondria of kinetoplastid protists. This type of editing corrects frameshifts, introduces start and stops codons, and often adds much of the coding sequence to create an open reading frame. The mitochondrial genome of trypanosomatids, the most extensively studied clade within the order Kinetoplastida, is composed of ∼50 maxicircles with limited coding capacity and thousands of minicircles. To produce functional mRNAs, a multitude of nuclear-encoded factors mediate interactions of maxicircle-encoded pre-mRNAs with a vast repertoire of minicircle-encoded guide RNAs. Editing reactions of mRNA cleavage, U-insertions or U-deletions, and ligation are catalyzed by the RNA editing core complex (RECC, the 20S editosome) while each step of this enzymatic cascade is directed by guide RNAs. These 50-60 nucleotide (nt) molecules are 3' uridylated by RET1 TUTase and stabilized via association with the gRNA binding complex (GRBC). Remarkably, the information transfer between maxicircle and minicircle transcriptomes does not rely on template-dependent polymerization of nucleic acids. Instead, intrinsic substrate specificities of key enzymes are largely responsible for the fidelity of editing. Conversely, the efficiency of editing is enhanced by assembling enzymes and RNA binding proteins into stable multiprotein complexes. WIREs RNA 2011 2 669-685 DOI: 10.1002/wrna.82 For further resources related to this article, please visit the WIREs website.
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MESH Headings
- Endonucleases/chemistry
- Endonucleases/genetics
- Endonucleases/metabolism
- Models, Biological
- Models, Molecular
- Protozoan Proteins/chemistry
- Protozoan Proteins/genetics
- Protozoan Proteins/metabolism
- RNA Editing/genetics
- RNA Editing/physiology
- RNA Helicases/chemistry
- RNA Helicases/genetics
- RNA Helicases/metabolism
- RNA, Guide, Kinetoplastida/genetics
- RNA, Guide, Kinetoplastida/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Protozoan/chemistry
- RNA, Protozoan/genetics
- RNA, Protozoan/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Trypanosoma/genetics
- Trypanosoma/metabolism
- Uridine/chemistry
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Affiliation(s)
- Ruslan Aphasizhev
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, USA.
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15
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Aphasizhev R, Aphasizheva I. Mitochondrial RNA processing in trypanosomes. Res Microbiol 2011; 162:655-63. [PMID: 21596134 DOI: 10.1016/j.resmic.2011.04.015] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Accepted: 04/04/2011] [Indexed: 01/20/2023]
Abstract
The mitochondrial genome of trypanosomes is composed of ∼50 maxicircles and thousands of minicircles. Maxi-(∼25 kb) and mini-(∼1 kb)circles are catenated and packed into a dense structure called a kinetoplast. Both types of circular DNA are transcribed by a phage-like RNA polymerase: maxicircles yield multicistronic rRNA and mRNA precursors, while guide RNA (gRNA) precursors are produced from minicircles. To function in mitochondrial translation, pre-mRNAs must undergo a nucleolytic processing and 3' modifications, and often uridine insertion/deletion editing. gRNAs, which represent short (50-60 nt) RNAs directing editing reactions, are produced by 3' nucleolytic processing of a much longer precursor followed by 3' uridylation. Ribosomal RNAs are excised from precursors and their 3' ends are also trimmed and uridylated. All tRNAs are imported from the cytoplasm and some are further modified and edited in the mitochondrial matrix. Historically, the fascinating phenomenon of RNA editing has been extensively studied as an isolated pathway in which nuclear-encoded proteins mediate interactions of maxi- and minicircle transcripts to create open reading frames. However, recent studies unraveled a highly integrated network of mitochondrial genome expression including critical pre- and post-editing 3' mRNA processing, and gRNA and rRNA maturation steps. Here we focus on RNA 3' adenylation and uridylation as processes essential for biogenesis, stability and functioning of mitochondrial RNAs.
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Affiliation(s)
- Ruslan Aphasizhev
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, B240 Medical Sciences I, Irvine, CA 92697, USA.
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16
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Zimmer SL, McEvoy SM, Li J, Qu J, Read LK. A novel member of the RNase D exoribonuclease family functions in mitochondrial guide RNA metabolism in Trypanosoma brucei. J Biol Chem 2011; 286:10329-40. [PMID: 21252235 PMCID: PMC3060487 DOI: 10.1074/jbc.m110.152439] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Revised: 01/18/2011] [Indexed: 12/22/2022] Open
Abstract
RNA turnover and RNA editing are essential for regulation of mitochondrial gene expression in Trypanosoma brucei. RNA turnover is controlled in part by RNA 3' adenylation and uridylation status, with trans-acting factors also impacting RNA homeostasis. However, little is known about the mitochondrial degradation machinery or its regulation in T. brucei. We have identified a mitochondrial exoribonuclease, TbRND, whose expression is highly up-regulated in the insect proliferative stage of the parasite. TbRND shares sequence similarity with RNase D family enzymes but differs from all reported members of this family in possessing a CCHC zinc finger domain. In vitro, TbRND exhibits 3' to 5' exoribonuclease activity, with specificity toward uridine homopolymers, including the 3' oligo(U) tails of guide RNAs (gRNAs) that provide the sequence information for RNA editing. Several lines of evidence generated from RNAi-mediated knockdown and overexpression cell lines indicate that TbRND functions in gRNA metabolism in vivo. First, TbRND depletion results in gRNA tails extended by 2-3 nucleotides on average. Second, overexpression of wild type but not catalytically inactive TbRND results in a substantial decrease in the total gRNA population and a consequent inhibition of RNA editing. The observed effects on the gRNA population are specific as rRNAs, which are also 3'-uridylated, are unaffected by TbRND depletion or overexpression. Finally, we show that gRNA binding proteins co-purify with TbRND. In summary, TbRND is a novel 3' to 5' exoribonuclease that appears to have evolved a function highly specific to the mitochondrion of trypanosomes.
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Affiliation(s)
- Sara L. Zimmer
- From the Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14214 and
| | - Sarah M. McEvoy
- From the Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14214 and
| | - Jun Li
- the Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Amherst, New York 14260
| | - Jun Qu
- the Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Amherst, New York 14260
| | - Laurie K. Read
- From the Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14214 and
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17
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Aphasizheva I, Aphasizhev R. RET1-catalyzed uridylylation shapes the mitochondrial transcriptome in Trypanosoma brucei. Mol Cell Biol 2010; 30:1555-67. [PMID: 20086102 PMCID: PMC2832499 DOI: 10.1128/mcb.01281-09] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 10/30/2009] [Accepted: 01/05/2010] [Indexed: 01/25/2023] Open
Abstract
RNA uridylylation is critical for the expression of the mitochondrial genome in trypanosomes. Short U tails are added to guide RNAs and rRNAs, while long A/U heteropolymers mark 3' ends of most mRNAs. Three divergent mitochondrial terminal uridylyl transferases (TUTases) are known: RET1 catalyzes guide RNA (gRNA) uridylylation, RET2 executes U insertion mRNA editing, and MEAT1 associates with the editosome-like complex. However, the activities responsible for 3' uridylylation of rRNAs and mRNAs, and the roles of these modifications, are unclear. To dissect the functions of mitochondrial TUTases, we investigated the effects of their repression and overexpression on abundance, processing, 3'-end status, and in vivo stability of major mitochondrially encoded RNA classes. We show that RET1 adds U tails to gRNAs, rRNAs, and select mRNAs and contributes U's into A/U heteropolymers. Furthermore, RET1's TUTase activity is required for the nucleolytic processing of gRNA, rRNA, and mRNA precursors. The U tail's presence does not affect the stability of gRNAs and rRNAs, while transcript-specific uridylylation triggers 3' to 5' mRNA decay. We propose that the minicircle-encoded antisense transcripts, which are stabilized by RET1-catalyzed uridylylation, may direct a nucleolytic cleavage of multicistronic precursors.
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Affiliation(s)
- Inna Aphasizheva
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, California 92697
| | - Ruslan Aphasizhev
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, California 92697
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18
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Fisk JC, Presnyak V, Ammerman ML, Read LK. Distinct and overlapping functions of MRP1/2 and RBP16 in mitochondrial RNA metabolism. Mol Cell Biol 2009; 29:5214-25. [PMID: 19620277 PMCID: PMC2747978 DOI: 10.1128/mcb.00520-09] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Revised: 05/29/2009] [Accepted: 07/14/2009] [Indexed: 01/05/2023] Open
Abstract
Mitochondrial RNA metabolism in Trypanosoma brucei is a complex process involving both extensive RNA editing and control of RNA stability. MRP1/2 and RBP16 are two factors that have been implicated in regulating the editing and stability of specific mRNAs. These two factors exhibit similar nonspecific RNA binding and RNA-annealing activities, suggesting that some of their actions may have been previously masked by functional redundancy. Here, we examine the functional interaction of MRP1/2 and RBP16 by separate and simultaneous RNA interference and by overexpressing RBP16 in an MRP1/2-depleted background. Simultaneous depletion of these factors resulted in synthetic lethality in procyclic trypanosomes. Analysis of mitochondrial RNAs in procyclic cells revealed distinct functions for MRP1/2 and RBP16 toward edited apocytochrome b mRNA, redundant functions in stabilization of edited ATPase subunit 6 and cytochrome oxidase subunit 3 mRNAs, and concentration-dependent positive and negative functions for RBP16 toward edited RPS12 mRNAs. While simultaneous MRP1/2-RBP16 depletion had no effect on the growth of bloodstream form cells, massive adverse effects on the levels of almost all mitochondrial RNAs were observed. These studies greatly expand our knowledge regarding the functions of MRP1/2 and RBP16 and suggest that both RNA-specific and life cycle stage-specific factors impact MRP1/2 and RBP16 functions.
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Affiliation(s)
- John C Fisk
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14214.
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19
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Osato D, Rogers K, Guo Q, Li F, Richmond G, Klug F, Simpson L. Uridine insertion/deletion RNA editing in trypanosomatid mitochondria: In search of the editosome. RNA (NEW YORK, N.Y.) 2009; 15:1338-44. [PMID: 19447916 PMCID: PMC2704074 DOI: 10.1261/rna.1642809] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The RNA ligase-containing or L-complex is the core complex involved in uridine insertion/deletion RNA editing in trypanosome mitochondria. Blue native gels of glycerol gradient-separated fractions of mitochondrial lysate from cells transfected with the TAP-tagged editing protein, LC-8 (TbMP44/KREPB5), show a approximately 1 MDa L-complex band and, in addition, two minor higher molecular weight REL1-containing complexes: one (L*a) co-sedimenting with the L-complex and running in the gel at around 1.2 MDa; the other (L*b) showing a continuous increase in molecular weight from 1 MDa to particles sedimenting over 70S. The L*b-complexes appear to be mainly composed of L-complex components, since polypeptide profiles of L- and L*b-complex gradient fractions were similar in composition and L*b-complex bands often degraded to L-complex bands after manipulation or freeze-thaw cycles. The L*a-complex may be artifactual since this gel shift can be produced by various experimental manipulations. However, the nature of the change and any cellular role remain to be determined. The L*b-complexes from both lysate and TAP pull-down were sensitive to RNase A digestion, suggesting that RNA is involved with the stability of the L*b-complexes. The MRP1/2 RNA binding complex is localized mainly in the L*b-complexes in substoichiometric amounts and this association is RNase sensitive. We suggest that the L*b-complexes may provide a scaffold for dynamic interaction with other editing factors during the editing process to form the active holoenzyme or "editosome."
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Affiliation(s)
- Daren Osato
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, USA
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20
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Mattiacio JL, Read LK. Evidence for a degradosome-like complex in the mitochondria of Trypanosoma brucei. FEBS Lett 2009; 583:2333-8. [PMID: 19540236 DOI: 10.1016/j.febslet.2009.06.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 06/11/2009] [Indexed: 12/21/2022]
Abstract
Mitochondrial RNA turnover in yeast involves the degradosome, composed of DSS-1 exoribonuclease and SUV3 RNA helicase. Here, we describe a degradosome-like complex, containing SUV3 and DSS-1 homologues, in the early branching protozoan, Trypanosoma brucei. TbSUV3 is mitochondrially localized and co-sediments with TbDSS-1 on glycerol gradients. Co-immunoprecipitation demonstrates that TbSUV3 and TbDSS-1 associate in a stable complex, which differs from the yeast degradosome in that it is not stably associated with mitochondrial ribosomes. This is the first report of a mitochondrial degradosome-like complex outside of yeast. Our data indicate an early evolutionary origin for the mitochondrial SUV3/DSS-1 containing complex.
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Affiliation(s)
- Jonelle L Mattiacio
- Depatment of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, SUNY Buffalo School of Medicine, Buffalo, NY 14214, USA
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21
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Koslowsky DJ. Complex interactions in the regulation of trypanosome mitochondrial gene expression. Trends Parasitol 2009; 25:252-5. [PMID: 19443271 DOI: 10.1016/j.pt.2009.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Revised: 03/13/2009] [Accepted: 03/19/2009] [Indexed: 02/04/2023]
Abstract
Trypanosomes undergo extreme physiological changes to adapt to different environments as they cycle between hosts. Adaptation to the different environments has evolved an energy metabolism involving a mitochondrion with an unusual genome. Recently, Aphasizhev and colleagues have identified two new protein complexes, a mitochondrial polyadenylation complex and a guide RNA stabilization complex, that provide novel insights into the coordinated expression of the mitochondrial genome.
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Affiliation(s)
- Donna J Koslowsky
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
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22
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Acestor N, Panigrahi AK, Carnes J, Zíková A, Stuart KD. The MRB1 complex functions in kinetoplastid RNA processing. RNA (NEW YORK, N.Y.) 2009; 15:277-86. [PMID: 19096045 PMCID: PMC2648719 DOI: 10.1261/rna.1353209] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Accepted: 10/24/2008] [Indexed: 05/20/2023]
Abstract
Mitochondrial (mt) gene expression in Trypanosoma brucei entails multiple types of RNA processing, including polycistronic transcript cleavage, mRNA editing, gRNA oligouridylation, and mRNA polyadenylation, which are catalyzed by various multiprotein complexes. We examined the novel mitochondrial RNA-binding 1 (MRB1) complex that has 16 associated proteins, four of which have motifs suggesting RNA interaction. RNase treatment or the lack of kDNA in mutants resulted in lower MRB1 complex sedimentation in gradients, indicating that MRB1 complex associates with kDNA transcripts. RNAi knockdowns of expression of the Tb10.406.0050 (TbRGGm, RGG motif), Tb927.6.1680 (C2H2 zinc finger), and Tb11.02.5390 (no known motif) MRB1 proteins each inhibited in vitro growth of procyclic form parasites and resulted in cells with abnormal numbers of nuclei. Knockdown of TbRGGm, but not the other two proteins, disrupted the MRB1 complex, indicating that it, but perhaps not the other two, is required for complex assembly and/or stability. The knockdowns resulted in similar but nonidentical patterns of altered in vivo abundances of edited, pre-edited, and preprocessed mt mRNAs, but did not appreciably affect the abundances of mRNAs that do not get edited. These results indicate that MRB1 complex is critical to the processing of mt RNAs, and although its specific function is unknown, it appears essential to parasite viability.
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Affiliation(s)
- Nathalie Acestor
- Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
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23
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3' adenylation determines mRNA abundance and monitors completion of RNA editing in T. brucei mitochondria. EMBO J 2008; 27:1596-608. [PMID: 18464794 DOI: 10.1038/emboj.2008.87] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Accepted: 04/02/2008] [Indexed: 11/08/2022] Open
Abstract
Expression of the mitochondrial genome in protozoan parasite Trypanosoma brucei is controlled post-transcriptionally and requires extensive U-insertion/deletion mRNA editing. In mitochondrial extracts, 3' adenylation reportedly influences degradation kinetics of synthetic edited and pre-edited mRNAs. We have identified and characterized a mitochondrial poly(A) polymerase, termed KPAP1, and determined major polypeptides in the polyadenylation complex. Inhibition of KPAP1 expression abrogates short and long A-tails typically found in mitochondrial mRNAs, and decreases the abundance of never-edited and edited transcripts. Pre-edited mRNAs are not destabilized by the lack of 3' adenylation, whereas short A-tails are required and sufficient to maintain the steady-state levels of partially edited, fully edited, and never-edited mRNAs. The editing directed by a single guide RNA is sufficient to impose a requirement for the short A-tail in edited molecules. Upon completion of the editing process, the short A-tails are extended as (A/U) heteropolymers into structures previously thought to be long poly(A) tails. These data provide the first direct evidence of functional interactions between 3' processing and editing of mitochondrial mRNAs in trypanosomes.
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Aphasizhev R, Aphasizheva I. Terminal RNA uridylyltransferases of trypanosomes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2007; 1779:270-80. [PMID: 18191648 DOI: 10.1016/j.bbagrm.2007.12.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Revised: 12/10/2007] [Accepted: 12/13/2007] [Indexed: 12/14/2022]
Abstract
Terminal RNA uridylyltransferases (TUTases) are functionally and structurally diverse nucleotidyl transferases that catalyze template-independent 3' uridylylation of RNAs. Within the DNA polymerase beta-type superfamily, TUTases are closely related to non-canonical poly(A) polymerases. Studies of U-insertion/deletion RNA editing in mitochondria of trypanosomatids identified the first TUTase proteins and their cellular functions: post-transcriptional uridylylation of guide RNAs by RNA editing TUTase 1 (RET1) and U-insertion mRNA editing by RNA editing TUTase 2 (RET2). The editing TUTases possess conserved catalytic and nucleotide base recognition domains, yet differ in quaternary structure, substrate specificity and processivity. The cytosolic TUTases TUT3 and TUT4 have also been identified in trypanosomes but their biological roles remain to be established. Structural analyses have revealed a mechanism of cognate nucleoside triphosphate selection by TUTases, which includes protein-UTP contacts as well as contribution of the RNA substrate. This review focuses on biological functions and structures of trypanosomal TUTases.
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Affiliation(s)
- Ruslan Aphasizhev
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697-4025, USA.
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25
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Mattiacio JL, Read LK. Roles for TbDSS-1 in RNA surveillance and decay of maturation by-products from the 12S rRNA locus. Nucleic Acids Res 2007; 36:319-29. [PMID: 18032430 PMCID: PMC2248759 DOI: 10.1093/nar/gkm690] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Trypanosoma brucei exoribonuclease, TbDSS-1, has been implicated in multiple aspects of mitochondrial RNA metabolism. Here, we investigate the role of TbDSS-1 in RNA processing and surveillance by analyzing 12S rRNA processing intermediates in TbDSS-1 RNAi cells. RNA fragments corresponding to leader sequence upstream of 12S rRNA accumulate upon TbDSS-1 depletion. The 5' extremity of 12S rRNA is generated by endonucleolytic cleavage, and TbDSS-1 degrades resulting upstream maturation by-products. RNAs with 5' ends at position -141 and 3' ends adjacent to the mature 5' end of 12S rRNA are common and invariably possess oligo(U) tails. 12S rRNAs with mature 3' ends and unprocessed 5' ends also accumulate in TbDSS-1 depleted cells, suggesting that these RNAs represent dead-end products normally destined for decay by TbDSS-1 in an RNA surveillance pathway. Together, these data indicate dual roles for TbDSS-1 in degradation of 12S rRNA maturation by-products and as part of a mitochondrial RNA surveillance pathway that eliminates stalled 12S processing intermediates. We further provide evidence that TbDSS-1 degrades RNAs originating upstream of the first gene on the minor strand of the mitochondrial maxicircle suggesting that TbDSS-1 also removes non-functional RNAs generated from other regions of the mitochondrial genome.
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Affiliation(s)
- Jonelle L Mattiacio
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, SUNY Buffalo School of Medicine, Buffalo, NY 14214, USA
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26
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Kao CY, Read LK. Targeted depletion of a mitochondrial nucleotidyltransferase suggests the presence of multiple enzymes that polymerize mRNA 3' tails in Trypanosoma brucei mitochondria. Mol Biochem Parasitol 2007; 154:158-69. [PMID: 17543398 PMCID: PMC2709527 DOI: 10.1016/j.molbiopara.2007.04.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Revised: 04/10/2007] [Accepted: 04/22/2007] [Indexed: 10/23/2022]
Abstract
Polyadenylation plays an important role in regulating RNA stability in Trypanosoma brucei mitochondria. To date, little is known about the enzymes responsible for the addition of mRNA 3' tails in this system. In this study, we characterize a trypanosome homolog of the human mitochondrial poly(A) polymerase, which we term kPAP2. kPAP2 is mitochondrially localized and expressed in both bloodstream and procyclic form trypanosomes. Targeted gene depletion using RNAi showed that kPAP2 is not required for T. brucei growth in either bloodstream or procyclic life stages, nor is it essential for differentiation from bloodstream to procyclic form. We also demonstrate that steady state abundance of several mitochondrial RNAs was largely unaffected upon kPAP2 down-regulation. Interestingly, mRNA 3' tail analysis of several mRNAs from both life cycle stages in uninduced kPAP2 RNAi cells demonstrated that tail length and uridine content are both regulated in a transcript-specific manner. mRNA-specific tail lengths were maintained upon kPAP2 depletion. However, the percentage of uridine residues in 3' tails was increased, and conversely the percentage of adenosine residues was decreased, in a distinct subset of mRNAs when kPAP2 levels were down-regulated. Thus, kPAP2 apparently contributes to the incorporation of adenosine residues in 3' tails of some, but not all, mitochondrial mRNAs. Together, these data suggest that multiple nucleotidyltransferases act on mitochondrial mRNA 3' ends, and that these enzymes are somewhat redundant and subject to complex regulation.
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Affiliation(s)
| | - Laurie K. Read
- Corresponding author: Dr. Laurie K. Read, Dept. of Microbiology and Immunology, 138 Farber Hall, Buffalo, NY 14214, Tel. 716-829-3307, FAX 716-829-2158,
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27
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Madej MJ, Alfonzo JD, Hüttenhofer A. Small ncRNA transcriptome analysis from kinetoplast mitochondria of Leishmania tarentolae. Nucleic Acids Res 2007; 35:1544-54. [PMID: 17287292 PMCID: PMC1865066 DOI: 10.1093/nar/gkm004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Revised: 12/21/2006] [Accepted: 12/22/2006] [Indexed: 11/12/2022] Open
Abstract
Gene expression in mitochondria of kinetoplastid protozoa requires RNA editing, a post-transcriptional process which involves insertion or deletion of uridine residues at specific sites within mitochondrial pre-mRNAs. Sequence specificity of the RNA editing process is mediated by oligo-uridylated small, non-coding RNAs, designated as guide RNAs (gRNAs). In this study, we have analyzed the small ncRNA transcriptome from kinetoplast mitochondria of Leishmania tarentolae by generating specialized cDNA libraries encoding size-selected RNA species. Through this screen, a significant number of novel oligo-uridylated RNA species, which we have termed oU-RNAs, has been identified. Most novel oU-RNAs are present as stable RNA species in mitochondria as assessed by northern blot analysis. Thereby, novel oU-RNAs show similar expression levels and sizes as previously reported for canonical gRNAs. Several oU-RNAs are transcribed from both strands of the maxicircle and minicircles components of the mitochondrial genome, from regions where up till now no transcription has been reported. Two stable oU-RNAs exhibit an anchor sequence in antisense orientation to known gRNAs and thus might regulate editing of respective pre-mRNAs. A number of oU-RNAs map in antisense orientation to non-edited protein-coding genes suggesting that they might function by a different mechanism. In addition, our screen shows that all kinetoplast-derived RNAs are prone to some degree of uridylation.
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MESH Headings
- Animals
- Cells, Cultured
- DNA, Circular/chemistry
- Gene Library
- Leishmania/genetics
- Leishmania/metabolism
- Mitochondria/genetics
- Mitochondria/metabolism
- Oligoribonucleotides/analysis
- Protozoan Proteins/genetics
- RNA/biosynthesis
- RNA/chemistry
- RNA/genetics
- RNA, Antisense/genetics
- RNA, Guide, Kinetoplastida/biosynthesis
- RNA, Guide, Kinetoplastida/chemistry
- RNA, Guide, Kinetoplastida/genetics
- RNA, Mitochondrial
- RNA, Untranslated/genetics
- Sequence Analysis, DNA
- Transcription, Genetic
- Uracil Nucleotides/analysis
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Affiliation(s)
- Monika J. Madej
- Innsbruck Biocenter, Division of Genomics and RNomics, Innsbruck Medical University, Fritz-Pregl-Strasse. 3, 6020 Innsbruck, Austria and Department of Microbiology, Ohio State Biochemistry Program and The RNA Group, The Ohio State University, 484 West 12th Ave., Columbus, OH 43210, USA
| | - Juan D. Alfonzo
- Innsbruck Biocenter, Division of Genomics and RNomics, Innsbruck Medical University, Fritz-Pregl-Strasse. 3, 6020 Innsbruck, Austria and Department of Microbiology, Ohio State Biochemistry Program and The RNA Group, The Ohio State University, 484 West 12th Ave., Columbus, OH 43210, USA
| | - Alexander Hüttenhofer
- Innsbruck Biocenter, Division of Genomics and RNomics, Innsbruck Medical University, Fritz-Pregl-Strasse. 3, 6020 Innsbruck, Austria and Department of Microbiology, Ohio State Biochemistry Program and The RNA Group, The Ohio State University, 484 West 12th Ave., Columbus, OH 43210, USA
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28
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Halbig K, Sacharidou A, De Nova-Ocampo M, Cruz-Reyes J. Preferential interaction of a 25kDa protein with an A6 pre-mRNA substrate for RNA editing in Trypanosoma brucei. Int J Parasitol 2006; 36:1295-304. [PMID: 16860325 DOI: 10.1016/j.ijpara.2006.05.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Revised: 05/14/2006] [Accepted: 05/15/2006] [Indexed: 11/23/2022]
Abstract
Mitochondrial gene expression in kinetoplastids is controlled after transcription, potentially at the levels of RNA maturation, stability and translation. Among these processes, RNA editing by U-insertion/deletion catalysed by multi-subunit editing complexes is best characterised at the molecular level. Nevertheless, mitochondrial RNA metabolism overall remains poorly understood, including the potential regulatory factors that may interact with the relevant catalytic molecular machines and/or RNA substrates. Here we report on a approximately 25kDa polypeptide in mitochondrial extracts that exhibits a preferential "zero-distance" photo-crosslinking interaction with an A6 pre-mRNA model substrate for RNA editing containing a single [(32)P] at the first editing site. The approximately 25kDa polypeptide purified away from editosomes upon ion-exchange chromatography and glycerol gradient sedimentation. Competition assays with homologous and heterologous transcripts suggest that the preferential recognition of the A6 substrate is based on relatively low-specificity RNA-protein contacts. Our mapping and substrate truncation analyses suggest that the crosslinking activity primarily targeted a predicted stem-loop region containing the first editing sites. Consistent with the notion that pre-mRNA folding may be required, pre-annealing with guide RNA abolished crosslinking. Interestingly, this preferential protein interaction with the A6 substrate seemed to require adenosine 5'-triphosphate but not hydrolysis. As in other biological systems, fine regulation in vivo may be brought about by transient networks of relatively low-specificity interactions in which multiple auxiliary factors bind to mRNAs and/or editing complexes in unique higher-order assemblies.
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Affiliation(s)
- Kari Halbig
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA
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29
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Goulah CC, Pelletier M, Read LK. Arginine methylation regulates mitochondrial gene expression in Trypanosoma brucei through multiple effector proteins. RNA (NEW YORK, N.Y.) 2006; 12:1545-55. [PMID: 16775306 PMCID: PMC1524885 DOI: 10.1261/rna.90106] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Arginine methylation is a post-translational modification that impacts gene expression in both the cytoplasm and nucleus. Here, we demonstrate that arginine methylation also affects mitochondrial gene expression in the protozoan parasite, Trypanosoma brucei. Down-regulation of the major trypanosome type I protein arginine methyltransferase, TbPRMT1, leads to destabilization of specific mitochondrial mRNAs. We provide evidence that some of these effects are mediated by the mitochondrial RNA-binding protein, RBP16, which we previously demonstrated affects both RNA editing and stability. TbPRMT1 catalyzes methylation of RBP16 in vitro. Further, MALDI-TOF-MS analysis of RBP16 isolated from TbPRMT1-depleted cells indicates that, in vivo, TbPRMT1 modifies two of the three known methylated arginine residues in RBP16. Expression of mutated, nonmethylatable RBP16 in T. brucei has a dominant negative effect, leading to destabilization of a subset of those mRNAs affected by TbPRMT1 depletion. Our results suggest that the specificity and multifunctional nature of RBP16 are due, at least in part, to the presence of differentially methylated forms of the protein. However, some effects of TbPRMT1 depletion on mitochondrial gene expression cannot be accounted for by RBP16 action. Thus, these data implicate additional, unknown methylproteins in mitochondrial gene regulation.
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Affiliation(s)
- Christopher C Goulah
- Department of Microbiology and Immunology and Witebsky Center for Microbial Pathogenesis and Immunology, SUNY Buffalo School of Medicine, Buffalo, NY 14214, USA
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30
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Sacharidou A, Cifuentes-Rojas C, Halbig K, Hernandez A, Dangott LJ, De Nova-Ocampo M, Cruz-Reyes J. RNA editing complex interactions with a site for full-round U deletion in Trypanosoma brucei. RNA (NEW YORK, N.Y.) 2006; 12:1219-28. [PMID: 16690999 PMCID: PMC1484423 DOI: 10.1261/rna.2295706] [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] [Indexed: 05/09/2023]
Abstract
Trypanosome U insertion and U deletion RNA editing of mitochondrial pre-mRNAs is catalyzed by multisubunit editing complexes as directed by partially complementary guide RNAs. The basic enzymatic activities and protein composition of these high-molecular mass complexes have been under intense study, but their specific protein interactions with functional pre-mRNA/gRNA substrates remains unknown. We show that editing complexes purified through extensive ion-exchange chromatography and immunoprecipitation make specific cross-linking interactions with A6 pre-mRNA containing a single 32P and photoreactive 4-thioU at the scissile bond of a functional site for full-round U deletion. At least four direct protein-RNA contacts are detected at this site by cross-linking. All four interactions are stimulated by unpaired residues just 5' of the pre-mRNA/gRNA anchor duplex, but strongly inhibited by pairing of the editing site region. Furthermore, competition analysis with homologous and heterologous transcripts suggests preferential contacts of the editing complex with the mRNA/gRNA duplex substrate. This apparent structural selectivity suggests that the RNA-protein interactions we observe may be involved in recognition of editing sites and/or catalysis in assembled complexes.
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Affiliation(s)
- Anastasia Sacharidou
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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31
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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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32
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Penschow JL, Sleve DA, Ryan CM, Read LK. TbDSS-1, an essential Trypanosoma brucei exoribonuclease homolog that has pleiotropic effects on mitochondrial RNA metabolism. EUKARYOTIC CELL 2005; 3:1206-16. [PMID: 15470249 PMCID: PMC522597 DOI: 10.1128/ec.3.5.1206-1216.2004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mitochondrial gene expression in trypanosomes is controlled primarily at the levels of RNA processing and RNA stability. This regulation undoubtedly involves numerous ribonucleases. Here we characterize the Trypanosoma brucei homolog of the yeast DSS-1 mitochondrial exoribonuclease, which we term TbDSS-1. Biochemical fractionation indicates that TbDSS-1 is mitochondrially localized, as predicted by its N-terminal sequence. In contrast to its yeast homolog, TbDSS-1 does not appear to be associated with mitochondrial ribosomes. Targeted downregulation of TbDSS-1 by RNA interference in procyclic-form T. brucei results in a severe growth defect. In addition, TbDSS-1 depletion leads to a decrease in the levels of never edited cytochrome oxidase subunit I (COI) mRNA and both unedited and edited COIII mRNAs, indicating this enzyme functions in the control of mitochondrial RNA abundance. We also observe a considerable reduction in the level of edited apocytochrome b (CYb) mRNA and a corresponding increase in unedited CYb mRNA, suggesting that TbDSS-1 functions, either directly or indirectly, in the control of RNA editing. The abundance of both gCYb[560] and gA6[149] guide RNAs is reduced upon TbDSS-1 depletion, although the reduction in gCYb[560] is much more dramatic. The significant reduction in gCYb levels could potentially account for the observed decrease in CYb RNA editing. Western blot analyses of mitochondrial RNA editing and stability factors indicate that the perturbations of RNA levels observed in TbDSS-1 knock-downs do not result from secondary effects on other mitochondrial proteins. In all, these data demonstrate that TbDSS-1 is an essential protein that plays a role in mitochondrial RNA stability and RNA editing.
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Affiliation(s)
- Jonelle L Penschow
- Department of Microbiology and Immunology, 138 Farber Hall, SUNY Buffalo School of Medicine, Buffalo, NY 14214, USA
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33
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Kao CY, Read LK. Opposing effects of polyadenylation on the stability of edited and unedited mitochondrial RNAs in Trypanosoma brucei. Mol Cell Biol 2005; 25:1634-44. [PMID: 15713623 PMCID: PMC549368 DOI: 10.1128/mcb.25.5.1634-1644.2005] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2004] [Revised: 10/11/2004] [Accepted: 12/07/2004] [Indexed: 11/20/2022] Open
Abstract
Mitochondrial RNAs in Trypanosoma brucei undergo posttranscriptional RNA editing and polyadenylation. We previously showed that polyadenylation stimulates turnover of unedited RNAs. Here, we investigated the role of polyadenylation in decay of edited RPS12 RNA. In in vitro turnover assays, nonadenylated fully edited RNA degrades significantly faster than its unedited counterpart. Rapid turnover of nonadenylated RNA is facilitated by editing at just six editing sites. Surprisingly, in direct contrast to unedited RNA, turnover of fully edited RNA is dramatically slowed by addition of a poly(A)20 tail. The same minimal edited sequence that stimulates decay of nonadenylated RNA is sufficient to switch the poly(A) tail from a destabilizing to a stabilizing element. Both nucleotide composition and length of the 3' extension are important for stabilization of edited RNA. Titration of poly(A) into RNA degradation reactions has no effect on turnover of polyadenylated edited RNA. These results suggest the presence of a protective protein(s) that simultaneously recognizes the poly(A) tail and small edited element and which blocks the action of a 3'-5' exonuclease. This study provides the first evidence for opposing effects of polyadenylation on RNA stability within a single organelle and suggests a novel and unique regulation of RNA turnover in this system.
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Affiliation(s)
- Chia-Ying Kao
- Department of Microbiology and Immunology, 138 Farber Hall, SUNY Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14214, USA
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34
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Abstract
Most mitochondrial mRNAs in kinetoplastids require editing, that is, the posttranscriptional insertion and deletion of uridine nucleotides that are specified by guide RNAs and catalyzed by multiprotein complexes. Recent studies have identified many of the proteins in these complexes, in addition to some of their functions and interactions. Although much remains unknown, a picture of highly organized complexes is emerging that shows that the complex that catalyzes the central steps of editing is partitioned into distinct insertion and deletion editing subcomplexes. These subcomplexes coordinate hundreds of ordered catalytic steps that function to produce a single mature mRNA. The dynamic processes, which might entail interactions among multiprotein complexes and changes in their composition and conformation, remain to be elucidated.
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Affiliation(s)
- Kenneth D Stuart
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA.
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35
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The ATPase subunit 6 gene of Leptomonas seymouri (Trypanosomatidae) is transcribed and edited as a polycistronic mRNA. Mol Biol 2005. [DOI: 10.1007/s11008-005-0007-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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36
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Clement SL, Mingler MK, Koslowsky DJ. An intragenic guide RNA location suggests a complex mechanism for mitochondrial gene expression in Trypanosoma brucei. EUKARYOTIC CELL 2004; 3:862-9. [PMID: 15302819 PMCID: PMC500885 DOI: 10.1128/ec.3.4.862-869.2004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2004] [Accepted: 06/04/2004] [Indexed: 11/20/2022]
Abstract
In Trypanosoma brucei, two classes of transcripts are produced from two distinct mitochondrial genome components. Guide RNAs (gRNAs) are usually minicircle encoded and exist as primary transcripts, while the maxicircle-encoded rRNAs and mRNAs are processed from a polycistronic precursor. The genes for the gRNAs gMURF2-II and gCYb(560) each have uncommon kinetoplast DNA (kDNA) locations that are not typically associated with transcription initiation events. We demonstrate that the conserved maxicircle gRNA gMURF2-II has an unusual location within the ND4 gene. This is the first report of a completely intragenic gene in kDNA. In addition, the gMURF2-II and ND4 transcripts are generated by distinctly different events; the ND4 mRNA is processed from a polycistronic precursor, while transcription of the gRNA initiates downstream of the 5' end of the ND4 gene. The gCYb(560) gene has an atypical minicircle location in that it is not flanked by the inverted repeat sequences that surround the majority of minicircle gRNA genes. Our data indicate that the mature gCYb(560) gRNA is also a primary transcript and that the 5'-end heterogeneity previously observed for this gRNA is a result of multiple transcription initiation sites and not of imprecise 5'-end processing. Together, these data indicate that gRNA genes represent individual transcription units, regardless of their genomic context, and suggest a complex mechanism for mitochondrial gene expression in T. brucei.
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Affiliation(s)
- Sandra L Clement
- 2209 Biomedical Physical Sciences Building, Michigan State University, East Lansing, MI 48824, USA
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37
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Halbig K, De Nova-Ocampo M, Cruz-Reyes J. Complete cycles of bloodstream trypanosome RNA editing in vitro. RNA (NEW YORK, N.Y.) 2004; 10:914-20. [PMID: 15146075 PMCID: PMC1370583 DOI: 10.1261/rna.5157704] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
RNA editing in kinetoplastid protists is required for the maturation of mitochondrial pre-mRNAs and occurs by protein-catalyzed cycles of uridylate insertion and deletion. During the complex life cycle of Trypanosoma brucei this process is differentially regulated in the mammalian bloodstream and insect procyclic stages. Complementary guide RNAs (gRNAs) direct editing, but the abundance of these transcripts is not developmentally controlled. The establishment of in vitro systems that recreate efficient RNA editing in bloodstream T. brucei would be valuable for mechanistic studies of regulation. Here we describe a robust in vitro system that reconstitutes full cycles of both U insertion and U deletion in bloodstream trypanosomes, and the first direct comparisons of the in vitro systems for strains of mammalian and insect stages.
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Affiliation(s)
- Kari Halbig
- Department of Biochemistry and Biophyisics, Texas A&M University, College Station, Texas 77843, USA
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38
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Koslowsky DJ, Reifur L, Yu LE, Chen W. Evidence for U-tail stabilization of gRNA/mRNA interactions in kinetoplastid RNA editing. RNA Biol 2004; 1:28-34. [PMID: 17194935 PMCID: PMC2762388 DOI: 10.4161/rna.1.1.898] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The most dramatic example of RNA editing is found in the mitochondria of trypanosomes. In these organisms, U-insertions/deletions can create mRNAs that are twice as large as the gene that encodes them. Guide RNAs (gRNAs) that are complementary to short stretches of the mature message direct the precise placements of the U residues. The binding of gRNA to mRNA is a fundamental step in RNA editing and understanding the relative importance of the elements that confer affinity and specificity on this interaction is critical to our understanding of the editing process. In this study, we have analyzed the relative binding affinities of two different gRNA/mRNA pairs. The affinity of gA6-14 for its message (ATPase 6) is high, with an apparent K(D) in the 5-10 nM range. In contrast, gCYb-558 has a low affinity for its cognate mRNA. Deletion of the gRNA U-tail caused a significant reduction in the binding affinity for only the gCYb-558 pair, and was observed only under physiological magnesium conditions. These results indicate that the U-tail contribution can differ substantially between the different gRNA/mRNA pairs. In addition, our results suggest that the efficiency of gRNA/mRNA interaction is highly dependent on thermodynamic parameters determined by the local sequences and their adopted structures surrounding the anchor-binding site.
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Affiliation(s)
- Donna J Koslowsky
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA.
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39
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Ryan CM, Militello KT, Read LK. Polyadenylation regulates the stability of Trypanosoma brucei mitochondrial RNAs. J Biol Chem 2003; 278:32753-62. [PMID: 12801929 DOI: 10.1074/jbc.m303552200] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Polyadenylation of RNAs plays a critical role in modulating rates of RNA turnover and ultimately in controlling gene expression in all systems examined to date. In mitochondria, the precise mechanisms by which RNAs are degraded, including the role of polyadenylation, are not well understood. Our previous in organello pulse-chase experiments suggest that poly(A) tails stimulate degradation of mRNAs in the mitochondria of the protozoan parasite Trypanosoma brucei (Militello, K. T., and Read, L. K. (2000) Mol. Cell. Biol. 21, 731-742). In this report, we developed an in vitro assay to directly examine the effects of specific 3'-sequences on RNA degradation. We found that a salt-extracted mitochondrial membrane fraction preferentially degraded polyadenylated mitochondrially and non-mitochondrially encoded RNAs over their non-adenylated counterparts. A poly(A) tail as short as 5 nucleotides was sufficient to stimulate rapid degradation, although an in vivo tail length of 20 adenosines supported the most rapid decay. A poly(U) extension did not promote rapid RNA degradation, and RNA turnover was slowed by the addition of uridine residues to the poly(A) tail. To stimulate degradation, the poly(A) element must be located at the 3' terminus of the RNA. Finally, we demonstrate that degradation of polyadenylated RNAs occurs in the 3' to 5' direction through the action of a hydrolytic exonuclease. These experiments demonstrate that the poly(A) tail can act as a cis-acting element to facilitate degradation of T. brucei mitochondrial mRNAs.
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Affiliation(s)
- Christopher M Ryan
- Department of Microbiology and the Witebsky Center for Microbial Pathogenesis and Immunology, School of Medicine and Biomedical Sciences, State University of New York, Buffalo, New York 14214, USA
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40
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Sbicego S, Alfonzo JD, Estévez AM, Rubio MAT, Kang X, Turck CW, Peris M, Simpson L. RBP38, a novel RNA-binding protein from trypanosomatid mitochondria, modulates RNA stability. EUKARYOTIC CELL 2003; 2:560-8. [PMID: 12796301 PMCID: PMC161464 DOI: 10.1128/ec.2.3.560-568.2003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We describe here the isolation and characterization of a novel RNA-binding protein, RBP38, from Leishmania tarentolae mitochondria. This protein does not contain any known RNA-binding motifs and is highly conserved among the trypanosomatids, but no homologues were found in other organisms. Recombinant LtRBP38 binds single and double-stranded (ds) RNA substrates with dissociation constants in the 100 nM range, as determined by fluorescence polarization analysis. Downregulation of expression of the homologous gene, TbRBP38, in procyclic Trypanosoma brucei by using conditional dsRNA interference resulted in 80% reduction of steady-state levels of RNAs transcribed from both maxicircle and minicircle DNA. In organello pulse-chase labeling experiments were used to determine the stability of RNAs in mitochondria that were depleted of TbRBP38. The half-life of metabolically labeled RNA decreased from approximately 160 to approximately 60 min after depletion. In contrast, there was no change in transcriptional activity. These observations suggest a role of RBP38 in stabilizing mitochondrial RNA.
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Affiliation(s)
- Sandro Sbicego
- Howard Hughes Medical Institute, University of California, Los Angeles, California 90095-1662, USA
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41
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Pelletier M, Read LK. RBP16 is a multifunctional gene regulatory protein involved in editing and stabilization of specific mitochondrial mRNAs in Trypanosoma brucei. RNA (NEW YORK, N.Y.) 2003; 9:457-68. [PMID: 12649497 PMCID: PMC1370412 DOI: 10.1261/rna.2160803] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2002] [Accepted: 12/27/2002] [Indexed: 05/20/2023]
Abstract
RBP16 is a Trypanosoma brucei mitochondrial RNA-binding protein that associates with guide RNAs (gRNAs), mRNAs, and ribosomal RNAs. Based on its inclusion in the multifunctional Y-box protein family and its ability to bind multiple RNA classes, we hypothesized that RBP16 plays a role in diverse aspects of mitochondrial gene regulation. To gain insight into RBP16 function, we generated cells expressing less than 10% of wild-type RBP16 levels by tetracycline-regulated RNA interference (RNAi). Poisoned primer extension analyses revealed that edited, but not unedited, CYb mRNA is reduced by approximately 98% in tetracycline-induced RBP16 RNAi cells, suggesting that RBP16 is critical for CYb RNA editing. The down-regulation of CYb editing in RBP16 RNAi transfectants apparently entails a defect in gRNA utilization, as gCYb[560] abundance is similar in uninduced and induced cells. We observed a surprising degree of specificity regarding the ability of RBP16 to modulate editing, as editing of mRNAs other than CYb is not significantly affected upon RBP16 disruption. However, the abundance of the never edited mitochondrial RNAs COI and ND4 is reduced by 70%-80% in RBP16 RNAi transfectants, indicating an additional role for RBP16 in the stabilization of these mRNAs. Analysis of RNAs bound to RBP16 immunoprecipitated from wild-type cells reveals that RBP16 is associated with multiple gRNA sequence classes in vivo, including those whose abundance and usage appear unaffected by RBP16 disruption. Overall, our results indicate that RBP16 is an accessory factor that regulates the editing and stability of specific populations of mitochondrial mRNAs.
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Affiliation(s)
- Michel Pelletier
- Department of Microbiology and Witebsky Center for Microbial Pathogenesis and Immunology, State University of New York-Buffalo School of Medicine, Buffalo, New York 14214, USA
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Grams J, Morris JC, Drew ME, Wang Z, Englund PT, Hajduk SL. A trypanosome mitochondrial RNA polymerase is required for transcription and replication. J Biol Chem 2002; 277:16952-9. [PMID: 11859084 DOI: 10.1074/jbc.m200662200] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Understanding mitochondrial transcription is a requisite first step toward understanding the regulation of mitochondrial gene expression in kinetoplastids. Here we report the identification and functional characterization of a mitochondrial RNA polymerase (mtRNAP) from Trypanosoma brucei, the first trans-acting factor involved in kinetoplast mitochondrial transcription to be identified. Using sequences conserved among the catalytic domains of the single-subunit mtRNAPs, we were able to obtain a full-length sequence for a candidate mtRNAP from T. brucei. Sequence comparison indicates that it shares homology in its catalytic domain with other single-subunit mtRNAPs, including functionally conserved residues that are identical in all single-subunit RNAPs. We used RNA interference to functionally knock out the gene product to determine whether the candidate gene represents an mtRNAP. As predicted for a mitochondrial specific RNA polymerase, reduction of the gene product resulted in a specific decrease of mitochondrial versus nuclear transcripts. Additionally, similar to the mtRNAP of other organisms, the mtRNAP characterized here is involved in replication of the mitochondrial genome. Thus, based on sequence comparison and functional studies, we have cloned an mtRNAP from trypanosomes.
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Affiliation(s)
- Jayleen Grams
- Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama, Birmingham, Alabama 35294, USA
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43
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Clement SL, Koslowsky DJ. Unusual organization of a developmentally regulated mitochondrial RNA polymerase (TBMTRNAP) gene in Trypanosoma brucei. Gene 2001; 272:209-18. [PMID: 11470527 PMCID: PMC2743126 DOI: 10.1016/s0378-1119(01)00538-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We report here the characterization of a developmentally regulated mitochondrial RNA polymerase transcript in the parasitic protozoan, Trypanosoma brucei. The 3822 bp protein-coding region of the T. brucei mitochondrial RNA polymerase (TBMTRNAP) gene is predicted to encode a 1274 amino acid polypeptide, the carboxyl-terminal domain of which exhibits 29-37% identity with the mitochondrial RNA polymerases from other organisms in the molecular databases. Interestingly, the TBMTRNAP mRNA is one of several mature mRNA species post-transcriptionally processed from a stable, polycistronic precursor. Alternative polyadenylation of the TBMTRNAP mRNA produces two mature transcripts that differ by 500 nt and that show stage-specific differences in abundance during the T. brucei life cycle. This alternative polyadenylation event appears to be accompanied by the alternative splicing of a high abundance, non-coding downstream transcript of unknown function. Our finding that the TBMTRNAP gene is transcribed into two distinct mRNAs subject to differential regulation during the T. brucei life cycle suggests that mitochondrial differentiation might be achieved in part through the regulated expression of this gene.
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MESH Headings
- Amino Acid Sequence
- Animals
- Cloning, Molecular
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Protozoan/chemistry
- DNA, Protozoan/genetics
- DNA-Directed RNA Polymerases/genetics
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Enzymologic
- Mitochondria/enzymology
- Molecular Sequence Data
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Trypanosoma brucei brucei/enzymology
- Trypanosoma brucei brucei/genetics
- Trypanosoma brucei brucei/growth & development
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Affiliation(s)
| | - Donna J. Koslowsky
- Corresponding author. Tel.: +1-517-432-3362; fax: +1-517-353-8957. E-mail address: (D.J. Koslowsky)
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Williams MA, Johzuka Y, Mulligan RM. Addition of non-genomically encoded nucleotides to the 3'-terminus of maize mitochondrial mRNAs: truncated rps12 mRNAs frequently terminate with CCA. Nucleic Acids Res 2000; 28:4444-51. [PMID: 11071931 PMCID: PMC113873 DOI: 10.1093/nar/28.22.4444] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The 3'-termini of maize mitochondrial RNAs were characterized by ligation of an anchor oligonucleotide, reverse transcription and amplification. DNA sequence analysis of cDNA clones for tRNA(Ser) and 18S rRNA confirmed the expected 3'-terminal nucleotides and demonstrated the accuracy and fidelity of the protocol. Analysis of cDNAs for rps12, cox2 and atp9 indicated that non-genomically encoded nucleotides were present at the 3'-terminus. rps12 cDNAs exhibited the highest degree of modification, with 94% of 35 cDNA clones analyzed containing one to four non-genomically encoded C or A residues; 83% of these cDNAs terminated with the trinucleotide CCA. DNA sequence and transcript mapping analyses demonstrated that four positions exhibited modified 3'-termini within a small region of the 3' flank of rps12 transcripts. These transcript termini represented low abundance, truncated forms of rps12 mRNAs which may be intermediates in degradation. cox2 mRNAs are also modified at a truncated position. Sixty percent of the cox2 cDNAs were modified with 1-5 nt that most frequently included A and C residues, but also included a few G and T residues. Non-genomically encoded nucleotides were detected in 27% of the atp9 cDNAs as a single C or A residue.
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MESH Headings
- 3' Untranslated Regions/genetics
- Arabidopsis Proteins
- Base Sequence
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- Electron Transport Complex IV/genetics
- Mitochondria/genetics
- Mitochondrial Proton-Translocating ATPases
- Molecular Sequence Data
- Plant Proteins/genetics
- Proteolipids/genetics
- Proton-Translocating ATPases/genetics
- RNA Processing, Post-Transcriptional
- RNA, Messenger/genetics
- RNA, Plant/genetics
- RNA, Ribosomal, 18S/genetics
- RNA, Transfer, Ser/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Analysis, DNA
- Zea mays/genetics
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Affiliation(s)
- M A Williams
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697-2300, USA
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Grams J, McManus MT, Hajduk SL. Processing of polycistronic guide RNAs is associated with RNA editing complexes in Trypanosoma brucei. EMBO J 2000; 19:5525-32. [PMID: 11032819 PMCID: PMC314002 DOI: 10.1093/emboj/19.20.5525] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2000] [Revised: 08/16/2000] [Accepted: 08/18/2000] [Indexed: 11/13/2022] Open
Abstract
In kinetoplastid mitochondrial mRNA editing, post-transcriptional insertion or deletion of uridines is templated by guide RNAs (gRNAs). Pre-mRNAs are encoded by maxicircles, while gRNAs are encoded by both maxicircles and minicircles. We have investigated minicircle transcription and the processing of gRNAs in Trypanosoma brucei. We find that minicircles are transcribed polycistronically and that transcripts are accurately processed by an approximately 19S complex. This gRNA processing activity co-purifies with RNA editing complexes, and both remain associated in 19S complexes. Furthermore, we show that RNA editing complexes associate preferentially with a polycistronic gRNA over non-processed RNAs. We propose that the approximately 19S complexes initially described as RNA editing complex I are gRNA processing complexes that cleave polycistronic gRNA transcripts into monocistrons.
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MESH Headings
- Animals
- Base Sequence
- DNA, Kinetoplast/genetics
- DNA, Kinetoplast/metabolism
- Genes/genetics
- Macromolecular Substances
- Mitochondria/genetics
- Models, Genetic
- Molecular Sequence Data
- Molecular Weight
- Nucleic Acid Conformation
- RNA/chemistry
- RNA/genetics
- RNA/metabolism
- RNA Editing
- RNA, Guide, Kinetoplastida/chemistry
- RNA, Guide, Kinetoplastida/genetics
- RNA, Guide, Kinetoplastida/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Mitochondrial
- Reverse Transcriptase Polymerase Chain Reaction
- Transcription, Genetic
- Trypanosoma brucei brucei/cytology
- Trypanosoma brucei brucei/genetics
- Trypanosoma brucei brucei/metabolism
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Affiliation(s)
- J Grams
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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46
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Militello KT, Read LK. UTP-dependent and -independent pathways of mRNA turnover in Trypanosoma brucei mitochondria. Mol Cell Biol 2000; 20:2308-16. [PMID: 10713154 PMCID: PMC85392 DOI: 10.1128/mcb.20.7.2308-2316.2000] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although primary transcripts are polycistronic in the mitochondria of Trypanosoma brucei, steady-state levels of mature, monocistronic RNAs change throughout the parasitic life cycle. This indicates that steady-state RNA abundance is controlled by posttranscriptional mechanisms involving differential RNA stability. In this study, in organello pulse-chase labeling experiments were used to analyze the stability of different T. brucei mitochondrial RNA populations. In this system, total RNA and rRNA are stable for many hours. In contrast, mRNAs can be degraded by two biochemically distinct turnover pathways. The first pathway results in the rapid degradation of mRNA (half-life [t(1/2)] of 11 to 18 min) and is dependent upon the presence of an mRNA poly(A) tail. Remarkably, this pathway also requires the addition of UTP and therefore is termed UTP dependent. The second pathway results in slow turnover of mitochondrial mRNA (t(1/2) of approximately 3 h) and is not dependent upon the presence of an mRNA poly(A) tail or the addition of exogenous UTP. In summary, these results demonstrate the presence of a novel, UTP-dependent degradation pathway for T. brucei mitochondrial mRNAs and reveal an unprecedented role for both UTP and mRNA polyadenylation in T. brucei mitochondrial gene expression.
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Affiliation(s)
- K T Militello
- Department of Microbiology and Center for Microbial Pathogenesis, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York 14214, USA
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47
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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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48
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Hotchkiss TL, Nerantzakis GE, Dills SC, Shang L, Read LK. Trypanosoma brucei poly(A) binding protein I cDNA cloning, expression, and binding to 5 untranslated region sequence elements. Mol Biochem Parasitol 1999; 98:117-29. [PMID: 10029314 DOI: 10.1016/s0166-6851(98)00156-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Poly(A) binding protein I (PABPI) is a highly conserved eukaryotic protein that binds mRNA poly(A) tails and functions in the regulation of translational efficiency and mRNA stability. As a first step in our investigation of the role(s) of mRNA poly(A) tails in posttranscriptional gene regulation in Trypanosoma brucei, we have cloned the cDNA encoding PABPI from this organism. The cDNA predicts a protein homologous to PABPI from other organisms and displaying conserved features of these proteins, including four RNA binding domains that span the N-terminal two-thirds of the protein. Comparison of northern blot data with the cDNA sequence indicates an unusually long 3' untranslated region (UTR) of approximately three kilobases. The 5 UTR contains both A-rich and AU repeat regions, the former being a ubiquitous property of PABPI 5' UTRs. T. brucei PABPI, expressed as a glutathione-S-transferase fusion protein, bound to RNA comprised of its full length 5' UTR in UV cross-linking experiments. This suggests that PABPI may play an autoregulatory role in its own expression. Competition experiments indicate that the A-rich region, but not the AU repeats, are involved in this binding.
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Affiliation(s)
- T L Hotchkiss
- Department of Microbiology and Center for Microbial Pathogenesis, SUNY Buffalo School of Medicine, NY 14214, USA
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49
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Alfonzo JD, Thiemann OH, Simpson L. Purification and characterization of MAR1. A mitochondrial associated ribonuclease from Leishmania tarentolae. J Biol Chem 1998; 273:30003-11. [PMID: 9792721 DOI: 10.1074/jbc.273.45.30003] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A relatively thermostable 22-kDa endoribonuclease (MAR1) was purified more than 10,000-fold from a mitochondrial extract of Leishmania tarentolae and the gene cloned. The purified nuclease has a Km of 100-145 +/- 33 nM and a Vmax of 1.8-2.9 +/- 2 nmol/min, depending on the RNA substrate, and yields a 3'-OH and a 5'-phosphate. Cleavage was limited to several specific sites in the substrate RNAs tested, but cleavage of pre-edited RNAs was generally independent of the addition of cognate guide RNA. The MAR1 gene was expressed in Escherichia coli or in L. tarentolae cells, and the recombinant protein was affinity-purified. The cleavage specificity of the recombinant enzyme from L. tarentolae was identical to that of the native enzyme. The single copy MAR1 gene maps to an 820-kilobase pair chromosome and contains an open reading frame of 579 nucleotides. The 18-amino acid N-terminal sequence shows characteristics of an uncleaved mitochondrial targeting sequence. Data base searching revealed two homologues of MAR1 corresponding to unidentified open reading frames in Caenorhabditis elegans (GenBankTM accession number Z69637) and Archaeoglobus fulgidus (GenBankTM accession number AE000943). The function of MAR1 in mitochondrial RNA metabolism in L. tarentolae remains to be determined.
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Affiliation(s)
- J D Alfonzo
- Howard Hughes Medical Institute, Los Angeles, California 90095-1662, USA
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