1
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Wenger C, Harsman A, Niemann M, Oeljeklaus S, von Känel C, Calderaro S, Warscheid B, Schneider A. The Mba1 homologue of Trypanosoma brucei is involved in the biogenesis of oxidative phosphorylation complexes. Mol Microbiol 2023; 119:537-550. [PMID: 36829306 DOI: 10.1111/mmi.15048] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023]
Abstract
Consistent with other eukaryotes, the Trypanosoma brucei mitochondrial genome encodes mainly hydrophobic core subunits of the oxidative phosphorylation system. These proteins must be co-translationally inserted into the inner mitochondrial membrane and are synthesized by the highly unique trypanosomal mitoribosomes, which have a much higher protein to RNA ratio than any other ribosome. Here, we show that the trypanosomal orthologue of the mitoribosome receptor Mba1 (TbMba1) is essential for normal growth of procyclic trypanosomes but redundant in the bloodstream form, which lacks an oxidative phosphorylation system. Proteomic analyses of TbMba1-depleted mitochondria from procyclic cells revealed reduced levels of many components of the oxidative phosphorylation system, most of which belong to the cytochrome c oxidase (Cox) complex, three subunits of which are mitochondrially encoded. However, the integrity of the mitoribosome and its interaction with the inner membrane were not affected. Pull-down experiments showed that TbMba1 forms a dynamic interaction network that includes the trypanosomal Mdm38/Letm1 orthologue and a trypanosome-specific factor that stabilizes the CoxI and CoxII mRNAs. In summary, our study suggests that the function of Mba1 in the biogenesis of membrane subunits of OXPHOS complexes is conserved among yeast, mammals and trypanosomes, which belong to two eukaryotic supergroups.
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Affiliation(s)
- Christoph Wenger
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Anke Harsman
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Moritz Niemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Silke Oeljeklaus
- Faculty of Chemistry and Pharmacy, Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Corinne von Känel
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Salvatore Calderaro
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Bettina Warscheid
- Faculty of Chemistry and Pharmacy, Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany.,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - André Schneider
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.,Institute for Advanced Study (Wissenschaftskolleg) Berlin, Berlin, Germany
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2
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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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3
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Maslov DA. Separating the Wheat from the Chaff: RNA Editing and Selection of Translatable mRNA in Trypanosome Mitochondria. Pathogens 2019; 8:E105. [PMID: 31323762 PMCID: PMC6789859 DOI: 10.3390/pathogens8030105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/14/2019] [Accepted: 07/16/2019] [Indexed: 11/16/2022] Open
Abstract
In the mitochondria of trypanosomes and related kinetoplastid protists, most mRNAs undergo a long and sophisticated maturation pathway before they can be productively translated by mitochondrial ribosomes. Some of the aspects of this pathway (identity of the promotors, transcription initiation, and termination signals) remain obscure, and some (post-transcriptional modification by U-insertion/deletion, RNA editing, 3'-end maturation) have been illuminated by research during the last decades. The RNA editing creates an open reading frame for a productive translation, but the fully edited mRNA often represents a minor fraction in the pool of pre-edited and partially edited precursors. Therefore, it has been expected that the final stages of the mRNA processing generate molecular hallmarks, which allow for the efficient and selective recognition of translation-competent templates. The general contours and several important details of this process have become known only recently and represent the subject of this review.
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Affiliation(s)
- Dmitri A Maslov
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA 92521, USA.
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4
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Yu H, Khalid MHB, Lu F, Sun F, Qu J, Liu B, Li W, Fu F. Isolation and identification of a vegetative organ-specific promoter from maize. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:277-287. [PMID: 30804649 PMCID: PMC6352524 DOI: 10.1007/s12298-018-0546-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 04/28/2018] [Accepted: 05/03/2018] [Indexed: 05/03/2023]
Abstract
To avoid the unregulated overexpression of the exogenous genes, specific or inducible expression is necessary for some exogenous genes in transgenic plants. But little is known about organ- or tissue-specific promoters in maize. In the present study, the expression of a maize pentatricopeptide repeat (PPR) protein encoding gene, GRMZM2G129783, was analyzed by RNA-sequencing data and confirmed by quantitative real time PCR. The results showed that the PPR GRMZM2G129783 gene specifically expressed in vegetative organs. Consequently, a 1830 bp sequence upstream of the start codon of the promoter for GRMZM2G129783 gene was isolated from maize genome (P 1830 ). To validate whether the promoter possesses the vegetative organ-specificity, the full-length and three 5'-end deletion fragments of P 1830 of different length (1387, 437, and 146 bp) were fused with glucuronidase (GUS) gene to generate promoter::GUS constructs and transformed into tobacco. The transient expression and fluorometric GUS assay in transgenic tobacco showed that all promoter could drive the expression of the GUS gene, the - 437 to - 146 bp region possessed some crucial elements for root-specific expression, and the shortest and optimal sequence to maintain transcription activity was 146 and 437 bp in length, respectively. These results indicate that the promoter of the PPR GRMZM2G129783 gene is a vegetative organ-specific promoter and will be useful in transgenic modification of commercial crops for moderate specific expression after further evaluation in monocotyledons.
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Affiliation(s)
- HaoQiang Yu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 People’s Republic of China
| | - Muhammad Hayder Bin Khalid
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 People’s Republic of China
| | - FengZhong Lu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 People’s Republic of China
| | - FuAi Sun
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 People’s Republic of China
| | - JingTao Qu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 People’s Republic of China
| | - BingLiang Liu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 People’s Republic of China
| | - WanChen Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 People’s Republic of China
| | - FengLing Fu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 People’s Republic of China
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5
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Kamba PF, Dickson DA, White NA, Ekstrom JL, Koslowsky DJ, Hoogstraten CG. The 27 kDa Trypanosoma brucei Pentatricopeptide Repeat Protein is a G-tract Specific RNA Binding Protein. Sci Rep 2018; 8:16989. [PMID: 30451852 PMCID: PMC6242908 DOI: 10.1038/s41598-018-34377-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/15/2018] [Indexed: 01/30/2023] Open
Abstract
Pentatricopeptide repeat (PPR) proteins, a helical repeat family of organellar RNA binding proteins, play essential roles in post-transcriptional RNA processing. In Trypanosoma brucei, an expanded family of PPR proteins localize to the parasite’s single mitochondrion, where they are believed to perform important roles in both RNA processing and translation. We studied the RNA binding specificity of the simplest T. brucei PPR protein (KRIPP11) using electrophoretic mobility shift assays, fluorescence anisotropy, circular dichroism spectroscopy, and in vitro selection. We found KRIPP11 to be an RNA binding protein with specificity for sequences of four or more consecutive guanosine residues (G-tracts). Such G-tracts are dramatically enriched in T. brucei mitochondrial transcripts that are destined for extensive uridine insertion/deletion editing but are not present in mRNAs following editing. We further found that the quadruplex oligoguanosine RNA conformation is preferentially recognized by KRIPP11 over other conformational forms, and is bound without disruption of the quadruplex structure. In combination with prior data demonstrating association of KRIPP11 with the small ribosomal subunit, these results suggest possible roles for KRIPP11 in bridging mRNA maturation and translation or in facilitating translation of unusual dual-coded open reading frames.
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Affiliation(s)
- Pakoyo F Kamba
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.,Graduate Program in Cell and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.,Makerere University, Kampala, Uganda
| | - David A Dickson
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.,Sackler School of Graduate Biomedical Sciences, Tufts University, Medford, Massachusetts, USA
| | - Neil A White
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.,Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Jennifer L Ekstrom
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.,Department of Food Science and Human Nutrition, Michigan State University, East Lansing, Michigan, USA
| | - Donna J Koslowsky
- Graduate Program in Cell and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, 48824-1319, USA
| | - Charles G Hoogstraten
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.
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6
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Yang Y, Wang Y, Jia L, Yang G, Xu X, Zhai H, He S, Li J, Dai X, Qin N, Zhu C, Liu Q. Involvement of an ABI-like protein and a Ca2+-ATPase in drought tolerance as revealed by transcript profiling of a sweetpotato somatic hybrid and its parents Ipomoea batatas (L.) Lam. and I. triloba L. PLoS One 2018; 13:e0193193. [PMID: 29466419 PMCID: PMC5821372 DOI: 10.1371/journal.pone.0193193] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 02/06/2018] [Indexed: 12/14/2022] Open
Abstract
Previously, we obtained the sweetpotato somatic hybrid KT1 from a cross between sweetpotato (Ipomoea batatas (L.) Lam.) cv. Kokei No. 14 and its drought-tolerant wild relative I. triloba L. KT1 not only inherited the thick storage root characteristic of Kokei No. 14 but also the drought-tolerance trait of I. triloba L. The aim of this study was to explore the molecular mechanism of the drought tolerance of KT1. Four-week-old in vitro-grown plants of KT1, Kokei No. 14, and I. triloba L. were subjected to a simulated drought stress treatment (30% PEG6000) for 0, 6, 12 and 24 h. Total RNA was extracted from samples at each time point, and then used for transcriptome sequencing. The gene transcript profiles of KT1 and its parents were compared to identify differentially expressed genes, and drought-related modules were screened by a weighted gene co-expression network analysis. The functions of ABI-like protein and Ca2+-ATPase, two proteins screened from the cyan and light yellow modules, were analyzed in terms of their potential roles in drought tolerance in KT1 and its parents. These analyses of the drought responses of KT1 and its somatic donors at the transcriptional level provide new annotations for the molecular mechanism of drought tolerance in the somatic hybrid KT1 and its parents.
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Affiliation(s)
- Yufeng Yang
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Yannan Wang
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Licong Jia
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Guohong Yang
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xinzhi Xu
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Hong Zhai
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Shaozhen He
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Junxia Li
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaodong Dai
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Na Qin
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Cancan Zhu
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Qingchang Liu
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
- * E-mail:
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7
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Gazestani VH, Hampton M, Shaw AK, Salavati R, Zimmer SL. Tail characteristics of Trypanosoma brucei mitochondrial transcripts are developmentally altered in a transcript-specific manner. Int J Parasitol 2017; 48:179-189. [PMID: 29100810 DOI: 10.1016/j.ijpara.2017.08.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/22/2017] [Accepted: 08/26/2017] [Indexed: 11/29/2022]
Abstract
The intricate life cycle of Trypanosoma brucei requires extensive regulation of gene expression levels of the mtRNAs for adaptation. Post-transcriptional gene regulatory programs, including unencoded mtRNA 3' tail additions, potentially play major roles in this adaptation process. Intriguingly, T. brucei mitochondrial transcripts possess two distinct unencoded 3' tails, each with a differing functional role; i.e., while one type is implicated in RNA stability (in-tails), the other type appears associated with translation (ex-tails). We examined the degree to which tail characteristics differ among cytochrome c oxidase subunits I and III (CO1 and CO3), and NADH dehydrogenase subunit 1 (ND1) transcripts, and to what extent these characteristics differ developmentally. We found that CO1, CO3 and ND1 transcripts possess longer in-tails in the mammalian life stage. By mathematically modelling states of in-tail and ex-tail addition, we determined that the typical length at which an in-tail is extended to become an ex-tail differs by transcript and, in the case of ND1, by life stage. To the best of our knowledge, we provide the first evidence that developmental differences exist in tail length distributions of mtRNAs, underscoring the potential involvement of in-tail and ex-tail populations in mitochondrial post-transcriptional regulation mechanisms.
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Affiliation(s)
- Vahid H Gazestani
- Institute of Parasitology, McGill University, Montreal, QC H9X 3V9, Canada
| | - Marshall Hampton
- Department of Mathematics and Statistics, University of Minnesota Duluth, Duluth, MN 55812, USA
| | - Aubie K Shaw
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA
| | - Reza Salavati
- Institute of Parasitology, McGill University, Montreal, QC H9X 3V9, Canada.
| | - Sara L Zimmer
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA.
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8
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Aphasizheva I, Maslov DA, Qian Y, Huang L, Wang Q, Costello CE, Aphasizhev R. Ribosome-associated pentatricopeptide repeat proteins function as translational activators in mitochondria of trypanosomes. Mol Microbiol 2016; 99:1043-58. [PMID: 26713541 DOI: 10.1111/mmi.13287] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2015] [Indexed: 12/20/2022]
Abstract
Mitochondrial ribosomes of Trypanosoma brucei are composed of 9S and 12S rRNAs, eubacterial-type ribosomal proteins, polypeptides lacking discernible motifs and approximately 20 pentatricopeptide repeat (PPR) RNA binding proteins. Several PPRs also populate the polyadenylation complex; among these, KPAF1 and KPAF2 function as general mRNA 3' adenylation/uridylation factors. The A/U-tail enables mRNA binding to the small ribosomal subunit and is essential for translation. The presence of A/U-tail also correlates with requirement for translation of certain mRNAs in mammalian and insect parasite stages. Here, we inquired whether additional PPRs activate translation of individual mRNAs. Proteomic analysis identified KRIPP1 and KRIPP8 as components of the small ribosomal subunit in mammalian and insect forms, but also revealed their association with the polyadenylation complex in the latter. RNAi knockdowns demonstrated essential functions of KRIPP1 and KRIPP8 in the actively respiring insect stage, but not in the mammalian stage. In the KRIPP1 knockdown, A/U-tailed mRNA encoding cytochrome c oxidase subunit 1 declined concomitantly with the de novo synthesis of this subunit whereas polyadenylation and translation of cyb mRNA were unaffected. In contrast, the KRIPP8 knockdown inhibited A/U-tailing and translation of both CO1 and cyb mRNAs. Our findings indicate that ribosome-associated PPRs may selectively activate mRNAs for translation.
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Affiliation(s)
- Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, MA, 02118, USA
| | - Dmitri A Maslov
- Department of Biology, University of California, Riverside, CA, 92521, USA
| | - Yu Qian
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, MA, 02118, USA
| | - Lan Huang
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Qi Wang
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Catherine E Costello
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, MA, 02118, USA.,Department of Biochemistry, Boston University School of Medicine, Boston, MA, 02118, USA
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9
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Ridlon L, Škodová I, Pan S, Lukeš J, Maslov DA. The importance of the 45 S ribosomal small subunit-related complex for mitochondrial translation in Trypanosoma brucei. J Biol Chem 2013; 288:32963-78. [PMID: 24089529 DOI: 10.1074/jbc.m113.501874] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The mitochondrial 45 S SSU* complex in Trypanosoma brucei contains the 9 S SSU ribosomal RNA, a set of SSU ribosomal proteins, several pentatricopeptide repeat (PPR) proteins, and proteins not typically found in ribosomes, including rhodanese domain protein (Rhod) and a 200-kDa coiled-coil protein. To investigate the function of this complex, PPR29, Rhod, 200-kDa protein, and mitochondrial ribosomal protein S17 were knocked down by RNAi in procyclic T. brucei. A growth retardation phenotype, a reduction in the amount of the 45 S SSU* complexes, and the preferential inhibition of synthesis of the cytochrome c oxidase subunit I over apocytochrome b were observed as early as day 2 postinduction of RNAi. On the contrary, the down-regulation of mitochondrial ribosomal protein L3 drastically reduced the amount of the large subunit and indiscriminately inhibited mitochondrial translation. The relative amounts of translation-competent, long poly(AU)-tailed cytochrome c oxidase subunit I and edited apocytochrome b mRNAs were selectively reduced by ablation of the 45 S SSU* complex. The formation of the 80 S translation complexes, identified by association of the long-tailed mRNAs with the mitoribosomes, was also disrupted. On the other hand, the relative amount of long-tailed edited RPS12 mRNA was not substantially affected, and there was no noticeable effect on the RPS12 translation complexes. In bloodstream trypanosomes, the amount of the 45 S complexes was drastically reduced compared with procyclics. We propose that the 45 S SSU* complex represents a factor required for normal mitochondrial translation that may have selective effects on different mRNAs.
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Affiliation(s)
- Lucie Ridlon
- From the Department of Biology, University of California, Riverside, California 92521
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10
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Aphasizhev R, Aphasizheva I. Emerging roles of PPR proteins in trypanosomes: switches, blocks, and triggers. RNA Biol 2013; 10:1495-500. [PMID: 24055869 PMCID: PMC3858432 DOI: 10.4161/rna.26215] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 08/16/2013] [Accepted: 08/19/2013] [Indexed: 01/05/2023] Open
Abstract
Mitochondrial genomes of trypanosomes are composed of catenated maxicircles and mini-circles that are densely packed into a nucleoprotein structure called the kinetoplast. Maxicircle DNA (~25 kb long, 20-50 copies) resembles a typical mitochondrial genome bearing rRNA and respiratory complex subunits genes, and also contains 12 cryptogenes whose transcripts require U-insertion/deletion editing to assemble protein-coding sequences. Production of guide RNAs for the editing process remains the only established function of mini-circle DNA (~1 kb, ~10000 copies). Although editing remains the most studied step in mRNA biogenesis, recent investigations illuminated complex nucleolytic processing and pre- and post-editing 3' modification events that ultimately create translation-competent mRNAs. Key mRNA 3' processing enzymes, such as KPAP1 poly(A) polymerase and RET1 TUTase, have been identified but the mechanisms regulating their activities remain poorly understood. Discoveries of multiple pentatricopeptide repeat-containing (PPR) proteins populating polyadenylation complex and ribosomal subunits opened exciting experimental prospects that may ultimately lead to an integrated picture of mitochondrial gene expression.
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Affiliation(s)
- Ruslan Aphasizhev
- Department of Molecular and Cell Biology; Boston University Goldman School of Dental Medicine; Boston, MA USA
| | - Inna Aphasizheva
- Department of Molecular and Cell Biology; Boston University Goldman School of Dental Medicine; Boston, MA USA
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11
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Identification of Pentatricopeptide Repeat Proteins in the Model Organism Dictyostelium discoideum. Int J Genomics 2013; 2013:586498. [PMID: 23998118 PMCID: PMC3753752 DOI: 10.1155/2013/586498] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 07/11/2013] [Indexed: 11/18/2022] Open
Abstract
Pentatricopeptide repeat (PPR) proteins are RNA binding proteins with functions in organelle RNA metabolism. They are found in all eukaryotes but have been most extensively studied in plants. We report on the identification of 12 PPR-encoding genes in the genome of the protist Dictyostelium discoideum, with potential homologs in other members of the same lineage and some predicted novel functions for the encoded gene products in protists. For one of the gene products, we show that it localizes to the mitochondria, and we also demonstrate that antisense inhibition of its expression leads to slower growth, a phenotype associated with mitochondrial dysfunction.
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12
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Filipovska A, Rackham O. Pentatricopeptide repeats: modular blocks for building RNA-binding proteins. RNA Biol 2013; 10:1426-32. [PMID: 23635770 DOI: 10.4161/rna.24769] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Pentatricopeptide repeat (PPR) proteins control diverse aspects of RNA metabolism across the eukaryotic domain. Recent computational and structural studies have provided new insights into how they recognize RNA, and show that the recognition is sequence-specific and modular. The modular code for RNA-binding by PPR proteins holds great promise for the engineering of new tools to target RNA and identifying RNAs bound by natural PPR proteins.
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Affiliation(s)
- Aleksandra Filipovska
- Western Australian Institute for Medical Research and Centre for Medical Research; The University of Western Australia; Perth, WA Australia; School of Chemistry and Biochemistry; The University of Western Australia; Crawley, WA Australia
| | - Oliver Rackham
- Western Australian Institute for Medical Research and Centre for Medical Research; The University of Western Australia; Perth, WA Australia; School of Chemistry and Biochemistry; The University of Western Australia; Crawley, WA Australia
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13
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Rackham O, Mercer TR, Filipovska A. The human mitochondrial transcriptome and the RNA-binding proteins that regulate its expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:675-95. [DOI: 10.1002/wrna.1128] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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Filipovska A, Rackham O. Modular recognition of nucleic acids by PUF, TALE and PPR proteins. MOLECULAR BIOSYSTEMS 2012; 8:699-708. [PMID: 22234420 DOI: 10.1039/c2mb05392f] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sequence specific binding of DNA and RNA is of fundamental importance in the regulation of cellular gene expression. Because of their modular structure repeat domain proteins are particularly well suited for these processes and have been widely adopted throughout evolution. Detailed biochemical and structural data has revealed the key residues responsible for recognition of RNA by Pumilio and FBF homology (PUF) repeat proteins and shown that the base specificity can be predicted and re-engineered. Recent work on the DNA-binding properties of transcription activator-like effector (TALE) proteins has shown that their specificity also relies on only a few key residues with a predictable code that can be used to design new DNA-binding proteins. Although less well understood, pentatricopeptide repeat (PPR) proteins contain motifs that appear to contribute to RNA recognition and comparisons to TALE and PUF proteins may help elucidate the code by which they recognize their RNA targets. Understanding how repeat proteins bind nucleic acids enables their biological roles to be uncovered and the design of engineered proteins with predictable RNA and DNA targets for use in biotechnology.
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15
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Kobayashi K, Kawabata M, Hisano K, Kazama T, Matsuoka K, Sugita M, Nakamura T. Identification and characterization of the RNA binding surface of the pentatricopeptide repeat protein. Nucleic Acids Res 2011; 40:2712-23. [PMID: 22127869 PMCID: PMC3315335 DOI: 10.1093/nar/gkr1084] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The expressions of chloroplast and mitochondria genes are tightly controlled by numerous nuclear-encoded proteins, mainly at the post-transcriptional level. Recent analyses have identified a large, plant-specific family of pentatricopeptide repeat (PPR) motif-containing proteins that are exclusively involved in RNA metabolism of organelle genes via sequence-specific RNA binding. A tandem array of PPR motifs within the protein is believed to facilitate the RNA interaction, although little is known of the mechanism. Here, we describe the RNA interacting framework of a PPR protein, Arabidopsis HCF152. First, we demonstrated that a Pfam model could be relevant to the PPR motif function. A series of proteins with two PPR motifs showed significant differences in their RNA binding affinities, indicating functional differences among PPR motifs. Mutagenesis and informatics analysis putatively identified five amino acids organizing its RNA binding surface [the 1st, 4th, 8th, 12th and ‘ii’(-2nd) amino acids] and their complex connections. SELEX (Systematic evolution of ligands by exponential enrichment) and nucleobase preference assays determined the nucleobases with high affinity for HCF152 and suggested several characteristic amino acids that may be involved in determining specificity and/or affinity of the PPR/RNA interaction.
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Affiliation(s)
- Keiko Kobayashi
- Faculty of Agriculture, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 812-8581, Japan
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16
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A trypanosomal pentatricopeptide repeat protein stabilizes the mitochondrial mRNAs of cytochrome oxidase subunits 1 and 2. EUKARYOTIC CELL 2011; 11:79-87. [PMID: 22058141 DOI: 10.1128/ec.05213-11] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The pentatricopeptide repeat (PPR) protein family consists of organellar proteins predicted to bind to specific RNA sequences. Plants have hundreds of distinct PPR proteins, whereas other eukaryotes generally have many fewer. The genome of the parasitic protozoon Trypanosoma brucei is predicted to encode more than 30 different PPR proteins, which is an extraordinarily high number for a nonplant organism. Here we report the characterization T. brucei PPR9 (TbPPR9). Epitope tagging shows that the protein is exclusively mitochondrially localized. Interestingly, while in induced RNA interference cell lines TbPPR9 is efficiently downregulated, the level of its mRNA is not affected. Ablation of TbPPR9 selectively abolishes oxidative but not mitochondrial substrate-level phosphorylation. The molecular basis of this phenotype is the fact that TbPPR9 is required for the stability of the cytochrome oxidase subunit 1 (COX1) and COX2 mRNAs. This is supported by the observation that ablation of TbPPR9 destabilizes the COX complex but not the cytochrome bc1 or the ATP synthase complex. Moreover, it was shown by blue native gel electrophoresis that TbPPR9 is present in a large complex of unknown composition.
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17
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Rackham O, Filipovska A. The role of mammalian PPR domain proteins in the regulation of mitochondrial gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:1008-16. [PMID: 22051507 DOI: 10.1016/j.bbagrm.2011.10.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 10/14/2011] [Accepted: 10/17/2011] [Indexed: 12/26/2022]
Abstract
Pentatricopeptide repeat (PPR) domain proteins are a large family of RNA-binding proteins that are involved in the maturation and translation of organelle transcripts in eukaryotes. They were first identified in plant organelles and their important role in mammalian mitochondrial gene regulation is now emerging. Mammalian PPR proteins, like their plant counterparts, have diverse roles in mitochondrial transcription, RNA metabolism and translation and consequently are important for mitochondrial function and cell health. Here we discuss the current knowledge about the seven mammalian PPR proteins identified to date and their roles in the regulation of mitochondrial gene expression. Furthermore we discuss the mitochondrial RNA targets of the mammalian PPR proteins and methods to investigate the RNA targets of these mitochondrial RNA-binding proteins. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.
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Affiliation(s)
- Oliver Rackham
- Western Australian Institute for Medical Research and Centre for Medical Research, The University of Western Australia, Perth, WA 6000, Australia
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18
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Madina BR, Kuppan G, Vashisht AA, Liang YH, Downey KM, Wohlschlegel JA, Ji X, Sze SH, Sacchettini JC, Read LK, Cruz-Reyes J. Guide RNA biogenesis involves a novel RNase III family endoribonuclease in Trypanosoma brucei. RNA (NEW YORK, N.Y.) 2011; 17:1821-30. [PMID: 21810935 PMCID: PMC3185915 DOI: 10.1261/rna.2815911] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 06/29/2011] [Indexed: 05/29/2023]
Abstract
The mitochondrial genome of kinetoplastids, including species of Trypanosoma and Leishmania, is an unprecedented DNA structure of catenated maxicircles and minicircles. Maxicircles represent the typical mitochondrial genome encoding components of the respiratory complexes and ribosomes. However, most mRNA sequences are cryptic, and their maturation requires a unique U insertion/deletion RNA editing. Minicircles encode hundreds of small guide RNAs (gRNAs) that partially anneal with unedited mRNAs and direct the extensive editing. Trypanosoma brucei gRNAs and mRNAs are transcribed as polycistronic precursors, which undergo processing preceding editing; however, the relevant nucleases are unknown. We report the identification and functional characterization of a close homolog of editing endonucleases, mRPN1 (mitochondrial RNA precursor-processing endonuclease 1), which is involved in gRNA biogenesis. Recombinant mRPN1 is a dimeric dsRNA-dependent endonuclease that requires Mg(2+), a critical catalytic carboxylate, and generates 2-nucleotide 3' overhangs. The cleavage specificity of mRPN1 is reminiscent of bacterial RNase III and thus is fundamentally distinct from editing endonucleases, which target a single scissile bond just 5' of short duplexes. An inducible knockdown of mRPN1 in T. brucei results in loss of gRNA and accumulation of precursor transcripts (pre-gRNAs), consistent with a role of mRPN1 in processing. mRPN1 stably associates with three proteins previously identified in relatively large complexes that do not contain mRPN1, and have been linked with multiple aspects of mitochondrial RNA metabolism. One protein, TbRGG2, directly binds mRPN1 and is thought to modulate gRNA utilization by editing complexes. The proposed participation of mRPN1 in processing of polycistronic RNA and its specific protein interactions in gRNA expression are discussed.
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Affiliation(s)
- Bhaskara Reddy Madina
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
| | - Gokulan Kuppan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
| | - Ajay A. Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095-1737, USA
| | - Yu-He Liang
- Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Kurtis M. Downey
- Department of Microbiology and Immunology, University at Buffalo, State University of New York, Buffalo, New York 14214, USA
| | - James A. Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095-1737, USA
| | - Xinhua Ji
- Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Sing-Hoi Sze
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - James C. Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
| | - Laurie K. Read
- Department of Microbiology and Immunology, University at Buffalo, State University of New York, Buffalo, New York 14214, USA
| | - Jorge Cruz-Reyes
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
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19
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Morey JS, Monroe EA, Kinney AL, Beal M, Johnson JG, Hitchcock GL, Van Dolah FM. Transcriptomic response of the red tide dinoflagellate, Karenia brevis, to nitrogen and phosphorus depletion and addition. BMC Genomics 2011; 12:346. [PMID: 21729317 PMCID: PMC3149589 DOI: 10.1186/1471-2164-12-346] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Accepted: 07/05/2011] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND The role of coastal nutrient sources in the persistence of Karenia brevis red tides in coastal waters of Florida is a contentious issue that warrants investigation into the regulation of nutrient responses in this dinoflagellate. In other phytoplankton studied, nutrient status is reflected by the expression levels of N- and P-responsive gene transcripts. In dinoflagellates, however, many processes are regulated post-transcriptionally. All nuclear encoded gene transcripts studied to date possess a 5' trans-spliced leader (SL) sequence suggestive, based on the trypanosome model, of post-transcriptional regulation. The current study therefore sought to determine if the transcriptome of K. brevis is responsive to nitrogen and phosphorus and is informative of nutrient status. RESULTS Microarray analysis of N-depleted K. brevis cultures revealed an increase in the expression of transcripts involved in N-assimilation (nitrate and ammonium transporters, glutamine synthetases) relative to nutrient replete cells. In contrast, a transcriptional signal of P-starvation was not apparent despite evidence of P-starvation based on their rapid growth response to P-addition. To study transcriptome responses to nutrient addition, the limiting nutrient was added to depleted cells and changes in global gene expression were assessed over the first 48 hours following nutrient addition. Both N- and P-addition resulted in significant changes in approximately 4% of genes on the microarray, using a significance cutoff of 1.7-fold and p ≤ 10-4. By far, the earliest responding genes were dominated in both nutrient treatments by pentatricopeptide repeat (PPR) proteins, which increased in expression up to 3-fold by 1 h following nutrient addition. PPR proteins are nuclear encoded proteins involved in chloroplast and mitochondria RNA processing. Correspondingly, other functions enriched in response to both nutrients were photosystem and ribosomal genes. CONCLUSIONS Microarray analysis provided transcriptomic evidence for N- but not P-limitation in K. brevis. Transcriptomic responses to the addition of either N or P suggest a concerted program leading to the reactivation of chloroplast functions. Even the earliest responding PPR protein transcripts possess a 5' SL sequence that suggests post-transcriptional control. Given the current state of knowledge of dinoflagellate gene regulation, it is currently unclear how these rapid changes in such transcript levels are achieved.
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Affiliation(s)
- Jeanine S Morey
- Marine Biotoxins Program, NOAA National Ocean Service, Center for Coastal Environmental Health and Biomolecular Research, 219 Fort Johnson Rd., Charleston, SC 29412, USA
| | - Emily A Monroe
- Marine Biotoxins Program, NOAA National Ocean Service, Center for Coastal Environmental Health and Biomolecular Research, 219 Fort Johnson Rd., Charleston, SC 29412, USA
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Dr. La Jolla, CA 92093, USA
| | - Amanda L Kinney
- Marine Biotoxins Program, NOAA National Ocean Service, Center for Coastal Environmental Health and Biomolecular Research, 219 Fort Johnson Rd., Charleston, SC 29412, USA
| | - Marion Beal
- Marine Biotoxins Program, NOAA National Ocean Service, Center for Coastal Environmental Health and Biomolecular Research, 219 Fort Johnson Rd., Charleston, SC 29412, USA
| | - Jillian G Johnson
- Marine Biotoxins Program, NOAA National Ocean Service, Center for Coastal Environmental Health and Biomolecular Research, 219 Fort Johnson Rd., Charleston, SC 29412, USA
| | - Gary L Hitchcock
- Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Cswy., Miami, FL 33149, USA
| | - Frances M Van Dolah
- Marine Biotoxins Program, NOAA National Ocean Service, Center for Coastal Environmental Health and Biomolecular Research, 219 Fort Johnson Rd., Charleston, SC 29412, USA
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20
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Kühl I, Dujeancourt L, Gaisne M, Herbert CJ, Bonnefoy N. A genome wide study in fission yeast reveals nine PPR proteins that regulate mitochondrial gene expression. Nucleic Acids Res 2011; 39:8029-41. [PMID: 21727087 PMCID: PMC3185421 DOI: 10.1093/nar/gkr511] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Pentatricopeptide repeat (PPR) proteins are particularly numerous in plant mitochondria and chloroplasts, where they are involved in different steps of RNA metabolism, probably due to the repeated 35 amino acid PPR motifs that are thought to mediate interactions with RNA. In non-photosynthetic eukaryotes only a handful of PPR proteins exist, for example the human LRPPRC, which is involved in a mitochondrial disease. We have conducted a systematic study of the PPR proteins in the fission yeast Schizosaccharomyces pombe and identified, in addition to the mitochondrial RNA polymerase, eight proteins all of which localized to the mitochondria, and showed some association with the membrane. The absence of all but one of these PPR proteins leads to a respiratory deficiency and modified patterns of steady state mt-mRNAs or newly synthesized mitochondrial proteins. Some cause a general defect, whereas others affect specific mitochondrial RNAs, either coding or non-coding: cox1, cox2, cox3, 15S rRNA, atp9 or atp6, sometimes leading to secondary defects. Interestingly, the two possible homologs of LRPPRC, ppr4 and ppr5, play opposite roles in the expression of the cox1 mt-mRNA, ppr4 being the first mRNA-specific translational activator identified in S. pombe, whereas ppr5 appears to be a general negative regulator of mitochondrial translation.
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Affiliation(s)
- Inge Kühl
- Centre de Génétique Moléculaire du CNRS, UPR3404, FRC3115, Avenue de Terrasse, 91198 Gif-sur-Yvette Cedex, France
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21
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Read LK, Zimmer SL, Ammerman ML. Marked for translation: long A/U tails as an interface between completion of RNA editing and ribosome recruitment. Mol Cell 2011; 42:6-8. [PMID: 21474064 DOI: 10.1016/j.molcel.2011.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The mechanism by which ribosomes select translatable mRNAs from the complex mixture of incompletely edited mRNAs in trypanosome mitochondria has remained a mystery. In this issue of Molecular Cell, Aphasizheva and colleagues (Aphasizheva et al., 2011) reveal a role for long 3' A/U tails in signaling ribosome recruitment to a fully edited, translatable mRNA.
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Affiliation(s)
- Laurie K Read
- Department of Microbiology and Immunology, SUNY Buffalo School of Medicine, Buffalo, NY 14214, USA.
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22
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The tetratricopeptide repeats (TPR)-like superfamily of proteins in Leishmania spp., as revealed by multi-relational data mining. Pattern Recognit Lett 2010. [DOI: 10.1016/j.patrec.2010.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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23
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Hernandez A, Madina BR, Ro K, Wohlschlegel JA, Willard B, Kinter MT, Cruz-Reyes J. REH2 RNA helicase in kinetoplastid mitochondria: ribonucleoprotein complexes and essential motifs for unwinding and guide RNA (gRNA) binding. J Biol Chem 2010; 285:1220-8. [PMID: 19850921 PMCID: PMC2801250 DOI: 10.1074/jbc.m109.051862] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Revised: 09/25/2009] [Indexed: 01/01/2023] Open
Abstract
Regulation of gene expression in kinetoplastid mitochondria is largely post-transcriptional and involves the orchestration of polycistronic RNA processing, 3'-terminal maturation, RNA editing, turnover, and translation; however, these processes remain poorly studied. Core editing complexes and their U-insertion/deletion activities are relatively well characterized, and a battery of ancillary factors has recently emerged. This study characterized a novel DExH-box RNA helicase, termed here REH2 (RNA editing associated helicase 2), in unique ribonucleoprotein complexes that exhibit unwinding and guide RNA binding activities, both of which required a double-stranded RNA-binding domain (dsRBD) and a functional helicase motif I of REH2. REH2 complexes and recently identified related particles share a multiprotein core but are distinguished by several differential polypeptides. Finally, REH2 associates transiently, via RNA, with editing complexes, mitochondrial ribosomes, and several ancillary factors that control editing and RNA stability. We propose that these putative higher order structures coordinate mitochondrial gene expression.
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Affiliation(s)
- Alfredo Hernandez
- From the Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Bhaskara Reddy Madina
- From the Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Kevin Ro
- the Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095-1737, and
| | - James A. Wohlschlegel
- the Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095-1737, and
| | - Belinda Willard
- the Department of Cell Biology, Cleveland Clinic Foundation, Cleveland, Ohio 44195
| | - Mike T. Kinter
- the Department of Cell Biology, Cleveland Clinic Foundation, Cleveland, Ohio 44195
| | - Jorge Cruz-Reyes
- From the Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
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24
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Abstract
In eukaryotes, RNA trans-splicing is an important RNA-processing form for the end-to-end ligation of primary transcripts that are derived from separately transcribed exons. So far, three different categories of RNA trans-splicing have been found in organisms as diverse as algae to man. Here, we review one of these categories: the trans-splicing of discontinuous group II introns, which occurs in chloroplasts and mitochondria of lower eukaryotes and plants. Trans-spliced exons can be predicted from DNA sequences derived from a large number of sequenced organelle genomes. Further molecular genetic analysis of mutants has unravelled proteins, some of which being part of high-molecular-weight complexes that promote the splicing process. Based on data derived from the alga Chlamydomonas reinhardtii, a model is provided which defines the composition of an organelle spliceosome. This will have a general relevance for understanding the function of RNA-processing machineries in eukaryotic organelles.
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Affiliation(s)
- Stephanie Glanz
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Bochum, Germany
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25
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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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26
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Weng J, Aphasizheva I, Etheridge RD, Huang L, Wang X, Falick AM, Aphasizhev R. Guide RNA-binding complex from mitochondria of trypanosomatids. Mol Cell 2008; 32:198-209. [PMID: 18951088 PMCID: PMC2645705 DOI: 10.1016/j.molcel.2008.08.023] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2008] [Revised: 07/14/2008] [Accepted: 08/18/2008] [Indexed: 12/16/2022]
Abstract
In the mitochondria of trypanosomatids, the majority of mRNAs undergo massive uracil-insertion/deletion editing. Throughout the processes of pre-mRNA polyadenylation, guide RNA (gRNA) uridylylation and annealing to mRNA, and editing reactions, several multiprotein complexes must engage in transient interactions to produce a template for protein synthesis. Here, we report the identification of a protein complex essential for gRNA stability. The gRNA-binding complex (GRBC) interacts with gRNA processing, editing, and polyadenylation machineries and with the mitochondrial edited mRNA stability (MERS1) factor. RNAi knockdown of the core subunits, GRBC1 and GRBC2, led to the elimination of gRNAs, thus inhibiting mRNA editing. Inhibition of MERS1 expression selectively abrogated edited mRNAs. Homologous proteins unique to the order of Kinetoplastida, GRBC1 and GRBC2, form a stable 200 kDa particle that directly binds gRNAs. Systematic analysis of RNA-mediated and RNA-independent interactions involving the GRBC and MERS1 suggests a unified model for RNA processing in the kinetoplast mitochondria.
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Affiliation(s)
- James Weng
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Inna Aphasizheva
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Ronald D. Etheridge
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Lan Huang
- Department of Physiology & Biophysics, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Xiaorong Wang
- Department of Physiology & Biophysics, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Arnold M. Falick
- Howard Hughes Medical Institute Mass Spectrometry Laboratory and Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Ruslan Aphasizhev
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697, USA
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27
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Williams-Carrier R, Kroeger T, Barkan A. Sequence-specific binding of a chloroplast pentatricopeptide repeat protein to its native group II intron ligand. RNA (NEW YORK, N.Y.) 2008; 14:1930-41. [PMID: 18669444 PMCID: PMC2525963 DOI: 10.1261/rna.1077708] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins are defined by degenerate 35-amino acid repeats that are related to the tetratricopeptide repeat (TPR). Most characterized PPR proteins mediate specific post-transcriptional steps in gene expression in mitochondria or chloroplasts. However, little is known about the structure of PPR proteins or the biochemical mechanisms through which they act. Here we establish features of PPR protein structure and nucleic acid binding activity through in vitro experiments with PPR5, which binds and stabilizes a chloroplast tRNA precursor harboring a group II intron. Recombinant PPR5 was shown to be monomeric by analytical ultracentrifugation and gel filtration. Circular dichroism spectroscopy showed that PPR5 has a high content of alpha helices, as predicted from the similarity between PPR and TPR motifs. PPR5 and another PPR protein, CRP1, bind with high affinity to single-stranded RNA, but bind poorly to single-stranded DNA or to double-stranded RNA or DNA. A specific PPR5 binding site was identified within its group II intron ligand. The minimal site spans approximately 45 nucleotides, encompasses two group II intron functional motifs, and overlaps the terminus of an in vivo RNA decay product. These results suggest mechanisms by which PPR5 influences both RNA stability and splicing.
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Affiliation(s)
- Rosalind Williams-Carrier
- Department of Biology, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
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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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Saha D, Prasad AM, Srinivasan R. Pentatricopeptide repeat proteins and their emerging roles in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2007; 45:521-34. [PMID: 17560114 DOI: 10.1016/j.plaphy.2007.03.026] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2006] [Accepted: 03/21/2007] [Indexed: 05/15/2023]
Abstract
Several protein families with tandem repeat motifs play a very important role in plant development and defense. The pentatricopeptide repeat (PPR) protein family, one of the largest families, is the most perplexing one in plants. PPR proteins have been implicated in many crucial functions broadly involving organelle biogenesis and plant development. PPR motifs are degenerate motifs, each with 35-amino-acid sequences and are present in tandem arrays of 2-27 repeats per protein. Although PPR proteins are found in other eukaryotes, their large number is probably required in plants to meet the specific needs of organellar gene expression. The repeats of PPR proteins form a superhelical structure to bind a specific ligand, probably a single-stranded RNA molecule, and modulate its expression. Functional studies on different PPR proteins have revealed their role in organellar RNA processing, fertility restoration in CMS plants, embryogenesis, and plant development. Functional genomic techniques can help identify the diverse roles of the PPR family of proteins in nucleus-organelle interaction and in plant development.
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Affiliation(s)
- D Saha
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India
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Pusnik M, Small I, Read LK, Fabbro T, Schneider A. Pentatricopeptide repeat proteins in Trypanosoma brucei function in mitochondrial ribosomes. Mol Cell Biol 2007; 27:6876-88. [PMID: 17646387 PMCID: PMC2099244 DOI: 10.1128/mcb.00708-07] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The pentatricopeptide repeat (PPR), a degenerate 35-amino-acid motif, defines a novel eukaryotic protein family. Plants have 400 to 500 distinct PPR proteins, whereas other eukaryotes generally have fewer than 5. The few PPR proteins that have been studied have roles in organellar gene expression, probably via direct interaction with RNA. Here we show that the parasitic protozoan Trypanosoma brucei encodes 28 distinct PPR proteins, an extraordinarily high number for a nonplant organism. A comparative analysis shows that seven out of eight selected PPR proteins are mitochondrially localized and essential for oxidative phosphorylation. Six of these are required for the stabilization of mitochondrial rRNAs and, like ribosomes, are associated with the mitochondrial membranes. Furthermore, one of the PPR proteins copurifies with the large subunit rRNA. Finally, ablation of all of the PPR proteins that were tested induces degradation of the other PPR proteins, indicating that they function in concert. Our results show that a significant number of trypanosomal PPR proteins are individually essential for the maintenance and/or biogenesis of mitochondrial rRNAs.
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Affiliation(s)
- Mascha Pusnik
- Department of Biology/Cell and Developmental Biology, University of Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
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Maslov DA, Spremulli LL, Sharma MR, Bhargava K, Grasso D, Falick AM, Agrawal RK, Parker CE, Simpson L. Proteomics and electron microscopic characterization of the unusual mitochondrial ribosome-related 45S complex in Leishmania tarentolae. Mol Biochem Parasitol 2007; 152:203-12. [PMID: 17292489 PMCID: PMC1885204 DOI: 10.1016/j.molbiopara.2007.01.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2006] [Revised: 12/29/2006] [Accepted: 01/12/2007] [Indexed: 11/20/2022]
Abstract
A novel type of ribonucleoprotein (RNP) complex has been described from the kinetoplast-mitochondria of Leishmania tarentolae. The complex, termed the 45S SSU*, contains the 9S small subunit rRNA but does not contain the 12S large subunit rRNA. This complex is the most stable and abundant mitochondrial RNP complex present in Leishmania. As shown by tandem mass spectrometry, the complex contains at least 39 polypeptides with a combined molecular mass of almost 2.1 MDa. These components include several homologs of small subunit ribosomal proteins (S5, S6, S8, S9, S11, S15, S16, S17, S18, MRPS29); however, most of the polypeptides present are unique. Only a few of them show recognizable motifs, such as protein-protein (coiled-coil, Rhodanese) or protein-RNA (pentatricopeptide repeat) interaction domains. A cryo-electron microscopy examination of the 45S SSU* fraction reveals that 27% of particles represent SSU homodimers arranged in a head-to-tail orientation, while the majority of particles are clearly different and show an asymmetric bilobed morphology. Multiple classes of two-dimensional averages were derived for the asymmetrical particles, probably reflecting random orientations of the particles and difficulties in correlating these views with the known projections of ribosomal complexes. One class of the two-dimensional averages shows a SSU moiety attached to a protein mass or masses in a monosome-like appearance. The combined mass spectrometry and electron microscopy data thus indicate that the majority 45S SSU* particles represents a heterodimeric complex in which the SSU of the Leishmania mitochondrial ribosome is associated with an additional protein mass. The biological role of these particles is not known.
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Affiliation(s)
- Dmitri A Maslov
- Department of Biology, University of California, Riverside, CA 92521, USA.
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Schmitz-Linneweber C, Williams-Carrier RE, Williams-Voelker PM, Kroeger TS, Vichas A, Barkan A. A pentatricopeptide repeat protein facilitates the trans-splicing of the maize chloroplast rps12 pre-mRNA. THE PLANT CELL 2006; 18:2650-63. [PMID: 17041147 PMCID: PMC1626628 DOI: 10.1105/tpc.106.046110] [Citation(s) in RCA: 149] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2006] [Revised: 08/23/2006] [Accepted: 09/18/2006] [Indexed: 05/12/2023]
Abstract
The pentatricopeptide repeat (PPR) is a degenerate 35-amino acid repeat motif that is widely distributed among eukaryotes. Genetic, biochemical, and bioinformatic data suggest that many PPR proteins influence specific posttranscriptional steps in mitochondrial or chloroplast gene expression and that they may typically bind RNA. However, biological functions have been determined for only a few PPR proteins, and with few exceptions, substrate RNAs are unknown. To gain insight into the functions and substrates of the PPR protein family, we characterized the maize (Zea mays) nuclear gene ppr4, which encodes a chloroplast-targeted protein harboring both a PPR tract and an RNA recognition motif. Microarray analysis of RNA that coimmunoprecipitates with PPR4 showed that PPR4 is associated in vivo with the first intron of the plastid rps12 pre-mRNA, a group II intron that is transcribed in segments and spliced in trans. ppr4 mutants were recovered through a reverse-genetic screen and shown to be defective for rps12 trans-splicing. The observations that PPR4 is associated in vivo with rps12-intron 1 and that it is also required for its splicing demonstrate that PPR4 is an rps12 trans-splicing factor. These findings add trans-splicing to the list of RNA-related functions associated with PPR proteins and suggest that plastid group II trans-splicing is performed by different machineries in vascular plants and algae.
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