1
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Afonin DA, Gerasimov ES, Škodová-Sveráková I, Záhonová K, Gahura O, Albanaz ATS, Myšková E, Bykova A, Paris Z, Lukeš J, Opperdoes FR, Horváth A, Zimmer SL, Yurchenko V. Blastocrithidia nonstop mitochondrial genome and its expression are remarkably insulated from nuclear codon reassignment. Nucleic Acids Res 2024; 52:3870-3885. [PMID: 38452217 DOI: 10.1093/nar/gkae168] [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: 06/20/2023] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
The canonical stop codons of the nuclear genome of the trypanosomatid Blastocrithidia nonstop are recoded. Here, we investigated the effect of this recoding on the mitochondrial genome and gene expression. Trypanosomatids possess a single mitochondrion and protein-coding transcripts of this genome require RNA editing in order to generate open reading frames of many transcripts encoded as 'cryptogenes'. Small RNAs that can number in the hundreds direct editing and produce a mitochondrial transcriptome of unusual complexity. We find B. nonstop to have a typical trypanosomatid mitochondrial genetic code, which presumably requires the mitochondrion to disable utilization of the two nucleus-encoded suppressor tRNAs, which appear to be imported into the organelle. Alterations of the protein factors responsible for mRNA editing were also documented, but they have likely originated from sources other than B. nonstop nuclear genome recoding. The population of guide RNAs directing editing is minimal, yet virtually all genes for the plethora of known editing factors are still present. Most intriguingly, despite lacking complex I cryptogene guide RNAs, these cryptogene transcripts are stochastically edited to high levels.
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MESH Headings
- Genome, Mitochondrial
- RNA Editing
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Open Reading Frames/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Trypanosomatina/genetics
- Trypanosomatina/metabolism
- Codon/genetics
- Mitochondria/genetics
- Mitochondria/metabolism
- Codon, Terminator/genetics
- RNA, Guide, Kinetoplastida/genetics
- RNA, Guide, Kinetoplastida/metabolism
- Genetic Code
- Protozoan Proteins/genetics
- Protozoan Proteins/metabolism
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Affiliation(s)
- Dmitry A Afonin
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Evgeny S Gerasimov
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russia
| | - Ingrid Škodová-Sveráková
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czechia
| | - Kristína Záhonová
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czechia
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV 252 50 Vestec, Czechia
- Division of Infectious Diseases, Department of Medicine, University of Alberta, T6G 2R3 Edmonton, Alberta, Canada
| | - Ondřej Gahura
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czechia
| | - Amanda T S Albanaz
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia
| | - Eva Myšková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czechia
| | - Anastassia Bykova
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia
| | - Zdeněk Paris
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czechia
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czechia
| | - Fred R Opperdoes
- De Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Anton Horváth
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia
| | - Sara L Zimmer
- University of Minnesota Medical School, Duluth Campus, Duluth, MN 55812, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia
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2
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Ovciarikova J, Shikha S, Lacombe A, Courjol F, McCrone R, Hussain W, Maclean A, Lemgruber L, Martins-Duarte ES, Gissot M, Sheiner L. Two ancient membrane pores mediate mitochondrial-nucleus membrane contact sites. J Cell Biol 2024; 223:e202304075. [PMID: 38456969 PMCID: PMC10923651 DOI: 10.1083/jcb.202304075] [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: 04/22/2023] [Revised: 11/28/2023] [Accepted: 01/29/2024] [Indexed: 03/09/2024] Open
Abstract
Coordination between nucleus and mitochondria is essential for cell survival, and thus numerous communication routes have been established between these two organelles over eukaryotic cell evolution. One route for organelle communication is via membrane contact sites, functional appositions formed by molecular tethers. We describe a novel nuclear-mitochondrial membrane contact site in the protozoan Toxoplasma gondii. We have identified specific contacts occurring at the nuclear pore and demonstrated an interaction between components of the nuclear pore and the mitochondrial protein translocon, highlighting them as molecular tethers. Genetic disruption of the nuclear pore or the TOM translocon components, TgNup503 or TgTom40, respectively, result in contact site reduction, supporting their potential involvement in this tether. TgNup503 depletion further leads to specific mitochondrial morphology and functional defects, supporting a role for nuclear-mitochondrial contacts in mediating their communication. The discovery of a contact formed through interaction between two ancient mitochondrial and nuclear complexes sets the ground for better understanding of mitochondrial-nuclear crosstalk in eukaryotes.
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Affiliation(s)
- Jana Ovciarikova
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Shikha Shikha
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Alice Lacombe
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Flavie Courjol
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019—UMR 9017—CIIL—Center for Infection and Immunity of Lille, University of Lille, Lille, France
| | - Rosalind McCrone
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Wasim Hussain
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Andrew Maclean
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Leandro Lemgruber
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Erica S. Martins-Duarte
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Mathieu Gissot
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019—UMR 9017—CIIL—Center for Infection and Immunity of Lille, University of Lille, Lille, France
| | - Lilach Sheiner
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
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3
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Britten NS, Butler JA. Ruthenium metallotherapeutics: novel approaches to combatting parasitic infections. Curr Med Chem 2022; 29:5159-5178. [DOI: 10.2174/0929867329666220401105444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/15/2022] [Accepted: 01/24/2022] [Indexed: 11/22/2022]
Abstract
Human parasitic infections cause a combined global mortality rate of over one million people per annum and represent some of the most challenging diseases for medical intervention. Current chemotherapeutic strategies often require prolonged treatment, coupled with subsequent drug-induced cytotoxic morbidity to the host, while resistance generation is also a major concern. Metals have been used extensively throughout the history of medicine, with more recent applications as anticancer and antimicrobial agents. Ruthenium metallotherapeutic antiparasitic agents are highly effective at targeting a range of key parasites, including the causative agents of malaria, trypanosomiasis, leishmaniasis, amoebiasis, toxoplasmosis and other orphan diseases, while demonstrating lower cytotoxicity profiles than current treatment strategies. Generally, such compounds also demonstrate activity against multiple cellular target sites within parasites, including inhibition of enzyme function, cell membrane perturbation, and alterations to metabolic pathways, therefore reducing the opportunity for resistance generation. This review provides a comprehensive and subjective analysis of the rapidly developing area of ruthenium metal-based antiparasitic chemotherapeutics, in the context of rational drug design and potential clinical approaches to combatting human parasitic infections.
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Affiliation(s)
- Nicole S. Britten
- Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, United Kingdom
| | - Jonathan A. Butler
- Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, United Kingdom
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Huang J, Wu S, Wang P, Wang G. Non-coding RNA Regulated Cross-Talk Between Mitochondria and Other Cellular Compartments. Front Cell Dev Biol 2021; 9:688523. [PMID: 34414182 PMCID: PMC8369480 DOI: 10.3389/fcell.2021.688523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/12/2021] [Indexed: 12/04/2022] Open
Abstract
Mitochondria are the main hubs for cellular energy production. Metabolites produced in mitochondria not only feed many important biosynthesis pathways but also function as signaling molecules. Mitochondrial biosynthesis requires collaboration of both nuclear and mitochondrial gene expression systems. In addition, mitochondria have to quickly respond to changes inside and outside the cells and have their own functional states reported to the nucleus and other cellular compartments. The underlying molecular mechanisms of these complex regulations have not been well understood. Recent evidence indicates that in addition to small molecules, non-coding RNAs may contribute to the communication between mitochondria and other cellular compartments and may even serve as signals. In this review, we summarize the current knowledge about mitochondrial non-coding RNAs (including nucleus-encoded non-coding RNAs that are imported into mitochondria and mitochondrion-encoded non-coding RNAs that are exported), their trafficking and their functions in co-regulation of mitochondrial and other cellular processes.
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Affiliation(s)
- Jinliang Huang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Sipeng Wu
- State Key laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Pengcheng Wang
- State Key laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Geng Wang
- State Key laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
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5
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Kulkarni S, Rubio MAT, Hegedűsová E, Ross RL, Limbach PA, Alfonzo JD, Paris Z. Preferential import of queuosine-modified tRNAs into Trypanosoma brucei mitochondrion is critical for organellar protein synthesis. Nucleic Acids Res 2021; 49:8247-8260. [PMID: 34244755 PMCID: PMC8373054 DOI: 10.1093/nar/gkab567] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 05/28/2021] [Accepted: 06/21/2021] [Indexed: 11/13/2022] Open
Abstract
Transfer RNAs (tRNAs) are key players in protein synthesis. To be fully active, tRNAs undergo extensive post-transcriptional modifications, including queuosine (Q), a hypermodified 7-deaza-guanosine present in the anticodon of several tRNAs in bacteria and eukarya. Here, molecular and biochemical approaches revealed that in the protozoan parasite Trypanosoma brucei, Q-containing tRNAs have a preference for the U-ending codons for asparagine, aspartate, tyrosine and histidine, analogous to what has been described in other systems. However, since a lack of tRNA genes in T. brucei mitochondria makes it essential to import a complete set from the cytoplasm, we surprisingly found that Q-modified tRNAs are preferentially imported over their unmodified counterparts. In turn, their absence from mitochondria has a pronounced effect on organellar translation and affects function. Although Q modification in T. brucei is globally important for codon selection, it is more so for mitochondrial protein synthesis. These results provide a unique example of the combined regulatory effect of codon usage and wobble modifications on protein synthesis; all driven by tRNA intracellular transport dynamics.
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Affiliation(s)
- Sneha Kulkarni
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Mary Anne T Rubio
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Eva Hegedűsová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Robert L Ross
- Metabolomics Mass Spectrometry Core, Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Juan D Alfonzo
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Zdeněk Paris
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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6
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The Diversity of the Mitochondrial Outer Membrane Protein Import Channels: Emerging Targets for Modulation. Molecules 2021; 26:molecules26134087. [PMID: 34279427 PMCID: PMC8272145 DOI: 10.3390/molecules26134087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 12/21/2022] Open
Abstract
The functioning of mitochondria and their biogenesis are largely based on the proper function of the mitochondrial outer membrane channels, which selectively recognise and import proteins but also transport a wide range of other molecules, including metabolites, inorganic ions and nucleic acids. To date, nine channels have been identified in the mitochondrial outer membrane of which at least half represent the mitochondrial protein import apparatus. When compared to the mitochondrial inner membrane, the presented channels are mostly constitutively open and consequently may participate in transport of different molecules and contribute to relevant changes in the outer membrane permeability based on the channel conductance. In this review, we focus on the channel structure, properties and transported molecules as well as aspects important to their modulation. This information could be used for future studies of the cellular processes mediated by these channels, mitochondrial functioning and therapies for mitochondria-linked diseases.
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7
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The immunogenic maturation of goat monocyte-derived dendritic cells and upregulation of toll-like receptors by five antigens of Haemonchus contortus in-vitro. Res Vet Sci 2021; 136:247-258. [PMID: 33721712 DOI: 10.1016/j.rvsc.2021.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 12/25/2022]
Abstract
Previously, it was found that several proteins of Haemonchus contortus were involved in the stimulation of the host immune system. However, the information about the selection of superlative antigens with immunogenic efficacies on host DCs is lacking. In the current study, the stimulatory effects of five recombinant proteins (elongation factor-1α, arginine kinase, ES-15, ES-24, and ADP-ribosylation factor 1) of H. contortus on the maturation of goat monocyte-derived dendritic cells (md-DCs) were reported. Recombinant proteins were purified separately in E. coli expression and incubated with isolated goat peripheral blood mononuclear cells (PBMC). Immunofluorescence assay (IFA) results confirmed the binding of these molecules to the md-DC's surface as compared to control groups. In the flow cytometry analysis, recombinant proteins induced md-DC stimulation via the up-regulation of the expression of the costimulatory molecule (CD80) and MHC-II. Quantitative RT-PCR data showed a significant increase in the expression of specific genes of the WNT and toll-like receptor (TLR) signaling pathways. The result of ELISA indicated the higher levels of cytokine (IL-10, IL-12, IFN-γ, and TNF-α) secretion in the md-DC compared to the negative (pET-32a His-Tag) and blank (PBS) control groups. The data gives valuable support in the selection of potential antigens for future studies on the immunomodulation of the host against the infection of H. contortus.
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8
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Tavares KCS, Casagrande Dambrós MG, Antunes ASL, Danziato PM, Stoco PH, Schlindwein AD, Moreira RS, Miletti LC. Selenocysteine in Trypanosoma evansi: Identification of the Genes selb, selc, seld, pstk, seltryp and the Selenophosphate Synthetase Protein. ACTA PROTOZOOL 2021. [DOI: 10.4467/16890027ap.21.003.14063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Selenoproteins have been described in all three domains of life and their function has been mainly associated with oxidative stress defense. Canonical elements required for selenoprotein production have been identified in members of the kinetoplastid group supporting the existence of a complete selenocysteine synthesis pathway in these organisms. Currently, nothing is known regarding the selenocysteine pathway in Trypanosoma evansi. In this study, we identified the expression of the elements selB, selC, selD, PSTK and selTRYP at the mRNA level in T. evansi. All translated proteins (selD, PSTK, selTRYP and selB) have the domains predicted and higher identity with Trypanosoma brucei. gambiense. The selenophosphate synthetase protein was localized in the cytoplasm. Our results support the existence of an active selenocysteine pathway in T. evansi.
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Affiliation(s)
- Kaio Cesar Simiano Tavares
- Laboratório de Hemoparasitas e Vetores Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC).; Experimental Biology Center (NUBEX), Universidade de Fortaleza
| | | | | | | | | | | | - Renato Simões Moreira
- Laboratório de Hemoparasitas e Vetores Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC); Instituto Federal de Santa Catarina (IFSC)
| | - Luiz Claudio Miletti
- Laboratório de Hemoparasitas e Vetores Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC)
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Shikha S, Huot JL, Schneider A, Niemann M. tRNA import across the mitochondrial inner membrane in T. brucei requires TIM subunits but is independent of protein import. Nucleic Acids Res 2020; 48:12269-12281. [PMID: 33231678 PMCID: PMC7708065 DOI: 10.1093/nar/gkaa1098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/20/2020] [Accepted: 11/03/2020] [Indexed: 01/27/2023] Open
Abstract
Mitochondrial tRNA import is widespread, but mechanistic insights of how tRNAs are translocated across mitochondrial membranes remain scarce. The parasitic protozoan T. brucei lacks mitochondrial tRNA genes. Consequently, it imports all organellar tRNAs from the cytosol. Here we investigated the connection between tRNA and protein translocation across the mitochondrial inner membrane. Trypanosomes have a single inner membrane protein translocase that consists of three heterooligomeric submodules, which all are required for import of matrix proteins. In vivo depletion of individual submodules shows that surprisingly only the integral membrane core module, including the protein import pore, but not the presequence-associated import motor are required for mitochondrial tRNA import. Thus we could uncouple import of matrix proteins from import of tRNAs even though both substrates are imported into the same mitochondrial subcompartment. This is reminiscent to the outer membrane where the main protein translocase but not on-going protein translocation is required for tRNA import. We also show that import of tRNAs across the outer and inner membranes are coupled to each other. Taken together, these data support the 'alternate import model', which states that tRNA and protein import while mechanistically independent use the same translocation pores but not at the same time.
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Affiliation(s)
- Shikha Shikha
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Jonathan L Huot
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - André Schneider
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Moritz Niemann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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10
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Barozai MYK, Chaudhuri M. Role of the translocase of the mitochondrial inner membrane in the import of tRNAs into mitochondria in Trypanosoma brucei. Gene 2020; 748:144705. [PMID: 32339625 PMCID: PMC7304388 DOI: 10.1016/j.gene.2020.144705] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 04/07/2020] [Accepted: 04/21/2020] [Indexed: 02/07/2023]
Abstract
Trypanosomatids are unicellular parasitic protozoa. Many of the species of this genera cause severe diseases in human, such as Leishmaniasis, African trypanosomiasis and Chagas disease. These parasites possess a single reticular mitochondrion with a concatenated structure of mitochondrial DNA known as kinetoplast or kDNA. kDNA encodes few essential mitochondrial proteins but no tRNAs. Therefore, trypanosomatid mitochondrion import a full set of nucleus-encoded tRNAs for mitochondrial translation. Recent advances indicated that mitochondrial protein translocases, particularly the subunits of the ATOM complex, are involved in the import of a tRNA in Trypanosoma brucei. However, the global picture and the role of the translocase components of the mitochondrial inner membrane (TbTims) are not well understood. Here we investigated the relative abundance of 16 different tRNAs in the cytosolic and mitochondrial fractions isolated from the six TbTims knockdown cell lines. We found that knockdown of TbTim17, one of the primary components of the TbTIM complex, reduced the abundance of all of these tRNAs into mitochondria and increased their abundance in the cytosol. Depletion of TbTim62, a TbTim17 associated proteins, also reduced the relative abundance of most of these tRNAs into mitochondria except for tRNAleu, tRNAmet, and tRNAglu. Whereas, knockdown of other TbTims, like TbTim50 and two small TbTims, TbTim10 and TbTim8/13, didn't have any effect on tRNA abundance either in the cytosol or mitochondria. Depletion of any of these TbTims showed minimal effect on the levels of total tRNAs in T. brucei. Absolute quantification of tRNA levels revealed that TbTim17 knockdown reduced the levels of different tRNAs in mitochondria from 3-6% to 0.8-1.4%, which is equivalent to ~70% reduction in average. Whereas, TbTim62 depletion showed somewhat selective effect. Overall, our results suggest that TbTim17 and TbTim62 are essential for tRNA import that further makes a connection between the tRNA and protein import into mitochondria in T. brucei.
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Affiliation(s)
- Muhammad Younas Khan Barozai
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN 37208, United States
| | - Minu Chaudhuri
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN 37208, United States.
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11
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Shikha S, Schneider A. The single CCA-adding enzyme of T. brucei has distinct functions in the cytosol and in mitochondria. J Biol Chem 2020; 295:6138-6150. [PMID: 32234763 DOI: 10.1074/jbc.ra119.011877] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 03/23/2020] [Indexed: 12/27/2022] Open
Abstract
tRNAs universally carry a CCA nucleotide triplet at their 3'-ends. In eukaryotes, the CCA is added post-transcriptionally by the CCA-adding enzyme (CAE). The mitochondrion of the parasitic protozoan Trypanosoma brucei lacks tRNA genes and therefore imports all of its tRNAs from the cytosol. This has generated interest in the tRNA modifications and their distribution in this organism, including how CCA is added to tRNAs. Here, using a BLAST search for genes encoding putative CAE proteins in T. brucei, we identified a single ORF, Tb927.9.8780, as a potential candidate. Knockdown of this putative protein, termed TbCAE, resulted in the accumulation of truncated tRNAs, abolished translation, and inhibited both total and mitochondrial CCA-adding activities, indicating that TbCAE is located both in the cytosol and mitochondrion. However, mitochondrially localized tRNAs were much less affected by the TbCAE ablation than the other tRNAs. Complementation assays revealed that the N-terminal 10 amino acids of TbCAE are dispensable for its activity and mitochondrial localization and that deletion of 10 further amino acids abolishes both. A growth arrest caused by the TbCAE knockdown was rescued by the expression of the cytosolic isoform of yeast CAE, even though it was not imported into mitochondria. This finding indicated that the yeast enzyme complements the essential function of TbCAE by adding CCA to the primary tRNA transcripts. Of note, ablation of the mitochondrial TbCAE activity, which likely has a repair function, only marginally affected growth.
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Affiliation(s)
- Shikha Shikha
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern CH-3012, Switzerland
| | - André Schneider
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern CH-3012, Switzerland.
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12
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Jelk J, Balmer V, Stibal D, Giannini F, Süss-Fink G, Bütikofer P, Furrer J, Hemphill A. Anti-parasitic dinuclear thiolato-bridged arene ruthenium complexes alter the mitochondrial ultrastructure and membrane potential in Trypanosoma brucei bloodstream forms. Exp Parasitol 2019; 205:107753. [DOI: 10.1016/j.exppara.2019.107753] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/20/2019] [Accepted: 08/25/2019] [Indexed: 01/28/2023]
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13
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Huot JL, Shikha S, Schneider A. Inducible orthogonal aminoacylation demonstrates that charging is required for mitochondrial tRNA import in Trypanosoma brucei. Sci Rep 2019; 9:10836. [PMID: 31346230 PMCID: PMC6658472 DOI: 10.1038/s41598-019-47268-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/10/2019] [Indexed: 01/12/2023] Open
Abstract
Orthogonal aminoacyl-tRNA synthetase/tRNA pairs have emerged as powerful means of site-specifically introducing non-standard amino acids into proteins in vivo. Using amino acids with crosslinking moieties this method allows the identification of transient protein-protein interactions. Here we have introduced a previously characterized evolved tyrosyl-tRNA synthetase/suppressor tRNATyr pair from E. coli into the parasitic protozoan Trypanosoma brucei. Upon addition of a suitable non-standard amino acid the suppressor tRNATyr was charged and allowed translation of a green fluorescent protein whose gene contained a nonsense mutation. - T. brucei is unusual in that its mitochondrion lacks tRNA genes indicating that all its organellar tRNAs are imported from the cytosol. Expression of the bacterial tyrosyl-tRNA synthetase in our system is tetracycline-inducible. We have therefore used it to demonstrate that cytosolic aminoacylation of the suppressor tRNATyr induces its import into the mitochondrion.
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Affiliation(s)
- Jonathan L Huot
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern, CH-3012, Switzerland.
| | - Shikha Shikha
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern, CH-3012, Switzerland
| | - André Schneider
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern, CH-3012, Switzerland.
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Import of Non-Coding RNAs into Human Mitochondria: A Critical Review and Emerging Approaches. Cells 2019; 8:cells8030286. [PMID: 30917553 PMCID: PMC6468882 DOI: 10.3390/cells8030286] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 03/19/2019] [Accepted: 03/23/2019] [Indexed: 01/26/2023] Open
Abstract
Mitochondria harbor their own genetic system, yet critically depend on the import of a number of nuclear-encoded macromolecules to ensure their expression. In all eukaryotes, selected non-coding RNAs produced from the nuclear genome are partially redirected into the mitochondria, where they participate in gene expression. Therefore, the mitochondrial RNome represents an intricate mixture of the intrinsic transcriptome and the extrinsic RNA importome. In this review, we summarize and critically analyze data on the nuclear-encoded transcripts detected in human mitochondria and outline the proposed molecular mechanisms of their mitochondrial import. Special attention is given to the various experimental approaches used to study the mitochondrial RNome, including some recently developed genome-wide and in situ techniques.
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Verechshagina NA, Konstantinov YM, Kamenski PA, Mazunin IO. Import of Proteins and Nucleic Acids into Mitochondria. BIOCHEMISTRY (MOSCOW) 2018; 83:643-661. [DOI: 10.1134/s0006297918060032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Käser S, Glauser I, Rettig J, Schneider A. The pseudo-dimeric tyrosyl-tRNA synthetase of T. brucei aminoacylates cytosolic and mitochondrial tRNATyr and requires both monomeric units for activity. Mol Biochem Parasitol 2018; 221:52-55. [DOI: 10.1016/j.molbiopara.2018.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/15/2018] [Accepted: 03/21/2018] [Indexed: 12/14/2022]
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tRNAs and proteins use the same import channel for translocation across the mitochondrial outer membrane of trypanosomes. Proc Natl Acad Sci U S A 2017; 114:E7679-E7687. [PMID: 28847952 DOI: 10.1073/pnas.1711430114] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial tRNA import is widespread, but the mechanism by which tRNAs are imported remains largely unknown. The mitochondrion of the parasitic protozoan Trypanosoma brucei lacks tRNA genes, and thus imports all tRNAs from the cytosol. Here we show that in T. brucei in vivo import of tRNAs requires four subunits of the mitochondrial outer membrane protein translocase but not the two receptor subunits, one of which is essential for protein import. The latter shows that it is possible to uncouple mitochondrial tRNA import from protein import. Ablation of the intermembrane space domain of the translocase subunit, archaic translocase of the outer membrane (ATOM)14, on the other hand, while not affecting the architecture of the translocase, impedes both protein and tRNA import. A protein import intermediate arrested in the translocation channel prevents both protein and tRNA import. In the presence of tRNA, blocking events of single-channel currents through the pore formed by recombinant ATOM40 were detected in electrophysiological recordings. These results indicate that both types of macromolecules use the same import channel across the outer membrane. However, while tRNA import depends on the core subunits of the protein import translocase, it does not require the protein import receptors, indicating that the two processes are not mechanistically linked.
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Characterization of the Activities of Dinuclear Thiolato-Bridged Arene Ruthenium Complexes against Toxoplasma gondii. Antimicrob Agents Chemother 2017; 61:AAC.01031-17. [PMID: 28652238 DOI: 10.1128/aac.01031-17] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/22/2017] [Indexed: 12/13/2022] Open
Abstract
The in vitro effects of 18 dinuclear thiolato-bridged arene ruthenium complexes (1 monohiolato compound, 4 dithiolato compounds, and 13 trithiolato compounds), originally designed as anticancer agents, on the apicomplexan parasite Toxoplasma gondii grown in human foreskin fibroblast (HFF) host cells were studied. Some trithiolato compounds exhibited antiparasitic efficacy at concentrations of 250 nM and below. Among those, complex 1 and complex 2 inhibited T. gondii proliferation with 50% inhibitory concentrations (IC50s) of 34 and 62 nM, respectively, and they did not affect HFFs at dosages of 200 μM or above, resulting in selectivity indices of >23,000. The IC50s of complex 9 were 1.2 nM for T. gondii and above 5 μM for HFFs. Transmission electron microscopy detected ultrastructural alterations in the matrix of the parasite mitochondria at the early stages of treatment, followed by a more pronounced destruction of tachyzoites. However, none of the three compounds applied at 250 nM for 15 days was parasiticidal. By affinity chromatography using complex 9 coupled to epoxy-activated Sepharose followed by mass spectrometry, T. gondii translation elongation factor 1α and two ribosomal proteins, RPS18 and RPL27, were identified to be potential binding proteins. In conclusion, organometallic ruthenium complexes exhibit promising activities against Toxoplasma, and the potential mechanisms of action of these compounds as well as their prospective applications for the treatment of toxoplasmosis are discussed.
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Murcha MW, Kubiszewski-Jakubiak S, Teixeira PF, Gügel IL, Kmiec B, Narsai R, Ivanova A, Megel C, Schock A, Kraus S, Berkowitz O, Glaser E, Philippar K, Maréchal-Drouard L, Soll J, Whelan J. Plant-Specific Preprotein and Amino Acid Transporter Proteins Are Required for tRNA Import into Mitochondria. PLANT PHYSIOLOGY 2016; 172:2471-2490. [PMID: 27789739 PMCID: PMC5129730 DOI: 10.1104/pp.16.01519] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 10/25/2016] [Indexed: 05/03/2023]
Abstract
A variety of eukaryotes, in particular plants, do not contain the required number of tRNAs to support the translation of mitochondria-encoded genes and thus need to import tRNAs from the cytosol. This study identified two Arabidopsis (Arabidopsis thaliana) proteins, Tric1 and Tric2 (for tRNA import component), which on simultaneous inactivation by T-DNA insertion lines displayed a severely delayed and chlorotic growth phenotype and significantly reduced tRNA import capacity into isolated mitochondria. The predicted tRNA-binding domain of Tric1 and Tric2, a sterile-α-motif at the C-terminal end of the protein, was required to restore tRNA uptake ability in mitochondria of complemented plants. The purified predicted tRNA-binding domain binds the T-arm of the tRNA for alanine with conserved lysine residues required for binding. T-DNA inactivation of both Tric proteins further resulted in an increase in the in vitro rate of in organello protein synthesis, which was mediated by a reorganization of the nuclear transcriptome, in particular of genes encoding a variety of proteins required for mitochondrial gene expression at both the transcriptional and translational levels. The characterization of Tric1/2 provides mechanistic insight into the process of tRNA import into mitochondria and supports the theory that the tRNA import pathway resulted from the repurposing of a preexisting protein import apparatus.
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Affiliation(s)
- Monika W Murcha
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.);
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.);
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.);
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.);
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.);
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Szymon Kubiszewski-Jakubiak
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Pedro F Teixeira
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Irene L Gügel
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Beata Kmiec
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Reena Narsai
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Aneta Ivanova
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Cyrille Megel
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Annette Schock
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Sabrina Kraus
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Oliver Berkowitz
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Elzbieta Glaser
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Katrin Philippar
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Laurence Maréchal-Drouard
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Jürgen Soll
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - James Whelan
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.);
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.);
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.);
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.);
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.);
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
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Salinas-Giegé T, Giegé R, Giegé P. tRNA biology in mitochondria. Int J Mol Sci 2015; 16:4518-59. [PMID: 25734984 PMCID: PMC4394434 DOI: 10.3390/ijms16034518] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/23/2015] [Accepted: 01/29/2015] [Indexed: 01/23/2023] Open
Abstract
Mitochondria are the powerhouses of eukaryotic cells. They are considered as semi-autonomous because they have retained genomes inherited from their prokaryotic ancestor and host fully functional gene expression machineries. These organelles have attracted considerable attention because they combine bacterial-like traits with novel features that evolved in the host cell. Among them, mitochondria use many specific pathways to obtain complete and functional sets of tRNAs as required for translation. In some instances, tRNA genes have been partially or entirely transferred to the nucleus and mitochondria require precise import systems to attain their pool of tRNAs. Still, tRNA genes have also often been maintained in mitochondria. Their genetic arrangement is more diverse than previously envisaged. The expression and maturation of mitochondrial tRNAs often use specific enzymes that evolved during eukaryote history. For instance many mitochondria use a eukaryote-specific RNase P enzyme devoid of RNA. The structure itself of mitochondrial encoded tRNAs is also very diverse, as e.g., in Metazoan, where tRNAs often show non canonical or truncated structures. As a result, the translational machinery in mitochondria evolved adapted strategies to accommodate the peculiarities of these tRNAs, in particular simplified identity rules for their aminoacylation. Here, we review the specific features of tRNA biology in mitochondria from model species representing the major eukaryotic groups, with an emphasis on recent research on tRNA import, maturation and aminoacylation.
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Affiliation(s)
- Thalia Salinas-Giegé
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg Cedex, France.
| | - Richard Giegé
- Institut de Biologie Moléculaire et Cellulaire, CNRS and Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France.
| | - Philippe Giegé
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg Cedex, France.
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21
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Shetty SP, Copeland PR. Selenocysteine incorporation: A trump card in the game of mRNA decay. Biochimie 2015; 114:97-101. [PMID: 25622574 DOI: 10.1016/j.biochi.2015.01.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 01/14/2015] [Indexed: 11/16/2022]
Abstract
The incorporation of the 21st amino acid, selenocysteine (Sec), occurs on mRNAs that harbor in-frame stop codons because the Sec-tRNA(Sec) recognizes a UGA codon. This sets up an intriguing interplay between translation elongation, translation termination and the complex machinery that marks mRNAs that contain premature termination codons for degradation, leading to nonsense mediated mRNA decay (NMD). In this review we discuss the intricate and complex relationship between this key quality control mechanism and the process of Sec incorporation in mammals.
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Affiliation(s)
- Sumangala P Shetty
- Department of Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, 675 Hoes Ln, Piscataway, NJ 08854, USA
| | - Paul R Copeland
- Department of Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, 675 Hoes Ln, Piscataway, NJ 08854, USA.
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22
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Suhandono S, Apriyanto A, Ihsani N. Isolation and characterization of three cassava elongation factor 1 alpha (MeEF1A) promoters. PLoS One 2014; 9:e84692. [PMID: 24404183 PMCID: PMC3880305 DOI: 10.1371/journal.pone.0084692] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 11/25/2013] [Indexed: 11/19/2022] Open
Abstract
In plant genetic engineering, the identification of gene promoters leading to particular expression patterns is crucial for the development of new genetically modified plant generations. This research was conducted in order to isolate and characterize several new promoters from cassava (Manihot esculenta Crantz) elongation factor 1 alpha (EF1A) gene family.Three promoters MeEF1A3, MeEF1A5 and MeEF1A6 were successfully isolated [corrected]. Sequence analyses showed that all of the promoters contain three conserved putative cis-acting elements which are located upstream of the transcription start site. These elements are included a TEF1, a TELO and TATA boxes. In addition, all of the promoters also have the 5'UTR intron but with a different lengths. These promoters were constructed translationally with gusA reporter gene (promoter::gusA fusion) in pBI-121 binary vector to build a new binary vector using Overlap Extension PCR Cloning (OEPC) technique. Transient expression assay that was done by using agroinfiltration method was used to show functionality of these promoters. Qualitative and quantitative analysis from GUS assay showed that these promoters were functional and conferred a specific activity in tobacco seedlings (Nicotiana tabacum), tomato fruits (Solanum lycopersicum) and banana fruits (Musa acuminata). We hypothesized that MeEF1A6 could be categorized as a constitutive promoter because it was able to drive the gene expression in all transformed tissue described in here and also comparable to CaMV35S. On the other hand, MeEF1A3 drove specific expression in the aerial parts of seedlings such as hypocotyl and cotyledon thus MeEF1A5 drove specific expression in fruit tissue. The results obtained from transient analysis showed that these promoters had a distinct activity although they came from same gene family. The DNA sequences identified here are new promoters potentially use for genetic engineering in cassava or other plants.
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Affiliation(s)
- Sony Suhandono
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Jawa Barat, Indonesia
| | - Ardha Apriyanto
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Jawa Barat, Indonesia
| | - Nisa Ihsani
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Jawa Barat, Indonesia
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Gowher A, Smirnov A, Tarassov I, Entelis N. Induced tRNA import into human mitochondria: implication of a host aminoacyl-tRNA-synthetase. PLoS One 2013; 8:e66228. [PMID: 23799079 PMCID: PMC3683045 DOI: 10.1371/journal.pone.0066228] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 05/02/2013] [Indexed: 11/19/2022] Open
Abstract
In human cell, a subset of small non-coding RNAs is imported into mitochondria from the cytosol. Analysis of the tRNA import pathway allowing targeting of the yeast tRNA(Lys)(CUU) into human mitochondria demonstrates a similarity between the RNA import mechanisms in yeast and human cells. We show that the cytosolic precursor of human mitochondrial lysyl-tRNA synthetase (preKARS2) interacts with the yeast tRNA(Lys)(CUU) and small artificial RNAs which contain the structural elements determining the tRNA mitochondrial import, and facilitates their internalization by isolated human mitochondria. The tRNA import efficiency increased upon addition of the glycolytic enzyme enolase, previously found to be an actor of the yeast RNA import machinery. Finally, the role of preKARS2 in the RNA mitochondrial import has been directly demonstrated in vivo, in cultured human cells transfected with the yeast tRNA and artificial importable RNA molecules, in combination with preKARS2 overexpression or downregulation by RNA interference. These findings suggest that the requirement of protein factors for the RNA mitochondrial targeting might be a conserved feature of the RNA import pathway in different organisms.
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Affiliation(s)
- Ali Gowher
- Department of Molecular and Cellular Genetics, UMR 7156 Génétique Moléculaire, Génomique, Microbiologie (GMGM), CNRS - Université de Strasbourg, Strasbourg, France
| | - Alexandre Smirnov
- Department of Molecular and Cellular Genetics, UMR 7156 Génétique Moléculaire, Génomique, Microbiologie (GMGM), CNRS - Université de Strasbourg, Strasbourg, France
| | - Ivan Tarassov
- Department of Molecular and Cellular Genetics, UMR 7156 Génétique Moléculaire, Génomique, Microbiologie (GMGM), CNRS - Université de Strasbourg, Strasbourg, France
| | - Nina Entelis
- Department of Molecular and Cellular Genetics, UMR 7156 Génétique Moléculaire, Génomique, Microbiologie (GMGM), CNRS - Université de Strasbourg, Strasbourg, France
- * E-mail:
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Mittal N, Subramanian G, Bütikofer P, Madhubala R. Unique posttranslational modifications in eukaryotic translation factors and their roles in protozoan parasite viability and pathogenesis. Mol Biochem Parasitol 2013; 187:21-31. [PMID: 23201129 DOI: 10.1016/j.molbiopara.2012.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 11/04/2012] [Accepted: 11/05/2012] [Indexed: 11/21/2022]
Abstract
Protozoan parasites are one of the major causes of diseases worldwide. The vector transmitted parasites exhibit complex life cycles involving interactions between humans, protozoa, and arthropods. In order to adapt themselves to the changing microenvironments, they have to undergo complex morphological and metabolic changes. These changes can be brought about by expressing a new pool of proteins in the cell or by modifying the existing repertoire of proteins via posttranslational modifications (PTMs). PTMs involve covalent modification and processing of proteins thereby modulating their functions. Some of these changes may involve PTMs of parasite proteins to help the parasite survive within the host and the vector. Out of many PTMs known, three are unique since they occur only on single proteins: ethanolamine phosphoglycerol (EPG) glutamate, hypusine and diphthamide. These modifications occur on eukaryotic elongation factor 1A (eEF1A), eukaryotic initiation factor 5A (eIF5A) and eukaryotic elongation factor 2 (eEF2), respectively. Interestingly, the proteins carrying these unique modifications are all involved in the elongation steps of translation. Here we review these unique PTMs, which are well conserved in protozoan parasites, and discuss their roles in viability and pathogenesis of parasites. Characterization of these modifications and studying their roles in physiology as well as pathogenesis will provide new insights in parasite biology, which may also help in developing new therapeutic interventions.
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Affiliation(s)
- Nimisha Mittal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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25
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Greganova E, Bütikofer P. Ethanolamine phosphoglycerol attachment to eEF1A is not essential for normal growth of Trypanosoma brucei. Sci Rep 2012; 2:254. [PMID: 22355766 PMCID: PMC3275919 DOI: 10.1038/srep00254] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 01/24/2012] [Indexed: 12/24/2022] Open
Abstract
Eukaryotic elongation factor 1A (eEF1A) is the only protein modified by ethanolamine phosphoglycerol (EPG). In mammals and plants, EPG is attached to conserved glutamate residues located in eEF1A domains II and III, whereas in the unicellular eukaryote, Trypanosoma brucei, a single EPG moiety is attached to domain III. A biosynthetic precursor of EPG and structural requirements for EPG attachment to T. brucei eEF1A have been reported, but the role of this unique protein modification in cellular growth and eEF1A function has remained elusive. Here we report, for the first time in a eukaryotic cell, a model system to study potential roles of EPG. By down-regulation of EF1A expression and subsequent complementation of eEF1A function using conditionally expressed exogenous eEF1A (mutant) proteins, we show that eEF1A lacking EPG complements trypanosomes deficient in endogenous eEF1A, demonstrating that EPG attachment is not essential for normal growth of T. brucei in culture.
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Seidman D, Johnson D, Gerbasi V, Golden D, Orlando R, Hajduk S. Mitochondrial membrane complex that contains proteins necessary for tRNA import in Trypanosoma brucei. J Biol Chem 2012; 287:8892-903. [PMID: 22267727 DOI: 10.1074/jbc.m111.300186] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mitochondrial genome of Trypanosoma brucei does not contain genes encoding tRNAs; instead this protozoan parasite must import nuclear-encoded tRNAs from the cytosol for mitochondrial translation. Previously, it has been shown that mitochondrial tRNA import requires ATP hydrolysis and a proteinaceous mitochondrial membrane component. However, little is known about the mitochondrial membrane proteins involved in tRNA binding and translocation into the mitochondrion. Here we report the purification of a mitochondrial membrane complex using tRNA affinity purification and have identified several protein components of the putative tRNA translocon by mass spectrometry. Using an in vivo tRNA import assay in combination with RNA interference, we have verified that two of these proteins, Tb11.01.4590 and Tb09.v1.0420, are involved in mitochondrial tRNA import. Using Protein C Epitope -Tobacco Etch Virus-Protein A Epitope (PTP)-tagged Tb11.01.4590, additional associated proteins were identified including Tim17 and other mitochondrial proteins necessary for mitochondrial protein import. Results presented here identify and validate two novel protein components of the putative tRNA translocon and provide additional evidence that mitochondrial tRNA and protein import have shared components in trypanosomes.
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Affiliation(s)
- David Seidman
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602-7229, USA
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27
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Wang G, Shimada E, Koehler CM, Teitell MA. PNPASE and RNA trafficking into mitochondria. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:998-1007. [PMID: 22023881 DOI: 10.1016/j.bbagrm.2011.10.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 09/26/2011] [Accepted: 10/07/2011] [Indexed: 10/16/2022]
Abstract
The mitochondrial genome encodes a very small fraction of the macromolecular components that are required to generate functional mitochondria. Therefore, most components are encoded within the nuclear genome and are imported into mitochondria from the cytosol. Understanding how mitochondria are assembled, function, and dysfunction in diseases requires detailed knowledge of mitochondrial import mechanisms and pathways. The import of nucleus-encoded RNAs is required for mitochondrial biogenesis and function, but unlike pre-protein import, the pathways and cellular machineries of RNA import are poorly defined, especially in mammals. Recent studies have shown that mammalian polynucleotide phosphorylase (PNPASE) localizes in the mitochondrial intermembrane space (IMS) to regulate the import of RNA. The identification of PNPASE as the first component of the RNA import pathway, along with a growing list of nucleus-encoded RNAs that are imported and newly developed assay systems for RNA import studies, suggest a unique opportunity is emerging to identify the factors and mechanisms that regulate RNA import into mammalian mitochondria. Here we summarize what is known in this fascinating area of mitochondrial biogenesis, identify areas that require further investigation, and speculate on the impact unraveling RNA import mechanisms and pathways will have for the field going forward. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.
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Affiliation(s)
- Geng Wang
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA
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28
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Abstract
The mitochondrial genomes of most eukaryotes lack a variable number of tRNA genes. This lack is compensated for by import of a small fraction of the corresponding cytosolic tRNAs. There are two broad mechanisms for the import of tRNAs into mitochondria. In the first one, the tRNA is coimported together with a mitochondrial precursor protein along the protein import pathway. It applies to the yeast tRNA(Lys) and has been elucidated in great detail. In the second more vaguely defined mechanism, which is mainly found in plants and protozoa, tRNAs are directly imported independent of cytosolic factors. However, results in plants indicate that direct import of tRNAs may nevertheless require some components of the protein import machinery. All imported tRNAs in all systems are of the eukaryotic type but need to be functionally integrated into the mitochondrial translation system of bacterial descent. For some tRNAs, this is not trivial and requires unique evolutionary adaptations.
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Affiliation(s)
- André Schneider
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland.
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29
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Rubio MAT, Hopper AK. Transfer RNA travels from the cytoplasm to organelles. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:802-17. [PMID: 21976284 DOI: 10.1002/wrna.93] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Transfer RNAs (tRNAs) encoded by the nuclear genome are surprisingly dynamic. Although tRNAs function in protein synthesis occurring on cytoplasmic ribosomes, tRNAs can transit from the cytoplasm to the nucleus and then again return to the cytoplasm by a process known as the tRNA retrograde process. Subsets of the cytoplasmic tRNAs are also imported into mitochondria and function in mitochondrial protein synthesis. The numbers of tRNA species that are imported into mitochondria differ among organisms, ranging from just a few to the entire set needed to decode mitochondrially encoded mRNAs. For some tRNAs, import is dependent on the mitochondrial protein import machinery, whereas the majority of tRNA mitochondrial import is independent of this machinery. Although cytoplasmic proteins and proteins located on the mitochondrial surface participating in the tRNA import process have been described for several organisms, the identity of these proteins differ among organisms. Likewise, the tRNA determinants required for mitochondrial import differ among tRNA species and organisms. Here, we present an overview and discuss the current state of knowledge regarding the mechanisms involved in the tRNA retrograde process and continue with an overview of tRNA import into mitochondria. Finally, we highlight areas of future research to understand the function and regulation of movement of tRNAs between the cytoplasm and organelles.
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Affiliation(s)
- Mary Anne T Rubio
- Department of Microbiology and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
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30
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In vivo study in Trypanosoma brucei links mitochondrial transfer RNA import to mitochondrial protein import. EMBO Rep 2011; 12:825-32. [PMID: 21720389 DOI: 10.1038/embor.2011.111] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 04/21/2011] [Accepted: 05/16/2011] [Indexed: 11/08/2022] Open
Abstract
Trypanosoma brucei imports all mitochondrial transfer RNAs (tRNAs) from the cytosol. By using cell lines that allow independent tetracycline-inducible RNA interference and isopropyl-β-D-thiogalactopyranoside-inducible expression of a tagged tRNA, we show that ablation of Tim17 and mitochondrial heat-shock protein 70, components of the inner-membrane protein translocation machinery, strongly inhibits import of newly synthesized tRNAs. These findings, together with previous results in yeast and plants, suggest that the requirement for mitochondrial protein-import factors might be a conserved feature of mitochondrial tRNA import in all systems.
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Abstract
Covalent modifications of proteins often modulate their biological functions or change their subcellular location. Among the many known protein modifications, three are exceptional in that they only occur on single proteins: ethanolamine phosphoglycerol, diphthamide and hypusine. Remarkably, the corresponding proteins carrying these modifications, elongation factor 1A, elongation factor 2 and initiation factor 5A, are all involved in elongation steps of translation. For diphthamide and, in part, hypusine, functional essentiality has been demonstrated, whereas no functional role has been reported so far for ethanolamine phosphoglycerol. We review the biosynthesis, attachment and physiological roles of these unique protein modifications and discuss common and separate features of the target proteins, which represent essential proteins in all organisms.
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Affiliation(s)
- Eva Greganova
- Institute for Biochemistry and Molecular Medicine, University of Berne, Berne, Switzerland
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32
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Niemann M, Schneider A, Cristodero M. Mitochondrial translation in trypanosomatids: a novel target for chemotherapy? Trends Parasitol 2011; 27:429-33. [PMID: 21531629 DOI: 10.1016/j.pt.2011.03.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 03/30/2011] [Accepted: 03/31/2011] [Indexed: 01/31/2023]
Abstract
Trypanosomatids cause widespread disease in humans and animals. Treatment of many of these diseases is hampered by the lack of efficient and safe drugs. New strategies for drug development are therefore urgently needed. It has long been known that the single mitochondrion of trypanosomatids exhibits many unique features. Recently, the mitochondrial translation machinery of trypanosomatids has been the focus of several studies, which revealed interesting variations to the mammalian system. It is the aim of this article to review these unique features and to discuss them in the larger biological context. It is our opinion that some of these features represent promising novel targets for chemotherapeutic intervention that should be studied in more detail.
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Affiliation(s)
- Moritz Niemann
- Department of Chemistry and Biochemistry, University of Bern, Freiestr. 3, 3012 Bern, Switzerland.
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Mitochondrial RNA import: from diversity of natural mechanisms to potential applications. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2011; 287:145-90. [PMID: 21414588 DOI: 10.1016/b978-0-12-386043-9.00004-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mitochondria, owing to their bacterial origin, still contain their own DNA. However, the majority of bacterial genes were lost or transferred to the nuclear genome and the biogenesis of the "present-day" mitochondria mainly depends on the expression of the nuclear genome. Thus, most mitochondrial proteins and a small number of mitochondrial RNAs (mostly tRNAs) expressed from nuclear genes need to be imported into the organelle. During evolution, macromolecule import systems were universally established. The processes of protein mitochondrial import are very well described in the literature. By contrast, deciphering the mitochondrial RNA import phenomenon is still a real challenge. The purpose of this review is to present a general survey of our present knowledge in this field in different model organisms, protozoa, plants, yeast, and mammals. Questions still under debate and major challenges are discussed. Mitochondria are involved in numerous human diseases. The targeting of macromolecule to mitochondria represents a promising way to fight mitochondrial disorders and recent developments in this area of research are presented.
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Smirnov A, Comte C, Mager-Heckel AM, Addis V, Krasheninnikov IA, Martin RP, Entelis N, Tarassov I. Mitochondrial enzyme rhodanese is essential for 5 S ribosomal RNA import into human mitochondria. J Biol Chem 2010; 285:30792-803. [PMID: 20663881 DOI: 10.1074/jbc.m110.151183] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
5 S rRNA is an essential component of ribosomes. In eukaryotic cells, it is distinguished by particularly complex intracellular traffic, including nuclear export and re-import. The finding that in mammalian cells 5 S rRNA can eventually escape its usual circuit toward nascent ribosomes to get imported into mitochondria has made the scheme more complex, and it has raised questions about both the mechanism of 5 S rRNA mitochondrial targeting and its function inside the organelle. Previously, we showed that import of 5 S rRNA into mitochondria requires unknown cytosolic proteins. Here, one of them was identified as mitochondrial thiosulfate sulfurtransferase, rhodanese. Rhodanese in its misfolded form was found to possess a strong and specific 5 S rRNA binding activity, exploiting sites found earlier to function as signals of 5 S rRNA mitochondrial localization. The interaction with 5 S rRNA occurs cotranslationally and results in formation of a stable complex in which rhodanese is preserved in a compact enzymatically inactive conformation. Human 5 S rRNA in a branched Mg(2+)-free form, upon its interaction with misfolded rhodanese, demonstrates characteristic functional traits of Hsp40 cochaperones implicated in mitochondrial precursor protein targeting, suggesting that it may use this mechanism to ensure its own mitochondrial localization. Finally, silencing of the rhodanese gene caused not only a proportional decrease of 5 S rRNA import but also a general inhibition of mitochondrial translation, indicating the functional importance of the imported 5 S rRNA inside the organelle.
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Affiliation(s)
- Alexandre Smirnov
- Department of Molecular and Cellular Genetics, UMR 7156, CNRS-University of Strasbourg, Strasbourg 67084, France
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35
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Kolesnikova O, Kazakova H, Comte C, Steinberg S, Kamenski P, Martin RP, Tarassov I, Entelis N. Selection of RNA aptamers imported into yeast and human mitochondria. RNA (NEW YORK, N.Y.) 2010; 16:926-941. [PMID: 20348443 PMCID: PMC2856887 DOI: 10.1261/rna.1914110] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2009] [Accepted: 02/01/2010] [Indexed: 05/29/2023]
Abstract
In the yeast Saccharomyces cerevisiae, nuclear DNA-encoded is partially imported into mitochondria. We previously found that the synthetic transcripts of yeast tRNA(Lys) and a number of their mutant versions could be specifically internalized by isolated yeast and human mitochondria. The mitochondrial targeting of tRNA(Lys) in yeast was shown to depend on the cytosolic precursor of mitochondrial lysyl-tRNA synthetase and the glycolytic enzyme enolase. Here we applied the approach of in vitro selection (SELEX) to broaden the spectrum of importable tRNA-derived molecules. We found that RNAs selected for their import into isolated yeast mitochondria have lost the potential to acquire a classical tRNA-shape. Analysis of conformational rearrangements in the importable RNAs by in-gel fluorescence resonance energy transfer (FRET) approach permitted us to suggest that protein factor binding and subsequent import require formation of an alternative structure, different from a classic L-form tRNA model. We show that in the complex with targeting protein factor, enolase 2, tRK1 adopts a particular conformation characterized by bringing together the 3'-end and the TPsiC loop. This is a first evidence for implication of RNA secondary structure rearrangement in the mechanism of mitochondrial import selectivity. Based on these data, a set of small RNA molecules with significantly improved efficiency of import into yeast and human mitochondria was constructed, opening the possibility of creating a new mitochondrial vector system able to target therapeutic oligoribonucleotides into deficient human mitochondria.
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MESH Headings
- Aptamers, Nucleotide/chemistry
- Aptamers, Nucleotide/genetics
- Aptamers, Nucleotide/metabolism
- Base Sequence
- Biological Transport, Active
- Fluorescence Resonance Energy Transfer
- Humans
- In Vitro Techniques
- Lysine-tRNA Ligase/metabolism
- Mitochondria/metabolism
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phosphopyruvate Hydratase/metabolism
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- SELEX Aptamer Technique
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Olga Kolesnikova
- UMR 7156, Université de Strasbourg/Centre National de la Recherche Scientifique (UdS/CNRS), 67084 Strasbourg, France
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36
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Pino P, Aeby E, Foth BJ, Sheiner L, Soldati T, Schneider A, Soldati-Favre D. Mitochondrial translation in absence of local tRNA aminoacylation and methionyl tRNA Met formylation in Apicomplexa. Mol Microbiol 2010; 76:706-18. [PMID: 20374492 DOI: 10.1111/j.1365-2958.2010.07128.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Apicomplexans possess three translationally active compartments: the cytosol, a single tubular mitochondrion, and a vestigial plastid organelle called apicoplast. Mitochondrion and apicoplast are of bacterial evolutionary origin and therefore depend on a bacterial-like translation machinery. The minimal mitochondrial genome contains only three ORFs, and in Toxoplasma gondii the absence of mitochondrial tRNA genes is compensated for by the import of cytosolic eukaryotic tRNAs. Although all compartments require a complete set of charged tRNAs, the apicomplexan nuclear genomes do not hold sufficient aminoacyl-tRNA synthetase (aaRSs) genes to be targeted individually to each compartment. This study reveals that aaRSs are either cytosolic, apicoplastic or shared between the two compartments by dual targeting but are absent from the mitochondrion. Consequently, tRNAs are very likely imported in their aminoacylated form. Furthermore, the unexpected absence of tRNA(Met) formyltransferase and peptide deformylase implies that the requirement for a specialized formylmethionyl-tRNA(Met) for translation initiation is bypassed in the mitochondrion of Apicomplexa.
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Affiliation(s)
- Paco Pino
- Department of Microbiology and Molecular Medicine, CMU, University of Geneva, 1 rue Michel-Servet, 1211 Geneva 4, Switzerland
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Lithgow T, Schneider A. Evolution of macromolecular import pathways in mitochondria, hydrogenosomes and mitosomes. Philos Trans R Soc Lond B Biol Sci 2010; 365:799-817. [PMID: 20124346 PMCID: PMC2817224 DOI: 10.1098/rstb.2009.0167] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
All eukaryotes require mitochondria for survival and growth. The origin of mitochondria can be traced down to a single endosymbiotic event between two probably prokaryotic organisms. Subsequent evolution has left mitochondria a collection of heterogeneous organelle variants. Most of these variants have retained their own genome and translation system. In hydrogenosomes and mitosomes, however, the entire genome was lost. All types of mitochondria import most of their proteome from the cytosol, irrespective of whether they have a genome or not. Moreover, in most eukaryotes, a variable number of tRNAs that are required for mitochondrial translation are also imported. Thus, import of macromolecules, both proteins and tRNA, is essential for mitochondrial biogenesis. Here, we review what is known about the evolutionary history of the two processes using a recently revised eukaryotic phylogeny as a framework. We discuss how the processes of protein import and tRNA import relate to each other in an evolutionary context.
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Affiliation(s)
- Trevor Lithgow
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Australia
| | - André Schneider
- Department of Chemistry and Biochemistry, University of Bern, Freiestr. 3, CH-3012 Bern, Switzerland
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A structural domain mediates attachment of ethanolamine phosphoglycerol to eukaryotic elongation factor 1A in Trypanosoma brucei. PLoS One 2010; 5:e9486. [PMID: 20209157 PMCID: PMC2830473 DOI: 10.1371/journal.pone.0009486] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Accepted: 02/10/2010] [Indexed: 11/19/2022] Open
Abstract
Ethanolamine phosphoglycerol (EPG) represents a protein modification that so far has only been found in eukaryotic elongation factor 1A (eEF1A). In mammals and plants, EPG is covalently attached to two conserved glutamate residues located in domains II and III of eEF1A. In contrast, Trypanosoma brucei eEF1A contains a single EPG attached to Glu362 in domain III. The sequence and/or structural requirements for covalent linkage of EPG to eEF1A have not been determined for any organism. Using a combination of biosynthetic labelling of parasites with tritiated ethanolamine and mass spectrometry analyses, we demonstrate that replacement of Glu362 in T. brucei eEF1A by site-directed mutagenesis prevents EPG attachment, whereas single or multiple amino acid substitutions around the attachment site are not critical. In addition, by expressing a series of eEF1A deletion mutants in T. brucei procyclic forms, we demonstrate that a peptide consisting of 80 amino acids of domain III of eEF1A is sufficient for EPG attachment to occur. Furthermore, EPG addition also occurs if domain III of eEF1A is fused to a soluble reporter protein. To our knowledge, this is the first report addressing amino acid sequence, or structure, requirements for EPG modification of eEF1A in any organism. Using T. brucei as a model organism, we show that amino acid substitutions around the modification site are not critical for EPG attachment and that a truncated version of domain III of eEF1A is sufficient to mediate EPG addition.
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Alfonzo JD, Söll D. Mitochondrial tRNA import--the challenge to understand has just begun. Biol Chem 2009; 390:717-22. [PMID: 19558325 DOI: 10.1515/bc.2009.101] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Mitochondrial translation is important for the synthesis of proteins involved in oxidative phosphorylation, which yields the bulk of the ATP made in cells. During evolution most mitochondria-containing organisms have lost tRNA genes from their mitochondrial genomes. Thus, to support the essential process of nuanced mitochondrial translation, mechanisms to actively transport tRNAs from the cytoplasm across the mitochondrial membranes into the mitochondrion have evolved. Here, we review the currently known tRNA import mechanisms, comment on recent discoveries of various import factors, and suggest a rationale for forces that lie behind the evolution of mitochondrial tRNA import.
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Affiliation(s)
- Juan D Alfonzo
- Department of Microbiology, Ohio State University Biochemistry Program and The Center for RNA Biology, The Ohio State University, Columbus, OH 43210-1292, USA.
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Bruske EI, Sendfeld F, Schneider A. Thiolated tRNAs of Trypanosoma brucei are imported into mitochondria and dethiolated after import. J Biol Chem 2009; 284:36491-36499. [PMID: 19875444 DOI: 10.1074/jbc.m109.064527] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
All mitochondrial tRNAs in Trypanosoma brucei derive from cytosolic tRNAs that are in part imported into mitochondria. Some trypanosomal tRNAs are thiolated in a compartment-specific manner. We have identified three proteins required for the thio modification of cytosolic tRNA(Gln), tRNA(Glu), and tRNA(Lys). RNA interference-mediated ablation of these proteins results in the cytosolic accumulation non-thio-modified tRNAs but does not increase their import. Moreover, in vitro import experiments showed that both thio-modified and non-thio-modified tRNA(Glu) can efficiently be imported into mitochondria. These results indicate that unlike previously suggested the cytosol-specific thio modifications do not function as antideterminants for mitochondrial tRNA import. Consistent with these results we showed by using inducible expression of a tagged tRNA(Glu) that it is mainly the thiolated form that is imported in vivo. Unexpectedly, the imported tRNA becomes dethiolated after import, which explains why the non-thiolated form is enriched in mitochondria. Finally, we have identified two genes required for thiolation of imported tRNA(Trp) whose wobble nucleotide is subject to mitochondrial C to U editing. Interestingly, down-regulation of thiolation resulted in an increase of edited tRNA(Trp) but did not affect growth.
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Affiliation(s)
- Ellen Inga Bruske
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Franziska Sendfeld
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - André Schneider
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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Paris Z, Rubio MAT, Lukes J, Alfonzo JD. Mitochondrial tRNA import in Trypanosoma brucei is independent of thiolation and the Rieske protein. RNA (NEW YORK, N.Y.) 2009; 15:1398-1406. [PMID: 19465685 PMCID: PMC2704085 DOI: 10.1261/rna.1589109] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Accepted: 04/13/2009] [Indexed: 05/27/2023]
Abstract
Due to a complete lack of the tRNA genes in the mitochondrial genome of Trypanosoma brucei, all tRNAs needed for mitochondrial translation have to be imported into the organelle from the cytosol. A previous study showed that the modified nucleotide s(2)U could act as a negative determinant for mitochondrial tRNA import in another kinetoplastid, Leishmania tarentolae. We have investigated whether the same type of cytosolic control for tRNA retention exists in T. brucei. Based on Northern analysis with subcellular RNA fractions and in vitro import assays, we demonstrate that silencing of the cysteine desulfurase, TbNfs (TbIscS), the key enzyme in tRNA thiolation (s(2)U) and Fe-S cluster formation in vivo, has no effect on tRNA partitioning. This observation is especially surprising in light of a recent report suggesting that in L. tropica the Rieske Fe-S protein is an essential component of the RNA import complex (RIC). In line with the above observation, we also show that down-regulation of the Rieske protein by RNA interference, similar to the TbNfs knockdowns, has no effect on import. The data presented here supports the view that in T. brucei: (1) s(2)U is not a negative determinant for tRNA import; (2) the Rieske protein is not an essential component of the import machinery, and (3) since the Rieske protein is essential for respiration and maintenance of inner mitochondrial membrane potential, neither process plays a critical role in tRNA import. We therefore suggest that the T. brucei import machinery differs substantially from what has been described in Leishmania.
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Affiliation(s)
- Zdenek Paris
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 37005 Ceské Budejovice (Budweis), Czech Republic
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Cascades of convergent evolution: the corresponding evolutionary histories of euglenozoans and dinoflagellates. Proc Natl Acad Sci U S A 2009; 106 Suppl 1:9963-70. [PMID: 19528647 DOI: 10.1073/pnas.0901004106] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The majority of eukaryotic diversity is hidden in protists, yet our current knowledge of processes and structures in the eukaryotic cell is almost exclusively derived from multicellular organisms. The increasing sensitivity of molecular methods and growing interest in microeukaryotes has only recently demonstrated that many features so far considered to be universal for eukaryotes actually exist in strikingly different versions. In other words, during their long evolutionary histories, protists have solved general biological problems in many more ways than previously appreciated. Interestingly, some groups have broken more rules than others, and the Euglenozoa and the Alveolata stand out in this respect. A review of the numerous odd features in these 2 groups allows us to draw attention to the high level of convergent evolution in protists, which perhaps reflects the limits that certain features can be altered. Moreover, the appearance of one deviation in an ancestor can constrain the set of possible downstream deviations in its descendents, so features that might be independent functionally, can still be evolutionarily linked. What functional advantage may be conferred by the excessive complexity of euglenozoan and alveolate gene expression, organellar genome structure, and RNA editing and processing has been thoroughly debated, but we suggest these are more likely the products of constructive neutral evolution, and as such do not necessarily confer any selective advantage at all.
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The canonical pathway for selenocysteine insertion is dispensable in Trypanosomes. Proc Natl Acad Sci U S A 2009; 106:5088-92. [PMID: 19279205 DOI: 10.1073/pnas.0901575106] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The micronutrient selenium is found in proteins as selenocysteine (Sec), the 21st amino acid cotranslationally inserted in response to a UGA codon. In vitro studies in archaea and mouse showed that Sec-tRNA(Sec) formation is a 3-step process starting with serylation of tRNA(Sec) by seryl-tRNA synthetase (SerRS), phosphorylation of serine to form phosphoserine (Sep)-tRNA(Sec) by phosphoseryl-tRNA(Sec) kinase (PSTK), and conversion to Sec-tRNA(Sec) by Sep-tRNA:Sec-tRNA synthase (SepSecS). However, a complete study of eukaryotic selenoprotein synthesis has been lacking. Here, we present an analysis of Sec-tRNA(Sec) formation in the parasitic protozoon Trypanosoma brucei in vivo. Null mutants of either PSTK or SepSecS abolished selenoprotein synthesis, demonstrating the essentiality of both enzymes for Sec-tRNA(Sec) formation. Growth of the 2 knockout strains was not impaired; thus, unlike mammals, trypanosomes do not require selenoproteins for viability. Analysis of conditional RNAi strains showed that SerRS, selenophosphate synthase, and the Sec-specific elongation factor, EFSec, are also essential for selenoprotein synthesis. These results with T. brucei imply that eukaryotes have a single pathway of Sec-tRNA(Sec) synthesis that requires Sep-tRNA(Sec) as an intermediate.
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Pusnik M, Charrière F, Mäser P, Waller RF, Dagley MJ, Lithgow T, Schneider A. The single mitochondrial porin of Trypanosoma brucei is the main metabolite transporter in the outer mitochondrial membrane. Mol Biol Evol 2008; 26:671-80. [PMID: 19091722 DOI: 10.1093/molbev/msn288] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
All mitochondria have integral outer membrane proteins with beta-barrel structures including the conserved metabolite transporter VDAC (voltage dependent anion channel) and the conserved protein import channel Tom40. Bioinformatic searches of the Trypanosoma brucei genome for either VDAC or Tom40 identified a single open reading frame, with sequence analysis suggesting that VDACs and Tom40s are ancestrally related and should be grouped into the same protein family: the mitochondrial porins. The single T. brucei mitochondrial porin is essential only under growth conditions that depend on oxidative phosphorylation. Mitochondria isolated from homozygous knockout cells did not produce adenosine-triphosphate (ATP) in response to added substrates, but ATP production was restored by physical disruption of the outer membrane. These results demonstrate that the mitochondrial porin identified in T. brucei is the main metabolite channel in the outer membrane and therefore the functional orthologue of VDAC. No distinct Tom40 was identified in T. brucei. In addition to mitochondrial proteins, T. brucei imports all mitochondrial tRNAs from the cytosol. Isolated mitochondria from the VDAC knockout cells import tRNA as efficiently as wild-type. Thus, unlike the scenario in plants, VDAC is not required for mitochondrial tRNA import in T. brucei.
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Affiliation(s)
- Mascha Pusnik
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
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Duchêne AM, Pujol C, Maréchal-Drouard L. Import of tRNAs and aminoacyl-tRNA synthetases into mitochondria. Curr Genet 2008; 55:1-18. [PMID: 19083240 DOI: 10.1007/s00294-008-0223-9] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Revised: 11/21/2008] [Accepted: 11/24/2008] [Indexed: 12/13/2022]
Abstract
During evolution, most of the bacterial genes from the ancestral endosymbiotic alpha-proteobacteria at the origin of mitochondria have been either lost or transferred to the nuclear genome. A crucial evolutionary step was the establishment of macromolecule import systems to allow the come back of proteins and RNAs into the organelle. Paradoxically, the few mitochondria-encoded protein genes remain essential and must be translated by a mitochondrial translation machinery mainly constituted by nucleus-encoded components. Two crucial partners of the mitochondrial translation machinery are the aminoacyl-tRNA synthetases and the tRNAs. All mitochondrial aminoacyl-tRNA synthetases and many tRNAs are imported from the cytosol into the mitochondria in eukaryotic cells. During the last few years, their origin and their import into the organelle have been studied in evolutionary distinct organisms and we review here what is known in this field.
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Affiliation(s)
- Anne-Marie Duchêne
- Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche du CNRS, Associated with Louis Pasteur University, 12 rue du Général Zimmer, 67084, Strasbourg Cedex, France.
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Regmi S, Rothberg KG, Hubbard JG, Ruben L. The RACK1 signal anchor protein from Trypanosoma brucei associates with eukaryotic elongation factor 1A: a role for translational control in cytokinesis. Mol Microbiol 2008; 70:724-45. [PMID: 18786142 PMCID: PMC2581647 DOI: 10.1111/j.1365-2958.2008.06443.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
RACK1 is a WD-repeat protein that forms signal complexes at appropriate locations in the cell. RACK1 homologues are core components of ribosomes from yeast, plants and mammals. In contrast, a cryo-EM analysis of trypanosome ribosomes failed to detect RACK1, thus eliminating an important translational regulatory mechanism. Here we report that TbRACK1 from Trypanosoma brucei associates with eukaryotic translation elongation factor-1a (eEF1A) as determined by tandem MS of TAP-TbRACK1 affinity eluates, co-sedimentation in a sucrose gradient, and co-precipitation assays. Consistent with these observations, sucrose gradient purified 80S monosomes and translating polysomes each contained TbRACK1. When RNAi was used to deplete cells of TbRACK1, a shift in the polysome profile was observed, while the phosphorylation of a ribosomal protein increased. Under these conditions, cell growth became hypersensitive to the translational inhibitor anisomycin. The kinetoplasts and nuclei were misaligned in the postmitotic cells, resulting in partial cleavage furrow ingression during cytokinesis. Overall, these findings identify eEF1A as a novel TbRACK1 binding partner and establish TbRACK1 as a component of the trypanosome translational apparatus. The synergy between anisomycin and TbRACK1 RNAi suggests that continued translation is required for complete ingression of the cleavage furrow.
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Affiliation(s)
- Sandesh Regmi
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275, USA
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Home P, Mukherjee S, Adhya S. A mosaic of RNA binding and protein interaction motifs in a bifunctional mitochondrial tRNA import factor from Leishmania tropica. Nucleic Acids Res 2008; 36:5552-61. [PMID: 18755708 PMCID: PMC2553583 DOI: 10.1093/nar/gkn536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Proteins that participate in the import of cytosolic tRNAs into mitochondria have been identified in several eukaryotic species, but the details of their interactions with tRNA and other proteins are unknown. In the kinetoplastid protozoon Leishmania tropica, multiple proteins are organized into a functional import complex. RIC8A, a tRNA-binding subunit of this complex, has a C-terminal domain that functions as subunit 6b of ubiquinol cytochrome c reductase (complex III). We show that the N-terminal domain, unique to kinetoplastid protozoa, is structurally similar to the appended S15/NS1 RNA-binding domain of aminoacyl tRNA synthetases, with a helix–turn–helix motif. Structure-guided mutagenesis coupled with in vitro assays showed that helix α1 contacts tRNA whereas helix α2 targets the protein for assembly into the import complex. Inducible expression of a helix 1-deleted variant in L. tropica resulted in formation of an inactive import complex, while the helix 2-deleted variant was unable to assemble in vivo. Moreover, a protein-interaction assay showed that the C-terminal domain makes allosteric contacts with import receptor RIC1 complexed with tRNA. These results help explain the origin of the bifunctionality of RIC8A, and the allosteric changes accompanying docking and release of tRNA during import.
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Affiliation(s)
- Pratik Home
- Genetic Engineering Laboratory, Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
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Salinas T, Duchêne AM, Maréchal-Drouard L. Recent advances in tRNA mitochondrial import. Trends Biochem Sci 2008; 33:320-9. [DOI: 10.1016/j.tibs.2008.04.010] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 04/22/2008] [Accepted: 04/22/2008] [Indexed: 02/02/2023]
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Signorell A, Jelk J, Rauch M, Bütikofer P. Phosphatidylethanolamine is the precursor of the ethanolamine phosphoglycerol moiety bound to eukaryotic elongation factor 1A. J Biol Chem 2008; 283:20320-9. [PMID: 18499667 DOI: 10.1074/jbc.m802430200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In addition to its conventional role during protein synthesis, eukaryotic elongation factor 1A is involved in other cellular processes. Several regions of interaction between eukaryotic elongation factor 1A and the translational apparatus or the cytoskeleton have been identified, yet the roles of the different post-translational modifications of eukaryotic elongation factor 1A are completely unknown. One amino acid modification, which so far has only been found in eukaryotic elongation factor 1A, consists of ethanolamine-phosphoglycerol attached to two glutamate residues that are conserved between mammals and plants. We now report that ethanolamine-phosphoglycerol is also present in eukaryotic elongation factor 1A of the protozoan parasite Trypanosoma brucei, indicating that this unique protein modification is of ancient origin. In addition, using RNA-mediated gene silencing against enzymes of the Kennedy pathway, we demonstrate that phosphatidylethanolamine is a direct precursor of the ethanolamine-phosphoglycerol moiety. Down-regulation of the expression of ethanolamine kinase and ethanolamine-phosphate cytidylyltransferase results in inhibition of phosphatidylethanolamine synthesis in T. brucei procyclic forms and, concomitantly, in a block in glycosylphosphatidylinositol attachment to procyclins and ethanolamine-phosphoglycerol modification of eukaryotic elongation factor 1A.
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Affiliation(s)
- Aita Signorell
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
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Basu S, Mukherjee S, Adhya S. Proton-guided movements of tRNA within the Leishmania mitochondrial RNA import complex. Nucleic Acids Res 2008; 36:1599-609. [PMID: 18250088 PMCID: PMC2275131 DOI: 10.1093/nar/gkn010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The RNA import complex (RIC) from the mitochondrion of the kinetoplastid protozoan Leishmania tropica contains two subunits that directly bind to import signals on two distinct subsets of tRNA and interact with each other allosterically. What happens to the tRNA subsequent to its loading on the complex is unknown. A third subunit-RIC9-has intrinsic affinity for both types of tRNA and is essential for import in vivo. Here we show that antibody against RIC9 inhibited the import of both types of tRNA into mitoplasts in vitro, but failed to inhibit the binding of these tRNAs to their respective receptors, indicating that RIC9 acts in a subsequent step. Using photoaffinity crosslinking-immunoprecipitation to detect translocation intermediates, it was observed that tRNA was transferred from its cognate receptor to RIC9, followed by translocation across the membrane and release as free tRNA in the inner compartment. Transfer required elevated temperatures and ATP, but ATP was substituted by acid pH. These tRNA movements were sensitive to uncouplers and inhibitors, suggesting distinct roles of the electrical and chemical components of the proton motive force generated by vectorial proton translocation accompanying ATP hydrolysis. By analysis of partially assembled complexes in L. tropica depleted of various subunits, and in vitro assembly assays, RIC9 was shown to make stable contacts with RIC8A, a tRNA receptor and RIC6, a membrane-embedded component. The results have implications for the mechanism of tRNA import.
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Affiliation(s)
- Sudarshana Basu
- Genetic Engineering Laboratory, Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Calcutta 700 032, India
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