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Horáková E, Vrbacký M, Tesařová M, Stříbrná E, Pilný J, Vavrušková Z, Vancová M, Sobotka R, Lukeš J, Perner J. Haptoglobin is dispensable for haemoglobin uptake by Trypanosoma brucei. Front Immunol 2024; 15:1441131. [PMID: 39114668 PMCID: PMC11304504 DOI: 10.3389/fimmu.2024.1441131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 06/19/2024] [Indexed: 08/10/2024] Open
Abstract
Haptoglobin is a plasma protein of mammals that plays a crucial role in vascular homeostasis by binding free haemoglobin released from ruptured red blood cells. Trypanosoma brucei can exploit this by internalising haptoglobin-haemoglobin complex to acquire host haem. Here, we investigated the impact of haptoglobin deficiency (Hp-/-) on T. brucei brucei infection and the parasite´s capacity to internalise haemoglobin in a Hp-/- mouse model. The infected Hp-/- mice exhibited normal disease progression, with minimal weight loss and no apparent organ pathology, similarly to control mice. While the proteomic profile of mouse sera significantly changed in response to T. b. brucei, no differences in the infection response markers of blood plasma between Hp-/- and control Black mice were observed. Similarly, very few quantitative differences were observed between the proteomes of parasites harvested from Hp-/- and Black mice, including both endogenous proteins and internalised host proteins. While haptoglobin was indeed absent from parasites isolated from Hp-/-mice, haemoglobin peptides were unexpectedly detected in parasites from both Hp-/- and Black mice. Combined, the data support the dispensability of haptoglobin for haemoglobin internalisation by T. b. brucei during infection in mice. Since the trypanosomes knock-outs for their haptoglobin-haemoglobin receptor (HpHbR) internalised significantly less haemoglobin from Hp-/- mice compared to those isolated from Black mice, it suggests that T. b. brucei employs also an HpHbR-independent haptoglobin-mediated mode for haemoglobin internalisation. Our study reveals a so-far hidden flexibility of haemoglobin acquisition by T. b. brucei and offers novel insights into alternative haemoglobin uptake pathways.
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Affiliation(s)
- Eva Horáková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Třeboň, Czechia
| | - Marek Vrbacký
- Institute of Physiology, Czech Academy of Sciences, Prague, Czechia
| | - Martina Tesařová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Eva Stříbrná
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Jan Pilný
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Třeboň, Czechia
| | - Zuzana Vavrušková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Marie Vancová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Roman Sobotka
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Třeboň, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Jan Perner
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
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He Z, Wu M, Tian H, Wang L, Hu Y, Han F, Zhou J, Wang Y, Zhou L. Euglena's atypical respiratory chain adapts to the discoidal cristae and flexible metabolism. Nat Commun 2024; 15:1628. [PMID: 38388527 PMCID: PMC10884005 DOI: 10.1038/s41467-024-46018-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/09/2024] [Indexed: 02/24/2024] Open
Abstract
Euglena gracilis, a model organism of the eukaryotic supergroup Discoba harbouring also clinically important parasitic species, possesses diverse metabolic strategies and an atypical electron transport chain. While structures of the electron transport chain complexes and supercomplexes of most other eukaryotic clades have been reported, no similar structure is currently available for Discoba, limiting the understandings of its core metabolism and leaving a gap in the evolutionary tree of eukaryotic bioenergetics. Here, we report high-resolution cryo-EM structures of Euglena's respirasome I + III2 + IV and supercomplex III2 + IV2. A previously unreported fatty acid synthesis domain locates on the tip of complex I's peripheral arm, providing a clear picture of its atypical subunit composition identified previously. Individual complexes are re-arranged in the respirasome to adapt to the non-uniform membrane curvature of the discoidal cristae. Furthermore, Euglena's conformationally rigid complex I is deactivated by restricting ubiquinone's access to its substrate tunnel. Our findings provide structural insights for therapeutic developments against euglenozoan parasite infections.
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Affiliation(s)
- Zhaoxiang He
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Mengchen Wu
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Hongtao Tian
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Liangdong Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yiqi Hu
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Fangzhu Han
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Jiancang Zhou
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China.
| | - Yong Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, 314400, China.
| | - Long Zhou
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
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Opperdoes FR, Záhonová K, Škodová-Sveráková I, Bučková B, Chmelová Ľ, Lukeš J, Yurchenko V. In silico prediction of the metabolism of Blastocrithidia nonstop, a trypanosomatid with non-canonical genetic code. BMC Genomics 2024; 25:184. [PMID: 38365628 PMCID: PMC10874023 DOI: 10.1186/s12864-024-10094-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Almost all extant organisms use the same, so-called canonical, genetic code with departures from it being very rare. Even more exceptional are the instances when a eukaryote with non-canonical code can be easily cultivated and has its whole genome and transcriptome sequenced. This is the case of Blastocrithidia nonstop, a trypanosomatid flagellate that reassigned all three stop codons to encode amino acids. RESULTS We in silico predicted the metabolism of B. nonstop and compared it with that of the well-studied human parasites Trypanosoma brucei and Leishmania major. The mapped mitochondrial, glycosomal and cytosolic metabolism contains all typical features of these diverse and important parasites. We also provided experimental validation for some of the predicted observations, concerning, specifically presence of glycosomes, cellular respiration, and assembly of the respiratory complexes. CONCLUSIONS In an unusual comparison of metabolism between a parasitic protist with a massively altered genetic code and its close relatives that rely on a canonical code we showed that the dramatic differences on the level of nucleic acids do not seem to be reflected in the metabolisms. Moreover, although the genome of B. nonstop is extremely AT-rich, we could not find any alterations of its pyrimidine synthesis pathway when compared to other trypanosomatids. Hence, we conclude that the dramatic alteration of the genetic code of B. nonstop has no significant repercussions on the metabolism of this flagellate.
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Affiliation(s)
- Fred R Opperdoes
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Kristína Záhonová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada
| | - Ingrid Škodová-Sveráková
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Barbora Bučková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Ľubomíra Chmelová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia.
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Prokopchuk G, Butenko A, Dacks JB, Speijer D, Field MC, Lukeš J. Lessons from the deep: mechanisms behind diversification of eukaryotic protein complexes. Biol Rev Camb Philos Soc 2023; 98:1910-1927. [PMID: 37336550 PMCID: PMC10952624 DOI: 10.1111/brv.12988] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 05/30/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
Genetic variation is the major mechanism behind adaptation and evolutionary change. As most proteins operate through interactions with other proteins, changes in protein complex composition and subunit sequence provide potentially new functions. Comparative genomics can reveal expansions, losses and sequence divergence within protein-coding genes, but in silico analysis cannot detect subunit substitutions or replacements of entire protein complexes. Insights into these fundamental evolutionary processes require broad and extensive comparative analyses, from both in silico and experimental evidence. Here, we combine data from both approaches and consider the gamut of possible protein complex compositional changes that arise during evolution, citing examples of complete conservation to partial and total replacement by functional analogues. We focus in part on complexes in trypanosomes as they represent one of the better studied non-animal/non-fungal lineages, but extend insights across the eukaryotes by extensive comparative genomic analysis. We argue that gene loss plays an important role in diversification of protein complexes and hence enhancement of eukaryotic diversity.
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Affiliation(s)
- Galina Prokopchuk
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- Faculty of ScienceUniversity of South BohemiaBranišovská 1160/31České Budějovice37005Czech Republic
| | - Anzhelika Butenko
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- Faculty of ScienceUniversity of South BohemiaBranišovská 1160/31České Budějovice37005Czech Republic
- Life Science Research Centre, Faculty of ScienceUniversity of OstravaChittussiho 983/10Ostrava71000Czech Republic
| | - Joel B. Dacks
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- Division of Infectious Diseases, Department of MedicineUniversity of Alberta1‐124 Clinical Sciences Building, 11350‐83 AvenueEdmontonT6G 2R3AlbertaCanada
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and the EnvironmentUniversity College LondonDarwin Building, Gower StreetLondonWC1E 6BTUK
| | - Dave Speijer
- Medical Biochemistry, Amsterdam UMCUniversity of AmsterdamMeibergdreef 15Amsterdam1105 AZThe Netherlands
| | - Mark C. Field
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- School of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- Faculty of ScienceUniversity of South BohemiaBranišovská 1160/31České Budějovice37005Czech Republic
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Das A, Liu T, Li H, Husain S. The RNA-binding protein RBP42 regulates cellular energy metabolism in mammalian-infective Trypanosoma brucei. mSphere 2023; 8:e0027323. [PMID: 37581443 PMCID: PMC10654194 DOI: 10.1128/msphere.00273-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/05/2023] [Indexed: 08/16/2023] Open
Abstract
RNA-binding proteins (RBPs) are key players in coordinated post-transcriptional regulation of functionally related genes, defined as RNA regulons. RNA regulons play particularly critical roles in parasitic trypanosomes, which exhibit unregulated co-transcription of long unrelated gene arrays. In this report, we present a systematic analysis of an essential RBP, RBP42, in the mammalian-infective bloodstream form of African trypanosome and show that RBP42 is a key regulator of parasite's central carbon and energy metabolism. Using individual-nucleotide resolution UV cross-linking and immunoprecipitation to identify genome-wide RBP42-RNA interactions, we show that RBP42 preferentially binds within the coding region of mRNAs encoding core metabolic enzymes. Global quantitative transcriptomic and proteomic analyses reveal that loss of RBP42 reduces the abundance of target mRNA-encoded proteins, but not target mRNA, suggesting a positive translational regulatory role of RBP42. Significant changes in central carbon metabolic intermediates, following loss of RBP42, further support its critical role in cellular energy metabolism. Trypanosoma brucei infection, transmitted through the bite of blood-feeding tsetse flies, causes deadly diseases in humans and livestock. This disease, if left untreated, is almost always fatal. Existing therapies are toxic and difficult to administer. During T. brucei's lifecycle in two different host environments, the parasite progresses through distinctive life stages with major morphological and metabolic changes, requiring precise alteration of parasite gene expression program. In the absence of regulated transcription, post-transcriptional processes mediated by RNA-binding proteins play critical roles in T. brucei gene regulation. In this study, we show that the RNA-binding protein RBP42 plays crucial roles in cellular energy metabolic regulation of this important human pathogen. Metabolic dysregulation observed in RBP42 knockdown cells offers a breadth of potential interest to researchers studying parasite biology and can also impact research in general eukaryotic biology.
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Affiliation(s)
- Anish Das
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - Tong Liu
- Center for Advanced Proteomics Research, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - Hong Li
- Center for Advanced Proteomics Research, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - Seema Husain
- Genomics Center, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
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6
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Pyrih J, Hammond M, Alves A, Dean S, Sunter JD, Wheeler RJ, Gull K, Lukeš J. Comprehensive sub-mitochondrial protein map of the parasitic protist Trypanosoma brucei defines critical features of organellar biology. Cell Rep 2023; 42:113083. [PMID: 37669165 DOI: 10.1016/j.celrep.2023.113083] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 06/30/2023] [Accepted: 08/17/2023] [Indexed: 09/07/2023] Open
Abstract
We have generated a high-confidence mitochondrial proteome (MitoTag) of the Trypanosoma brucei procyclic stage containing 1,239 proteins. For 337 of these, a mitochondrial localization had not been described before. We use the TrypTag dataset as a foundation and take advantage of the properties of the fluorescent protein tag that causes aberrant but fortuitous accumulation of tagged matrix and inner membrane proteins near the kinetoplast (mitochondrial DNA). Combined with transmembrane domain predictions, this characteristic allowed categorization of 1,053 proteins into mitochondrial sub-compartments, the detection of unique matrix-localized fucose and methionine synthesis, and the identification of new kinetoplast proteins, which showed kinetoplast-linked pyrimidine synthesis. Moreover, disruption of targeting signals by tagging allowed mapping of the mode of protein targeting to these sub-compartments, identifying a set of C-tail anchored outer mitochondrial membrane proteins and mitochondrial carriers likely employing multiple target peptides. This dataset represents a comprehensive, updated mapping of the mitochondrion.
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Affiliation(s)
- Jan Pyrih
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Department of Biochemistry, University of Cambridge, Cambridge, UK; Faculty of Science, University of Ostrava, Ostrava, Czech Republic.
| | - Michael Hammond
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | | | - Samuel Dean
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | | | - Richard John Wheeler
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Keith Gull
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic.
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Jamabo M, Bentley SJ, Macucule-Tinga P, Tembo P, Edkins AL, Boshoff A. In silico analysis of the HSP90 chaperone system from the African trypanosome, Trypanosoma brucei. Front Mol Biosci 2022; 9:947078. [PMID: 36213128 PMCID: PMC9538636 DOI: 10.3389/fmolb.2022.947078] [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] [Received: 05/18/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
African trypanosomiasis is a neglected tropical disease caused by Trypanosoma brucei (T. brucei) and spread by the tsetse fly in sub-Saharan Africa. The trypanosome relies on heat shock proteins for survival in the insect vector and mammalian host. Heat shock protein 90 (HSP90) plays a crucial role in the stress response at the cellular level. Inhibition of its interactions with chaperones and co-chaperones is being explored as a potential therapeutic target for numerous diseases. This study provides an in silico overview of HSP90 and its co-chaperones in both T. brucei brucei and T. brucei gambiense in relation to human and other trypanosomal species, including non-parasitic Bodo saltans and the insect infecting Crithidia fasciculata. A structural analysis of T. brucei HSP90 revealed differences in the orientation of the linker and C-terminal domain in comparison to human HSP90. Phylogenetic analysis displayed the T. brucei HSP90 proteins clustering into three distinct groups based on subcellular localizations, namely, cytosol, mitochondria, and endoplasmic reticulum. Syntenic analysis of cytosolic HSP90 genes revealed that T. b. brucei encoded for 10 tandem copies, while T. b. gambiense encoded for three tandem copies; Leishmania major (L. major) had the highest gene copy number with 17 tandem copies. The updated information on HSP90 from recently published proteomics on T. brucei was examined for different life cycle stages and subcellular localizations. The results show a difference between T. b. brucei and T. b. gambiense with T. b. brucei encoding a total of twelve putative HSP90 genes, while T. b. gambiense encodes five HSP90 genes. Eighteen putative co-chaperones were identified with one notable absence being cell division cycle 37 (Cdc37). These results provide an updated framework on approaching HSP90 and its interactions as drug targets in the African trypanosome.
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Affiliation(s)
- Miebaka Jamabo
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, South Africa
| | | | | | - Praise Tembo
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, South Africa
| | - Adrienne Lesley Edkins
- Department of Biochemistry and Microbiology, Biomedical Biotechnology Research Unit (BioBRU), Rhodes University, Grahamstown, South Africa
| | - Aileen Boshoff
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, South Africa
- *Correspondence: Aileen Boshoff,
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Valach M, Gonzalez Alcazar JA, Sarrasin M, Lang BF, Gray MW, Burger G. An Unexpectedly Complex Mitoribosome in Andalucia godoyi, a Protist with the Most Bacteria-like Mitochondrial Genome. Mol Biol Evol 2021; 38:788-804. [PMID: 32886790 PMCID: PMC7947838 DOI: 10.1093/molbev/msaa223] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The mitoribosome, as known from studies in model organisms, deviates considerably from its ancestor, the bacterial ribosome. Deviations include substantial reduction of the mitochondrial ribosomal RNA (mt-rRNA) structure and acquisition of numerous mitochondrion-specific (M) mitoribosomal proteins (mtRPs). A broadly accepted view assumes that M-mtRPs compensate for structural destabilization of mt-rRNA resulting from its evolutionary remodeling. Since most experimental information on mitoribosome makeup comes from eukaryotes having derived mitochondrial genomes and mt-rRNAs, we tested this assumption by investigating the mitochondrial translation machinery of jakobids, a lineage of unicellular protists with the most bacteria-like mitochondrial genomes. We report here proteomics analyses of the Andalucia godoyi small mitoribosomal subunit and in silico transcriptomic and comparative genome analyses of four additional jakobids. Jakobids have mt-rRNA structures that minimally differ from their bacterial counterparts. Yet, with at least 31 small subunit and 44 large subunit mtRPs, the mitoriboproteome of Andalucia is essentially as complex as that in animals or fungi. Furthermore, the relatively high conservation of jakobid sequences has helped to clarify the identity of several mtRPs, previously considered to be lineage-specific, as divergent homologs of conserved M-mtRPs, notably mS22 and mL61. The coexistence of bacteria-like mt-rRNAs and a complex mitoriboproteome refutes the view that M-mtRPs were ancestrally recruited to stabilize deviations of mt-rRNA structural elements. We postulate instead that the numerous M-mtRPs acquired in the last eukaryotic common ancestor allowed mt-rRNAs to pursue a broad range of evolutionary trajectories across lineages: from dramatic reduction to acquisition of novel elements to structural conservatism.
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Affiliation(s)
- Matus Valach
- Department of Biochemistry and Molecular Medicine, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - José Angel Gonzalez Alcazar
- Department of Biochemistry and Molecular Medicine, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - Matt Sarrasin
- Department of Biochemistry and Molecular Medicine, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - B Franz Lang
- Department of Biochemistry and Molecular Medicine, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - Michael W Gray
- Department of Biochemistry and Molecular Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Gertraud Burger
- Department of Biochemistry and Molecular Medicine, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
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9
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Hierro-Yap C, Šubrtová K, Gahura O, Panicucci B, Dewar C, Chinopoulos C, Schnaufer A, Zíková A. Bioenergetic consequences of F oF 1-ATP synthase/ATPase deficiency in two life cycle stages of Trypanosoma brucei. J Biol Chem 2021; 296:100357. [PMID: 33539923 PMCID: PMC7949148 DOI: 10.1016/j.jbc.2021.100357] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/23/2020] [Accepted: 01/28/2021] [Indexed: 12/17/2022] Open
Abstract
Mitochondrial ATP synthase is a reversible nanomotor synthesizing or hydrolyzing ATP depending on the potential across the membrane in which it is embedded. In the unicellular parasite Trypanosoma brucei, the direction of the complex depends on the life cycle stage of this digenetic parasite: in the midgut of the tsetse fly vector (procyclic form), the FoF1–ATP synthase generates ATP by oxidative phosphorylation, whereas in the mammalian bloodstream form, this complex hydrolyzes ATP and maintains mitochondrial membrane potential (ΔΨm). The trypanosome FoF1–ATP synthase contains numerous lineage-specific subunits whose roles remain unknown. Here, we seek to elucidate the function of the lineage-specific protein Tb1, the largest membrane-bound subunit. In procyclic form cells, Tb1 silencing resulted in a decrease of FoF1–ATP synthase monomers and dimers, rerouting of mitochondrial electron transfer to the alternative oxidase, reduced growth rate and cellular ATP levels, and elevated ΔΨm and total cellular reactive oxygen species levels. In bloodstream form parasites, RNAi silencing of Tb1 by ∼90% resulted in decreased FoF1–ATPase monomers and dimers, but it had no apparent effect on growth. The same findings were obtained by silencing of the oligomycin sensitivity-conferring protein, a conserved subunit in T. brucei FoF1–ATP synthase. However, as expected, nearly complete Tb1 or oligomycin sensitivity-conferring protein suppression was lethal because of the inability to sustain ΔΨm. The diminishment of FoF1–ATPase complexes was further accompanied by a decreased ADP/ATP ratio and reduced oxygen consumption via the alternative oxidase. Our data illuminate the often diametrically opposed bioenergetic consequences of FoF1–ATP synthase loss in insect versus mammalian forms of the parasite.
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Affiliation(s)
- Carolina Hierro-Yap
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Karolína Šubrtová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Institute of Immunology and Infection Research, University of Edinburgh, United Kingdom
| | - Ondřej Gahura
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Brian Panicucci
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Caroline Dewar
- Institute of Immunology and Infection Research, University of Edinburgh, United Kingdom
| | | | - Achim Schnaufer
- Institute of Immunology and Infection Research, University of Edinburgh, United Kingdom
| | - Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic.
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10
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Opperdoes FR, Butenko A, Zakharova A, Gerasimov ES, Zimmer SL, Lukeš J, Yurchenko V. The Remarkable Metabolism of Vickermania ingenoplastis: Genomic Predictions. Pathogens 2021; 10:68. [PMID: 33466586 PMCID: PMC7828693 DOI: 10.3390/pathogens10010068] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/08/2021] [Accepted: 01/12/2021] [Indexed: 11/16/2022] Open
Abstract
A recently redescribed two-flagellar trypanosomatid Vickermania ingenoplastis is insensitive to the classical inhibitors of respiration and thrives under anaerobic conditions. Using genomic and transcriptomic data, we analyzed its genes of the core metabolism and documented that subunits of the mitochondrial respiratory complexes III and IV are ablated, while those of complexes I, II, and V are all present, along with an alternative oxidase. This explains the previously reported conversion of glucose to acetate and succinate by aerobic fermentation. Glycolytic pyruvate is metabolized to acetate and ethanol by pyruvate dismutation, whereby a unique type of alcohol dehydrogenase (shared only with Phytomonas spp.) processes an excess of reducing equivalents formed under anaerobic conditions, leading to the formation of ethanol. Succinate (formed to maintain the glycosomal redox balance) is converted to propionate by a cyclic process involving three enzymes of the mitochondrial methyl-malonyl-CoA pathway, via a cyclic process, which results in the formation of additional ATP. The unusual structure of the V. ingenoplastis genome and its similarity with that of Phytomonas spp. imply their relatedness or convergent evolution. Nevertheless, a critical difference between these two trypanosomatids is that the former has significantly increased its genome size by gene duplications, while the latter streamlined its genome.
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Affiliation(s)
- Fred R. Opperdoes
- De Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Anzhelika Butenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (A.B.); (A.Z.)
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic;
| | - Alexandra Zakharova
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (A.B.); (A.Z.)
| | - Evgeny S. Gerasimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119435 Moscow, Russia
| | - Sara L. Zimmer
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, Duluth, MN 558812, USA;
| | - Julius Lukeš
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic;
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice (Budweis), Czech Republic
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (A.B.); (A.Z.)
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119435 Moscow, Russia
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11
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Abstract
Complex I (NADH dehydrogenase) is the first enzyme in the respiratory chain. It catalyses the electron transfer from NADH to ubiquinone that is associated with proton pumping out of the matrix. In this study, we characterized NADH dehydrogenase activity in seven monoxenous trypanosomatid species: Blechomonas ayalai, Herpetomonas tarakana, Kentomonas sorsogonicus, Leptomonas seymouri, Novymonas esmeraldas, Sergeia podlipaevi and Wallacemonas raviniae. We also investigated the subunit composition of the complex I in dixenous Phytomonas serpens, in which its presence and activity have been previously documented. In addition to P. serpens, the complex I is functionally active in N. esmeraldas and S. podlipaevi. We also identified 24-32 subunits of the complex I in individual species by using mass spectrometry. Among them, for the first time, we recognized several proteins of the mitochondrial DNA origin.
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12
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Smith Jr. JT, Doleželová E, Tylec B, Bard JE, Chen R, Sun Y, Zíková A, Read LK. Developmental regulation of edited CYb and COIII mitochondrial mRNAs is achieved by distinct mechanisms in Trypanosoma brucei. Nucleic Acids Res 2020; 48:8704-8723. [PMID: 32738044 PMCID: PMC7470970 DOI: 10.1093/nar/gkaa641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 01/01/2023] Open
Abstract
Trypanosoma brucei is a parasitic protozoan that undergoes a complex life cycle involving insect and mammalian hosts that present dramatically different nutritional environments. Mitochondrial metabolism and gene expression are highly regulated to accommodate these environmental changes, including regulation of mRNAs that require extensive uridine insertion/deletion (U-indel) editing for their maturation. Here, we use high throughput sequencing and a method for promoting life cycle changes in vitro to assess the mechanisms and timing of developmentally regulated edited mRNA expression. We show that edited CYb mRNA is downregulated in mammalian bloodstream forms (BSF) at the level of editing initiation and/or edited mRNA stability. In contrast, edited COIII mRNAs are depleted in BSF by inhibition of editing progression. We identify cell line-specific differences in the mechanisms abrogating COIII mRNA editing, including the possible utilization of terminator gRNAs that preclude the 3' to 5' progression of editing. By examining the developmental timing of altered mitochondrial mRNA levels, we also reveal transcript-specific developmental checkpoints in epimastigote (EMF), metacyclic (MCF), and BSF. These studies represent the first analysis of the mechanisms governing edited mRNA levels during T. brucei development and the first to interrogate U-indel editing in EMF and MCF life cycle stages.
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Affiliation(s)
- Joseph T Smith Jr.
- Department of Microbiology and Immunology, University at Buffalo – Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Eva Doleželová
- Institute of Parasitology, Biology Centre Czech Academy of Science, České Budejovice, Czech Republic
| | - Brianna Tylec
- Department of Microbiology and Immunology, University at Buffalo – Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Jonathan E Bard
- Genomics and Bioinformatics Core, University at Buffalo, Buffalo, NY 14203, USA
| | - Runpu Chen
- Department of Computer Science and Engineering, University at Buffalo, Buffalo, NY 14260, USA
| | - Yijun Sun
- Department of Microbiology and Immunology, University at Buffalo – Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Alena Zíková
- Institute of Parasitology, Biology Centre Czech Academy of Science, České Budejovice, Czech Republic
| | - Laurie K Read
- Department of Microbiology and Immunology, University at Buffalo – Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
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13
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Pyrih J, Rašková V, Škodová-Sveráková I, Pánek T, Lukeš J. ZapE/Afg1 interacts with Oxa1 and its depletion causes a multifaceted phenotype. PLoS One 2020; 15:e0234918. [PMID: 32579605 PMCID: PMC7314023 DOI: 10.1371/journal.pone.0234918] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 06/04/2020] [Indexed: 11/19/2022] Open
Abstract
ZapE/Afg1 is a component of the inner cell membrane of some eubacteria and the inner mitochondrial membrane of eukaryotes. This protein is involved in FtsZ-dependent division of eubacteria. In the yeast and human mitochondrion, ZapE/Afg1 likely interacts with Oxa1 and facilitates the degradation of mitochondrion-encoded subunits of respiratory complexes. Furthermore, the depletion of ZapE increases resistance to apoptosis, decreases oxidative stress tolerance, and impacts mitochondrial protein homeostasis. It remains unclear whether ZapE is a multifunctional protein, or whether some of the described effects are just secondary phenotypes. Here, we have analyzed the functions of ZapE in Trypanosoma brucei, a parasitic protist, and an important model organism. Using a newly developed proximity-dependent biotinylation approach (BioID2), we have identified the inner mitochondrial membrane insertase Oxa1 among three putative interacting partners of ZapE, which is present in two paralogs. RNAi-mediated depletion of both ZapE paralogs likely affected the function of respiratory complexes I and IV. Consistently, we show that the distribution of mitochondrial ZapE is restricted only to organisms with Oxa1, respiratory complexes, and a mitochondrial genome. We propose that the evolutionarily conserved interaction of ZapE with Oxa1, which is required for proper insertion of many inner mitochondrial membrane proteins, is behind the multifaceted phenotype caused by the ablation of ZapE.
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Affiliation(s)
- Jan Pyrih
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- * E-mail: (JL); (JP)
| | - Vendula Rašková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Ingrid Škodová-Sveráková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, Comenius University, Bratislava, Slovakia
| | - Tomáš Pánek
- Faculty of Sciences, University of Ostrava, Ostrava, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic
- * E-mail: (JL); (JP)
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14
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Doleželová E, Kunzová M, Dejung M, Levin M, Panicucci B, Regnault C, Janzen CJ, Barrett MP, Butter F, Zíková A. Cell-based and multi-omics profiling reveals dynamic metabolic repurposing of mitochondria to drive developmental progression of Trypanosoma brucei. PLoS Biol 2020; 18:e3000741. [PMID: 32520929 PMCID: PMC7307792 DOI: 10.1371/journal.pbio.3000741] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 06/22/2020] [Accepted: 05/27/2020] [Indexed: 12/23/2022] Open
Abstract
Mitochondrial metabolic remodeling is a hallmark of the Trypanosoma brucei digenetic life cycle because the insect stage utilizes a cost-effective oxidative phosphorylation (OxPhos) to generate ATP, while bloodstream cells switch to aerobic glycolysis. Due to difficulties in acquiring enough parasites from the tsetse fly vector, the dynamics of the parasite's metabolic rewiring in the vector have remained obscure. Here, we took advantage of in vitro-induced differentiation to follow changes at the RNA, protein, and metabolite levels. This multi-omics and cell-based profiling showed an immediate redirection of electron flow from the cytochrome-mediated pathway to an alternative oxidase (AOX), an increase in proline consumption, elevated activity of complex II, and certain tricarboxylic acid (TCA) cycle enzymes, which led to mitochondrial membrane hyperpolarization and increased reactive oxygen species (ROS) levels. Interestingly, these ROS molecules appear to act as signaling molecules driving developmental progression because ectopic expression of catalase, a ROS scavenger, halted the in vitro-induced differentiation. Our results provide insights into the mechanisms of the parasite's mitochondrial rewiring and reinforce the emerging concept that mitochondria act as signaling organelles through release of ROS to drive cellular differentiation.
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Affiliation(s)
- Eva Doleželová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Michaela Kunzová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Mario Dejung
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Michal Levin
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Brian Panicucci
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Clément Regnault
- Welcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Christian J. Janzen
- Welcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Michael P. Barrett
- Department of Cell and Developmental Biology, Biocenter, University Wuerzburg, Wuerzburg, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
- * E-mail:
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15
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Luévano-Martínez LA, Girard RMBM, Alencar MB, Silber AM. ATP regulates the activity of an alternative oxidase in Trypanosoma brucei. FEBS Lett 2020; 594:2150-2158. [PMID: 32279308 DOI: 10.1002/1873-3468.13790] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 02/05/2023]
Abstract
The reduced mitochondrial respiratory chain from the bloodstream forms of Trypanosoma brucei is composed of only a membrane-bound glycerol-3-phosphate dehydrogenase and an alternative oxidase. Since these enzymes are not proton pumps, their functions are restricted to the maintenance of the redox balance in the glycosome by means of the dihydroxyacetone phosphate/glycerol-3-phosphate shuttle. Additionally, an F1 Fo -ATP synthase functions as an ATP-hydrolysing enzyme to establish the proton motive force necessary to maintain the basic functions of mitochondria. In this report, we studied the interplay between the alternative oxidase and ATP synthase, and we found that, in addition to its role as a proton pump, ATP synthase contributes to maintain safe levels of ATP to prevent the inhibition of the alternative oxidase by ATP.
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Affiliation(s)
- Luis Alberto Luévano-Martínez
- Laboratory of Biochemistry of Tryps - LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil
| | - Richard M B M Girard
- Laboratory of Biochemistry of Tryps - LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil
| | - Mayke Bezerra Alencar
- Laboratory of Biochemistry of Tryps - LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil
| | - Ariel Mariano Silber
- Laboratory of Biochemistry of Tryps - LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil
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16
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Butenko A, Opperdoes FR, Flegontova O, Horák A, Hampl V, Keeling P, Gawryluk RMR, Tikhonenkov D, Flegontov P, Lukeš J. Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids. BMC Biol 2020; 18:23. [PMID: 32122335 PMCID: PMC7052976 DOI: 10.1186/s12915-020-0754-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/17/2020] [Indexed: 12/24/2022] Open
Abstract
Background The Euglenozoa are a protist group with an especially rich history of evolutionary diversity. They include diplonemids, representing arguably the most species-rich clade of marine planktonic eukaryotes; trypanosomatids, which are notorious parasites of medical and veterinary importance; and free-living euglenids. These different lifestyles, and particularly the transition from free-living to parasitic, likely require different metabolic capabilities. We carried out a comparative genomic analysis across euglenozoan diversity to see how changing repertoires of enzymes and structural features correspond to major changes in lifestyles. Results We find a gradual loss of genes encoding enzymes in the evolution of kinetoplastids, rather than a sudden decrease in metabolic capabilities corresponding to the origin of parasitism, while diplonemids and euglenids maintain more metabolic versatility. Distinctive characteristics of molecular machines such as kinetochores and the pre-replication complex that were previously considered specific to parasitic kinetoplastids were also identified in their free-living relatives. Therefore, we argue that they represent an ancestral rather than a derived state, as thought until the present. We also found evidence of ancient redundancy in systems such as NADPH-dependent thiol-redox. Only the genus Euglena possesses the combination of trypanothione-, glutathione-, and thioredoxin-based systems supposedly present in the euglenozoan common ancestor, while other representatives of the phylum have lost one or two of these systems. Lastly, we identified convergent losses of specific metabolic capabilities between free-living kinetoplastids and ciliates. Although this observation requires further examination, it suggests that certain eukaryotic lineages are predisposed to such convergent losses of key enzymes or whole pathways. Conclusions The loss of metabolic capabilities might not be associated with the switch to parasitic lifestyle in kinetoplastids, and the presence of a highly divergent (or unconventional) kinetochore machinery might not be restricted to this protist group. The data derived from the transcriptomes of free-living early branching prokinetoplastids suggests that the pre-replication complex of Trypanosomatidae is a highly divergent version of the conventional machinery. Our findings shed light on trends in the evolution of metabolism in protists in general and open multiple avenues for future research.
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Affiliation(s)
- Anzhelika Butenko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Fred R Opperdoes
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Olga Flegontova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Vladimír Hampl
- Faculty of Science, Charles University, Biocev, Vestec, Czech Republic
| | - Patrick Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada
| | | | - Denis Tikhonenkov
- Department of Botany, University of British Columbia, Vancouver, Canada.,Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia
| | - Pavel Flegontov
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic. .,Faculty of Science, University of Ostrava, Ostrava, Czech Republic. .,Present address: Department of Genetics, Harvard Medical School, Boston, USA.
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic. .,Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic.
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17
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Schädeli D, Serricchio M, Ben Hamidane H, Loffreda A, Hemphill A, Beneke T, Gluenz E, Graumann J, Bütikofer P. Cardiolipin depletion–induced changes in theTrypanosoma bruceiproteome. FASEB J 2019; 33:13161-13175. [DOI: 10.1096/fj.201901184rr] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- David Schädeli
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Mauro Serricchio
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | | | - Alessio Loffreda
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Andrew Hemphill
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Tom Beneke
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Eva Gluenz
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | | | - Peter Bütikofer
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
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18
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Trenaman A, Glover L, Hutchinson S, Horn D. A post-transcriptional respiratome regulon in trypanosomes. Nucleic Acids Res 2019; 47:7063-7077. [PMID: 31127277 PMCID: PMC6648352 DOI: 10.1093/nar/gkz455] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/25/2019] [Accepted: 05/10/2019] [Indexed: 12/21/2022] Open
Abstract
Post-transcriptional regulons coordinate the expression of groups of genes in eukaryotic cells, yet relatively few have been characterized. Parasitic trypanosomatids are particularly good models for studies on such mechanisms because they exhibit almost exclusive polycistronic, and unregulated, transcription. Here, we identify the Trypanosoma brucei ZC3H39/40 RNA-binding proteins as regulators of the respiratome; the mitochondrial electron transport chain (complexes I-IV) and the FoF1-ATP synthase (complex V). A high-throughput RNAi screen initially implicated both ZC3H proteins in variant surface glycoprotein (VSG) gene silencing. This link was confirmed and both proteins were shown to form a cytoplasmic ZC3H39/40 complex. Transcriptome and mRNA-interactome analyses indicated that the impact on VSG silencing was indirect, while the ZC3H39/40 complex specifically bound and stabilized transcripts encoding respiratome-complexes. Quantitative proteomic analyses revealed specific positive control of >20 components from complexes I, II and V. Our findings establish a link between the mitochondrial respiratome and VSG gene silencing in bloodstream form T. brucei. They also reveal a major respiratome regulon controlled by the conserved trypanosomatid ZC3H39/40 RNA-binding proteins.
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Affiliation(s)
- Anna Trenaman
- The Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Lucy Glover
- The Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Sebastian Hutchinson
- The Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - David Horn
- The Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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19
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Bentley SJ, Jamabo M, Boshoff A. The Hsp70/J-protein machinery of the African trypanosome, Trypanosoma brucei. Cell Stress Chaperones 2019; 24:125-148. [PMID: 30506377 PMCID: PMC6363631 DOI: 10.1007/s12192-018-0950-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 11/06/2018] [Accepted: 11/12/2018] [Indexed: 12/28/2022] Open
Abstract
The etiological agent of the neglected tropical disease African trypanosomiasis, Trypanosoma brucei, possesses an expanded and diverse repertoire of heat shock proteins, which have been implicated in cytoprotection, differentiation, as well as progression and transmission of the disease. Hsp70 plays a crucial role in proteostasis, and inhibition of its interactions with co-chaperones is emerging as a potential therapeutic target for numerous diseases. In light of genome annotations and the release of the genome sequence of the human infective subspecies, an updated and current in silico overview of the Hsp70/J-protein machinery in both T. brucei brucei and T. brucei gambiense was conducted. Functional, structural, and evolutionary analyses of the T. brucei Hsp70 and J-protein families were performed. The Hsp70 and J-proteins from humans and selected kinetoplastid parasites were used to assist in identifying proteins from T. brucei, as well as the prediction of potential Hsp70-J-protein partnerships. The Hsp70 and J-proteins were mined from numerous genome-wide proteomics studies, which included different lifecycle stages and subcellular localisations. In this study, 12 putative Hsp70 proteins and 67 putative J-proteins were identified to be encoded on the genomes of both T. brucei subspecies. Interestingly there are 6 type III J-proteins that possess tetratricopeptide repeat-containing (TPR) motifs. Overall, it is envisioned that the results of this study will provide a future context for studying the biology of the African trypanosome and evaluating Hsp70 and J-protein interactions as potential drug targets.
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Affiliation(s)
| | - Miebaka Jamabo
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, South Africa
| | - Aileen Boshoff
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, South Africa.
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20
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Valach M, Léveillé-Kunst A, Gray MW, Burger G. Respiratory chain Complex I of unparalleled divergence in diplonemids. J Biol Chem 2018; 293:16043-16056. [PMID: 30166340 DOI: 10.1074/jbc.ra118.005326] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial genes of Euglenozoa (Kinetoplastida, Diplonemea, and Euglenida) are notorious for being barely recognizable, raising the question of whether such divergent genes actually code for functional proteins. Here we demonstrate the translation and identify the function of five previously unassigned y genes encoded by mitochondrial DNA (mtDNA) of diplonemids. As is the rule in diplonemid mitochondria, y genes are fragmented, with gene pieces transcribed separately and then trans-spliced to form contiguous mRNAs. Further, y transcripts undergo massive RNA editing, including uridine insertions that generate up to 16-residue-long phenylalanine tracts, a feature otherwise absent from conserved mitochondrial proteins. By protein sequence analyses, MS, and enzymatic assays in Diplonema papillatum, we show that these y genes encode the subunits Nad2, -3, -4L, -6, and -9 of the respiratory chain Complex I (CI; NADH:ubiquinone oxidoreductase). The few conserved residues of these proteins are essentially those involved in proton pumping across the inner mitochondrial membrane and in coupling ubiquinone reduction to proton pumping (Nad2, -3, -4L, and -6) and in interactions with subunits containing electron-transporting Fe-S clusters (Nad9). Thus, in diplonemids, 10 CI subunits are mtDNA-encoded. Further, MS of D. papillatum CI allowed identification of 26 conventional and 15 putative diplonemid-specific nucleus-encoded components. Most conventional accessory subunits are well-conserved but unusually long, possibly compensating for the streamlined mtDNA-encoded components and for missing, otherwise widely distributed, conventional subunits. Finally, D. papillatum CI predominantly exists as a supercomplex I:III:IV that is exceptionally stable, making this protist an organism of choice for structural studies.
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Affiliation(s)
- Matus Valach
- From the Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec H3T 1J4, Canada and
| | - Alexandra Léveillé-Kunst
- From the Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec H3T 1J4, Canada and
| | - Michael W Gray
- the Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Gertraud Burger
- From the Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec H3T 1J4, Canada and
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Miranda-Astudillo HV, Yadav KNS, Colina-Tenorio L, Bouillenne F, Degand H, Morsomme P, Boekema EJ, Cardol P. The atypical subunit composition of respiratory complexes I and IV is associated with original extra structural domains in Euglena gracilis. Sci Rep 2018; 8:9698. [PMID: 29946152 PMCID: PMC6018760 DOI: 10.1038/s41598-018-28039-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 06/14/2018] [Indexed: 11/10/2022] Open
Abstract
In mitochondrial oxidative phosphorylation, electron transfer from NADH or succinate to oxygen by a series of large protein complexes in the inner mitochondrial membrane (complexes I-IV) is coupled to the generation of an electrochemical proton gradient, the energy of which is utilized by complex V to generate ATP. In Euglena gracilis, a non-parasitic secondary green alga related to trypanosomes, these respiratory complexes totalize more than 40 Euglenozoa-specific subunits along with about 50 classical subunits described in other eukaryotes. In the present study the Euglena proton-pumping complexes I, III, and IV were purified from isolated mitochondria by a two-steps liquid chromatography approach. Their atypical subunit composition was further resolved and confirmed using a three-steps PAGE analysis coupled to mass spectrometry identification of peptides. The purified complexes were also observed by electron microscopy followed by single-particle analysis. Even if the overall structures of the three oxidases are similar to the structure of canonical enzymes (e.g. from mammals), additional atypical domains were observed in complexes I and IV: an extra domain located at the tip of the peripheral arm of complex I and a "helmet-like" domain on the top of the cytochrome c binding region in complex IV.
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Affiliation(s)
- H V Miranda-Astudillo
- Laboratoire de Génétique et Physiologie des microalgues, InBioS/Phytosystems, Institut de Botanique, Université de Liège, Liege, Belgium
| | - K N S Yadav
- Department of Electron Microscopy, Groningen Biological Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - L Colina-Tenorio
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico, Mexico
| | - F Bouillenne
- InBioS/Center for Protein Engineering, Université de Liège, Liege, Belgium
| | - H Degand
- Institut des Sciences de la Vie, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - P Morsomme
- Institut des Sciences de la Vie, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - E J Boekema
- Department of Electron Microscopy, Groningen Biological Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - P Cardol
- Laboratoire de Génétique et Physiologie des microalgues, InBioS/Phytosystems, Institut de Botanique, Université de Liège, Liege, Belgium.
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Divergent Small Tim Homologues Are Associated with TbTim17 and Critical for the Biogenesis of TbTim17 Protein Complexes in Trypanosoma brucei. mSphere 2018; 3:3/3/e00204-18. [PMID: 29925672 PMCID: PMC6010621 DOI: 10.1128/msphere.00204-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/27/2018] [Indexed: 12/18/2022] Open
Abstract
The small Tim proteins belong to a group of mitochondrial intermembrane space chaperones that aid in the import of mitochondrial inner membrane proteins with internal targeting signals. Trypanosoma brucei, the protozoan parasite that causes African trypanosomiasis, possesses multiple small Tim proteins that include homologues of T. brucei Tim9 (TbTim9) and Tim10 (TbTim10) and a unique small Tim that shares homology with both Tim8 and Tim13 (TbTim8/13). Here, we found that these three small TbTims are expressed as soluble mitochondrial intermembrane space proteins. Coimmunoprecipitation and mass spectrometry analysis showed that the small TbTims stably associated with each other and with TbTim17, the major component of the mitochondrial inner membrane translocase in T. brucei Yeast two-hybrid analysis indicated direct interactions among the small TbTims; however, their interaction patterns appeared to be different from those of their counterparts in yeast and humans. Knockdown of the small TbTims reduced cell growth and decreased the steady-state level of TbTim17 and T. brucei ADP/ATP carrier (TbAAC), two polytopic mitochondrial inner membrane proteins. Knockdown of small TbTims also reduced the matured complexes of TbTim17 in mitochondria. Depletion of any of the small TbTims reduced TbTim17 import moderately but greatly hampered the stability of the TbTim17 complexes in T. brucei Altogether, our results revealed that TbTim9, TbTim10, and TbTim8/13 interact with each other, associate with TbTim17, and play a crucial role in the integrity and maintenance of the levels of TbTim17 complexes.IMPORTANCETrypanosoma brucei is the causative agent of African sleeping sickness. The parasite's mitochondrion represents a useful source for potential chemotherapeutic targets. Similarly to yeast and humans, mitochondrial functions depend on the import of proteins that are encoded in the nucleus and made in the cytosol. Even though the machinery involved in this mitochondrial protein import process is becoming clearer in T. brucei, a comprehensive picture of protein complex composition and function is still lacking. In this study, we characterized three T. brucei small Tim proteins, TbTim9, TbTim10, and TbTim8/13. Although the parasite does not have the classical TIM22 complex that imports mitochondrial inner membrane proteins containing internal targeting signals in yeast or humans, we found that these small TbTims associate with TbTim17, the major subunit of the TbTIM complex in T. brucei, and play an essential role in the stability of the TbTim17 complexes. Therefore, these divergent proteins are critical for mitochondrial protein biogenesis in T. brucei.
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Zimmer SL, Simpson RM, Read LK. High throughput sequencing revolution reveals conserved fundamentals of U-indel editing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1487. [PMID: 29888550 DOI: 10.1002/wrna.1487] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/26/2018] [Accepted: 04/30/2018] [Indexed: 01/18/2023]
Abstract
Among Euglenozoans, mitochondrial RNA editing occurs in the diplonemids and in the kinetoplastids that include parasitic trypanosomes. Yet U-indel editing, in which open reading frames (ORFs) on mRNAs are generated by insertion and deletion of uridylates in locations dictated by guide RNAs, appears confined to kinetoplastids. The nature of guide RNA and edited mRNA populations has been cursorily explored in a surprisingly extensive number of species over the years, although complete sets of fully edited mRNAs for most kinetoplast genomes are largely missing. Now, however, high throughput sequencing technologies have had an enormous impact on what we know and will learn about the mechanisms, benefits, and final edited products of U-indel editing. Tools including PARERS, TREAT, and T-Aligner function to organize and make sense of U-indel mRNA transcriptomes, which are comprised of mRNAs harboring uridylate indels both consistent and inconsistent with translatable products. From high throughput sequencing data come arguments that partially edited mRNAs containing "junction regions" of noncanonical editing are editing intermediates, and conversely, arguments that they are dead-end products. These data have also revealed that the percent of a given transcript population that is fully or partially edited varies dramatically between transcripts and organisms. Outstanding questions that are being addressed include the prevalence of sequences that apparently encode alternative ORFs, diversity of editing events in ORF termini and 5' and 3' untranslated regions, and the differences that exist in this byzantine process between species. High throughput sequencing technologies will also undoubtedly be harnessed to probe U-indel editing's evolutionary origins. This article is categorized under: RNA Processing > RNA Editing and Modification RNA Evolution and Genomics > Computational Analyses of RNA.
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Affiliation(s)
- Sara L Zimmer
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, Minnesota
| | - Rachel M Simpson
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Laurie K Read
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
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Kalem MC, Gerasimov ES, Vu PK, Zimmer SL. Gene expression to mitochondrial metabolism: Variability among cultured Trypanosoma cruzi strains. PLoS One 2018; 13:e0197983. [PMID: 29847594 PMCID: PMC5976161 DOI: 10.1371/journal.pone.0197983] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/11/2018] [Indexed: 11/18/2022] Open
Abstract
The insect-transmitted protozoan parasite Trypanosoma cruzi experiences changes in nutrient availability and rate of flux through different metabolic pathways across its life cycle. The species encompasses much genetic diversity of both the nuclear and mitochondrial genomes among isolated strains. The genetic or expression variation of both genomes are likely to impact metabolic responses to environmental stimuli, and even steady state metabolic function, among strains. To begin formal characterization these differences, we compared aspects of metabolism between genetically similar strains CL Brener and Tulahuen with less similar Esmeraldo and Sylvio X10 strains in a culture environment. Epimastigotes of all strains took up glucose at similar rates. However, the degree of medium acidification that could be observed when glucose was absent from the medium varied by strain, indicating potential differences in excreted metabolic byproducts. Our main focus was differences related to electron transport chain function. We observed differences in ATP-coupled respiration and maximal respiratory capacity, mitochondrial membrane potential, and mitochondrial morphology between strains, despite the fact that abundances of two nuclear-encoded proteins of the electron transport chain are similar between strains. RNA sequencing reveals strain-specific differences in abundances of mRNAs encoding proteins of the respiratory chain but also other metabolic processes. From these differences in metabolism and mitochondrial phenotypes we have generated tentative models for the differential metabolic fluxes or differences in gene expression that may underlie these results.
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Affiliation(s)
- Murat C. Kalem
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota, United States of America
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth campus, Duluth, Minnesota, United States of America
| | | | - Pamela K. Vu
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota, United States of America
| | - Sara L. Zimmer
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth campus, Duluth, Minnesota, United States of America
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Abstract
Sleeping sickness is a neglected tropical disease caused by Trypanosoma brucei parasites, affecting the poorest communities in sub-Saharan Africa. The great efforts done by the scientific community, local governments, and non-governmental organizations (NGOs) via active patients' screening, vector control, and introduction of improved treatment regimens have significantly contributed to the reduction of human African trypanosomiasis (HAT) incidence during the last 15 years. Consequently, the WHO has announced the objective of HAT elimination as a public health problem by 2020. Studies at both parasite and host levels have improved our understanding of the parasite biology and the mechanisms of parasite interaction with its mammalian host. In this review, the impact that 'omics studies have had on sleeping sickness by revealing novel properties of parasite's subcellular organelles are summarized, by highlighting changes induced in the host during the infection and by proposing potential disease markers and therapeutic targets.
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Affiliation(s)
- Natalia Tiberti
- Translational Biomarker Group, University of Geneva, Geneva, Switzerland
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Zíková A, Verner Z, Nenarokova A, Michels PAM, Lukeš J. A paradigm shift: The mitoproteomes of procyclic and bloodstream Trypanosoma brucei are comparably complex. PLoS Pathog 2017; 13:e1006679. [PMID: 29267392 PMCID: PMC5739487 DOI: 10.1371/journal.ppat.1006679] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- * E-mail:
| | - Zdeněk Verner
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Sciences, Charles University, Prague, Czech Republic
| | - Anna Nenarokova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Paul A. M. Michels
- Centre for Immunity, Infection and Evolution, The University of Edinburgh, Edinburgh, United Kingdom
| | - Julius Lukeš
- 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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Charting organellar importomes by quantitative mass spectrometry. Nat Commun 2017; 8:15272. [PMID: 28485388 PMCID: PMC5436138 DOI: 10.1038/ncomms15272] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 03/15/2017] [Indexed: 11/08/2022] Open
Abstract
Protein import into organelles is essential for all eukaryotes and facilitated by multi-protein translocation machineries. Analysing whether a protein is transported into an organelle is largely restricted to single constituents. This renders knowledge about imported proteins incomplete, limiting our understanding of organellar biogenesis and function. Here we introduce a method that enables charting an organelle's importome. The approach relies on inducible RNAi-mediated knockdown of an essential subunit of a translocase to impair import and quantitative mass spectrometry. To highlight its potential, we established the mitochondrial importome of Trypanosoma brucei, comprising 1,120 proteins including 331 new candidates. Furthermore, the method allows for the identification of proteins with dual or multiple locations and the substrates of distinct protein import pathways. We demonstrate the specificity and versatility of this ImportOmics method by targeting import factors in mitochondria and glycosomes, which demonstrates its potential for globally studying protein import and inventories of organelles. Knowing the specific protein content of individual organelles is necessary for an integrated understanding of cellular physiology. Here the authors describe a mass spectrometry-based approach to identify the substrates of distinct protein import pathways and define organellar proteomes.
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28
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Gazestani VH, Yip CW, Nikpour N, Berghuis N, Salavati R. TrypsNetDB: An integrated framework for the functional characterization of trypanosomatid proteins. PLoS Negl Trop Dis 2017; 11:e0005368. [PMID: 28158179 PMCID: PMC5310917 DOI: 10.1371/journal.pntd.0005368] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 02/15/2017] [Accepted: 01/28/2017] [Indexed: 12/27/2022] Open
Abstract
Trypanosomatid parasites cause serious infections in humans and production losses in livestock. Due to the high divergence from other eukaryotes, such as humans and model organisms, the functional roles of many trypanosomatid proteins cannot be predicted by homology-based methods, rendering a significant portion of their proteins as uncharacterized. Recent technological advances have led to the availability of multiple systematic and genome-wide datasets on trypanosomatid parasites that are informative regarding the biological role(s) of their proteins. Here, we report TrypsNetDB (http://trypsNetDB.org), a web-based resource for the functional annotation of 16 different species/strains of trypanosomatid parasites. The database not only visualizes the network context of the queried protein(s) in an intuitive way but also examines the response of the represented network in more than 50 different biological contexts and its enrichment for various biological terms and pathways, protein sequence signatures, and potential RNA regulatory elements. The interactome core of the database, as of Jan 23, 2017, contains 101,187 interactions among 13,395 trypanosomatid proteins inferred from 97 genome-wide and focused studies on the interactome of these organisms. Methods to predict protein function based on sequences enable the rapid annotation of newly sequenced genomes. However, as most of these methods rely on homology-based approaches, non-conserved proteins in trypanosomatids remain elusive for annotation, rendering approximately half of the sequenced proteins uncharacterized. In this study, we developed a user friendly integrated database, TrypsNetDB, which fills multiple gaps in the field by depositing the current interactome knowledge on trypanosomatid proteins and combining this information with other available resources accompanied by related statistical analyses. The database allows automatic inter-species mapping of available data to better characterize the queried proteins in the species of interest. The database is built on fast and reliable ASP.Net framework and provides (i) a significant increase in the genome-wide functional annotation of trypanosomatid proteins, (ii) potential novel targets for therapeutics against trypanosomatids, and (iii) a robust methodology that can be adapted for the functional annotation of other non-model organisms.
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Affiliation(s)
- Vahid H. Gazestani
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec, Canada
| | - Chun Wai Yip
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec, Canada
| | - Najmeh Nikpour
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec, Canada
| | - Natasha Berghuis
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec, Canada
| | - Reza Salavati
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec, Canada
- * E-mail:
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29
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Mantilla BS, Marchese L, Casas-Sánchez A, Dyer NA, Ejeh N, Biran M, Bringaud F, Lehane MJ, Acosta-Serrano A, Silber AM. Proline Metabolism is Essential for Trypanosoma brucei brucei Survival in the Tsetse Vector. PLoS Pathog 2017; 13:e1006158. [PMID: 28114403 PMCID: PMC5289646 DOI: 10.1371/journal.ppat.1006158] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 02/02/2017] [Accepted: 12/29/2016] [Indexed: 01/18/2023] Open
Abstract
Adaptation to different nutritional environments is essential for life cycle completion by all Trypanosoma brucei sub-species. In the tsetse fly vector, L-proline is among the most abundant amino acids and is mainly used by the fly for lactation and to fuel flight muscle. The procyclic (insect) stage of T. b. brucei uses L-proline as its main carbon source, relying on an efficient catabolic pathway to convert it to glutamate, and then to succinate, acetate and alanine as the main secreted end products. Here we investigated the essentiality of an undisrupted proline catabolic pathway in T. b. brucei by studying mitochondrial Δ1-pyrroline-5-carboxylate dehydrogenase (TbP5CDH), which catalyzes the irreversible conversion of gamma-glutamate semialdehyde (γGS) into L-glutamate and NADH. In addition, we provided evidence for the absence of a functional proline biosynthetic pathway. TbP5CDH expression is developmentally regulated in the insect stages of the parasite, but absent in bloodstream forms grown in vitro. RNAi down-regulation of TbP5CDH severely affected the growth of procyclic trypanosomes in vitro in the absence of glucose, and altered the metabolic flux when proline was the sole carbon source. Furthermore, TbP5CDH knocked-down cells exhibited alterations in the mitochondrial inner membrane potential (ΔΨm), respiratory control ratio and ATP production. Also, changes in the proline-glutamate oxidative capacity slightly affected the surface expression of the major surface glycoprotein EP-procyclin. In the tsetse, TbP5CDH knocked-down cells were impaired and thus unable to colonize the fly’s midgut, probably due to the lack of glucose between bloodmeals. Altogether, our data show that the regulated expression of the proline metabolism pathway in T. b. brucei allows this parasite to adapt to the nutritional environment of the tsetse midgut. Bloodsucking insects play a major role in the transmission of pathogens that cause major tropical diseases. Their capacity to transmit these diseases is directly associated with the availability and turnover of energy sources. Proline is the main readily-mobilizable fuel of the tsetse fly, which is the vector of sub-species of Trypanosoma brucei parasites that cause human sleeping sickness and are partly responsible for animal trypanosomiasis (Nagana disease) in sub-Saharan Africa. Once trypanosomes are ingested from an infected host by the tsetse, the parasites encounter an environment that is poor in glucose (as it is rapidly metabolized by the fly) but rich in proline, which then becomes the main carbon source once the parasite differentiates into the first insect (procyclic) stage. In this work, we provide evidence on the essentiality of T. b. brucei proline catabolism for procyclic survival within the tsetse’s digestive tract, as this organism is unable to synthesize this amino acid and strictly depends on the proline provided by the fly. We also show that parasites deficient in TbP5CDH, a mitochondrial enzyme involved in the proline degradative pathway, failed to proliferate in vitro, showed a diminished respiratory capacity, and showed compromised maintenance of energy levels and metabolic flux when proline was offered as the main carbon source. Thus, the integrity of the trypanosome proline degradation pathway is needed to maintain essential functions related to parasite bioenergetics, replication and infectivity within the insect host. Our observations answer a long-standing question on the role of parasite proline metabolism in tsetse-trypanosome interplay.
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Affiliation(s)
- Brian S. Mantilla
- Laboratory of Biochemistry of Tryps - LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Letícia Marchese
- Laboratory of Biochemistry of Tryps - LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Aitor Casas-Sánchez
- Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Naomi A. Dyer
- Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Nicholas Ejeh
- Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Marc Biran
- Centre de Résonance Magnétique des Systemes Biologiques, Université Bordeaux, Bordeaux, France
| | - Frédéric Bringaud
- Centre de Résonance Magnétique des Systemes Biologiques, Université Bordeaux, Bordeaux, France
| | - Michael J. Lehane
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Alvaro Acosta-Serrano
- Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- * E-mail: (AMS); (AAS)
| | - Ariel M. Silber
- Laboratory of Biochemistry of Tryps - LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- * E-mail: (AMS); (AAS)
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Alkhaldi AAM, Martinek J, Panicucci B, Dardonville C, Zíková A, de Koning HP. Trypanocidal action of bisphosphonium salts through a mitochondrial target in bloodstream form Trypanosoma brucei. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2015; 6:23-34. [PMID: 27054061 PMCID: PMC4805778 DOI: 10.1016/j.ijpddr.2015.12.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/03/2015] [Accepted: 12/07/2015] [Indexed: 12/21/2022]
Abstract
Lipophilic bisphosphonium salts are among the most promising antiprotozoal leads currently under investigation. As part of their preclinical evaluation we here report on their mode of action against African trypanosomes, the etiological agents of sleeping sickness. The bisphosphonium compounds CD38 and AHI-9 exhibited rapid inhibition of Trypanosoma brucei growth, apparently the result of cell cycle arrest that blocked the replication of mitochondrial DNA, contained in the kinetoplast, thereby preventing the initiation of S-phase. Incubation with either compound led to a rapid reduction in mitochondrial membrane potential, and ATP levels decreased by approximately 50% within 1 h. Between 4 and 8 h, cellular calcium levels increased, consistent with release from the depolarized mitochondria. Within the mitochondria, the Succinate Dehydrogenase complex (SDH) was investigated as a target for bisphosphonium salts, but while its subunit 1 (SDH1) was present at low levels in the bloodstream form trypanosomes, the assembled complex was hardly detectable. RNAi knockdown of the SDH1 subunit produced no growth phenotype, either in bloodstream or in the procyclic (insect) forms and we conclude that in trypanosomes SDH is not the target for bisphosphonium salts. Instead, the compounds inhibited ATP production in intact mitochondria, as well as the purified F1 ATPase, to a level that was similar to 1 mM azide. Co-incubation with azide and bisphosphonium compounds did not inhibit ATPase activity more than either product alone. The results show that, in T. brucei, bisphosphonium compounds do not principally act on succinate dehydrogenase but on the mitochondrial FoF1 ATPase. Bisphosphonium salts display highly promising antiprotozoal activity. It has been reported that, in Leishmania, they act on the mitochondrial SDH complex. We show that in Trypanosoma brucei SDH is not essential and not the drug target. Instead, we present strong evidence that the F1F0 ATPase is the target.
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Affiliation(s)
- Abdulsalam A M Alkhaldi
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Jan Martinek
- Institute of Parasitology, Biology Centre & Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Brian Panicucci
- Institute of Parasitology, Biology Centre & Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | | | - Alena Zíková
- Institute of Parasitology, Biology Centre & Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
| | - Harry P de Koning
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.
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Wyllie S, Foth BJ, Kelner A, Sokolova AY, Berriman M, Fairlamb AH. Nitroheterocyclic drug resistance mechanisms in Trypanosoma brucei. J Antimicrob Chemother 2015; 71:625-34. [PMID: 26581221 PMCID: PMC4743696 DOI: 10.1093/jac/dkv376] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 10/15/2015] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES The objective of this study was to identify the mechanisms of resistance to nifurtimox and fexinidazole in African trypanosomes. METHODS Bloodstream-form Trypanosoma brucei were selected for resistance to nifurtimox and fexinidazole by stepwise exposure to increasing drug concentrations. Clones were subjected to WGS to identify putative resistance genes. Transgenic parasites modulating expression of genes of interest were generated and drug susceptibility phenotypes determined. RESULTS Nifurtimox-resistant (NfxR) and fexinidazole-resistant (FxR) parasites shared reciprocal cross-resistance suggestive of a common mechanism of action. Previously, a type I nitroreductase (NTR) has been implicated in nitro drug activation. WGS of resistant clones revealed that NfxR parasites had lost >100 kb from one copy of chromosome 7, rendering them hemizygous for NTR as well as over 30 other genes. FxR parasites retained both copies of NTR, but lost >70 kb downstream of one NTR allele, decreasing NTR transcription by half. A single knockout line of NTR displayed 1.6- and 1.9-fold resistance to nifurtimox and fexinidazole, respectively. Since NfxR and FxR parasites are ∼6- and 20-fold resistant to nifurtimox and fexinidazole, respectively, additional factors must be involved. Overexpression and knockout studies ruled out a role for a putative oxidoreductase (Tb927.7.7410) and a hypothetical gene (Tb927.1.1050), previously identified in a genome-scale RNAi screen. CONCLUSIONS NTR was confirmed as a key resistance determinant, either by loss of one gene copy or loss of gene expression. Further work is required to identify which of the many dozens of SNPs identified in the drug-resistant cell lines contribute to the overall resistance phenotype.
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Affiliation(s)
- Susan Wyllie
- Division of Biological Chemistry and Drug Discovery, Wellcome Trust Building, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Bernardo J Foth
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Anna Kelner
- Division of Biological Chemistry and Drug Discovery, Wellcome Trust Building, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Antoaneta Y Sokolova
- Division of Biological Chemistry and Drug Discovery, Wellcome Trust Building, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Alan H Fairlamb
- Division of Biological Chemistry and Drug Discovery, Wellcome Trust Building, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
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Mbang-Benet DE, Sterkers Y, Crobu L, Sarrazin A, Bastien P, Pagès M. RNA interference screen reveals a high proportion of mitochondrial proteins essential for correct cell cycle progress in Trypanosoma brucei. BMC Genomics 2015; 16:297. [PMID: 25888089 PMCID: PMC4445814 DOI: 10.1186/s12864-015-1505-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 03/30/2015] [Indexed: 12/20/2022] Open
Abstract
Background Trypanosomatid parasites possess a single mitochondrion which is classically involved in the energetic metabolism of the cell, but also, in a much more original way, through its single and complex DNA (termed kinetoplast), in the correct progress of cell division. In order to identify proteins potentially involved in the cell cycle, we performed RNAi knockdowns of 101 genes encoding mitochondrial proteins using procyclic cells of Trypanosoma brucei. Results A major cell growth reduction was observed in 10 cases and a moderate reduction in 29 other cases. These data are overall in agreement with those previously obtained by a case-by-case approach performed on chromosome 1 genes, and quantitatively with those obtained by “high-throughput phenotyping using parallel sequencing of RNA interference targets” (RIT-seq). Nevertheless, a detailed analysis revealed many qualitative discrepancies with the RIT-seq-based approach. Moreover, for 37 out of 39 mutants for which a moderate or severe growth defect was observed here, we noted abnormalities in the cell cycle progress, leading to increased proportions of abnormal cell cycle stages, such as cells containing more than 2 kinetoplasts (K) and/or more than 2 nuclei (N), and modified proportions of the normal phenotypes (1N1K, 1N2K and 2N2K). Conclusions These data, together with the observation of other abnormal phenotypes, show that all the corresponding mitochondrial proteins are involved, directly or indirectly, in the correct progress or, less likely, in the regulation, of the cell cycle in T. brucei. They also show how post-genomics analyses performed on a case-by-case basis may yield discrepancies with global approaches. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1505-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diane-Ethna Mbang-Benet
- Université Montpellier 1, UFR Médecine, Laboratoire de Parasitologie-Mycologie, CHRU de Montpellier, 39, Avenue Charles Flahault, 34295, Montpellier, Cedex 5, France. .,CNRS 5290 - IRD 224 - Université Montpellier (UMR "MiVEGEC"), Montpellier, France.
| | - Yvon Sterkers
- Université Montpellier 1, UFR Médecine, Laboratoire de Parasitologie-Mycologie, CHRU de Montpellier, 39, Avenue Charles Flahault, 34295, Montpellier, Cedex 5, France. .,CNRS 5290 - IRD 224 - Université Montpellier (UMR "MiVEGEC"), Montpellier, France. .,Département de Parasitologie-Mycologie, CHRU (Centre Hospitalier Universitaire de Montpellier), Montpellier, France.
| | - Lucien Crobu
- CNRS 5290 - IRD 224 - Université Montpellier (UMR "MiVEGEC"), Montpellier, France.
| | - Amélie Sarrazin
- Montpellier RIO Imaging Facility, Montpellier BIOCAMPUS, UMS3426, Arnaud de Villeneuve Campus Imaging Facility - Institut de Génétique Humaine-CNRS, Montpellier, France.
| | - Patrick Bastien
- Université Montpellier 1, UFR Médecine, Laboratoire de Parasitologie-Mycologie, CHRU de Montpellier, 39, Avenue Charles Flahault, 34295, Montpellier, Cedex 5, France. .,CNRS 5290 - IRD 224 - Université Montpellier (UMR "MiVEGEC"), Montpellier, France. .,Département de Parasitologie-Mycologie, CHRU (Centre Hospitalier Universitaire de Montpellier), Montpellier, France.
| | - Michel Pagès
- Université Montpellier 1, UFR Médecine, Laboratoire de Parasitologie-Mycologie, CHRU de Montpellier, 39, Avenue Charles Flahault, 34295, Montpellier, Cedex 5, France. .,CNRS 5290 - IRD 224 - Université Montpellier (UMR "MiVEGEC"), Montpellier, France.
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Mantilla BS, Paes LS, Pral EMF, Martil DE, Thiemann OH, Fernández-Silva P, Bastos EL, Silber AM. Role of Δ1-pyrroline-5-carboxylate dehydrogenase supports mitochondrial metabolism and host-cell invasion of Trypanosoma cruzi. J Biol Chem 2015; 290:7767-90. [PMID: 25623067 PMCID: PMC4367278 DOI: 10.1074/jbc.m114.574525] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 12/30/2014] [Indexed: 01/03/2023] Open
Abstract
Proline is crucial for energizing critical events throughout the life cycle of Trypanosoma cruzi, the etiological agent of Chagas disease. The proline breakdown pathway consists of two oxidation steps, both of which produce reducing equivalents as follows: the conversion of proline to Δ(1)-pyrroline-5-carboxylate (P5C), and the subsequent conversion of P5C to glutamate. We have identified and characterized the Δ(1)-pyrroline-5-carboxylate dehydrogenase from T. cruzi (TcP5CDH) and report here on how this enzyme contributes to a central metabolic pathway in this parasite. Size-exclusion chromatography, two-dimensional gel electrophoresis, and small angle x-ray scattering analysis of TcP5CDH revealed an oligomeric state composed of two subunits of six protomers. TcP5CDH was found to complement a yeast strain deficient in PUT2 activity, confirming the enzyme's functional role; and the biochemical parameters (Km, kcat, and kcat/Km) of the recombinant TcP5CDH were determined, exhibiting values comparable with those from T. cruzi lysates. In addition, TcP5CDH exhibited mitochondrial staining during the main stages of the T. cruzi life cycle. mRNA and enzymatic activity levels indicated the up-regulation (6-fold change) of TcP5CDH during the infective stages of the parasite. The participation of P5C as an energy source was also demonstrated. Overall, we propose that this enzymatic step is crucial for the viability of both replicative and infective forms of T. cruzi.
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Affiliation(s)
- Brian S Mantilla
- From the Instituto de Ciências Biomédicas, Departamento de Parasitologia, Universidade de São Paulo, 05508-000 São Paulo, Brazil
| | - Lisvane S Paes
- From the Instituto de Ciências Biomédicas, Departamento de Parasitologia, Universidade de São Paulo, 05508-000 São Paulo, Brazil
| | - Elizabeth M F Pral
- From the Instituto de Ciências Biomédicas, Departamento de Parasitologia, Universidade de São Paulo, 05508-000 São Paulo, Brazil
| | - Daiana E Martil
- the Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, and
| | - Otavio H Thiemann
- the Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, and
| | - Patricio Fernández-Silva
- the Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, 50013 Zaragoza Spain
| | - Erick L Bastos
- Instituto de Química, Departamento de Química Fundamental, Universidade de São Paulo, 13560-590 São Paulo, Brazil, and
| | - Ariel M Silber
- From the Instituto de Ciências Biomédicas, Departamento de Parasitologia, Universidade de São Paulo, 05508-000 São Paulo, Brazil,
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Šubrtová K, Panicucci B, Zíková A. ATPaseTb2, a unique membrane-bound FoF1-ATPase component, is essential in bloodstream and dyskinetoplastic trypanosomes. PLoS Pathog 2015; 11:e1004660. [PMID: 25714685 PMCID: PMC4340940 DOI: 10.1371/journal.ppat.1004660] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 01/06/2015] [Indexed: 12/21/2022] Open
Abstract
In the infectious stage of Trypanosoma brucei, an important parasite of humans and livestock, the mitochondrial (mt) membrane potential (Δψm) is uniquely maintained by the ATP hydrolytic activity and subsequent proton pumping of the essential FoF1-ATPase. Intriguingly, this multiprotein complex contains several trypanosome-specific subunits of unknown function. Here, we demonstrate that one of the largest novel subunits, ATPaseTb2, is membrane-bound and localizes with monomeric and multimeric assemblies of the FoF1-ATPase. Moreover, RNAi silencing of ATPaseTb2 quickly leads to a significant decrease of the Δψm that manifests as a decreased growth phenotype, indicating that the FoF1-ATPase is impaired. To further explore the function of this protein, we employed a trypanosoma strain that lacks mtDNA (dyskinetoplastic, Dk) and thus subunit a, an essential component of the proton pore in the membrane Fo-moiety. These Dk cells generate the Δψm by combining the hydrolytic activity of the matrix-facing F1-ATPase and the electrogenic exchange of ATP4- for ADP3- by the ATP/ADP carrier (AAC). Surprisingly, in addition to the expected presence of F1-ATPase, the monomeric and multimeric FoF1-ATPase complexes were identified. In fact, the immunoprecipitation of a F1-ATPase subunit demonstrated that ATPaseTb2 was a component of these complexes. Furthermore, RNAi studies established that the membrane-bound ATPaseTb2 subunit is essential for maintaining normal growth and the Δψm of Dk cells. Thus, even in the absence of subunit a, a portion of the FoF1-ATPase is assembled in Dk cells.
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Affiliation(s)
- Karolína Šubrtová
- Institute of Parasitology, Biology Centre, CAS, České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Brian Panicucci
- Institute of Parasitology, Biology Centre, CAS, České Budějovice, Czech Republic
| | - Alena Zíková
- Institute of Parasitology, Biology Centre, CAS, České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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Verner Z, Basu S, Benz C, Dixit S, Dobáková E, Faktorová D, Hashimi H, Horáková E, Huang Z, Paris Z, Peña-Diaz P, Ridlon L, Týč J, Wildridge D, Zíková A, Lukeš J. Malleable mitochondrion of Trypanosoma brucei. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 315:73-151. [PMID: 25708462 DOI: 10.1016/bs.ircmb.2014.11.001] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The importance of mitochondria for a typical aerobic eukaryotic cell is undeniable, as the list of necessary mitochondrial processes is steadily growing. Here, we summarize the current knowledge of mitochondrial biology of an early-branching parasitic protist, Trypanosoma brucei, a causative agent of serious human and cattle diseases. We present a comprehensive survey of its mitochondrial pathways including kinetoplast DNA replication and maintenance, gene expression, protein and metabolite import, major metabolic pathways, Fe-S cluster synthesis, ion homeostasis, organellar dynamics, and other processes. As we describe in this chapter, the single mitochondrion of T. brucei is everything but simple and as such rivals mitochondria of multicellular organisms.
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Affiliation(s)
- Zdeněk Verner
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Present address: Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Present address: Faculty of Sciences, Charles University, Prague, Czech Republic
| | - Somsuvro Basu
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic; Present address: Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Germany
| | - Corinna Benz
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Sameer Dixit
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Eva Dobáková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Present address: Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Drahomíra Faktorová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Hassan Hashimi
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Eva Horáková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic
| | - Zhenqiu Huang
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Zdeněk Paris
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic
| | - Priscila Peña-Diaz
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic
| | - Lucie Ridlon
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic; Present address: Salk Institute, La Jolla, San Diego, USA
| | - Jiří Týč
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - David Wildridge
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic
| | - Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
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36
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The ADP/ATP carrier and its relationship to oxidative phosphorylation in ancestral protist trypanosoma brucei. EUKARYOTIC CELL 2015; 14:297-310. [PMID: 25616281 DOI: 10.1128/ec.00238-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The highly conserved ADP/ATP carrier (AAC) is a key energetic link between the mitochondrial (mt) and cytosolic compartments of all aerobic eukaryotic cells, as it exchanges the ATP generated inside the organelle for the cytosolic ADP. Trypanosoma brucei, a parasitic protist of medical and veterinary importance, possesses a single functional AAC protein (TbAAC) that is related to the human and yeast ADP/ATP carriers. However, unlike previous studies performed with these model organisms, this study showed that TbAAC is most likely not a stable component of either the respiratory supercomplex III+IV or the ATP synthasome but rather functions as a physically separate entity in this highly diverged eukaryote. Therefore, TbAAC RNA interference (RNAi) ablation in the insect stage of T. brucei does not impair the activity or arrangement of the respiratory chain complexes. Nevertheless, RNAi silencing of TbAAC caused a severe growth defect that coincides with a significant reduction of mt ATP synthesis by both substrate and oxidative phosphorylation. Furthermore, TbAAC downregulation resulted in a decreased level of cytosolic ATP, a higher mt membrane potential, an elevated amount of reactive oxygen species, and a reduced consumption of oxygen in the mitochondria. Interestingly, while TbAAC has previously been demonstrated to serve as the sole ADP/ATP carrier for ADP influx into the mitochondria, our data suggest that a second carrier for ATP influx may be present and active in the T. brucei mitochondrion. Overall, this study provides more insight into the delicate balance of the functional relationship between TbAAC and the oxidative phosphorylation (OXPHOS) pathway in an early diverged eukaryote.
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37
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Mitochondrial respiration and genomic analysis provide insight into the influence of the symbiotic bacterium on host trypanosomatid oxygen consumption. Parasitology 2014; 142:352-62. [PMID: 25160925 DOI: 10.1017/s0031182014001139] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Certain trypanosomatids co-evolve with an endosymbiotic bacterium in a mutualistic relationship that is characterized by intense metabolic exchanges. Symbionts were able to respire for up to 4 h after isolation from Angomonas deanei. FCCP (carbonyl cyanide-4-(trifluoromethoxy)phenylhydrazone) similarly increased respiration in wild-type and aposymbiotic protozoa, though a higher maximal O2 consumption capacity was observed in the symbiont-containing cells. Rotenone, a complex I inhibitor, did not affect A. deanei respiration, whereas TTFA (thenoyltrifluoroacetone), a complex II activity inhibitor, completely blocked respiration in both strains. Antimycin A and cyanide, inhibitors of complexes III and IV, respectively, abolished O2 consumption, but the aposymbiotic protozoa were more sensitive to both compounds. Oligomycin did not affect cell respiration, whereas carboxyatractyloside (CAT), an inhibitor of the ADP-ATP translocator, slightly reduced O2 consumption. In the A. deanei genome, sequences encoding most proteins of the respiratory chain are present. The symbiont genome lost part of the electron transport system (ETS), but complex I, a cytochrome d oxidase, and FoF1-ATP synthase remain. In conclusion, this work suggests that the symbiont influences the mitochondrial respiration of the host protozoan.
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38
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Duarte M, Tomás AM. The mitochondrial complex I of trypanosomatids--an overview of current knowledge. J Bioenerg Biomembr 2014; 46:299-311. [PMID: 24961227 DOI: 10.1007/s10863-014-9556-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 06/17/2014] [Indexed: 01/23/2023]
Abstract
The contribution of trypanosomatid mitochondrial complex I for energy transduction has long been debated. Herein, we summarize current knowledge on the composition and relevance of this enzyme. Bioinformatic and proteomic analyses allowed the identification of many conserved and trypanosomatid-specific subunits of NADH:ubiquinone oxidoreductase, revealing a multifunctional enzyme capable of performing bioenergetic activities and possibly, also of functioning in fatty acid metabolism. A multimeric structure organized in 5 domains of more than 2 MDa is predicted, in contrast to the 1 MDa described for mammalian complex I. The relevance of mitochondrial complex I within the Trypanosomatidae family is quite diverse with its NADH oxidation activity being dispensable for both procyclic and bloodstream Trypanosoma brucei, whereas in Phytomonas serpens the enzyme is the only respiratory complex able to sustain membrane potential. Aside from complex I, trypanosomatid mitochondria contain a type II NADH dehydrogenase and a NADH-dependent fumarate reductase as alternative electron entry points into the respiratory chain and thus, some trypanosomatids may have bypassed the need for complex I. The involvement of each of these enzymes in the maintenance of the mitochondrial redox balance in trypanosomatids is still an open question and requires further investigation.
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Affiliation(s)
- Margarida Duarte
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180, Porto, Portugal,
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Verner Z, Čermáková P, Škodová I, Kováčová B, Lukeš J, Horváth A. Comparative analysis of respiratory chain and oxidative phosphorylation in Leishmania tarentolae, Crithidia fasciculata, Phytomonas serpens and procyclic stage of Trypanosoma brucei. Mol Biochem Parasitol 2014; 193:55-65. [DOI: 10.1016/j.molbiopara.2014.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 02/05/2014] [Accepted: 02/06/2014] [Indexed: 10/25/2022]
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Rodrigues JCF, Godinho JLP, de Souza W. Biology of human pathogenic trypanosomatids: epidemiology, lifecycle and ultrastructure. Subcell Biochem 2014; 74:1-42. [PMID: 24264239 DOI: 10.1007/978-94-007-7305-9_1] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Leishmania and Trypanosoma belong to the Trypanosomatidae family and cause important human infections such as leishmaniasis, Chagas disease, and sleeping sickness. Leishmaniasis, caused by protozoa belonging to Leishmania, affects about 12 million people worldwide and can present different clinical manifestations, i.e., visceral leishmaniasis (VL), cutaneous leishmaniasis (CL), mucocutaneous leishmaniasis (MCL), diffuse cutaneous leishmaniasis (DCL), and post-kala-azar dermal leishmaniasis (PKDL). Chagas disease, also known as American trypanosomiasis, is caused by Trypanosoma cruzi and is mainly prevalent in Latin America but is increasingly occurring in the United States, Canada, and Europe. Sleeping sickness or human African trypanosomiasis (HAT), caused by two sub-species of Trypanosoma brucei (i.e., T. b. rhodesiense and T. b. gambiense), occurs only in sub-Saharan Africa countries. These pathogenic trypanosomatids alternate between invertebrate and vertebrate hosts throughout their lifecycles, and different developmental stages can live inside the host cells and circulate in the bloodstream or in the insect gut. Trypanosomatids have a classical eukaryotic ultrastructural organization with some of the same main organelles found in mammalian host cells, while also containing special structures and organelles that are absent in other eukaryotic organisms. For example, the mitochondrion is ramified and contains a region known as the kinetoplast, which houses the mitochondrial DNA. Also, the glycosomes are specialized peroxisomes containing glycolytic pathway enzymes. Moreover, a layer of subpellicular microtubules confers mechanic rigidity to the cell. Some of these structures have been investigated to determine their function and identify potential enzymes and metabolic pathways that may constitute targets for new chemotherapeutic drugs.
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Affiliation(s)
- Juliany Cola Fernandes Rodrigues
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil,
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A multiple aminoacyl-tRNA synthetase complex that enhances tRNA-aminoacylation in African trypanosomes. Mol Cell Biol 2013; 33:4872-88. [PMID: 24126051 DOI: 10.1128/mcb.00711-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genes for all cytoplasmic and potentially all mitochondrial aminoacyl-tRNA synthetases (aaRSs) were identified, and all those tested by RNA interference were found to be essential for the growth of Trypanosoma brucei. Some of these enzymes were localized to the cytoplasm or mitochondrion, but most were dually localized to both cellular compartments. Cytoplasmic T. brucei aaRSs were organized in a multiprotein complex in both bloodstream and procyclic forms. The multiple aminoacyl-tRNA synthetase (MARS) complex contained at least six aaRS enzymes and three additional non-aaRS proteins. Steady-state kinetic studies showed that association in the MARS complex enhances tRNA-aminoacylation efficiency, which is in part dependent on a MARS complex-associated protein (MCP), named MCP2, that binds tRNAs and increases their aminoacylation by the complex. Conditional repression of MCP2 in T. brucei bloodstream forms resulted in reduced parasite growth and infectivity in mice. Thus, association in a MARS complex enhances tRNA-aminoacylation and contributes to parasite fitness. The MARS complex may be part of a cellular regulatory system and a target for drug development.
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Cristodero M, Mani J, Oeljeklaus S, Aeberhard L, Hashimi H, Ramrath DJF, Lukeš J, Warscheid B, Schneider A. Mitochondrial translation factors of Trypanosoma brucei: elongation factor-Tu has a unique subdomain that is essential for its function. Mol Microbiol 2013; 90:744-55. [PMID: 24033548 DOI: 10.1111/mmi.12397] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2013] [Indexed: 11/28/2022]
Abstract
Mitochondrial translation in the parasitic protozoan Trypanosoma brucei relies on imported eukaryotic-type tRNAs as well as on bacterial-type ribosomes that have the shortest known rRNAs. Here we have identified the mitochondrial translation elongation factors EF-Tu, EF-Ts, EF-G1 and release factor RF1 of trypanosomatids and show that their ablation impairs growth and oxidative phosphorylation. In vivo labelling experiments and a SILAC-based analysis of the global proteomic changes induced by EF-Tu RNAi directly link EF-Tu to mitochondrial translation. Moreover, EF-Tu RNAi reveals downregulation of many nuclear encoded subunits of cytochrome oxidase as well as of components of the bc1-complex, whereas most cytosolic ribosomal proteins were upregulated. Interestingly, T. brucei EF-Tu has a 30-amino-acid-long, highly charged subdomain, which is unique to trypanosomatids. A combination of RNAi and complementation experiments shows that this subdomain is essential for EF-Tu function, but that it can be replaced by a similar sequence found in eukaryotic EF-1a, the cytosolic counterpart of EF-Tu. A recent cryo-electron microscopy study revealed that trypanosomatid mitochondrial ribosomes have a unique intersubunit space that likely harbours the EF-Tu binding site. These findings suggest that the trypanosomatid-specific EF-Tu subdomain serves as an adaption for binding to these unusual mitochondrial ribosomes.
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Affiliation(s)
- Marina Cristodero
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
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Abstract
SIGNIFICANCE In the single mitochondrion of protozoan trypanosomatid parasites there are several sites for the generation and elimination of reactive oxygen species (ROS), a class of molecules that exhibit a dual role in cells, either as regulatory mediators or as cytotoxic effectors. RECENT ADVANCES Formation of ROS in trypanosomatid mitochondria can be induced by various drug compounds. Importantly, it can also be triggered by specific physiologic stimuli, indicating that this phenomenon may occur in living parasites as well. Elimination of ROS in these organelles is attributed to the activity of two iron-dependent superoxide dismutases (FeSODs) and up to three different peroxidases (a cytochrome c peroxidase and two thiol peroxidases). CRITICAL ISSUES Data regarding the formation of ROS in trypanosomatid mitochondria are limited and nonsystematic. Another critical issue refers to the exact contribution of mitochondrial FeSODs and peroxidases for ROS removal, given that their antioxidant activity is not essential when abrogated individually. This suggests some level of functional overlapping or that ROS produced in mitochondria under normal conditions can be removed noncatalytically. Also still unsolved is the mechanism by which mitochondrial thiol peroxidases are regenerated to their reduced (active) form. FUTURE DIRECTIONS The production of intramitochondrial ROS under physiologic conditions and their implication in parasite biology should be further clarified. The relative importance of enzymatic versus nonenzymatic mechanisms for ROS elimination in trypanosomatid mitochondria also requires investigation. Simultaneous depletion of several redundant antioxidant enzymes and determination of noncatalytic antioxidants are possible ways to achieve this.
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Affiliation(s)
- Ana M Tomás
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.
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Trypanosoma brucei Tb927.2.6100 is an essential protein associated with kinetoplast DNA. EUKARYOTIC CELL 2013; 12:970-8. [PMID: 23650088 DOI: 10.1128/ec.00352-12] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The mitochondrial DNA of trypanosomatid protozoa consists of a complex, intercatenated network of tens of maxicircles and thousands of minicircles. This structure, called kinetoplast DNA (kDNA), requires numerous proteins and multiprotein complexes for replication, segregation, and transcription. In this study, we used a proteomic approach to identify proteins that are associated with the kDNA network. We identified a novel protein encoded by Tb927.2.6100 that was present in a fraction enriched for kDNA and colocalized the protein with kDNA by fluorescence microscopy. RNA interference (RNAi) knockdown of its expression resulted in a growth defect and changes in the proportion of kinetoplasts and nuclei in the cell population. RNAi also resulted in shrinkage and loss of the kinetoplasts, loss of maxicircle and minicircle components of kDNA at similar rates, and (perhaps secondarily) loss of edited and pre-edited mRNA. These results indicate that the Tb927.2.6100 protein is essential for the maintenance of kDNA.
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Abstract
Faithful transmission of genetic material is essential for the survival of all organisms. Eukaryotic chromosome segregation is driven by the kinetochore that assembles onto centromeric DNA to capture spindle microtubules and govern the movement of chromosomes. Its molecular mechanism has been actively studied in conventional model eukaryotes, such as yeasts, worms, flies and human. However, these organisms are closely related in the evolutionary time scale and it therefore remains unclear whether all eukaryotes use a similar mechanism. The evolutionary origins of the segregation apparatus also remain enigmatic. To gain insights into these questions, it is critical to perform comparative studies. Here, we review our current understanding of the mitotic mechanism in Trypanosoma brucei, an experimentally tractable kinetoplastid parasite that branched early in eukaryotic history. No canonical kinetochore component has been identified, and the design principle of kinetochores might be fundamentally different in kinetoplastids. Furthermore, these organisms do not appear to possess a functional spindle checkpoint that monitors kinetochore-microtubule attachments. With these unique features and the long evolutionary distance from other eukaryotes, understanding the mechanism of chromosome segregation in T. brucei should reveal fundamental requirements for the eukaryotic segregation machinery, and may also provide hints about the origin and evolution of the segregation apparatus.
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Affiliation(s)
- Bungo Akiyoshi
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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Mach J, Poliak P, Matušková A, Žárský V, Janata J, Lukeš J, Tachezy J. An Advanced System of the Mitochondrial Processing Peptidase and Core Protein Family in Trypanosoma brucei and Multiple Origins of the Core I Subunit in Eukaryotes. Genome Biol Evol 2013; 5:860-75. [PMID: 23563972 PMCID: PMC3673636 DOI: 10.1093/gbe/evt056] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2013] [Indexed: 01/20/2023] Open
Abstract
Mitochondrial processing peptidase (MPP) consists of α and β subunits that catalyze the cleavage of N-terminal mitochondrial-targeting sequences (N-MTSs) and deliver preproteins to the mitochondria. In plants, both MPP subunits are associated with the respiratory complex bc1, which has been proposed to represent an ancestral form. Subsequent duplication of MPP subunits resulted in separate sets of genes encoding soluble MPP in the matrix and core proteins (cp1 and cp2) of the membrane-embedded bc1 complex. As only α-MPP was duplicated in Neurospora, its single β-MPP functions in both MPP and bc1 complexes. Herein, we investigated the MPP/core protein family and N-MTSs in the kinetoplastid Trypanosoma brucei, which is often considered one of the most ancient eukaryotes. Analysis of N-MTSs predicted in 336 mitochondrial proteins showed that trypanosomal N-MTSs were comparable with N-MTSs from other organisms. N-MTS cleavage is mediated by a standard heterodimeric MPP, which is present in the matrix of procyclic and bloodstream trypanosomes, and its expression is essential for the parasite. Distinct Genes encode cp1 and cp2, and in the bloodstream forms the expression of cp1 is downregulated along with the bc1 complex. Phylogenetic analysis revealed that all eukaryotic lineages include members with a Neurospora-type MPP/core protein family, whereas cp1 evolved independently in metazoans, some fungi and kinetoplastids. Evolution of cp1 allowed the independent regulation of respiration and protein import, which is essential for the procyclic and bloodstream forms of T. brucei. These results indicate that T. brucei possesses a highly derived MPP/core protein family that likely evolved in response to its complex life cycle and does not appear to have an ancient character proposed earlier for this eukaryote.
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Affiliation(s)
- Jan Mach
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Pavel Poliak
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Budweis, Czech Republic
| | - Anna Matušková
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Vojtěch Žárský
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jiří Janata
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Budweis, Czech Republic
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
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Li L, Nelson CJ, Carrie C, Gawryluk RMR, Solheim C, Gray MW, Whelan J, Millar AH. Subcomplexes of ancestral respiratory complex I subunits rapidly turn over in vivo as productive assembly intermediates in Arabidopsis. J Biol Chem 2012; 288:5707-17. [PMID: 23271729 DOI: 10.1074/jbc.m112.432070] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Subcomplexes of mitochondrial respiratory complex I (CI; EC 1.6.5.3) are shown to turn over in vivo, and we propose a role in an ancestral assembly pathway. By progressively labeling Arabidopsis cell cultures with (15)N and isolating mitochondria, we have identified CI subcomplexes through differences in (15)N incorporation into their protein subunits. The 200-kDa subcomplex, containing the ancestral γ-carbonic anhydrase (γ-CA), γ-carbonic anhydrase-like, and 20.9-kDa subunits, had a significantly higher turnover rate than intact CI or CI+CIII(2). In vitro import of precursors for these CI subunits demonstrated rapid generation of subcomplexes and revealed that their specific abundance varied when different ancestral subunits were imported. Time course studies of precursor import showed the further assembly of these subcomplexes into CI and CI+CIII(2), indicating that the subcomplexes are productive intermediates of assembly. The strong transient incorporation of new subunits into the 200-kDa subcomplex in a γ-CA mutant is consistent with this subcomplex being a key initiator of CI assembly in plants. This evidence alongside the pattern of coincident occurrence of genes encoding these particular proteins broadly in eukaryotes, except for opisthokonts, provides a framework for the evolutionary conservation of these accessory subunits and evidence of their function in ancestral CI assembly.
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Affiliation(s)
- Lei Li
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Western Australia, Australia
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Niemann M, Wiese S, Mani J, Chanfon A, Jackson C, Meisinger C, Warscheid B, Schneider A. Mitochondrial outer membrane proteome of Trypanosoma brucei reveals novel factors required to maintain mitochondrial morphology. Mol Cell Proteomics 2012; 12:515-28. [PMID: 23221899 DOI: 10.1074/mcp.m112.023093] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Trypanosoma brucei is a unicellular parasite that causes devastating diseases in humans and animals. It diverged from most other eukaryotes very early in evolution and, as a consequence, has an unusual mitochondrial biology. Moreover, mitochondrial functions and morphology are highly regulated throughout the life cycle of the parasite. The outer mitochondrial membrane defines the boundary of the organelle. Its properties are therefore key for understanding how the cytosol and mitochondria communicate and how the organelle is integrated into the metabolism of the whole cell. We have purified the mitochondrial outer membrane of T. brucei and characterized its proteome using label-free quantitative mass spectrometry for protein abundance profiling in combination with statistical analysis. Our results show that the trypanosomal outer membrane proteome consists of 82 proteins, two-thirds of which have never been associated with mitochondria before. 40 proteins share homology with proteins of known functions. The function of 42 proteins, 33 of which are specific to trypanosomatids, remains unknown. 11 proteins are essential for the disease-causing bloodstream form of T. brucei and therefore may be exploited as novel drug targets. A comparison with the outer membrane proteome of yeast defines a set of 17 common proteins that are likely present in the mitochondrial outer membrane of all eukaryotes. Known factors involved in the regulation of mitochondrial morphology are virtually absent in T. brucei. Interestingly, RNAi-mediated ablation of three outer membrane proteins of unknown function resulted in a collapse of the network-like mitochondrion of procyclic cells and for the first time identified factors that control mitochondrial shape in T. brucei.
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Affiliation(s)
- Moritz Niemann
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
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49
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Fisk JC, Li J, Wang H, Aletta JM, Qu J, Read LK. Proteomic analysis reveals diverse classes of arginine methylproteins in mitochondria of trypanosomes. Mol Cell Proteomics 2012; 12:302-11. [PMID: 23152538 DOI: 10.1074/mcp.m112.022533] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Arginine (arg) methylation is a widespread posttranslational modification of proteins that impacts numerous cellular processes such as chromatin remodeling, RNA processing, DNA repair, and cell signaling. Known arg methylproteins arise mostly from yeast and mammals, and are almost exclusively nuclear and cytoplasmic. Trypanosoma brucei is an early branching eukaryote whose genome encodes five putative protein arg methyltransferases, and thus likely contains a plethora of arg methylproteins. Additionally, trypanosomes and related organisms possess a unique mitochondrion that undergoes dramatic developmental regulation and uses novel RNA editing and mitochondrial DNA replication mechanisms. Here, we performed a global mass spectrometric analysis of the T. brucei mitochondrion to identify new arg methylproteins in this medically relevant parasite. Enabling factors of this work are use of a combination digestion with two orthogonal enzymes, an efficient offline two dimensional chromatography separation, and high-resolution mass spectrometry analysis with two complementary activations. This approach led to the comprehensive, sensitive and confident identification and localization of methylarg at a proteome level. We identified 167 arg methylproteins with wide-ranging functions including metabolism, transport, chaperoning, RNA processing, translation, and DNA replication. Our data suggest that arg methylproteins in trypanosome mitochondria possess both trypanosome-specific and evolutionarily conserved modifications, depending on the protein targeted. This study is the first comprehensive analysis of mitochondrial arg methylation in any organism, and represents a significant advance in our knowledge of the range of arg methylproteins and their sites of modification. Moreover, these studies establish T. brucei as a model organism for the study of posttranslational modifications.
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Affiliation(s)
- John C Fisk
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14124, USA
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50
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Disparate phenotypic effects from the knockdown of various Trypanosoma brucei cytochrome c oxidase subunits. Mol Biochem Parasitol 2012; 184:90-8. [PMID: 22569586 DOI: 10.1016/j.molbiopara.2012.04.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 04/27/2012] [Accepted: 04/28/2012] [Indexed: 10/28/2022]
Abstract
The Trypanosoma brucei cytochrome c oxidase (respiratory complex IV) is a very divergent complex containing a surprisingly high number of trypanosomatid-specific subunits with unknown function. To gain insight into the functional organization of this large protein complex, the expression of three novel subunits (TbCOX VII, TbCOX X and TbCOX 6080) were down-regulated by RNA interference. We demonstrate that all three subunits are important for the proper function of complex IV and the growth of the procyclic stage of T. brucei. These phenotypes were manifested by the structural instability of the complex when these indispensible subunits were repressed. Furthermore, the impairment of cytochrome c oxidase resulted in other severe mitochondrial phenotypes, such as a decreased mitochondrial membrane potential, reduced ATP production via oxidative phoshorylation and redirection of oxygen consumption to the trypanosome-specific alternative oxidase, TAO. Interestingly, the inspected subunits revealed some disparate phenotypes, particularly regarding the activity of cytochrome c reductase (respiratory complex III). While the activity of complex III was down-regulated in RNAi induced cells for TbCOX X and TbCOX 6080, the TbCOX VII silenced cell line actually exhibited higher levels of complex III activity and elevated levels of ROS formation. This result suggests that the examined subunits may have different functional roles within complex IV of T. brucei, perhaps involving the ability to communicate between sequential enzymes in the respiratory chain. In summary, by characterizing the function of three hypothetical components of complex IV, we are able to assign these proteins as genuine and indispensable subunits of the procyclic T. brucei cytochrome c oxidase, an essential component of the respiratory chain in these evolutionary ancestral and medically important parasites.
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