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Novák LVF, Treitli SC, Pyrih J, Hałakuc P, Pipaliya SV, Vacek V, Brzoň O, Soukal P, Eme L, Dacks JB, Karnkowska A, Eliáš M, Hampl V. Genomics of Preaxostyla Flagellates Illuminates the Path Towards the Loss of Mitochondria. PLoS Genet 2023; 19:e1011050. [PMID: 38060519 PMCID: PMC10703272 DOI: 10.1371/journal.pgen.1011050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023] Open
Abstract
The notion that mitochondria cannot be lost was shattered with the report of an oxymonad Monocercomonoides exilis, the first eukaryote arguably without any mitochondrion. Yet, questions remain about whether this extends beyond the single species and how this transition took place. The Oxymonadida is a group of gut endobionts taxonomically housed in the Preaxostyla which also contains free-living flagellates of the genera Trimastix and Paratrimastix. The latter two taxa harbour conspicuous mitochondrion-related organelles (MROs). Here we report high-quality genome and transcriptome assemblies of two Preaxostyla representatives, the free-living Paratrimastix pyriformis and the oxymonad Blattamonas nauphoetae. We performed thorough comparisons among all available genomic and transcriptomic data of Preaxostyla to further decipher the evolutionary changes towards amitochondriality, endobiosis, and unstacked Golgi. Our results provide insights into the metabolic and endomembrane evolution, but most strikingly the data confirm the complete loss of mitochondria for all three oxymonad species investigated (M. exilis, B. nauphoetae, and Streblomastix strix), suggesting the amitochondriate status is common to a large part if not the whole group of Oxymonadida. This observation moves this unique loss to 100 MYA when oxymonad lineage diversified.
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Affiliation(s)
- Lukáš V. F. Novák
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
- Université de Bretagne Occidentale, CNRS, Unité Biologie et Ecologie des Ecosystèmes Marins Profonds BEEP, IUEM, Plouzané, France
| | - Sebastian C. Treitli
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
- RG Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jan Pyrih
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
| | - Paweł Hałakuc
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Poland
| | - Shweta V. Pipaliya
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Vojtěch Vacek
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
| | - Ondřej Brzoň
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
| | - Petr Soukal
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
| | - Laura Eme
- Ecology, Systematics, and Evolution Unit, Université Paris-Saclay, CNRS, Orsay, France
| | - Joel B. Dacks
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Poland
| | - Marek Eliáš
- University of Ostrava, Faculty of Science, Department of Biology and Ecology, Ostrava, Czech Republic
| | - Vladimír Hampl
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
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Záhonová K, Füssy Z, Stairs CW, Leger MM, Tachezy J, Čepička I, Roger AJ, Hampl V. Comparative analysis of mitochondrion-related organelles in anaerobic amoebozoans. Microb Genom 2023; 9. [PMID: 37994879 DOI: 10.1099/mgen.0.001143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023] Open
Abstract
Archamoebae comprises free-living or endobiotic amoebiform protists that inhabit anaerobic or microaerophilic environments and possess mitochondrion-related organelles (MROs) adapted to function anaerobically. We compared in silico reconstructed MRO proteomes of eight species (six genera) and found that the common ancestor of Archamoebae possessed very few typical components of the protein translocation machinery, electron transport chain and tricarboxylic acid cycle. On the other hand, it contained a sulphate activation pathway and bacterial iron-sulphur (Fe-S) assembly system of MIS-type. The metabolic capacity of the MROs, however, varies markedly within this clade. The glycine cleavage system is widely conserved among Archamoebae, except in Entamoeba, probably owing to its role in catabolic function or one-carbon metabolism. MRO-based pyruvate metabolism was dispensed within subgroups Entamoebidae and Rhizomastixidae, whereas sulphate activation could have been lost in isolated cases of Rhizomastix libera, Mastigamoeba abducta and Endolimax sp. The MIS (Fe-S) assembly system was duplicated in the common ancestor of Mastigamoebidae and Pelomyxidae, and one of the copies took over Fe-S assembly in their MRO. In Entamoebidae and Rhizomastixidae, we hypothesize that Fe-S cluster assembly in both compartments may be facilitated by dual localization of the single system. We could not find evidence for changes in metabolic functions of the MRO in response to changes in habitat; it appears that such environmental drivers do not strongly affect MRO reduction in this group of eukaryotes.
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Affiliation(s)
- Kristína Záhonová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czechia
- Life Science Research Centre, Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | - Zoltán Füssy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Courtney W Stairs
- Centre for Comparative Genomics and Evolutionary Bioinformatics, and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Present address: Microbiology Research Group, Department of Biology, Lund University, Lund, Sweden
| | - Michelle M Leger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Present address: Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Andrew J Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
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Zítek J, King MS, Peña-Diaz P, Pyrihová E, King AC, Kunji ERS, Hampl V. The free-living flagellate Paratrimastix pyriformis uses a distinct mitochondrial carrier to balance adenine nucleotide pools. Arch Biochem Biophys 2023; 742:109638. [PMID: 37192692 PMCID: PMC10251735 DOI: 10.1016/j.abb.2023.109638] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/12/2023] [Accepted: 05/13/2023] [Indexed: 05/18/2023]
Abstract
Paratrimastix pyriformis is a free-living flagellate thriving in low-oxygen freshwater sediments. It belongs to the group Metamonada along with human parasites, such as Giardia and Trichomonas. Like other metamonads, P. pyriformis has a mitochondrion-related organelle (MRO) which in this protist is primarily involved in one-carbon folate metabolism. The MRO contains four members of the solute carrier family 25 (SLC25) responsible for the exchange of metabolites across the mitochondrial inner membrane. Here, we characterise the function of the adenine nucleotide carrier PpMC1 by thermostability shift and transport assays. We show that it transports ATP, ADP and, to a lesser extent, AMP, but not phosphate. The carrier is distinct in function and origin from both ADP/ATP carriers and ATP-Mg/phosphate carriers, and it most likely represents a distinct class of adenine nucleotide carriers.
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Affiliation(s)
- Justyna Zítek
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, 252 50, Czech Republic
| | - Martin S King
- Medical Research Council Mitochondrial Biology Unit, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Priscila Peña-Diaz
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, 252 50, Czech Republic
| | - Eva Pyrihová
- Medical Research Council Mitochondrial Biology Unit, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom; University of Stavanger, Department of Chemistry, Bioscience, And Environmental Engineering, Richard Johnsens Gate 4, N-4021, Stavanger, Norway
| | - Alannah C King
- Medical Research Council Mitochondrial Biology Unit, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Edmund R S Kunji
- Medical Research Council Mitochondrial Biology Unit, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom.
| | - Vladimír Hampl
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, 252 50, Czech Republic.
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Speijer D. How mitochondria showcase evolutionary mechanisms and the importance of oxygen. Bioessays 2023; 45:e2300013. [PMID: 36965057 DOI: 10.1002/bies.202300013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/10/2023] [Accepted: 03/14/2023] [Indexed: 03/27/2023]
Abstract
Darwinian evolution can be simply stated: natural selection of inherited variations increasing differential reproduction. However, formulated thus, links with biochemistry, cell biology, ecology, and population dynamics remain unclear. To understand interactive contributions of chance and selection, higher levels of biological organization (e.g., endosymbiosis), complexities of competing selection forces, and emerging biological novelties (such as eukaryotes or meiotic sex), we must analyze actual examples. Focusing on mitochondria, I will illuminate how biology makes sense of life's evolution, and the concepts involved. First, looking at the bacterium - mitochondrion transition: merging with an archaeon, it lost its independence, but played a decisive role in eukaryogenesis, as an extremely efficient aerobic ATP generator and internal ROS source. Second, surveying later mitochondrion adaptations and diversifications illustrates concepts such as constructive neutral evolution, dynamic interactions between endosymbionts and hosts, the contingency of life histories, and metabolic reprogramming. Without oxygen, mitochondria disappear; with (intermittent) oxygen diversification occurs in highly complex ways, especially upon (temporary) phototrophic substrate supply. These expositions show the Darwinian model to be a highly fruitful paradigm.
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Affiliation(s)
- Dave Speijer
- Department of Medical Biochemistry, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands
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Onuț-Brännström I, Stairs CW, Campos KIA, Thorén MH, Ettema TJG, Keeling PJ, Bass D, Burki F. A Mitosome With Distinct Metabolism in the Uncultured Protist Parasite Paramikrocytos canceri (Rhizaria, Ascetosporea). Genome Biol Evol 2023; 15:7039708. [PMID: 36790104 PMCID: PMC9998036 DOI: 10.1093/gbe/evad022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/13/2023] [Accepted: 02/07/2023] [Indexed: 02/16/2023] Open
Abstract
Ascetosporea are endoparasites of marine invertebrates that include economically important pathogens of aquaculture species. Owing to their often-minuscule cell sizes, strict intracellular lifestyle, lack of cultured representatives and minimal availability of molecular data, these unicellular parasites remain poorly studied. Here, we sequenced and assembled the genome and transcriptome of Paramikrocytos canceri, an endoparasite isolated from the European edible crab Cancer pagurus. Using bioinformatic predictions, we show that P. canceri likely possesses a mitochondrion-related organelle (MRO) with highly reduced metabolism, resembling the mitosomes of other parasites but with key differences. Like other mitosomes, this MRO is predicted to have reduced metabolic capacity and lack an organellar genome and function in iron-sulfur cluster (ISC) pathway-mediated Fe-S cluster biosynthesis. However, the MRO in P. canceri is uniquely predicted to produce ATP via a partial glycolytic pathway and synthesize phospholipids de novo through the CDP-DAG pathway. Heterologous gene expression confirmed that proteins from the ISC and CDP-DAG pathways retain mitochondrial targeting sequences that are recognized by yeast mitochondria. This represents a unique combination of metabolic pathways in an MRO, including the first reported case of a mitosome-like organelle able to synthesize phospholipids de novo. Some of these phospholipids, such as phosphatidylserine, are vital in other protist endoparasites that invade their host through apoptotic mimicry.
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Affiliation(s)
- Ioana Onuț-Brännström
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden
| | - Courtney W Stairs
- Microbiology Research Group, Department of Biology, Lund University, Lund, Sweden
| | | | - Markus Hiltunen Thorén
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - David Bass
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, United Kingdom.,Department of Life Sciences, The Natural History Museum, London, United Kingdom.,Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Fabien Burki
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Leger MM, Stairs C. Eukaryotic evolution: Spatial proteomics sheds light on mitochondrial reduction. Curr Biol 2022; 32:R1308-R1311. [PMID: 36473440 DOI: 10.1016/j.cub.2022.10.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multi-organelle spatial proteomics has revolutionized animal cell biology, but its use in protists has so far been limited. A new study delivers the first such proteome of a free-living protist, uncovering a previously overlooked function of highly reduced mitochondria.
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Affiliation(s)
- Michelle M Leger
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Pg. Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain.
| | - Courtney Stairs
- Microbiology Research Group, Department of Biology, Lund University, Sölvegatan 35, 223 62 Lund, Sweden.
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