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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Kučerová J, Zdrha A, Shinde A, Harant K, Hrdý I, Tachezy J. The divergent ER-mitochondria encounter structures (ERMES) are conserved in parabasalids but lost in several anaerobic lineages with hydrogenosomes. BMC Biol 2023; 21:259. [PMID: 37968591 PMCID: PMC10648710 DOI: 10.1186/s12915-023-01765-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/09/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND The endoplasmic reticulum (ER)-mitochondria membrane contact sites (MCS) are extensively studied in aerobic eukaryotes; however, little is known about MCS in anaerobes with reduced forms of mitochondria named hydrogenosomes. In several eukaryotic lineages, the direct physical tether between ER and the outer mitochondrial membrane is formed by ER-mitochondria encounter structure (ERMES). The complex consists of four core proteins (Mmm1, Mmm2, Mdm12, and Mdm10) which are involved in phospholipid trafficking. Here we investigated ERMES distribution in organisms bearing hydrogenosomes and employed Trichomonas vaginalis as a model to estimate ERMES cellular localization, structure, and function. RESULTS Homology searches revealed that Parabasalia-Anaeramoebae, anaerobic jakobids, and anaerobic fungi are lineages with hydrogenosomes that retain ERMES, while ERMES components were gradually lost in Fornicata, and are absent in Preaxostyla and Archamoebae. In T. vaginalis and other parabasalids, three ERMES components were found with the expansion of Mmm1. Immunofluorescence microscopy confirmed that Mmm1 localized in ER, while Mdm12 and Mmm2 were partially localized in hydrogenosomes. Pull-down assays and mass spectrometry of the ERMES components identified a parabasalid-specific Porin2 as a substitute for the Mdm10. ERMES modeling predicted a formation of a continuous hydrophobic tunnel of TvMmm1-TvMdm12-TvMmm2 that is anchored via Porin2 to the hydrogenosomal outer membrane. Phospholipid-ERMES docking and Mdm12-phospholipid dot-blot indicated that ERMES is involved in the transport of phosphatidylinositol phosphates. The absence of enzymes involved in hydrogenosomal phospholipid metabolism implies that ERMES is not involved in the exchange of substrates between ER and hydrogenosomes but in the unidirectional import of phospholipids into hydrogenosomal membranes. CONCLUSIONS Our investigation demonstrated that ERMES mediates ER-hydrogenosome interactions in parabasalid T. vaginalis, while the complex was lost in several other lineages with hydrogenosomes.
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Affiliation(s)
- Jitka Kučerová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242, Vestec, Czech Republic
| | - Alois Zdrha
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242, Vestec, Czech Republic
| | - Abhishek Shinde
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242, Vestec, Czech Republic
| | - Karel Harant
- OMICS Proteomics Laboratory, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242, Vestec, Czech Republic
| | - Ivan Hrdý
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242, Vestec, Czech Republic
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242, Vestec, Czech Republic.
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Abstract
This review is dedicated to the 50th anniversary of the discovery of hydrogenosomes by Miklós Müller and Donald Lindmark, which we will celebrate the following year. It was a long journey from the first observation of enigmatic rows of granules in trichomonads at the end of the 19th century to their first biochemical characterization in 1973. The key experiments by Müller and Lindmark revealed that the isolated granules contain hydrogen-producing hydrogenase, similar to some anaerobic bacteria-a discovery that gave birth to the field of hydrogenosomes. It is also important to acknowledge the parallel work of the team of Apolena Čerkasovová, Jiří Čerkasov, and Jaroslav Kulda, who demonstrated that these granules, similar to mitochondria, produce ATP. However, the evolutionary origin of hydrogenosomes remained enigmatic until the turn of the millennium, when it was finally accepted that hydrogenosomes and mitochondria evolved from a common ancestor. After a historical introduction, the review provides an overview of hydrogenosome biogenesis, hydrogenosomal protein import, and the relationship between the peculiar structure of membrane translocases and its low inner membrane potential due to the lack of respiratory complexes. Next, it summarizes the current state of knowledge on energy metabolism, the oxygen defense system, and iron/sulfur cluster assembly.
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Affiliation(s)
- Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic
| | - Abhijith Makki
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic
| | - Ivan Hrdý
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic
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Abstract
Monocercomonoides exilis is considered the first known eukaryote to completely lack mitochondria. This conclusion is based primarily on a genomic and transcriptomic study which failed to identify any mitochondrial hallmark proteins. However, the available genome assembly has limited contiguity and around 1.5 % of the genome sequence is represented by unknown bases. To improve the contiguity, we re-sequenced the genome and transcriptome of M. exilis using Oxford Nanopore Technology (ONT). The resulting draft genome is assembled in 101 contigs with an N50 value of 1.38 Mbp, almost 20 times higher than the previously published assembly. Using a newly generated ONT transcriptome, we further improve the gene prediction and add high quality untranslated region (UTR) annotations, in which we identify two putative polyadenylation signals present in the 3′UTR regions and characterise the Kozak sequence in the 5′UTR regions. All these improvements are reflected by higher BUSCO genome completeness values. Regardless of an overall more complete genome assembly without missing bases and a better gene prediction, we still failed to identify any mitochondrial hallmark genes, thus further supporting the hypothesis on the absence of mitochondrion.
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Affiliation(s)
- Sebastian Cristian Treitli
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252 42 Vestec, Czech Republic
| | - Priscila Peña-Diaz
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252 42 Vestec, Czech Republic
| | - Paweł Hałakuc
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252 42 Vestec, Czech Republic
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Abstract
Trichomonas vaginalis is an anaerobic/microaerophilic protist parasite which causes trichomoniasis, one of the most prevalent sexually transmitted diseases worldwide. T. vaginalis not only is important as a human pathogen but also is of great biological interest because of its peculiar cell biology and metabolism, in earlier times fostering the erroneous notion that this microorganism is at the root of eukaryotic evolution. This review summarizes the major advances in the last five years in the T. vaginalis field with regard to genetics, molecular biology, ecology, and pathogenicity of the parasite.
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Affiliation(s)
- David Leitsch
- Department of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Vienna, Austria
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Ferdigg A, Dimmer KS, Rapaport D, Vitali DG. Hydrogenosomal tail-anchored proteins are targeted to both mitochondria and ER upon their expression in yeast cells. PLoS One 2020; 15:e0237982. [PMID: 32817700 PMCID: PMC7446849 DOI: 10.1371/journal.pone.0237982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 08/06/2020] [Indexed: 11/18/2022] Open
Abstract
Some organisms, like Trichomonas vaginalis, contain mitochondria-related hydrogen-producing organelles, called hydrogenosomes. The protein targeting into these organelles is proposed to be similar to the well-studied mitochondria import. Indeed, S. cerevisiae mitochondria and T. vaginalis hydrogenosomes share some components of protein import complexes. However, it is still unknown whether targeting signals directing substrate proteins to hydrogenosomes can support in other eukaryotes specific mitochondrial localization. To address this issue, we investigated the intracellular localization of three hydrogenosomal tail-anchored proteins expressed in yeast cells. We observed that these proteins were targeted to both mitochondria and ER with a variable dependency on the mitochondrial MIM complex. Our results suggest that the targeting signal of TA proteins are only partially conserved between hydrogenosomes and yeast mitochondria.
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Affiliation(s)
- Andrè Ferdigg
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Kai S. Dimmer
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
- * E-mail: (DR); (DGV)
| | - Daniela G. Vitali
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
- * E-mail: (DR); (DGV)
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