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Audoor S, Bilcke G, Pargana K, Belišová D, Thierens S, Van Bel M, Sterck L, Rijsdijk N, Annunziata R, Ferrante MI, Vandepoele K, Vyverman W. Transcriptional chronology reveals conserved genes involved in pennate diatom sexual reproduction. Mol Ecol 2024; 33:e17320. [PMID: 38506152 DOI: 10.1111/mec.17320] [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: 08/30/2023] [Revised: 01/23/2024] [Accepted: 03/07/2024] [Indexed: 03/21/2024]
Abstract
Sexual reproduction is a major driver of adaptation and speciation in eukaryotes. In diatoms, siliceous microalgae with a unique cell size reduction-restitution life cycle and among the world's most prolific primary producers, sex also acts as the main mechanism for cell size restoration through the formation of an expanding auxospore. However, the molecular regulators of the different stages of sexual reproduction and size restoration are poorly explored. Here, we combined RNA sequencing with the assembly of a 55 Mbp reference genome for Cylindrotheca closterium to identify patterns of gene expression during different stages of sexual reproduction. These were compared with a corresponding transcriptomic time series of Seminavis robusta to assess the degree of expression conservation. Integrative orthology analysis revealed 138 one-to-one orthologues that are upregulated during sex in both species, among which 56 genes consistently upregulated during cell pairing and gametogenesis, and 11 genes induced when auxospores are present. Several early, sex-specific transcription factors and B-type cyclins were also upregulated during sex in other pennate and centric diatoms, pointing towards a conserved core regulatory machinery for meiosis and gametogenesis across diatoms. Furthermore, we find molecular evidence that the pheromone-induced cell cycle arrest is short-lived in benthic diatoms, which may be linked to their active mode of mate finding through gliding. Finally, we exploit the temporal resolution of our comparative analysis to report the first marker genes for auxospore identity called AAE1-3 ("Auxospore-Associated Expression"). Altogether, we introduce a multi-species model of the transcriptional dynamics during size restoration in diatoms and highlight conserved gene expression dynamics during different stages of sexual reproduction.
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Affiliation(s)
- Sien Audoor
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Ghent, Ghent, Belgium
| | - Gust Bilcke
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Ghent, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Katerina Pargana
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Ghent, Ghent, Belgium
| | - Darja Belišová
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Ghent, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Sander Thierens
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Michiel Van Bel
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Lieven Sterck
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Nadine Rijsdijk
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Ghent, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | | | - Maria Immacolata Ferrante
- Stazione Zoologica Anton Dohrn, Naples, Italy
- Associate to the National Institute of Oceanography and Applied Geophysics, Trieste, Italy
| | - Klaas Vandepoele
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for AI & Computational Biology, VIB, Ghent, Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Ghent, Ghent, Belgium
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Verner Z, Žárský V, Le T, Narayanasamy RK, Rada P, Rozbeský D, Makki A, Belišová D, Hrdý I, Vancová M, Lender C, König C, Bruchhaus I, Tachezy J. Anaerobic peroxisomes in Entamoeba histolytica metabolize myo-inositol. PLoS Pathog 2021; 17:e1010041. [PMID: 34780573 PMCID: PMC8629394 DOI: 10.1371/journal.ppat.1010041] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 06/12/2021] [Revised: 11/29/2021] [Accepted: 10/18/2021] [Indexed: 11/19/2022] Open
Abstract
Entamoeba histolytica is believed to be devoid of peroxisomes, like most anaerobic protists. In this work, we provided the first evidence that peroxisomes are present in E. histolytica, although only seven proteins responsible for peroxisome biogenesis (peroxins) were identified (Pex1, Pex6, Pex5, Pex11, Pex14, Pex16, and Pex19). Targeting matrix proteins to peroxisomes is reduced to the PTS1-dependent pathway mediated via the soluble Pex5 receptor, while the PTS2 receptor Pex7 is absent. Immunofluorescence microscopy showed that peroxisomal markers (Pex5, Pex14, Pex16, Pex19) are present in vesicles distinct from mitosomes, the endoplasmic reticulum, and the endosome/phagosome system, except Pex11, which has dual localization in peroxisomes and mitosomes. Immunoelectron microscopy revealed that Pex14 localized to vesicles of approximately 90-100 nm in diameter. Proteomic analyses of affinity-purified peroxisomes and in silico PTS1 predictions provided datasets of 655 and 56 peroxisomal candidates, respectively; however, only six proteins were shared by both datasets, including myo-inositol dehydrogenase (myo-IDH). Peroxisomal NAD-dependent myo-IDH appeared to be a dimeric enzyme with high affinity to myo-inositol (Km 0.044 mM) and can utilize also scyllo-inositol, D-glucose and D-xylose as substrates. Phylogenetic analyses revealed that orthologs of myo-IDH with PTS1 are present in E. dispar, E. nutalli and E. moshkovskii but not in E. invadens, and form a monophyletic clade of mostly peroxisomal orthologs with free-living Mastigamoeba balamuthi and Pelomyxa schiedti. The presence of peroxisomes in E. histolytica and other archamoebae breaks the paradigm of peroxisome absence in anaerobes and provides a new potential target for the development of antiparasitic drugs.
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Affiliation(s)
- Zdeněk Verner
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Vojtěch Žárský
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Tien Le
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ravi Kumar Narayanasamy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Petr Rada
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Daniel Rozbeský
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Abhijith Makki
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Darja Belišová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ivan Hrdý
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Marie Vancová
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, Ceske Budejovice, Czech Republic
| | - Corinna Lender
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Constantin König
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Iris Bruchhaus
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
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