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Foučková M, Uhrová K, Kubánková A, Pánek T, Čepička I. Lighting lantern above Psalteriomonadidae: Unveiling novel diversity within the genus Psalteriomonas (Discoba: Heterolobosea). Eur J Protistol 2024; 93:126052. [PMID: 38302295 DOI: 10.1016/j.ejop.2024.126052] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
Psalteriomonadidae are a small family of anaerobic free-living protists belonging to Heterolobosea, Discoba. We cultured 74 new strains of mostly amoeboid Psalteriomonadidae obtained from mainly freshwater habitats and sequenced their 18S rRNA gene. Based on the phylogenetic analysis and genetic distances, we report multiple novel species, four of which we formally describe based on the light-microscopic morphology (Psalteriomonas minuta, P. australis, P. fimbriata, and P. parva). We also examined the ultrastructure of two Psalteriomonas species using transmission electron microscopy. We transfer Sawyeria marylandensis into the genus Psalteriomonas and synonymize Sawyeria with Psalteriomonas. In addition, we studied the flagellate stage of P. marylandensis comb. nov. for the first time, using light and scanning electron microscopy.
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Affiliation(s)
- Martina Foučková
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 128 00, Czech Republic
| | - Kristýna Uhrová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 128 00, Czech Republic
| | - Aneta Kubánková
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 128 00, Czech Republic
| | - Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 128 00, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 128 00, Czech Republic.
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Rotterová J, Pánek T, Salomaki ED, Kotyk M, Táborský P, Kolísko M, Čepička I. Single cell transcriptomics reveals UAR codon reassignment in Palmarella salina (Metopida, Armophorea) and confirms Armophorida belongs to APM clade. Mol Phylogenet Evol 2024; 191:107991. [PMID: 38092322 DOI: 10.1016/j.ympev.2023.107991] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 12/04/2023] [Accepted: 12/09/2023] [Indexed: 12/17/2023]
Abstract
Anaerobes have emerged in several major lineages of ciliates, but the number of independent transitions to anaerobiosis among ciliates is unknown. The APM clade (Armophorea, Muranotrichea, Parablepharismea) represents the largest clade of obligate anaerobes among ciliates and contains free-living marine and freshwater representatives as well as gut endobionts of animals. The evolution of APM group has only recently started getting attention, and our knowledge on its phylogeny and genetics is still limited to a fraction of taxa. While ciliates portray a wide array of alternatives to the standard genetic code across numerous classes, the APM ciliates were considered to be the largest group using exclusively standard nuclear genetic code. In this study, we present a pan-ciliate phylogenomic analysis with emphasis on the APM clade, bringing the first phylogenomic analysis of the family Tropidoatractidae (Armophorea) and confirming the position of Armophorida within Armophorea. We include five newly sequenced single cell transcriptomes from marine, freshwater, and endobiotic APM ciliates - Palmarella salina, Anteclevelandella constricta, Nyctotherus sp., Caenomorpha medusula, and Thigmothrix strigosa. We report the first discovery of an alternative nuclear genetic code among APM ciliates, used by Palmarella salina (Tropidoatractidae, Armophorea), but not by its close relative, Tropidoatractus sp., and provide a comparative analysis of stop codon identity and frequency indicating the precedency to the UAG codon loss/reassignment over the UAA codon reassignment in the specific ancestor of Palmarella. Comparative genomic and proteomic studies of this group may help explain the constraints that underlie UAR stop-to-sense reassignment, the most frequent type of alternative nuclear genetic code, not only in ciliates, but eukaryotes in general.
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Affiliation(s)
- Johana Rotterová
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic; Department of Marine Sciences, University of Puerto Rico Mayagüez, Mayagüez, PR, USA.
| | - Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
| | - Eric D Salomaki
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice 370 05, Czech Republic; Center for Computational Biology of Human Disease and Center for Computation and Visualization, Brown University, Providence, Rhode Island, USA
| | - Michael Kotyk
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
| | - Petr Táborský
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
| | - Martin Kolísko
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice 370 05, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic.
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3
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Del Campo J, Carlos-Oliveira M, Čepička I, Hehenberger E, Horák A, Karnkowska A, Kolisko M, Lara E, Lukeš J, Pánek T, Piwosz K, Richter DJ, Škaloud P, Sutak R, Tachezy J, Hampl V. The protist cultural renaissance. Trends Microbiol 2024; 32:128-131. [PMID: 38102035 DOI: 10.1016/j.tim.2023.11.010] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/20/2023] [Accepted: 11/24/2023] [Indexed: 12/17/2023]
Abstract
Protists are key players in the biosphere. Here, we provide a perspective on integrating protist culturing with omics approaches, imaging, and high-throughput single-cell manipulation strategies, concluding with actions required for a successful return of the golden age of protist culturing.
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Affiliation(s)
- Javier Del Campo
- Biodiversity Program, Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Catalonia, Spain.
| | - Maria Carlos-Oliveira
- Functional Genomics and Evolution Program, Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Elisabeth Hehenberger
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic; Department of Molecular Biology, University of South Bohemia, České Budějovice, Czech Republic
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Martin Kolisko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic; Department of Molecular Biology, University of South Bohemia, České Budějovice, Czech Republic
| | - Enrique Lara
- Department of Mycology, Real Jardín Botánico-CSIC, Madrid, Spain
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic; Department of Molecular Biology, University of South Bohemia, České Budějovice, Czech Republic
| | - Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Kasia Piwosz
- Department of Fisheries Oceanography and Marine Ecology, National Marine Fisheries Research Institute, Gdynia, Poland
| | - Daniel J Richter
- Functional Genomics and Evolution Program, Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Pavel Škaloud
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Robert Sutak
- Department of Parasitology, Faculty of Science, BIOCEV, Charles University, Vestec, Czech Republic
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, BIOCEV, Charles University, Vestec, Czech Republic
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, BIOCEV, Charles University, Vestec, Czech Republic
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Jones RE, Tice AK, Eliáš M, Eme L, Kolísko M, Nenarokov S, Pánek T, Rokas A, Salomaki E, Strassert JFH, Shen XX, Žihala D, Brown MW. Create, Analyze, and Visualize Phylogenomic Datasets Using PhyloFisher. Curr Protoc 2024; 4:e969. [PMID: 38265166 DOI: 10.1002/cpz1.969] [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] [Indexed: 01/25/2024]
Abstract
PhyloFisher is a software package written primarily in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that consist of protein sequences from eukaryotic organisms. Unlike many existing phylogenomic pipelines, PhyloFisher comes with a manually curated database of 240 protein-coding genes, a subset of a previous phylogenetic dataset sampled from 304 eukaryotic taxa. The software package can also utilize a user-created database of eukaryotic proteins, which may be more appropriate for shallow evolutionary questions. PhyloFisher is also equipped with a set of utilities to aid in running routine analyses, such as the prediction of alternative genetic codes, removal of genes and/or taxa based on occupancy/completeness of the dataset, testing for amino acid compositional heterogeneity among sequences, removal of heterotachious and/or fast-evolving sites, removal of fast-evolving taxa, supermatrix creation from randomly resampled genes, and supermatrix creation from nucleotide sequences. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Constructing a phylogenomic dataset Basic Protocol 2: Performing phylogenomic analyses Support Protocol 1: Installing PhyloFisher Support Protocol 2: Creating a custom phylogenomic database.
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Affiliation(s)
- Robert E Jones
- Department of Biological Sciences, Mississippi State University, Starkville, Mississippi, USA
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Starkville, Mississippi, USA
| | - Alexander K Tice
- Department of Biological Sciences, Mississippi State University, Starkville, Mississippi, USA
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Starkville, Mississippi, USA
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Laura Eme
- Unité d'Ecologie, Systématique et Evolution, CNRS, Université Paris-Saclay France, Orsay, France
| | - Martin Kolísko
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice Czech Republic, USA
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Serafim Nenarokov
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice Czech Republic, USA
| | - Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Eric Salomaki
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice Czech Republic, USA
- Center for Computational Biology of Human Disease and Center for Computation and Visualization, Brown University, Providence, Rhode Island, USA
| | - Jürgen F H Strassert
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Xing-Xing Shen
- Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - David Žihala
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Starkville, Mississippi, USA
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Starkville, Mississippi, USA
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Sheikh S, Pánek T, Gahura O, Týč J, Záhonová K, Lukeš J, Eliáš M, Hashimi H. A novel group of dynamin-related proteins shared by eukaryotes and giant viruses is able to remodel mitochondria from within the matrix. Mol Biol Evol 2023:7190697. [PMID: 37279941 DOI: 10.1093/molbev/msad134] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/05/2023] [Accepted: 06/04/2023] [Indexed: 06/08/2023] Open
Abstract
The diverse GTPases of the dynamin superfamily play various roles in the cell, as exemplified by the dynamin-related proteins (DRPs) Mgm1 and Opa1, which remodel the mitochondrial inner membrane in fungi and metazoans, respectively. Via an exhaustive search of genomic and metagenomic databases we found previously unknown DRP types occurring in diverse eukaryotes and giant viruses (phylum Nucleocytoviricota). One novel DRP clade, termed MidX, combined hitherto uncharacterized proteins from giant viruses and six distantly related eukaryote taxa (Stramenopiles, Telonemia, Picozoa, Amoebozoa, Apusomonadida, and Choanoflagellata). MidX stood out because it was not only predicted to be mitochondria-targeted, but also to assume a tertiary structure not observed in other DRPs before. To understand how MidX affects mitochondria, we exogenously expressed MidX from Hyperionvirus in the kinetoplastid Trypanosoma brucei, which lacks Mgm1 or Opa1 orthologs. MidX massively affected mitochondrial morphology from inside the matrix, where it closely associates with the inner membrane. This unprecedented mode of action is contrasts to those of Mgm1 and Opa1, which mediate inner membrane remodeling in the intermembrane space. We speculate that MidX was acquired in Nucleocytoviricota evolution by horizontal gene transfer from eukaryotes and is used by giant viruses to remodel host mitochondria during infection. MidX's unique structure may be an adaptation for reshaping mitochondria from the inside. Finally, Mgm1 forms a sister to MidX and not Opa1 in our phylogenetic analysis, throwing into question the long-presumed homology of these DRPs with similar roles in sister lineages.
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Affiliation(s)
- Shaghayegh Sheikh
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ondřej Gahura
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jiří Týč
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Kristína Záhonová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - 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
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Hassan Hashimi
- 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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Pilátová J, Pánek T, Oborník M, Čepička I, Mojzeš P. Revisiting biocrystallization: purine crystalline inclusions are widespread in eukaryotes. ISME J 2022; 16:2290-2294. [PMID: 35672454 PMCID: PMC9381591 DOI: 10.1038/s41396-022-01264-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 11/09/2022]
Abstract
Despite the widespread occurrence of intracellular crystalline inclusions in unicellular eukaryotes, scant attention has been paid to their composition, functions, and evolutionary origins. Using Raman microscopy, we examined >200 species from all major eukaryotic supergroups. We detected cellular crystalline inclusions in 77% species out of which 80% is composed of purines, such as anhydrous guanine (62%), guanine monohydrate (2%), uric acid (12%) and xanthine (4%). Our findings shifts the paradigm assuming predominance of calcite and oxalates. Purine crystals emerge in microorganisms in all habitats, e.g., in freshwater algae, endosymbionts of reef-building corals, deadly parasites, anaerobes in termite guts, or slime molds. Hence, purine biocrystallization is a general and ancestral eukaryotic process likely present in the last eukaryotic common ancestor (LECA) and here we propose two proteins omnipresent in eukaryotes that are likely in charge of their metabolism: hypoxanthine-guanine phosphoribosyl transferase and equilibrative nucleoside transporter. Purine crystalline inclusions are multifunctional structures representing high-capacity and rapid-turnover reserves of nitrogen and optically active elements, e.g., used in light sensing. Thus, we anticipate our work to be a starting point for further studies spanning from cell biology to global ecology, with potential applications in biotechnologies, bio-optics, or in human medicine.
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Affiliation(s)
- Jana Pilátová
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague 2, Czech Republic.
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Prague 2, Czech Republic.
- Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Czech Republic.
| | - Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University, Prague 2, Czech Republic
| | - Miroslav Oborník
- Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Czech Republic
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague 2, Czech Republic
| | - Peter Mojzeš
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Prague 2, Czech Republic
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Azuma T, Pánek T, Tice AK, Kayama M, Kobayashi M, Miyashita H, Suzaki T, Yabuki A, Brown MW, Kamikawa R. An enigmatic stramenopile sheds light on early evolution in Ochrophyta plastid organellogenesis. Mol Biol Evol 2022; 39:6555011. [PMID: 35348760 PMCID: PMC9004409 DOI: 10.1093/molbev/msac065] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ochrophyta is an algal group belonging to the Stramenopiles and comprises diverse lineages of algae which contribute significantly to the oceanic ecosystems as primary producers. However, early evolution of the plastid organelle in Ochrophyta is not fully understood. In this study, we provide a well-supported tree of the Stramenopiles inferred by the large-scale phylogenomic analysis that unveils the eukaryvorous (nonphotosynthetic) protist Actinophrys sol (Actinophryidae) is closely related to Ochrophyta. We used genomic and transcriptomic data generated from A. sol to detect molecular traits of its plastid and we found no evidence of plastid genome and plastid-mediated biosynthesis, consistent with previous ultrastructural studies that did not identify any plastids in Actinophryidae. Moreover, our phylogenetic analyses of particular biosynthetic pathways provide no evidence of a current and past plastid in A. sol. However, we found more than a dozen organellar aminoacyl-tRNA synthases (aaRSs) that are of algal origin. Close relationships between aaRS from A. sol and their ochrophyte homologs document gene transfer of algal genes that happened before the divergence of Actinophryidae and Ochrophyta lineages. We further showed experimentally that organellar aaRSs of A. sol are targeted exclusively to mitochondria, although organellar aaRSs in Ochrophyta are dually targeted to mitochondria and plastids. Together, our findings suggested that the last common ancestor of Actinophryidae and Ochrophyta had not yet completed the establishment of host–plastid partnership as seen in the current Ochrophyta species, but acquired at least certain nuclear-encoded genes for the plastid functions.
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Affiliation(s)
- Tomonori Azuma
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida nihonmatsu cho, Sakyo ku, Kyoto, Kyoto, Japan
| | - Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Alexander K Tice
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Motoki Kayama
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida nihonmatsu cho, Sakyo ku, Kyoto, Kyoto, Japan
| | | | - Hideaki Miyashita
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida nihonmatsu cho, Sakyo ku, Kyoto, Kyoto, Japan
| | | | - Akinori Yabuki
- Japan Agency for Marine-Earth Science and Technology, Japan
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Ryoma Kamikawa
- Graduate School of Agriculture, Kyoto University, Kitashirakawa oiwake cho, Sakyo ku, Kyoto, Kyoto, Japan
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Pánek T, Barcytė D, Treitli SC, Záhonová K, Sokol M, Ševčíková T, Zadrobílková E, Jaške K, Yubuki N, Čepička I, Eliáš M. A new lineage of non-photosynthetic green algae with extreme organellar genomes. BMC Biol 2022; 20:66. [PMID: 35296310 PMCID: PMC8928634 DOI: 10.1186/s12915-022-01263-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/22/2022] [Indexed: 12/27/2022] Open
Abstract
Background The plastid genomes of the green algal order Chlamydomonadales tend to expand their non-coding regions, but this phenomenon is poorly understood. Here we shed new light on organellar genome evolution in Chlamydomonadales by studying a previously unknown non-photosynthetic lineage. We established cultures of two new Polytoma-like flagellates, defined their basic characteristics and phylogenetic position, and obtained complete organellar genome sequences and a transcriptome assembly for one of them. Results We discovered a novel deeply diverged chlamydomonadalean lineage that has no close photosynthetic relatives and represents an independent case of photosynthesis loss. To accommodate these organisms, we establish the new genus Leontynka, with two species (L. pallida and L. elongata) distinguishable through both their morphological and molecular characteristics. Notable features of the colourless plastid of L. pallida deduced from the plastid genome (plastome) sequence and transcriptome assembly include the retention of ATP synthase, thylakoid-associated proteins, the carotenoid biosynthesis pathway, and a plastoquinone-based electron transport chain, the latter two modules having an obvious functional link to the eyespot present in Leontynka. Most strikingly, the ~362 kbp plastome of L. pallida is by far the largest among the non-photosynthetic eukaryotes investigated to date due to an extreme proliferation of sequence repeats. These repeats are also present in coding sequences, with one repeat type found in the exons of 11 out of 34 protein-coding genes, with up to 36 copies per gene, thus affecting the encoded proteins. The mitochondrial genome of L. pallida is likewise exceptionally large, with its >104 kbp surpassed only by the mitogenome of Haematococcus lacustris among all members of Chlamydomonadales hitherto studied. It is also bloated with repeats, though entirely different from those in the L. pallida plastome, which contrasts with the situation in H. lacustris where both the organellar genomes have accumulated related repeats. Furthermore, the L. pallida mitogenome exhibits an extremely high GC content in both coding and non-coding regions and, strikingly, a high number of predicted G-quadruplexes. Conclusions With its unprecedented combination of plastid and mitochondrial genome characteristics, Leontynka pushes the frontiers of organellar genome diversity and is an interesting model for studying organellar genome evolution. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01263-w.
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Affiliation(s)
- Tomáš Pánek
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 00, Ostrava, Czech Republic.,Department of Zoology, Faculty of Science, Charles University, 128 43, Prague, Czech Republic
| | - Dovilė Barcytė
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 00, Ostrava, Czech Republic
| | - Sebastian C Treitli
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, 252 42, Vestec, Czech Republic
| | - Kristína Záhonová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 00, Ostrava, Czech Republic
| | - Martin Sokol
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 00, Ostrava, Czech Republic
| | - Tereza Ševčíková
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 00, Ostrava, Czech Republic
| | - Eliška Zadrobílková
- Department of Zoology, Faculty of Science, Charles University, 128 43, Prague, Czech Republic
| | - Karin Jaške
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 00, Ostrava, Czech Republic
| | - Naoji Yubuki
- Department of Zoology, Faculty of Science, Charles University, 128 43, Prague, Czech Republic.,Bioimaging Facility, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, 128 43, Prague, Czech Republic
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 00, Ostrava, Czech Republic.
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9
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Stairs CW, Táborský P, Salomaki ED, Kolisko M, Pánek T, Eme L, Hradilová M, Vlček Č, Jerlström-Hultqvist J, Roger AJ, Čepička I. Anaeramoebae are a divergent lineage of eukaryotes that shed light on the transition from anaerobic mitochondria to hydrogenosomes. Curr Biol 2021; 31:5605-5612.e5. [PMID: 34710348 DOI: 10.1016/j.cub.2021.10.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/07/2021] [Accepted: 10/05/2021] [Indexed: 01/02/2023]
Abstract
Discoveries of diverse microbial eukaryotes and their inclusion in comprehensive phylogenomic analyses have crucially re-shaped the eukaryotic tree of life in the 21st century.1 At the deepest level, eukaryotic diversity comprises 9-10 "supergroups." One of these supergroups, the Metamonada, is particularly important to our understanding of the evolutionary dynamics of eukaryotic cells, including the remodeling of mitochondrial function. All metamonads thrive in low-oxygen environments and lack classical aerobic mitochondria, instead possessing mitochondrion-related organelles (MROs) with metabolisms that are adapted to low-oxygen conditions. These MROs lack an organellar genome, do not participate in the Krebs cycle and oxidative phosphorylation,2 and often synthesize ATP by substrate-level phosphorylation coupled to hydrogen production.3,4 The events that occurred during the transition from an oxygen-respiring mitochondrion to a functionally streamlined MRO early in metamonad evolution remain largely unknown. Here, we report transcriptomes of two recently described, enigmatic, anaerobic protists from the genus Anaeramoeba.5 Using phylogenomic analysis, we show that these species represent a divergent, phylum-level lineage in the tree of metamonads, emerging as a sister group of the Parabasalia and reordering the deep branching order of the metamonad tree. Metabolic reconstructions of the Anaeramoeba MROs reveal many "classical" mitochondrial features previously not seen in metamonads, including a disulfide relay import system, propionate production, and amino acid metabolism. Our findings suggest that the cenancestor of Metamonada likely had MROs with more classical mitochondrial features than previously anticipated and demonstrate how discoveries of novel lineages of high taxonomic rank continue to transform our understanding of early eukaryote evolution.
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Affiliation(s)
- Courtney W Stairs
- Department of Biology, Lund University, Sölvegatan 35, 223 62 Lund, Sweden.
| | - Petr Táborský
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague, Czech Republic
| | - Eric D Salomaki
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Martin Kolisko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague, Czech Republic
| | - Laura Eme
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, 91400 Orsay, France
| | - Miluše Hradilová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Čestmír Vlček
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Jon Jerlström-Hultqvist
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College St. Halifax, NS B3H 4R2, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College St. Halifax, NS B3H 4R2, Canada
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague, Czech Republic.
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10
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Abstract
Cristae are infoldings of the mitochondrial inner membrane jutting into the organelle's innermost compartment from narrow stems at their base called crista junctions. They are emblematic of aerobic mitochondria, being the fabric for the molecular machinery driving cellular respiration. Electron microscopy revealed that diverse eukaryotes possess cristae of different shapes. Yet, crista diversity has not been systematically examined in light of our current knowledge about eukaryotic evolution. Since crista form and function are intricately linked, we take a holistic view of factors that may underlie both crista diversity and the adherence of cristae to a recognizable form. Based on electron micrographs of 226 species from all major lineages, we propose a rational crista classification system that postulates cristae as variations of two general morphotypes: flat and tubulo-vesicular. The latter is most prevalent and likely ancestral, but both morphotypes are found interspersed throughout the eukaryotic tree. In contrast, crista junctions are remarkably conserved, supporting their proposed role as diffusion barriers that sequester cristae contents. Since cardiolipin, ATP synthase dimers, the MICOS complex, and dynamin-like Opa1/Mgm1 are known to be involved in shaping cristae, we examined their variation in the context of crista diversity. Moreover, we have identified both commonalities and differences that may collectively be manifested as diverse variations of crista form and function.
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Affiliation(s)
- Tomáš Pánek
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava 710 00, Czech Republic
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava 710 00, Czech Republic
| | - Marie Vancová
- Institute of Parasitology, Biology Center, Czech Academy of Sciences and Faculty of Science, University of South Bohemia, České Budějovice 370 05, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Center, Czech Academy of Sciences and Faculty of Science, University of South Bohemia, České Budějovice 370 05, Czech Republic
| | - Hassan Hashimi
- Institute of Parasitology, Biology Center, Czech Academy of Sciences and Faculty of Science, University of South Bohemia, České Budějovice 370 05, Czech Republic.
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11
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Horváthová L, Žárský V, Pánek T, Derelle R, Pyrih J, Motyčková A, Klápšťová V, Vinopalová M, Marková L, Voleman L, Klimeš V, Petrů M, Vaitová Z, Čepička I, Hryzáková K, Harant K, Gray MW, Chami M, Guilvout I, Francetic O, Franz Lang B, Vlček Č, Tsaousis AD, Eliáš M, Doležal P. Analysis of diverse eukaryotes suggests the existence of an ancestral mitochondrial apparatus derived from the bacterial type II secretion system. Nat Commun 2021; 12:2947. [PMID: 34011950 PMCID: PMC8134430 DOI: 10.1038/s41467-021-23046-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 03/22/2021] [Indexed: 12/14/2022] Open
Abstract
The type 2 secretion system (T2SS) is present in some Gram-negative eubacteria and used to secrete proteins across the outer membrane. Here we report that certain representative heteroloboseans, jakobids, malawimonads and hemimastigotes unexpectedly possess homologues of core T2SS components. We show that at least some of them are present in mitochondria, and their behaviour in biochemical assays is consistent with the presence of a mitochondrial T2SS-derived system (miT2SS). We additionally identified 23 protein families co-occurring with miT2SS in eukaryotes. Seven of these proteins could be directly linked to the core miT2SS by functional data and/or sequence features, whereas others may represent different parts of a broader functional pathway, possibly also involving the peroxisome. Its distribution in eukaryotes and phylogenetic evidence together indicate that the miT2SS-centred pathway is an ancestral eukaryotic trait. Our findings thus have direct implications for the functional properties of the early mitochondrion. Bacteria use the type 2 secretion system to secrete enzymes and toxins across the outer membrane to the environment. Here the authors analyse the T2SS pathway in three protist lineages and suggest that the early mitochondrion may have been capable of secreting proteins into the cytosol.
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Affiliation(s)
- Lenka Horváthová
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Vojtěch Žárský
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Tomáš Pánek
- Faculty of Science, Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic.,Faculty of Science, Department of Zoology, Charles University, Prague 2, Czech Republic
| | - Romain Derelle
- School of Biosciences, University of Birmingham, Edgbaston, UK
| | - Jan Pyrih
- Laboratory of Molecular & Evolutionary Parasitology, RAPID group, School of Biosciences, University of Kent, Canterbury, UK.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Alžběta Motyčková
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Veronika Klápšťová
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Martina Vinopalová
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Lenka Marková
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Luboš Voleman
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Vladimír Klimeš
- Faculty of Science, Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic
| | - Markéta Petrů
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Zuzana Vaitová
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ivan Čepička
- Faculty of Science, Department of Zoology, Charles University, Prague 2, Czech Republic
| | - Klára Hryzáková
- Faculty of Science, Department of Genetics and Microbiology, Charles University, Prague 2, Czech Republic
| | - Karel Harant
- Faculty of Science, Proteomic core facility, Charles University, BIOCEV, Vestec, Czech Republic
| | - Michael W Gray
- Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada
| | - Mohamed Chami
- Center for Cellular Imaging and NanoAnalytics, University of Basel, Basel, Switzerland
| | - Ingrid Guilvout
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Olivera Francetic
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - B Franz Lang
- Robert Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Montréal, Montreal, QC, Canada
| | - Čestmír Vlček
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague 4, Czech Republic
| | - Anastasios D Tsaousis
- Laboratory of Molecular & Evolutionary Parasitology, RAPID group, School of Biosciences, University of Kent, Canterbury, UK
| | - Marek Eliáš
- Faculty of Science, Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic.
| | - Pavel Doležal
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic.
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12
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Pyrih J, Pánek T, Durante IM, Rašková V, Cimrhanzlová K, Kriegová E, Tsaousis AD, Eliáš M, Lukeš J. Vestiges of the Bacterial Signal Recognition Particle-Based Protein Targeting in Mitochondria. Mol Biol Evol 2021; 38:3170-3187. [PMID: 33837778 PMCID: PMC8321541 DOI: 10.1093/molbev/msab090] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 02/23/2021] [Indexed: 12/22/2022] Open
Abstract
The main bacterial pathway for inserting proteins into the plasma membrane relies on the signal recognition particle (SRP), composed of the Ffh protein and an associated RNA component, and the SRP-docking protein FtsY. Eukaryotes use an equivalent system of archaeal origin to deliver proteins into the endoplasmic reticulum, whereas a bacteria-derived SRP and FtsY function in the plastid. Here we report on the presence of homologs of the bacterial Ffh and FtsY proteins in various unrelated plastid-lacking unicellular eukaryotes, namely Heterolobosea, Alveida, Goniomonas, and Hemimastigophora. The monophyly of novel eukaryotic Ffh and FtsY groups, predicted mitochondrial localization experimentally confirmed for Naegleria gruberi, and a strong alphaproteobacterial affinity of the Ffh group, collectively suggest that they constitute parts of an ancestral mitochondrial signal peptide-based protein-targeting system inherited from the last eukaryotic common ancestor, but lost from the majority of extant eukaryotes. The ability of putative signal peptides, predicted in a subset of mitochondrial-encoded N. gruberi proteins, to target a reporter fluorescent protein into the endoplasmic reticulum of Trypanosoma brucei, likely through their interaction with the cytosolic SRP, provided further support for this notion. We also illustrate that known mitochondrial ribosome-interacting proteins implicated in membrane protein targeting in opisthokonts (Mba1, Mdm38, and Mrx15) are broadly conserved in eukaryotes and nonredundant with the mitochondrial SRP system. Finally, we identified a novel mitochondrial protein (MAP67) present in diverse eukaryotes and related to the signal peptide-binding domain of Ffh, which may well be a hitherto unrecognized component of the mitochondrial membrane protein-targeting machinery.
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Affiliation(s)
- Jan Pyrih
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Laboratory of Molecular and Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Tomáš Pánek
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.,Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ignacio Miguel Durante
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Vendula Rašková
- 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
| | - Kristýna Cimrhanzlová
- 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
| | - Eva Kriegová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Anastasios D Tsaousis
- Laboratory of Molecular and Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - 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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13
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Pánek T, Břežný M, Kilnar J, Winocur D. Complex causes of landslides after ice sheet retreat: Post-LGM mass movements in the Northern Patagonian Icefield region. Sci Total Environ 2021; 758:143684. [PMID: 33288266 DOI: 10.1016/j.scitotenv.2020.143684] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 06/12/2023]
Abstract
Although the dynamics of individual rock-slope failures above recently shrinking glaciers have received increasing study, less is known about the spatial distribution of landslides in paraglacial settings. Here, we present a landslide inventory for large deglaciated area (~100,000 km2) situated within the Last Glacial Maximum (LGM) limits of the Northern Patagonian Icefield (NPI). Using satellite images and the TanDEM-X digital elevation model, we mapped a total of 15,543 landslides, among which 1006 are deep-seated landslides (DSLs) with area ≥0.01 km2. The distribution of DSLs is highly asymmetric in a W-E transect of the NPI region, with pronounced clustering along the semi-arid eastern front of the Patagonian Andes. The most strongly affected domain is volcanic tablelands overlying weak Miocene sedimentary rocks, but DSLs tend to also cluster along recently deglaciated (i.e. since the end of the 19th century) eastern margin of the NPI. Compared with other high mountain regions, alpine valleys of the Patagonian Andes are affected by DSLs only in <1% of their area, an order of magnitude lower than in other reported deglaciated mountains. The modest incidence of DSLs in the Patagonian Andes is due to dominance of hard granitoid rocks and relatively weak historical seismic activity. We conclude that 1) geological conditions control the distribution of DSLs and their types in the NPI region; 2) paraglacial effects play secondary (although locally important) roles in the origin of DSLs; 3) local clusters of large DSLs originate due to specifics of the post-LGM landscape evolution, involving drawdowns of glacial lakes and incision of rivers into the unconsolidated deposits; and 4) increased abundance of landslides above the recently shrinking margin of the NPI results from the repeated Holocene fluctuations of glacier snouts around the Little Ice Age (LIA) glacier limits and the spatial coincidence of glacial debuttressing effects with the presence of active faults.
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Affiliation(s)
- Tomáš Pánek
- Department of Physical Geography and Geoecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic.
| | - Michal Břežný
- Department of Physical Geography and Geoecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Jakub Kilnar
- Department of Physical Geography and Geoecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Diego Winocur
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Ciencias Geologicas, Intendente Güiraldes 2160, C1428EGA CABA, Argentina; Instituto de Estudios Andinos (IDEAN), UBA-CONICET, Argentina
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14
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Füssy Z, Vinopalová M, Treitli SC, Pánek T, Smejkalová P, Čepička I, Doležal P, Hampl V. Retortamonads from vertebrate hosts share features of anaerobic metabolism and pre-adaptations to parasitism with diplomonads. Parasitol Int 2021; 82:102308. [PMID: 33626397 PMCID: PMC7985675 DOI: 10.1016/j.parint.2021.102308] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/26/2021] [Accepted: 02/11/2021] [Indexed: 12/17/2022]
Abstract
Although the mitochondria of extant eukaryotes share a single origin, functionally these organelles diversified to a great extent, reflecting lifestyles of the organisms that host them. In anaerobic protists of the group Metamonada, mitochondria are present in reduced forms (also termed hydrogenosomes or mitosomes) and a complete loss of mitochondrion in Monocercomonoides exilis (Metamonada:Preaxostyla) has also been reported. Within metamonads, retortamonads from the gastrointestinal tract of vertebrates form a sister group to parasitic diplomonads (e.g. Giardia and Spironucleus) and have also been hypothesized to completely lack mitochondria. We obtained transcriptomic data from Retortamonas dobelli and R. caviae and searched for enzymes of the core metabolism as well as mitochondrion- and parasitism-related proteins. Our results indicate that retortamonads have a streamlined metabolism lacking pathways for metabolites they are probably capable of obtaining from prey bacteria or their environment, reminiscent of the biochemical arrangement in other metamonads. Retortamonads were surprisingly found do encode homologs of components of Giardia's remarkable ventral disk, as well as homologs of regulatory NEK kinases and secreted lytic enzymes known for involvement in host colonization by Giardia. These can be considered pre-adaptations of these intestinal microorganisms to parasitism. Furthermore, we found traces of the mitochondrial metabolism represented by iron‑sulfur cluster assembly subunits, subunits of mitochondrial translocation and chaperone machinery and, importantly, [FeFe]‑hydrogenases and hydrogenase maturases (HydE, HydF and HydG). Altogether, our results strongly suggest that a remnant mitochondrion is still present.
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Affiliation(s)
- Zoltán Füssy
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic.
| | - Martina Vinopalová
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
| | | | - Tomáš Pánek
- Charles University, Faculty of Science, Department of Zoology, Prague, Czech Republic
| | - Pavla Smejkalová
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic; Charles University, Faculty of Science, Department of Parasitology, Prague, Czech Republic
| | - Ivan Čepička
- Charles University, Faculty of Science, Department of Zoology, Prague, Czech Republic
| | - Pavel Doležal
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
| | - Vladimír Hampl
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic.
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15
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Kovalinka T, Pánek T, Kováčová B, Horváth A. Orientation of FtsH protease homologs in Trypanosoma brucei inner mitochondrial membrane and its evolutionary implications. Mol Biochem Parasitol 2020; 238:111282. [DOI: 10.1016/j.molbiopara.2020.111282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/10/2020] [Accepted: 05/07/2020] [Indexed: 12/18/2022]
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16
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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: 1.3] [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: 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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17
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Rotterová J, Salomaki E, Pánek T, Bourland W, Žihala D, Táborský P, Edgcomb VP, Beinart RA, Kolísko M, Čepička I. Genomics of New Ciliate Lineages Provides Insight into the Evolution of Obligate Anaerobiosis. Curr Biol 2020; 30:2037-2050.e6. [PMID: 32330419 DOI: 10.1016/j.cub.2020.03.064] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/10/2020] [Accepted: 03/24/2020] [Indexed: 02/07/2023]
Abstract
Oxygen plays a crucial role in energetic metabolism of most eukaryotes. Yet adaptations to low-oxygen concentrations leading to anaerobiosis have independently arisen in many eukaryotic lineages, resulting in a broad spectrum of reduced and modified mitochondrion-related organelles (MROs). In this study, we present the discovery of two new class-level lineages of free-living marine anaerobic ciliates, Muranotrichea, cl. nov. and Parablepharismea, cl. nov., that, together with the class Armophorea, form a major clade of obligate anaerobes (APM ciliates) within the Spirotrichea, Armophorea, and Litostomatea (SAL) group. To deepen our understanding of the evolution of anaerobiosis in ciliates, we predicted the mitochondrial metabolism of cultured representatives from all three classes in the APM clade by using transcriptomic and metagenomic data and performed phylogenomic analyses to assess their evolutionary relationships. The predicted mitochondrial metabolism of representatives from the APM ciliates reveals functional adaptations of metabolic pathways that were present in their last common ancestor and likely led to the successful colonization and diversification of the group in various anoxic environments. Furthermore, we discuss the possible relationship of Parablepharismea to the uncultured deep-sea class Cariacotrichea on the basis of single-gene analyses. Like most anaerobic ciliates, all studied species of the APM clade host symbionts, which we propose to be a significant accelerating factor in the transitions to an obligately anaerobic lifestyle. Our results provide an insight into the evolutionary mechanisms of early transitions to anaerobiosis and shed light on fine-scale adaptations in MROs over a relatively short evolutionary time frame.
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Affiliation(s)
- Johana Rotterová
- Department of Zoology, Faculty of Science, Charles University, Prague 128 43, Czech Republic.
| | - Eric Salomaki
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice 370 05, Czech Republic
| | - Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - William Bourland
- Department of Biological Sciences, Boise State University, Boise, ID 83725-1515, USA
| | - David Žihala
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava 710 00, Czech Republic
| | - Petr Táborský
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice 370 05, Czech Republic
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Roxanne A Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - Martin Kolísko
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice 370 05, Czech Republic; Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague 128 43, Czech Republic
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18
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Kolisko M, Flegontova O, Karnkowska A, Lax G, Maritz JM, Pánek T, Táborský P, Carlton JM, Čepička I, Horák A, Lukeš J, Simpson AGB, Tai V. EukRef-excavates: seven curated SSU ribosomal RNA gene databases. Database (Oxford) 2020; 2020:5996027. [PMID: 33216898 PMCID: PMC7678783 DOI: 10.1093/database/baaa080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/04/2020] [Accepted: 08/28/2020] [Indexed: 12/14/2022]
Abstract
The small subunit ribosomal RNA (SSU rRNA) gene is a widely used molecular marker to study the diversity of life. Sequencing of SSU rRNA gene amplicons has become a standard approach for the investigation of the ecology and diversity of microbes. However, a well-curated database is necessary for correct classification of these data. While available for many groups of Bacteria and Archaea, such reference databases are absent for most eukaryotes. The primary goal of the EukRef project (eukref.org) is to close this gap and generate well-curated reference databases for major groups of eukaryotes, especially protists. Here we present a set of EukRef-curated databases for the excavate protists—a large assemblage that includes numerous taxa with divergent SSU rRNA gene sequences, which are prone to misclassification. We identified 6121 sequences, 625 of which were obtained from cultures, 3053 from cell isolations or enrichments and 2419 from environmental samples. We have corrected the classification for the majority of these curated sequences. The resulting publicly available databases will provide phylogenetically based standards for the improved identification of excavates in ecological and microbiome studies, as well as resources to classify new discoveries in excavate diversity.
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Affiliation(s)
- Martin Kolisko
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budeějovice (Budweis), Czech Republic.,Faculty of Science, University of South Bohemia, 370 05 České Budeějovice (Budweis), Czech Republic
| | - Olga Flegontova
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budeějovice (Budweis), Czech Republic
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, 02-089 Warsaw, Poland.,Department of Parasitology, BIOCEV, Faculty of Science, Charles University, 128 43 Vestec, Czech Republic
| | - Gordon Lax
- Department of Biology and Centre of Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Julia M Maritz
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Tomáš Pánek
- Department of Zoology, Charles University, 128 00 Prague, Czech Republic
| | - Petr Táborský
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budeějovice (Budweis), Czech Republic
| | - Jane M Carlton
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Ivan Čepička
- Department of Zoology, Charles University, 128 00 Prague, Czech Republic
| | - Aleš Horák
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budeějovice (Budweis), Czech Republic.,Faculty of Science, University of South Bohemia, 370 05 České Budeějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budeějovice (Budweis), Czech Republic.,Faculty of Science, University of South Bohemia, 370 05 České Budeějovice (Budweis), Czech Republic
| | - Alastair G B Simpson
- Department of Biology and Centre of Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Vera Tai
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada
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19
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Karnkowska A, Treitli SC, Brzoň O, Novák L, Vacek V, Soukal P, Barlow LD, Herman EK, Pipaliya SV, Pánek T, Žihala D, Petrželková R, Butenko A, Eme L, Stairs CW, Roger AJ, Eliáš M, Dacks JB, Hampl V. The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion. Mol Biol Evol 2019; 36:2292-2312. [PMID: 31387118 PMCID: PMC6759080 DOI: 10.1093/molbev/msz147] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The discovery that the protist Monocercomonoides exilis completely lacks mitochondria demonstrates that these organelles are not absolutely essential to eukaryotic cells. However, the degree to which the metabolism and cellular systems of this organism have adapted to the loss of mitochondria is unknown. Here, we report an extensive analysis of the M. exilis genome to address this question. Unexpectedly, we find that M. exilis genome structure and content is similar in complexity to other eukaryotes and less "reduced" than genomes of some other protists from the Metamonada group to which it belongs. Furthermore, the predicted cytoskeletal systems, the organization of endomembrane systems, and biosynthetic pathways also display canonical eukaryotic complexity. The only apparent preadaptation that permitted the loss of mitochondria was the acquisition of the SUF system for Fe-S cluster assembly and the loss of glycine cleavage system. Changes in other systems, including in amino acid metabolism and oxidative stress response, were coincident with the loss of mitochondria but are likely adaptations to the microaerophilic and endobiotic niche rather than the mitochondrial loss per se. Apart from the lack of mitochondria and peroxisomes, we show that M. exilis is a fully elaborated eukaryotic cell that is a promising model system in which eukaryotic cell biology can be investigated in the absence of mitochondria.
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Affiliation(s)
- Anna Karnkowska
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
- Department of Molecular Phylogenetics and Evolution, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Sebastian C Treitli
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Ondřej Brzoň
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Lukáš Novák
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Vojtěch Vacek
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Petr Soukal
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Lael D Barlow
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Canada
| | - Emily K Herman
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Canada
| | - Shweta V Pipaliya
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Canada
| | - Tomáš Pánek
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - David Žihala
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Romana Petrželková
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Anzhelika Butenko
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Laura Eme
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Courtney W Stairs
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Joel B Dacks
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Canada
| | - Vladimír Hampl
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
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20
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Lahr DJG, Kosakyan A, Lara E, Mitchell EAD, Morais L, Porfirio-Sousa AL, Ribeiro GM, Tice AK, Pánek T, Kang S, Brown MW. Phylogenomics and Morphological Reconstruction of Arcellinida Testate Amoebae Highlight Diversity of Microbial Eukaryotes in the Neoproterozoic. Curr Biol 2019; 29:991-1001.e3. [PMID: 30827918 DOI: 10.1016/j.cub.2019.01.078] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 10/26/2018] [Accepted: 01/30/2019] [Indexed: 11/26/2022]
Abstract
Life was microbial for the majority of Earth's history, but as very few microbial lineages leave a fossil record, the Precambrian evolution of life remains shrouded in mystery. Shelled (testate) amoebae stand out as an exception with rich documented diversity in the Neoproterozoic as vase-shaped microfossils (VSMs). While there is general consensus that most of these can be attributed to the Arcellinida lineage in Amoebozoa, it is still unclear whether they can be used as key fossils for interpretation of early eukaryotic evolution. Here, we present a well-resolved phylogenomic reconstruction based on 250 genes, obtained using single-cell transcriptomic techniques from a representative selection of 19 Arcellinid testate amoeba taxa. The robust phylogenetic framework enables deeper interpretations of evolution in this lineage and demanded an updated classification of the group. Additionally, we performed reconstruction of ancestral morphologies, yielding hypothetical ancestors remarkably similar to existing Neoproterozoic VSMs. We demonstrate that major lineages of testate amoebae were already diversified before the Sturtian glaciation (720 mya), supporting the hypothesis that massive eukaryotic diversification took place in the early Neoproterozoic and congruent with the interpretation that VSM are arcellinid testate amoebae.
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Affiliation(s)
- Daniel J G Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, Brazil.
| | - Anush Kosakyan
- Department of Zoology, Institute of Biosciences, University of São Paulo, Brazil; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, 37005, České Budějovice, Czech Republic
| | - Enrique Lara
- Real Jardín Botánico, CSIC, Plaza Murillo 2, ES 28014 Madrid, Spain; Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Edward A D Mitchell
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland; Botanical Garden of Neuchâtel, Pertuis-du-Sault 58, 2000 Neuchâtel, Switzerland
| | - Luana Morais
- Department of Geophysics, Institute of Astronomy, Geophysics and Atmospheric Sciences, University of São Paulo, Brazil
| | | | - Giulia M Ribeiro
- Department of Zoology, Institute of Biosciences, University of São Paulo, Brazil
| | - Alexander K Tice
- Department of Biological Sciences, Mississippi State University, Starkville, MS, USA; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, USA
| | - Tomáš Pánek
- Department of Biological Sciences, Mississippi State University, Starkville, MS, USA; Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic
| | - Seungho Kang
- Department of Biological Sciences, Mississippi State University, Starkville, MS, USA; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, USA
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Starkville, MS, USA; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, USA.
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21
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Kang S, Tice AK, Spiegel FW, Silberman JD, Pánek T, Cepicka I, Kostka M, Kosakyan A, Alcântara DMC, Roger AJ, Shadwick LL, Smirnov A, Kudryavtsev A, Lahr DJG, Brown MW. Between a Pod and a Hard Test: The Deep Evolution of Amoebae. Mol Biol Evol 2017; 34:2258-2270. [PMID: 28505375 PMCID: PMC5850466 DOI: 10.1093/molbev/msx162] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Amoebozoa is the eukaryotic supergroup sister to Obazoa, the lineage that contains the animals and Fungi, as well as their protistan relatives, and the breviate and apusomonad flagellates. Amoebozoa is extraordinarily diverse, encompassing important model organisms and significant pathogens. Although amoebozoans are integral to global nutrient cycles and present in nearly all environments, they remain vastly understudied. We present a robust phylogeny of Amoebozoa based on broad representative set of taxa in a phylogenomic framework (325 genes). By sampling 61 taxa using culture-based and single-cell transcriptomics, our analyses show two major clades of Amoebozoa, Discosea, and Tevosa. This phylogeny refutes previous studies in major respects. Our results support the hypothesis that the last common ancestor of Amoebozoa was sexual and flagellated, it also may have had the ability to disperse propagules from a sporocarp-type fruiting body. Overall, the main macroevolutionary patterns in Amoebozoa appear to result from the parallel losses of homologous characters of a multiphase life cycle that included flagella, sex, and sporocarps rather than independent acquisition of convergent features.
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Affiliation(s)
- Seungho Kang
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS.,Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS
| | - Alexander K Tice
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS.,Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS
| | | | | | - Tomáš Pánek
- Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic
| | - Ivan Cepicka
- Department of Zoology, Charles University, Prague, Czech Republic
| | - Martin Kostka
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Českě Budějovice, Czech Republic.,Department of Parasitology, University of South Bohemia, Českě Budějovice, Czech Republic
| | - Anush Kosakyan
- Department of Zoology, University of São Paulo, São Paulo, Brazil
| | | | - Andrew J Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Lora L Shadwick
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR
| | - Alexey Smirnov
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Alexander Kudryavtsev
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Daniel J G Lahr
- Department of Zoology, University of São Paulo, São Paulo, Brazil
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS.,Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS
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22
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Táborský P, Pánek T, Čepička I. Anaeramoebidae fam. nov., a Novel Lineage of Anaerobic Amoebae and Amoeboflagellates of Uncertain Phylogenetic Position. Protist 2017; 168:495-526. [DOI: 10.1016/j.protis.2017.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 07/17/2017] [Accepted: 07/27/2017] [Indexed: 12/18/2022]
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23
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Pánek T, Žihala D, Sokol M, Derelle R, Klimeš V, Hradilová M, Zadrobílková E, Susko E, Roger AJ, Čepička I, Eliáš M. Nuclear genetic codes with a different meaning of the UAG and the UAA codon. BMC Biol 2017; 15:8. [PMID: 28193262 PMCID: PMC5304391 DOI: 10.1186/s12915-017-0353-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 01/23/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Departures from the standard genetic code in eukaryotic nuclear genomes are known for only a handful of lineages and only a few genetic code variants seem to exist outside the ciliates, the most creative group in this regard. Most frequent code modifications entail reassignment of the UAG and UAA codons, with evidence for at least 13 independent cases of a coordinated change in the meaning of both codons. However, no change affecting each of the two codons separately has been documented, suggesting the existence of underlying evolutionary or mechanistic constraints. RESULTS Here, we present the discovery of two new variants of the nuclear genetic code, in which UAG is translated as an amino acid while UAA is kept as a termination codon (along with UGA). The first variant occurs in an organism noticed in a (meta)transcriptome from the heteropteran Lygus hesperus and demonstrated to be a novel insect-dwelling member of Rhizaria (specifically Sainouroidea). This first documented case of a rhizarian with a non-canonical genetic code employs UAG to encode leucine and represents an unprecedented change among nuclear codon reassignments. The second code variant was found in the recently described anaerobic flagellate Iotanema spirale (Metamonada: Fornicata). Analyses of transcriptomic data revealed that I. spirale uses UAG to encode glutamine, similarly to the most common variant of a non-canonical code known from several unrelated eukaryotic groups, including hexamitin diplomonads (also a lineage of fornicates). However, in these organisms, UAA also encodes glutamine, whereas it is the primary termination codon in I. spirale. Along with phylogenetic evidence for distant relationship of I. spirale and hexamitins, this indicates two independent genetic code changes in fornicates. CONCLUSIONS Our study documents, for the first time, that evolutionary changes of the meaning of UAG and UAA codons in nuclear genomes can be decoupled and that the interpretation of the two codons by the cytoplasmic translation apparatus is mechanistically separable. The latter conclusion has interesting implications for possibilities of genetic code engineering in eukaryotes. We also present a newly developed generally applicable phylogeny-informed method for inferring the meaning of reassigned codons.
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Affiliation(s)
- Tomáš Pánek
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00, Ostrava, Czech Republic
| | - David Žihala
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00, Ostrava, Czech Republic
| | - Martin Sokol
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00, Ostrava, Czech Republic
| | - Romain Derelle
- Unité d'Ecologie, Systématique et Evolution, Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud/Paris-Saclay, AgroParisTech, Orsay, France
| | - Vladimír Klimeš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00, Ostrava, Czech Republic
| | - Miluše Hradilová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20, Prague, Czech Republic
| | - Eliška Zadrobílková
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 00, Prague, Czech Republic
| | - Edward Susko
- Department of Mathematics and Statistics, Dalhousie University, Halifax, NS, B3H 4R2, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada
| | - Andrew J Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
- Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Toronto, ON, Canada
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 00, Prague, Czech Republic
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00, Ostrava, Czech Republic.
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24
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Pánek T, Zadrobílková E, Walker G, Brown MW, Gentekaki E, Hroudová M, Kang S, Roger AJ, Tice AK, Vlček Č, Čepička I. First multigene analysis of Archamoebae (Amoebozoa: Conosa) robustly reveals its phylogeny and shows that Entamoebidae represents a deep lineage of the group. Mol Phylogenet Evol 2016; 98:41-51. [PMID: 26826602 DOI: 10.1016/j.ympev.2016.01.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 01/17/2016] [Accepted: 01/19/2016] [Indexed: 10/22/2022]
Abstract
Archamoebae is an understudied group of anaerobic free-living or endobiotic protists that constitutes the major anaerobic lineage of the supergroup Amoebozoa. Hitherto, the phylogeny of Archamoebae was based solely on SSU rRNA and actin genes, which did not resolve relationships among the main lineages of the group. Because of this uncertainty, several different scenarios had been proposed for the phylogeny of the Archamoebae. In this study, we present the first multigene phylogenetic analysis that includes members of Pelomyxidae, and Rhizomastixidae. The analysis clearly shows that Mastigamoebidae, Pelomyxidae and Rhizomastixidae form a clade of mostly free-living, amoeboid flagellates, here called Pelobiontida. The predominantly endobiotic and aflagellated Entamoebidae represents a separate, deep-branching lineage, Entamoebida. Therefore, two unique evolutionary events, horizontal transfer of the nitrogen fixation system from bacteria and transfer of the sulfate activation pathway to mitochondrial derivatives, predate the radiation of recent lineages of Archamoebae. The endobiotic lifestyle has arisen at least three times independently during the evolution of the group. We also present new ultrastructural data that clarifies the primary divergence among the family Mastigamoebidae which had previously been inferred from phylogenetic analyses based on SSU rDNA.
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Affiliation(s)
- Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44 Prague, Czech Republic.
| | - Eliška Zadrobílková
- Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44 Prague, Czech Republic; Centre for Epidemiology and Microbiology, National Institute of Public Health, Srobarova 48, 100 42 Prague, Czech Republic
| | - Giselle Walker
- Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44 Prague, Czech Republic
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Miluše Hroudová
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics, Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Seungho Kang
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Andrew J Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS B3H 4R2, Canada; Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Alexander K Tice
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Čestmír Vlček
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics, Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44 Prague, Czech Republic
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25
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Pánek T, Táborský P, Pachiadaki MG, Hroudová M, Vlček Č, Edgcomb VP, Čepička I. Combined Culture-Based and Culture-Independent Approaches Provide Insights into Diversity of Jakobids, an Extremely Plesiomorphic Eukaryotic Lineage. Front Microbiol 2015; 6:1288. [PMID: 26635756 PMCID: PMC4649034 DOI: 10.3389/fmicb.2015.01288] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/03/2015] [Indexed: 11/13/2022] Open
Abstract
We used culture-based and culture-independent approaches to discover diversity and ecology of anaerobic jakobids (Excavata: Jakobida), an overlooked, deep-branching lineage of free-living nanoflagellates related to Euglenozoa. Jakobids are among a few lineages of nanoflagellates frequently detected in anoxic habitats by PCR-based studies, however only two strains of a single jakobid species have been isolated from those habitats. We recovered 712 environmental sequences and cultured 21 new isolates of anaerobic jakobids that collectively represent at least ten different species in total, from which four are uncultured. Two cultured species have never been detected by environmental, PCR-based methods. Surprisingly, culture-based and culture-independent approaches were able to reveal a relatively high proportion of overall species diversity of anaerobic jakobids—60 or 80%, respectively. Our phylogenetic analyses based on SSU rDNA and six protein-coding genes showed that anaerobic jakobids constitute a clade of morphologically similar, but genetically and ecologically diverse protists—Stygiellidae fam. nov. Our investigation combines culture-based and environmental molecular-based approaches to capture a wider extent of species diversity and shows Stygiellidae as a group that ordinarily inhabits anoxic, sulfide- and ammonium-rich marine habitats worldwide.
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Affiliation(s)
- Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University in Prague Prague, Czech Republic
| | - Petr Táborský
- Department of Zoology, Faculty of Science, Charles University in Prague Prague, Czech Republic
| | - Maria G Pachiadaki
- Geology and Geophysics Department, Woods Hole Oceanographic Institution Woods Hole, MA, USA
| | - Miluše Hroudová
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics, Czech Academy of Sciences Prague, Czech Republic
| | - Čestmír Vlček
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics, Czech Academy of Sciences Prague, Czech Republic
| | - Virginia P Edgcomb
- Geology and Geophysics Department, Woods Hole Oceanographic Institution Woods Hole, MA, USA
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University in Prague Prague, Czech Republic
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Zhang Q, Táborský P, Silberman JD, Pánek T, Čepička I, Simpson AGB. Marine Isolates of Trimastix marina Form a Plesiomorphic Deep-branching Lineage within Preaxostyla, Separate from Other Known Trimastigids (Paratrimastix n. gen.). Protist 2015; 166:468-91. [PMID: 26312987 DOI: 10.1016/j.protis.2015.07.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 06/12/2015] [Accepted: 07/02/2015] [Indexed: 11/17/2022]
Abstract
Trimastigids are free-living, anaerobic protists that are closely related to the symbiotic oxymonads, forming together the taxon Preaxostyla (Excavata: Metamonada). We isolated fourteen new strains morphologically corresponding to two species assigned to Trimastix (until now the only genus of trimastigids), Trimastix marina and Trimastix pyriformis. Unexpectedly, marine strains of Trimastix marina branch separately from freshwater strains of this morphospecies in SSU rRNA gene trees, and instead form the sister group of all other Preaxostyla. This position is confirmed by three-gene phylogenies. Ultrastructural examination of a marine isolate of Trimastix marina demonstrates a combination of trimastigid-like features (e.g. preaxostyle-like I fibre) and ancestral characters (e.g. absence of thickened flagellar vane margins), consistent with inclusion of marine T. marina within Preaxostyla, but also supporting its distinctiveness from 'freshwater T. marina' and its deep-branching position within Preaxostyla. Since these results indicate paraphyly of Trimastix as currently understood, we transfer the other better-studied trimastigids to Paratrimastix n. gen. and Paratrimastigidae n. fam. The freshwater form previously identified as T. marina is described as Paratrimastix eleionoma n. sp., and Trimastix pyriformis becomes Paratrimastix pyriformis n. comb. Because of its phylogenetic position, 'true' Trimastix is potentially important for understanding the evolution of mitochondrion-related organelles in metamonads.
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Affiliation(s)
- Qianqian Zhang
- Department of Biology, Dalhousie University, Halifax, B3H 4R2, Canada; Yantai Institute of Coastal Zone Research, Chinese Academy of Science, Yantai 264003, China
| | - Petr Táborský
- Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44 Prague 2, Czech Republic
| | - Jeffrey D Silberman
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44 Prague 2, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44 Prague 2, Czech Republic
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Céza V, Pánek T, Smejkalová P, Čepička I. Molecular and morphological diversity of the genus Hypotrichomonas (Parabasalia: Hypotrichomonadida), with descriptions of six new species. Eur J Protistol 2015; 51:158-72. [PMID: 25855142 DOI: 10.1016/j.ejop.2015.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 02/09/2015] [Accepted: 02/09/2015] [Indexed: 11/30/2022]
Abstract
The genus HypotrichomonasLee, 1960 belongs to the small parabasalian class Hypotrichomonadea. Although five Hypotrichomonas species have been described from intestines of lizards and birds, some descriptions were brief and incomplete. Only the type species H. acosta has been observed repeatedly. We have established 23 strains of the genus Hypotrichomonas in culture. Phylogenetic and morphological analyses showed that these isolates represent eight distinct species, six of which are novel. Three of the species showed unusual morphology, such as a reduced undulating membrane, absence of the free part of the recurrent flagellum or a costa-like fiber. Our strains were isolated from a wide range of hosts including cockroaches, frogs, tortoises, lizards, snakes, marsupials, pigs, rodents, and primates. The genus Hypotrichomonas thus contains a relatively large number of species that differ in morphology, phylogenetic position and host range. It is remarkable that such diversity of hypotrichomonads was previously undetected, although a number of studies dealt with intestinal trichomonads of vertebrates and invertebrates. Our results indicate that the diversity of the genus Hypotrichomonas as well as of the whole Parabasalia is still only poorly understood, and the lineages described so far likely represent only a small fraction of the true diversity of parabasalids.
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Affiliation(s)
- Vít Céza
- Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, Prague 2, Czech Republic
| | - Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, Prague 2, Czech Republic
| | - Pavla Smejkalová
- Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, Prague 2, Czech Republic; Department of Parasitology, Faculty of Science, Charles University in Prague, Vinicna 7, Prague 2, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, Prague 2, Czech Republic.
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Yubuki N, Pánek T, Yabuki A, Čepička I, Takishita K, Inagaki Y, Leander BS. Morphological Identities of Two Different Marine Stramenopile Environmental Sequence Clades: Bicosoeca kenaiensis
(Hilliard, 1971) and Cantina marsupialis
(Larsen and Patterson, 1990) gen. nov., comb. nov. J Eukaryot Microbiol 2015; 62:532-42. [DOI: 10.1111/jeu.12207] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 12/09/2014] [Accepted: 12/19/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Naoji Yubuki
- The Departments of Botany and Zoology; Beaty Biodiversity Research Centre and Museum; University of British Columbia; Vancouver British Columbia V6T 1Z4 Canada
| | - Tomáš Pánek
- Department of Zoology; Faculty of Science; Charles University in Prague; Prague 128 44 Czech Republic
| | - Akinori Yabuki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC); Yokosuka Kanagawa 237-0061 Japan
| | - Ivan Čepička
- Department of Zoology; Faculty of Science; Charles University in Prague; Prague 128 44 Czech Republic
| | - Kiyotaka Takishita
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC); Yokosuka Kanagawa 237-0061 Japan
| | - Yuji Inagaki
- Center for Computational Sciences and Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba Ibaraki 305-8577 Japan
| | - Brian S. Leander
- The Departments of Botany and Zoology; Beaty Biodiversity Research Centre and Museum; University of British Columbia; Vancouver British Columbia V6T 1Z4 Canada
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Pánek T, Simpson AG, Hampl V, Čepička I. Creneis carolina gen. et sp. nov. (Heterolobosea), a Novel Marine Anaerobic Protist with Strikingly Derived Morphology and Life Cycle. Protist 2014; 165:542-67. [DOI: 10.1016/j.protis.2014.05.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 05/05/2014] [Accepted: 05/28/2014] [Indexed: 11/29/2022]
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Pánek T, Ptáčková E, Čepička I. Survey on diversity of marine/saline anaerobic Heterolobosea (Excavata: Discoba) with description of seven new species. Int J Syst Evol Microbiol 2014; 64:2280-2304. [PMID: 24729392 DOI: 10.1099/ijs.0.063487-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Diversity of the anaerobic Heterolobosea (Excavata: Discoba) is only poorly understood, especially in marine environments. We have isolated and cultured 16 strains of anaerobic heteroloboseid amoebae and flagellates from brackish, marine and saline anoxic habitats worldwide. Phylogenetic analyses of SSU rDNA sequences and light-microscopic observations showed that all the strains belong to the family Psalteriomonadidae, the main anaerobic lineage of Heterolobosea, and that they represent eight species from the genera Monopylocystis, Harpagon and Pseudoharpagon. Seven species are newly isolated and described here as Monopylocystis minor n. sp., Monopylocystis robusta n. sp., Monopylocystis elegans n. sp., Monopylocystis disparata n. sp., Harpagon salinus n. sp., Pseudoharpagon longus n. sp. and Pseudoharpagon tertius n. sp. Amoebae, cysts and the ultrastructure of the genus Pseudoharpagon are presented for the first time.
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Affiliation(s)
- Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44 Prague, Czech Republic
| | - Eliška Ptáčková
- Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44 Prague, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44 Prague, Czech Republic
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Pánek T, Silberman JD, Yubuki N, Leander BS, Cepicka I. Diversity, Evolution and Molecular Systematics of the Psalteriomonadidae, the Main Lineage of Anaerobic/Microaerophilic Heteroloboseans (Excavata: Discoba). Protist 2012; 163:807-31. [DOI: 10.1016/j.protis.2011.11.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 10/19/2011] [Accepted: 11/01/2011] [Indexed: 12/01/2022]
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Pánek T, Hradecký J, Minár J, Šilhán K. Recurrent landslides predisposed by fault-induced weathering of flysch in the Western Carpathians. ACTA ACUST UNITED AC 2010. [DOI: 10.1144/egsp23.11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AbstractThe interrelationship between slope deformation and fault-induced weathering as a predisposing factor for the development of sliding is analysed through several case studies from the Western Carpathians in the Czech Republic. The study area comprises flysch nappes with alternating sandstone and shale of different permeability. These lithological structures are affected by systems of faults. Recurring slope instability is found associated with zones of deep weathering in tectonically weakened areas. Climatic variability of landslide activity can be identified during the Holocene by means of radiocarbon dating and pollen analysis. Areas affected by recurring landsliding suggest gradual and cyclic landslide frequency.
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Affiliation(s)
- T. Pánek
- Department of Physical Geography and Geoecology, Faculty of Science, University of Ostrava, Chittussiho 10, Ostrava 710 00, Czech Republic
| | - J. Hradecký
- Department of Physical Geography and Geoecology, Faculty of Science, University of Ostrava, Chittussiho 10, Ostrava 710 00, Czech Republic
| | - J. Minár
- Department of Physical Geography and Geoecology, Faculty of Science, University of Ostrava, Chittussiho 10, Ostrava 710 00, Czech Republic
| | - K. Šilhán
- Department of Physical Geography and Geoecology, Faculty of Science, University of Ostrava, Chittussiho 10, Ostrava 710 00, Czech Republic
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