1
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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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2
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Lukeš J, Čepička I, Kolísko M. Evolution: No end in sight for novel incredible (heterotrophic) protists. Curr Biol 2024; 34:R55-R58. [PMID: 38262358 DOI: 10.1016/j.cub.2023.10.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
The microbial eukaryotes known as protists are of immense importance for our understanding of eukaryotic biology. Although it is often difficult to convince funding bodies to sponsor research projects aimed at finding new protist lineages, such discoveries usually provide new and fundamental insights into cell and evolutionary biology, and ecology.
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Affiliation(s)
- Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, and Faculty of Science, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic.
| | - Ivan Čepička
- Department of Zoology, Faculty of Sciences, Charles University, 12800 Prague, Czech Republic
| | - Martin Kolísko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, and Faculty of Science, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic
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3
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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] [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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4
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Brabec J, Salomaki ED, Kolísko M, Scholz T, Kuchta R. The evolution of endoparasitism and complex life cycles in parasitic platyhelminths. Curr Biol 2023; 33:4269-4275.e3. [PMID: 37729914 DOI: 10.1016/j.cub.2023.08.064] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 01/27/2023] [Revised: 07/05/2023] [Accepted: 08/22/2023] [Indexed: 09/22/2023]
Abstract
Within flatworms, the vast majority of parasitism is innate to Neodermata, the most derived and diversified group of the phylum Platyhelminthes.1,2 The four major lineages of Neodermata maintain various combinations of life strategies.3 They include both externally (ecto-) and internally feeding (endo-) parasites. Some lineages complete their life cycles directly by infecting a single host, whereas others succeed only through serial infections of multiple hosts of various vertebrate and invertebrate groups. Food sources and modes of digestion add further combinatorial layers to the often incompletely understood mosaic of neodermatan life histories. Their evolutionary trajectories have remained molecularly unresolved because of conflicting evolutionary inferences and a lack of genomic data.4 Here, we generated transcriptomes for nine early branching neodermatan representatives and performed detailed phylogenomic analyses to address these critical gaps. Polyopisthocotylea, mostly hematophagous ectoparasites, form a group with the mostly hematophagous but endoparasitic trematodes (Trematoda), rather than sharing a common ancestor with Monopisthocotylea, ectoparasitic epithelial feeders. Phylogenetic placement of the highly specialized endoparasitic Cestoda alters depending on the model. Regardless of this uncertainty, this study brings an unconventional perspective on the evolution of platyhelminth parasitism, rejecting a common origin for the endoparasitic lifestyle intrinsic to cestodes and trematodes. Instead, our data indicate that complex life cycles and invasion of vertebrates' gut lumen, the hallmark features of these parasites, evolved independently within Neodermata. We propose the demise of the traditionally recognized class Monogenea and the promotion of its two subclasses to the class level as Monopisthocotyla new class and Polyopisthocotyla new class.
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Affiliation(s)
- Jan Brabec
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice 37005, Czech Republic.
| | - Eric D Salomaki
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice 37005, Czech Republic; Center for Computational Biology of Human Disease and Center for Computation and Visualization, Brown University, 180 George St, Providence, RI 02906, USA
| | - Martin Kolísko
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice 37005, Czech Republic
| | - Tomáš Scholz
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice 37005, Czech Republic
| | - Roman Kuchta
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice 37005, Czech Republic
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5
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Obiol A, López-Escardó D, Salomaki ED, Wiśniewska MM, Forn I, Sà E, Vaqué D, Kolísko M, Massana R. Gene expression dynamics of natural assemblages of heterotrophic flagellates during bacterivory. Microbiome 2023; 11:134. [PMID: 37322519 PMCID: PMC10268365 DOI: 10.1186/s40168-023-01571-5] [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] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 05/12/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Marine heterotrophic flagellates (HF) are dominant bacterivores in the ocean, where they represent the trophic link between bacteria and higher trophic levels and participate in the recycling of inorganic nutrients for regenerated primary production. Studying their activity and function in the ecosystem is challenging since most of the HFs in the ocean are still uncultured. In the present work, we investigated gene expression of natural HF communities during bacterivory in four unamended seawater incubations. RESULTS The most abundant species growing in our incubations belonged to the taxonomic groups MAST-4, MAST-7, Chrysophyceae, and Telonemia. Gene expression dynamics were similar between incubations and could be divided into three states based on microbial counts, each state displaying distinct expression patterns. The analysis of samples where HF growth was highest revealed some highly expressed genes that could be related to bacterivory. Using available genomic and transcriptomic references, we identified 25 species growing in our incubations and used those to compare the expression levels of these specific genes. Video Abstract CONCLUSIONS: Our results indicate that several peptidases, together with some glycoside hydrolases and glycosyltransferases, are more expressed in phagotrophic than in phototrophic species, and thus could be used to infer the process of bacterivory in natural assemblages.
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Affiliation(s)
- Aleix Obiol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spain.
| | - David López-Escardó
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spain
| | - Eric D Salomaki
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Monika M Wiśniewska
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Irene Forn
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spain
| | - Elisabet Sà
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spain
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spain
| | - Martin Kolísko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spain.
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6
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Alama-Bermejo G, Meyer E, Atkinson SD, Holzer AS, Wiśniewska MM, Kolísko M, Bartholomew JL. Transcriptome-Wide Comparisons and Virulence Gene Polymorphisms of Host-Associated Genotypes of the Cnidarian Parasite Ceratonova shasta in Salmonids. Genome Biol Evol 2021; 12:1258-1276. [PMID: 32467979 PMCID: PMC7487138 DOI: 10.1093/gbe/evaa109] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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] [Accepted: 05/25/2020] [Indexed: 12/15/2022] Open
Abstract
Ceratonova shasta is an important myxozoan pathogen affecting the health of salmonid fishes in the Pacific Northwest of North America. Ceratonova shasta exists as a complex of host-specific genotypes, some with low to moderate virulence, and one that causes a profound, lethal infection in susceptible hosts. High throughput sequencing methods are powerful tools for discovering the genetic basis of these host/virulence differences, but deep sequencing of myxozoans has been challenging due to extremely fast molecular evolution of this group, yielding strongly divergent sequences that are difficult to identify, and unavoidable host contamination. We designed and optimized different bioinformatic pipelines to address these challenges. We obtained a unique set of comprehensive, host-free myxozoan RNA-seq data from C. shasta genotypes of varying virulence from different salmonid hosts. Analyses of transcriptome-wide genetic distances and maximum likelihood multigene phylogenies elucidated the evolutionary relationship between lineages and demonstrated the limited resolution of the established Internal Transcribed Spacer marker for C. shasta genotype identification, as this marker fails to differentiate between biologically distinct genotype II lineages from coho salmon and rainbow trout. We further analyzed the data sets based on polymorphisms in two gene groups related to virulence: cell migration and proteolytic enzymes including their inhibitors. The developed single-nucleotide polymorphism-calling pipeline identified polymorphisms between genotypes and demonstrated that variations in both motility and protease genes were associated with different levels of virulence of C. shasta in its salmonid hosts. The prospective use of proteolytic enzymes as promising candidates for targeted interventions against myxozoans in aquaculture is discussed. We developed host-free transcriptomes of a myxozoan model organism from strains that exhibited different degrees of virulence, as a unique source of data that will foster functional gene analyses and serve as a base for the development of potential therapeutics for efficient control of these parasites.
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Affiliation(s)
- Gema Alama-Bermejo
- Department of Microbiology, Oregon State University.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic.,Centro de Investigación Aplicada y Transferencia Tecnológica en Recursos Marinos Almirante Storni (CIMAS), CCT CONICET - CENPAT, San Antonio Oeste, Argentina
| | - Eli Meyer
- Department of Integrative Biology, Oregon State University
| | | | - Astrid S Holzer
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Monika M Wiśniewska
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Martin Kolísko
- Institute of Parasitology, Biology Centre of the 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
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7
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Lhotská Z, Jirků M, Hložková O, Brožová K, Jirsová D, Stensvold CR, Kolísko M, Jirků Pomajbíková K. A Study on the Prevalence and Subtype Diversity of the Intestinal Protist Blastocystis sp. in a Gut-Healthy Human Population in the Czech Republic. Front Cell Infect Microbiol 2020; 10:544335. [PMID: 33123491 PMCID: PMC7573152 DOI: 10.3389/fcimb.2020.544335] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [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: 03/20/2020] [Accepted: 09/10/2020] [Indexed: 12/14/2022] Open
Abstract
Blastocystis sp. is a common intestinal protist colonizing the human intestine the prevalence of which varies across non-industrialized and industrialized countries. Its role in the human gut ecosystem remains unclear due to persisting gaps in knowledge of epidemiology and factors affecting gut colonization. Here, we aimed to expand the knowledge of the epidemiology of Blastocystis sp. in the gut-healthy humans in one of the industrialized European countries, including the distribution of its subtypes, the correlation between its occurrence and several factors such as lifestyle, contact with animals, age, and sex. A total of 288 stool samples were obtained from asymptomatic individuals over the entire age-range and 136 samples from animals with which the volunteers were in frequent contact. All samples were examined in parallel by PCR and xenic in vitro culture. Blastocystis sp. was detected in samples from both human and non-human hosts. In humans, the overall prevalence was 24% and eight subtypes were found; in animals, the prevalence was 10%, and only five subtypes were detected. A higher incidence of Blastocystis sp. was observed in individuals (i) traveling outside Europe, (ii) in frequent contact with livestock, and (iii) over 50 years of age. We found no effect on gender on Blastocystis sp. colonization. Summary This study provides data on the prevalence and diversity of the gut protist Blastocystis sp. and its subtypes in a gut-healthy human population with emphasis on several factors such as contact with animals, lifestyle, age, and gender.
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Affiliation(s)
- Zuzana Lhotská
- Biology Center, Institute of Parasitology, The Czech Academy of Sciences, České Budějovice, Czechia.,Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Milan Jirků
- Biology Center, Institute of Parasitology, The Czech Academy of Sciences, České Budějovice, Czechia
| | - Oldřiška Hložková
- Biology Center, Institute of Parasitology, The Czech Academy of Sciences, České Budějovice, Czechia
| | - Kristýna Brožová
- Biology Center, Institute of Parasitology, The Czech Academy of Sciences, České Budějovice, Czechia.,Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Dagmar Jirsová
- Biology Center, Institute of Parasitology, The Czech Academy of Sciences, České Budějovice, Czechia
| | | | - Martin Kolísko
- Biology Center, Institute of Parasitology, The Czech Academy of Sciences, České Budějovice, Czechia.,Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Kateřina Jirků Pomajbíková
- Biology Center, Institute of Parasitology, The Czech Academy of Sciences, České Budějovice, Czechia.,Faculty of Science, University of South Bohemia, České Budějovice, Czechia
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8
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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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9
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Mathur V, Kolísko M, Hehenberger E, Irwin NAT, Leander BS, Kristmundsson Á, Freeman MA, Keeling PJ. Multiple Independent Origins of Apicomplexan-Like Parasites. Curr Biol 2019; 29:2936-2941.e5. [PMID: 31422883 DOI: 10.1016/j.cub.2019.07.019] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [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: 05/22/2019] [Revised: 05/28/2019] [Accepted: 07/08/2019] [Indexed: 01/08/2023]
Abstract
The apicomplexans are a group of obligate animal pathogens that include Plasmodium (malaria), Toxoplasma (toxoplasmosis), and Cryptosporidium (cryptosporidiosis) [1]. They are an extremely diverse and specious group but are nevertheless united by a distinctive suite of cytoskeletal and secretory structures related to infection, called the apical complex, which is used to recognize and gain entry into animal host cells. The apicomplexans are also known to have evolved from free-living photosynthetic ancestors and retain a relict plastid (the apicoplast), which is non-photosynthetic but houses a number of other essential metabolic pathways [2]. Their closest relatives include a mix of both photosynthetic algae (chromerids) and non-photosynthetic microbial predators (colpodellids) [3]. Genomic analyses of these free-living relatives have revealed a great deal about how the alga-parasite transition may have taken place, as well as origins of parasitism more generally [4]. Here, we show that, despite the surprisingly complex origin of apicomplexans from algae, this transition actually occurred at least three times independently. Using single-cell genomics and transcriptomics from diverse uncultivated parasites, we find that two genera previously classified within the Apicomplexa, Piridium and Platyproteum, form separately branching lineages in phylogenomic analyses. Both retain cryptic plastids with genomic and metabolic features convergent with apicomplexans. These findings suggest a predilection in this lineage for both the convergent loss of photosynthesis and transition to parasitism, resulting in multiple lineages of superficially similar animal parasites.
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Affiliation(s)
- Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Martin Kolísko
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Institute of Parasitology, Biology Centre, Czech Acad. Sci., Branišovská 31, České Budějovice 370 05, Czech Republic
| | - Elisabeth Hehenberger
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; GEOMAR - Helmholtz Centre for Ocean Research, Duesternbrooker Weg 20, 24105 Kiel, Germany
| | - Nicholas A T Irwin
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Brian S Leander
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Árni Kristmundsson
- Institute for Experimental Pathology, University of Iceland, Keldur. Keldnavegur 3, 112 Reykjavík, Iceland
| | - Mark A Freeman
- Ross University School of Veterinary Medicine, PO Box 334, Basseterre, St. Kitts, West Indies
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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10
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Vacek V, Novák LVF, Treitli SC, Táborský P, Cepicka I, Kolísko M, Keeling PJ, Hampl V. Fe-S Cluster Assembly in Oxymonads and Related Protists. Mol Biol Evol 2019; 35:2712-2718. [PMID: 30184127 PMCID: PMC6231488 DOI: 10.1093/molbev/msy168] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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] [Indexed: 01/06/2023] Open
Abstract
The oxymonad Monocercomonoides exilis was recently reported to be the first eukaryote that has completely lost the mitochondrial compartment. It was proposed that an important prerequisite for such a radical evolutionary step was the acquisition of the SUF Fe–S cluster assembly pathway from prokaryotes, making the mitochondrial ISC pathway dispensable. We have investigated genomic and transcriptomic data from six oxymonad species and their relatives, composing the group Preaxostyla (Metamonada, Excavata), for the presence and absence of enzymes involved in Fe–S cluster biosynthesis. None possesses enzymes of mitochondrial ISC pathway and all apparently possess the SUF pathway, composed of SufB, C, D, S, and U proteins, altogether suggesting that the transition from ISC to SUF preceded their last common ancestor. Interestingly, we observed that SufDSU were fused in all three oxymonad genomes, and in the genome of Paratrimastix pyriformis. The donor of the SUF genes is not clear from phylogenetic analyses, but the enzyme composition of the pathway and the presence of SufDSU fusion suggests Firmicutes, Thermotogae, Spirochaetes, Proteobacteria, or Chloroflexi as donors. The inventory of the downstream CIA pathway enzymes is consistent with that of closely related species that retain ISC, indicating that the switch from ISC to SUF did not markedly affect the downstream process of maturation of cytosolic and nuclear Fe–S proteins.
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Affiliation(s)
- Vojtech Vacek
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Lukáš V F Novák
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Sebastian C Treitli
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Petr Táborský
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ivan Cepicka
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Kolísko
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Czech Republic.,Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
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11
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Pyrihová E, Motycková A, Voleman L, Wandyszewska N, Fišer R, Seydlová G, Roger A, Kolísko M, Doležal P. A Single Tim Translocase in the Mitosomes of Giardia intestinalis Illustrates Convergence of Protein Import Machines in Anaerobic Eukaryotes. Genome Biol Evol 2018; 10:2813-2822. [PMID: 30265292 PMCID: PMC6200312 DOI: 10.1093/gbe/evy215] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [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] [Accepted: 09/27/2018] [Indexed: 11/14/2022] Open
Abstract
Mitochondria have evolved diverse forms across eukaryotic diversity in adaptation to anoxia. Mitosomes are the simplest and the least well-studied type of anaerobic mitochondria. Transport of proteins via TIM complexes, composed of three proteins of the Tim17 protein family (Tim17/22/23), is one of the key unifying aspects of mitochondria and mitochondria-derived organelles. However, multiple experimental and bioinformatic attempts have so far failed to identify the nature of TIM in mitosomes of the anaerobic metamonad protist, Giardia intestinalis, one of the few experimental models for mitosome biology. Here, we present the identification of a single G. intestinalis Tim17 protein (GiTim17), made possible only by the implementation of a metamonad-specific hidden Markov model. While very divergent in primary sequence and in predicted membrane topology, experimental data suggest that GiTim17 is an inner membrane mitosomal protein, forming a disulphide-linked dimer. We suggest that the peculiar GiTim17 sequence reflects adaptation to the unusual, detergent resistant, inner mitosomal membrane. Specific pull-down experiments indicate interaction of GiTim17 with mitosomal Tim44, the tethering component of the import motor complex. Analysis of TIM complexes across eukaryote diversity suggests that a "single Tim" translocase is a convergent adaptation of mitosomes in anaerobic protists, with Tim22 and Tim17 (but not Tim23), providing the protein backbone.
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Affiliation(s)
- Eva Pyrihová
- Department of Parasitology, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Alžbeta Motycková
- Department of Parasitology, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Luboš Voleman
- Department of Parasitology, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Natalia Wandyszewska
- Department of Parasitology, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Radovan Fišer
- Department of Genetics and Microbiology, Charles University, Praha 2, Czech Republic
| | - Gabriela Seydlová
- Department of Genetics and Microbiology, Charles University, Praha 2, Czech Republic
| | - Andrew Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Martin Kolísko
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada.,Biology Centre CAS, České Budějovice, Czech Republic
| | - Pavel Doležal
- Department of Parasitology, Faculty of Science, Charles University, Vestec, Czech Republic
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12
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Pyrih J, Pyrihová E, Kolísko M, Stojanovová D, Basu S, Harant K, Haindrich AC, Doležal P, Lukeš J, Roger A, Tachezy J. Minimal cytosolic iron-sulfur cluster assembly machinery of Giardia intestinalis is partially associated with mitosomes. Mol Microbiol 2016; 102:701-714. [PMID: 27582265 DOI: 10.1111/mmi.13487] [Citation(s) in RCA: 13] [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] [Accepted: 08/21/2016] [Indexed: 01/10/2023]
Abstract
Iron-sulfur (Fe-S) clusters are essential cofactors that enable proteins to transport electrons, sense signals, or catalyze chemical reactions. The maturation of dozens of Fe-S proteins in various compartments of every eukaryotic cell is driven by several assembly pathways. The ubiquitous cytosolic Fe-S cluster assembly (CIA) pathway, typically composed of eight highly conserved proteins, depends on mitochondrial Fe-S cluster assembly (ISC) machinery. Giardia intestinalis contains one of the smallest eukaryotic genomes and the mitosome, an extremely reduced mitochondrion. Because the only pathway known to be retained within this organelle is the synthesis of Fe-S clusters mediated by ISC machinery, a likely function of the mitosome is to cooperate with the CIA pathway. We investigated the cellular localization of CIA components in G. intestinalis and the origin and distribution of CIA-related components and Tah18-like proteins in other Metamonada. We show that orthologs of Tah18 and Dre2 are missing in these eukaryotes. In Giardia, all CIA components are exclusively cytosolic, with the important exception of Cia2 and two Nbp35 paralogs, which are present in the mitosomes. We propose that the dual localization of Cia2 and Nbp35 proteins in Giardia might represent a novel connection between the ISC and the CIA pathways.
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Affiliation(s)
- Jan Pyrih
- Department of Parasitology, Charles University in Prague, Vestec, 252 42, Czech Republic
| | - Eva Pyrihová
- Department of Parasitology, Charles University in Prague, Vestec, 252 42, Czech Republic
| | - Martin Kolísko
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Darja Stojanovová
- Department of Parasitology, Charles University in Prague, Vestec, 252 42, Czech Republic
| | - Somsuvro Basu
- Institute of Parasitology, Biology Centre, České Budějovice, Budweis, 37005, Czech Republic
| | - Karel Harant
- Department of Parasitology, Charles University in Prague, Vestec, 252 42, Czech Republic
| | - Alexander C Haindrich
- Institute of Parasitology, Biology Centre, České Budějovice, Budweis, 37005, Czech Republic.,Faculty of Sciences, University of South Bohemia, České Budějovice, Budweis, 37005, Czech Republic
| | - Pavel Doležal
- Department of Parasitology, Charles University in Prague, Vestec, 252 42, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, České Budějovice, Budweis, 37005, Czech Republic.,Faculty of Sciences, University of South Bohemia, České Budějovice, Budweis, 37005, Czech Republic.,Canadian Institute for Advanced Research, Toronto, ON, M5G 1Z8, Canada
| | - Andrew Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada.,Canadian Institute for Advanced Research, Toronto, ON, M5G 1Z8, Canada
| | - Jan Tachezy
- Department of Parasitology, Charles University in Prague, Vestec, 252 42, Czech Republic
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