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Žárský V, Klimeš V, Pačes J, Vlček Č, Hradilová M, Beneš V, Nývltová E, Hrdý I, Pyrih J, Mach J, Barlow L, Stairs CW, Eme L, Hall N, Eliáš M, Dacks JB, Roger A, Tachezy J. The Mastigamoeba balamuthi Genome and the Nature of the Free-Living Ancestor of Entamoeba. Mol Biol Evol 2021; 38:2240-2259. [PMID: 33528570 PMCID: PMC8136499 DOI: 10.1093/molbev/msab020] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The transition of free-living organisms to parasitic organisms is a mysterious process that occurs in all major eukaryotic lineages. Parasites display seemingly unique features associated with their pathogenicity; however, it is important to distinguish ancestral preconditions to parasitism from truly new parasite-specific functions. Here, we sequenced the genome and transcriptome of anaerobic free-living Mastigamoeba balamuthi and performed phylogenomic analysis of four related members of the Archamoebae, including Entamoeba histolytica, an important intestinal pathogen of humans. We aimed to trace gene histories throughout the adaptation of the aerobic ancestor of Archamoebae to anaerobiosis and throughout the transition from a free-living to a parasitic lifestyle. These events were associated with massive gene losses that, in parasitic lineages, resulted in a reduction in structural features, complete losses of some metabolic pathways, and a reduction in metabolic complexity. By reconstructing the features of the common ancestor of Archamoebae, we estimated preconditions for the evolution of parasitism in this lineage. The ancestor could apparently form chitinous cysts, possessed proteolytic enzyme machinery, compartmentalized the sulfate activation pathway in mitochondrion-related organelles, and possessed the components for anaerobic energy metabolism. After the split of Entamoebidae, this lineage gained genes encoding surface membrane proteins that are involved in host–parasite interactions. In contrast, gene gains identified in the M. balamuthi lineage were predominantly associated with polysaccharide catabolic processes. A phylogenetic analysis of acquired genes suggested an essential role of lateral gene transfer in parasite evolution (Entamoeba) and in adaptation to anaerobic aquatic sediments (Mastigamoeba).
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Affiliation(s)
- Vojtěch Žárský
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Vladimír Klimeš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jan Pačes
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Čestmír Vlček
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Miluše Hradilová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Vladimír Beneš
- European Molecular Biology Laboratory (EMBL), Genomics Core Facility, Heidelberg, Germany
| | - Eva Nývltová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ivan Hrdý
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Jan Pyrih
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Jan Mach
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Lael Barlow
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Courtney W Stairs
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada.,Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Laura Eme
- Diversity, Ecology and Evolution of Microbes (DEEM), Unité Ecologie Systématique Evolution Université Paris-Saclay, Orsay, France
| | - Neil Hall
- The Earlham Institute, Norwich Research Park, Norwich, United Kingdom.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Joel B Dacks
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.,Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, AB, Canada.,Institute of Parasitology, Biology Centre, CAS, v.v.i., Ceske Budejovice, Czech Republic
| | - Andrew Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
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Metabolic Reconstruction Elucidates the Lifestyle of the Last Diplomonadida Common Ancestor. mSystems 2020; 5:5/6/e00774-20. [PMID: 33361320 PMCID: PMC7762791 DOI: 10.1128/msystems.00774-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Diplomonads are a group of microbial eukaryotes found in oxygen-poor environments. There are both parasitic (e.g., Giardia intestinalis) and free-living (e.g., Trepomonas) members in the group. The identification of ancestral traits is essential to understanding the evolution of any group. In the case of parasitic groups, this helps us understand the adaptation to this lifestyle and a particular host. Most diplomonads are parasites, but there are free-living members of the group nested among the host-associated diplomonads. Furthermore, most of the close relatives within Fornicata are free-living organisms. This leaves the lifestyle of the ancestor unclear. Here, we present metabolic maps of four different diplomonad species. We identified 853 metabolic reactions and 147 pathways present in at least one of the analyzed diplomonads. Our study suggests that diplomonads represent a metabolically diverse group in which differences correlate with different environments (e.g., the detoxification of arsenic). Using a parsimonious analysis, we also provide a description of the putative metabolism of the last Diplomonadida common ancestor. Our results show that the acquisition and loss of reactions have shaped metabolism since this common ancestor. There is a net loss of reaction in all branches leading to parasitic diplomonads, suggesting an ongoing reduction in the metabolic capacity. Important traits present in host-associated diplomonads (e.g., virulence factors and the synthesis of UDP-N-acetyl-d-galactosamine) are shared with free-living relatives. The last Diplomonadida common ancestor most likely already had acquired important enzymes for the salvage of nucleotides and had a reduced capacity to synthesize nucleotides, lipids, and amino acids de novo, suggesting that it was an obligate host-associated organism. IMPORTANCE Diplomonads are a group of microbial eukaryotes found in oxygen-poor environments. There are both parasitic (e.g., Giardia intestinalis) and free-living (e.g., Trepomonas) members in the group. Diplomonads are well known for their anaerobic metabolism, which has been studied for many years. Here, we reconstructed whole metabolic networks of four extant diplomonad species as well as their ancestors, using a bioinformatics approach. We show that the metabolism within the group is under constant change throughout evolutionary time, in response to the environments that the different lineages explore. Both gene losses and gains are responsible for the adaptation processes. Interestingly, it appears that the last Diplomonadida common ancestor had a metabolism that is more similar to extant parasitic than free-living diplomonads. This suggests that the host-associated lifestyle of parasitic diplomonads, such as the human parasite G. intestinalis, is an old evolutionary adaptation.
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Hunter ES, Paight C, Lane CE. Metabolic Contributions of an Alphaproteobacterial Endosymbiont in the Apicomplexan Cardiosporidium cionae. Front Microbiol 2020; 11:580719. [PMID: 33335517 PMCID: PMC7737231 DOI: 10.3389/fmicb.2020.580719] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/05/2020] [Indexed: 12/27/2022] Open
Abstract
Apicomplexa is a diverse protistan phylum composed almost exclusively of metazoan-infecting parasites, including the causative agents of malaria, cryptosporidiosis, and toxoplasmosis. A single apicomplexan genus, Nephromyces, was described in 2010 as a mutualist partner to its tunicate host. Here we present genomic and transcriptomic data from the parasitic sister species to this mutualist, Cardiosporidium cionae, and its associated bacterial endosymbiont. Cardiosporidium cionae and Nephromyces both infect tunicate hosts, localize to similar organs within these hosts, and maintain bacterial endosymbionts. Though many other protists are known to harbor bacterial endosymbionts, these associations are completely unknown in Apicomplexa outside of the Nephromycidae clade. Our data indicate that a vertically transmitted α-proteobacteria has been retained in each lineage since Nephromyces and Cardiosporidium diverged. This α-proteobacterial endosymbiont has highly reduced metabolic capabilities, but contributes the essential amino acid lysine, and essential cofactor lipoic acid to C. cionae. This partnership likely reduces resource competition with the tunicate host. However, our data indicate that the contribution of the single α-proteobacterial endosymbiont in C. cionae is minimal compared to the three taxa of endosymbionts present in the Nephromyces system, and is a potential explanation for the virulence disparity between these lineages.
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Affiliation(s)
- Elizabeth Sage Hunter
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - Christopher Paight
- Department of Ecology, Evolution & Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Christopher E. Lane
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
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Butenko A, Hammond M, Field MC, Ginger ML, Yurchenko V, Lukeš J. Reductionist Pathways for Parasitism in Euglenozoans? Expanded Datasets Provide New Insights. Trends Parasitol 2020; 37:100-116. [PMID: 33127331 DOI: 10.1016/j.pt.2020.10.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 12/21/2022]
Abstract
The unicellular trypanosomatids belong to the phylum Euglenozoa and all known species are obligate parasites. Distinct lineages infect plants, invertebrates, and vertebrates, including humans. Genome data for marine diplonemids, together with freshwater euglenids and free-living kinetoplastids, the closest known nonparasitic relatives to trypanosomatids, recently became available. Robust phylogenetic reconstructions across Euglenozoa are now possible and place the results of parasite-focused studies into an evolutionary context. Here we discuss recent advances in identifying the factors shaping the evolution of Euglenozoa, focusing on ancestral features generally considered parasite-specific. Remarkably, most of these predate the transition(s) to parasitism, suggesting that the presence of certain preconditions makes a significant lifestyle change more likely.
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Affiliation(s)
- Anzhelika Butenko
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Science, University of Ostrava, Ostrava, Czech Republic.
| | - Michael Hammond
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Mark C Field
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; School of Life Sciences, University of Dundee, Dundee, UK
| | - Michael L Ginger
- School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Vyacheslav Yurchenko
- Faculty of Science, University of Ostrava, Ostrava, Czech Republic; Martsinovsky Institute of Medical Parasitology, Sechenov University, Moscow, Russia
| | - Julius Lukeš
- Biology Centre, Institute of Parasitology, 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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5
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Lu Y, Ocaña-Pallarès E, López-Escardó D, Dennis SR, Monaghan MT, Ruiz-Trillo I, Spaak P, Wolinska J. Revisiting the phylogenetic position of Caullerya mesnili (Ichthyosporea), a common Daphnia parasite, based on 22 protein-coding genes. Mol Phylogenet Evol 2020; 151:106891. [PMID: 32562822 DOI: 10.1016/j.ympev.2020.106891] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 06/05/2020] [Accepted: 06/10/2020] [Indexed: 02/01/2023]
Abstract
Caullerya mesnili is a common and virulent parasite of the water flea, Daphnia. It was classified within the Haplosporidia (Rhizaria) for over a century. However, a recent molecular phylogeny based on the 18S rRNA gene suggested it belonged to the Ichthyosporea, a class of protists closely related to animals within the Opisthokonta clade. The exact phylogenetic position of C. mesnili remained uncertain because it appeared in the 18S rRNA tree with a very long branch and separated from all other taxa, suggesting that its position could be artifactual. A better understanding of its phylogenetic position has been constrained by a lack of molecular markers and the difficulty of obtaining a suitable quantity and quality of DNA from in vitro cultures, as this intracellular parasite cannot be cultured without its host. We isolated and collected spores of C. mesnili and sequenced genomic libraries. Phylogenetic analyses of a newly generated multi-protein data set (22 proteins, 4998 amino acids) and of sequences from the 18S rRNA gene both placed C. mesnili within the Ichthyophonida sub-clade of Ichthyosporea, as sister-taxon to Abeoforma whisleri and Pirum gemmata. Our study highlights the utility of metagenomic approaches for obtaining genomic information from intracellular parasites and for more accurate phylogenetic placement in evolutionary studies.
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Affiliation(s)
- Yameng Lu
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany; Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland.
| | - Eduard Ocaña-Pallarès
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - David López-Escardó
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain; Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Stuart R Dennis
- Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | - Michael T Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany; Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany; Institut für Biologie, Freie Universität Berlin (FU), Berlin, Germany
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain; Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona 08028, Catalonia, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Catalonia, Spain
| | - Piet Spaak
- Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | - Justyna Wolinska
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany; Institut für Biologie, Freie Universität Berlin (FU), Berlin, Germany
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Butenko A, Opperdoes FR, Flegontova O, Horák A, Hampl V, Keeling P, Gawryluk RMR, Tikhonenkov D, Flegontov P, Lukeš J. Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids. BMC Biol 2020; 18:23. [PMID: 32122335 PMCID: PMC7052976 DOI: 10.1186/s12915-020-0754-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/17/2020] [Indexed: 12/24/2022] Open
Abstract
Background The Euglenozoa are a protist group with an especially rich history of evolutionary diversity. They include diplonemids, representing arguably the most species-rich clade of marine planktonic eukaryotes; trypanosomatids, which are notorious parasites of medical and veterinary importance; and free-living euglenids. These different lifestyles, and particularly the transition from free-living to parasitic, likely require different metabolic capabilities. We carried out a comparative genomic analysis across euglenozoan diversity to see how changing repertoires of enzymes and structural features correspond to major changes in lifestyles. Results We find a gradual loss of genes encoding enzymes in the evolution of kinetoplastids, rather than a sudden decrease in metabolic capabilities corresponding to the origin of parasitism, while diplonemids and euglenids maintain more metabolic versatility. Distinctive characteristics of molecular machines such as kinetochores and the pre-replication complex that were previously considered specific to parasitic kinetoplastids were also identified in their free-living relatives. Therefore, we argue that they represent an ancestral rather than a derived state, as thought until the present. We also found evidence of ancient redundancy in systems such as NADPH-dependent thiol-redox. Only the genus Euglena possesses the combination of trypanothione-, glutathione-, and thioredoxin-based systems supposedly present in the euglenozoan common ancestor, while other representatives of the phylum have lost one or two of these systems. Lastly, we identified convergent losses of specific metabolic capabilities between free-living kinetoplastids and ciliates. Although this observation requires further examination, it suggests that certain eukaryotic lineages are predisposed to such convergent losses of key enzymes or whole pathways. Conclusions The loss of metabolic capabilities might not be associated with the switch to parasitic lifestyle in kinetoplastids, and the presence of a highly divergent (or unconventional) kinetochore machinery might not be restricted to this protist group. The data derived from the transcriptomes of free-living early branching prokinetoplastids suggests that the pre-replication complex of Trypanosomatidae is a highly divergent version of the conventional machinery. Our findings shed light on trends in the evolution of metabolism in protists in general and open multiple avenues for future research.
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Affiliation(s)
- Anzhelika Butenko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Fred R Opperdoes
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Olga Flegontova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Aleš Horák
- 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
| | - Vladimír Hampl
- Faculty of Science, Charles University, Biocev, Vestec, Czech Republic
| | - Patrick Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada
| | | | - Denis Tikhonenkov
- Department of Botany, University of British Columbia, Vancouver, Canada.,Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia
| | - Pavel Flegontov
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic. .,Faculty of Science, University of Ostrava, Ostrava, Czech Republic. .,Present address: Department of Genetics, Harvard Medical School, Boston, USA.
| | - 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.
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7
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Abstract
The uptake of host-derived nutrients is key to the growth and survival of Toxoplasma gondii parasites. Nutrients are acquired via solute transporters that localize to the plasma membrane of the parasites. In this chapter, we describe methodology by which the uptake of solutes via plasma membrane transporters may be monitored and characterized. These assays, used here to investigate the uptake of amino acids into parasites, have broad applicability in measuring the uptake of a diverse range of solutes.
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Affiliation(s)
- Esther Rajendran
- Research School of Biology, Australian National University, Acton, ACT, Australia
| | - Kiaran Kirk
- Research School of Biology, Australian National University, Acton, ACT, Australia
| | - Giel G van Dooren
- Research School of Biology, Australian National University, Acton, ACT, Australia.
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8
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Campo J, Bass D, Keeling PJ. The eukaryome: Diversity and role of microeukaryotic organisms associated with animal hosts. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13490] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Javier Campo
- Marine Biology and Ecology Department Rosenstiel School of Marine and Atmospheric Science University of Miami Miami FL USA
| | - David Bass
- Department of Life Sciences The Natural History Museum London UK
- CEFAS Weymouth UK
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Janouškovec J, Paskerova GG, Miroliubova TS, Mikhailov KV, Birley T, Aleoshin VV, Simdyanov TG. Apicomplexan-like parasites are polyphyletic and widely but selectively dependent on cryptic plastid organelles. eLife 2019; 8:49662. [PMID: 31418692 PMCID: PMC6733595 DOI: 10.7554/elife.49662] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/14/2019] [Indexed: 12/22/2022] Open
Abstract
The phylum Apicomplexa comprises human pathogens such as Plasmodium but is also an under-explored hotspot of evolutionary diversity central to understanding the origins of parasitism and non-photosynthetic plastids. We generated single-cell transcriptomes for all major apicomplexan groups lacking large-scale sequence data. Phylogenetic analysis reveals that apicomplexan-like parasites are polyphyletic and their similar morphologies emerged convergently at least three times. Gregarines and eugregarines are monophyletic, against most expectations, and rhytidocystids and Eleutheroschizon are sister lineages to medically important taxa. Although previously unrecognized, plastids in deep-branching apicomplexans are common, and they contain some of the most divergent and AT-rich genomes ever found. In eugregarines, however, plastids are either abnormally reduced or absent, thus increasing known plastid losses in eukaryotes from two to four. Environmental sequences of ten novel plastid lineages and structural innovations in plastid proteins confirm that plastids in apicomplexans and their relatives are widespread and share a common, photosynthetic origin. Microscopic parasites known collectively as apicomplexans are responsible for several infectious diseases in humans including malaria and toxoplasmosis. The cells of the malaria parasite and many other apicomplexans contain compartments known as cryptic chloroplasts that produce molecules the parasites need to survive. Cryptic chloroplasts are similar to the chloroplasts found in plant cells, but unlike plants the compartments in apicomplexans are unable to harvest energy from sunlight. Since the cells of humans and other animals do not contain chloroplasts, cryptic chloroplasts are a potential target for new drugs to treat diseases caused by apicomplexans. However, it remains unclear how widespread cryptic chloroplasts are in these parasites, largely because few apicomplexans have been successfully grown in the laboratory. To address this question, Janouškovec et al. used an approach called single-cell transcriptomics to study ten different apicomplexans. This provided new data about the genetic make-up of each parasite that the team analysed to find out how they are related to one another. The analysis revealed that, unexpectedly, apicomplexan parasites do not share a close common ancestor and are therefore not a natural grouping from an evolutionary perspective. Instead, their similar physical appearances and lifestyles evolved independently on at least three separate occasions. Further analysis demonstrated that cryptic chloroplasts are common in apicomplexan parasites, including in lineages where they were not previously known to exist. However, at least three lineages of apicomplexans have independently lost their cryptic chloroplasts. The findings of Janouškovec et al. shed new light on the importance of chloroplasts in the evolution of life and may help develop new treatments for diseases caused by apicomplexan parasites. Several drugs targeting the cryptic chloroplasts in malaria parasites are currently in clinical trials, and this work suggests that these drugs may also have the potential to be used against other apicomplexan parasites in the future.
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Affiliation(s)
- Jan Janouškovec
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Gita G Paskerova
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, St. Petersburg, Russian Federation
| | - Tatiana S Miroliubova
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, St. Petersburg, Russian Federation.,Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russian Federation
| | - Kirill V Mikhailov
- Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation.,Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - Thomas Birley
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Vladimir V Aleoshin
- Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation.,Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - Timur G Simdyanov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russian Federation
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10
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Kokina A, Ozolina Z, Liepins J. Purine auxotrophy: Possible applications beyond genetic marker. Yeast 2019; 36:649-656. [PMID: 31334866 DOI: 10.1002/yea.3434] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/12/2019] [Accepted: 07/16/2019] [Indexed: 01/09/2023] Open
Abstract
Exploring new drug candidates or drug targets against many illnesses is necessary as "traditional" treatments lose their effectivity. Cancer and sicknesses caused by protozoan parasites are among these diseases. Cell purine metabolism is an important drug target. Theoretically, inhibiting purine metabolism could stop the proliferation of unwanted cells. Purine metabolism is similar across all eukaryotes. However, some medically important organisms or cell lines rely on their host purine metabolism. Protozoans causing malaria, leishmaniasis, or toxoplasmosis are purine auxotrophs. Some cancer forms have also lost the ability to synthesize purines de novo. Budding yeast can serve as an effective model for eukaryotic purine metabolism, and thus, purine auxotrophic strains could be an important tool. In this review, we present the common principles of purine metabolism in eukaryotes, effects of purine starvation in eukaryotic cells, and purine-starved Saccharomyces cerevisiae as a model for purine depletion-elicited metabolic states with applications in evolution studies and pharmacology. Purine auxotrophic yeast strains behave differently when growing in media with sufficient supplementation with adenine or in media depleted of adenine (starvation). In the latter, they undergo cell cycle arrest at G1/G0 and become stress resistant. Importantly, similar effects have also been observed among parasitic protozoans or cancer cells. We consider that studies on metabolic changes caused by purine auxotrophy could reveal new options for parasite or cancer therapy. Further, knowledge on phenotypic changes will improve the use of auxotrophic strains in high-throughput screening for primary drug candidates.
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Affiliation(s)
- Agnese Kokina
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Zane Ozolina
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Janis Liepins
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
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11
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Coccia M. The theory of technological parasitism for the measurement of the evolution of technology and technological forecasting. TECHNOLOGICAL FORECASTING AND SOCIAL CHANGE 2019; 141:289-304. [DOI: 10.1016/j.techfore.2018.12.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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12
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Parker KER, Fairweather SJ, Rajendran E, Blume M, McConville MJ, Bröer S, Kirk K, van Dooren GG. The tyrosine transporter of Toxoplasma gondii is a member of the newly defined apicomplexan amino acid transporter (ApiAT) family. PLoS Pathog 2019; 15:e1007577. [PMID: 30742695 PMCID: PMC6386423 DOI: 10.1371/journal.ppat.1007577] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 02/22/2019] [Accepted: 01/12/2019] [Indexed: 12/20/2022] Open
Abstract
Apicomplexan parasites are auxotrophic for a range of amino acids which must be salvaged from their host cells, either through direct uptake or degradation of host proteins. Here, we describe a family of plasma membrane-localized amino acid transporters, termed the Apicomplexan Amino acid Transporters (ApiATs), that are ubiquitous in apicomplexan parasites. Functional characterization of the ApiATs of Toxoplasma gondii indicate that several of these transporters are important for intracellular growth of the tachyzoite stage of the parasite, which is responsible for acute infections. We demonstrate that the ApiAT protein TgApiAT5-3 is an exchanger for aromatic and large neutral amino acids, with particular importance for L-tyrosine scavenging and amino acid homeostasis, and that TgApiAT5-3 is critical for parasite virulence. Our data indicate that T. gondii expresses additional proteins involved in the uptake of aromatic amino acids, and we present a model for the uptake and homeostasis of these amino acids. Our findings identify a family of amino acid transporters in apicomplexans, and highlight the importance of amino acid scavenging for the biology of this important phylum of intracellular parasites. The Apicomplexa comprise a large number of parasitic protozoa that have obligate intracellular lifestyles and cause significant human and animal diseases, including malaria, cryptosporidiosis, toxoplasmosis, coccidiosis in poultry, and various cattle fevers. Apicomplexans must scavenge essential nutrients from their hosts in order to proliferate and cause disease, including a range of amino acids. The direct uptake of these nutrients is presumed to be mediated by transporter proteins located in the plasma membrane of intracellular stages, although the identities of these proteins are poorly defined. Using a combination of bioinformatic, genetic, cell biological, and physiological approaches, we have characterized an apicomplexan-specific family of plasma membrane-localized transporter proteins that we have called the Apicomplexan Amino acid Transporters (ApiATs). We show that TgApiAT5-3, a member of the family in the apicomplexan Toxoplasma gondii, is an exchanger for aromatic and large neutral amino acids. In particular, it is critical for uptake of tyrosine, and for parasite virulence in a mouse infection model. We conclude that ApiATs are a family of plasma membrane transporters that play crucial roles in amino acid scavenging by apicomplexan parasites.
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Affiliation(s)
- Kathryn E. R. Parker
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | | | - Esther Rajendran
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Martin Blume
- Department of Biochemistry and Molecular Biology and the Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, VIC, Australia
- Robert Koch Institute, Berlin, Germany
| | - Malcolm J. McConville
- Department of Biochemistry and Molecular Biology and the Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, VIC, Australia
| | - Stefan Bröer
- Research School of Biology, Australian National University, Canberra, ACT, Australia
- * E-mail: (GGVD); (KK); (SB)
| | - Kiaran Kirk
- Research School of Biology, Australian National University, Canberra, ACT, Australia
- * E-mail: (GGVD); (KK); (SB)
| | - Giel G. van Dooren
- Research School of Biology, Australian National University, Canberra, ACT, Australia
- * E-mail: (GGVD); (KK); (SB)
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13
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Paight C, Slamovits CH, Saffo MB, Lane CE. Nephromyces Encodes a Urate Metabolism Pathway and Predicted Peroxisomes, Demonstrating That These Are Not Ancient Losses of Apicomplexans. Genome Biol Evol 2019; 11:41-53. [PMID: 30500900 PMCID: PMC6320678 DOI: 10.1093/gbe/evy251] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2018] [Indexed: 12/21/2022] Open
Abstract
The phylum Apicomplexa is a quintessentially parasitic lineage, whose members infect a broad range of animals. One exception to this may be the apicomplexan genus Nephromyces, which has been described as having a mutualistic relationship with its host. Here we analyze transcriptome data from Nephromyces and its parasitic sister taxon, Cardiosporidium, revealing an ancestral purine degradation pathway thought to have been lost early in apicomplexan evolution. The predicted localization of many of the purine degradation enzymes to peroxisomes, and the in silico identification of a full set of peroxisome proteins, indicates that loss of both features in other apicomplexans occurred multiple times. The degradation of purines is thought to play a key role in the unusual relationship between Nephromyces and its host. Transcriptome data confirm previous biochemical results of a functional pathway for the utilization of uric acid as a primary nitrogen source for this unusual apicomplexan.
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Affiliation(s)
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Mary Beth Saffo
- Department of Biological Sciences, University of Rhode Island
- Smithsonian National Museum of Natural History, Washington, District of Columbia
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14
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Costa-Martins AG, Lima L, Alves JMP, Serrano MG, Buck GA, Camargo EP, Teixeira MMG. Genome-wide identification of evolutionarily conserved Small Heat-Shock and eight other proteins bearing α-crystallin domain-like in kinetoplastid protists. PLoS One 2018; 13:e0206012. [PMID: 30346990 PMCID: PMC6197667 DOI: 10.1371/journal.pone.0206012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/04/2018] [Indexed: 11/18/2022] Open
Abstract
Small Heat-Shock Proteins (sHSPs) and other proteins bearing alpha-crystallin domains (ACD) participate in defense against heat and oxidative stress and play important roles in cell cycle, cytoskeleton dynamics, and immunological and pathological mechanisms in eukaryotes. However, little is known about these proteins in early-diverging lineages of protists such as the kinetoplastids. Here, ACD-like proteins (ACDp) were investigated in genomes of 61 species of 12 kinetoplastid genera, including Trypanosoma spp. (23 species of mammals, reptiles and frogs), Leishmania spp. (mammals and lizards), trypanosomatids of insects, Phytomonas spp. of plants, and bodonids. Comparison of ACDps based on domain architecture, predicted tertiary structure, phylogeny and genome organization reveals a kinetoplastid evolutionarily conserved repertoire, which diversified prior to trypanosomatid adaptation to parasitic life. We identified 9 ACDp orthologs classified in 8 families of TryACD: four previously recognized (HSP20, Tryp23A, Tryp23B and ATOM69), and four characterized for the first time in kinetoplastids (TryACDP, TrySGT1, TryDYX1C1 and TryNudC). A single copy of each ortholog was identified in each genome alongside TryNudC1/TrypNudC2 homologs and, overall, ACDPs were under strong selection pressures at main phylogenetic lineages. Transcripts of all ACDPs were identified across the life stages of T. cruzi, T. brucei and Leishmania spp., but proteomic profiles suggested that most ACDPs may be species- and stage-regulated. Our findings establish the basis for functional studies, and provided evolutionary and structural support for an underestimated repertoire of ACDps in the kinetoplastids.
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Affiliation(s)
- André G Costa-Martins
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Luciana Lima
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.,INCT-EpiAmO-Instituto Nacional de Epidemiologia na Amazônia Ocidental, Porto Velho, RO, Brazil
| | - João Marcelo P Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Myrna G Serrano
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Gregory A Buck
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Erney P Camargo
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.,INCT-EpiAmO-Instituto Nacional de Epidemiologia na Amazônia Ocidental, Porto Velho, RO, Brazil
| | - Marta M G Teixeira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.,INCT-EpiAmO-Instituto Nacional de Epidemiologia na Amazônia Ocidental, Porto Velho, RO, Brazil
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15
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Coccia M. A theory of classification and evolution of technologies within a Generalised Darwinism. TECHNOLOGY ANALYSIS & STRATEGIC MANAGEMENT 2018. [DOI: 10.1080/09537325.2018.1523385] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mario Coccia
- CNR – National Research Council of Italy, Moncalieri, Italy
- Arizona State University, Tempe, AZ, USA
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16
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Ginger M, Field MC. Making the pathogen: Evolution and adaptation in parasitic protists. Mol Biochem Parasitol 2018; 209:1-2. [PMID: 27919329 DOI: 10.1016/j.molbiopara.2016.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Michael Ginger
- Department of Life Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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17
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Gazanion E, Vergnes B. Protozoan Parasite Auxotrophies and Metabolic Dependencies. EXPERIENTIA SUPPLEMENTUM (2012) 2018; 109:351-375. [PMID: 30535605 DOI: 10.1007/978-3-319-74932-7_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Diseases caused by protozoan parasites have a major impact on world health. These early branching eukaryotes cause significant morbidity and mortality in humans and livestock. During evolution, protozoan parasites have evolved toward complex life cycles in multiple host organisms with different nutritional resources. The conservation of functional metabolic pathways required for these successive environments is therefore a prerequisite for parasitic lifestyle. Nevertheless, parasitism drives genome evolution toward gene loss and metabolic dependencies (including strict auxotrophy), especially for obligatory intracellular parasites. In this chapter, we will compare and contrast how protozoan parasites have perfected this metabolic adaptation by focusing on specific auxotrophic pathways and scavenging strategies used by clinically relevant apicomplexan and trypanosomatid parasites to access host's nutritional resources. We will further see how these metabolic dependencies have in turn been exploited for therapeutic purposes against these human pathogens.
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Affiliation(s)
- Elodie Gazanion
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Baptiste Vergnes
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France.
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18
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Extensive flagellar remodeling during the complex life cycle of Paratrypanosoma, an early-branching trypanosomatid. Proc Natl Acad Sci U S A 2017; 114:11757-11762. [PMID: 29078369 DOI: 10.1073/pnas.1712311114] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Paratrypanosoma confusum is a monoxenous kinetoplastid flagellate that constitutes the most basal branch of the highly diverse parasitic trypanosomatids, which include human pathogens Trypanosoma and Leishmania This makes Paratrypanosoma uniquely informative for the evolution of obligatory parasitism from free-living lifestyle and the evolution of human parasitism in some trypanosomatid lineages. It has typical promastigote morphology but also forms surface-attached haptomonads and amastigotes. Haptomonads form by attachment to a surface via a large bulge at the base of the flagellum, which is then remodeled into a thin attachment pad associated with flagellum shortening. Promastigotes and haptomonads multiply by binary division, and the progeny of a haptomonad can either remain attached or grow a flagellum and resume swimming. Whole genome sequencing and transcriptome profiling, in combination with analysis of the cell ultrastructure, reveal how the cell surface and metabolism are adapted to parasitism and how characteristic cytoskeletal features are conserved. Our data demonstrate that surface attachment by the flagellum and the flagellar pocket, a Leishmania-like flagellum attachment zone, and a Trypanosoma cruzi-like cytostome are ancestral features, while evolution of extant trypanosomatids, including the human parasites, is associated with genome streamlining and diversification of membrane proteins.
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19
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Abstract
The increasing prevalence of infections involving intracellular apicomplexan parasites such as Plasmodium, Toxoplasma, and Cryptosporidium (the causative agents of malaria, toxoplasmosis, and cryptosporidiosis, respectively) represent a significant global healthcare burden. Despite their significance, few treatments are available; a situation that is likely to deteriorate with the emergence of new resistant strains of parasites. To lay the foundation for programs of drug discovery and vaccine development, genome sequences for many of these organisms have been generated, together with large-scale expression and proteomic datasets. Comparative analyses of these datasets are beginning to identify the molecular innovations supporting both conserved processes mediating fundamental roles in parasite survival and persistence, as well as lineage-specific adaptations associated with divergent life-cycle strategies. The challenge is how best to exploit these data to derive insights into parasite virulence and identify those genes representing the most amenable targets. In this review, we outline genomic datasets currently available for apicomplexans and discuss biological insights that have emerged as a consequence of their analysis. Of particular interest are systems-based resources, focusing on areas of metabolism and host invasion that are opening up opportunities for discovering new therapeutic targets.
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Affiliation(s)
| | - John Parkinson
- a Program in Molecular Structure and Function , Hospital for Sick Children , Toronto , Ontario , Canada
- b Departments of Biochemistry, Molecular Genetics and Computer Science , University of Toronto , Toronto , Ontario , Canada
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21
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Yubuki N, Zadrobílková E, Čepička I. Ultrastructure and Molecular Phylogeny of Iotanema spirale gen. nov. et sp. nov., a New Lineage of Endobiotic Fornicata with Strikingly Simplified Ultrastructure. J Eukaryot Microbiol 2016; 64:422-433. [PMID: 27749017 DOI: 10.1111/jeu.12376] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 09/30/2016] [Accepted: 10/12/2016] [Indexed: 12/19/2022]
Abstract
Fornicata (Metamonada) is a group of Excavata living in low-oxygen environments and lacking conventional mitochondria. It includes free-living Carpediemonas-like organisms from marine habitats and predominantly parasitic/commensal retortamonads and diplomonads. Current modest knowledge of biodiversity of Fornicata limits our ability to draw a complete picture of the evolutionary history in this group. Here, we report the discovery of a novel fornicate, Iotanema spirale gen. nov. et sp. nov., obtained from fresh feces of the gecko Phelsuma madagascariensis. Our phylogenetic analyses of the small subunit ribosomal RNA gene demonstrate that I. spirale is closely related to the free-living, marine strain PCS and the Carpediemonas-like organism Hicanonectes teleskopos within Fornicata. Iotanema spirale exhibits several features uncommon to fornicates, such as a single flagellum, a highly reduced cytoskeletal system, and the lack of the excavate ventral groove, but shares these characters with the poorly known genus Caviomonas. Therefore, I. spirale is accommodated within the family Caviomonadidae, which represents the third known endobiotic lineage of Fornicata. This study improves our understanding of character evolution within Fornicata when placed within the molecular phylogenetic context.
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Affiliation(s)
- Naoji Yubuki
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, Prague, 128 44, Czech Republic
| | - Eliška Zadrobílková
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, Prague, 128 44, Czech Republic.,Centre for Epidemiology and Microbiology, National Institute of Public Health, Srobarova 48, Prague, 100 42, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, Prague, 128 44, Czech Republic
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22
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Opperdoes FR, Butenko A, Flegontov P, Yurchenko V, Lukeš J. Comparative Metabolism of Free-living Bodo saltans
and Parasitic Trypanosomatids. J Eukaryot Microbiol 2016; 63:657-78. [DOI: 10.1111/jeu.12315] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/10/2016] [Accepted: 03/20/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Fred R. Opperdoes
- de Duve Institute; Université Catholique de Louvain; Brussels B-1200 Belgium
| | - Anzhelika Butenko
- Life Science Research Centre; Faculty of Science; University of Ostrava; Ostrava 710 00 Czech Republic
| | - Pavel Flegontov
- Life Science Research Centre; Faculty of Science; University of Ostrava; Ostrava 710 00 Czech Republic
- Biology Centre; Institute of Parasitology; Czech Academy of Sciences; České Budějovice (Budweis) 370 05 Czech Republic
- A.A. Kharkevich Institute for Information Transmission Problems; Russian Academy of Sciences; Moscow 127 051 Russia
| | - Vyacheslav Yurchenko
- Life Science Research Centre; Faculty of Science; University of Ostrava; Ostrava 710 00 Czech Republic
- Biology Centre; Institute of Parasitology; Czech Academy of Sciences; České Budějovice (Budweis) 370 05 Czech Republic
- Faculty of Science; Institute of Environmental Technologies; University of Ostrava; Ostrava 710 00 Czech Republic
| | - Julius Lukeš
- Biology Centre; Institute of Parasitology; Czech Academy of Sciences; České Budějovice (Budweis) 370 05 Czech Republic
- Faculty of Science; University of South Bohemia; České Budějovice (Budweis) 370 05 Czech Republic
- Canadian Institute for Advanced Research; Toronto ON M5G 1Z8 Canada
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