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Guiry MD. How many species of algae are there? A reprise. Four kingdoms, 14 phyla, 63 classes and still growing. JOURNAL OF PHYCOLOGY 2024; 60:214-228. [PMID: 38245909 DOI: 10.1111/jpy.13431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/22/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
To date (1 November 2023), the online database AlgaeBase has documented 50,589 species of living algae and 10,556 fossil species here referred to four kingdoms (Eubacteria, Chromista, Plantae, and Protozoa), 14 phyla, and 63 classes. The algae are the third most speciose grouping of plant-like organisms after the flowering plants (≈382,000 species) and fungi (≈170,000 species, including lichens) but are the least well defined of all the botanical groupings. Priority is given to phyla and class names that are familiar to phycologists and that are nomenclaturally valid. The most species-rich phylum is the Heterokontophyta to which 18 classes are referred with 21,052 living species and which is dominated by the diatoms in three classes with 18,673 species (16,427 living; 2239 fossil). The next most species-rich phyla are the red algae (7276 living), the green algae (6851 living), the blue-green algae (Cyanobacteria, 5723 living), the charophytes (4950 living, including the Charophyceae, 511 species living, and the Zygnematophyceae, 4335 living species), Dinoflagellata (2956 living, including the Dinophyceae, 2828 extant), and haptophytes (Haptophyta 1722 species, 517 living).
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Affiliation(s)
- Michael D Guiry
- AlgaeBase, Ryan Institute, University of Galway, University Road, Galway, Ireland
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2
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Lax G, Cho A, Keeling PJ. Phylogenomics of novel ploeotid taxa contribute to the backbone of the euglenid tree. J Eukaryot Microbiol 2023; 70:e12973. [PMID: 36912454 DOI: 10.1111/jeu.12973] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 03/14/2023]
Abstract
Euglenids are a diverse group of flagellates that inhabit most environments and exhibit many different nutritional modes. The most prominent euglenids are phototrophs, but phagotrophs constitute the majority of phylogenetic diversity of euglenids. They are pivotal to our understanding of euglenid evolution, yet we are only starting to understand relationships amongst phagotrophs, with the backbone of the tree being most elusive. Ploeotids make up most of this backbone diversity-yet despite their morphological similarities, SSU rDNA analyses and multigene analyses show that they are non-monophyletic. As more ploeotid diversity is sampled, known taxa have coalesced into some subgroups (e.g. Alistosa), but the relationships amongst these are not always supported and some taxa remain unsampled for multigene phylogenetics. Here, we used light microscopy and single-cell transcriptomics to characterize five ploeotid euglenids and place them into a multigene phylogenetic framework. Our analyses place Decastava in Alistosa; while Hemiolia branches with Liburna, establishing the novel clade Karavia. We describe Hemiolia limna, a freshwater-dwelling species in an otherwise marine clade. Intriguingly, two undescribed ploeotids are found to occupy pivotal positions in the tree: Chelandium granulatum nov. gen. nov. sp. branches as sister to Olkasia, and Gaulosia striata nov. gen. nov. sp. remains an orphan taxon.
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Affiliation(s)
- Gordon Lax
- Department of Botany, University of British Columbia, Vancouver, V6T 1Z4, British Columbia, Canada
| | - Anna Cho
- Department of Botany, University of British Columbia, Vancouver, V6T 1Z4, British Columbia, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, V6T 1Z4, British Columbia, Canada
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3
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Rackevei AS, Karnkowska A, Wolf M. 18S rDNA sequence-structure phylogeny of the Euglenophyceae (Euglenozoa, Euglenida). J Eukaryot Microbiol 2023; 70:e12959. [PMID: 36478494 DOI: 10.1111/jeu.12959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/14/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
The phylogeny of Euglenophyceae (Euglenozoa, Euglenida) has been discussed for decades with new genera being described in the last few years. In this study, we reconstruct a phylogeny using 18S rDNA sequence and structural data simultaneously. Using homology modeling, individual secondary structures were predicted. Sequence-structure data are encoded and automatically aligned. Here, we present a sequence-structure neighbor-joining tree of more than 300 taxa classified as Euglenophyceae. Profile neighbor-joining was used to resolve the basal branching pattern. Neighbor-joining, maximum parsimony, and maximum likelihood analyses were performed using sequence-structure information for manually chosen subsets. All analyses supported the monophyly of Eutreptiella, Discoplastis, Lepocinclis, Strombomonas, Cryptoglena, Monomorphina, Euglenaria, and Colacium. Well-supported topologies were generally consistent with previous studies using a combined dataset of genetic markers. Our study supports the simultaneous use of sequence and structural data to reconstruct more accurate and robust trees. The average bootstrap value is significantly higher than the average bootstrap value obtained from sequence-only analyses, which is promising for resolving relationships between more closely related taxa.
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Affiliation(s)
- Antonia S Rackevei
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Matthias Wolf
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
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Hałakuc P, Karnkowska A, Milanowski R. Typical structure of rRNA coding genes in diplonemids points to two independent origins of the bizarre rDNA structures of euglenozoans. BMC Ecol Evol 2022; 22:59. [PMID: 35534840 PMCID: PMC9082867 DOI: 10.1186/s12862-022-02014-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 04/22/2022] [Indexed: 12/02/2022] Open
Abstract
Background Members of Euglenozoa (Discoba) are known for unorthodox rDNA organization. In Euglenida rDNA is located on extrachromosomal circular DNA. In Kinetoplastea and Euglenida the core of the large ribosomal subunit, typically formed by the 28S rRNA, consists of several smaller rRNAs. They are the result of the presence of additional internal transcribed spacers (ITSs) in the rDNA. Diplonemea is the third of the main groups of Euglenozoa and its members are known to be among the most abundant and diverse protists in the oceans. Despite that, the rRNA of only one diplonemid species, Diplonema papillatum, has been examined so far and found to exhibit continuous 28S rRNA. Currently, the rDNA organization has not been researched for any diplonemid. Herein we investigate the structure of rRNA genes in classical (Diplonemidae) and deep-sea diplonemids (Eupelagonemidae), representing the majority of known diplonemid diversity. The results fill the gap in knowledge about diplonemid rDNA and allow better understanding of the evolution of the fragmented structure of the rDNA in Euglenozoa. Results We used available genomic (culture and single-cell) sequencing data to assemble complete or almost complete rRNA operons for three classical and six deep-sea diplonemids. The rDNA sequences acquired for several euglenids and kinetoplastids were used to provide the background for the analysis. In all nine diplonemids, 28S rRNA seems to be contiguous, with no additional ITSs detected. Similarly, no additional ITSs were detected in basal prokinetoplastids. However, we identified five additional ITSs in the 28S rRNA of all analysed metakinetoplastids, and up to twelve in euglenids. Only three of these share positions, and they cannot be traced back to their common ancestor. Conclusions Presented results indicate that independent origin of additional ITSs in euglenids and kinetoplastids seems to be the most likely. The reason for such unmatched fragmentation remains unknown, but for some reason euglenozoan ribosomes appear to be prone to 28S rRNA fragmentation. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02014-9.
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Nowruzi B, Shishir MA, Porzani SJ, Ferdous UT. Exploring the Interactions between Algae and Bacteria. Mini Rev Med Chem 2022; 22:2596-2607. [PMID: 35507745 DOI: 10.2174/1389557522666220504141047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/01/2022] [Accepted: 03/17/2022] [Indexed: 11/22/2022]
Abstract
Humans have used algae for hundreds of years to make various products viz. agar, fertilizer, food, and pigments. Algae are also used in bioremediation to clean up polluted water and as essential laboratory tools in genomics, proteomics, and other research applications such as environmental warnings. Several special features of algae, including the oxygenic photosynthesis, higher yield in biomass, growth on the non-arable lands, their survival in a wide range of water supplies (contaminated or filtered waters), the production of necessary byproducts and biofuels, the enhancement of soil productivity, and the greenhouse gas emissions, etc. altogether rendered them as vital bio-resources in the sustainable development. Algae and bacteria have been assumed to coexist from the early stages of the development of the earth, and a wide variety of interactions were observed between them which have influenced the ecosystems ranging from the oceans to the lichens. Research has shown that bacteria and algae interact synergistically, especially roseobacter-algae interactions being the most common. These interactions are common to all ecosystems and characterize their primary efficiency. The commercialization of algae for industrial purposes, an important field, is also influenced by this interaction which frequently results in bacterial infections among the consumers. However, the recent findings have revealed that the bacteria improve algal growth and support flocculation which are very crucial in algal biotechnology. Some of the most exciting advancements in the area of algal biotic interactions and potential difficulties were reviewed in this article. Information gleaned in this study would provide a firm foundation for launching more contemporaneous research efforts in understanding and utilizing the algal species in biotechnology industries and medical sectors.
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Affiliation(s)
- Bahareh Nowruzi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Samaneh J Porzani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Umme Tamanna Ferdous
- Aquatic Animal Health and Therapeutics Laboratory (AquaHealth), Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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Cavalier-Smith T. Ciliary transition zone evolution and the root of the eukaryote tree: implications for opisthokont origin and classification of kingdoms Protozoa, Plantae, and Fungi. PROTOPLASMA 2022; 259:487-593. [PMID: 34940909 PMCID: PMC9010356 DOI: 10.1007/s00709-021-01665-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 05/03/2021] [Indexed: 05/19/2023]
Abstract
I thoroughly discuss ciliary transition zone (TZ) evolution, highlighting many overlooked evolutionarily significant ultrastructural details. I establish fundamental principles of TZ ultrastructure and evolution throughout eukaryotes, inferring unrecognised ancestral TZ patterns for Fungi, opisthokonts, and Corticata (i.e., kingdoms Plantae and Chromista). Typical TZs have a dense transitional plate (TP), with a previously overlooked complex lattice as skeleton. I show most eukaryotes have centriole/TZ junction acorn-V filaments (whose ancestral function was arguably supporting central pair microtubule-nucleating sites; I discuss their role in centriole growth). Uniquely simple malawimonad TZs (without TP, simpler acorn) pinpoint the eukaryote tree's root between them and TP-bearers, highlighting novel superclades. I integrate TZ/ciliary evolution with the best multiprotein trees, naming newly recognised major eukaryote clades and revise megaclassification of basal kingdom Protozoa. Recent discovery of non-photosynthetic phagotrophic flagellates with genome-free plastids (Rhodelphis), the sister group to phylum Rhodophyta (red algae), illuminates plant and chromist early evolution. I show previously overlooked marked similarities in cell ultrastructure between Rhodelphis and Picomonas, formerly considered an early diverging chromist. In both a nonagonal tube lies between their TP and an annular septum surrounding their 9+2 ciliary axoneme. Mitochondrial dense condensations and mitochondrion-linked smooth endomembrane cytoplasmic partitioning cisternae further support grouping Picomonadea and Rhodelphea as new plant phylum Pararhoda. As Pararhoda/Rhodophyta form a robust clade on site-heterogeneous multiprotein trees, I group Pararhoda and Rhodophyta as new infrakingdom Rhodaria of Plantae within subkingdom Biliphyta, which also includes Glaucophyta with fundamentally similar TZ, uniquely in eukaryotes. I explain how biliphyte TZs generated viridiplant stellate-structures.
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Belyaev AO, Zagumyonnyi DG, Mylnikov AP, Tikhonenkov DV. The Morphology, Ultrastructure and Molecular Phylogeny of a New Soil-Dwelling Kinetoplastid Avlakibodo gracilis gen. et sp. nov. (Neobodonida; Kinetoplastea). Protist 2022; 173:125885. [DOI: 10.1016/j.protis.2022.125885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 04/29/2022] [Accepted: 05/02/2022] [Indexed: 01/04/2023]
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8
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Tashyreva D, Simpson A, Prokopchuk G, Škodová-Sveráková I, Butenko A, Hammond M, George EE, Flegontova O, Záhonová K, Faktorová D, Yabuki A, Horák A, Keeling PJ, Lukeš J. Diplonemids – A Review on “New“ Flagellates on the Oceanic Block. Protist 2022; 173:125868. [DOI: 10.1016/j.protis.2022.125868] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/26/2022] [Accepted: 02/28/2022] [Indexed: 11/15/2022]
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9
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Verma S, Toppo K, Nayaka S. Comprehensive checklist of algal class Chlorophyceae (sensu Fritsch, 1935) for Uttar Pradesh, India, with updated taxonomic status. JOURNAL OF THREATENED TAXA 2021. [DOI: 10.11609/jott.6508.13.14.20218-20248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Uttar Pradesh is an active center for algal research in India, but regional checklists are not available. Checklists of algae reported from class Chlorophyceae (sensu Fritsch, 1935) are presented here, with taxonomic status updated per AlgaeBase. The checklist covers algae from 17 types of habitats and includes 749 species, 166 varities and six forma, belonging to four phyla, 11 classes, 26 orders, 64 families and 161 genera. Charophyta is the dominant phylum with 519 infrageneric taxa (species, varities, forma), while Chlorophyta is represented by 389 taxa. Zygnematophyceae is the dominant class with 465 infrageneric taxa under two orders, six families and 29 genera. Chlorophyceae has 305 infrageneric taxa under five orders, 33 families, and 76 genera. Cosmarium is the most speciose genus with 163 taxa, followed by Oedogonium (79), Spirogyra (72), and Closterium (54). Our study revealed that of 75 districts in Uttar Pradesh only 40 are explored for algae, with Prayagraj and Lucknow recording 266 and 144 taxa respectively.
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Škodová-Sveráková I, Záhonová K, Juricová V, Danchenko M, Moos M, Baráth P, Prokopchuk G, Butenko A, Lukáčová V, Kohútová L, Bučková B, Horák A, Faktorová D, Horváth A, Šimek P, Lukeš J. Highly flexible metabolism of the marine euglenozoan protist Diplonema papillatum. BMC Biol 2021; 19:251. [PMID: 34819072 PMCID: PMC8611851 DOI: 10.1186/s12915-021-01186-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/08/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The phylum Euglenozoa is a group of flagellated protists comprising the diplonemids, euglenids, symbiontids, and kinetoplastids. The diplonemids are highly abundant and speciose, and recent tools have rendered the best studied representative, Diplonema papillatum, genetically tractable. However, despite the high diversity of diplonemids, their lifestyles, ecological functions, and even primary energy source are mostly unknown. RESULTS We designed a metabolic map of D. papillatum cellular bioenergetic pathways based on the alterations of transcriptomic, proteomic, and metabolomic profiles obtained from cells grown under different conditions. Comparative analysis in the nutrient-rich and nutrient-poor media, as well as the absence and presence of oxygen, revealed its capacity for extensive metabolic reprogramming that occurs predominantly on the proteomic rather than the transcriptomic level. D. papillatum is equipped with fundamental metabolic routes such as glycolysis, gluconeogenesis, TCA cycle, pentose phosphate pathway, respiratory complexes, β-oxidation, and synthesis of fatty acids. Gluconeogenesis is uniquely dominant over glycolysis under all surveyed conditions, while the TCA cycle represents an eclectic combination of standard and unusual enzymes. CONCLUSIONS The identification of conventional anaerobic enzymes reflects the ability of this protist to survive in low-oxygen environments. Furthermore, its metabolism quickly reacts to restricted carbon availability, suggesting a high metabolic flexibility of diplonemids, which is further reflected in cell morphology and motility, correlating well with their extreme ecological valence.
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Affiliation(s)
- Ingrid Škodová-Sveráková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.
- Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia.
| | - Kristína Záhonová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Valéria Juricová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Maksym Danchenko
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Martin Moos
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Peter Baráth
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
- Medirex Group Academy n.o., Trnava, Slovakia
| | - Galina Prokopchuk
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - 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
| | | | - Lenka Kohútová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Barbora Bučková
- Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Drahomíra Faktorová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Anton Horváth
- Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Petr Šimek
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic.
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Borges AR, Engstler M, Wolf M. 18S rRNA gene sequence-structure phylogeny of the Trypanosomatida (Kinetoplastea, Euglenozoa) with special reference to Trypanosoma. Eur J Protistol 2021; 81:125824. [PMID: 34352687 DOI: 10.1016/j.ejop.2021.125824] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 06/08/2021] [Accepted: 07/06/2021] [Indexed: 11/30/2022]
Abstract
Parasites of the order Trypanosomatida are known due to their medical relevance. Despite the progress made in the past decades on understanding the evolution of this group of organisms, there are still many open questions that require robust phylogenetic markers to increase the resolution of trees. Using two known 18S rRNA gene template structures (from Trypanosoma cruzi Chagas, 1909 and Trypanosoma brucei Plimmer and Bradford, 1899), individual 18S rRNA gene secondary structures were predicted by homology modeling. Sequences and their secondary structures, automatically encoded by a 12-letter alphabet (each nucleotide with its three structural states, paired left, paired right, unpaired), were simultaneously aligned. Sequence-structure trees were generated by neighbor joining and/or maximum likelihood. The reconstructed trees allowed us to discuss not only the big picture of trypanosomatid phylogeny but also a comprehensive sampling of trypanosomes evaluated in the context of trypanosomatid diversity. The robust support (bootstrap > 75) for well-known clades and critical branches suggests that the simultaneous use of 18S rRNA sequence and secondary structure data can reconstruct robust phylogenetic trees and can be used by the trypanosomatid research community for future analysis.
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Affiliation(s)
- Alyssa R Borges
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Markus Engstler
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Matthias Wolf
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
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12
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Srivastava S, Usmani Z, Atanasov AG, Singh VK, Singh NP, Abdel-Azeem AM, Prasad R, Gupta G, Sharma M, Bhargava A. Biological Nanofactories: Using Living Forms for Metal Nanoparticle Synthesis. Mini Rev Med Chem 2021; 21:245-265. [PMID: 33198616 DOI: 10.2174/1389557520999201116163012] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/21/2020] [Accepted: 09/08/2020] [Indexed: 11/22/2022]
Abstract
Metal nanoparticles are nanosized entities with dimensions of 1-100 nm that are increasingly in demand due to applications in diverse fields like electronics, sensing, environmental remediation, oil recovery and drug delivery. Metal nanoparticles possess large surface energy and properties different from bulk materials due to their small size, large surface area with free dangling bonds and higher reactivity. High cost and pernicious effects associated with the chemical and physical methods of nanoparticle synthesis are gradually paving the way for biological methods due to their eco-friendly nature. Considering the vast potentiality of microbes and plants as sources, biological synthesis can serve as a green technique for the synthesis of nanoparticles as an alternative to conventional methods. A number of reviews are available on green synthesis of nanoparticles but few have focused on covering the entire biological agents in this process. Therefore present paper describes the use of various living organisms like bacteria, fungi, algae, bryophytes and tracheophytes in the biological synthesis of metal nanoparticles, the mechanisms involved and the advantages associated therein.
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Affiliation(s)
- Shilpi Srivastava
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | - Zeba Usmani
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | | | | | | | - Ahmed M Abdel-Azeem
- Botany Department, Faculty of Science, University of Suez Canal, Ismailia, Egypt
| | - Ram Prasad
- Department of Botany, Mahatma Gandhi Central University, Motihari, Bihar, India
| | - Govind Gupta
- Sage School of Agriculture, Sage University, Bhopal, India
| | - Minaxi Sharma
- Department of Food Technology, Akal College of Agriculture, Eternal University, Baru Sahib, Himachal Pradesh, India
| | - Atul Bhargava
- Department of Botany, Mahatma Gandhi Central University, Motihari, Bihar, India
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13
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Kostygov AY, Karnkowska A, Votýpka J, Tashyreva D, Maciszewski K, Yurchenko V, Lukeš J. Euglenozoa: taxonomy, diversity and ecology, symbioses and viruses. Open Biol 2021; 11:200407. [PMID: 33715388 PMCID: PMC8061765 DOI: 10.1098/rsob.200407] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Euglenozoa is a species-rich group of protists, which have extremely diverse lifestyles and a range of features that distinguish them from other eukaryotes. They are composed of free-living and parasitic kinetoplastids, mostly free-living diplonemids, heterotrophic and photosynthetic euglenids, as well as deep-sea symbiontids. Although they form a well-supported monophyletic group, these morphologically rather distinct groups are almost never treated together in a comparative manner, as attempted here. We present an updated taxonomy, complemented by photos of representative species, with notes on diversity, distribution and biology of euglenozoans. For kinetoplastids, we propose a significantly modified taxonomy that reflects the latest findings. Finally, we summarize what is known about viruses infecting euglenozoans, as well as their relationships with ecto- and endosymbiotic bacteria.
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Affiliation(s)
- Alexei Y Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.,Zoological Institute, Russian Academy of Sciences, St Petersburg, Russia
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Jan Votýpka
- Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Daria Tashyreva
- Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Kacper Maciszewski
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.,Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia
| | - Julius Lukeš
- 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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Tikhonenkov DV, Gawryluk RMR, Mylnikov AP, Keeling PJ. First finding of free-living representatives of Prokinetoplastina and their nuclear and mitochondrial genomes. Sci Rep 2021; 11:2946. [PMID: 33536456 PMCID: PMC7859406 DOI: 10.1038/s41598-021-82369-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/19/2021] [Indexed: 01/30/2023] Open
Abstract
Kinetoplastids are heterotrophic flagellated protists, including important parasites of humans and animals (trypanosomatids), and ecologically important free-living bacterial consumers (bodonids). Phylogenies have shown that the earliest-branching kinetoplastids are all parasites or obligate endosymbionts, whose highly-derived state makes reconstructing the ancestral state of the group challenging. We have isolated new strains of unusual free-living flagellates that molecular phylogeny shows to be most closely related to endosymbiotic and parasitic Perkinsela and Ichthyobodo species that, together with unidentified environmental sequences, form the clade at the base of kinetoplastids. These strains are therefore the first described free-living prokinetoplastids, and potentially very informative in understanding the evolution and ancestral states of morphological and molecular characteristics described in other kinetoplastids. Overall, we find that these organisms morphologically and ultrastructurally resemble some free-living bodonids and diplonemids, and possess nuclear genomes with few introns, polycistronic mRNA expression, high coding density, and derived traits shared with other kinetoplastids. Their genetic repertoires are more diverse than the best-studied free-living kinetoplastids, which is likely a reflection of their higher metabolic potential. Mitochondrial RNAs of these new species undergo the most extensive U insertion/deletion editing reported so far, and limited deaminative C-to-U and A-to-I editing, but we find no evidence for mitochondrial trans-splicing.
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Affiliation(s)
- Denis V. Tikhonenkov
- grid.4886.20000 0001 2192 9124Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, 152742 Russia ,grid.446209.d0000 0000 9203 3563AquaBioSafe Laboratory, University of Tyumen, 625003 Tyumen, Russia
| | - Ryan M. R. Gawryluk
- grid.143640.40000 0004 1936 9465Department of Biology, University of Victoria, Victoria, British Columbia V8W 2Y2 Canada
| | - Alexander P. Mylnikov
- grid.4886.20000 0001 2192 9124Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, 152742 Russia
| | - Patrick J. Keeling
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4 Canada
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15
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Lax G, Kolisko M, Eglit Y, Lee WJ, Yubuki N, Karnkowska A, Leander BS, Burger G, Keeling PJ, Simpson AGB. Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs. Mol Phylogenet Evol 2021; 159:107088. [PMID: 33545276 DOI: 10.1016/j.ympev.2021.107088] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 01/24/2021] [Accepted: 01/26/2021] [Indexed: 12/22/2022]
Abstract
Euglenids are a well-known group of single-celled eukaryotes, with phototrophic, osmotrophic and phagotrophic members. Phagotrophs represent most of the phylogenetic diversity of euglenids, and gave rise to the phototrophs and osmotrophs, but their evolutionary relationships are poorly understood. Symbiontids, in contrast, are anaerobes that are alternatively inferred to be derived euglenids, or a separate euglenozoan group. Most phylogenetic studies of euglenids have examined the SSU rDNA only, which is often highly divergent. Also, many phagotrophic euglenids (and symbiontids) are uncultured, restricting collection of other molecular data. We generated transcriptome data for 28 taxa, mostly using a single-cell approach, and conducted the first multigene phylogenetic analyses of euglenids to include phagotrophs and symbiontids. Euglenids are recovered as monophyletic, with symbiontids forming an independent branch within Euglenozoa. Spirocuta, the clade of flexible euglenids that contains both the phototrophs (Euglenophyceae) and osmotrophs (Aphagea), is robustly resolved, with the ploeotid Olkasia as its sister group, forming the new taxon Olkaspira. Ploeotids are paraphyletic, although Ploeotiidae (represented by Ploeotia spp.), Lentomonas, and Keelungia form a robust clade (new taxon Alistosa). Petalomonadida branches robustly as sister to other euglenids in outgroup-rooted analyses. Within Spirocuta, Euglenophyceae is a robust clade that includes Rapaza, and Anisonemia is a well-supported monophyletic group containing Anisonemidae (Anisonema and Dinema spp.), 'Heteronema II' (represented by H. vittatum), and a clade of Neometanema plus Aphagea. Among 'peranemid' phagotrophs, Chasmostoma branches with included Urceolus, and Peranema with the undescribed 'Jenningsia II', while other relationships are weakly supported and consequently the closest sister group to Euglenophyceae remains unresolved. Our results are inconsistent with recent inferences that Entosiphon is the evolutionarily pivotal sister either to other euglenids, or to Spirocuta. At least three transitions between posterior and anterior flagellar gliding occurred in euglenids, with the phylogenetic positions and directions of those transitions remaining ambiguous.
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Affiliation(s)
- G Lax
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada; Department of Botany, University of British Columbia, Vancouver, Canada(1)
| | - M Kolisko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Y Eglit
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
| | - W J Lee
- Department of Environment and Energy Engineering, Kyungnam University, Changwon, Republic of Korea
| | - N Yubuki
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, Orsay, France; Department of Zoology, University of British Columbia, Vancouver, Canada
| | - A Karnkowska
- Institute of Evolutionary Biology, Faculty of Biology, University of Warsaw, Poland
| | - B S Leander
- Department of Zoology, University of British Columbia, Vancouver, Canada
| | - G Burger
- Robert-Cedergren Centre for Bioinformatics and Genomics, Biochemistry Department, Université de Montréal, Montréal, Canada
| | - P J Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada(1)
| | - A G B Simpson
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada.
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16
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Yabuki A, Kawato M, Nagano Y, Tsuchida S, Yoshida T, Fujiwara Y. Structural Comparison of Diplonemid Communities around the Izu Peninsula, Japan. Microbes Environ 2021; 36:ME21012. [PMID: 34121037 PMCID: PMC8209450 DOI: 10.1264/jsme2.me21012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/07/2021] [Indexed: 11/28/2022] Open
Abstract
Diplonemea (diplonemids) is one of the most abundant and species-rich protist groups in marine environments; however, their community structures among local and seasonal samples have not yet been compared. In the present study, we analyzed four diplonemid community structures around the Izu Peninsula, Japan using barcode sequences amplified from environmental DNA. These sequences and the results of statistical analyses indicated that communities at the same site were more similar to each other than those in the same season. Environmental variables were also measured, and their influence on diplonemid community structures was examined. Salinity, electrical conductivity, and temperature, and their correlated variables, appeared to influence the structures of diplonemid communities, which was consistent with previous findings; however, since the results obtained did not reach statistical significance, further studies are required. A comparison of each diplonemid community indicated that some lineages were unique to specific samples, while others were consistently detected in all samples. Members of the latter type are cosmopolitan candidates and may be better adapted to the environments of the studied area. Future studies that focus on the more adaptive members will provide a more detailed understanding of the mechanisms by which diplonemids are widely distributed in marine environments and will facilitate their utilization as indicator organisms to monitor environmental changes.
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Affiliation(s)
- Akinori Yabuki
- Deep-Sea Biodiversity Research Group, Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima, Yokosuka, Kanagawa 2370061, Japan
| | - Masaru Kawato
- Deep-Sea Biodiversity Research Group, Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima, Yokosuka, Kanagawa 2370061, Japan
| | - Yuriko Nagano
- Deep-Sea Biodiversity Research Group, Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima, Yokosuka, Kanagawa 2370061, Japan
| | - Shinji Tsuchida
- Deep-Sea Biodiversity Research Group, Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima, Yokosuka, Kanagawa 2370061, Japan
| | - Takao Yoshida
- Deep-Sea Biodiversity Research Group, Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima, Yokosuka, Kanagawa 2370061, Japan
| | - Yoshihiro Fujiwara
- Deep-Sea Biodiversity Research Group, Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima, Yokosuka, Kanagawa 2370061, Japan
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17
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Menaa F, Wijesinghe PAUI, Thiripuranathar G, Uzair B, Iqbal H, Khan BA, Menaa B. Ecological and Industrial Implications of Dynamic Seaweed-Associated Microbiota Interactions. Mar Drugs 2020; 18:md18120641. [PMID: 33327517 PMCID: PMC7764995 DOI: 10.3390/md18120641] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/09/2020] [Accepted: 12/13/2020] [Indexed: 02/07/2023] Open
Abstract
Seaweeds are broadly distributed and represent an important source of secondary metabolites (e.g., halogenated compounds, polyphenols) eliciting various pharmacological activities and playing a relevant ecological role in the anti-epibiosis. Importantly, host (as known as basibiont such as algae)–microbe (as known as epibiont such as bacteria) interaction (as known as halobiont) is a driving force for coevolution in the marine environment. Nevertheless, halobionts may be fundamental (harmless) or detrimental (harmful) to the functioning of the host. In addition to biotic factors, abiotic factors (e.g., pH, salinity, temperature, nutrients) regulate halobionts. Spatiotemporal and functional exploration of such dynamic interactions appear crucial. Indeed, environmental stress in a constantly changing ocean may disturb complex mutualistic relations, through mechanisms involving host chemical defense strategies (e.g., secretion of secondary metabolites and antifouling chemicals by quorum sensing). It is worth mentioning that many of bioactive compounds, such as terpenoids, previously attributed to macroalgae are in fact produced or metabolized by their associated microorganisms (e.g., bacteria, fungi, viruses, parasites). Eventually, recent metagenomics analyses suggest that microbes may have acquired seaweed associated genes because of increased seaweed in diets. This article retrospectively reviews pertinent studies on the spatiotemporal and functional seaweed-associated microbiota interactions which can lead to the production of bioactive compounds with high antifouling, theranostic, and biotechnological potential.
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Affiliation(s)
- Farid Menaa
- Department of Nanomedicine, California Innovations Corporation, San Diego, CA 92037, USA;
- Correspondence: or
| | - P. A. U. I. Wijesinghe
- College of Chemical Sciences, Institute of Chemistry Ceylon, Rajagiriya 10107, Sri Lanka; (P.A.U.I.W.); (G.T.)
| | - Gobika Thiripuranathar
- College of Chemical Sciences, Institute of Chemistry Ceylon, Rajagiriya 10107, Sri Lanka; (P.A.U.I.W.); (G.T.)
| | - Bushra Uzair
- Department of Biological Sciences, International Islamic University, Islamabad 44000, Pakistan;
| | - Haroon Iqbal
- Department of Pharmaceutics, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China;
| | - Barkat Ali Khan
- Department of Pharmacy, Gomal University, Dera Ismail Khan 29050, Pakistan;
| | - Bouzid Menaa
- Department of Nanomedicine, California Innovations Corporation, San Diego, CA 92037, USA;
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18
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Flegontova O, Flegontov P, Londoño PAC, Walczowski W, Šantić D, Edgcomb VP, Lukeš J, Horák A. Environmental determinants of the distribution of planktonic diplonemids and kinetoplastids in the oceans. Environ Microbiol 2020; 22:4014-4031. [PMID: 32779301 DOI: 10.1111/1462-2920.15190] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/07/2020] [Indexed: 12/26/2022]
Abstract
We analysed a widely used barcode, the V9 region of the 18S rRNA gene, to study the effect of environmental conditions on the distribution of two related heterotrophic protistan lineages in marine plankton, kinetoplastids and diplonemids. We relied on a major published dataset (Tara Oceans) where samples from the mesopelagic zone were available from just 32 of 123 locations, and both groups are most abundant in this zone. To close sampling gaps and obtain more information from the deeper ocean, we collected 57 new samples targeting especially the mesopelagic zone. We sampled in three geographic regions: the Arctic, two depth transects in the Adriatic Sea, and the anoxic Cariaco Basin. In agreement with previous studies, both protist groups are most abundant and diverse in the mesopelagic zone. In addition to that, we found that their abundance, richness, and community structure also depend on geography, oxygen concentration, salinity, temperature, and other environmental variables reflecting the abundance of algae and nutrients. Both groups studied here demonstrated similar patterns, although some differences were also observed. Kinetoplastids and diplonemids prefer tropical regions and nutrient-rich conditions and avoid high oxygen concentration, high salinity, and high density of algae.
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Affiliation(s)
- Olga Flegontova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Pavel Flegontov
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Paula Andrea Castañeda Londoño
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Biocenter, University of Würzburg, Würzburg, Germany
| | | | | | - Virginia P Edgcomb
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Department of Molecular Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Department of Molecular Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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19
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Lax G, Simpson AGB. The Molecular Diversity of Phagotrophic Euglenids Examined Using Single-cell Methods. Protist 2020; 171:125757. [PMID: 33126020 DOI: 10.1016/j.protis.2020.125757] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/29/2020] [Accepted: 08/05/2020] [Indexed: 01/16/2023]
Abstract
Euglenids are a diverse group of euglenozoan flagellates that includes phototrophs, osmotrophs, and phagotrophs. Despite making up most of the phylogenetic diversity of euglenids, phagotrophs remain understudied, and recent work has focused on 'deep-branching' groups. Spirocuta is the large clade encompassing all flexible euglenids including the phototroph and primary osmotroph clades, plus various phagotrophs. Understanding the phylogenetic diversity of phagotrophic spirocutes is crucial for tracing euglenid evolution, including how phototrophs arose. We used single-cell approaches to greatly increase sampling of SSU rDNA for phagotrophic euglenids, particularly spirocutes, including the first sequences from Urceolus, Jenningsia, Chasmostoma, and Sphenomonas, and expanded coverage for Dinema and Heteronema sensu lato, amongst others. Urceolus monophyly is unconfirmed. Organisms referred to Jenningsia form two distinct clades. Heteronema vittatum and similar cells branch separately from Heteronema (c.f.) globuliferum and Teloprocta/Heteronema scaphurum, while Dinema appears as 2-3 clades. Sphenomonas is monophyletic and the deepest branch within Petalomonadida. The census of genera markedly underestimates the phylogenetic diversity of phagotrophs, but taxonomic restraint is necessary when sequences are not available from type species or reasonable surrogates. SSU rDNA phylogenies do not resolve most deep relationships within Spirocuta, but identify units of diversity to sample in future multigene analyses.
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Affiliation(s)
- Gordon Lax
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada
| | - Alastair G B Simpson
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada.
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20
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Gao F, Voncken F, Colasante C. The mitochondrial phosphate carrier TbMCP11 is essential for mitochondrial function in the procyclic form of Trypanosoma brucei. Mol Biochem Parasitol 2020; 237:111275. [PMID: 32353560 DOI: 10.1016/j.molbiopara.2020.111275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/02/2020] [Accepted: 03/24/2020] [Indexed: 01/24/2023]
Abstract
Conserved amongst all eukaryotes is a family of mitochondrial carrier proteins (SLC25A) responsible for the import of various solutes across the inner mitochondrial membrane. We previously reported that the human parasite Trypanosoma brucei possesses 26 SLC25A proteins (TbMCPs) amongst which two, TbMCP11 and TbMCP8, were predicted to function as phosphate importers. The transport of inorganic phosphate into the mitochondrion is a prerequisite to drive ATP synthesis by substrate level and oxidative phosphorylation and thus crucial for cell viability. In this paper we describe the functional characterization of TbMCP11. In procyclic form T. brucei, the RNAi of TbMCP11 blocked ATP synthesis on mitochondrial substrates, caused a drop of the mitochondrial oxygen consumption and drastically reduced cell viability. The functional complementation in yeast and mitochondrial swelling experiments suggested a role for TbMCP11 as inorganic phosphate carrier. Interestingly, procyclic form T. brucei cells in which TbMCP11 was depleted displayed an inability to either replicate or divide the kinetoplast DNA, which resulted in a severe cytokinesis defect.
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Affiliation(s)
- Fei Gao
- Department of Neuroscience, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0AH, United Kingdom
| | - Frank Voncken
- Department of Biomedical Sciences, School of Life Sciences, University of Hull, Cottingham Road, Hull, HU6 7RX, United Kingdom
| | - Claudia Colasante
- Institute for Anatomy and Cell Biology, Division of Medical Cell Biology, Aulweg 123, University of Giessen, 35392, Giessen, Germany.
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21
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Medkour H, Varloud M, Davoust B, Mediannikov O. New Molecular Approach for the Detection of Kinetoplastida Parasites of Medical and Veterinary Interest. Microorganisms 2020; 8:E356. [PMID: 32131458 PMCID: PMC7143920 DOI: 10.3390/microorganisms8030356] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 02/26/2020] [Accepted: 03/01/2020] [Indexed: 01/03/2023] Open
Abstract
Kinetoplastids are protozoa containing a range of ubiquitous free_living species-pathogens of invertebrates, vertebrates and even some plants. Some of them are causative agents of canine vector-borne diseases. Their diagnosis is often missing in a gold standard. Here, we proposed a molecular approach for the diagnosis and study of Kinetoplastida. The TaqMan qPCR assays target the following genes: 24Sa LSU of Kinetoplastida, 28S LSU of Leishmania/ Trypanosoma spp., 5.8S rRNA of Trypanosoma spp., 18S SSU of Leishmania spp., kinetoplast minicircle DNA (kDNA) of L. donovani complex and kDNA of L. infantum, were designed, validated for their sensitivity (Se) and specificity (Sp) in silico and in vitro using a panel of known DNAs. They were then used to screen 369 blood samples (358 dogs, 2 equids, 9 monkeys). In addition, new 28S LSU primer sets are presented to use for Kinetoplastida's identification by PCR/sequencing. All qPCRs showed consistently high analytical sensitivities and reproducibility. They detect approximately 0.01 parasite/ mL blood for the kDNA based- qPCRs and at least a single cell-equivalent of rDNA for the other systems. Based on the sequencing results, after screening, Se and Sp were: 0. 919 and 0.971, 0.853 and 0.979, 1.00 and 0.987, 0.826 and 0.995 for all of Kinetoplastida, Leishmania/ Trypanosoma, Trypanosoma, Leishmania spp. specific qPCRs, respectively. kDNA based qPCRs were more sensitive and specific (Se: 1.00; Sp: 0.997). PCR/sequencing allowed the detection of Kinetoplastids in animal blood samples such as L. infantum, L. guyanensis, T. congolense, T. evansi and Bodo spp. The molecular approach proposed here is useful for epidemiological studies, fundamental research such as screening for new Kinetoplastida species, diagnosis and therapeutic follow-up. In addition, researchers are free to choose the molecular tools adapted to their aims.
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Affiliation(s)
- Hacène Medkour
- IHU Méditerranée Infection - Microbes, Evolution, Phylogeny and Infection (MEΦI), 13385 Marseille CEDEX 05, France; (H.M.); (B.D.)
- UMR Aix-Marseille Université, IRD, APHM -19-21, Bd Jean Moulin, 13385 Marseille CEDEX 05, France
- PADESCA Laboratory, Veterinary Science Institute, University Constantine 1, El Khroub 25100, Algeria
| | | | - Bernard Davoust
- IHU Méditerranée Infection - Microbes, Evolution, Phylogeny and Infection (MEΦI), 13385 Marseille CEDEX 05, France; (H.M.); (B.D.)
- UMR Aix-Marseille Université, IRD, APHM -19-21, Bd Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Oleg Mediannikov
- IHU Méditerranée Infection - Microbes, Evolution, Phylogeny and Infection (MEΦI), 13385 Marseille CEDEX 05, France; (H.M.); (B.D.)
- UMR Aix-Marseille Université, IRD, APHM -19-21, Bd Jean Moulin, 13385 Marseille CEDEX 05, France
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22
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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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23
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von Känel C, Muñoz-Gómez SA, Oeljeklaus S, Wenger C, Warscheid B, Wideman JG, Harsman A, Schneider A. Homologue replacement in the import motor of the mitochondrial inner membrane of trypanosomes. eLife 2020; 9:52560. [PMID: 32105215 PMCID: PMC7064343 DOI: 10.7554/elife.52560] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/26/2020] [Indexed: 01/13/2023] Open
Abstract
Many mitochondrial proteins contain N-terminal presequences that direct them to the organelle. The main driving force for their translocation across the inner membrane is provided by the presequence translocase-associated motor (PAM) which contains the J-protein Pam18. Here, we show that in the PAM of Trypanosoma brucei the function of Pam18 has been replaced by the non-orthologous euglenozoan-specific J-protein TbPam27. TbPam27 is specifically required for the import of mitochondrial presequence-containing but not for carrier proteins. Similar to yeast Pam18, TbPam27 requires an intact J-domain to function. Surprisingly, T. brucei still contains a bona fide Pam18 orthologue that, while essential for normal growth, is not involved in protein import. Thus, during evolution of kinetoplastids, Pam18 has been replaced by TbPam27. We propose that this replacement is linked to the transition from two ancestral and functionally distinct TIM complexes, found in most eukaryotes, to the single bifunctional TIM complex present in trypanosomes.
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Affiliation(s)
- Corinne von Känel
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Sergio A Muñoz-Gómez
- Center for Mechanisms of Evolution, Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, United States
| | - Silke Oeljeklaus
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Christoph Wenger
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Bettina Warscheid
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Jeremy G Wideman
- Center for Mechanisms of Evolution, Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, United States
| | - Anke Harsman
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Andre Schneider
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
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24
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Schoenle A, Hohlfeld M, Rosse M, Filz P, Wylezich C, Nitsche F, Arndt H. Global comparison of bicosoecid Cafeteria-like flagellates from the deep ocean and surface waters, with reorganization of the family Cafeteriaceae. Eur J Protistol 2020; 73:125665. [PMID: 31978633 DOI: 10.1016/j.ejop.2019.125665] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 12/11/2019] [Accepted: 12/16/2019] [Indexed: 02/04/2023]
Abstract
Cafeteria is one of the most common and ecologically significant genera of heterotrophic nanoflagellates in marine plankton. We could isolate and cultivate 29 strains morphologically similar to Cafeteria obtained from surface waters and the deep sea all over the world's ocean. Morphological characterization obtained by high resolution microscopy revealed only small differences between the strains. Sequencing the type material of the type species C. roenbergensis (CCAP 1900/1) and molecular analyses (18S rDNA, 28S rDNA) of newly isolated strains resulted in a revision and separation of the Cafeteriaceae into two known species (C. roenbergensis, C. mylnikovii) and six new species (C. maldiviensis, C. biegae, C. loberiensis, C. chilensis, C. graefeae, C. burkhardae). Many deposited Cafeteria sequences at GenBank and most of our own sequences clustered within one clade (C. burkhardae) with a p-distance of 5% to strain CCAP 1900/1. Only C. maldiviensis clustered together with the type species C. roenbergensis. While C. burkhardae seems to have a cosmopolitan distribution, the distribution of the other species seems to be more restricted. A strain from the Angola Basin had a p-distance of 10% to Cafeteria species and clustered separately within the Anoecales requiring the erection of a new genus, Bilabrum gen. nov., with B. latius sp. nov. as type species.
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Affiliation(s)
- Alexandra Schoenle
- University of Cologne, Biocenter, Institute of Zoology, General Ecology, 50674 Cologne, Germany
| | - Manon Hohlfeld
- University of Cologne, Biocenter, Institute of Zoology, General Ecology, 50674 Cologne, Germany
| | - Mona Rosse
- University of Cologne, Biocenter, Institute of Zoology, General Ecology, 50674 Cologne, Germany
| | - Paulina Filz
- University of Cologne, Biocenter, Institute of Zoology, General Ecology, 50674 Cologne, Germany
| | - Claudia Wylezich
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Südufer 10, D-17493 Greifswald, Insel Riems, Germany
| | - Frank Nitsche
- University of Cologne, Biocenter, Institute of Zoology, General Ecology, 50674 Cologne, Germany
| | - Hartmut Arndt
- University of Cologne, Biocenter, Institute of Zoology, General Ecology, 50674 Cologne, Germany.
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25
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Kolisko M, Flegontova O, Karnkowska A, Lax G, Maritz JM, Pánek T, Táborský P, Carlton JM, Čepička I, Horák A, Lukeš J, Simpson AGB, Tai V. EukRef-excavates: seven curated SSU ribosomal RNA gene databases. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5996027. [PMID: 33216898 PMCID: PMC7678783 DOI: 10.1093/database/baaa080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/04/2020] [Accepted: 08/28/2020] [Indexed: 12/14/2022]
Abstract
The small subunit ribosomal RNA (SSU rRNA) gene is a widely used molecular marker to study the diversity of life. Sequencing of SSU rRNA gene amplicons has become a standard approach for the investigation of the ecology and diversity of microbes. However, a well-curated database is necessary for correct classification of these data. While available for many groups of Bacteria and Archaea, such reference databases are absent for most eukaryotes. The primary goal of the EukRef project (eukref.org) is to close this gap and generate well-curated reference databases for major groups of eukaryotes, especially protists. Here we present a set of EukRef-curated databases for the excavate protists—a large assemblage that includes numerous taxa with divergent SSU rRNA gene sequences, which are prone to misclassification. We identified 6121 sequences, 625 of which were obtained from cultures, 3053 from cell isolations or enrichments and 2419 from environmental samples. We have corrected the classification for the majority of these curated sequences. The resulting publicly available databases will provide phylogenetically based standards for the improved identification of excavates in ecological and microbiome studies, as well as resources to classify new discoveries in excavate diversity.
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Affiliation(s)
- Martin Kolisko
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budeějovice (Budweis), Czech Republic.,Faculty of Science, University of South Bohemia, 370 05 České Budeějovice (Budweis), Czech Republic
| | - Olga Flegontova
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budeějovice (Budweis), Czech Republic
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, 02-089 Warsaw, Poland.,Department of Parasitology, BIOCEV, Faculty of Science, Charles University, 128 43 Vestec, Czech Republic
| | - Gordon Lax
- Department of Biology and Centre of Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Julia M Maritz
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Tomáš Pánek
- Department of Zoology, Charles University, 128 00 Prague, Czech Republic
| | - Petr Táborský
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budeějovice (Budweis), Czech Republic
| | - Jane M Carlton
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Ivan Čepička
- Department of Zoology, Charles University, 128 00 Prague, Czech Republic
| | - Aleš Horák
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budeějovice (Budweis), Czech Republic.,Faculty of Science, University of South Bohemia, 370 05 České Budeějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budeějovice (Budweis), Czech Republic.,Faculty of Science, University of South Bohemia, 370 05 České Budeějovice (Budweis), Czech Republic
| | - Alastair G B Simpson
- Department of Biology and Centre of Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Vera Tai
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada
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26
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Wideman JG, Lax G, Leonard G, Milner DS, Rodríguez-Martínez R, Simpson AGB, Richards TA. A single-cell genome reveals diplonemid-like ancestry of kinetoplastid mitochondrial gene structure. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190100. [PMID: 31587636 PMCID: PMC6792441 DOI: 10.1098/rstb.2019.0100] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Euglenozoa comprises euglenids, kinetoplastids, and diplonemids, with each group exhibiting different and highly unusual mitochondrial genome organizations. Although they are sister groups, kinetoplastids and diplonemids have very distinct mitochondrial genome architectures, requiring widespread insertion/deletion RNA editing and extensive trans-splicing, respectively, in order to generate functional transcripts. The evolutionary history by which these differing processes arose remains unclear. Using single-cell genomics, followed by small sub unit ribosomal DNA and multigene phylogenies, we identified an isolated marine cell that branches on phylogenetic trees as a sister to known kinetoplastids. Analysis of single-cell amplified genomic material identified multiple mitochondrial genome contigs. These revealed a gene architecture resembling that of diplonemid mitochondria, with small fragments of genes encoded out of order and or on different contigs, indicating that these genes require extensive trans-splicing. Conversely, no requirement for kinetoplastid-like insertion/deletion RNA-editing was detected. Additionally, while we identified some proteins so far only found in kinetoplastids, we could not unequivocally identify mitochondrial RNA editing proteins. These data invite the hypothesis that extensive genome fragmentation and trans-splicing were the ancestral states for the kinetoplastid-diplonemid clade but were lost during the kinetoplastid radiation. This study demonstrates that single-cell approaches can successfully retrieve lineages that represent important new branches on the tree of life, and thus can illuminate major evolutionary and functional transitions in eukaryotes. This article is part of a discussion meeting issue ‘Single cell ecology’.
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Affiliation(s)
- Jeremy G Wideman
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.,Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
| | - Gordon Lax
- Department of Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
| | - Guy Leonard
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - David S Milner
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Raquel Rodríguez-Martínez
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.,Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Alastair G B Simpson
- Department of Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
| | - Thomas A Richards
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
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27
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Schoenle A, Živaljić S, Prausse D, Voß J, Jakobsen K, Arndt H. New phagotrophic euglenids from deep sea and surface waters of the Atlantic Ocean (Keelungia nitschei, Petalomonas acorensis, Ploeotia costaversata). Eur J Protistol 2019; 69:102-116. [DOI: 10.1016/j.ejop.2019.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 10/27/2022]
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28
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Vesteg M, Hadariová L, Horváth A, Estraño CE, Schwartzbach SD, Krajčovič J. Comparative molecular cell biology of phototrophic euglenids and parasitic trypanosomatids sheds light on the ancestor of Euglenozoa. Biol Rev Camb Philos Soc 2019; 94:1701-1721. [PMID: 31095885 DOI: 10.1111/brv.12523] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 04/30/2019] [Accepted: 05/02/2019] [Indexed: 01/23/2023]
Abstract
Parasitic trypanosomatids and phototrophic euglenids are among the most extensively studied euglenozoans. The phototrophic euglenid lineage arose relatively recently through secondary endosymbiosis between a phagotrophic euglenid and a prasinophyte green alga that evolved into the euglenid secondary chloroplast. The parasitic trypanosomatids (i.e. Trypanosoma spp. and Leishmania spp.) and the freshwater phototrophic euglenids (i.e. Euglena gracilis) are the most evolutionary distant lineages in the Euglenozoa phylogenetic tree. The molecular and cell biological traits they share can thus be considered as ancestral traits originating in the common euglenozoan ancestor. These euglenozoan ancestral traits include common mitochondrial presequence motifs, respiratory chain complexes containing various unique subunits, a unique ATP synthase structure, the absence of mitochondria-encoded transfer RNAs (tRNAs), a nucleus with a centrally positioned nucleolus, closed mitosis without dissolution of the nuclear membrane and nucleoli, a nuclear genome containing the unusual 'J' base (β-D-glucosyl-hydroxymethyluracil), processing of nucleus-encoded precursor messenger RNAs (pre-mRNAs) via spliced-leader RNA (SL-RNA) trans-splicing, post-transcriptional gene silencing by the RNA interference (RNAi) pathway and the absence of transcriptional regulation of nuclear gene expression. Mitochondrial uridine insertion/deletion RNA editing directed by guide RNAs (gRNAs) evolved in the ancestor of the kinetoplastid lineage. The evolutionary origin of other molecular features known to be present only in either kinetoplastids (i.e. polycistronic transcripts, compaction of nuclear genomes) or euglenids (i.e. monocistronic transcripts, huge genomes, many nuclear cis-spliced introns, polyproteins) is unclear.
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Affiliation(s)
- Matej Vesteg
- Department of Biology and Ecology, Faculty of Natural Sciences, Matej Bel University, 974 01, Banská Bystrica, Slovakia
| | - Lucia Hadariová
- Biotechnology and Biomedicine Center of the Academy of Sciences and Charles University in Vestec (BIOCEV), 252 50, Vestec, Czech Republic.,Department of Parasitology, Faculty of Science, Charles University in Prague, 128 44, Prague, Czech Republic
| | - Anton Horváth
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, 842 15, Bratislava, Slovakia
| | - Carlos E Estraño
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152-3560, USA
| | - Steven D Schwartzbach
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152-3560, USA
| | - Juraj Krajčovič
- Department of Biology, Faculty of Natural Sciences, University of ss. Cyril and Methodius, 917 01, Trnava, Slovakia
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29
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Morphological, Ultrastructural, Motility and Evolutionary Characterization of Two New Hemistasiidae Species. Protist 2019; 170:259-282. [PMID: 31154071 DOI: 10.1016/j.protis.2019.04.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 03/26/2019] [Accepted: 04/04/2019] [Indexed: 11/21/2022]
Abstract
Until now, Hemistasia phaeocysticola was the only representative of the monogeneric family Hemistasiidae available in culture. Here we describe two new axenized hemistasiids isolated from Tokyo Bay, Japan. Like in other diplonemids, cellular organization of these heterotrophic protists is characterized by a distinct apical papilla, a tubular cytopharynx contiguous with a deep flagellar pocket, and a highly branched mitochondrion with lamellar cristae. Both hemistasiids also bear a prominent digestive vacuole, peripheral lacunae, and paraflagellar rods, are highly motile and exhibit diverse morphologies in culture. We argue that significant differences in molecular phylogenetics and ultrastructure between these new species and H. phaeocysticola are on the generic level. Therefore, we have established two new genera within Hemistasiidae - Artemidia gen. n. and Namystynia gen. n. to accommodate Artemidia motanka, sp. n. and Namystynia karyoxenos, sp. n., respectively. A. motanka permanently carries tubular extrusomes, while in N. karyoxenos, they are present only in starving cells. An additional remarkable feature of the latter species is the presence, in both the cytoplasm and the nucleus, of the endosymbiotic rickettsiid Candidatus Sneabacter namystus.
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30
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Lax G, Lee WJ, Eglit Y, Simpson A. Ploeotids Represent Much of the Phylogenetic Diversity of Euglenids. Protist 2019; 170:233-257. [PMID: 31102975 DOI: 10.1016/j.protis.2019.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/19/2019] [Accepted: 03/01/2019] [Indexed: 11/26/2022]
Abstract
Ploeotids are an assemblage of rigid phagotrophic euglenids that have 10-12 pellicular strips and glide on their posterior flagellum. Molecular phylogenies place them as a poorly resolved, likely paraphyletic assemblage outside the Spirocuta clade of flexible euglenids, which includes the well-known phototrophs and primary osmotrophs. Here, we report SSU rRNA gene sequences from 38 ploeotids, using both single-cell and culture-based methods. Several contain group I or non-canonical introns. Our phylogenetic analyses place ploeotids in 8 distinct clades: Olkasia n. gen., Hemiolia n. gen., Liburna n. gen., Lentomonas, Decastava, Keelungia, Ploeotiidae, and Entosiphon. Ploeotia vitrea, the type of Ploeotia, is closely related to P. oblonga and Serpenomonas costata, but not to Lentomonas. Ploeotia cf. vitrea sensu Lax and Simpson 2013 is not related to P. vitrea and has a different pellicle strip architecture (as imaged by scanning electron microscopy): it instead represents a novel genus and species, Olkasia polycarbonata. We also describe new genera, Hemiolia and Liburna, for the morphospecies Anisonema trepidum and A. glaciale. A recent system proposing 13 suprafamilial taxa that include ploeotids is not supported by our phylogenies. The exact relationships between ploeotid groups remain unresolved and multigene phylogenetics or phylogenomics are needed to address this uncertainty.
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Affiliation(s)
- Gordon Lax
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada
| | - Won Je Lee
- Department of Environment and Energy Engineering, Kyungnam University, Changwon, Republic of Korea
| | - Yana Eglit
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada
| | - Alastair Simpson
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada.
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31
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Bondarenko N, Glotova A, Nassonova E, Masharsky A, Polev D, Smirnov A. The complete mitochondrial genome of Paravannella minima (Amoebozoa, Discosea, Vannellida). Eur J Protistol 2019; 68:80-87. [PMID: 30716623 DOI: 10.1016/j.ejop.2019.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 12/24/2018] [Accepted: 01/09/2019] [Indexed: 10/27/2022]
Abstract
We present a complete sequence and describe the organization of the mitochondrial genome of the amoeba Paravannella minima (Amoebooza, Discosea, Vannellida). This tiny species represents a branch at the base of Vannellida tree, to the moment being its earliest-branching lineage. The circular mitochondrial DNA of this species has 53,464 bp in length and contains 30 protein-coding genes, 2 ribosomal RNAs, 23 transfer RNAs, and 15 open reading frames. This genome is significantly longer and contains more protein-coding genes than any yet sequenced mitochondrial genome of vannellid amoebae. Unlike the previously sequenced mitochondrial genomes of Vannellida, which should be translated using the "Table 4" (the mold, protozoan, and coelenterate mitochondrial code), that of P. minima can be properly translated using the universal genetic code.
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Affiliation(s)
- Natalya Bondarenko
- Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia.
| | - Anna Glotova
- Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
| | - Elena Nassonova
- Laboratory of Cytology of Unicellular Organisms, Institute of Cytology RAS, Tikhoretsky Ave. 4, 194064 St. Petersburg, Russia
| | - Alexey Masharsky
- Core Facility Centre for Molecular and Cell Technologies, St. Petersburg State University, Botanicheskaya ul. 17, Stary Peterhof, 198504 St. Petersburg, Russia
| | - Dmitry Polev
- Core Facility Centre Biobank, St. Petersburg State University, Botanicheskaya ul. 17, Stary Peterhof, 198504 St. Petersburg, Russia
| | - Alexey Smirnov
- Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
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32
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Vieira CB, Praça YR, Bentes KLDS, Santiago PB, Silva SMM, Silva GDS, Motta FN, Bastos IMD, de Santana JM, de Araújo CN. Triatomines: Trypanosomatids, Bacteria, and Viruses Potential Vectors? Front Cell Infect Microbiol 2018; 8:405. [PMID: 30505806 PMCID: PMC6250844 DOI: 10.3389/fcimb.2018.00405] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/29/2018] [Indexed: 12/17/2022] Open
Abstract
Triatominae bugs are the vectors of Chagas disease, a major concern to public health especially in Latin America, where vector-borne Chagas disease has undergone resurgence due mainly to diminished triatomine control in many endemic municipalities. Although the majority of Triatominae species occurs in the Americas, species belonging to the genus Linshcosteus occur in India, and species belonging to the Triatoma rubrofasciata complex have been also identified in Africa, the Middle East, South-East Asia, and in the Western Pacific. Not all of Triatominae species have been found to be infected with Trypanosoma cruzi, but the possibility of establishing vector transmission to areas where Chagas disease was previously non-endemic has increased with global population mobility. Additionally, the worldwide distribution of triatomines is concerning, as they are able to enter in contact and harbor other pathogens, leading us to wonder if they would have competence and capacity to transmit them to humans during the bite or after successful blood feeding, spreading other infectious diseases. In this review, we searched the literature for infectious agents transmitted to humans by Triatominae. There are reports suggesting that triatomines may be competent vectors for pathogens such as Serratia marcescens, Bartonella, and Mycobacterium leprae, and that triatomine infection with other microrganisms may interfere with triatomine-T. cruzi interactions, altering their competence and possibly their capacity to transmit Chagas disease.
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Affiliation(s)
- Caroline Barreto Vieira
- Programa de Pós-Graduação em Ciências Médicas, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil
| | - Yanna Reis Praça
- Programa de Pós-Graduação em Ciências Médicas, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil
| | - Kaio Luís da Silva Bentes
- Laboratório de Interação Patógeno-Hospedeiro, Instituto de Ciências Biológicas, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Paula Beatriz Santiago
- Laboratório de Interação Patógeno-Hospedeiro, Instituto de Ciências Biológicas, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Sofia Marcelino Martins Silva
- Laboratório de Interação Patógeno-Hospedeiro, Instituto de Ciências Biológicas, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Gabriel dos Santos Silva
- Laboratório de Interação Patógeno-Hospedeiro, Instituto de Ciências Biológicas, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Flávia Nader Motta
- Laboratório de Interação Patógeno-Hospedeiro, Instituto de Ciências Biológicas, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
- Faculdade de Ceilândia, Universidade de Brasília, Brasília, Brazil
| | - Izabela Marques Dourado Bastos
- Laboratório de Interação Patógeno-Hospedeiro, Instituto de Ciências Biológicas, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Jaime Martins de Santana
- Laboratório de Interação Patógeno-Hospedeiro, Instituto de Ciências Biológicas, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Carla Nunes de Araújo
- Laboratório de Interação Patógeno-Hospedeiro, Instituto de Ciências Biológicas, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
- Faculdade de Ceilândia, Universidade de Brasília, Brasília, Brazil
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33
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Goodenough U, Roth R, Kariyawasam T, He A, Lee JH. Epiplasts: Membrane Skeletons and Epiplastin Proteins in Euglenids, Glaucophytes, Cryptophytes, Ciliates, Dinoflagellates, and Apicomplexans. mBio 2018; 9:e02020-18. [PMID: 30377285 PMCID: PMC6212826 DOI: 10.1128/mbio.02020-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 09/17/2018] [Indexed: 01/03/2023] Open
Abstract
Animals and amoebae assemble actin/spectrin-based plasma membrane skeletons, forming what is often called the cell cortex, whereas euglenids and alveolates (ciliates, dinoflagellates, and apicomplexans) have been shown to assemble a thin, viscoelastic, actin/spectrin-free membrane skeleton, here called the epiplast. Epiplasts include a class of proteins, here called the epiplastins, with a head/medial/tail domain organization, whose medial domains have been characterized in previous studies by their low-complexity amino acid composition. We have identified two additional features of the medial domains: a strong enrichment of acid/base amino acid dyads and a predicted β-strand/random coil secondary structure. These features have served to identify members in two additional unicellular eukaryotic radiations-the glaucophytes and cryptophytes-as well as additional members in the alveolates and euglenids. We have analyzed the amino acid composition and domain structure of 219 epiplastin sequences and have used quick-freeze deep-etch electron microscopy to visualize the epiplasts of glaucophytes and cryptophytes. We define epiplastins as proteins encoded in organisms that assemble epiplasts, but epiplastin-like proteins, of unknown function, are also encoded in Insecta, Basidiomycetes, and Caulobacter genomes. We discuss the diverse cellular traits that are supported by epiplasts and propose evolutionary scenarios that are consonant with their distribution in extant eukaryotes.IMPORTANCE Membrane skeletons associate with the inner surface of the plasma membrane to provide support for the fragile lipid bilayer and an elastic framework for the cell itself. Several radiations, including animals, organize such skeletons using actin/spectrin proteins, but four major radiations of eukaryotic unicellular organisms, including disease-causing parasites such as Plasmodium, have been known to construct an alternative and essential skeleton (the epiplast) using a class of proteins that we term epiplastins. We have identified epiplastins in two additional radiations and present images of their epiplasts using electron microscopy. We analyze the sequences and secondary structure of 219 epiplastins and present an in-depth overview and analysis of their known and posited roles in cellular organization and parasite infection. An understanding of epiplast assembly may suggest therapeutic approaches to combat infectious agents such as Plasmodium as well as approaches to the engineering of useful viscoelastic biofilms.
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Affiliation(s)
- Ursula Goodenough
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - Robyn Roth
- Center for Cellular Imaging, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Thamali Kariyawasam
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amelia He
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jae-Hyeok Lee
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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dos Santos Júnior ADCM, Ricart CAO, Pontes AH, Fontes W, de Souza AR, Castro MS, de Sousa MV, de Lima BD. Proteome analysis of Phytomonas serpens, a phytoparasite of medical interest. PLoS One 2018; 13:e0204818. [PMID: 30303999 PMCID: PMC6179244 DOI: 10.1371/journal.pone.0204818] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 09/15/2018] [Indexed: 02/04/2023] Open
Abstract
The protozoan Phytomonas serpens (class Kinetoplastea) is an important phytoparasite that has gained medical importance due to its similarities to Trypanosoma cruzi, the etiological agent of Chagas disease. The present work describes the first proteome analysis of P. serpens. The parasite was separated into cytosolic and high density organelle fractions, which, together with total cell extract, were subjected to LC-MS/MS analyses. Protein identification was conducted using a comprehensive database composed of genome sequences of other related kinetoplastids. A total of 1,540 protein groups were identified among the three sample fractions. Sequences from Phytomonas sp. in the database allowed the highest number of identifications, with T. cruzi and T. brucei the human pathogens providing the greatest contribution to the identifications. Based on the proteomics data obtained, we proposed a central metabolic map of P. serpens, which includes all enzymes of the citric acid cycle. Data also revealed a new range of proteins possibly responsible for immunological cross-reactivity between P. serpens and T. cruzi.
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Affiliation(s)
- Agenor de Castro Moreira dos Santos Júnior
- Laboratory Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasília, Brasília, Federal District, Brazil
- Laboratory of Gene Biology, Department of Cell Biology, University of Brasília, Brasília, Federal District, Brazil
| | - Carlos André Ornelas Ricart
- Laboratory Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasília, Brasília, Federal District, Brazil
| | - Arthur Henriques Pontes
- Laboratory Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasília, Brasília, Federal District, Brazil
| | - Wagner Fontes
- Laboratory Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasília, Brasília, Federal District, Brazil
| | - Agnelo Rodrigues de Souza
- Laboratory Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasília, Brasília, Federal District, Brazil
- Laboratory of Gene Biology, Department of Cell Biology, University of Brasília, Brasília, Federal District, Brazil
| | - Mariana Souza Castro
- Laboratory Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasília, Brasília, Federal District, Brazil
| | - Marcelo Valle de Sousa
- Laboratory Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasília, Brasília, Federal District, Brazil
| | - Beatriz Dolabela de Lima
- Laboratory of Gene Biology, Department of Cell Biology, University of Brasília, Brasília, Federal District, Brazil
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Okamoto N, Gawryluk RMR, Del Campo J, Strassert JFH, Lukeš J, Richards TA, Worden AZ, Santoro AE, Keeling PJ. A Revised Taxonomy of Diplonemids Including the Eupelagonemidae n. fam. and a Type Species, Eupelagonema oceanica n. gen. & sp. J Eukaryot Microbiol 2018; 66:519-524. [PMID: 30080299 DOI: 10.1111/jeu.12679] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 06/16/2018] [Accepted: 07/12/2018] [Indexed: 12/20/2022]
Abstract
Recent surveys of marine microbial diversity have identified a previously unrecognized lineage of diplonemid protists as being among the most diverse heterotrophic eukaryotes in global oceans. Despite their monophyly (and assumed importance), they lack a formal taxonomic description, and are informally known as deep-sea pelagic diplonemids (DSPDs) or marine diplonemids. Recently, we documented morphology and molecular sequences from several DSPDs, one of which is particularly widespread and abundant in environmental sequence data. To simplify the communication of future work on this important group, here we formally propose to erect the family Eupelagonemidae to encompass this clade, as well as a formal genus and species description for the apparently most abundant phylotype, Eupelagonema oceanica, for which morphological information and single-cell amplified genome data are currently available.
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Affiliation(s)
- Noriko Okamoto
- Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Boulevard, British Columbia, Canada
| | - Ryan M R Gawryluk
- Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Boulevard, British Columbia, Canada
| | - Javier Del Campo
- Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Boulevard, British Columbia, Canada
| | - Jürgen F H Strassert
- Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Boulevard, British Columbia, Canada
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Faculty of Sciences, University of South Bohemia, Branišovská 31, 370 05, České Budějovice (Budweis), Czech Republic
| | - Thomas A Richards
- Biosciences, University of Exeter, Geoffrey Pope Building, Exeter, EX4 4QD, United Kingdom
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, California, 95039, USA
| | - Alyson E Santoro
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, 93106, USA
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Boulevard, British Columbia, Canada
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Yubuki N, Leander BS. Diversity and Evolutionary History of the Symbiontida (Euglenozoa). Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00100] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Farming, slaving and enslavement: histories of endosymbioses during kinetoplastid evolution. Parasitology 2018; 145:1311-1323. [PMID: 29895336 DOI: 10.1017/s0031182018000781] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Parasitic trypanosomatids diverged from free-living kinetoplastid ancestors several hundred million years ago. These parasites are relatively well known, due in part to several unusual cell biological and molecular traits and in part to the significance of a few - pathogenic Leishmania and Trypanosoma species - as aetiological agents of serious neglected tropical diseases. However, the majority of trypanosomatid biodiversity is represented by osmotrophic monoxenous parasites of insects. In two lineages, novymonads and strigomonads, osmotrophic lifestyles are supported by cytoplasmic endosymbionts, providing hosts with macromolecular precursors and vitamins. Here we discuss the two independent origins of endosymbiosis within trypanosomatids and subsequently different evolutionary trajectories that see entrainment vs tolerance of symbiont cell divisions cycles within those of the host. With the potential to inform on the transition to obligate parasitism in the trypanosomatids, interest in the biology and ecology of free-living, phagotrophic kinetoplastids is beginning to enjoy a renaissance. Thus, we take the opportunity to additionally consider the wider relevance of endosymbiosis during kinetoplastid evolution, including the indulged lifestyle and reductive evolution of basal kinetoplastid Perkinsela.
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Záhonová K, Petrželková R, Valach M, Yazaki E, Tikhonenkov DV, Butenko A, Janouškovec J, Hrdá Š, Klimeš V, Burger G, Inagaki Y, Keeling PJ, Hampl V, Flegontov P, Yurchenko V, Eliáš M. Extensive molecular tinkering in the evolution of the membrane attachment mode of the Rheb GTPase. Sci Rep 2018; 8:5239. [PMID: 29588502 PMCID: PMC5869587 DOI: 10.1038/s41598-018-23575-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/15/2018] [Indexed: 02/07/2023] Open
Abstract
Rheb is a conserved and widespread Ras-like GTPase involved in cell growth regulation mediated by the (m)TORC1 kinase complex and implicated in tumourigenesis in humans. Rheb function depends on its association with membranes via prenylated C-terminus, a mechanism shared with many other eukaryotic GTPases. Strikingly, our analysis of a phylogenetically rich sample of Rheb sequences revealed that in multiple lineages this canonical and ancestral membrane attachment mode has been variously altered. The modifications include: (1) accretion to the N-terminus of two different phosphatidylinositol 3-phosphate-binding domains, PX in Cryptista (the fusion being the first proposed synapomorphy of this clade), and FYVE in Euglenozoa and the related undescribed flagellate SRT308; (2) acquisition of lipidic modifications of the N-terminal region, namely myristoylation and/or S-palmitoylation in seven different protist lineages; (3) acquisition of S-palmitoylation in the hypervariable C-terminal region of Rheb in apusomonads, convergently to some other Ras family proteins; (4) replacement of the C-terminal prenylation motif with four transmembrane segments in a novel Rheb paralog in the SAR clade; (5) loss of an evident C-terminal membrane attachment mechanism in Tremellomycetes and some Rheb paralogs of Euglenozoa. Rheb evolution is thus surprisingly dynamic and presents a spectacular example of molecular tinkering.
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Affiliation(s)
- Kristína Záhonová
- Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Romana Petrželková
- Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Matus Valach
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
| | - Euki Yazaki
- Institute for Biological Sciences, University of Tsukuba, Tsukuba, Japan
| | - Denis V Tikhonenkov
- Laboratory of Microbiology, Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia
| | - Anzhelika Butenko
- Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jan Janouškovec
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Štěpánka Hrdá
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Vladimír Klimeš
- Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Gertraud Burger
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
| | - Yuji Inagaki
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Pavel Flegontov
- Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Vyacheslav Yurchenko
- Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Marek Eliáš
- Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.
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Tomasini N. Introgression of the Kinetoplast DNA: An Unusual Evolutionary Journey in Trypanosoma cruzi. Curr Genomics 2018; 19:133-139. [PMID: 29491741 PMCID: PMC5814961 DOI: 10.2174/1389202918666170815124832] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/02/2017] [Accepted: 04/16/2017] [Indexed: 11/22/2022] Open
Abstract
INTRODUCTION Phylogenetic relationships between different lineages of Trypanosoma cruzi, the agent of Chagas disease, have been controversial for several years. However, recent phylogenetic and phylogenomic analyses clarified the nuclear relationships among such lineages. However, incongruence between nuclear and kinetoplast DNA phylogenies has emerged as a new challenge. This incongruence implies several events of mitochondrial introgression at evolutionary level. However, the mechanism that gave origin to introgressed lineages is unknown. Here, I will review and discuss how maxicircles of the kinetoplast were horizontally and vertically transferred between different lineages of T. cruzi. CONCLUSION Finally, I will discuss what we know - and what we don't - about the kDNA transference and inheritance in the context of sexual reproduction in this parasite.
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Affiliation(s)
- Nicolás Tomasini
- Instituto de Patología Experimental, Facultad de Ciencias de la Salud, Universidad Nacional de Salta, CONICET, Salta, Argentina
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Cavalier-Smith T. Kingdom Chromista and its eight phyla: a new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences. PROTOPLASMA 2018; 255:297-357. [PMID: 28875267 PMCID: PMC5756292 DOI: 10.1007/s00709-017-1147-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/18/2017] [Indexed: 05/18/2023]
Abstract
In 1981 I established kingdom Chromista, distinguished from Plantae because of its more complex chloroplast-associated membrane topology and rigid tubular multipartite ciliary hairs. Plantae originated by converting a cyanobacterium to chloroplasts with Toc/Tic translocons; most evolved cell walls early, thereby losing phagotrophy. Chromists originated by enslaving a phagocytosed red alga, surrounding plastids by two extra membranes, placing them within the endomembrane system, necessitating novel protein import machineries. Early chromists retained phagotrophy, remaining naked and repeatedly reverted to heterotrophy by losing chloroplasts. Therefore, Chromista include secondary phagoheterotrophs (notably ciliates, many dinoflagellates, Opalozoa, Rhizaria, heliozoans) or walled osmotrophs (Pseudofungi, Labyrinthulea), formerly considered protozoa or fungi respectively, plus endoparasites (e.g. Sporozoa) and all chromophyte algae (other dinoflagellates, chromeroids, ochrophytes, haptophytes, cryptophytes). I discuss their origin, evolutionary diversification, and reasons for making chromists one kingdom despite highly divergent cytoskeletons and trophic modes, including improved explanations for periplastid/chloroplast protein targeting, derlin evolution, and ciliary/cytoskeletal diversification. I conjecture that transit-peptide-receptor-mediated 'endocytosis' from periplastid membranes generates periplastid vesicles that fuse with the arguably derlin-translocon-containing periplastid reticulum (putative red algal trans-Golgi network homologue; present in all chromophytes except dinoflagellates). I explain chromist origin from ancestral corticates and neokaryotes, reappraising tertiary symbiogenesis; a chromist cytoskeletal synapomorphy, a bypassing microtubule band dextral to both centrioles, favoured multiple axopodial origins. I revise chromist higher classification by transferring rhizarian subphylum Endomyxa from Cercozoa to Retaria; establishing retarian subphylum Ectoreta for Foraminifera plus Radiozoa, apicomonad subclasses, new dinozoan classes Myzodinea (grouping Colpovora gen. n., Psammosa), Endodinea, Sulcodinea, and subclass Karlodinia; and ranking heterokont Gyrista as phylum not superphylum.
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Faktorová D, Valach M, Kaur B, Burger G, Lukeš J. Mitochondrial RNA Editing and Processing in Diplonemid Protists. RNA METABOLISM IN MITOCHONDRIA 2018. [DOI: 10.1007/978-3-319-78190-7_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
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Cavalier-Smith T. Euglenoid pellicle morphogenesis and evolution in light of comparative ultrastructure and trypanosomatid biology: Semi-conservative microtubule/strip duplication, strip shaping and transformation. Eur J Protistol 2017; 61:137-179. [DOI: 10.1016/j.ejop.2017.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 08/19/2017] [Accepted: 09/05/2017] [Indexed: 11/27/2022]
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Shiratori T, Thakur R, Ishida KI. Pseudophyllomitus vesiculosus (Larsen and Patterson 1990) Lee, 2002, a Poorly Studied Phagotrophic Biflagellate is the First Characterized Member of Stramenopile Environmental Clade MAST-6. Protist 2017; 168:439-451. [PMID: 28822908 DOI: 10.1016/j.protis.2017.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 06/20/2017] [Accepted: 06/21/2017] [Indexed: 01/17/2023]
Abstract
There are many eukaryotic lineages that are exclusively composed of environmental sequences and lack information about which species are included. Regarding stramenopiles, at least 18 environmental lineages, known as marine stramenopiles (MAST), have been recognized. Since each MAST lineage forms deep branches in the stramenopiles, the characterization of MAST members is key to understanding the diversity and evolution of stramenopiles. In this study, we established a culture of Pseudophyllomitus vesiculosus, which is a poorly studied phagotrophic flagellate of uncertain taxonomic position. Our molecular phylogenetic analyses based on small subunit ribosomal RNA gene sequences robustly supported the inclusion of P. vesiculosus in the MAST-6 clade. Our microscopic observations indicated that P. vesiculosus shared characteristics with stramenopiles, including an anterior flagellum that exhibits sinusoidal waves and bears tubular mastigonemes. The flagellar apparatus of P. vesiculosus was also similar to that of other stramenopiles in having a transitional helix and five microtubular roots (R1-R4 and S tubules) including R2 that split into two bands. On the other hand, P. vesiculosus was distinguished from other deep-branching stramenopiles by the combination of flagellar apparatus characteristics. Based on the phylogenetic analyses and microscopic observations, we established Pseudophyllomitidae fam. nov in stramenopiles.
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Affiliation(s)
- Takashi Shiratori
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.
| | - Rabindra Thakur
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Ken-Ichiro Ishida
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
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Ultrastructural and immunocytochemical investigation of paramylon combined with new 18S rDNA-based secondary structure analysis clarifies phylogenetic affiliation of Entosiphon sulcatum (Euglenida: Euglenozoa). ORG DIVERS EVOL 2017. [DOI: 10.1007/s13127-017-0330-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Evolutionary Lessons from Species with Unique Kinetochores. CENTROMERES AND KINETOCHORES 2017; 56:111-138. [DOI: 10.1007/978-3-319-58592-5_5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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