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Opperdoes FR, Záhonová K, Škodová-Sveráková I, Bučková B, Chmelová Ľ, Lukeš J, Yurchenko V. In silico prediction of the metabolism of Blastocrithidia nonstop, a trypanosomatid with non-canonical genetic code. BMC Genomics 2024; 25:184. [PMID: 38365628 PMCID: PMC10874023 DOI: 10.1186/s12864-024-10094-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Almost all extant organisms use the same, so-called canonical, genetic code with departures from it being very rare. Even more exceptional are the instances when a eukaryote with non-canonical code can be easily cultivated and has its whole genome and transcriptome sequenced. This is the case of Blastocrithidia nonstop, a trypanosomatid flagellate that reassigned all three stop codons to encode amino acids. RESULTS We in silico predicted the metabolism of B. nonstop and compared it with that of the well-studied human parasites Trypanosoma brucei and Leishmania major. The mapped mitochondrial, glycosomal and cytosolic metabolism contains all typical features of these diverse and important parasites. We also provided experimental validation for some of the predicted observations, concerning, specifically presence of glycosomes, cellular respiration, and assembly of the respiratory complexes. CONCLUSIONS In an unusual comparison of metabolism between a parasitic protist with a massively altered genetic code and its close relatives that rely on a canonical code we showed that the dramatic differences on the level of nucleic acids do not seem to be reflected in the metabolisms. Moreover, although the genome of B. nonstop is extremely AT-rich, we could not find any alterations of its pyrimidine synthesis pathway when compared to other trypanosomatids. Hence, we conclude that the dramatic alteration of the genetic code of B. nonstop has no significant repercussions on the metabolism of this flagellate.
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Affiliation(s)
- Fred R Opperdoes
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Kristína Záhonová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada
| | - Ingrid Škodová-Sveráková
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Barbora Bučková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Ľubomíra Chmelová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia.
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Valach M, Moreira S, Petitjean C, Benz C, Butenko A, Flegontova O, Nenarokova A, Prokopchuk G, Batstone T, Lapébie P, Lemogo L, Sarrasin M, Stretenowich P, Tripathi P, Yazaki E, Nara T, Henrissat B, Lang BF, Gray MW, Williams TA, Lukeš J, Burger G. Recent expansion of metabolic versatility in Diplonema papillatum, the model species of a highly speciose group of marine eukaryotes. BMC Biol 2023; 21:99. [PMID: 37143068 PMCID: PMC10161547 DOI: 10.1186/s12915-023-01563-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/10/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Diplonemid flagellates are among the most abundant and species-rich of known marine microeukaryotes, colonizing all habitats, depths, and geographic regions of the world ocean. However, little is known about their genomes, biology, and ecological role. RESULTS We present the first nuclear genome sequence from a diplonemid, the type species Diplonema papillatum. The ~ 280-Mb genome assembly contains about 32,000 protein-coding genes, likely co-transcribed in groups of up to 100. Gene clusters are separated by long repetitive regions that include numerous transposable elements, which also reside within introns. Analysis of gene-family evolution reveals that the last common diplonemid ancestor underwent considerable metabolic expansion. D. papillatum-specific gains of carbohydrate-degradation capability were apparently acquired via horizontal gene transfer. The predicted breakdown of polysaccharides including pectin and xylan is at odds with reports of peptides being the predominant carbon source of this organism. Secretome analysis together with feeding experiments suggest that D. papillatum is predatory, able to degrade cell walls of live microeukaryotes, macroalgae, and water plants, not only for protoplast feeding but also for metabolizing cell-wall carbohydrates as an energy source. The analysis of environmental barcode samples shows that D. papillatum is confined to temperate coastal waters, presumably acting in bioremediation of eutrophication. CONCLUSIONS Nuclear genome information will allow systematic functional and cell-biology studies in D. papillatum. It will also serve as a reference for the highly diverse diplonemids and provide a point of comparison for studying gene complement evolution in the sister group of Kinetoplastida, including human-pathogenic taxa.
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Affiliation(s)
- Matus Valach
- Department of Biochemistry, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, QC, Canada.
| | - Sandrine Moreira
- Department of Biochemistry, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, QC, Canada
| | - Celine Petitjean
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Corinna Benz
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Anzhelika Butenko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Olga Flegontova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Anna Nenarokova
- School of Biological Sciences, University of Bristol, Bristol, UK
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Galina Prokopchuk
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Tom Batstone
- School of Biological Sciences, University of Bristol, Bristol, UK
- Present address: High Performance Computing Centre, Bristol, UK
| | - Pascal Lapébie
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix Marseille Université, Marseille, France
| | - Lionnel Lemogo
- Department of Biochemistry, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, QC, Canada
- Present address: Environment Climate Change Canada, Dorval, QC, Canada
| | - Matt Sarrasin
- Department of Biochemistry, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, QC, Canada
| | - Paul Stretenowich
- Department of Biochemistry, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, QC, Canada
- Present address: Canadian Centre for Computational Genomics; McGill Genome Centre, McGill University, Montreal, QC, Canada
| | - Pragya Tripathi
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Euki Yazaki
- RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS), Hirosawa, Wako, Saitama, Japan
| | - Takeshi Nara
- Laboratory of Molecular Parasitology, Graduate School of Life Science and Technology, Iryo Sosei University, Iwaki City, Fukushima, Japan
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix Marseille Université, Marseille, France
- Present address: DTU Bioengineering, Technical University of Denmark, Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - B Franz Lang
- Department of Biochemistry, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, QC, Canada
| | - Michael W Gray
- Department of Biochemistry and Molecular Biology, Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Gertraud Burger
- Department of Biochemistry, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, QC, Canada.
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Current Status of Regulatory Non-Coding RNAs Research in the Tritryp. Noncoding RNA 2022; 8:ncrna8040054. [PMID: 35893237 PMCID: PMC9326685 DOI: 10.3390/ncrna8040054] [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: 05/14/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 11/23/2022] Open
Abstract
Trypanosomatids are protozoan parasites that cause devastating vector-borne human diseases. Gene expression regulation of these organisms depends on post-transcriptional control in responding to diverse environments while going through multiple developmental stages of their complex life cycles. In this scenario, non-coding RNAs (ncRNAs) are excellent candidates for a very efficient, quick, and economic strategy to regulate gene expression. The advent of high throughput RNA sequencing technologies show the presence and deregulation of small RNA fragments derived from canonical ncRNAs. This review seeks to depict the ncRNA landscape in trypanosomatids, focusing on the small RNA fragments derived from functional RNA molecules observed in RNA sequencing studies. Small RNA fragments derived from canonical ncRNAs (tsRNAs, snsRNAs, sdRNAs, and sdrRNAs) were identified in trypanosomatids. Some of these RNAs display changes in their levels associated with different environments and developmental stages, demanding further studies to determine their functional characterization and potential roles. Nevertheless, a comprehensive and detailed ncRNA annotation for most trypanosomatid genomes is still needed, allowing better and more extensive comparative and functional studies.
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Beilstein S, El Phil R, Sahraoui SS, Scapozza L, Kaiser M, Mäser P. Laboratory Selection of Trypanosomatid Pathogens for Drug Resistance. Pharmaceuticals (Basel) 2022; 15:ph15020135. [PMID: 35215248 PMCID: PMC8879015 DOI: 10.3390/ph15020135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 11/16/2022] Open
Abstract
The selection of parasites for drug resistance in the laboratory is an approach frequently used to investigate the mode of drug action, estimate the risk of emergence of drug resistance, or develop molecular markers for drug resistance. Here, we focused on the How rather than the Why of laboratory selection, discussing different experimental set-ups based on research examples with Trypanosoma brucei, Trypanosoma cruzi, and Leishmania spp. The trypanosomatids are particularly well-suited to illustrate different strategies of selecting for drug resistance, since it was with African trypanosomes that Paul Ehrlich performed such an experiment for the first time, more than a century ago. While breakthroughs in reverse genetics and genome editing have greatly facilitated the identification and validation of candidate resistance mutations in the trypanosomatids, the forward selection of drug-resistant mutants still relies on standard in vivo models and in vitro culture systems. Critical questions are: is selection for drug resistance performed in vivo or in vitro? With the mammalian or with the insect stages of the parasites? Under steady pressure or by sudden shock? Is a mutagen used? While there is no bona fide best approach, we think that a methodical consideration of these questions provides a helpful framework for selection of parasites for drug resistance in the laboratory.
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Affiliation(s)
- Sabina Beilstein
- Department Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland; (S.B.); (M.K.)
- Swiss TPH, University of Basel, Petersplatz 1, 4002 Basel, Switzerland
| | - Radhia El Phil
- School of Pharmaceutical Sciences, University of Geneva, 1205 Geneva, Switzerland; (R.E.P.); (S.S.S.); (L.S.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
| | - Suzanne Sherihan Sahraoui
- School of Pharmaceutical Sciences, University of Geneva, 1205 Geneva, Switzerland; (R.E.P.); (S.S.S.); (L.S.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
| | - Leonardo Scapozza
- School of Pharmaceutical Sciences, University of Geneva, 1205 Geneva, Switzerland; (R.E.P.); (S.S.S.); (L.S.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
| | - Marcel Kaiser
- Department Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland; (S.B.); (M.K.)
- Swiss TPH, University of Basel, Petersplatz 1, 4002 Basel, Switzerland
| | - Pascal Mäser
- Department Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland; (S.B.); (M.K.)
- Swiss TPH, University of Basel, Petersplatz 1, 4002 Basel, Switzerland
- Correspondence: ; Tel.: +41-61-284-8338
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Analyses of Leishmania-LRV Co-Phylogenetic Patterns and Evolutionary Variability of Viral Proteins. Viruses 2021; 13:v13112305. [PMID: 34835111 PMCID: PMC8624691 DOI: 10.3390/v13112305] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/09/2021] [Indexed: 01/07/2023] Open
Abstract
Leishmania spp. are important pathogens causing a vector-borne disease with a broad range of clinical manifestations from self-healing ulcers to the life-threatening visceral forms. Presence of Leishmania RNA virus (LRV) confers survival advantage to these parasites by suppressing anti-leishmanial immunity in the vertebrate host. The two viral species, LRV1 and LRV2 infect species of the subgenera Viannia and Leishmania, respectively. In this work we investigated co-phylogenetic patterns of leishmaniae and their viruses on a small scale (LRV2 in L. major) and demonstrated their predominant coevolution, occasionally broken by intraspecific host switches. Our analysis of the two viral genes, encoding the capsid and RNA-dependent RNA polymerase (RDRP), revealed them to be under the pressure of purifying selection, which was considerably stronger for the former gene across the whole tree. The selective pressure also differs between the LRV clades and correlates with the frequency of interspecific host switches. In addition, using experimental (capsid) and predicted (RDRP) models we demonstrated that the evolutionary variability across the structure is strikingly different in these two viral proteins.
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Lax C, Tahiri G, Patiño-Medina JA, Cánovas-Márquez JT, Pérez-Ruiz JA, Osorio-Concepción M, Navarro E, Calo S. The Evolutionary Significance of RNAi in the Fungal Kingdom. Int J Mol Sci 2020; 21:E9348. [PMID: 33302447 PMCID: PMC7763443 DOI: 10.3390/ijms21249348] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 12/18/2022] Open
Abstract
RNA interference (RNAi) was discovered at the end of last millennium, changing the way scientists understood regulation of gene expression. Within the following two decades, a variety of different RNAi mechanisms were found in eukaryotes, reflecting the evolutive diversity that RNAi entails. The essential silencing mechanism consists of an RNase III enzyme called Dicer that cleaves double-stranded RNA (dsRNA) generating small interfering RNAs (siRNAs), a hallmark of RNAi. These siRNAs are loaded into the RNA-induced silencing complex (RISC) triggering the cleavage of complementary messenger RNAs by the Argonaute protein, the main component of the complex. Consequently, the expression of target genes is silenced. This mechanism has been thoroughly studied in fungi due to their proximity to the animal phylum and the conservation of the RNAi mechanism from lower to higher eukaryotes. However, the role and even the presence of RNAi differ across the fungal kingdom, as it has evolved adapting to the particularities and needs of each species. Fungi have exploited RNAi to regulate a variety of cell activities as different as defense against exogenous and potentially harmful DNA, genome integrity, development, drug tolerance, or virulence. This pathway has offered versatility to fungi through evolution, favoring the enormous diversity this kingdom comprises.
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Affiliation(s)
- Carlos Lax
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, 30100 Murcia, Spain; (C.L.); (G.T.); (J.T.C.-M.); (J.A.P.-R.); (M.O.-C.); (E.N.)
| | - Ghizlane Tahiri
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, 30100 Murcia, Spain; (C.L.); (G.T.); (J.T.C.-M.); (J.A.P.-R.); (M.O.-C.); (E.N.)
| | - José Alberto Patiño-Medina
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, Michoacán CP 58030, Mexico;
| | - José T. Cánovas-Márquez
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, 30100 Murcia, Spain; (C.L.); (G.T.); (J.T.C.-M.); (J.A.P.-R.); (M.O.-C.); (E.N.)
| | - José A. Pérez-Ruiz
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, 30100 Murcia, Spain; (C.L.); (G.T.); (J.T.C.-M.); (J.A.P.-R.); (M.O.-C.); (E.N.)
| | - Macario Osorio-Concepción
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, 30100 Murcia, Spain; (C.L.); (G.T.); (J.T.C.-M.); (J.A.P.-R.); (M.O.-C.); (E.N.)
| | - Eusebio Navarro
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, 30100 Murcia, Spain; (C.L.); (G.T.); (J.T.C.-M.); (J.A.P.-R.); (M.O.-C.); (E.N.)
| | - Silvia Calo
- School of Natural and Exact Sciences, Pontificia Universidad Católica Madre y Maestra, 51033 Santiago de los Caballeros, Dominican Republic
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Svoboda P. Key Mechanistic Principles and Considerations Concerning RNA Interference. FRONTIERS IN PLANT SCIENCE 2020; 11:1237. [PMID: 32903622 PMCID: PMC7438612 DOI: 10.3389/fpls.2020.01237] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 07/28/2020] [Indexed: 05/03/2023]
Abstract
Canonical RNAi, one of the so-called RNA-silencing mechanisms, is defined as sequence-specific RNA degradation induced by long double-stranded RNA (dsRNA). RNAi occurs in four basic steps: (i) processing of long dsRNA by RNase III Dicer into small interfering RNA (siRNA) duplexes, (ii) loading of one of the siRNA strands on an Argonaute protein possessing endonucleolytic activity, (iii) target recognition through siRNA basepairing, and (iv) cleavage of the target by the Argonaute's endonucleolytic activity. This basic pathway diversified and blended with other RNA silencing pathways employing small RNAs. In some organisms, RNAi is extended by an amplification loop employing an RNA-dependent RNA polymerase, which generates secondary siRNAs from targets of primary siRNAs. Given the high specificity of RNAi and its presence in invertebrates, it offers an opportunity for highly selective pest control. The aim of this text is to provide an introductory overview of key mechanistic aspects of RNA interference for understanding its potential and constraints for its use in pest control.
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Kleschenko Y, Grybchuk D, Matveeva NS, Macedo DH, Ponirovsky EN, Lukashev AN, Yurchenko V. Molecular Characterization of Leishmania RNA virus 2 in Leishmania major from Uzbekistan. Genes (Basel) 2019; 10:genes10100830. [PMID: 31640177 PMCID: PMC6826456 DOI: 10.3390/genes10100830] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 12/15/2022] Open
Abstract
Here we report sequence and phylogenetic analysis of two new isolates of Leishmania RNA virus 2 (LRV2) found in Leishmania major isolated from human patients with cutaneous leishmaniasis in south Uzbekistan. These new virus-infected flagellates were isolated in the same region of Uzbekistan and the viral sequences differed by only nineteen SNPs, all except one being silent mutations. Therefore, we concluded that they belong to a single LRV2 species. New viruses are closely related to the LRV2-Lmj-ASKH documented in Turkmenistan in 1995, which is congruent with their shared host (L. major) and common geographical origin.
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Affiliation(s)
- Yuliya Kleschenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119435 Moscow, Russia.
| | - Danyil Grybchuk
- Life Sciences Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic.
- CEITEC-Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
| | - Nadezhda S Matveeva
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119435 Moscow, Russia.
- Department of Molecular Biology, Faculty of Biology, Moscow State University, 119991 Moscow, Russia.
| | - Diego H Macedo
- Life Sciences Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic.
| | - Evgeny N Ponirovsky
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119435 Moscow, Russia.
| | - Alexander N Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119435 Moscow, Russia.
| | - Vyacheslav Yurchenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119435 Moscow, Russia.
- Life Sciences Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic.
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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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Double-stranded RNA reduces growth rates of the gut parasite Crithidia mellificae. Parasitol Res 2019; 118:715-721. [DOI: 10.1007/s00436-018-6176-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 12/11/2018] [Indexed: 10/27/2022]
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11
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Bradwell KR, Koparde VN, Matveyev AV, Serrano MG, Alves JMP, Parikh H, Huang B, Lee V, Espinosa-Alvarez O, Ortiz PA, Costa-Martins AG, Teixeira MMG, Buck GA. Genomic comparison of Trypanosoma conorhini and Trypanosoma rangeli to Trypanosoma cruzi strains of high and low virulence. BMC Genomics 2018; 19:770. [PMID: 30355302 PMCID: PMC6201504 DOI: 10.1186/s12864-018-5112-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 09/25/2018] [Indexed: 01/09/2023] Open
Abstract
Background Trypanosoma conorhini and Trypanosoma rangeli, like Trypanosoma cruzi, are kinetoplastid protist parasites of mammals displaying divergent hosts, geographic ranges and lifestyles. Largely nonpathogenic T. rangeli and T. conorhini represent clades that are phylogenetically closely related to the T. cruzi and T. cruzi-like taxa and provide insights into the evolution of pathogenicity in those parasites. T. rangeli, like T. cruzi is endemic in many Latin American countries, whereas T. conorhini is tropicopolitan. T. rangeli and T. conorhini are exclusively extracellular, while T. cruzi has an intracellular stage in the mammalian host. Results Here we provide the first comprehensive sequence analysis of T. rangeli AM80 and T. conorhini 025E, and provide a comparison of their genomes to those of T. cruzi G and T. cruzi CL, respectively members of T. cruzi lineages TcI and TcVI. We report de novo assembled genome sequences of the low-virulent T. cruzi G, T. rangeli AM80, and T. conorhini 025E ranging from ~ 21–25 Mbp, with ~ 10,000 to 13,000 genes, and for the highly virulent and hybrid T. cruzi CL we present a ~ 65 Mbp in-house assembled haplotyped genome with ~ 12,500 genes per haplotype. Single copy orthologs of the two T. cruzi strains exhibited ~ 97% amino acid identity, and ~ 78% identity to proteins of T. rangeli or T. conorhini. Proteins of the latter two organisms exhibited ~ 84% identity. T. cruzi CL exhibited the highest heterozygosity. T. rangeli and T. conorhini displayed greater metabolic capabilities for utilization of complex carbohydrates, and contained fewer retrotransposons and multigene family copies, i.e. trans-sialidases, mucins, DGF-1, and MASP, compared to T. cruzi. Conclusions Our analyses of the T. rangeli and T. conorhini genomes closely reflected their phylogenetic proximity to the T. cruzi clade, and were largely consistent with their divergent life cycles. Our results provide a greater context for understanding the life cycles, host range expansion, immunity evasion, and pathogenesis of these trypanosomatids. Electronic supplementary material The online version of this article (10.1186/s12864-018-5112-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katie R Bradwell
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA.,Present address: Institute for Genome Sciences, University of Maryland, Baltimore, MD, USA
| | - Vishal N Koparde
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA
| | - Andrey V Matveyev
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA.,Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Myrna G Serrano
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA.,Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - João M P Alves
- Department of Parasitology, ICB, University of São Paulo, São Paulo, SP, Brazil
| | - Hardik Parikh
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA.,Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Bernice Huang
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA.,Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Vladimir Lee
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA
| | | | - Paola A Ortiz
- Department of Parasitology, ICB, University of São Paulo, São Paulo, SP, Brazil
| | | | - Marta M G Teixeira
- Department of Parasitology, ICB, University of São Paulo, São Paulo, SP, Brazil
| | - Gregory A Buck
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA. .,Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA.
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12
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Richter DJ, Fozouni P, Eisen MB, King N. Gene family innovation, conservation and loss on the animal stem lineage. eLife 2018; 7:34226. [PMID: 29848444 PMCID: PMC6040629 DOI: 10.7554/elife.34226] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 05/26/2018] [Indexed: 02/06/2023] Open
Abstract
Choanoflagellates, the closest living relatives of animals, can provide unique insights into the changes in gene content that preceded the origin of animals. However, only two choanoflagellate genomes are currently available, providing poor coverage of their diversity. We sequenced transcriptomes of 19 additional choanoflagellate species to produce a comprehensive reconstruction of the gains and losses that shaped the ancestral animal gene repertoire. We identified ~1944 gene families that originated on the animal stem lineage, of which only 39 are conserved across all animals in our study. In addition, ~372 gene families previously thought to be animal-specific, including Notch, Delta, and homologs of the animal Toll-like receptor genes, instead evolved prior to the animal-choanoflagellate divergence. Our findings contribute to an increasingly detailed portrait of the gene families that defined the biology of the Urmetazoan and that may underpin core features of extant animals. All animals, from sea sponges and reef-building corals to elephants and humans, share a single common ancestor that lived over half a billion years ago. This single-celled predecessor evolved the ability to develop into a creature made up of many cells with specialized jobs. Reconstructing the steps in this evolutionary process has been difficult because the earliest animals were soft-bodied and microscopic and did not leave behind fossils that scientists can study. Though their bodies have since disintegrated, many of the instructions for building the first animals live on in genes that were passed on to life forms that still exist. Scientists are trying to retrace those genes back to the first animal by comparing the genomes of living animals with their closest relatives, the choanoflagellates. Choanoflagellates are single-celled, colony-forming organisms that live in waters around the world. Comparisons with choanoflagellates may help scientists identify which genes were necessary to help animals evolve and diversify into so many different species. So far, 1,000 animal and two choanoflagellate genomes have been sequenced. But the gene repertoires of most species of choanoflagellates have yet to be analyzed. Now, Richter et al. have cataloged the genes of 19 more species of choanoflagellates. This added information allowed them to recreate the likely gene set of the first animal and to identify genetic changes that occurred during animal evolution. The analyses showed that modern animals lost about a quarter of the genes present in their last common ancestor with choanoflagellates and gained an equal number of new genes. Richter et al. identified several dozen core animal genes that were gained and subsequently preserved throughout animal evolution. Many of these are necessary so that an embryo can develop properly, but the precise roles of some core genes remain a mystery. Most other genes that emerged in the first animals have been lost in at least one living animal. The study of Richter et al. also showed that some very important genes in animals, including genes essential for early development and genes that help the immune system detect pathogens, predate animals. These key genes trace back to animals’ last common ancestor with choanoflagellates and may have evolved new roles in animals.
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Affiliation(s)
- Daniel J Richter
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Sorbonne Universités, UPMC Univ Paris 06, CNRS UMR 7144, Adaptation et Diversité en Milieu Marin, Équipe EPEP, Station Biologique de Roscoff, Roscoff, France
| | - Parinaz Fozouni
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Medical Scientist Training Program, Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, United States.,Gladstone Institutes, San Francisco, United States
| | - Michael B Eisen
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Nicole King
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
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Grybchuk D, Kostygov AY, Macedo DH, d'Avila-Levy CM, Yurchenko V. RNA viruses in trypanosomatid parasites: a historical overview. Mem Inst Oswaldo Cruz 2018. [PMID: 29513877 PMCID: PMC5851034 DOI: 10.1590/0074-02760170487] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Viruses of trypanosomatids are now being extensively studied because of their diversity and the roles they play in flagellates' biology. Among the most prominent examples are leishmaniaviruses implicated in pathogenesis of Leishmania parasites. Here, we present a historical overview of this field, starting with early reports of virus-like particles on electron microphotographs, and culminating in detailed molecular descriptions of viruses obtained using modern next generation sequencing-based techniques. Because of their diversity, different life cycle strategies and host specificity, we believe that trypanosomatids are a fertile ground for further explorations to better understand viral evolution, routes of transitions, and molecular mechanisms of adaptation to different hosts.
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Affiliation(s)
- Danyil Grybchuk
- University of Ostrava, Faculty of Science, Life Science Research Centre, Ostrava, Czech Republic
| | - Alexei Y Kostygov
- University of Ostrava, Faculty of Science, Life Science Research Centre, Ostrava, Czech Republic
| | - Diego H Macedo
- University of Ostrava, Faculty of Science, Life Science Research Centre, Ostrava, Czech Republic
| | - Claudia M d'Avila-Levy
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Estudos Integrados em Protozoologia, Coleção de Protozoários, Rio de Janeiro, RJ, Brasil
| | - Vyacheslav Yurchenko
- University of Ostrava, Faculty of Science, Life Science Research Centre, Ostrava, Czech Republic
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Viral discovery and diversity in trypanosomatid protozoa with a focus on relatives of the human parasite Leishmania. Proc Natl Acad Sci U S A 2017; 115:E506-E515. [PMID: 29284754 DOI: 10.1073/pnas.1717806115] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Knowledge of viral diversity is expanding greatly, but many lineages remain underexplored. We surveyed RNA viruses in 52 cultured monoxenous relatives of the human parasite Leishmania (Crithidia and Leptomonas), as well as plant-infecting PhytomonasLeptomonas pyrrhocoris was a hotbed for viral discovery, carrying a virus (Leptomonas pyrrhocoris ostravirus 1) with a highly divergent RNA-dependent RNA polymerase missed by conventional BLAST searches, an emergent clade of tombus-like viruses, and an example of viral endogenization. A deep-branching clade of trypanosomatid narnaviruses was found, notable as Leptomonas seymouri bearing Narna-like virus 1 (LepseyNLV1) have been reported in cultures recovered from patients with visceral leishmaniasis. A deep-branching trypanosomatid viral lineage showing strong affinities to bunyaviruses was termed "Leishbunyavirus" (LBV) and judged sufficiently distinct to warrant assignment within a proposed family termed "Leishbunyaviridae" Numerous relatives of trypanosomatid viruses were found in insect metatranscriptomic surveys, which likely arise from trypanosomatid microbiota. Despite extensive sampling we found no relatives of the totivirus Leishmaniavirus (LRV1/2), implying that it was acquired at about the same time the Leishmania became able to parasitize vertebrates. As viruses were found in over a quarter of isolates tested, many more are likely to be found in the >600 unsurveyed trypanosomatid species. Viral loss was occasionally observed in culture, providing potentially isogenic virus-free lines enabling studies probing the biological role of trypanosomatid viruses. These data shed important insights on the emergence of viruses within an important trypanosomatid clade relevant to human disease.
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