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Chmelová Ľ, Kraeva N, Saura A, Krayzel A, Vieira CS, Ferreira TN, Soares RP, Bučková B, Galan A, Horáková E, Vojtková B, Sádlová J, Malysheva MN, Butenko A, Prokopchuk G, Frolov AO, Lukeš J, Horváth A, Škodová-Sveráková I, Feder D, Yu Kostygov A, Yurchenko V. Intricate balance of dually-localized catalase modulates infectivity of Leptomonas seymouri (Kinetoplastea: Trypanosomatidae). Int J Parasitol 2024:S0020-7519(24)00077-8. [PMID: 38663543 DOI: 10.1016/j.ijpara.2024.04.007] [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: 12/05/2023] [Revised: 03/24/2024] [Accepted: 04/19/2024] [Indexed: 05/02/2024]
Abstract
Nearly all aerobic organisms are equipped with catalases, powerful enzymes scavenging hydrogen peroxide and facilitating defense against harmful reactive oxygen species. In trypanosomatids, this enzyme was not present in the common ancestor, yet it had been independently acquired by different lineages of monoxenous trypanosomatids from different bacteria at least three times. This observation posited an obvious question: why was catalase so "sought after" if many trypanosomatid groups do just fine without it? In this work, we analyzed subcellular localization and function of catalase in Leptomonas seymouri. We demonstrated that this enzyme is present in the cytoplasm and a subset of glycosomes, and that its cytoplasmic retention is H2O2-dependent. The ablation of catalase in this parasite is not detrimental in vivo, while its overexpression resulted in a substantially higher parasite load in the experimental infection of Dysdercus peruvianus. We propose that the capacity of studied flagellates to modulate the catalase activity in the midgut of its insect host facilitates their development and protects them from oxidative damage at elevated temperatures.
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Affiliation(s)
- Ľubomíra Chmelová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Natalya Kraeva
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Andreu Saura
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Adam Krayzel
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Cecilia Stahl Vieira
- Universidade Federal Fluminense, Instituto de Biologia, Programa de Pós-Graduação em Ciências e Biotecnologia, Niterói, Brazil
| | - Tainá Neves Ferreira
- Universidade Federal Fluminense, Instituto de Biologia, Programa de Pós-Graduação em Ciências e Biotecnologia, Niterói, Brazil
| | - Rodrigo Pedro Soares
- Biotechnology Applied to Pathogens (BAP), Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Barbora Bučková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Arnau Galan
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Eva Horáková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Barbora Vojtková
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czechia
| | - Jovana Sádlová
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czechia
| | - Marina N Malysheva
- Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia
| | - Anzhelika Butenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia; Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Galina Prokopchuk
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia; Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Alexander O Frolov
- Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia; Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Anton Horváth
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Ingrid Škodová-Sveráková
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia; Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Denise Feder
- Universidade Federal Fluminense, Instituto de Biologia, Programa de Pós-Graduação em Ciências e Biotecnologia, Niterói, Brazil; Universidade Federal Fluminense, Instituto de Biologia, Laboratório de Biologia de Insetos, Niterói, Brazil; Instituto Nacional de Entomologia Molecular, Rio de Janeiro, Brazil
| | - Alexei Yu Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia; Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia.
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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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Kostygov AY, Chmelová Ľ, Reichl J, Jászayová A, Votýpka J, Fuehrer HP, Yurchenko V. Parasites of firebugs in Austria with focus on the "micro"-diversity of the cosmopolitan trypanosomatid Leptomonas pyrrhocoris. Parasitol Res 2023; 123:27. [PMID: 38072883 PMCID: PMC10710968 DOI: 10.1007/s00436-023-08080-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023]
Abstract
In this work, we investigated parasites of the firebug Pyrrhocoris apterus in Austria and demonstrated that in addition to the extensively studied Leptomonas pyrrhocoris, it can also be infected by Blastocrithidia sp. and by a mermithid, which for the first time has been characterized using molecular methods. This diversity can be explained by the gregarious lifestyle, as well as the coprophagous and cannibalistic behavior of the insect hosts that makes them susceptible to various parasites. In addition, we showed no tight association of the L. pyrrhocoris haplotypes and geographical locations (at least, considering the relatively small scale of locations in Austria) implying that the natural populations of L. pyrrhocoris are mixed due to the mobility of their firebug hosts.
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Affiliation(s)
| | | | - Julia Reichl
- Institute of Parasitology, University of Veterinary Medicine Vienna, Vienna, Austria
- Institute for Medical Microbiology and Hygiene, AGES - Austrian Agency for Health and Food Safety, Vienna, Austria
| | | | - Jan Votýpka
- Faculty of Science, Charles University, Prague, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Hans-Peter Fuehrer
- Institute of Parasitology, University of Veterinary Medicine Vienna, Vienna, Austria
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Tullume-Vergara PO, Caicedo KYO, Tantalean JFC, Serrano MG, Buck GA, Teixeira MMG, Shaw JJ, Alves JMP. Genomes of Endotrypanum monterogeii from Panama and Zelonia costaricensis from Brazil: Expansion of Multigene Families in Leishmaniinae Parasites That Are Close Relatives of Leishmania spp. Pathogens 2023; 12:1409. [PMID: 38133293 PMCID: PMC10747355 DOI: 10.3390/pathogens12121409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/10/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
The Leishmaniinae subfamily of the Trypanosomatidae contains both genus Zelonia (monoxenous) and Endotrypanum (dixenous). They are amongst the nearest known relatives of Leishmania, which comprises many human pathogens widespread in the developing world. These closely related lineages are models for the genomic biology of monoxenous and dixenous parasites. Herein, we used comparative genomics to identify the orthologous groups (OGs) shared among 26 Leishmaniinae species to investigate gene family expansion/contraction and applied two phylogenomic approaches to confirm relationships within the subfamily. The Endotrypanum monterogeii and Zelonia costaricensis genomes were assembled, with sizes of 29.9 Mb and 38.0 Mb and 9.711 and 12.201 predicted protein-coding genes, respectively. The genome of E. monterogeii displayed a higher number of multicopy cell surface protein families, including glycoprotein 63 and glycoprotein 46, compared to Leishmania spp. The genome of Z. costaricensis presents expansions of BT1 and amino acid transporters and proteins containing leucine-rich repeat domains, as well as a loss of ABC-type transporters. In total, 415 and 85 lineage-specific OGs were identified in Z. costaricensis and E. monterogeii. The evolutionary relationships within the subfamily were confirmed using the supermatrix (3384 protein-coding genes) and supertree methods. Overall, this study showed new expansions of multigene families in monoxenous and dixenous parasites of the subfamily Leishmaniinae.
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Affiliation(s)
- Percy O. Tullume-Vergara
- Department of Parasitology, Institute for Biomedical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 1374, Sao Paulo 05508-000, SP, Brazil; (P.O.T.-V.); (K.Y.O.C.); (J.F.C.T.); (M.M.G.T.); (J.J.S.)
| | - Kelly Y. O. Caicedo
- Department of Parasitology, Institute for Biomedical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 1374, Sao Paulo 05508-000, SP, Brazil; (P.O.T.-V.); (K.Y.O.C.); (J.F.C.T.); (M.M.G.T.); (J.J.S.)
| | - Jose F. C. Tantalean
- Department of Parasitology, Institute for Biomedical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 1374, Sao Paulo 05508-000, SP, Brazil; (P.O.T.-V.); (K.Y.O.C.); (J.F.C.T.); (M.M.G.T.); (J.J.S.)
| | - Myrna G. Serrano
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, 1101 E Marshall St., Richmond, VA 23298, USA; (M.G.S.); (G.A.B.)
| | - Gregory A. Buck
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, 1101 E Marshall St., Richmond, VA 23298, USA; (M.G.S.); (G.A.B.)
| | - Marta M. G. Teixeira
- Department of Parasitology, Institute for Biomedical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 1374, Sao Paulo 05508-000, SP, Brazil; (P.O.T.-V.); (K.Y.O.C.); (J.F.C.T.); (M.M.G.T.); (J.J.S.)
| | - Jeffrey J. Shaw
- Department of Parasitology, Institute for Biomedical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 1374, Sao Paulo 05508-000, SP, Brazil; (P.O.T.-V.); (K.Y.O.C.); (J.F.C.T.); (M.M.G.T.); (J.J.S.)
| | - Joao M. P. Alves
- Department of Parasitology, Institute for Biomedical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 1374, Sao Paulo 05508-000, SP, Brazil; (P.O.T.-V.); (K.Y.O.C.); (J.F.C.T.); (M.M.G.T.); (J.J.S.)
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Macedo DH, Grybchuk D, Režnarová J, Votýpka J, Klocek D, Yurchenko T, Ševčík J, Magri A, Dolinská MU, Záhonová K, Lukeš J, Servienė E, Jászayová A, Serva S, Malysheva MN, Frolov AO, Yurchenko V, Kostygov AY. Diversity of RNA viruses in the cosmopolitan monoxenous trypanosomatid Leptomonas pyrrhocoris. BMC Biol 2023; 21:191. [PMID: 37697369 PMCID: PMC10496375 DOI: 10.1186/s12915-023-01687-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 08/22/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Trypanosomatids are parasitic flagellates well known because of some representatives infecting humans, domestic animals, and cultural plants. Many trypanosomatid species bear RNA viruses, which, in the case of human pathogens Leishmania spp., influence the course of the disease. One of the close relatives of leishmaniae, Leptomonas pyrrhocoris, has been previously shown to harbor viruses of the groups not documented in other trypanosomatids. At the same time, this species has a worldwide distribution and high prevalence in the natural populations of its cosmopolitan firebug host. It therefore represents an attractive model to study the diversity of RNA viruses. RESULTS We surveyed 106 axenic cultures of L. pyrrhocoris and found that 64 (60%) of these displayed 2-12 double-stranded RNA fragments. The analysis of next-generation sequencing data revealed four viral groups with seven species, of which up to five were simultaneously detected in a single trypanosomatid isolate. Only two of these species, a tombus-like virus and an Ostravirus, were earlier documented in L. pyrrhocoris. In addition, there were four new species of Leishbuviridae, the family encompassing trypanosomatid-specific viruses, and a new species of Qinviridae, the family previously known only from metatranscriptomes of invertebrates. Currently, this is the only qinvirus with an unambiguously determined host. Our phylogenetic inferences suggest reassortment in the tombus-like virus owing to the interaction of different trypanosomatid strains. Two of the new Leishbuviridae members branch early on the phylogenetic tree of this family and display intermediate stages of genomic segment reduction between insect Phenuiviridae and crown Leishbuviridae. CONCLUSIONS The unprecedented wide range of viruses in one protist species and the simultaneous presence of up to five viral species in a single Leptomonas pyrrhocoris isolate indicate the uniqueness of this flagellate. This is likely determined by the peculiarity of its firebug host, a highly abundant cosmopolitan species with several habits ensuring wide distribution and profuseness of L. pyrrhocoris, as well as its exposure to a wider spectrum of viruses compared to other trypanosomatids combined with a limited ability to transmit these viruses to its relatives. Thus, L. pyrrhocoris represents a suitable model to study the adoption of new viruses and their relationships with a protist host.
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Affiliation(s)
- Diego H Macedo
- Faculty of Science, University of Ostrava, 710 00, Ostrava, Czech Republic
- University of Stockholm, Stockholm, Sweden
| | - Danyil Grybchuk
- Faculty of Science, University of Ostrava, 710 00, Ostrava, Czech Republic
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
| | - Jana Režnarová
- Faculty of Science, University of Ostrava, 710 00, Ostrava, Czech Republic
- University Hospital in Ostrava, Ostrava, Czech Republic
| | - Jan Votýpka
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic
- Faculty of Science, Charles University, 128 44, Prague, Czech Republic
| | - Donnamae Klocek
- Faculty of Science, University of Ostrava, 710 00, Ostrava, Czech Republic
| | - Tatiana Yurchenko
- Faculty of Science, University of Ostrava, 710 00, Ostrava, Czech Republic
| | - Jan Ševčík
- Faculty of Science, University of Ostrava, 710 00, Ostrava, Czech Republic
| | - Alice Magri
- Faculty of Science, University of Ostrava, 710 00, Ostrava, Czech Republic
- Department of Veterinary Medical Sciences, Alma Mater Studiorum - University of Bologna, Ozzano Dell'Emilia, 40064, Bologna, Italy
| | - Michaela Urda Dolinská
- Department of Epizootiology, Parasitology and Protection of One Health, University of Veterinary Medicine and Pharmacy, 041 81, Košice, Slovakia
| | - Kristína Záhonová
- Faculty of Science, University of Ostrava, 710 00, Ostrava, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic
- Faculty of Science, Charles University, BIOCEV, 252 50, Vestec, Czech Republic
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic
- Faculty of Sciences, University of South Bohemia, 370 05, České Budějovice, Czech Republic
| | - Elena Servienė
- Laboratory of Genetics, Institute of Botany, Nature Research Centre, 08412, Vilnius, Lithuania
| | - Alexandra Jászayová
- Faculty of Science, University of Ostrava, 710 00, Ostrava, Czech Republic
- Institute of Parasitology, Slovak Academy of Sciences, 040 01, Košice, Slovakia
- University of Veterinary Medicine and Pharmacy, 041 81, Košice, Slovakia
| | - Saulius Serva
- Department of Biochemistry and Molecular Biology, Institute of Biosciences, Vilnius University, 10257, Vilnius, Lithuania
| | - Marina N Malysheva
- Zoological Institute of Russian Academy of Sciences, 199034, St. Petersburg, Russia
| | - Alexander O Frolov
- Zoological Institute of Russian Academy of Sciences, 199034, St. Petersburg, Russia
| | | | - Alexei Yu Kostygov
- Faculty of Science, University of Ostrava, 710 00, Ostrava, Czech Republic.
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6
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Albanaz ATS, Carrington M, Frolov AO, Ganyukova AI, Gerasimov ES, Kostygov AY, Lukeš J, Malysheva MN, Votýpka J, Zakharova A, Záhonová K, Zimmer SL, Yurchenko V, Butenko A. Shining the spotlight on the neglected: new high-quality genome assemblies as a gateway to understanding the evolution of Trypanosomatidae. BMC Genomics 2023; 24:471. [PMID: 37605127 PMCID: PMC10441713 DOI: 10.1186/s12864-023-09591-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/15/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND Protists of the family Trypanosomatidae (phylum Euglenozoa) have gained notoriety as parasites affecting humans, domestic animals, and agricultural plants. However, the true extent of the group's diversity spreads far beyond the medically and veterinary relevant species. We address several knowledge gaps in trypanosomatid research by undertaking sequencing, assembly, and analysis of genomes from previously overlooked representatives of this protistan group. RESULTS We assembled genomes for twenty-one trypanosomatid species, with a primary focus on insect parasites and Trypanosoma spp. parasitizing non-human hosts. The assemblies exhibit sizes consistent with previously sequenced trypanosomatid genomes, ranging from approximately 18 Mb for Obscuromonas modryi to 35 Mb for Crithidia brevicula and Zelonia costaricensis. Despite being the smallest, the genome of O. modryi has the highest content of repetitive elements, contributing nearly half of its total size. Conversely, the highest proportion of unique DNA is found in the genomes of Wallacemonas spp., with repeats accounting for less than 8% of the assembly length. The majority of examined species exhibit varying degrees of aneuploidy, with trisomy being the most frequently observed condition after disomy. CONCLUSIONS The genome of Obscuromonas modryi represents a very unusual, if not unique, example of evolution driven by two antidromous forces: i) increasing dependence on the host leading to genomic shrinkage and ii) expansion of repeats causing genome enlargement. The observed variation in somy within and between trypanosomatid genera suggests that these flagellates are largely predisposed to aneuploidy and, apparently, exploit it to gain a fitness advantage. High heterogeneity in the genome size, repeat content, and variation in chromosome copy numbers in the newly-sequenced species highlight the remarkable genome plasticity exhibited by trypanosomatid flagellates. These new genome assemblies are a robust foundation for future research on the genetic basis of life cycle changes and adaptation to different hosts in the family Trypanosomatidae.
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Affiliation(s)
- Amanda T S Albanaz
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00, Ostrava, Czech Republic
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Alexander O Frolov
- Zoological Institute of the Russian Academy of Sciences, 199034, St. Petersburg, Russia
| | - Anna I Ganyukova
- Zoological Institute of the Russian Academy of Sciences, 199034, St. Petersburg, Russia
| | - Evgeny S Gerasimov
- Faculty of Biology, M. V. Lomonosov Moscow State University, 119991, Moscow, Russia
- Martsinovsky Institute of Medical Parasitology, Sechenov University, 119435, Moscow, Russia
| | - Alexei Y Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00, Ostrava, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic
- Faculty of Sciences, University of South Bohemia, 370 05, České Budějovice, Czech Republic
| | - Marina N Malysheva
- Zoological Institute of the Russian Academy of Sciences, 199034, St. Petersburg, Russia
| | - Jan Votýpka
- Institute of Parasitology, Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic
- Department of Parasitology, Faculty of Science, Charles University, 128 44, Prague, Czech Republic
| | - Alexandra Zakharova
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00, Ostrava, Czech Republic
| | - Kristína Záhonová
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00, Ostrava, Czech Republic
- Institute of Parasitology, Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, 252 50, Vestec, Czech Republic
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, T6G 2G3, Canada
| | - Sara L Zimmer
- Duluth Campus, University of Minnesota Medical School, Duluth, MN, 55812, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00, Ostrava, Czech Republic.
| | - Anzhelika Butenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00, Ostrava, Czech Republic.
- Institute of Parasitology, Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic.
- Faculty of Sciences, University of South Bohemia, 370 05, České Budějovice, Czech Republic.
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7
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Mendoza‐Roldan JA, Votýpka J, Bandi C, Epis S, Modrý D, Tichá L, Volf P, Otranto D. Leishmania tarentolae: A new frontier in the epidemiology and control of the leishmaniases. Transbound Emerg Dis 2022; 69:e1326-e1337. [PMID: 35839512 PMCID: PMC9804434 DOI: 10.1111/tbed.14660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/22/2022] [Accepted: 07/11/2022] [Indexed: 01/05/2023]
Abstract
Leishmaniasis (or the leishmaniases), classified as a neglected tropical parasitic disease, is found in parts of the tropics, subtropics and southern Europe. Leishmania parasites are transmitted by the bite of phlebotomine sand flies and million cases of human infection occur annually. Leishmania tarentolae has been historically considered a non-pathogenic protozoan of reptiles, which has been studied mainly for its potential biotechnological applications. However, some strains of L. tarentolae appear to be transiently infective to mammals. In areas where leishmaniasis is endemic, recent molecular diagnostics and serological positivity to L. tarentolae in humans and dogs have spurred interest in the interactions between these mammalian hosts, reptiles and Leishmania infantum, the main aetiologic agent of human and canine leishmaniasis. In this review, we discuss the systematics and biology of L. tarentolae in the insect vectors and the vertebrate hosts and address questions about evolution of reptilian leishmaniae. Furthermore, we discuss the possible usefulness of L. tarentolae for new vaccination strategies.
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Affiliation(s)
| | - Jan Votýpka
- Department of Parasitology, Faculty of ScienceCharles UniversityPragueCzech Republic,Biology Centre, Institute of ParasitologyCzech Academy of SciencesČeské BudějoviceCzech Republic
| | - Claudio Bandi
- Department of Biosciences and Pediatric CRC “Romeo ed Enrica Invernizzi”University of MilanMilanItaly
| | - Sara Epis
- Department of Biosciences and Pediatric CRC “Romeo ed Enrica Invernizzi”University of MilanMilanItaly
| | - David Modrý
- Biology Centre, Institute of ParasitologyCzech Academy of SciencesČeské BudějoviceCzech Republic,Department of Botany and Zoology, Faculty of ScienceMasaryk UniversityBrnoCzech Republic,Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural ResourcesCzech University of Life SciencesPragueCzech Republic
| | - Lucie Tichá
- Department of Parasitology, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Petr Volf
- Department of Parasitology, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Domenico Otranto
- Department of Veterinary MedicineUniversity of BariValenzanoItaly,Department of Pathobiology, Faculty of Veterinary ScienceBu‐Ali Sina UniversityHamedanIran
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8
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Guimarães RCS, Marialva EF, Feijó JA, Pereira-Silva JW, Martins-Campos KM, Gontijo CMF, Pereira AAS, Rios-Velasquez CM, Pessoa FAC. Trypanosomatids in Phlebotomine Sand Flies (Diptera: Phlebotominae) From Anthropic and Sinantropic Landscapes in a Rural Settlement in the Brazilian Amazon. JOURNAL OF MEDICAL ENTOMOLOGY 2022; 59:681-692. [PMID: 35022773 DOI: 10.1093/jme/tjab208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Indexed: 06/14/2023]
Abstract
Trypanosomatids (Kinetoplastida:Trypanosomatidae) protozoa are a diverse group of obligate parasites. The genera Trypanosoma and Leishmania are the most studied because of their medical importance. This work aims to evaluate the effects of anthropization processes on the composition of the phlebotomine sand fly fauna and the natural infection by Trypanosomatids, with emphasis on Leishmania. At all 3,186 sand flies were collected, distributed in 13 genera and 52 species, being Ny. umbratilis the most abundant species. There was no difference in the diversity between canopy and soil environments. The species abundance and richness were higher in the forest environment while species diversity and evenness were highest in the forest edge. The ITS1 region was used by PCR-RFLP to identify the fragment profiles of Leishmania species, followed by genetic sequencing. Here were analyzed 100 pools of female sand flies, being six positive for DNA parasite. PCR-RFLP fragment patterns similar to Endotrypanum sp. were observed in Nyssomyia anduzei, Psychodopygus amazonensis and Lutzomyia gomezi, and those fragments similar to Leishmania (Leishmania) amazonensis were observed in Bichromomyia flaviscutellata. ITS1 sequencing confirmed the presence of Leishmania sp. in Bi. flaviscutellata, and Leishmania (Viannia) naiffi in Ny. anduzei, Psychodopygus amazonensis, and Lu. gomezi. This is the first record of Lu. gomezi and Ps. amazonensis infection by L. naiffi in the State of Amazonas. These results show the trypanosomatid infection in sandflies from different landscapes in a rural settlement, and the finding of species infected with L.(V.) naiffi suggest that they can develop a role in the transmission cycle of leishmaniasis.
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Affiliation(s)
- R C S Guimarães
- Programa de Pós-Graduação em Condições de Vida e Situações de Saúde na Amazônia - PPGVIDA. Instituto Leônidas e Maria Deane - ILMD Fiocruz Amazônia, Rua Teresina, 476 Adrianópolis, Manaus, Amazonas, Brasil
| | - E F Marialva
- Laboratório de Ecologia de Doenças Transmissíveis na Amazonia - EDTA Instituto Leônidas e Maria Deane - ILMD Fiocruz Amazônia, Rua Teresina, 476 Adrianópolis, Manaus, Amazonas, Brasil
| | - J A Feijó
- Laboratório de Ecologia de Doenças Transmissíveis na Amazonia - EDTA Instituto Leônidas e Maria Deane - ILMD Fiocruz Amazônia, Rua Teresina, 476 Adrianópolis, Manaus, Amazonas, Brasil
| | - J W Pereira-Silva
- Laboratório de Ecologia de Doenças Transmissíveis na Amazonia - EDTA Instituto Leônidas e Maria Deane - ILMD Fiocruz Amazônia, Rua Teresina, 476 Adrianópolis, Manaus, Amazonas, Brasil
| | - K M Martins-Campos
- Laboratório de Ecologia de Doenças Transmissíveis na Amazonia - EDTA Instituto Leônidas e Maria Deane - ILMD Fiocruz Amazônia, Rua Teresina, 476 Adrianópolis, Manaus, Amazonas, Brasil
| | - C M F Gontijo
- Grupo de Estudos em Leishmanioses, Centro de Pesquisas Rene Rachou, Fundação Oswaldo Cruz, Avenida Augusto de Lima, 1715 Barro Preto, CEP 30190-002, Belo Horizonte, Minas Gerais, Brasil
| | - A A S Pereira
- Grupo de Estudos em Leishmanioses, Centro de Pesquisas Rene Rachou, Fundação Oswaldo Cruz, Avenida Augusto de Lima, 1715 Barro Preto, CEP 30190-002, Belo Horizonte, Minas Gerais, Brasil
| | - C M Rios-Velasquez
- Laboratório de Ecologia de Doenças Transmissíveis na Amazonia - EDTA Instituto Leônidas e Maria Deane - ILMD Fiocruz Amazônia, Rua Teresina, 476 Adrianópolis, Manaus, Amazonas, Brasil
| | - F A C Pessoa
- Laboratório de Ecologia de Doenças Transmissíveis na Amazonia - EDTA Instituto Leônidas e Maria Deane - ILMD Fiocruz Amazônia, Rua Teresina, 476 Adrianópolis, Manaus, Amazonas, Brasil
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9
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Genomics of Trypanosomatidae: Where We Stand and What Needs to Be Done? Pathogens 2021; 10:pathogens10091124. [PMID: 34578156 PMCID: PMC8472099 DOI: 10.3390/pathogens10091124] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/26/2021] [Accepted: 08/31/2021] [Indexed: 01/18/2023] Open
Abstract
Trypanosomatids are easy to cultivate and they are (in many cases) amenable to genetic manipulation. Genome sequencing has become a standard tool routinely used in the study of these flagellates. In this review, we summarize the current state of the field and our vision of what needs to be done in order to achieve a more comprehensive picture of trypanosomatid evolution. This will also help to illuminate the lineage-specific proteins and pathways, which can be used as potential targets in treating diseases caused by these parasites.
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10
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A New Model Trypanosomatid, Novymonas esmeraldas: Genomic Perception of Its " Candidatus Pandoraea novymonadis" Endosymbiont. mBio 2021; 12:e0160621. [PMID: 34399629 PMCID: PMC8406214 DOI: 10.1128/mbio.01606-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The closest relative of human pathogen Leishmania, the trypanosomatid Novymonas esmeraldas, harbors a bacterial endosymbiont “Candidatus Pandoraea novymonadis.” Based on genomic data, we performed a detailed characterization of the metabolic interactions of both partners. While in many respects the metabolism of N. esmeraldas resembles that of other Leishmaniinae, the endosymbiont provides the trypanosomatid with heme, essential amino acids, purines, some coenzymes, and vitamins. In return, N. esmeraldas shares with the bacterium several nonessential amino acids and phospholipids. Moreover, it complements its carbohydrate metabolism and urea cycle with enzymes missing from the “Ca. Pandoraea novymonadis” genome. The removal of the endosymbiont from N. esmeraldas results in a significant reduction of the overall translation rate, reduced expression of genes involved in lipid metabolism and mitochondrial respiratory activity, and downregulation of several aminoacyl-tRNA synthetases, enzymes involved in the synthesis of some amino acids, as well as proteins associated with autophagy. At the same time, the genes responsible for protection against reactive oxygen species and DNA repair become significantly upregulated in the aposymbiotic strain of this trypanosomatid. By knocking out a component of its flagellum, we turned N. esmeraldas into a new model trypanosomatid that is amenable to genetic manipulation using both conventional and CRISPR-Cas9-mediated approaches.
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11
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Becvar T, Vojtkova B, Siriyasatien P, Votypka J, Modry D, Jahn P, Bates P, Carpenter S, Volf P, Sadlova J. Experimental transmission of Leishmania (Mundinia) parasites by biting midges (Diptera: Ceratopogonidae). PLoS Pathog 2021; 17:e1009654. [PMID: 34115806 PMCID: PMC8221790 DOI: 10.1371/journal.ppat.1009654] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/23/2021] [Accepted: 05/18/2021] [Indexed: 12/23/2022] Open
Abstract
Leishmania parasites, causative agents of leishmaniasis, are currently divided into four subgenera: Leishmania, Viannia, Sauroleishmania and Mundinia. The recently established subgenus Mundinia has a wide geographical distribution and contains five species, three of which have the potential to infect and cause disease in humans. While the other Leishmania subgenera are transmitted exclusively by phlebotomine sand flies (Diptera: Psychodidae), natural vectors of Mundinia remain uncertain. This study investigates the potential of sand flies and biting midges of the genus Culicoides (Diptera: Ceratopogonidae) to transmit Leishmania parasites of the subgenus Mundinia. Sand flies (Phlebotomus argentipes, P. duboscqi and Lutzomyia migonei) and Culicoides biting midges (Culicoides sonorensis) were exposed to five Mundinia species through a chicken skin membrane and dissected at specific time intervals post bloodmeal. Potentially infected insects were also allowed to feed on ear pinnae of anaesthetized BALB/c mice and the presence of Leishmania DNA was subsequently confirmed in the mice using polymerase chain reaction analyses. In C. sonorensis, all Mundinia species tested were able to establish infection at a high rate, successfully colonize the stomodeal valve and produce a higher proportion of metacyclic forms than in sand flies. Subsequently, three parasite species, L. martiniquensis, L. orientalis and L. sp. from Ghana, were transmitted to the host mouse ear by C. sonorensis bite. In contrast, transmission experiments entirely failed with P. argentipes, although colonisation of the stomodeal valve was observed for L. orientalis and L. martiniquensis and metacyclic forms of L. orientalis were recorded. This laboratory-based transmission of Mundinia species highlights that Culicoides are potential vectors of members of this ancestral subgenus of Leishmania and we suggest further studies in endemic areas to confirm their role in the lifecycles of neglected pathogens. Leishmania parasites are causative agents of leishmaniasis, a disease affecting millions of humans worldwide. It is widely accepted that these flagellates are transmitted exclusively by phlebotomine sand flies (Diptera: Phlebotominae). Reservoir hosts and insect vectors for the newly established Leishmania subgenus Mundinia, however, remain poorly understood. Preliminary evidence from field-based studies discovered biting midges (Diptera: Ceratopogonidae) that were naturally infected by L. (Mundinia) macropodum in Australia. This surprising finding led us to carry out a detailed laboratory study aimed at comparison of the development of all currently known species of the subgenus Mundinia in both putative vector families. We found that all five Mundinia species developed successfully in C. sonorensis and the successful transmission of three Mundinia species from infected insects to mice was demonstrated for the first time. This is the first detailed in vivo evidence that biting midges can act as competent vectors of Leishmania parasites of the subgenus Mundinia and has considerable epidemiological implications for control of these neglected pathogens.
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Affiliation(s)
- Tomas Becvar
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Barbora Vojtkova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Padet Siriyasatien
- Vector Biology and Vector Borne Disease Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jan Votypka
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - David Modry
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Veterinary Sciences/CINeZ, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Petr Jahn
- Equine Clinic, University of Veterinary Sciences, Brno, Czech Republic
| | - Paul Bates
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom
| | - Simon Carpenter
- Entomology Group, The Pirbright Institute, Pirbright, Surrey, United Kingdom
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jovana Sadlova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
- * E-mail:
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12
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Midha S, Rigden DJ, Siozios S, Hurst GDD, Jackson AP. Bodo saltans (Kinetoplastida) is dependent on a novel Paracaedibacter-like endosymbiont that possesses multiple putative toxin-antitoxin systems. THE ISME JOURNAL 2021; 15:1680-1694. [PMID: 33452479 PMCID: PMC8163844 DOI: 10.1038/s41396-020-00879-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/03/2020] [Accepted: 12/09/2020] [Indexed: 12/30/2022]
Abstract
Bacterial endosymbiosis has been instrumental in eukaryotic evolution, and includes both mutualistic, dependent and parasitic associations. Here we characterize an intracellular bacterium inhabiting the flagellated protist Bodo saltans (Kinetoplastida). We present a complete bacterial genome comprising a 1.39 Mb circular chromosome with 40.6% GC content. Fluorescent in situ hybridisation confirms that the endosymbiont is located adjacent to the nuclear membrane, and a detailed model of its intracellular niche is generated using serial block-face scanning electron microscopy. Phylogenomic analysis shows that the endosymbiont belongs to the Holosporales, most closely related to other α-proteobacterial endosymbionts of ciliates and amoebae. Comparative genomics indicates that it has a limited metabolism and is nutritionally host-dependent. However, the endosymbiont genome does encode diverse symbiont-specific secretory proteins, including a type VI secretion system and three separate toxin-antitoxin systems. We show that these systems are actively transcribed and hypothesize they represent a mechanism by which B. saltans becomes addicted to its endosymbiont. Consistent with this idea, attempts to cure Bodo of endosymbionts led to rapid and uniform cell death. This study adds kinetoplastid flagellates to ciliates and amoebae as hosts of Paracaedibacter-like bacteria, suggesting that these antagonistic endosymbioses became established very early in Eukaryotic evolution.
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Affiliation(s)
- Samriti Midha
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Ic2 Liverpool Science Park, 146 Brownlow Hill, Liverpool, L3 5RF, UK.
| | - Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool, L69 7ZB, UK
| | - Stefanos Siozios
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Ic2 Liverpool Science Park, 146 Brownlow Hill, Liverpool, L3 5RF, UK
| | - Gregory D D Hurst
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Ic2 Liverpool Science Park, 146 Brownlow Hill, Liverpool, L3 5RF, UK
| | - Andrew P Jackson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Ic2 Liverpool Science Park, 146 Brownlow Hill, Liverpool, L3 5RF, UK
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13
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The Maze Pathway of Coevolution: A Critical Review over the Leishmania and Its Endosymbiotic History. Genes (Basel) 2021; 12:genes12050657. [PMID: 33925663 PMCID: PMC8146029 DOI: 10.3390/genes12050657] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 01/10/2023] Open
Abstract
The description of the genus Leishmania as the causative agent of leishmaniasis occurred in the modern age. However, evolutionary studies suggest that the origin of Leishmania can be traced back to the Mesozoic era. Subsequently, during its evolutionary process, it achieved worldwide dispersion predating the breakup of the Gondwana supercontinent. It is assumed that this parasite evolved from monoxenic Trypanosomatidae. Phylogenetic studies locate dixenous Leishmania in a well-supported clade, in the recently named subfamily Leishmaniinae, which also includes monoxenous trypanosomatids. Virus-like particles have been reported in many species of this family. To date, several Leishmania species have been reported to be infected by Leishmania RNA virus (LRV) and Leishbunyavirus (LBV). Since the first descriptions of LRVs decades ago, differences in their genomic structures have been highlighted, leading to the designation of LRV1 in L. (Viannia) species and LRV2 in L. (Leishmania) species. There are strong indications that viruses that infect Leishmania spp. have the ability to enhance parasitic survival in humans as well as in experimental infections, through highly complex and specialized mechanisms. Phylogenetic analyses of these viruses have shown that their genomic differences correlate with the parasite species infected, suggesting a coevolutionary process. Herein, we will explore what has been described in the literature regarding the relationship between Leishmania and endosymbiotic Leishmania viruses and what is known about this association that could contribute to discussions about the worldwide dispersion of Leishmania.
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14
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Dario MA, Lisboa CV, Silva MV, Herrera HM, Rocha FL, Furtado MC, Moratelli R, Rodrigues Roque AL, Jansen AM. Crithidia mellificae infection in different mammalian species in Brazil. INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2021; 15:58-69. [PMID: 33981571 PMCID: PMC8085711 DOI: 10.1016/j.ijppaw.2021.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/05/2021] [Accepted: 04/05/2021] [Indexed: 11/17/2022]
Abstract
Crithidia mellificae, a monoxenous trypanosomatid considered restricted to insects, was recently reported to infect a bat. Herein, C. mellificae has been demonstrated to have a wider range of vertebrate hosts and distribution in Brazilian biomes than once thought. Parasites isolated from haemocultures were characterized using V7V8 SSU rDNA and glyceraldehyde 3-phosphate dehydrogenase genes. Coatis (Nasua nasua) in the Cerrado; marmosets (Callithrix sp.) and bats (Carollia perspicillata, Myotis lavali, M. izecksohni, Artibeus lituratus) in the Atlantic Forest; crab-eating foxes (Cerdocyon thous) and ocelot (Leopardus pardalis) in the Pantanal biomes were infected by trypanosomatids that displayed choanomastigote forms in haemoculture in Giemsa-stained slide smears. Molecular characterization and phylogenetic inference confirmed the infection of C. mellificae in these animals. Moreover, slight differences in C. mellificae sequences were observed. Crithidia mellificae growth curves were counted at 27°C, 36°C and 37°C, and the morphotypes were able to grow and survive for up to 16 days. Serological titers for C. mellificae were observed in nonhuman primates, demonstrating that this parasite is able to induce a humoral immune response in an infected mammal. These results showed that host specificity in trypanosomatids is complex and far from understood.
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Affiliation(s)
- Maria Augusta Dario
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cristiane Varella Lisboa
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marlon Vicente Silva
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Heitor Miraglia Herrera
- Programa de Pós-Graduação em Ciências Ambientais e Sustentabilidade Agropecuária, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - Fabiana Lopes Rocha
- Programa de Pós-graduação em Ecologia e Monitoramento Ambiental, Universidade Federal da Paraíba, Rio Tinto, Paraíba, Brazil
- IUCN SSC Species Survival Center. Parque das Aves, Foz do Iguaçú, Paraná, Brazil
| | | | - Ricardo Moratelli
- Fiocruz Mata Atlântica, Fundação Oswaldo Cruz Rio de Janeiro, Rio de Janeiro, Brazil
| | - André Luiz Rodrigues Roque
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana Maria Jansen
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
- Corresponding author.
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15
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Gerasimov ES, Gasparyan AA, Afonin DA, Zimmer SL, Kraeva N, Lukeš J, Yurchenko V, Kolesnikov A. Complete minicircle genome of Leptomonas pyrrhocoris reveals sources of its non-canonical mitochondrial RNA editing events. Nucleic Acids Res 2021; 49:3354-3370. [PMID: 33660779 PMCID: PMC8034629 DOI: 10.1093/nar/gkab114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 02/03/2021] [Accepted: 02/09/2021] [Indexed: 01/24/2023] Open
Abstract
Uridine insertion/deletion (U-indel) editing of mitochondrial mRNA, unique to the protistan class Kinetoplastea, generates canonical as well as potentially non-productive editing events. While the molecular machinery and the role of the guide (g) RNAs that provide required information for U-indel editing are well understood, little is known about the forces underlying its apparently error-prone nature. Analysis of a gRNA:mRNA pair allows the dissection of editing events in a given position of a given mitochondrial transcript. A complete gRNA dataset, paired with a fully characterized mRNA population that includes non-canonically edited transcripts, would allow such an analysis to be performed globally across the mitochondrial transcriptome. To achieve this, we have assembled 67 minicircles of the insect parasite Leptomonas pyrrhocoris, with each minicircle typically encoding one gRNA located in one of two similar-sized units of different origin. From this relatively narrow set of annotated gRNAs, we have dissected all identified mitochondrial editing events in L. pyrrhocoris, the strains of which dramatically differ in the abundance of individual minicircle classes. Our results support a model in which a multitude of editing events are driven by a limited set of gRNAs, with individual gRNAs possessing an inherent ability to guide canonical and non-canonical editing.
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Affiliation(s)
- Evgeny S Gerasimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow 119435, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russia
| | - Anna A Gasparyan
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Dmitry A Afonin
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Sara L Zimmer
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, Duluth, MN 55812, USA
| | - Natalya Kraeva
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice (Budweis), Czech Republic
| | - Vyacheslav Yurchenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow 119435, Russia
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Alexander Kolesnikov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
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16
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Genome Analysis of Endotrypanum and Porcisia spp., Closest Phylogenetic Relatives of Leishmania, Highlights the Role of Amastins in Shaping Pathogenicity. Genes (Basel) 2021; 12:genes12030444. [PMID: 33804709 PMCID: PMC8004069 DOI: 10.3390/genes12030444] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/15/2021] [Accepted: 03/18/2021] [Indexed: 02/07/2023] Open
Abstract
While numerous genomes of Leishmania spp. have been sequenced and analyzed, an understanding of the evolutionary history of these organisms remains limited due to the unavailability of the sequence data for their closest known relatives, Endotrypanum and Porcisia spp., infecting sloths and porcupines. We have sequenced and analyzed genomes of three members of this clade in order to fill this gap. Their comparative analyses revealed only minute differences from Leishmaniamajor genome in terms of metabolic capacities. We also documented that the number of genes under positive selection on the Endotrypanum/Porcisia branch is rather small, with the flagellum-related group of genes being over-represented. Most significantly, the analysis of gene family evolution revealed a substantially reduced repertoire of surface proteins, such as amastins and biopterin transporters BT1 in the Endotrypanum/Porcisia species when compared to amastigote-dwelling Leishmania. This reduction was especially pronounced for δ-amastins, a subfamily of cell surface proteins crucial in the propagation of Leishmania amastigotes inside vertebrate macrophages and, apparently, dispensable for Endotrypanum/Porcisia, which do not infect such cells.
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17
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Sádlová J, Podešvová L, Bečvář T, Bianchi C, Gerasimov ES, Saura A, Glanzová K, Leštinová T, Matveeva NS, Chmelová Ľ, Mlacovská D, Spitzová T, Vojtková B, Volf P, Yurchenko V, Kraeva N. Catalase impairs Leishmania mexicana development and virulence. Virulence 2021; 12:852-867. [PMID: 33724149 PMCID: PMC7971327 DOI: 10.1080/21505594.2021.1896830] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Catalase is one of the most abundant enzymes on Earth. It decomposes hydrogen peroxide, thus protecting cells from dangerous reactive oxygen species. The catalase-encoding gene is conspicuously absent from the genome of most representatives of the family Trypanosomatidae. Here, we expressed this protein from the Leishmania mexicana Β-TUBULIN locus using a novel bicistronic expression system, which relies on the 2A peptide of Teschovirus A. We demonstrated that catalase-expressing parasites are severely compromised in their ability to develop in insects, to be transmitted and to infect mice, and to cause clinical manifestation in their mammalian host. Taken together, our data support the hypothesis that the presence of catalase is not compatible with the dixenous life cycle of Leishmania, resulting in loss of this gene from the genome during the evolution of these parasites.
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Affiliation(s)
- Jovana Sádlová
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Lucie Podešvová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Tomáš Bečvář
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Claretta Bianchi
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Evgeny S Gerasimov
- Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Andreu Saura
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Kristýna Glanzová
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tereza Leštinová
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Nadezhda S Matveeva
- Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow, Russia.,Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia
| | - Ľubomíra Chmelová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Denisa Mlacovská
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Tatiana Spitzová
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Barbora Vojtková
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - 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
| | - Natalya Kraeva
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
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18
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Frolov AO, Kostygov AY, Yurchenko V. Development of Monoxenous Trypanosomatids and Phytomonads in Insects. Trends Parasitol 2021; 37:538-551. [PMID: 33714646 DOI: 10.1016/j.pt.2021.02.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 11/30/2022]
Abstract
In this review, we summarize the current data on development of monoxenous trypanosomatids and phytomonads in various insects. Of these, Diptera and Hemiptera are the main host groups, and, consequently, most available information concerns their parasites. Within the insect body, the midgut and hindgut are the predominant colonization sites; in addition, some trypanosomatids can invade the foregut, Malpighian tubules, hemolymph, and/or salivary glands. Differences in the intestinal structure and biology of the host determine the variety of parasites' developmental and transmission strategies. Meanwhile, similar mechanisms are used by unrelated trypanosomatids, reflecting the limited range of options to achieve the same goal.
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Affiliation(s)
- Alexander O Frolov
- Zoological Institute of the Russian Academy of Sciences, St Petersburg, Russia.
| | - Alexei Y Kostygov
- Zoological Institute of the Russian Academy of Sciences, St Petersburg, Russia; Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.
| | - 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.
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19
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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: 77] [Impact Index Per Article: 25.7] [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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20
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Abstract
Telomeres are the ends of linear eukaryotic chromosomes facilitating the resolution of the ‘end replication and protection’ problems, associated with linearity. At the nucleotide level, telomeres typically represent stretches of tandemly arranged telomeric repeats, which vary in length and sequence among different groups of organisms. Recently, a composition of the telomere-associated protein complex has been scrutinized in Trypanosoma brucei. In this work, we subjected proteins from that list to a more detailed bioinformatic analysis and delineated a core set of 20 conserved proteins putatively associated with telomeres in trypanosomatids. Out of these, two proteins (Ku70 and Ku80) are conspicuously missing in representatives of the genus Blastocrithidia, yet telomeres in these species do not appear to be affected. In this work, based on the analysis of a large set of trypanosomatids widely different in their phylogenetic position and life strategies, we demonstrated that telomeres of trypanosomatids are diverse in length, even within groups of closely related species. Our analysis showed that the expression of two proteins predicted to be associated with telomeres (those encoding telomerase and telomere-associated hypothetical protein orthologous to Tb927.6.4330) may directly affect and account for the differences in telomere length within the species of the Leishmania mexicana complex.
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21
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Maruyama SR, Rogerio LA, Freitas PD, Teixeira MMG, Ribeiro JMC. Total Ortholog Median Matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes. Sci Rep 2021; 11:3791. [PMID: 33589693 PMCID: PMC7884790 DOI: 10.1038/s41598-021-81926-w] [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: 06/17/2020] [Accepted: 01/05/2021] [Indexed: 11/09/2022] Open
Abstract
The increasing number of available genomic data allowed the development of phylogenomic analytical tools. Current methods compile information from single gene phylogenies, whether based on topologies or multiple sequence alignments. Generally, phylogenomic analyses elect gene families or genomic regions to construct phylogenomic trees. Here, we presented an alternative approach for Phylogenomics, named TOMM (Total Ortholog Median Matrix), to construct a representative phylogram composed by amino acid distance measures of all pairwise ortholog protein sequence pairs from desired species inside a group of organisms. The procedure is divided two main steps, (1) ortholog detection and (2) creation of a matrix with the median amino acid distance measures of all pairwise orthologous sequences. We tested this approach within three different group of organisms: Kinetoplastida protozoa, hematophagous Diptera vectors and Primates. Our approach was robust and efficacious to reconstruct the phylogenetic relationships for the three groups. Moreover, novel branch topologies could be achieved, providing insights about some phylogenetic relationships between some taxa.
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Affiliation(s)
- Sandra Regina Maruyama
- Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos (UFSCar), São Carlos, SP, 13565-905, Brazil.
| | - Luana Aparecida Rogerio
- Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos (UFSCar), São Carlos, SP, 13565-905, Brazil
| | - Patricia Domingues Freitas
- Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos (UFSCar), São Carlos, SP, 13565-905, Brazil
| | | | - José Marcos Chaves Ribeiro
- Vector Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12735 Twinbrook Parkway rm 2E32, Rockville, MD, 20852, USA.
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22
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Lukeš J, Tesařová M, Yurchenko V, Votýpka J. Characterization of a new cosmopolitan genus of trypanosomatid parasites, Obscuromonas gen. nov. (Blastocrithidiinae subfam. nov.). Eur J Protistol 2021; 79:125778. [PMID: 33706204 DOI: 10.1016/j.ejop.2021.125778] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/10/2020] [Accepted: 01/19/2021] [Indexed: 01/28/2023]
Abstract
The expanding phylogenetic tree of trypanosomatid flagellates (Kinetoplastea: Trypanosomatidae) contains a long-known and phylogenetically well-supported species-rich lineage that was provisionally named as the 'jaculum' clade. Its members were found in representatives of several unrelated families of heteropteran bugs captured in South and Central America, Europe, Africa, and Asia. However, this group resisted introduction into the culture, a needed prerequisite for its proper characterization. Here we describe four new cultivable species, which parasitize various parts of their hosts' intestine, including the thoracic and abdominal part of the midgut, hindgut, and Malpighian tubules. Morphologically, the cultured flagellates vary from relatively short stumpy promastigotes to long slender leptomonad cells. Some species form straphangers (cyst-like amastigotes) both in vivo and in vitro, initially attached to the basal part of the flagellum of the mother cell, from which they subsequently detach. To formally classify this enigmatic monophyletic cosmopolitan clade, we erected Obscuromonas gen. nov., including five species: O. modryi sp. nov. (isolated from the true bug host species Riptortus linearis captured in the Philippines), O. volfi sp. nov. (from Catorhintha selector, Curaçao), O. eliasi sp. nov. (from Graptostethus servus, Papua New Guinea), O. oborniki sp. nov. (from Aspilocoryphus unimaculatus, Madagascar), and O. jaculum comb. nov. (from Nepa cinerea, France). Obscuromonas along with the genus Blastocrithidia belongs to the newly established Blastocrithidiinae subfam. nov.
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Affiliation(s)
- 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
| | - Martina Tesařová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Vyacheslav Yurchenko
- Faculty of Science, University of Ostrava, Ostrava, Czech Republic; Martsinovsky Institute of Medical Parasitology, Sechenov University, Moscow, Russia
| | - Jan Votýpka
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Science, Charles University, Prague, Czech Republic.
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23
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Abstract
Complex I (NADH dehydrogenase) is the first enzyme in the respiratory chain. It catalyses the electron transfer from NADH to ubiquinone that is associated with proton pumping out of the matrix. In this study, we characterized NADH dehydrogenase activity in seven monoxenous trypanosomatid species: Blechomonas ayalai, Herpetomonas tarakana, Kentomonas sorsogonicus, Leptomonas seymouri, Novymonas esmeraldas, Sergeia podlipaevi and Wallacemonas raviniae. We also investigated the subunit composition of the complex I in dixenous Phytomonas serpens, in which its presence and activity have been previously documented. In addition to P. serpens, the complex I is functionally active in N. esmeraldas and S. podlipaevi. We also identified 24-32 subunits of the complex I in individual species by using mass spectrometry. Among them, for the first time, we recognized several proteins of the mitochondrial DNA origin.
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24
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Durante IM, Butenko A, Rašková V, Charyyeva A, Svobodová M, Yurchenko V, Hashimi H, Lukeš J. Large-Scale Phylogenetic Analysis of Trypanosomatid Adenylate Cyclases Reveals Associations with Extracellular Lifestyle and Host-Pathogen Interplay. Genome Biol Evol 2020; 12:2403-2416. [PMID: 33104188 PMCID: PMC7719234 DOI: 10.1093/gbe/evaa226] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2020] [Indexed: 12/14/2022] Open
Abstract
Receptor adenylate cyclases (RACs) on the surface of trypanosomatids are important players in the host–parasite interface. They detect still unidentified environmental signals that affect the parasites’ responses to host immune challenge, coordination of social motility, and regulation of cell division. A lesser known class of oxygen-sensing adenylate cyclases (OACs) related to RACs has been lost in trypanosomes and expanded mostly in Leishmania species and related insect-dwelling trypanosomatids. In this work, we have undertaken a large-scale phylogenetic analysis of both classes of adenylate cyclases (ACs) in trypanosomatids and the free-living Bodo saltans. We observe that the expanded RAC repertoire in trypanosomatids with a two-host life cycle is not only associated with an extracellular lifestyle within the vertebrate host, but also with a complex path through the insect vector involving several life cycle stages. In Trypanosoma brucei, RACs are split into two major clades, which significantly differ in their expression profiles in the mammalian host and the insect vector. RACs of the closely related Trypanosoma congolense are intermingled within these two clades, supporting early RAC diversification. Subspecies of T. brucei that have lost the capacity to infect insects exhibit high numbers of pseudogenized RACs, suggesting many of these proteins have become redundant upon the acquisition of a single-host life cycle. OACs appear to be an innovation occurring after the expansion of RACs in trypanosomatids. Endosymbiont-harboring trypanosomatids exhibit a diversification of OACs, whereas these proteins are pseudogenized in Leishmania subgenus Viannia. This analysis sheds light on how ACs have evolved to allow diverse trypanosomatids to occupy multifarious niches and assume various lifestyles.
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Affiliation(s)
- Ignacio Miguel Durante
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czechia
| | - Anzhelika Butenko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czechia.,Life Science Research Centre, Faculty of Science, University of Ostrava, Czechia
| | - Vendula Rašková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czechia.,Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czechia
| | - Arzuv Charyyeva
- Life Science Research Centre, Faculty of Science, University of Ostrava, Czechia
| | - Michaela Svobodová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czechia
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Czechia.,Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russian Federation
| | - Hassan Hashimi
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czechia.,Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czechia
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czechia.,Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czechia
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25
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Rogozin IB, Charyyeva A, Sidorenko IA, Babenko VN, Yurchenko V. Frequent Recombination Events in Leishmania donovani: Mining Population Data. Pathogens 2020; 9:pathogens9070572. [PMID: 32679679 PMCID: PMC7400496 DOI: 10.3390/pathogens9070572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/24/2020] [Accepted: 07/13/2020] [Indexed: 11/21/2022] Open
Abstract
The Leishmania donovani species complex consists of all L. donovani and L. infantum strains mainly responsible for visceral leishmaniasis (VL). It was suggested that genome rearrangements in Leishmania spp. occur very often, thus enabling parasites to adapt to the different environmental conditions. Some of these rearrangements may be directly linked to the virulence or explain the reduced efficacy of antimonial drugs in some isolates. In the current study, we focused on a large-scale analysis of putative gene conversion events using publicly available datasets. Previous population study of L. donovani suggested that population variability of L. donovani is relatively low, however the authors used masking procedures and strict read selection criteria. We decided to re-analyze DNA-seq data without masking sequences, because we were interested in the most dynamic fraction of the genome. The majority of samples have an excess of putative gene conversion/recombination events in the noncoding regions, however we found an overall excess of putative intrachromosomal gene conversion/recombination in the protein coding genes, compared to putative interchromosomal gene conversion/recombination events.
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Affiliation(s)
- Igor B. Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA;
| | - Arzuv Charyyeva
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
| | - Ivan A. Sidorenko
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (I.A.S.); (V.N.B.)
| | - Vladimir N. Babenko
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (I.A.S.); (V.N.B.)
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119435 Moscow, Russia
- Correspondence:
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26
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Diversity of phlebotomine sand flies and molecular detection of trypanosomatids in Brumadinho, Minas Gerais, Brazil. PLoS One 2020; 15:e0234445. [PMID: 32579586 PMCID: PMC7314019 DOI: 10.1371/journal.pone.0234445] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/25/2020] [Indexed: 02/08/2023] Open
Abstract
This study aimed to describe the sand fly fauna and detect trypanosomatids in these insects from Casa Branca, state of Minas Gerais, Brazil, an endemic area of both visceral (VL) and tegumentary leishmaniasis (TL). Sand flies were collected bimonthly from May 2013 to July 2014, using automatic light traps exposed for three consecutive nights in peridomiciliary areas of nine houses with previous reports of VL and TL. ITS1-PCR and DNA sequencing were performed for trypanosomatids identification. A total of 16,771 sand flies were collected belonging to 23 species. The most abundant species was Nyssomyia whitmani (Antunes & Coutinho, 1939) (70.9%), followed by Lutzomyia longipalpis (Lutz & Neiva, 1912) (15.2%) and Migonemyia migonei (França, 1920) (9.1%). Leishmania amazonensis DNA was detected in Ny. whitmani (four pools) and Le. braziliensis DNA was detected in Psychodopygus lloydi (one pool). In seven pools of Ny. whitmani and in one pool of Lu. longipalpis positive for Leishmania DNA, the parasite species was not determined due to the low quality of the sequences. Moreover, DNA of Herpetomonas spp. was detected in Ny. whitmani (two pools) and Cortelezzii complex (one pool). DNA of Crithidia spp. was detected in Ny. whitmani and Ps. lloydi (both one pool). Our results suggest that Ny. whitmani may be involved in the transmission of Le. amazonensis in the study area. The molecular detection of Le. amazonensis suggests the presence of this species in a sylvatic cycle between vertebrate and invertebrate hosts in the region of Casa Branca. Our data also reveal the occurrence of other non-Leishmania trypanosomatids in sand flies in Casa Branca District.
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27
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Boucinha C, Caetano AR, Santos HLC, Helaers R, Vikkula M, Branquinha MH, dos Santos ALS, Grellier P, Morelli KA, d‘Avila-Levy CM. Analysing ambiguities in trypanosomatids taxonomy by barcoding. Mem Inst Oswaldo Cruz 2020; 115:e200504. [PMID: 32578684 PMCID: PMC7304411 DOI: 10.1590/0074-02760200504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/06/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Biodiversity screens and phylogenetic studies are dependent on reliable DNA sequences in public databases. Biological collections possess vouchered specimens with a traceable history. Therefore, DNA sequencing of samples available at institutional collections can greatly contribute to taxonomy, and studies on evolution and biodiversity. METHODS We sequenced part of the glycosomal glyceraldehyde phosphate dehydrogenase (gGAPDH) and the SSU rRNA (V7/V8) genes from 102 trypanosomatid cultures, which are available on request at www.colprot.fiocruz.br. OBJECTIVE The main objective of this work was to use phylogenetic inferences, using the obtained DNA sequences and those from representatives of all Trypanosomatidae genera, to generate phylogenetic trees that can simplify new isolates screenings. FINDINGS A DNA sequence is provided for the first time for several isolates, the phylogenetic analysis allowed the classification or reclassification of several specimens, identification of candidates for new genera and species, as well as the taxonomic validation of several deposits. MAIN CONCLUSIONS This survey aimed at presenting a list of validated species and their associated DNA sequences combined with a short historical overview of each isolate, which can support taxonomic and biodiversity research and promote culture collections.
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Affiliation(s)
- Carolina Boucinha
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Estudos Integrados em Protozoologia, Coleção de Protozoários da Fiocruz, Rio de Janeiro, RJ, Brasil
| | - Amanda R Caetano
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Estudos Integrados em Protozoologia, Coleção de Protozoários da Fiocruz, Rio de Janeiro, RJ, Brasil
| | - Helena LC Santos
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Estudos Integrados em Protozoologia, Coleção de Protozoários da Fiocruz, Rio de Janeiro, RJ, Brasil
| | - Raphael Helaers
- University of Louvain, de Duve Institute, Laboratory of Human Molecular Genetics, Brussels, Belgium
| | - Miikka Vikkula
- University of Louvain, de Duve Institute, Laboratory of Human Molecular Genetics, Brussels, Belgium
| | - Marta Helena Branquinha
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Rio de Janeiro, Brasil
| | | | - Philippe Grellier
- Muséum National d‘Histoire Naturelle, Unité Molécules de Communication et Adaptation des Microorganisme, Paris, France
| | - Karina Alessandra Morelli
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Estudos Integrados em Protozoologia, Coleção de Protozoários da Fiocruz, Rio de Janeiro, RJ, Brasil
- Universidade do Estado do Rio de Janeiro, Instituto de Biologia Roberto Alcântara Gomes, Departamento de Ecologia, Rio de Janeiro, RJ, Brasil
| | - Claudia Masini d‘Avila-Levy
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Estudos Integrados em Protozoologia, Coleção de Protozoários da Fiocruz, Rio de Janeiro, RJ, Brasil
- University of Louvain, de Duve Institute, Laboratory of Human Molecular Genetics, Brussels, Belgium
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28
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Škodová-Sveráková I, Záhonová K, Bučková B, Füssy Z, Yurchenko V, Lukeš J. Catalase and Ascorbate Peroxidase in Euglenozoan Protists. Pathogens 2020; 9:pathogens9040317. [PMID: 32344595 PMCID: PMC7237987 DOI: 10.3390/pathogens9040317] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 11/16/2022] Open
Abstract
In this work, we studied the biochemical properties and evolutionary histories of catalase (CAT) and ascorbate peroxidase (APX), two central enzymes of reactive oxygen species detoxification, across the highly diverse clade Eugenozoa. This clade encompasses free-living phototrophic and heterotrophic flagellates, as well as obligate parasites of insects, vertebrates, and plants. We present evidence of several independent acquisitions of CAT by horizontal gene transfers and evolutionary novelties associated with the APX presence. We posit that Euglenozoa recruit these detoxifying enzymes for specific molecular tasks, such as photosynthesis in euglenids and membrane-bound peroxidase activity in kinetoplastids and some diplonemids.
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Affiliation(s)
- Ingrid Škodová-Sveráková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic;
- Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Correspondence: (I.Š.-S.); (J.L.)
| | - Kristína Záhonová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic;
- Faculty of Science, Charles University, BIOCEV, 128 00 Prague, Czech Republic;
| | - Barbora Bučková
- Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
| | - Zoltán Füssy
- Faculty of Science, Charles University, BIOCEV, 128 00 Prague, Czech Republic;
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119435 Moscow, Russia
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic;
- Faculty of Sciences, University of South Bohemia, 370 05 České Budějovice (Budweis), Czech Republic
- Correspondence: (I.Š.-S.); (J.L.)
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Grybchuk D, Macedo DH, Kleschenko Y, Kraeva N, Lukashev AN, Bates PA, Kulich P, Leštinová T, Volf P, Kostygov AY, Yurchenko V. The First Non-LRV RNA Virus in Leishmania. Viruses 2020; 12:v12020168. [PMID: 32024293 PMCID: PMC7077295 DOI: 10.3390/v12020168] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 01/21/2020] [Accepted: 01/29/2020] [Indexed: 12/25/2022] Open
Abstract
In this work, we describe the first Leishmania-infecting leishbunyavirus-the first virus other than Leishmania RNA virus (LRV) found in trypanosomatid parasites. Its host is Leishmania martiniquensis, a human pathogen causing infections with a wide range of manifestations from asymptomatic to severe visceral disease. This virus (LmarLBV1) possesses many characteristic features of leishbunyaviruses, such as tripartite organization of its RNA genome, with ORFs encoding RNA-dependent RNA polymerase, surface glycoprotein, and nucleoprotein on L, M, and S segments, respectively. Our phylogenetic analyses suggest that LmarLBV1 originated from leishbunyaviruses of monoxenous trypanosomatids and, probably, is a result of genomic re-assortment. The LmarLBV1 facilitates parasites' infectivity in vitro in primary murine macrophages model. The discovery of a virus in L. martiniquensis poses the question of whether it influences pathogenicity of this parasite in vivo, similarly to the LRV in other Leishmania species.
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Affiliation(s)
- Danyil Grybchuk
- Life Science Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic; (D.G.); (D.H.M.); (N.K.)
- Central European Institute of Technology, Masaryk University, 60177 Brno, Czech Republic
| | - Diego H. Macedo
- Life Science Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic; (D.G.); (D.H.M.); (N.K.)
| | - Yulia Kleschenko
- Martsinovsky Institute of Medical Parasitology, Sechenov University, Moscow 119435, Russia, (A.N.L.)
| | - Natalya Kraeva
- Life Science Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic; (D.G.); (D.H.M.); (N.K.)
| | - Alexander N. Lukashev
- Martsinovsky Institute of Medical Parasitology, Sechenov University, Moscow 119435, Russia, (A.N.L.)
| | - Paul A. Bates
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YE, UK;
| | - Pavel Kulich
- Laboratory of Electron Microscopy, Veterinary Research Institute, 62100 Brno, Czech Republic;
| | - Tereza Leštinová
- Department of Parasitology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (T.L.); (P.V.)
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (T.L.); (P.V.)
| | - Alexei Y. Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic; (D.G.); (D.H.M.); (N.K.)
- Laboratory of Cellular and Molecular Protistology, Zoological Institute of the Russian Academy of Sciences, St. Petersburg 199034, Russia
- Correspondence: (A.Y.K.); (V.Y.)
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic; (D.G.); (D.H.M.); (N.K.)
- Martsinovsky Institute of Medical Parasitology, Sechenov University, Moscow 119435, Russia, (A.N.L.)
- Correspondence: (A.Y.K.); (V.Y.)
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LmxM.22.0250-Encoded Dual Specificity Protein/Lipid Phosphatase Impairs Leishmania mexicana Virulence In Vitro. Pathogens 2019; 8:pathogens8040241. [PMID: 31744234 PMCID: PMC6969907 DOI: 10.3390/pathogens8040241] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/08/2019] [Accepted: 11/13/2019] [Indexed: 11/30/2022] Open
Abstract
Protein phosphorylation/dephosphorylation is an important regulatory mechanism that controls many key physiological processes. Numerous pathogens successfully use kinases and phosphatases to internalize, replicate, and survive, modifying the host′s phosphorylation profile or signal transduction pathways. Multiple phosphatases and kinases from diverse bacterial pathogens have been implicated in human infections before. In this work, we have identified and characterized the dual specificity protein/lipid phosphatase LmDUSP1 as a novel virulence factor governing Leishmania mexicana infection. The LmDUSP1-encoding gene (LmxM.22.0250 in L. mexicana) has been acquired from bacteria via horizontal gene transfer. Importantly, its orthologues have been associated with virulence in several bacterial species, such as Mycobacterium tuberculosis and Listeria monocytogenes. Leishmania mexicana with ablated LmxM.22.0250 demonstrated severely attenuated virulence in the experimental infection of primary mouse macrophages, suggesting that this gene facilitates Leishmania pathogenicity in vertebrates. Despite significant upregulation of LmxM.22.0250 expression in metacyclic promastigotes, its ablation did not affect the ability of mutant cells to differentiate into virulent stages in insects. It remains to be further investigated which specific biochemical pathways involve LmDUSP1 and how this facilitates the parasite′s survival in the host. One of the interesting possibilities is that LmDUSP1 may target host′s substrate(s), thereby affecting its signal transduction pathways.
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Horáková E, Faktorová D, Kraeva N, Kaur B, Van Den Abbeele J, Yurchenko V, Lukeš J. Catalase compromises the development of the insect and mammalian stages of Trypanosoma brucei. FEBS J 2019; 287:964-977. [PMID: 31593329 DOI: 10.1111/febs.15083] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 06/21/2019] [Accepted: 10/04/2019] [Indexed: 12/14/2022]
Abstract
Catalase is a widespread heme-containing enzyme, which converts hydrogen peroxide (H2 O2 ) to water and molecular oxygen, thereby protecting cells from the toxic effects of H2 O2 . Trypanosoma brucei is an aerobic protist, which conspicuously lacks this potent enzyme, present in virtually all organisms exposed to oxidative stress. To uncover the reasons for its absence in T. brucei, we overexpressed different catalases in procyclic and bloodstream stages of the parasite. The heterologous enzymes originated from the related insect-confined trypanosomatid Crithidia fasciculata and the human. While the trypanosomatid enzyme (cCAT) operates at low temperatures, its human homolog (hCAT) is adapted to the warm-blooded environment. Despite the presence of peroxisomal targeting signal in hCAT, both human and C. fasciculata catalases localized to the cytosol of T. brucei. Even though cCAT was efficiently expressed in both life cycle stages, the enzyme was active in the procyclic stage, increasing cell's resistance to the H2 O2 stress, yet its activity was suppressed in the cultured bloodstream stage. Surprisingly, following the expression of hCAT, the ability to establish the T. brucei infection in the tsetse fly midgut was compromised. In the mouse model, hCAT attenuated parasitemia and, consequently, increased the host's survival. Hence, we suggest that the activity of catalase in T. brucei is beneficial in vitro, yet it becomes detrimental for parasite's proliferation in both invertebrate and vertebrate hosts, leading to an inability to carry this, otherwise omnipresent, enzyme.
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Affiliation(s)
- Eva Horáková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Drahomíra Faktorová
- 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
| | - Natalia Kraeva
- Life Science Research Centre, Faculty of Science, University of Ostrava, Czech Republic
| | - Binnypreet Kaur
- 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
| | - Jan Van Den Abbeele
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Czech Republic.,Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia
| | - 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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Butenko A, Kostygov AY, Sádlová J, Kleschenko Y, Bečvář T, Podešvová L, Macedo DH, Žihala D, Lukeš J, Bates PA, Volf P, Opperdoes FR, Yurchenko V. Comparative genomics of Leishmania (Mundinia). BMC Genomics 2019; 20:726. [PMID: 31601168 PMCID: PMC6787982 DOI: 10.1186/s12864-019-6126-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 09/20/2019] [Indexed: 12/31/2022] Open
Abstract
Background Trypanosomatids of the genus Leishmania are parasites of mammals or reptiles transmitted by bloodsucking dipterans. Many species of these flagellates cause important human diseases with clinical symptoms ranging from skin sores to life-threatening damage of visceral organs. The genus Leishmania contains four subgenera: Leishmania, Sauroleishmania, Viannia, and Mundinia. The last subgenus has been established recently and remains understudied, although Mundinia contains human-infecting species. In addition, it is interesting from the evolutionary viewpoint, representing the earliest branch within the genus and possibly with a different type of vector. Here we analyzed the genomes of L. (M.) martiniquensis, L. (M.) enriettii and L. (M.) macropodum to better understand the biology and evolution of these parasites. Results All three genomes analyzed were approximately of the same size (~ 30 Mb) and similar to that of L. (Sauroleishmania) tarentolae, but smaller than those of the members of subgenera Leishmania and Viannia, or the genus Endotrypanum (~ 32 Mb). This difference was explained by domination of gene losses over gains and contractions over expansions at the Mundinia node, although only a few of these genes could be identified. The analysis predicts significant changes in the Mundinia cell surface architecture, with the most important ones relating to losses of LPG-modifying side chain galactosyltransferases and arabinosyltransferases, as well as β-amastins. Among other important changes were gene family contractions for the oxygen-sensing adenylate cyclases and FYVE zinc finger-containing proteins. Conclusions We suggest that adaptation of Mundinia to different vectors and hosts has led to alternative host-parasite relationships and, thereby, made some proteins redundant. Thus, the evolution of genomes in the genus Leishmania and, in particular, in the subgenus Mundinia was mainly shaped by host (or vector) switches.
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Affiliation(s)
- Anzhelika Butenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.,Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budejovice (Budweis), Czech Republic
| | - Alexei Y Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.,Zoological Institute of the Russian Academy of Sciences, St Petersburg, Russia
| | - Jovana Sádlová
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Yuliya Kleschenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia
| | - Tomáš Bečvář
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Lucie Podešvová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Diego H Macedo
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - David Žihala
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Julius Lukeš
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budejovice (Budweis), Czech Republic.,Faculty of Sciences, University of South Bohemia, České Budejovice (Budweis), Czech Republic
| | - Paul A Bates
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, UK
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Fred R Opperdoes
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - 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.
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Evolutionary Insight into the Trypanosomatidae Using Alignment-Free Phylogenomics of the Kinetoplast. Pathogens 2019; 8:pathogens8030157. [PMID: 31540520 PMCID: PMC6789588 DOI: 10.3390/pathogens8030157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/10/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022] Open
Abstract
Advancements in next-generation sequencing techniques have led to a substantial increase in the genomic information available for analyses in evolutionary biology. As such, this data requires the exponential growth in bioinformatic methods and expertise required to understand such vast quantities of genomic data. Alignment-free phylogenomics offer an alternative approach for large-scale analyses that may have the potential to address these challenges. The evolutionary relationships between various species within the trypanosomatid family, specifically members belonging to the genera Leishmania and Trypanosoma have been extensively studies over the last 30 years. However, there is a need for a more exhaustive analysis of the Trypanosomatidae, summarising the evolutionary patterns amongst the entire family of these important protists. The mitochondrial DNA of the trypanosomatids, better known as the kinetoplast, represents a valuable taxonomic marker given its unique presence across all kinetoplastid protozoans. The aim of this study was to validate the reliability and robustness of alignment-free approaches for phylogenomic analyses and its applicability to reconstruct the evolutionary relationships between the trypanosomatid family. In the present study, alignment-free analyses demonstrated the strength of these methods, particularly when dealing with large datasets compared to the traditional phylogenetic approaches. We present a maxicircle genome phylogeny of 46 species spanning the trypanosomatid family, demonstrating the superiority of the maxicircle for the analysis and taxonomic resolution of the Trypanosomatidae.
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Abstract
In this study, we sequenced and analyzed the genomes of 40 strains, in addition to the already-reported two type strains, of two Crithidia species infecting bumblebees in Alaska and Central Europe and demonstrated that different strains of Crithidia bombi and C. expoeki vary considerably in terms of single nucleotide polymorphisms and gene copy number. Based on the genomic structure, phylogenetic analyses, and the pattern of copy number variation, we confirmed the status of C. expoeki as a separate species. The Alaskan populations appear to be clearly separated from those of Central Europe. This pattern fits a scenario of rapid host-parasite coevolution, where the selective advantage of a given parasite strain is only temporary. This study provides helpful insights into possible scenarios of selection and diversification of trypanosomatid parasites.IMPORTANCE A group of trypanosomatid flagellates includes several well-studied medically and economically important parasites of vertebrates and plants. Nevertheless, the vast majority of trypanosomatids infect only insects (mostly flies and true bugs) and, because of that, has attracted little research attention in the past. Of several hundred trypanosomatid species, only four can infect bees (honeybees and bumblebees). Because of such scarcity, these parasites are severely understudied. We analyzed whole-genome information for a total of 42 representatives of bee-infecting trypanosomatids collected in Central Europe and Alaska from a population genetics point of view. Our data shed light on the evolution, selection, and diversification in this important group of trypanosomatid parasites.
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Klatt S, Simpson L, Maslov DA, Konthur Z. Leishmania tarentolae: Taxonomic classification and its application as a promising biotechnological expression host. PLoS Negl Trop Dis 2019; 13:e0007424. [PMID: 31344033 PMCID: PMC6657821 DOI: 10.1371/journal.pntd.0007424] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In this review, we summarize the current knowledge concerning the eukaryotic protozoan parasite Leishmania tarentolae, with a main focus on its potential for biotechnological applications. We will also discuss the genus, subgenus, and species-level classification of this parasite, its life cycle and geographical distribution, and similarities and differences to human-pathogenic species, as these aspects are relevant for the evaluation of biosafety aspects of L. tarentolae as host for recombinant DNA/protein applications. Studies indicate that strain LEM-125 but not strain TARII/UC of L. tarentolae might also be capable of infecting mammals, at least transiently. This could raise the question of whether the current biosafety level of this strain should be reevaluated. In addition, we will summarize the current state of biotechnological research involving L. tarentolae and explain why this eukaryotic parasite is an advantageous and promising human recombinant protein expression host. This summary includes overall biotechnological applications, insights into its protein expression machinery (especially on glycoprotein and antibody fragment expression), available expression vectors, cell culture conditions, and its potential as an immunotherapy agent for human leishmaniasis treatment. Furthermore, we will highlight useful online tools and, finally, discuss possible future applications such as the humanization of the glycosylation profile of L. tarentolae or the expression of mammalian recombinant proteins in amastigote-like cells of this species or in amastigotes of avirulent human-pathogenic Leishmania species.
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Affiliation(s)
- Stephan Klatt
- Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- * E-mail: (SK); (ZK)
| | - Larry Simpson
- Department of Microbiology, Immunology and Molecular Genetics, Geffen School of Medicine at UCLA, University of California, Los Angeles, California, United States of America
| | - Dmitri A. Maslov
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, California, United States of America
| | - Zoltán Konthur
- Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- * E-mail: (SK); (ZK)
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Maslov DA. Separating the Wheat from the Chaff: RNA Editing and Selection of Translatable mRNA in Trypanosome Mitochondria. Pathogens 2019; 8:pathogens8030105. [PMID: 31323762 PMCID: PMC6789859 DOI: 10.3390/pathogens8030105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/14/2019] [Accepted: 07/16/2019] [Indexed: 11/16/2022] Open
Abstract
In the mitochondria of trypanosomes and related kinetoplastid protists, most mRNAs undergo a long and sophisticated maturation pathway before they can be productively translated by mitochondrial ribosomes. Some of the aspects of this pathway (identity of the promotors, transcription initiation, and termination signals) remain obscure, and some (post-transcriptional modification by U-insertion/deletion, RNA editing, 3′-end maturation) have been illuminated by research during the last decades. The RNA editing creates an open reading frame for a productive translation, but the fully edited mRNA often represents a minor fraction in the pool of pre-edited and partially edited precursors. Therefore, it has been expected that the final stages of the mRNA processing generate molecular hallmarks, which allow for the efficient and selective recognition of translation-competent templates. The general contours and several important details of this process have become known only recently and represent the subject of this review.
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Affiliation(s)
- Dmitri A Maslov
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA 92521, USA.
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Abstract
Phylogenetics is an important component of the systems biology approach. Knowledge about evolution of the genus Leishmania is essential to understand various aspects of basic biology of these parasites, such as parasite-host or parasite-vector relationships, biogeography, or epidemiology. Here, we present a comprehensive guideline for performing phylogenetic studies based on DNA sequence data, but with principles that can be adapted to protein sequences or other molecular markers. It is presented as a compilation of the most commonly used genetic targets for phylogenetic studies of Leishmania, including their respective primers for amplification and references, as well as details of PCR assays. Guidelines are, then, presented to choose the best targets in relation to the types of samples under study. Finally, and importantly, instructions are given to obtain optimal sequences, alignments, and datasets for the subsequent data analysis and phylogenetic inference. Different bioinformatics methods and software for phylogenetic inference are presented and explained. This chapter aims to provide a compilation of methods and generic guidelines to conduct phylogenetics of Leishmania for nonspecialists.
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Affiliation(s)
- Katrin Kuhls
- Molekulare Biotechnologie und Funktionelle Genomik, Technische Hochschule Wildau, Wildau, Germany.
| | - Isabel Mauricio
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisbon, Portugal
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Ceccarelli M, Diotallevi A, Andreoni F, Vitale F, Galluzzi L, Magnani M. Exploiting genetic polymorphisms in metabolic enzymes for rapid screening of Leishmania infantum genotypes. Parasit Vectors 2018; 11:572. [PMID: 30382928 PMCID: PMC6211443 DOI: 10.1186/s13071-018-3143-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 10/10/2018] [Indexed: 11/30/2022] Open
Abstract
Background Leishmania infantum is the aetiological agent of visceral leishmaniasis (VL) and cutaneous leishmaniasis (CL). Numerous strains and/or zymodemes have been identified and characterized by multilocus enzyme electrophoresis (MLEE). MLEE is considered the reference method for L. infantum parasite typing and it is based upon enzyme electrophoretic mobility analysis from promastigote cultures. However, the MLEE technique is cumbersome, time-consuming and does not detect silent genetic mutations or nucleotide changes that give rise to amino acid changes that do not alter electrophoretic mobility. As a result of these difficulties, many DNA-based typing methods have been developed over the past few years. However, relative to the enzymes utilized in MLEE analysis, we observed a shortage of DNA sequences available in the GenBank database or an absolute lack of sequences belonging to specific zymodemes. The aims of the present study were to (i) implement the number of sequences coding for metabolic enzymes used in MLEE; (ii) identify polymorphisms that characterize L. infantum zymodemes most prevalent in the Mediterranean basin; and (iii) exploit these polymorphisms to develop a rapid screening test that would give results comparable with existing MLEE typing. Results Partial sequences of seven metabolic enzyme genes (malic enzyme, 6-phosphogluconate dehydrogenase, mitochondrial isocitrate dehydrogenase, glucose-6-phosphate isomerase, glucose-6-phosphate dehydrogenase, phosphoglucomutase and mannose phosphate isomerase) were obtained from 11 L. infantum strains. The comparison of these sequences with those obtained from GenBank allowed for the identification of a few polymorphisms that could distinguish several zymodemes. In particular, the polymorphism 390T>G in the malic enzyme gene has been exploited to develop a high-resolution melt (HRM)-based assay to rapidly differentiate the genotype 390T, associated with zymodemes MON-1, MON-72 and MON-201, evidencing a partial agreement between genotyping results and MLEE. The assay has been successfully applied to L. infantum clinical isolates and clinical samples. Conclusions A HRM-based assay for rapid identification of genotypes associated with the most common L. infantum zymodemes in the Mediterranean basin has been developed and its potential application in epidemiological research for L. infantum population screening, without parasite isolation and culturing, has been demonstrated. Electronic supplementary material The online version of this article (10.1186/s13071-018-3143-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marcello Ceccarelli
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, PU, Italy
| | - Aurora Diotallevi
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, PU, Italy
| | - Francesca Andreoni
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, PU, Italy
| | - Fabrizio Vitale
- Istituto Zooprofilattico Sperimentale of Sicily "A Mirri", Palermo, PA, Italy
| | - Luca Galluzzi
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, PU, Italy.
| | - Mauro Magnani
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, PU, Italy
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Grybchuk D, Kostygov AY, Macedo DH, Votýpka J, Lukeš J, Yurchenko V. RNA Viruses in Blechomonas (Trypanosomatidae) and Evolution of Leishmaniavirus. mBio 2018; 9:e01932-18. [PMID: 30327446 PMCID: PMC6191543 DOI: 10.1128/mbio.01932-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 09/11/2018] [Indexed: 01/25/2023] Open
Abstract
In this work, we analyzed viral prevalence in trypanosomatid parasites (Blechomonas spp.) infecting Siphonaptera and discovered nine species of viruses from three different groups (leishbunyaviruses, narnaviruses, and leishmaniaviruses). Most of the flagellate isolates bore two or three viral types (mixed infections). Although no new viral groups were documented in Blechomonas spp., our findings are important for the comprehension of viral evolution. The discovery of bunyaviruses in blechomonads was anticipated, since these viruses have envelopes facilitating their interspecific transmission and have already been found in various trypanosomatids and metatranscriptomes with trypanosomatid signatures. In this work, we also provided evidence that even representatives of the family Narnaviridae are capable of host switching and evidently have accomplished switches multiple times in the course of their evolution. The most unexpected finding was the presence of leishmaniaviruses, a group previously solely confined to the human pathogens Leishmania spp. From phylogenetic inferences and analyses of the life cycles of Leishmania and Blechomonas, we concluded that a common ancestor of leishmaniaviruses most likely infected Leishmania first and was acquired by Blechomonas by horizontal transfer. Our findings demonstrate that evolution of leishmaniaviruses is more complex than previously thought and includes occasional host switching.IMPORTANCE Flagellates belonging to the genus Leishmania are important human parasites. Some strains of different Leishmania species harbor viruses (leishmaniaviruses), which facilitate metastatic spread of the parasites, thus aggravating the disease. Up until now, these viruses were known to be hosted only by Leishmania Here, we analyzed viral distribution in Blechomonas, a related group of flagellates parasitizing fleas, and revealed that they also bear leishmaniaviruses. Our findings shed light on the entangled evolution of these viruses. In addition, we documented that Blechomonas can be also infected by leishbunyaviruses and narnaviruses, viral groups known from other insects' flagellates.
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Affiliation(s)
- Danyil Grybchuk
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Alexei Y Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Diego H Macedo
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jan Votýpka
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budejovice (Budweis), Czech Republic
| | - Julius Lukeš
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budejovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budejovice (Budweis), Czech Republic
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budejovice (Budweis), Czech Republic
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia
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Recent advances in trypanosomatid research: genome organization, expression, metabolism, taxonomy and evolution. Parasitology 2018; 146:1-27. [PMID: 29898792 DOI: 10.1017/s0031182018000951] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Unicellular flagellates of the family Trypanosomatidae are obligatory parasites of invertebrates, vertebrates and plants. Dixenous species are aetiological agents of a number of diseases in humans, domestic animals and plants. Their monoxenous relatives are restricted to insects. Because of the high biological diversity, adaptability to dramatically different environmental conditions, and omnipresence, these protists have major impact on all biotic communities that still needs to be fully elucidated. In addition, as these organisms represent a highly divergent evolutionary lineage, they are strikingly different from the common 'model system' eukaryotes, such as some mammals, plants or fungi. A number of excellent reviews, published over the past decade, were dedicated to specialized topics from the areas of trypanosomatid molecular and cell biology, biochemistry, host-parasite relationships or other aspects of these fascinating organisms. However, there is a need for a more comprehensive review that summarizing recent advances in the studies of trypanosomatids in the last 30 years, a task, which we tried to accomplish with the current paper.
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Trypanosomatids Are Much More than Just Trypanosomes: Clues from the Expanded Family Tree. Trends Parasitol 2018; 34:466-480. [PMID: 29605546 DOI: 10.1016/j.pt.2018.03.002] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 02/17/2018] [Accepted: 03/02/2018] [Indexed: 11/22/2022]
Abstract
Trypanosomes and leishmanias are widely known parasites of humans. However, they are just two out of several phylogenetic lineages that constitute the family Trypanosomatidae. Although dixeny - the ability to infect two hosts - is a derived trait of vertebrate-infecting parasites, the majority of trypanosomatids are monoxenous. Like their common ancestor, the monoxenous Trypanosomatidae are mostly parasites or commensals of insects. This review covers recent advances in the study of insect trypanosomatids, highlighting their diversity as well as genetic, morphological and biochemical complexity, which, until recently, was underappreciated. The investigation of insect trypanosomatids is providing an important foundation for understanding the origin and evolution of parasitism, including colonization of vertebrates and the appearance of human pathogens.
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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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Schmid-Hempel P, Aebi M, Barribeau S, Kitajima T, du Plessis L, Schmid-Hempel R, Zoller S. The genomes of Crithidia bombi and C. expoeki, common parasites of bumblebees. PLoS One 2018; 13:e0189738. [PMID: 29304093 PMCID: PMC5755769 DOI: 10.1371/journal.pone.0189738] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 11/30/2017] [Indexed: 11/19/2022] Open
Abstract
Trypanosomatids (Trypanosomatidae, Kinetoplastida) are flagellated protozoa containing many parasites of medical or agricultural importance. Among those, Crithidia bombi and C. expoeki, are common parasites in bumble bees around the world, and phylogenetically close to Leishmania and Leptomonas. They have a simple and direct life cycle with one host, and partially castrate the founding queens greatly reducing their fitness. Here, we report the nuclear genome sequences of one clone of each species, extracted from a field-collected infection. Using a combination of Roche 454 FLX Titanium, Pacific Biosciences PacBio RS, and Illumina GA2 instruments for C. bombi, and PacBio for C. expoeki, we could produce high-quality and well resolved sequences. We find that these genomes are around 32 and 34 MB, with 7,808 and 7,851 annotated genes for C. bombi and C. expoeki, respectively-which is somewhat less than reported from other trypanosomatids, with few introns, and organized in polycistronic units. A large fraction of genes received plausible functional support in comparison primarily with Leishmania and Trypanosoma. Comparing the annotated genes of the two species with those of six other trypanosomatids (C. fasciculata, L. pyrrhocoris, L. seymouri, B. ayalai, L. major, and T. brucei) shows similar gene repertoires and many orthologs. Similar to other trypanosomatids, we also find signs of concerted evolution in genes putatively involved in the interaction with the host, a high degree of synteny between C. bombi and C. expoeki, and considerable overlap with several other species in the set. A total of 86 orthologous gene groups show signatures of positive selection in the branch leading to the two Crithidia under study, mostly of unknown function. As an example, we examined the initiating glycosylation pathway of surface components in C. bombi, finding it deviates from most other eukaryotes and also from other kinetoplastids, which may indicate rapid evolution in the extracellular matrix that is involved in interactions with the host. Bumble bees are important pollinators and Crithidia-infections are suspected to cause substantial selection pressure on their host populations. These newly sequenced genomes provide tools that should help better understand host-parasite interactions in these pollinator pathogens.
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Affiliation(s)
| | - Markus Aebi
- Institute of Microbiology, ETH Zurich, Zürich, Switzerland
| | - Seth Barribeau
- Institute of Integrative Biology (IBZ), ETH Zurich, Zürich, Switzerland
| | | | - Louis du Plessis
- Institute of Integrative Biology (IBZ), ETH Zurich, Zürich, Switzerland
| | | | - Stefan Zoller
- Genetic Diversity Centre (GDC), ETH Zurich, Zürich, Switzerland
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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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