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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, Albanaz ATS, Butenko A, Gerasimov ES, Lukeš J, Yurchenko V. Phylogenetic framework to explore trait evolution in Trypanosomatidae. Trends Parasitol 2024; 40:96-99. [PMID: 38065790 DOI: 10.1016/j.pt.2023.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/23/2023] [Accepted: 11/23/2023] [Indexed: 02/10/2024]
Abstract
The number of sequenced trypanosomatid genomes has reached a critical point so that they are now available for almost all genera and subgenera. Based on this, we inferred a phylogenomic tree and propose it as a framework to study trait evolution together with some examples of how to do it.
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Affiliation(s)
- Alexei Yu Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia.
| | - Amanda T S Albanaz
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia
| | - Anzhelika Butenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia; Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budějovice, Czechia; Faculty of Sciences, University of South Bohemia, 370 05 České Budějovice, Czechia
| | - Evgeny S Gerasimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Julius Lukeš
- Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budějovice, Czechia; Faculty of Sciences, University of South Bohemia, 370 05 České Budějovice, Czechia
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia.
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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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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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5
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Takamiya NT, Rogerio LA, Torres C, Leonel JAF, Vioti G, de Sousa Oliveira TMF, Valeriano KC, Porcino GN, de Miranda Santos IKF, Costa CHN, Costa DL, Ferreira TS, Gurgel-Gonçalves R, da Silva JS, Teixeira FR, De Almeida RP, Ribeiro JMC, Maruyama SR. Parasite Detection in Visceral Leishmaniasis Samples by Dye-Based qPCR Using New Gene Targets of Leishmania infantum and Crithidia. Trop Med Infect Dis 2023; 8:405. [PMID: 37624343 PMCID: PMC10457869 DOI: 10.3390/tropicalmed8080405] [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: 07/03/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
Visceral leishmaniasis (VL) is a neglected disease considered a serious public health problem, especially in endemic countries. Several studies have discovered monoxenous trypanosomatids (Leptomonas and Crithidia) in patients with VL. In different situations of leishmaniasis, investigations have examined cases of co-infection between Leishmania spp. and Crithidia spp. These coinfections have been observed in a wide range of vertebrate hosts, indicating that they are not rare. Diagnostic techniques require improvements and more robust tools to accurately detect the causative agent of VL. This study aimed to develop a real-time quantitative dye-based PCR (qPCR) assay capable of distinguishing Leishmania infantum from Crithidia-related species and to estimate the parasite load in samples of VL from humans and animals. The primer LinJ31_2420 targets an exclusive phosphatase of L. infantum; the primer Catalase_LVH60-12060_1F targets the catalase gene of Crithidia. Therefore, primers were designed to detect L. infantum and Crithidia sp. LVH60A (a novel trypanosomatid isolated from VL patients in Brazil), in samples related to VL. These primers were considered species-specific, based on sequence analysis using genome data retrieved from the TriTryp database and the genome assembling of Crithidia sp. LVH60A strain, in addition to experimental and clinical data presented herein. This novel qPCR assay was highly accurate in identifying and quantifying L. infantum and Crithidia sp. LVH60A in samples obtained experimentally (in vitro and in vivo) or collected from hosts (humans, dogs, cats, and vectors). Importantly, the screening of 62 cultured isolates from VL patients using these primers surprisingly revealed that 51 parasite cultures were PCR+ for Crithidia sp. In addition, qPCR assays identified the co-infection of L. infantum with Crithidia sp. LVH60A in two new VL cases in Brazil, confirming the suspicion of co-infection in a previously reported case of fatal VL. We believe that the species-specific genes targeted in this study can be helpful for the molecular diagnosis of VL, as well as for elucidating suspected co-infections with monoxenous-like trypanosomatids, which is a neglected fact of a neglected disease.
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Affiliation(s)
- Nayore Tamie Takamiya
- Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos (UFSCar), São Carlos 13565-905, SP, Brazil; (N.T.T.); (F.R.T.)
| | - Luana Aparecida Rogerio
- Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos (UFSCar), São Carlos 13565-905, SP, Brazil; (N.T.T.); (F.R.T.)
| | - Caroline Torres
- Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos (UFSCar), São Carlos 13565-905, SP, Brazil; (N.T.T.); (F.R.T.)
| | - João Augusto Franco Leonel
- Post-Graduate Program in Experimental Epidemiology Applied to Zoonoses at the Faculty of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo 05508-270, SP, Brazil
| | - Geovanna Vioti
- Post-Graduate Program in Experimental Epidemiology Applied to Zoonoses at the Faculty of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo 05508-270, SP, Brazil
| | - Tricia Maria Ferreira de Sousa Oliveira
- Post-Graduate Program in Experimental Epidemiology Applied to Zoonoses at the Faculty of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo 05508-270, SP, Brazil
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga 13635-900, SP, Brazil
| | - Karoline Camila Valeriano
- Ribeirão Preto Medical School, University of São Paulo, FMRP-USP, Ribeirão Preto 14049-900, SP, Brazil
| | | | | | - Carlos H. N. Costa
- Natan Portela Institute of Tropical Diseases, Teresina 64002-510, PI, Brazil
| | | | - Tauana Sousa Ferreira
- Laboratory of Medical Parasitology and Vector Biology, Faculty of Medicine, University of Brasília, Brasília 70910-900, DF, Brazil
| | - Rodrigo Gurgel-Gonçalves
- Laboratory of Medical Parasitology and Vector Biology, Faculty of Medicine, University of Brasília, Brasília 70910-900, DF, Brazil
| | - João Santana da Silva
- Fiocruz-Bi-Institutional Translational Medicine Project, Oswaldo Cruz Foundation, Ribeirão Preto 14040-900, SP, Brazil
| | - Felipe Roberti Teixeira
- Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos (UFSCar), São Carlos 13565-905, SP, Brazil; (N.T.T.); (F.R.T.)
| | - Roque Pacheco De Almeida
- Department of Medicine, Center for Biology and Health Sciences, Federal University of Sergipe (UFS), Aracaju 49060-108, SE, Brazil
| | - José M. C. Ribeiro
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, NIH/NIAID, Rockville, MD 20892, USA
| | - Sandra Regina Maruyama
- Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos (UFSCar), São Carlos 13565-905, SP, Brazil; (N.T.T.); (F.R.T.)
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Gerasimov ES, Novozhilova TS, Zimmer SL, Yurchenko V. Kinetoplast Genome of Leishmania spp. Is under Strong Purifying Selection. Trop Med Infect Dis 2023; 8:384. [PMID: 37624322 PMCID: PMC10458658 DOI: 10.3390/tropicalmed8080384] [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: 06/28/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
Instability is an intriguing characteristic of many protist genomes, and trypanosomatids are not an exception in this respect. Some regions of trypanosomatid genomes evolve fast. For instance, the trypanosomatid mitochondrial (kinetoplast) genome consists of fairly conserved maxicircle and minicircle molecules that can, nevertheless, possess high nucleotide substitution rates between closely related strains. Recent experiments have demonstrated that rapid laboratory evolution can result in the non-functionality of multiple genes of kinetoplast genomes due to the accumulation of mutations or loss of critical genomic components. An example of a loss of critical components is the reported loss of entire minicircle classes in Leishmania tarentolae during laboratory cultivation, which results in an inability to generate some correctly encoded genes. In the current work, we estimated the evolutionary rates of mitochondrial and nuclear genome regions of multiple natural Leishmania spp. We analyzed synonymous and non-synonymous substitutions and, rather unexpectedly, found that the coding regions of kinetoplast maxicircles are among the most variable regions of both genomes. In addition, we demonstrate that synonymous substitutions greatly predominate among maxicircle coding regions and that most maxicircle genes show signs of purifying selection. These results imply that maxicircles in natural Leishmania populations remain functional despite their high mutation rate.
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Affiliation(s)
- Evgeny S. Gerasimov
- Department of Molecular Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, 127051 Moscow, Russia
| | - Tatiana S. Novozhilova
- Department of Molecular Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Sara L. Zimmer
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, Duluth, MN 55812, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
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Anti-Trypanosomatidae Activity of Essential Oils and Their Main Components from Selected Medicinal Plants. Molecules 2023; 28:molecules28031467. [PMID: 36771132 PMCID: PMC9920086 DOI: 10.3390/molecules28031467] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Kinetoplastida is a group of flagellated protozoa characterized by the presence of a kinetoplast, a structure which is part of a large mitochondria and contains DNA. Parasites of this group include genera such as Leishmania, that cause disease in humans and animals, and Phytomonas, that are capable of infecting plants. Due to the lack of treatments, the low efficacy, or the high toxicity of the employed therapeutic agents there is a need to seek potential alternative treatments. In the present work, the antiparasitic activity on Leishmania infantum and Phytomonas davidi of 23 essential oils (EOs) from plants of the Lamiaceae and Asteraceae families, extracted by hydrodistillation (HD) at laboratory scale and steam distillation (SD) in a pilot plant, were evaluated. The chemical compositions of the EOs were determined by gas chromatography-mass spectrometry. Additionally, the cytotoxic activity on mammalian cells of the major components from the most active EOs was evaluated, and their anti-Phytomonas and anti-Leishmania effects analyzed. L. infantum was more sensitive to the EOs than P. davidi. The EOs with the best anti-kinetoplastid activity were S. montana, T. vulgaris, M. suaveolens, and L. luisieri. Steam distillation increased the linalyl acetate, β-caryophyllene, and trans-α-necrodyl acetate contents of the EOs, and decreased the amount of borneol and 1,8 cineol. The major active components of the EOs were tested, with thymol being the strongest anti-Phytomonas compound followed by carvacrol. Our study identified potential treatments against kinetoplastids.
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8
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Zakharova A, Albanaz ATS, Opperdoes FR, Škodová-Sveráková I, Zagirova D, Saura A, Chmelová L, Gerasimov ES, Leštinová T, Bečvář T, Sádlová J, Volf P, Lukeš J, Horváth A, Butenko A, Yurchenko V. Leishmania guyanensis M4147 as a new LRV1-bearing model parasite: Phosphatidate phosphatase 2-like protein controls cell cycle progression and intracellular lipid content. PLoS Negl Trop Dis 2022; 16:e0010510. [PMID: 35749562 PMCID: PMC9232130 DOI: 10.1371/journal.pntd.0010510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/17/2022] [Indexed: 12/11/2022] Open
Abstract
Leishmaniasis is a parasitic vector-borne disease caused by the protistan flagellates of the genus Leishmania. Leishmania (Viannia) guyanensis is one of the most common causative agents of the American tegumentary leishmaniasis. It has previously been shown that L. guyanensis strains that carry the endosymbiotic Leishmania RNA virus 1 (LRV1) cause more severe form of the disease in a mouse model than those that do not. The presence of the virus was implicated into the parasite’s replication and spreading. In this respect, studying the molecular mechanisms of cellular control of viral infection is of great medical importance. Here, we report ~30.5 Mb high-quality genome assembly of the LRV1-positive L. guyanensis M4147. This strain was turned into a model by establishing the CRISPR-Cas9 system and ablating the gene encoding phosphatidate phosphatase 2-like (PAP2L) protein. The orthologue of this gene is conspicuously absent from the genome of an unusual member of the family Trypanosomatidae, Vickermania ingenoplastis, a species with mostly bi-flagellated cells. Our analysis of the PAP2L-null L. guyanensis showed an increase in the number of cells strikingly resembling the bi-flagellated V. ingenoplastis, likely as a result of the disruption of the cell cycle, significant accumulation of phosphatidic acid, and increased virulence compared to the wild type cells. Worldwide, over one million people are getting infected by the parasitic flagellates of the genus Leishmania annually leading to ~30,000 deaths. Notably, there is still no approved vaccine against human leishmaniases. A range of methods of forward and reverse genetics has recently been developed for several model Leishmania species. Unfortunately, these methods are often not transferrable to non-model species, which may be of even greater medical importance. Leishmania guyanensis is one of such cases. It frequently carries a symbiotic RNA virus that contributes to the development of a more aggressive form of leishmaniasis in an experimental murine model. In order to establish and optimize the system for genetic manipulations in L. guyanensis, we sequenced and annotated its genome. Next, we applied the CRISPR-Cas9 technology to target a gene of interest. This approach was validated by ablating a gene encoding a protein involved in lipid metabolism. In this work, we document that deletion of this gene leads to the disturbance of cell cycle and affects the ratio of critical intracellular lipids. We believe that our study will facilitate research into more effective treatment of leishmaniases.
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Affiliation(s)
- Alexandra Zakharova
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Amanda T. S. Albanaz
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Fred R. Opperdoes
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Ingrid Škodová-Sveráková
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Diana Zagirova
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Andreu Saura
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Lˇubomíra Chmelová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Evgeny S. Gerasimov
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Tereza Leštinová
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tomáš Bečvář
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jovana Sádlová
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - 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
| | - Anton Horváth
- Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Anzhelika Butenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- 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
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- * E-mail:
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Mutation Characteristics and Phylogenetic Analysis of Five Leishmania Clinical Isolates. Animals (Basel) 2022; 12:ani12030321. [PMID: 35158645 PMCID: PMC8833617 DOI: 10.3390/ani12030321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/19/2022] [Accepted: 01/24/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Leishmaniasis, a neglected tropical disease, is caused by infection with the Leishmania species, threatening millions of people in approximately 100 endemic countries. The emergence of antimony-resistant Leishmania strains have brought difficulties to the treatment and elimination of leishmaniasis. This study performed genome-wide resequencing and phylogenetic analysis of five isolates from the Leishmania donovani complex, focusing on finding mutations related to antimony resistance and virulence of the newly isolated Leishmania strain L_HCZ in 2016. By combining whole-genome sequencing and whole-genome phylogenetic analysis, Leishmania isolates L_801, L_9044 and L_Liu were identified as Leishmania donovani, and L_HCZ as Leishmania infantum. By discovering genome-wide single-nucleotide polymorphisms and structural variations, we identified mutations of drug resistance-related genes in the antimony-resistant Leishmania isolate L_HCZ. The new Leishmania isolate L_HCZ has strong virulence and strong drug resistance, which should be taken seriously by the relevant health departments and scientific researchers. Abstract Leishmaniasis is a neglected tropical disease threatening millions of people worldwide. The emergence of antimony-resistant Leishmania strains have brought difficulties to the treatment and elimination of leishmaniasis. This study performed genome sequencing, phylogenetic analysis and mutation analysis of five Leishmania clinical isolates, especially the Leishmania strain L_HCZ isolated in 2016, which shows strong virulence and antimony resistance. By phylogenetic analysis, four isolates (L_DD8, L_801, L_Liu and L_9044) were identified as Leishmania donovani, the isolate L_HCZ was identified as Leishmania infantum and the isolate L_DD8 as a standard strain of L.donovani. Genome-wide mutation analysis was applied to identify mutations related to the drug resistance and virulence of the newly isolated L_HCZ. Compared with the other four Leishmania isolates, L_HCZ had the most mutations in genes associated with antimony resistance, including the ABC transporter, ascorbate-dependent peroxidase, gamma–glutamylcysteine synthetase, glucose-6-phosphate 1-dehydrogenase, ATP-binding cassette protein subfamily A and multi-drug resistance protein-like genes. Among the genes associated with virulence, L_HCZ had the most mutations in cysteine peptidase A, cysteine peptidase B, cysteine peptidase C, heat-shock protein 70, gp63, acid phosphatase, kinesin k39, kinesin, phosphoglycan beta 1, amastin-like surface protein and amastin-like proteins. The mutations in L_HCZ might possibly contribute to its antimony resistance and strong virulence in clinical patients. Whole-genome resequencing has exhibited broad application prospects and may be put into clinical use in the future for parasite identifying and epidemiological investigations.
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Chmelová Ľ, Bianchi C, Albanaz ATS, Režnarová J, Wheeler R, Kostygov AY, Kraeva N, Yurchenko V. Comparative Analysis of Three Trypanosomatid Catalases of Different Origin. Antioxidants (Basel) 2021; 11:46. [PMID: 35052550 PMCID: PMC8773446 DOI: 10.3390/antiox11010046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/16/2021] [Accepted: 12/23/2021] [Indexed: 11/16/2022] Open
Abstract
Most trypanosomatid flagellates do not have catalase. In the evolution of this group, the gene encoding catalase has been independently acquired at least three times from three different bacterial groups. Here, we demonstrate that the catalase of Vickermania was obtained by horizontal gene transfer from Gammaproteobacteria, extending the list of known bacterial sources of this gene. Comparative biochemical analyses revealed that the enzymes of V. ingenoplastis, Leptomonas pyrrhocoris, and Blastocrithidia sp., representing the three independent catalase-bearing trypanosomatid lineages, have similar properties, except for the unique cyanide resistance in the catalase of the latter species.
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Affiliation(s)
- Ľubomíra Chmelová
- Life Science Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic; (Ľ.C.); (C.B.); (A.T.S.A.); (J.R.); (A.Y.K.); (N.K.)
| | - Claretta Bianchi
- Life Science Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic; (Ľ.C.); (C.B.); (A.T.S.A.); (J.R.); (A.Y.K.); (N.K.)
| | - Amanda T. S. Albanaz
- Life Science Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic; (Ľ.C.); (C.B.); (A.T.S.A.); (J.R.); (A.Y.K.); (N.K.)
| | - Jana Režnarová
- Life Science Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic; (Ľ.C.); (C.B.); (A.T.S.A.); (J.R.); (A.Y.K.); (N.K.)
| | - Richard Wheeler
- Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK;
| | - Alexei Yu. Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic; (Ľ.C.); (C.B.); (A.T.S.A.); (J.R.); (A.Y.K.); (N.K.)
- Zoological Institute of the Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Natalya Kraeva
- Life Science Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic; (Ľ.C.); (C.B.); (A.T.S.A.); (J.R.); (A.Y.K.); (N.K.)
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic; (Ľ.C.); (C.B.); (A.T.S.A.); (J.R.); (A.Y.K.); (N.K.)
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119435 Moscow, Russia
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