1
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Afonin DA, Gerasimov ES, Škodová-Sveráková I, Záhonová K, Gahura O, Albanaz ATS, Myšková E, Bykova A, Paris Z, Lukeš J, Opperdoes FR, Horváth A, Zimmer SL, Yurchenko V. Blastocrithidia nonstop mitochondrial genome and its expression are remarkably insulated from nuclear codon reassignment. Nucleic Acids Res 2024; 52:3870-3885. [PMID: 38452217 DOI: 10.1093/nar/gkae168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
The canonical stop codons of the nuclear genome of the trypanosomatid Blastocrithidia nonstop are recoded. Here, we investigated the effect of this recoding on the mitochondrial genome and gene expression. Trypanosomatids possess a single mitochondrion and protein-coding transcripts of this genome require RNA editing in order to generate open reading frames of many transcripts encoded as 'cryptogenes'. Small RNAs that can number in the hundreds direct editing and produce a mitochondrial transcriptome of unusual complexity. We find B. nonstop to have a typical trypanosomatid mitochondrial genetic code, which presumably requires the mitochondrion to disable utilization of the two nucleus-encoded suppressor tRNAs, which appear to be imported into the organelle. Alterations of the protein factors responsible for mRNA editing were also documented, but they have likely originated from sources other than B. nonstop nuclear genome recoding. The population of guide RNAs directing editing is minimal, yet virtually all genes for the plethora of known editing factors are still present. Most intriguingly, despite lacking complex I cryptogene guide RNAs, these cryptogene transcripts are stochastically edited to high levels.
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MESH Headings
- Genome, Mitochondrial
- RNA Editing
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Open Reading Frames/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Trypanosomatina/genetics
- Trypanosomatina/metabolism
- Codon/genetics
- Mitochondria/genetics
- Mitochondria/metabolism
- Codon, Terminator/genetics
- RNA, Guide, Kinetoplastida/genetics
- RNA, Guide, Kinetoplastida/metabolism
- Genetic Code
- Protozoan Proteins/genetics
- Protozoan Proteins/metabolism
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Affiliation(s)
- Dmitry A Afonin
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Evgeny S Gerasimov
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russia
| | - Ingrid Škodová-Sveráková
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czechia
| | - Kristína Záhonová
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czechia
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV 252 50 Vestec, Czechia
- Division of Infectious Diseases, Department of Medicine, University of Alberta, T6G 2R3 Edmonton, Alberta, Canada
| | - Ondřej Gahura
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czechia
| | - Amanda T S Albanaz
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia
| | - Eva Myšková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czechia
| | - Anastassia Bykova
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia
| | - Zdeněk Paris
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czechia
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czechia
| | - Fred R Opperdoes
- De Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Anton Horváth
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia
| | - Sara L Zimmer
- 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, Czechia
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2
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Tannières M, Breugnot D, Bon MC, Grodowitz MJ. Cultivation of monoxenous trypanosomatids: A minireview. J Invertebr Pathol 2024; 203:108047. [PMID: 38142929 DOI: 10.1016/j.jip.2023.108047] [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: 04/07/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
Abstract
Trypanosomatids are obligatory parasites, some of which are responsible for important human and animal diseases, but the vast majority of trypanosomatids are restricted to invertebrate hosts. Isolation and in vitro cultivation of trypanosomatids from insect hosts enable their description, characterization, and subsequently genetic and genomic studies. However, exact nutritional requirements are still unknown for most trypanosomatids and thus very few defined media are available. This mini review provides information about the role of different ingredients, recommendations and advice on essential supplements and important physicochemical parameters of culture media with the aim of facilitating first attempts to cultivate insect-infesting trypanosomatids, with a focus on monoxenous trypanosomatids.
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Affiliation(s)
- M Tannières
- USDA-ARS European Biological Control Laboratory, 810 avenue du campus Agropolis, 34980 Montferrier sur Lez, France.
| | - D Breugnot
- USDA-ARS European Biological Control Laboratory, 810 avenue du campus Agropolis, 34980 Montferrier sur Lez, France
| | - M C Bon
- USDA-ARS European Biological Control Laboratory, 810 avenue du campus Agropolis, 34980 Montferrier sur Lez, France
| | - M J Grodowitz
- USDA-ARS European Biological Control Laboratory, 810 avenue du campus Agropolis, 34980 Montferrier sur Lez, France; USDA-ARS National Biological Control Laboratory, 59 Lee Road, Stoneville, MS 38776, USA
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3
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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: 8] [Impact Index Per Article: 8.0] [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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Zeke A, Gibson TJ, Dobson L. Linear motifs regulating protein secretion, sorting and autophagy in Leishmania parasites are diverged with respect to their host equivalents. PLoS Comput Biol 2024; 20:e1011902. [PMID: 38363808 PMCID: PMC10903960 DOI: 10.1371/journal.pcbi.1011902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 02/29/2024] [Accepted: 02/08/2024] [Indexed: 02/18/2024] Open
Abstract
The pathogenic, tropical Leishmania flagellates belong to an early-branching eukaryotic lineage (Kinetoplastida) with several unique features. Unfortunately, they are poorly understood from a molecular biology perspective, making development of mechanistically novel and selective drugs difficult. Here, we explore three functionally critical targeting short linear motif systems as well as their receptors in depth, using a combination of structural modeling, evolutionary sequence divergence and deep learning. Secretory signal peptides, endoplasmic reticulum (ER) retention motifs (KDEL motifs), and autophagy signals (motifs interacting with ATG8 family members) are ancient and essential components of cellular life. Although expected to be conserved amongst the kinetoplastids, we observe that all three systems show a varying degree of divergence from their better studied equivalents in animals, plants, or fungi. We not only describe their behaviour, but also build models that allow the prediction of localization and potential functions for several uncharacterized Leishmania proteins. The unusually Ala/Val-rich secretory signal peptides, endoplasmic reticulum resident proteins ending in Asp-Leu-COOH and atypical ATG8-like proteins are all unique molecular features of kinetoplastid parasites. Several of their critical protein-protein interactions could serve as targets of selective antimicrobial agents against Leishmaniasis due to their systematic divergence from the host.
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Affiliation(s)
- Andras Zeke
- Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Budapest, Hungary
| | - Toby J. Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Laszlo Dobson
- Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Budapest, Hungary
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
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Ribeiro JM, Silva PA, Costa-Silva HM, Santi AMM, Murta SMF. Deletion of the lipid droplet protein kinase gene affects lipid droplets biogenesis, parasite infectivity, and resistance to trivalent antimony in Leishmania infantum. PLoS Negl Trop Dis 2024; 18:e0011880. [PMID: 38236929 PMCID: PMC10795987 DOI: 10.1371/journal.pntd.0011880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 12/21/2023] [Indexed: 01/22/2024] Open
Abstract
The Lipid Droplet Protein Kinase (LDK) facilitates lipid droplet (LD) biogenesis, organelles involved in various metabolic and signaling functions in trypanosomatids. As LDK's function has not been previously explored in Leishmania spp., we utilized CRISPR/Cas9 technology to generate LDK-knockout lines of Leishmania infantum to investigate its role in this parasite. Our findings demonstrate that LDK is not an essential gene for L. infantum, as its deletion did not impede parasite survival. Furthermore, removing LDK did not impact the growth of promastigote forms of L. infantum lacking LDK. However, a noticeable reduction in LDs occurred during the stationary phase of parasite growth following LDK deletion. In the presence of myriocin, a LD inducer, LDK-knockout parasites displayed reduced LD abundance during both logarithmic and stationary growth phases compared to control parasites. Moreover, an infection analysis involving THP-1 cells revealed that 72 h post-infection, LDK-knockout L. infantum lines exhibited fewer infected macrophages and intracellular amastigotes than control parasites. LDK-knockout L. infantum lines also displayed 1.7 to 1.8 -fold greater resistance to trivalent antimony than control parasites. There were no observed alterations in susceptibility to amphotericin B, miltefosine, or menadione in LDK-knockout L. infantum lines. Our results suggest that LDK plays a crucial role in the biogenesis and/or maintenance of LDs in L. infantum, as well as in parasite infectivity and resistance to trivalent antimony.
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Affiliation(s)
- Juliana Martins Ribeiro
- Grupo Genômica Funcional de Parasitos, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Paula Alves Silva
- Grupo Genômica Funcional de Parasitos, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Héllida Marina Costa-Silva
- Grupo Genômica Funcional de Parasitos, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Ana Maria Murta Santi
- Grupo Genômica Funcional de Parasitos, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Silvane Maria Fonseca Murta
- Grupo Genômica Funcional de Parasitos, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, Minas Gerais, Brazil
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Povelones ML, Holmes NA, Povelones M. A sticky situation: When trypanosomatids attach to insect tissues. PLoS Pathog 2023; 19:e1011854. [PMID: 38128049 PMCID: PMC10734937 DOI: 10.1371/journal.ppat.1011854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
Transmission of trypanosomatids to their mammalian hosts requires a complex series of developmental transitions in their insect vectors, including stable attachment to an insect tissue. While there are many ultrastructural descriptions of attached cells, we know little about the signaling events and molecular mechanisms involved in this process. Each trypanosomatid species attaches to a specific tissue in the insect at a particular stage of its life cycle. Attachment is mediated by the flagellum, which is modified to accommodate a filament-rich plaque within an expanded region of the flagellar membrane. Attachment immediately precedes differentiation to the mammal-infectious stage and in some cases a direct mechanistic link has been demonstrated. In this review, we summarize the current state of knowledge of trypanosomatid attachment in insects, including structure, function, signaling, candidate molecules, and changes in gene expression. We also highlight remaining questions about this process and how the field is poised to address them through modern approaches.
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Affiliation(s)
- Megan L. Povelones
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
| | - Nikki A. Holmes
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
| | - Michael Povelones
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
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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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9
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Rusman F, Díaz AG, Ponce T, Floridia-Yapur N, Barnabé C, Diosque P, Tomasini N. Wide reference databases for typing Trypanosoma cruzi based on amplicon sequencing of the minicircle hypervariable region. PLoS Negl Trop Dis 2023; 17:e0011764. [PMID: 37956210 PMCID: PMC10681310 DOI: 10.1371/journal.pntd.0011764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/27/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Trypanosoma cruzi, the etiological agent of Chagas Disease, exhibits remarkable genetic diversity and is classified into different Discrete Typing Units (DTUs). Strain typing techniques are crucial for studying T. cruzi, because their DTUs have significant biological differences from one another. However, there is currently no methodological strategy for the direct typing of biological materials that has sufficient sensitivity, specificity, and reproducibility. The high diversity and copy number of the minicircle hypervariable regions (mHVRs) makes it a viable target for typing. METHODOLOGY/PRINCIPAL FINDINGS Approximately 24 million reads obtained by amplicon sequencing of the mHVR were analyzed for 62 strains belonging to the six main T. cruzi DTUs. To build reference databases of mHVR diversity for each DTU and to evaluate this target as a typing tool. Strains of the same DTU shared more mHVR clusters than strains of different DTUs, and clustered together. Different identity thresholds were used to build the reference sets of the mHVR sequences (85% and 95%, respectively). The 95% set had a higher specificity and was more suited for detecting co-infections, whereas the 85% set was excellent for identifying the primary DTU of a sample. The workflow's capacity for typing samples obtained from cultures, a set of whole-genome data, under various simulated PCR settings, in the presence of co-infecting lineages and for blood samples was also assessed. CONCLUSIONS/SIGNIFICANCE We present reference databases of mHVR sequences and an optimized typing workflow for T. cruzi including a simple online tool for deep amplicon sequencing analysis (https://ntomasini.github.io/cruzityping/). The results show that the workflow displays an equivalent resolution to that of the other typing methods. Owing to its specificity, sensitivity, relatively low cost, and simplicity, the proposed workflow could be an alternative for screening different types of samples.
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Affiliation(s)
- Fanny Rusman
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental Dr. Miguel Ángel Basombrío, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
| | - Anahí G. Díaz
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental Dr. Miguel Ángel Basombrío, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
| | - Tatiana Ponce
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental Dr. Miguel Ángel Basombrío, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
| | - Noelia Floridia-Yapur
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental Dr. Miguel Ángel Basombrío, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
| | - Christian Barnabé
- Institut de Recherche pour le Développement (IRD), UMR INTERTRYP IRD-CIRAD, University of Montpellier, Montpellier, France
| | - Patricio Diosque
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental Dr. Miguel Ángel Basombrío, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
| | - Nicolás Tomasini
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental Dr. Miguel Ángel Basombrío, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
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10
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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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11
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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: 6] [Impact Index Per Article: 6.0] [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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12
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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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13
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Dubey AP, Tylec BL, Mishra A, Sortino K, Chen R, Sun Y, Read LK. KREH1 RNA helicase activity promotes utilization of initiator gRNAs across multiple mRNAs in trypanosome RNA editing. Nucleic Acids Res 2023; 51:5791-5809. [PMID: 37140035 PMCID: PMC10287954 DOI: 10.1093/nar/gkad292] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/04/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023] Open
Abstract
Mitochondrial U-indel RNA editing in kinetoplastid protozoa is directed by trans-acting gRNAs and mediated by a holoenzyme with associated factors. Here, we examine the function of the holoenzyme-associated KREH1 RNA helicase in U-indel editing. We show that KREH1 knockout (KO) impairs editing of a small subset of mRNAs. Overexpression of helicase-dead mutants results in expanded impairment of editing across multiple transcripts, suggesting the existence of enzymes that can compensate for KREH1 in KO cells. In depth analysis of editing defects using quantitative RT-PCR and high-throughput sequencing reveals compromised editing initiation and progression in both KREH1-KO and mutant-expressing cells. In addition, these cells exhibit a distinct defect in the earliest stages of editing in which the initiator gRNA is bypassed, and a small number of editing events takes place just outside this region. Wild type KREH1 and a helicase-dead KREH1 mutant interact similarly with RNA and holoenzyme, and overexpression of both similarly disorders holoenzyme homeostasis. Thus, our data support a model in which KREH1 RNA helicase activity facilitates remodeling of initiator gRNA-mRNA duplexes to permit accurate utilization of initiating gRNAs on multiple transcripts.
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Affiliation(s)
- Ashutosh P Dubey
- Dept. of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Brianna L Tylec
- Dept. of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Amartya Mishra
- Dept. of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Katherine Sortino
- Dept. of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Runpu Chen
- Dept. of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Yijun Sun
- Dept. of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Laurie K Read
- Dept. of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
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14
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Žárský V, Karnkowska A, Boscaro V, Trznadel M, Whelan TA, Hiltunen-Thorén M, Onut-Brännström I, Abbott CL, Fast NM, Burki F, Keeling PJ. Contrasting outcomes of genome reduction in mikrocytids and microsporidians. BMC Biol 2023; 21:137. [PMID: 37280585 DOI: 10.1186/s12915-023-01635-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/26/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Intracellular symbionts often undergo genome reduction, losing both coding and non-coding DNA in a process that ultimately produces small, gene-dense genomes with few genes. Among eukaryotes, an extreme example is found in microsporidians, which are anaerobic, obligate intracellular parasites related to fungi that have the smallest nuclear genomes known (except for the relic nucleomorphs of some secondary plastids). Mikrocytids are superficially similar to microsporidians: they are also small, reduced, obligate parasites; however, as they belong to a very different branch of the tree of eukaryotes, the rhizarians, such similarities must have evolved in parallel. Since little genomic data are available from mikrocytids, we assembled a draft genome of the type species, Mikrocytos mackini, and compared the genomic architecture and content of microsporidians and mikrocytids to identify common characteristics of reduction and possible convergent evolution. RESULTS At the coarsest level, the genome of M. mackini does not exhibit signs of extreme genome reduction; at 49.7 Mbp with 14,372 genes, the assembly is much larger and gene-rich than those of microsporidians. However, much of the genomic sequence and most (8075) of the protein-coding genes code for transposons, and may not contribute much of functional relevance to the parasite. Indeed, the energy and carbon metabolism of M. mackini share several similarities with those of microsporidians. Overall, the predicted proteome involved in cellular functions is quite reduced and gene sequences are extremely divergent. Microsporidians and mikrocytids also share highly reduced spliceosomes that have retained a strikingly similar subset of proteins despite having reduced independently. In contrast, the spliceosomal introns in mikrocytids are very different from those of microsporidians in that they are numerous, conserved in sequence, and constrained to an exceptionally narrow size range (all 16 or 17 nucleotides long) at the shortest extreme of known intron lengths. CONCLUSIONS Nuclear genome reduction has taken place many times and has proceeded along different routes in different lineages. Mikrocytids show a mix of similarities and differences with other extreme cases, including uncoupling the actual size of a genome with its functional reduction.
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Affiliation(s)
- Vojtečh Žárský
- Department of Botany, University of British Columbia, V6T 1Z4, Vancouver, 3529-6270 University Boulevard, BC, Canada
| | - Anna Karnkowska
- Department of Botany, University of British Columbia, V6T 1Z4, Vancouver, 3529-6270 University Boulevard, BC, Canada
- Institute of Evolutionary Biology, Faculty of Biology, University of Warsaw, 02-089, Warsaw, Poland
| | - Vittorio Boscaro
- Department of Botany, University of British Columbia, V6T 1Z4, Vancouver, 3529-6270 University Boulevard, BC, Canada.
| | - Morelia Trznadel
- Department of Botany, University of British Columbia, V6T 1Z4, Vancouver, 3529-6270 University Boulevard, BC, Canada
| | - Thomas A Whelan
- Department of Botany, University of British Columbia, V6T 1Z4, Vancouver, 3529-6270 University Boulevard, BC, Canada
| | - Markus Hiltunen-Thorén
- Department of Organismal Biology, Uppsala University, Norbyv. 18D, 752 36, Uppsala, Sweden
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Ioana Onut-Brännström
- Department of Organismal Biology, Uppsala University, Norbyv. 18D, 752 36, Uppsala, Sweden
- Department of Ecology and Genetics, Uppsala University, 752 36, Uppsala, Sweden
- Natural History Museum, University of Oslo, 0562, Oslo, Norway
| | - Cathryn L Abbott
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, V9T 6N7, Canada
| | - Naomi M Fast
- Department of Botany, University of British Columbia, V6T 1Z4, Vancouver, 3529-6270 University Boulevard, BC, Canada
| | - Fabien Burki
- Department of Organismal Biology, Uppsala University, Norbyv. 18D, 752 36, Uppsala, Sweden
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, V6T 1Z4, Vancouver, 3529-6270 University Boulevard, BC, Canada.
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15
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Camacho E, González-de la Fuente S, Solana JC, Tabera L, Carrasco-Ramiro F, Aguado B, Requena JM. Leishmania infantum (JPCM5) Transcriptome, Gene Models and Resources for an Active Curation of Gene Annotations. Genes (Basel) 2023; 14:genes14040866. [PMID: 37107624 PMCID: PMC10137940 DOI: 10.3390/genes14040866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/25/2023] [Accepted: 04/01/2023] [Indexed: 04/08/2023] Open
Abstract
Leishmania infantum is one of the causative agents of visceral leishmaniases, the most severe form of leishmaniasis. An improved assembly for the L. infantum genome was published five years ago, yet delineation of its transcriptome remained to be accomplished. In this work, the transcriptome annotation was attained by a combination of both short and long RNA-seq reads. The good agreement between the results derived from both methodologies confirmed that transcript assembly based on Illumina RNA-seq and further delimitation according to the positions of spliced leader (SAS) and poly-A (PAS) addition sites is an adequate strategy to annotate the transcriptomes of Leishmania, a procedure previously used for transcriptome annotation in other Leishmania species and related trypanosomatids. These analyses also confirmed that the Leishmania transcripts boundaries are relatively slippery, showing extensive heterogeneity at the 5′- and 3′-ends. However, the use of RNA-seq reads derived from the PacBio technology (referred to as Iso-Seq) allowed the authors to uncover some complex transcription patterns occurring at particular loci that would be unnoticed by the use of short RNA-seq reads alone. Thus, Iso-Seq analysis provided evidence that transcript processing at particular loci would be more dynamic than expected. Another noticeable finding was the observation of a case of allelic heterozygosity based on the existence of chimeric Iso-Seq reads that might be generated by an event of intrachromosomal recombination. In addition, we are providing the L. infantum gene models, including both UTRs and CDS regions, that would be helpful for undertaking whole-genome expression studies. Moreover, we have built the foundations of a communal database for the active curation of both gene/transcript models and functional annotations for genes and proteins.
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Affiliation(s)
- Esther Camacho
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Departamento de Biología Molecular, Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | | | - Jose Carlos Solana
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Departamento de Biología Molecular, Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Laura Tabera
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Genomic and NGS Facility (GENGS), 28049 Madrid, Spain
| | - Fernando Carrasco-Ramiro
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Genomic and NGS Facility (GENGS), 28049 Madrid, Spain
| | - Begoña Aguado
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Genomic and NGS Facility (GENGS), 28049 Madrid, Spain
| | - Jose M. Requena
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Departamento de Biología Molecular, Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
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Barranco-Gómez O, De Paula JC, Parada JS, Gómez-Moracho T, Marfil AV, Zafra M, Orantes Bermejo FJ, Osuna A, De Pablos LM. Development of a TaqMan qPCR assay for trypanosomatid multi-species detection and quantification in insects. Parasit Vectors 2023; 16:69. [PMID: 36788540 PMCID: PMC9930332 DOI: 10.1186/s13071-023-05687-3] [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: 11/24/2022] [Accepted: 01/30/2023] [Indexed: 02/16/2023] Open
Abstract
BACKGROUND Trypanosomatid parasites are widely distributed in nature and can have a monoxenous or dixenous life-cycle. These parasites thrive in a wide number of insect orders, some of which have an important economic and environmental value, such as bees. The objective of this study was to develop a robust and sensitive real-time quantitative PCR (qPCR) assay for detecting trypanosomatid parasites in any type of parasitized insect sample. METHODS A TaqMan qPCR assay based on a trypanosomatid-conserved region of the α-tubulin gene was standardized and evaluated. The limits of detection, sensitivity and versatility of the α-tubulin TaqMan assay were tested and validated using field samples of honeybee workers, wild bees, bumblebees and grasshoppers, as well as in the human infective trypanosomatid Leishmania major. RESULTS The assay showed a detection limit of 1 parasite equivalent/µl and successfully detected trypanosomatids in 10 different hosts belonging to the insect orders Hymenoptera and Orthoptera. The methodology was also tested using honeybee samples from four apiaries (n = 224 worker honeybees) located in the Alpujarra region (Granada, Spain). Trypanosomatids were detected in 2.7% of the honeybees, with an intra-colony prevalence of 0% to 13%. Parasite loads in the four different classes of insects ranged from 40.6 up to 1.1 × 108 cell equivalents per host. CONCLUSIONS These results show that the α-tubulin TaqMan qPCR assay described here is a versatile diagnostic tool for the accurate detection and quantification of trypanosomatids in a wide range of environmental settings.
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Affiliation(s)
- Olga Barranco-Gómez
- Departamento de Parasitología, Grupo de Bioquímica y Parasitología Molecular CTS-183, Universidad de Granada, Granada, Spain.,Institute of Biotechnology, University of Granada, Granada, Spain
| | - Jessica Carreira De Paula
- Departamento de Parasitología, Grupo de Bioquímica y Parasitología Molecular CTS-183, Universidad de Granada, Granada, Spain.,Institute of Biotechnology, University of Granada, Granada, Spain
| | - Jennifer Solano Parada
- Departamento de Parasitología, Grupo de Bioquímica y Parasitología Molecular CTS-183, Universidad de Granada, Granada, Spain.,Institute of Biotechnology, University of Granada, Granada, Spain
| | - Tamara Gómez-Moracho
- Departamento de Parasitología, Grupo de Bioquímica y Parasitología Molecular CTS-183, Universidad de Granada, Granada, Spain.,Institute of Biotechnology, University of Granada, Granada, Spain
| | - Ana Vic Marfil
- Departamento de Parasitología, Grupo de Bioquímica y Parasitología Molecular CTS-183, Universidad de Granada, Granada, Spain
| | - María Zafra
- Departamento de Parasitología, Grupo de Bioquímica y Parasitología Molecular CTS-183, Universidad de Granada, Granada, Spain
| | | | - Antonio Osuna
- Departamento de Parasitología, Grupo de Bioquímica y Parasitología Molecular CTS-183, Universidad de Granada, Granada, Spain.,Institute of Biotechnology, University of Granada, Granada, Spain
| | - Luis Miguel De Pablos
- Departamento de Parasitología, Grupo de Bioquímica y Parasitología Molecular CTS-183, Universidad de Granada, Granada, Spain. .,Institute of Biotechnology, University of Granada, Granada, Spain.
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17
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Kachale A, Pavlíková Z, Nenarokova A, Roithová A, Durante IM, Miletínová P, Záhonová K, Nenarokov S, Votýpka J, Horáková E, Ross RL, Yurchenko V, Beznosková P, Paris Z, Valášek LS, Lukeš J. Short tRNA anticodon stem and mutant eRF1 allow stop codon reassignment. Nature 2023; 613:751-758. [PMID: 36631608 DOI: 10.1038/s41586-022-05584-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 11/18/2022] [Indexed: 01/13/2023]
Abstract
Cognate tRNAs deliver specific amino acids to translating ribosomes according to the standard genetic code, and three codons with no cognate tRNAs serve as stop codons. Some protists have reassigned all stop codons as sense codons, neglecting this fundamental principle1-4. Here we analyse the in-frame stop codons in 7,259 predicted protein-coding genes of a previously undescribed trypanosomatid, Blastocrithidia nonstop. We reveal that in this species in-frame stop codons are underrepresented in genes expressed at high levels and that UAA serves as the only termination codon. Whereas new tRNAsGlu fully cognate to UAG and UAA evolved to reassign these stop codons, the UGA reassignment followed a different path through shortening the anticodon stem of tRNATrpCCA from five to four base pairs (bp). The canonical 5-bp tRNATrp recognizes UGG as dictated by the genetic code, whereas its shortened 4-bp variant incorporates tryptophan also into in-frame UGA. Mimicking this evolutionary twist by engineering both variants from B. nonstop, Trypanosoma brucei and Saccharomyces cerevisiae and expressing them in the last two species, we recorded a significantly higher readthrough for all 4-bp variants. Furthermore, a gene encoding B. nonstop release factor 1 acquired a mutation that specifically restricts UGA recognition, robustly potentiating the UGA reassignment. Virtually the same strategy has been adopted by the ciliate Condylostoma magnum. Hence, we describe a previously unknown, universal mechanism that has been exploited in unrelated eukaryotes with reassigned stop codons.
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Affiliation(s)
- Ambar Kachale
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic
| | - Zuzana Pavlíková
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Anna Nenarokova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic.,School of Biological Sciences, University of Bristol, Bristol, UK
| | - Adriana Roithová
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Ignacio M Durante
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Petra Miletínová
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Kristína Záhonová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic.,Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Serafim Nenarokov
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic
| | - Jan Votýpka
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic
| | - Eva Horáková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Institute of Microbiology, Czech Academy of Sciences, Třeboň, Czech Republic
| | | | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Petra Beznosková
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Zdeněk Paris
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic. .,Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic.
| | | | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic. .,Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic.
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18
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Kostygov AY, Malysheva MN, Ganyukova AI, Razygraev AV, Drachko DO, Yurchenko V, Agasoi VV, Frolov AO. The Roles of Mosquitoes in the Circulation of Monoxenous Trypanosomatids in Temperate Climates. Pathogens 2022; 11:1326. [PMID: 36422578 PMCID: PMC9695722 DOI: 10.3390/pathogens11111326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 08/23/2023] Open
Abstract
Monoxenous (insect-restricted) trypanosomatids are highly diverse and abundant in nature. While many papers focus on the taxonomy and distribution of these parasites, studies on their biology are still scarce. In particular, this concerns trypanosomatids inhabiting the ubiquitous mosquitoes. To shed light on the circulation of monoxenous trypanosomatids with the participation of mosquitoes, we performed a multifaceted study combining the examination of naturally- and experimentally-infected insects using light and electron microscopy and molecular identification of parasites. Our examination of overwintering mosquitoes (genera Culex and Culiseta) revealed that their guts contained living trypanosomatids, which can be spread during the next season. Experimental infections with Crithidia spp. demonstrated that imagines represent permissive hosts, while larvae are resistant to these parasites. We argue that for the parasites with wide specificity, mosquitoes act as facultative hosts. Other trypanosomatids may have specific adaptations for vertical transmission in these insects at the expense of their potential to infect a wider range of hosts and, consequently, abundance in nature.
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Affiliation(s)
- Alexei Y. Kostygov
- Zoological Institute of the Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Marina N. Malysheva
- 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
| | - Alexey V. Razygraev
- Zoological Institute of the Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Daria O. Drachko
- Zoological Institute of the Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic
| | - Vera V. Agasoi
- Zoological Institute of the Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Alexander O. Frolov
- Zoological Institute of the Russian Academy of Sciences, 199034 St. Petersburg, Russia
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19
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Mitochondrial RNA editing in Trypanoplasma borreli: new tools, new revelations. Comput Struct Biotechnol J 2022; 20:6388-6402. [DOI: 10.1016/j.csbj.2022.11.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
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20
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Santos FM, Sano NY, Liberal SC, Dario MA, Nantes WAG, Alves FM, da Silva AR, De Oliveira CE, Roque ALR, Herrera HM, Jansen AM. Kinetoplastid Species Maintained by a Small Mammal Community in the Pantanal Biome. Pathogens 2022; 11:pathogens11101205. [PMID: 36297262 PMCID: PMC9612235 DOI: 10.3390/pathogens11101205] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/15/2022] [Accepted: 10/18/2022] [Indexed: 11/24/2022] Open
Abstract
Kinetoplastids include species economically important in agriculture, livestock, and human health. We evaluated the richness of kinetoplastids that infect small mammals in patches of unflooded forests in the Pantanal biome, an area where we hypothesize that its diversity is higher than currently recognized. Hemocultures (HC) and Next Generation Sequencing (NGS) targeting the 18S rDNA gene were employed for the detection of kinetoplastids. We grouped the positive samples into pools for each small mammal species (Monodelphis domestica, Thylamys macrurus, Oecomys mamorae, Thrichomys fosteri, Clyomys laticeps, and Holochilus chacarius). Eight parasite species were identified: Leishmania amazonensis, L. infantum; Trypanosoma cascavelli (HC + NGS), T. cruzi, T. lainsoni, T. rangeli (HC + NGS), Trypanosoma sp. DID, and Neobodo sp. The use of a tool as sensitive as NGS has increased our awareness of the diversity of kinetoplastids, as well as their host range, with emphasis on the species O. mamorae (seven kinetoplastid species, excepting T. cascavelli in a pool of nine individuals) and T. macrurus (four kinetoplastid species in a single individual). Furthermore, L. infantum and L. amazonensis infections were described in small mammals from this region for the first time. These findings make it mandatory to revisit the kinetoplastids/host associations proposed so far.
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Affiliation(s)
- Filipe Martins Santos
- Programa de Pós-Graduação em Ciências Ambientais e Sustentabilidade Agropecuária, Universidade Católica Dom Bosco (UCDB), Campo Grande 79117-010, Brazil
- Correspondence:
| | - Nayara Yoshie Sano
- Programa de Pós-Graduação em Ecologia e Conservação, Universidade Federal do Mato Grosso do Sul (UFMS), Campo Grande 79070-900, Brazil
| | - Sany Caroline Liberal
- Programa de Pós-Graduação em Ciências Ambientais e Sustentabilidade Agropecuária, Universidade Católica Dom Bosco (UCDB), Campo Grande 79117-010, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco (UCDB), Campo Grande 79117-010, Brazil
| | - Maria Augusta Dario
- Laboratório de Biologia de Tripanossomatídeos, Instituto Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
| | - Wesley Arruda Gimenes Nantes
- Programa de Pós-Graduação em Ciências Ambientais e Sustentabilidade Agropecuária, Universidade Católica Dom Bosco (UCDB), Campo Grande 79117-010, Brazil
| | - Fernanda Moreira Alves
- Laboratório de Biologia de Tripanossomatídeos, Instituto Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
- Programa de Pós-Graduação em Biologia Parasitária, Instituto Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
| | | | - Carina Elisei De Oliveira
- Programa de Pós-Graduação em Ciências Ambientais e Sustentabilidade Agropecuária, Universidade Católica Dom Bosco (UCDB), Campo Grande 79117-010, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco (UCDB), Campo Grande 79117-010, Brazil
| | - André Luiz Rodrigues Roque
- Laboratório de Biologia de Tripanossomatídeos, Instituto Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
| | - Heitor Miraglia Herrera
- Programa de Pós-Graduação em Ciências Ambientais e Sustentabilidade Agropecuária, Universidade Católica Dom Bosco (UCDB), Campo Grande 79117-010, Brazil
- Programa de Pós-Graduação em Ecologia e Conservação, Universidade Federal do Mato Grosso do Sul (UFMS), Campo Grande 79070-900, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco (UCDB), Campo Grande 79117-010, Brazil
| | - Ana Maria Jansen
- Programa de Pós-Graduação em Ciências Ambientais e Sustentabilidade Agropecuária, Universidade Católica Dom Bosco (UCDB), Campo Grande 79117-010, Brazil
- Laboratório de Biologia de Tripanossomatídeos, Instituto Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
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21
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Abrahim M, Machado E, Alvarez-Valín F, de Miranda AB, Catanho M. Uncovering Pseudogenes and Intergenic Protein-coding Sequences in TriTryps' Genomes. Genome Biol Evol 2022; 14:6754225. [PMID: 36208292 PMCID: PMC9576210 DOI: 10.1093/gbe/evac142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/14/2022] [Accepted: 09/20/2022] [Indexed: 01/24/2023] Open
Abstract
Trypanosomatids belong to a remarkable group of unicellular, parasitic organisms of the order Kinetoplastida, an early diverging branch of the phylogenetic tree of eukaryotes, exhibiting intriguing biological characteristics affecting gene expression (intronless polycistronic transcription, trans-splicing, and RNA editing), metabolism, surface molecules, and organelles (compartmentalization of glycolysis, variation of the surface molecules, and unique mitochondrial DNA), cell biology and life cycle (phagocytic vacuoles evasion and intricate patterns of cell morphogenesis). With numerous genomic-scale data of several trypanosomatids becoming available since 2005 (genomes, transcriptomes, and proteomes), the scientific community can further investigate the mechanisms underlying these unusual features and address other unexplored phenomena possibly revealing biological aspects of the early evolution of eukaryotes. One fundamental aspect comprises the processes and mechanisms involved in the acquisition and loss of genes throughout the evolutionary history of these primitive microorganisms. Here, we present a comprehensive in silico analysis of pseudogenes in three major representatives of this group: Leishmania major, Trypanosoma brucei, and Trypanosoma cruzi. Pseudogenes, DNA segments originating from altered genes that lost their original function, are genomic relics that can offer an essential record of the evolutionary history of functional genes, as well as clues about the dynamics and evolution of hosting genomes. Scanning these genomes with functional proteins as proxies to reveal intergenic regions with protein-coding features, relying on a customized threshold to distinguish statistically and biologically significant sequence similarities, and reassembling remnant sequences from their debris, we found thousands of pseudogenes and hundreds of open reading frames, with particular characteristics in each trypanosomatid: mutation profile, number, content, density, codon bias, average size, single- or multi-copy gene origin, number and type of mutations, putative primitive function, and transcriptional activity. These features suggest a common process of pseudogene formation, different patterns of pseudogene evolution and extant biological functions, and/or distinct genome organization undertaken by those parasites during evolution, as well as different evolutionary and/or selective pressures acting on distinct lineages.
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Affiliation(s)
- Mayla Abrahim
- Laboratório de Tecnologia Imunológica, Instituto de Tecnologia em Imunobiológicos, Vice-Diretoria de Desenvolvimento Tecnológico, Bio-Manguinhos, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Edson Machado
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fiocruz, Brazil
| | - Fernando Alvarez-Valín
- Unidad de Genómica Evolutiva, Sección Biomatemática, Universidad de la República del Uruguay, Montevideo, Uruguay
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22
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Bezerra MJR, Moura DMN, Freire ER, Holetz FB, Reis CRS, Monteiro TTS, Pinto ARS, Zhang N, Rezende AM, Pereira-Neves A, Figueiredo RCBQ, Clayton C, Field MC, Carrington M, de Melo Neto OP. Distinct mRNA and protein interactomes highlight functional differentiation of major eIF4F-like complexes from Trypanosoma brucei. Front Mol Biosci 2022; 9:971811. [PMID: 36275617 PMCID: PMC9585242 DOI: 10.3389/fmolb.2022.971811] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Gene expression in pathogenic protozoans of the family Trypanosomatidae has several novel features, including multiple eIF4F-like complexes involved in protein synthesis. The eukaryotic eIF4F complex, formed mainly by eIF4E and eIF4G subunits, is responsible for the canonical selection of mRNAs required for the initiation of mRNA translation. The best-known complexes implicated in translation in trypanosomatids are based on two related pairs of eIF4E and eIF4G subunits (EIF4E3/EIF4G4 and EIF4E4/EIF4G3), whose functional distinctions remain to be fully described. Here, to define interactomes associated with both complexes in Trypanosoma brucei procyclic forms, we performed parallel immunoprecipitation experiments followed by identification of proteins co-precipitated with the four tagged eIF4E and eIF4G subunits. A number of different protein partners, including RNA binding proteins and helicases, specifically co-precipitate with each complex. Highlights with the EIF4E4/EIF4G3 pair include RBP23, PABP1, EIF4AI and the CRK1 kinase. Co-precipitated partners with the EIF4E3/EIF4G4 pair are more diverse and include DRBD2, PABP2 and different zinc-finger proteins and RNA helicases. EIF4E3/EIF4G4 are essential for viability and to better define their role, we further investigated their phenotypes after knockdown. Depletion of either EIF4E3/EIF4G4 mRNAs lead to aberrant morphology with a more direct impact on events associated with cytokinesis. We also sought to identify those mRNAs differentially associated with each complex through CLIP-seq with the two eIF4E subunits. Predominant among EIF4E4-bound transcripts are those encoding ribosomal proteins, absent from those found with EIF4E3, which are generally more diverse. RNAi mediated depletion of EIF4E4, which does not affect proliferation, does not lead to changes in mRNAs or proteins associated with EIF4E3, confirming a lack of redundancy and distinct roles for the two complexes.
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Affiliation(s)
- Maria J. R. Bezerra
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
- Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | | | - Eden R. Freire
- Carlos Chagas Institute, Oswaldo Cruz Foundation, Curitiba, Pernambuco, Brazil
| | - Fabiola B. Holetz
- Carlos Chagas Institute, Oswaldo Cruz Foundation, Curitiba, Pernambuco, Brazil
| | | | | | - Adriana R. S. Pinto
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
| | - Ning Zhang
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Antonio M. Rezende
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
| | | | | | - Christine Clayton
- Heidelberg University Center for Molecular Biology, Heidelberg, Germany
| | - Mark C. Field
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Osvaldo P. de Melo Neto
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
- *Correspondence: Osvaldo P. de Melo Neto,
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23
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Sending the message: specialized RNA export mechanisms in trypanosomes. Trends Parasitol 2022; 38:854-867. [PMID: 36028415 PMCID: PMC9894534 DOI: 10.1016/j.pt.2022.07.008] [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: 10/19/2021] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 02/04/2023]
Abstract
Export of RNA from the nucleus is essential for all eukaryotic cells and has emerged as a major step in the control of gene expression. mRNA molecules are required to complete a complex series of processing events and pass a quality control system to protect the cytoplasm from the translation of aberrant proteins. Many of these events are highly conserved across eukaryotes, reflecting their ancient origin, but significant deviation from a canonical pathway as described from animals and fungi has emerged in the trypanosomatids. With significant implications for the mechanisms that control gene expression and hence differentiation, responses to altered environments and fitness as a parasite, these deviations may also reveal additional, previously unsuspected, mRNA export pathways.
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Bartolomé C, Buendía-Abad M, Ornosa C, De la Rúa P, Martín-Hernández R, Higes M, Maside X. Bee Trypanosomatids: First Steps in the Analysis of the Genetic Variation and Population Structure of Lotmaria passim, Crithidia bombi and Crithidia mellificae. MICROBIAL ECOLOGY 2022; 84:856-867. [PMID: 34609533 PMCID: PMC9622509 DOI: 10.1007/s00248-021-01882-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Trypanosomatids are among the most prevalent parasites in bees but, despite the fact that their impact on the colonies can be quite important and that their infectivity may potentially depend on their genotypes, little is known about the population diversity of these pathogens. Here we cloned and sequenced three non-repetitive single copy loci (DNA topoisomerase II, glyceraldehyde-3-phosphate dehydrogenase and RNA polymerase II large subunit, RPB1) to produce new genetic data from Crithidia bombi, C. mellificae and Lotmaria passim isolated from honeybees and bumblebees. These were analysed by applying population genetic tools in order to quantify and compare their variability within and between species, and to obtain information on their demography and population structure. The general pattern for the three species was that (1) they were subject to the action of purifying selection on nonsynonymous variants, (2) the levels of within species diversity were similar irrespective of the host, (3) there was evidence of recombination among haplotypes and (4) they showed no haplotype structuring according to the host. C. bombi exhibited the lowest levels of synonymous variation (πS= 0.06 ± 0.04 %) - and a mutation frequency distribution compatible with a population expansion after a bottleneck - that contrasted with the extensive polymorphism displayed by C. mellificae (πS= 2.24 ± 1.00 %), which likely has a more ancient origin. L. passim showed intermediate values (πS= 0.40 ± 0.28 %) and an excess of variants a low frequencies probably linked to the spread of this species to new geographical areas.
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Affiliation(s)
- Carolina Bartolomé
- Grupo de Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Galicia, Spain.
- Instituto de Investigación Sanitaria de Santiago (IDIS), 15706, Santiago de Compostela, Galicia, Spain.
| | - María Buendía-Abad
- Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal (IRIAF), Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, 19180, Marchamalo, Spain
| | - Concepción Ornosa
- Departamento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Pilar De la Rúa
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, 30100, Murcia, Spain
| | - Raquel Martín-Hernández
- Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal (IRIAF), Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, 19180, Marchamalo, Spain
- Instituto de Recursos Humanos para la Ciencia y la Tecnología, Fundación Parque Científico Tecnológico de Albacete, 02006, Albacete, Spain
| | - Mariano Higes
- Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal (IRIAF), Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, 19180, Marchamalo, Spain
| | - Xulio Maside
- Grupo de Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Galicia, Spain
- Instituto de Investigación Sanitaria de Santiago (IDIS), 15706, Santiago de Compostela, Galicia, Spain
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25
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Differences in Charge Distribution in Leishmania tarentolae Leishmanolysin Result in a Reduced Enzymatic Activity. Int J Mol Sci 2022; 23:ijms23147660. [PMID: 35887004 PMCID: PMC9321319 DOI: 10.3390/ijms23147660] [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: 06/06/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 02/04/2023] Open
Abstract
Leishmania tarentolae is a non-pathogenic trypanosomatid isolated from lizards widely used for heterologous protein expression and extensively studied to understand the pathogenic mechanisms of leishmaniasis. The repertoire of leishmanolysin genes was reported to be expanded in L. tarentolae genome, but no proteolytic activity was detected. Here, we analyzed L. tarentolae leishmanolysin proteins from the genome to the structural levels and evaluated the enzymatic activity of the wild-type and overexpressing mutants of leishmanolysin. A total of 61 leishmanolysin sequences were retrieved from the L. tarentolae genome. Five of them were selected for phylogenetic analysis, and for three of them, we built 3D models based on the crystallographic structure of L. major ortholog. Molecular dynamics simulations of these models disclosed a less negative electrostatic potential compared to the template. Subsequently, L. major LmjF.10.0460 and L. tarentolae LtaP10.0650 leishmanolysins were cloned in a pLEXSY expression system into L. tarentolae. Proteins from the wild-type and the overexpressing parasites were submitted to enzymatic analysis. Our results revealed that L. tarentolae leishmanolysins harbor a weak enzymatic activity about three times less abundant than L. major leishmanolysin. Our findings strongly suggest that the less negative electrostatic potential of L. tarentolae leishmanolysin can be the reason for the reduced proteolytic activity detected in this parasite.
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26
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Gerasimov ES, Ramirez-Barrios R, Yurchenko V, Zimmer SL. Trypanosoma cruzi strain and starvation-driven mitochondrial RNA editing and transcriptome variability. RNA (NEW YORK, N.Y.) 2022; 28:993-1012. [PMID: 35470233 PMCID: PMC9202582 DOI: 10.1261/rna.079088.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 04/07/2022] [Indexed: 05/09/2023]
Abstract
Trypanosoma cruzi is a unicellular protistan parasitic species that is comprised of strains and isolates exhibiting high levels of genetic and metabolic variability. In the insect vector, it is known to be highly responsive to starvation, a signal for progression to a life stage in which it can infect mammalian cells. Most mRNAs encoded in its mitochondrion require the targeted insertion and deletion of uridines to become translatable transcripts. This study defined differences in uridine-insertion/deletion RNA editing among three strains and established the mechanism whereby abundances of edited (and, thus, translatable) mitochondrial gene products increase during starvation. Our approach utilized our custom T-Aligner toolkit to describe transcriptome-wide editing events and reconstruct editing products from high-throughput sequencing data. We found that the relative abundance of mitochondrial transcripts and the proportion of mRNAs that are edited varies greatly between analyzed strains, a characteristic that could potentially impact metabolic capacity. Starvation typically led to an increase in overall editing activity rather than affecting a specific step in the process. We also determined that transcripts CR3, CR4, and ND3 produce multiple open reading frames that, if translated, would generate different proteins. Finally, we quantitated the inherent flexibility of editing in T. cruzi and found it to be higher relative to that in a related trypanosomatid lineage. Over time, new editing domains or patterns could prove advantageous to the organism and become more widespread within individual transcriptomes or among strains.
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Affiliation(s)
- Evgeny S Gerasimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russia
| | - Roger Ramirez-Barrios
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, Duluth, Minnesota 55812, USA
| | - 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, Moscow 119435, Russia
| | - Sara L Zimmer
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, Duluth, Minnesota 55812, USA
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Dario MA, Furtado C, Lisboa CV, de Oliveira F, Santos FM, D’Andrea PS, Roque ALR, Xavier SCDC, Jansen AM. Trypanosomatid Richness Among Rats, Opossums, and Dogs in the Caatinga Biome, Northeast Brazil, a Former Endemic Area of Chagas Disease. Front Cell Infect Microbiol 2022; 12:851903. [PMID: 35795183 PMCID: PMC9251133 DOI: 10.3389/fcimb.2022.851903] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/11/2022] [Indexed: 12/22/2022] Open
Abstract
Parasites are important components of the immense n-dimensional trophic network that connects all living beings because they, among others, forge biodiversity and deeply influence ecological evolution and host behavior. In this sense, the influence of Trypanosomatidae remains unknown. The aim of this study was to determine trypanosomatid infection and richness in rats, opossums, and dogs in the semiarid Caatinga biome. We submitted DNA samples from trypanosomatids obtained through axenic cultures of the blood of these mammals to mini exon multiplex-PCR, Sanger, and next-generation sequencing targeting the 18S rDNA gene. Phylogenetic analyses were performed to identify genetic diversity in the Trypanosomatidae family. Shannon, Simpson, equability, and beta-diversity indices were calculated per location and per mammalian host. Dogs were surveyed for trypanosomatid infection through hemocultures and serological assays. The examined mammal species of this area of the Caatinga biome exhibited an enormous trypanosomatid species/genotypes richness. Ten denoised Operational Taxonomic Units (ZOTUs), including three species (Trypanosoma cruzi, Trypanosoma rangeli and Crithidia mellificae) and one Trypanosoma sp. five genotypes/lineages (T. cruzi DTU TcI, TcII, and TcIV; T. rangeli A and B) and four DTU TcI haplotypes (ZOTU1, ZOTU2, ZOTU5, and ZOTU10 merged), as well as 13 Amplicon Sequence Variants (ASVs), including five species (T. cruzi, T. rangeli, C. mellificae, Trypanosoma dionisii, and Trypanosoma lainsoni), five genotypes/lineages (same as the ZOTUs) and six DTU TcI haplotypes (ASV, ASV1, ASV2, ASV3, ASV5 and ASV13), were identified in single and mixed infections. We observed that trypanosomatids present a broad host spectrum given that species related to a single host are found in other mammals from different taxa. Concomitant infections between trypanosomatids and new host-parasite relationships have been reported, and this immense diversity in mammals raised questions, such as how this can influence the course of the infection in these animals and its transmissibility. Dogs demonstrated a high infection rate by T. cruzi as observed by positive serological results (92% in 2005 and 76% in 2007). The absence of positive parasitological tests confirmed their poor infectivity potential but their importance as sentinel hosts of T. cruzi transmission.
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Affiliation(s)
- Maria Augusta Dario
- Trypanosomatid Biology Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
- *Correspondence: Maria Augusta Dario,
| | - Carolina Furtado
- Genetic Laboratory, National Cancer Institute, Rio de Janeiro, Brazil
| | - Cristiane Varella Lisboa
- Trypanosomatid Biology Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Felipe de Oliveira
- Trypanosomatid Biology Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Filipe Martins Santos
- Environmental Sciences and Agricultural Sustainability Postgraduation, Dom Bosco Catholic University, Campo Grande, Brazil
| | - Paulo Sérgio D’Andrea
- Wild Mammal Reservoirs Biology and Parasitology Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - André Luiz Rodrigues Roque
- Trypanosomatid Biology Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | | | - Ana Maria Jansen
- Trypanosomatid Biology Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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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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African trypanosome strategies for conquering new hosts and territories: the end of monophyly? Trends Parasitol 2022; 38:724-736. [DOI: 10.1016/j.pt.2022.05.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 11/22/2022]
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Díaz E, Febres A, Giammarresi M, Silva A, Vanegas O, Gomes C, Ponte-Sucre A. G Protein-Coupled Receptors as Potential Intercellular Communication Mediators in Trypanosomatidae. Front Cell Infect Microbiol 2022; 12:812848. [PMID: 35651757 PMCID: PMC9149261 DOI: 10.3389/fcimb.2022.812848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
Abstract
Detection and transduction of environmental signals, constitute a prerequisite for successful parasite invasion; i.e., Leishmania transmission, survival, pathogenesis and disease manifestation and dissemination, with diverse molecules functioning as inter-cellular signaling ligands. Receptors [i.e., G protein-coupled receptors (GPCRs)] and their associated transduction mechanisms, well conserved through evolution, specialize in this function. However, canonical GPCR-related signal transduction systems have not been described in Leishmania, although orthologs, with reduced domains and function, have been identified in Trypanosomatidae. These inter-cellular communication means seem to be essential for multicellular and unicellular organism’s survival. GPCRs are flexible in their molecular architecture and may interact with the so-called receptor activity-modifying proteins (RAMPs), which modulate their function, changing GPCRs pharmacology, acting as chaperones and regulating signaling and/or trafficking in a receptor-dependent manner. In the skin, vasoactive- and neuro- peptides released in response to the noxious stimuli represented by the insect bite may trigger parasite physiological responses, for example, chemotaxis. For instance, in Leishmania (V.) braziliensis, sensory [Substance P, SP, chemoattractant] and autonomic [Vasoactive Intestinal Peptide, VIP, and Neuropeptide Y, NPY, chemorepellent] neuropeptides at physiological levels stimulate in vitro effects on parasite taxis. VIP and NPY chemotactic effects are impaired by their corresponding receptor antagonists, suggesting that the stimulated responses might be mediated by putative GPCRs (with essential conserved receptor domains); the effect of SP is blocked by [(D-Pro 2, D-Trp7,9]-Substance P (10-6 M)] suggesting that it might be mediated by neurokinin-1 transmembrane receptors. Additionally, vasoactive molecules like Calcitonin Gene-Related Peptide [CGRP] and Adrenomedullin [AM], exert a chemorepellent effect and increase the expression of a 24 kDa band recognized in western blot analysis by (human-)-RAMP-2 antibodies. In-silico search oriented towards GPCRs-like receptors and signaling cascades detected a RAMP-2-aligned sequence corresponding to Leishmania folylpolyglutamate synthase and a RAMP-3 aligned protein, a hypothetical Leishmania protein with yet unknown function, suggesting that in Leishmania, CGRP and AM activities may be modulated by RAMP- (-2) and (-3) homologs. The possible presence of proteins and molecules potentially involved in GPCRs cascades, i.e., RAMPs, signpost conservation of ancient signaling systems associated with responses, fundamental for cell survival, (i.e., taxis and migration) and may constitute an open field for description of pharmacophores against Leishmania parasites.
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Affiliation(s)
- Emilia Díaz
- Laboratory of Molecular Physiology, Institute of Experimental Medicine, School of Medicine Luis Razetti, Faculty of Medicine, Universidad Central de Venezuela, Caracas, Venezuela
| | - Anthony Febres
- Section of Infectious Diseases, Baylor College of Medicine, TX, United States
| | - Michelle Giammarresi
- Laboratory of Molecular Physiology, Institute of Experimental Medicine, School of Medicine Luis Razetti, Faculty of Medicine, Universidad Central de Venezuela, Caracas, Venezuela
| | - Adrian Silva
- Laboratory of Molecular Physiology, Institute of Experimental Medicine, School of Medicine Luis Razetti, Faculty of Medicine, Universidad Central de Venezuela, Caracas, Venezuela
| | - Oriana Vanegas
- Pediatric Gastroenterology, University of Iowa, Iowa City, IA, United States
| | - Carlos Gomes
- Royal Berkshire NHS, Foundation Trust, Light House Lab, Bracknell, United Kingdom
| | - Alicia Ponte-Sucre
- Laboratory of Molecular Physiology, Institute of Experimental Medicine, School of Medicine Luis Razetti, Faculty of Medicine, Universidad Central de Venezuela, Caracas, Venezuela
- Medical Mission Institute, Würzburg, Germany
- *Correspondence: Alicia Ponte-Sucre,
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31
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Oldrieve GR, Malacart B, López-Vidal J, Matthews KR. The genomic basis of host and vector specificity in non-pathogenic trypanosomatids. Biol Open 2022; 11:bio059237. [PMID: 35373253 PMCID: PMC9099014 DOI: 10.1242/bio.059237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/25/2022] [Indexed: 11/20/2022] Open
Abstract
Trypanosoma theileri, a non-pathogenic parasite of bovines, has a predicted surface protein architecture that likely aids survival in its mammalian host. Their surface proteins are encoded by genes which account for ∼10% of their genome. A non-pathogenic parasite of sheep, Trypanosoma melophagium, is transmitted by the sheep ked and is closely related to T. theileri. To explore host and vector specificity between these species, we sequenced the T. melophagium genome and transcriptome and an annotated draft genome was assembled. T. melophagium was compared to 43 kinetoplastid genomes, including T. theileri. T. melophagium and T. theileri have an AT biased genome, the greatest bias of publicly available trypanosomatids. This trend may result from selection acting to decrease the genomic nucleotide cost. The T. melophagium genome is 6.3Mb smaller than T. theileri and large families of proteins, characteristic of the predicted surface of T. theileri, were found to be absent or greatly reduced in T. melophagium. Instead, T. melophagium has modestly expanded protein families associated with the avoidance of complement-mediated lysis. We propose that the contrasting genomic features of these species is linked to their mode of transmission from their insect vector to their mammalian host. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Guy R. Oldrieve
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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Dario MA, Lisboa CV, Xavier SCDC, D’Andrea PS, Roque ALR, Jansen AM. Trypanosoma Species in Small Nonflying Mammals in an Area With a Single Previous Chagas Disease Case. Front Cell Infect Microbiol 2022; 12:812708. [PMID: 35223545 PMCID: PMC8873152 DOI: 10.3389/fcimb.2022.812708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/03/2022] [Indexed: 11/29/2022] Open
Abstract
Trypanosomatids are hemoflagellate parasites that even though they have been increasingly studied, many aspects of their biology and taxonomy remain unknown. The aim of this study was to investigate the Trypanosoma sp. transmission cycle in nonflying small mammals in an area where a case of acute Chagas disease occurred in Mangaratiba municipality, Rio de Janeiro state. Three expeditions were conducted in the area: the first in 2012, soon after the human case, and two others in 2015. Sylvatic mammals were captured and submitted to blood collection for trypanosomatid parasitological and serological exams. Dogs from the surrounding areas where the sylvatic mammals were captured were also tested for T. cruzi infection. DNA samples were extracted from blood clots and positive hemocultures, submitted to polymerase chain reaction targeting SSU rDNA and gGAPDH genes, sequenced and phylogenetic analysed. Twenty-one wild mammals were captured in 2012, mainly rodents, and 17 mammals, mainly marsupials, were captured in the two expeditions conducted in 2015. Only four rodents demonstrated borderline serological T. cruzi test (IFAT), two in 2012 and two in 2015. Trypanosoma janseni was the main Trypanosoma species identified, and isolates were obtained solely from Didelphis aurita. In addition to biological differences, molecular differences are suggestive of genetic diversity in this flagellate species. Trypanosoma sp. DID was identified in blood clots from D. aurita in single and mixed infections with T. janseni. Concerning dogs, 12 presented mostly borderline serological titers for T. cruzi and no positive hemoculture. In blood clots from 11 dogs, T. cruzi DNA was detected and characterized as TcI (n = 9) or TcII (n = 2). Infections by Trypanosoma rangeli lineage E (n = 2) and, for the first time, Trypanosoma caninum, Trypanosoma dionisii, and Crithidia mellificae (n = 1 each) were also detected in dogs. We concluded that despite the low mammalian species richness and degraded environment, a high Trypanosoma species richness species was being transmitted with the predominance of T. janseni and not T. cruzi, as would be expected in a locality of an acute case of Chagas disease.
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Affiliation(s)
- Maria Augusta Dario
- Laboratory of Trypanosomatid Biology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
- *Correspondence: Maria Augusta Dario,
| | - Cristiane Varella Lisboa
- Laboratory of Trypanosomatid Biology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | | | - Paulo Sérgio D’Andrea
- Laboratory of Biology and Parasitology of Wild Reservoir Mammals, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - André Luiz Rodrigues Roque
- Laboratory of Trypanosomatid Biology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Ana Maria Jansen
- Laboratory of Trypanosomatid Biology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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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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Gallo-Francisco PH, Brocchi M, Giorgio S. Leishmania and its relationships with bacteria. Future Microbiol 2022; 17:199-218. [PMID: 35040703 DOI: 10.2217/fmb-2021-0133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Leishmaniasis is a zoonotic and neglected disease, which represents an important public health problem worldwide. Different species of Leishmania are associated with different manifestations, and a practical problem that can worsen the condition of hosts infected with Leishmania is the secondary infection caused by bacteria. This review aims to examine the importance and prevalence of bacteria co-infection during leishmaniasis and the nature of this ecological relationship. In the cases discussed in this review, the facilitation phenomenon, defined as any interaction where the action of one organism has a beneficial effect on an organism of another species, was considered in the Leishmania-bacteria interaction, as well as the effects on one another and their consequences for the host.
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Affiliation(s)
- Pedro H Gallo-Francisco
- Department of Animal Biology, Biology Institute, State University of Campinas, Campinas SP, 13083-862, Brazil
| | - Marcelo Brocchi
- Department of Genetics, Microbiology & Immunology, Biology Institute, State University of Campinas, Campinas SP, Brazil
| | - Selma Giorgio
- Department of Animal Biology, Biology Institute, State University of Campinas, Campinas SP, 13083-862, Brazil
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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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Su BX, Wang JF, Yang TB, Hide G, Lai DH, Lun ZR. A new species of mammalian trypanosome, Trypanosoma (Megatrypanum) bubalisi sp. nov., found in the freshwater leech Hirudinaria manillensis. Int J Parasitol 2021; 52:253-264. [PMID: 34863800 DOI: 10.1016/j.ijpara.2021.10.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 11/17/2022]
Abstract
Leeches have long been considered potential vectors for the aquatic lineage of trypanosomes, while bloodsucking insects are generally considered as the vectors for the terrestrial lineage of trypanosomes. The freshwater leech, Hirudinaria manillensis, is a widely distributed species in southern China and could potentially act as the vector for trypanosomes. Prior to this study, no trypanosomes had been reported from this leech. However, in this study, leeches were collected from three different places in Guangdong province, China, and a large number of flagellates were isolated and successfully cultured in vitro. Based on morphology, these flagellates looked like a typical trypanosome species. Analysis was carried out on the molecular sequences of the 18S rRNA gene and the glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH) gene. To our surprise, these flagellates were identified as likely to be a mammalian trypanosome belonging to the clade containing Trypanosoma (Megatrypanum) theileri but they are significantly different from the typical TthI and TthII stocks. Analyses of blood composition indicated that the source of the blood meal in these leeches was from the water buffalo (Bubalus bubalis). To further test if this flagellate from the freshwater leech was indeed a mammalian trypanosome, we transferred the trypanosomes cultured at 27-37 °C and they were able to successfully adapt to this mammalian body temperature, providing further supporting evidence. Due to the significant genetic differences from other related trypanosomes in the subgenus Megatrypanum, we propose that this flagellate, isolated from H. manillensis, is a new species and have named it Trypanosoma bubalisi. Our results indicate that freshwater leeches may be a potential vector of this new mammalian trypanosome.
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Affiliation(s)
- Bi-Xiu Su
- Guangdong Provincial Key Laboratory of Aquatic Economic Animals, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, The People's Republic of China
| | - Ju-Feng Wang
- Guangdong Provincial Key Laboratory of Aquatic Economic Animals, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, The People's Republic of China
| | - Ting-Bao Yang
- Guangdong Provincial Key Laboratory of Aquatic Economic Animals, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, The People's Republic of China
| | - Geoff Hide
- Ecosystems and Environment Research Centre and Biomedical Research Centre, School of Science, Engineering and Environment, University of Salford, Salford M5 4WT, UK
| | - De-Hua Lai
- Guangdong Provincial Key Laboratory of Aquatic Economic Animals, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, The People's Republic of China.
| | - Zhao-Rong Lun
- Guangdong Provincial Key Laboratory of Aquatic Economic Animals, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, The People's Republic of China; Ecosystems and Environment Research Centre and Biomedical Research Centre, School of Science, Engineering and Environment, University of Salford, Salford M5 4WT, UK.
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Poláková E, Albanaz ATS, Zakharova A, Novozhilova TS, Gerasimov ES, Yurchenko V. Ku80 is involved in telomere maintenance but dispensable for genomic stability in Leishmania mexicana. PLoS Negl Trop Dis 2021; 15:e0010041. [PMID: 34965251 PMCID: PMC8716037 DOI: 10.1371/journal.pntd.0010041] [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: 07/13/2021] [Accepted: 11/30/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Telomeres are indispensable for genome stability maintenance. They are maintained by the telomere-associated protein complex, which include Ku proteins and a telomerase among others. Here, we investigated a role of Ku80 in Leishmania mexicana. Leishmania is a genus of parasitic protists of the family Trypanosomatidae causing a vector-born disease called leishmaniasis. METHODOLOGY/PRINCIPAL FINDINGS We used the previously established CRISPR/Cas9 system to mediate ablation of Ku80- and Ku70-encoding genes in L. mexicana. Complete knock-outs of both genes were confirmed by Southern blotting, whole-genome Illumina sequencing, and RT-qPCR. Resulting telomeric phenotypes were subsequently investigated using Southern blotting detection of terminal restriction fragments. The genome integrity in the Ku80- deficient cells was further investigated by whole-genome sequencing. Our work revealed that telomeres in the ΔKu80 L. mexicana are elongated compared to those of the wild type. This is a surprising finding considering that in another model trypanosomatid, Trypanosoma brucei, they are shortened upon ablation of the same gene. A telomere elongation phenotype has been documented in other species and associated with a presence of telomerase-independent alternative telomere lengthening pathway. Our results also showed that Ku80 appears to be not involved in genome stability maintenance in L. mexicana. CONCLUSION/SIGNIFICANCE Ablation of the Ku proteins in L. mexicana triggers telomere elongation, but does not have an adverse impact on genome integrity.
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Affiliation(s)
- Ester Poláková
- 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
| | - Alexandra Zakharova
- 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
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - 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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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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 02/19/2021] [Accepted: 02/24/2021] [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
| | | | - 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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Škodová-Sveráková I, Záhonová K, Juricová V, Danchenko M, Moos M, Baráth P, Prokopchuk G, Butenko A, Lukáčová V, Kohútová L, Bučková B, Horák A, Faktorová D, Horváth A, Šimek P, Lukeš J. Highly flexible metabolism of the marine euglenozoan protist Diplonema papillatum. BMC Biol 2021; 19:251. [PMID: 34819072 PMCID: PMC8611851 DOI: 10.1186/s12915-021-01186-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/08/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The phylum Euglenozoa is a group of flagellated protists comprising the diplonemids, euglenids, symbiontids, and kinetoplastids. The diplonemids are highly abundant and speciose, and recent tools have rendered the best studied representative, Diplonema papillatum, genetically tractable. However, despite the high diversity of diplonemids, their lifestyles, ecological functions, and even primary energy source are mostly unknown. RESULTS We designed a metabolic map of D. papillatum cellular bioenergetic pathways based on the alterations of transcriptomic, proteomic, and metabolomic profiles obtained from cells grown under different conditions. Comparative analysis in the nutrient-rich and nutrient-poor media, as well as the absence and presence of oxygen, revealed its capacity for extensive metabolic reprogramming that occurs predominantly on the proteomic rather than the transcriptomic level. D. papillatum is equipped with fundamental metabolic routes such as glycolysis, gluconeogenesis, TCA cycle, pentose phosphate pathway, respiratory complexes, β-oxidation, and synthesis of fatty acids. Gluconeogenesis is uniquely dominant over glycolysis under all surveyed conditions, while the TCA cycle represents an eclectic combination of standard and unusual enzymes. CONCLUSIONS The identification of conventional anaerobic enzymes reflects the ability of this protist to survive in low-oxygen environments. Furthermore, its metabolism quickly reacts to restricted carbon availability, suggesting a high metabolic flexibility of diplonemids, which is further reflected in cell morphology and motility, correlating well with their extreme ecological valence.
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Affiliation(s)
- Ingrid Škodová-Sveráková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.
- Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia.
| | - Kristína Záhonová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Valéria Juricová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Maksym Danchenko
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Martin Moos
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Peter Baráth
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
- Medirex Group Academy n.o., Trnava, Slovakia
| | - Galina Prokopchuk
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Anzhelika Butenko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | | | - Lenka Kohútová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Barbora Bučková
- Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Drahomíra Faktorová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Anton Horváth
- Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Petr Šimek
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic.
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Wheeler RJ. A resource for improved predictions of Trypanosoma and Leishmania protein three-dimensional structure. PLoS One 2021; 16:e0259871. [PMID: 34762696 PMCID: PMC8584756 DOI: 10.1371/journal.pone.0259871] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/27/2021] [Indexed: 12/30/2022] Open
Abstract
AlphaFold2 and RoseTTAfold represent a transformative advance for predicting protein structure. They are able to make very high-quality predictions given a high-quality alignment of the protein sequence with related proteins. These predictions are now readily available via the AlphaFold database of predicted structures and AlphaFold or RoseTTAfold Colaboratory notebooks for custom predictions. However, predictions for some species tend to be lower confidence than model organisms. Problematic species include Trypanosoma cruzi and Leishmania infantum: important unicellular eukaryotic human parasites in an early-branching eukaryotic lineage. The cause appears to be due to poor sampling of this branch of life (Discoba) in the protein sequences databases used for the AlphaFold database and ColabFold. Here, by comprehensively gathering openly available protein sequence data for Discoba species, significant improvements to AlphaFold2 protein structure prediction over the AlphaFold database and ColabFold are demonstrated. This is made available as an easy-to-use tool for the parasitology community in the form of Colaboratory notebooks for generating multiple sequence alignments and AlphaFold2 predictions of protein structure for Trypanosoma, Leishmania and related species.
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Affiliation(s)
- Richard John Wheeler
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
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Berbigier AP, Barros JHDS, Pontes ES, Lisboa CV, Gentile R, Xavier SCDC, Jansen AM, Roque ALR. Trypanosomatid Richness in Wild and Synanthropic Small Mammals from a Biological Station in Rio de Janeiro, Brazil. Pathogens 2021; 10:pathogens10111442. [PMID: 34832597 PMCID: PMC8620513 DOI: 10.3390/pathogens10111442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 11/16/2022] Open
Abstract
Trypanosomatids are diverse and can infect several host species, including small mammals (rodents and marsupials). Between 2012 and 2014, 91 small mammals were surveyed for trypanosomatid infection in the Estação Biológica FIOCRUZ Mata Atlântica (EFMA), an Atlantic Forest area in Rio de Janeiro that presents different levels of conserved and degraded areas. Blood, skin, liver, and spleen samples were submitted to parasitological, serological, and molecular assays to detect the infection and determine the taxonomic status of their parasites. Sixty-eight individuals (74.7%; n = 91) were infected by trypanosomatids, including fourteen mixed infected by different trypanosomatid parasites. These hosts were infected by: T. cruzi DTU TcI (n = 12), T. cruzi DTU TcIV (n = 2), T. janseni (n = 15), T. dionisii (n = 1), and T. rangeli A (n = 1) detected in blood or tissue cultures, in addition to T. cruzi DTU TcI (n = 9) and Leishmania sp. (n = 1) only by the molecular diagnosis. Serological diagnosis was positive in 38 (71.6%) individuals for T. cruzi, the same amount for Leishmania spp., and 23 (43.3%) individuals were mixed infected. These data indicate a remarkable richness of trypanosomatid species/genotypes infecting small mammals, even in a disturbed area with low mammal species diversity—as is the case of the EFMA—reinforcing the generalist aspect of these parasites.
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Affiliation(s)
- Alice Pereira Berbigier
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil; (A.P.B.); (J.H.d.S.B.); (E.S.P.); (C.V.L.); (S.C.d.C.X.); (A.M.J.)
| | - Juliana Helena da Silva Barros
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil; (A.P.B.); (J.H.d.S.B.); (E.S.P.); (C.V.L.); (S.C.d.C.X.); (A.M.J.)
| | - Edilene Sousa Pontes
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil; (A.P.B.); (J.H.d.S.B.); (E.S.P.); (C.V.L.); (S.C.d.C.X.); (A.M.J.)
| | - Cristiane Varella Lisboa
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil; (A.P.B.); (J.H.d.S.B.); (E.S.P.); (C.V.L.); (S.C.d.C.X.); (A.M.J.)
| | - Rosana Gentile
- Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil;
| | - Samanta Cristina das Chagas Xavier
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil; (A.P.B.); (J.H.d.S.B.); (E.S.P.); (C.V.L.); (S.C.d.C.X.); (A.M.J.)
| | - Ana Maria Jansen
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil; (A.P.B.); (J.H.d.S.B.); (E.S.P.); (C.V.L.); (S.C.d.C.X.); (A.M.J.)
| | - André Luiz Rodrigues Roque
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil; (A.P.B.); (J.H.d.S.B.); (E.S.P.); (C.V.L.); (S.C.d.C.X.); (A.M.J.)
- Correspondence: ; Tel.: +55-(21)-2562-1416; Fax: +55-(21)-2562-1609
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Austen JM, Barbosa AD. Diversity and Epidemiology of Bat Trypanosomes: A One Health Perspective. Pathogens 2021; 10:pathogens10091148. [PMID: 34578180 PMCID: PMC8465530 DOI: 10.3390/pathogens10091148] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 11/17/2022] Open
Abstract
Bats (order Chiroptera) have been increasingly recognised as important reservoir hosts for human and animal pathogens worldwide. In this context, molecular and microscopy-based investigations to date have revealed remarkably high diversity of Trypanosoma spp. harboured by bats, including species of recognised medical and veterinary importance such as Trypanosoma cruzi and Trypanosoma evansi (aetiological agents of Chagas disease and Surra, respectively). This review synthesises current knowledge on the diversity, taxonomy, evolution and epidemiology of bat trypanosomes based on both molecular studies and morphological records. In addition, we use a One Health approach to discuss the significance of bats as reservoirs (and putative vectors) of T. cruzi, with a focus on the complex associations between intra-specific genetic diversity and eco-epidemiology of T. cruzi in sylvatic and domestic ecosystems. This article also highlights current knowledge gaps on the biological implications of trypanosome co-infections in a single host, as well as the prevalence, vectors, life-cycle, host-range and clinical impact of most bat trypanosomes recorded to date. Continuous research efforts involving molecular surveillance of bat trypanosomes are required for improved disease prevention and control, mitigation of biosecurity risks and potential spill-over events, ultimately ensuring the health of humans, domestic animals and wildlife globally.
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Affiliation(s)
- Jill M. Austen
- Centre for Biosecurity and One Health, Harry Butler Institute, Murdoch University, Murdoch, WA 6150, Australia
- Correspondence: (J.M.A.); (A.D.B.)
| | - Amanda D. Barbosa
- Centre for Biosecurity and One Health, Harry Butler Institute, Murdoch University, Murdoch, WA 6150, Australia
- CAPES Foundation, Ministry of Education of Brazil, Brasilia 70040-020, DF, Brazil
- Correspondence: (J.M.A.); (A.D.B.)
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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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Buendía-Abad M, García-Palencia P, de Pablos LM, Alunda JM, Osuna A, Martín-Hernández R, Higes M. First description of Lotmaria passim and Crithidia mellificae haptomonad stages in the honeybee hindgut. Int J Parasitol 2021; 52:65-75. [PMID: 34416272 DOI: 10.1016/j.ijpara.2021.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 12/22/2022]
Abstract
The remodelling of flagella into attachment structures is a common and important event in the trypanosomatid life cycle. Lotmaria passim and Crithidia mellificae can parasitize Apis mellifera, and as a result they might have a significant impact on honeybee health. However, there are details of their life cycle and the mechanisms underlying their pathogenicity in this host that remain unclear. Here we show that both L. passim promastigotes and C. mellificae choanomastigotes differentiate into haptomonad stages covering the ileum and rectum of honeybees. These haptomonad cells remain attached to the host surface via zonular hemidesmosome-like structures, as revealed by transmission electron microscopy. This work describes for the first known time the haptomonad morphotype of these species and their hemidesmosome-like attachments in A. mellifera, a key trait used by other trypanosomatid species to proliferate in the insect host hindgut.
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Affiliation(s)
- María Buendía-Abad
- Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), IRIAF - Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal, Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, Marchamalo, Spain.
| | - Pilar García-Palencia
- Departamento de Medicina Veterinaria y Cirugía Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Luis Miguel de Pablos
- Departamento de Parasitología, Grupo de Bioquímica y Parasitología Molecular CTS-183, Universidad de Granada, Granada, Spain
| | - José María Alunda
- Departamento de Sanidad Animal, Grupo ICPVet, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Antonio Osuna
- Departamento de Parasitología, Grupo de Bioquímica y Parasitología Molecular CTS-183, Universidad de Granada, Granada, Spain
| | - Raquel Martín-Hernández
- Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), IRIAF - Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal, Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, Marchamalo, Spain; Instituto de Recursos Humanos para la Ciencia y la Tecnología (INCRECYT-FEDER), Fundación Parque Científico y Tecnológico de Castilla - La Mancha, Albacete, Spain
| | - Mariano Higes
- Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), IRIAF - Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal, Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, Marchamalo, Spain
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Hendrickx S, Reis-Cunha JL, Forrester S, Jeffares DC, Caljon G. Experimental Selection of Paromomycin Resistance in Leishmania donovani Amastigotes Induces Variable Genomic Polymorphisms. Microorganisms 2021; 9:microorganisms9081546. [PMID: 34442625 PMCID: PMC8398221 DOI: 10.3390/microorganisms9081546] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 01/07/2023] Open
Abstract
The relatively high post-treatment relapse rates of paromomycin (PMM) in visceral leishmaniasis treatment and the swift emergence of experimental drug resistance challenge its broad application and urge for rational use and monitoring of resistance. However, no causal molecular mechanisms to Leishmania PMM resistance have been identified so far. To gain insights into potential resistance mechanisms, twelve experimentally selected Leishmania donovani clonal lines and the non-cloned preselection population, with variable degrees of PMM resistance, were subjected to whole genome sequencing. To identify genomic variations potentially associated with resistance, SNPs, Indels, chromosomal somy and gene copy number variations were compared between the different parasite lines. A total of 11 short nucleotide variations and the copy number alterations in 39 genes were correlated to PMM resistance. Some of the identified genes are involved in transcription, translation and protein turn-over (transcription elongation factor-like protein, RNA-binding protein, ribosomal protein L1a, 60S ribosomal protein L6, eukaryotic translation initiation factor 4E-1, proteasome regulatory non-ATP-ase subunit 3), virulence (major surface protease gp63, protein-tyrosine phosphatase 1-like protein), mitochondrial function (ADP/ATP mitochondrial carrier-like protein), signaling (phosphatidylinositol 3-related kinase, protein kinase putative and protein-tyrosine phosphatase 1-like protein) and vesicular trafficking (ras-related protein RAB1). These results indicate that, in Leishmania, the aminoglycoside PMM affects protein translational processes and underlines the complex and probably multifactorial origin of resistance.
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Affiliation(s)
- Sarah Hendrickx
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Antwerp, Belgium;
| | - João Luís Reis-Cunha
- Department of Biology and York Biomedical Research Institute, University of York, York YO31 5DD, UK; (J.L.R.-C.); (S.F.)
| | - Sarah Forrester
- Department of Biology and York Biomedical Research Institute, University of York, York YO31 5DD, UK; (J.L.R.-C.); (S.F.)
| | - Daniel C. Jeffares
- Department of Biology and York Biomedical Research Institute, University of York, York YO31 5DD, UK; (J.L.R.-C.); (S.F.)
- Correspondence: (D.C.J.); (G.C.); Tel.: +32-3-265-26-01 (G.C.)
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Antwerp, Belgium;
- Correspondence: (D.C.J.); (G.C.); Tel.: +32-3-265-26-01 (G.C.)
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46
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Zuma AA, Dos Santos Barrias E, de Souza W. Basic Biology of Trypanosoma cruzi. Curr Pharm Des 2021; 27:1671-1732. [PMID: 33272165 DOI: 10.2174/1381612826999201203213527] [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: 06/27/2020] [Revised: 10/01/2020] [Accepted: 10/08/2020] [Indexed: 11/22/2022]
Abstract
The present review addresses basic aspects of the biology of the pathogenic protozoa Trypanosoma cruzi and some comparative information of Trypanosoma brucei. Like eukaryotic cells, their cellular organization is similar to that of mammalian hosts. However, these parasites present structural particularities. That is why the following topics are emphasized in this paper: developmental stages of the life cycle in the vertebrate and invertebrate hosts; the cytoskeleton of the protozoa, especially the sub-pellicular microtubules; the flagellum and its attachment to the protozoan body through specialized junctions; the kinetoplast-mitochondrion complex, including its structural organization and DNA replication; glycosome and its role in the metabolism of the cell; acidocalcisome, describing its morphology, biochemistry, and functional role; cytostome and the endocytic pathway; the organization of the endoplasmic reticulum and Golgi complex; the nucleus, describing its structural organization during interphase and division; and the process of interaction of the parasite with host cells. The unique characteristics of these structures also make them interesting chemotherapeutic targets. Therefore, further understanding of cell biology aspects contributes to the development of drugs for chemotherapy.
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Affiliation(s)
- Aline A Zuma
- Laboratorio de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho - Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Emile Dos Santos Barrias
- Laboratorio de Metrologia Aplicada a Ciencias da Vida, Diretoria de Metrologia Aplicada a Ciencias da Vida - Instituto Nacional de Metrologia, Qualidade e Tecnologia (Inmetro), Rio de Janeiro, Brazil
| | - Wanderley de Souza
- Laboratorio de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho - Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Callejas-Hernández F, Herreros-Cabello A, Del Moral-Salmoral J, Fresno M, Gironès N. The Complete Mitochondrial DNA of Trypanosoma cruzi: Maxicircles and Minicircles. Front Cell Infect Microbiol 2021; 11:672448. [PMID: 34268138 PMCID: PMC8277381 DOI: 10.3389/fcimb.2021.672448] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/04/2021] [Indexed: 11/13/2022] Open
Abstract
The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA or kDNA or mtDNA, consists of a few maxicircles and thousands of minicircles concatenated together into a huge complex network. These structures present species-specific sizes, from 20 to 40 Kb in maxicircles and from 0.5 to 10 Kb in minicircles. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles contain coding guide RNAs involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. The knowledge about this mitochondrial genome is especially relevant since the expression of nuclear and mitochondrial genes involved in oxidative phosphorylation must be coordinated. In Trypanosoma cruzi (T. cruzi), the mtDNA has a dual relevance; the production of energy, and its use as a phylogenetic marker due to its high conservation among strains. Therefore, this study aimed to assemble, annotate, and analyze the complete repertoire of maxicircle and minicircle sequences of different T. cruzi strains by using DNA sequencing. We assembled and annotated the complete maxicircle sequence of the Y and Bug2148 strains. For Bug2148, our results confirm that the maxicircle sequence is the longest assembled to date, and is composed of 21 genes, most of them conserved among Trypanosomatid species. In agreement with previous results, T. cruzi minicircles show a conserved structure around 1.4 Kb, with four highly conserved regions and other four hypervariable regions interspersed between them. However, our results suggest that the parasite minicircles display several sizes and numbers of conserved and hypervariable regions, contrary to those previous studies. Besides, this heterogeneity is also reflected in the three conserved sequence blocks of the conserved regions that play a key role in the minicircle replication. Our results using sequencing technologies of second and third-generation indicate that the different consensus sequences of the maxicircles and minicircles seem to be more complex than previously described indicating at least four different groups in T. cruzi minicircles.
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Affiliation(s)
- Francisco Callejas-Hernández
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
| | - Alfonso Herreros-Cabello
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
| | - Javier Del Moral-Salmoral
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
| | - Manuel Fresno
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain.,Instituto Sanitario de Investigación de la Princesa, Group 12, Madrid, Spain
| | - Núria Gironès
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain.,Instituto Sanitario de Investigación de la Princesa, Group 12, Madrid, Spain
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Skalický T, Alves JMP, Morais AC, Režnarová J, Butenko A, Lukeš J, Serrano MG, Buck GA, Teixeira MMG, Camargo EP, Sanders M, Cotton JA, Yurchenko V, Kostygov AY. Endosymbiont Capture, a Repeated Process of Endosymbiont Transfer with Replacement in Trypanosomatids Angomonas spp. Pathogens 2021; 10:pathogens10060702. [PMID: 34200026 PMCID: PMC8229890 DOI: 10.3390/pathogens10060702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022] Open
Abstract
Trypanosomatids of the subfamily Strigomonadinae bear permanent intracellular bacterial symbionts acquired by the common ancestor of these flagellates. However, the cospeciation pattern inherent to such relationships was revealed to be broken upon the description of Angomonas ambiguus, which is sister to A. desouzai, but bears an endosymbiont genetically close to that of A. deanei. Based on phylogenetic inferences, it was proposed that the bacterium from A. deanei had been horizontally transferred to A. ambiguus. Here, we sequenced the bacterial genomes from two A. ambiguus isolates, including a new one from Papua New Guinea, and compared them with the published genome of the A. deanei endosymbiont, revealing differences below the interspecific level. Our phylogenetic analyses confirmed that the endosymbionts of A. ambiguus were obtained from A. deanei and, in addition, demonstrated that this occurred more than once. We propose that coinfection of the same blowfly host and the phylogenetic relatedness of the trypanosomatids facilitate such transitions, whereas the drastic difference in the occurrence of the two trypanosomatid species determines the observed direction of this process. This phenomenon is analogous to organelle (mitochondrion/plastid) capture described in multicellular organisms and, thereafter, we name it endosymbiont capture.
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Affiliation(s)
- Tomáš Skalický
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic; (T.S.); (A.B.); (J.L.)
| | - João M. P. Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (J.M.P.A.); (A.C.M.); (M.M.G.T.); (E.P.C.)
| | - Anderson C. Morais
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (J.M.P.A.); (A.C.M.); (M.M.G.T.); (E.P.C.)
| | - Jana Režnarová
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (J.R.); (V.Y.)
| | - Anzhelika Butenko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic; (T.S.); (A.B.); (J.L.)
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (J.R.); (V.Y.)
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic; (T.S.); (A.B.); (J.L.)
- Faculty of Sciences, University of South Bohemia, 370 05 České Budějovice (Budweis), Czech Republic
| | - Myrna G. Serrano
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23298-0678, USA; (M.G.S.); (G.A.B.)
| | - Gregory A. Buck
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23298-0678, USA; (M.G.S.); (G.A.B.)
| | - Marta M. G. Teixeira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (J.M.P.A.); (A.C.M.); (M.M.G.T.); (E.P.C.)
| | - Erney P. Camargo
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (J.M.P.A.); (A.C.M.); (M.M.G.T.); (E.P.C.)
| | - Mandy Sanders
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; (M.S.); (J.A.C.)
| | - James A. Cotton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; (M.S.); (J.A.C.)
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (J.R.); (V.Y.)
- 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; (J.R.); (V.Y.)
- Zoological Institute of the Russian Academy of Sciences, 199034 St. Petersburg, Russia
- Correspondence:
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Aphasizheva I, Aphasizhev R. Mitochondrial RNA quality control in trypanosomes. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1638. [PMID: 33331073 PMCID: PMC9805618 DOI: 10.1002/wrna.1638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 01/04/2023]
Abstract
Unicellular parasites Trypanosoma brucei spp. cause African human and animal trypanosomiasis, a spectrum of diseases that jeopardize public health and afflict the economy in sub-Saharan Africa. These hemoflagellates are distinguished by a single mitochondrion, which contains a kinetoplast nucleoid composed of DNA and histone-like proteins. Kinetoplast DNA (kDNA) represents a densely packed network of interlinked relaxed circular molecules: a few ~23-kb maxicircles encoding ribosomal RNAs (rRNAs) and proteins, and approximately 5,000 1-kb minicircles bearing guide RNA (gRNA) genes. The transcription start site defines the mRNA's 5' terminus while the primary RNA is remodeled into a monocistronic messenger by 3'-5' exonucleolytic trimming, 5' and 3' end modifications, and, in most cases, by internal U-insertion/deletion editing. Ribosomal and guide RNA precursors are also trimmed, and the processed molecules are uridylated. For 35 years, mRNA editing has attracted a major effort, but more recently the essential pre- and postediting processing and turnover events have been discovered and the key effectors have been identified. Among these, pentatricopeptide repeat (PPR) RNA binding proteins emerged as conduits coupling modifications of mRNA termini with internal sequence changes introduced by editing. Among 39 annotated PPRs, 20 belong to ribosomal subunits or assembly intermediates, four function as polyadenylation factors, a single factor directs 5' mRNA modification, and one protein is found in F1-ATPase. Nuclear and mitochondrial RNases P consist of a single PPR polypeptide, PRORP1 and PROP2, respectively. Here, we review PPR-mediated mitochondrial processes and discuss their potential roles in mRNA maturation, quality control, translational activation, and decay. This article is categorized under: RNA Processing > Capping and 5' End Modifications RNA Processing > 3' End Processing RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, Massachusetts
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, Massachusetts,Department of Biochemistry, Boston University Medical Campus, Boston, Massachusetts
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50
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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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