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Sabalette KB, Campo VA, Sotelo-Silveira JR, Smircich P, De Gaudenzi JG. Transcriptomic analysis of N-terminal mutated Trypanosoma cruzi UBP1 knockdown underlines the importance of this RNA-binding protein in parasite development. PLoS Negl Trop Dis 2024; 18:e0012179. [PMID: 38758959 PMCID: PMC11139272 DOI: 10.1371/journal.pntd.0012179] [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: 12/08/2023] [Revised: 05/30/2024] [Accepted: 04/30/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND During its life cycle, the human pathogen Trypanosoma cruzi must quickly adapt to different environments, in which the variation in the gene expression of the regulatory U-rich RNA-binding protein 1 (TcUBP1) plays a crucial role. We have previously demonstrated that the overexpression of TcUBP1 in insect-dwelling epimastigotes orchestrates an RNA regulon to promote differentiation to infective forms. METHODS In an attempt to generate TcUBP1 knockout parasites by using CRISPR-Cas9 technology, in the present study, we obtained a variant transcript that encodes a protein with 95% overall identity and a modified N-terminal sequence. The expression of this mutant protein, named TcUBP1mut, was notably reduced compared to that of the endogenous form found in normal cells. TcUBP1mut-knockdown epimastigotes exhibited normal growth and differentiation into infective metacyclic trypomastigotes and were capable of infecting mammalian cells. RESULTS We analyzed the RNA-Seq expression profiles of these parasites and identified 276 up- and 426 downregulated genes with respect to the wildtype control sample. RNA-Seq comparison across distinct developmental stages revealed that the transcriptomic profile of these TcUBP1mut-knockdown epimastigotes significantly differs not only from that of epimastigotes in the stationary phase but also from the gene expression landscape characteristic of infective forms. This is both contrary to and consistent with the results of our recent study involving TcUBP1-overexpressing cells. CONCLUSION Together, our findings demonstrate that the genes exhibiting opposite changes under overexpression and knockdown conditions unveil key mRNA targets regulated by TcUBP1. These mostly encompass transcripts that encode for trypomastigote-specific surface glycoproteins and ribosomal proteins, supporting a role for TcUBP1 in determining the molecular characteristics of the infective stage.
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Affiliation(s)
- Karina B. Sabalette
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín—Consejo Nacional de Investigaciones Científicas y Técnicas, General San Martín, Prov. de Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, General San Martín, Prov. de Buenos Aires, Argentina
| | - Vanina A. Campo
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín—Consejo Nacional de Investigaciones Científicas y Técnicas, General San Martín, Prov. de Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, General San Martín, Prov. de Buenos Aires, Argentina
| | - José R. Sotelo-Silveira
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
- Instituto de Biología, School of Sciences, Universidad de la República, Montevideo, Uruguay
| | - Pablo Smircich
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
- Instituto de Biología, School of Sciences, Universidad de la República, Montevideo, Uruguay
| | - Javier G. De Gaudenzi
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín—Consejo Nacional de Investigaciones Científicas y Técnicas, General San Martín, Prov. de Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, General San Martín, Prov. de Buenos Aires, Argentina
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Souza-Melo N, de Lima Alcantara C, Vidal JC, Rocha GM, de Souza W. Implications of Flagellar Attachment Zone Proteins TcGP72 and TcFLA-1BP in Morphology, Proliferation, and Intracellular Dynamics in Trypanosoma cruzi. Pathogens 2023; 12:1367. [PMID: 38003831 PMCID: PMC10675206 DOI: 10.3390/pathogens12111367] [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: 10/16/2023] [Revised: 11/05/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
The highly adaptable parasite Trypanosoma cruzi undergoes complex developmental stages to exploit host organisms effectively. Each stage involves the expression of specific proteins and precise intracellular structural organization. These morphological changes depend on key structures that control intracellular components' growth and redistribution. In trypanosomatids, the flagellar attachment zone (FAZ) connects the flagellum to the cell body and plays a pivotal role in cell expansion and structural rearrangement. While FAZ proteins are well-studied in other trypanosomatids, there is limited knowledge about specific components, organization, and function in T. cruzi. This study employed the CRISPR/Cas9 system to label endogenous genes and conduct deletions to characterize FAZ-specific proteins during epimastigote cell division and metacyclogenesis. In T. cruzi, these proteins exhibited distinct organization compared to their counterparts in T. brucei. TcGP72 is anchored to the flagellar membrane, while TcFLA-1BP is anchored to the membrane lining the cell body. We identified unique features in the organization and function of the FAZ in T. cruzi compared to other trypanosomatids. Deleting these proteins had varying effects on intracellular structures, cytokinesis, and metacyclogenesis. This study reveals specific variations that directly impact the success of cell division and differentiation of this parasite.
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Affiliation(s)
- Normanda Souza-Melo
- Laboratório de Ultraestrutura Celular Hertha Meyer, Centro de Pesquisas em Medicina de Precisão, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21491-590, Brazil; (C.d.L.A.); (J.C.V.); (G.M.R.)
| | - Carolina de Lima Alcantara
- Laboratório de Ultraestrutura Celular Hertha Meyer, Centro de Pesquisas em Medicina de Precisão, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21491-590, Brazil; (C.d.L.A.); (J.C.V.); (G.M.R.)
| | - Juliana Cunha Vidal
- Laboratório de Ultraestrutura Celular Hertha Meyer, Centro de Pesquisas em Medicina de Precisão, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21491-590, Brazil; (C.d.L.A.); (J.C.V.); (G.M.R.)
| | - Gustavo Miranda Rocha
- Laboratório de Ultraestrutura Celular Hertha Meyer, Centro de Pesquisas em Medicina de Precisão, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21491-590, Brazil; (C.d.L.A.); (J.C.V.); (G.M.R.)
| | - Wanderley de Souza
- Laboratório de Ultraestrutura Celular Hertha Meyer, Centro de Pesquisas em Medicina de Precisão, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21491-590, Brazil; (C.d.L.A.); (J.C.V.); (G.M.R.)
- Centro de Estudos Biomédicos-CMABio, Escola Superior de Saúde, Universidade do Estado do Amazonas-UEA, Manaus 69065-000, Brazil
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Marcelino TDP, Fala AM, da Silva MM, Souza-Melo N, Malvezzi AM, Klippel AH, Zoltner M, Padilla-Mejia N, Kosto S, Field MC, Burle-Caldas GDA, Teixeira SMR, Couñago RM, Massirer KB, Schenkman S. Identification of inhibitors for the transmembrane Trypanosoma cruzi eIF2α kinase relevant for parasite proliferation. J Biol Chem 2023; 299:104857. [PMID: 37230387 PMCID: PMC10300260 DOI: 10.1016/j.jbc.2023.104857] [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: 03/05/2023] [Revised: 05/02/2023] [Accepted: 05/05/2023] [Indexed: 05/27/2023] Open
Abstract
The TcK2 protein kinase of Trypanosoma cruzi, the causative agent of Chagas disease, is structurally similar to the human kinase PERK, which phosphorylates the initiation factor eIF2α and, in turn, inhibits translation initiation. We have previously shown that absence of TcK2 kinase impairs parasite proliferation within mammalian cells, positioning it as a potential target for treatment of Chagas disease. To better understand its role in the parasite, here we initially confirmed the importance of TcK2 in parasite proliferation by generating CRISPR/Cas9 TcK2-null cells, albeit they more efficiently differentiate into infective forms. Proteomics indicates that the TcK2 knockout of proliferative forms expresses proteins including trans-sialidases, normally restricted to infective and nonproliferative trypomastigotes explaining decreased proliferation and better differentiation. TcK2 knockout cells lost phosphorylation of eukaryotic initiation factor 3 and cyclic AMP responsive-like element, recognized to promote growth, likely explaining both decreased proliferation and augmented differentiation. To identify specific inhibitors, a library of 379 kinase inhibitors was screened by differential scanning fluorimetry using a recombinant TcK2 encompassing the kinase domain and selected molecules were tested for kinase inhibition. Only Dasatinib and PF-477736, inhibitors of Src/Abl and ChK1 kinases, showed inhibitory activity with IC50 of 0.2 ± 0.02 mM and 0.8 ± 0.1, respectively. In infected cells Dasatinib inhibited growth of parental amastigotes (IC50 = 0.6 ± 0.2 mM) but not TcK2 of depleted parasites (IC50 > 34 mM) identifying Dasatinib as a potential lead for development of therapeutics for Chagas disease targeting TcK2.
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Affiliation(s)
- Tiago de Paula Marcelino
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Angela Maria Fala
- Center for Molecular Biology and Genetic Engineering - CBMEG, Center of Medicinal Chemistry - CQMED, Structural Genomics Consortium - SGC, University of Campinas - UNICAMP, Campinas, SP, Brazil
| | - Matheus Monteiro da Silva
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Normanda Souza-Melo
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Amaranta Muniz Malvezzi
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Angélica Hollunder Klippel
- Center for Molecular Biology and Genetic Engineering - CBMEG, Center of Medicinal Chemistry - CQMED, Structural Genomics Consortium - SGC, University of Campinas - UNICAMP, Campinas, SP, Brazil; Departamento de Ciências Biológicas da Faculdade de Ciências Farmacêuticas da Universidade Estadual Paulista "Júlio de Mesquita Filho"-Unesp, Araraquara, SP, Brazil
| | - Martin Zoltner
- Drug Discovery and Evaluation Unit, Department of Parasitology, Faculty of Science, Charles University in Prague, BIOCEV, Vestec, Czech Republic
| | | | - Samantha Kosto
- School of Life Sciences, University of Dundee, Dundee, UK
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, UK; Biology Centre, Institute of Parasitology, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | | | | | - Rafael Miguez Couñago
- Center for Molecular Biology and Genetic Engineering - CBMEG, Center of Medicinal Chemistry - CQMED, Structural Genomics Consortium - SGC, University of Campinas - UNICAMP, Campinas, SP, Brazil
| | - Katlin Brauer Massirer
- Center for Molecular Biology and Genetic Engineering - CBMEG, Center of Medicinal Chemistry - CQMED, Structural Genomics Consortium - SGC, University of Campinas - UNICAMP, Campinas, SP, Brazil.
| | - Sergio Schenkman
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
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RNA-seq reveals that overexpression of TcUBP1 switches the gene expression pattern towards that of the infective form of Trypanosoma cruzi. J Biol Chem 2023; 299:104623. [PMID: 36935010 PMCID: PMC10141520 DOI: 10.1016/j.jbc.2023.104623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/19/2023] Open
Abstract
Trypanosomes regulate gene expression mainly by using post-transcriptional mechanisms. Key factors responsible for carrying out this regulation are RNA-binding proteins (RBPs), affecting subcellular localization, translation, and/or transcript stability. Trypanosoma cruzi U-rich RBP 1 (TcUBP1) is a small protein that modulates the expression of several surface glycoproteins of the trypomastigote infective stage of the parasite. Its mRNA targets are known but the impact of its overexpression at the transcriptome level in the insect-dwelling epimastigote cells has not yet been investigated. Thus, in the present study, by using a tetracycline-inducible system, we generated a population of TcUBP1-overexpressing parasites and analyzed its effect by RNA-seq methodology. This allowed us to identify 793 up- and 371 down-regulated genes with respect to the wild-type control sample. Among the up-regulated genes, it was possible to identify members coding for the TcS superfamily, MASP, MUCI/II, and protein kinases, whereas among the down-regulated transcripts, we found mainly genes coding for ribosomal, mitochondrial, and synthetic pathway proteins. RNA-seq comparison with two previously published datasets revealed that the expression profile of this TcUBP1-overexpressing replicative epimastigote form resembles the transition to the infective metacyclic trypomastigote stage. We identified novel cis-regulatory elements in the 3'-untranslated region of the affected transcripts and confirmed that UBP1m -a signature TcUBP1 binding element previously characterized in our lab- is enriched in the list of stabilized genes. We can conclude that the overall effect of TcUBP1 overexpression on the epimastigote transcriptome is mainly the stabilization of mRNAs coding for proteins that are important for parasite infection.
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Burle-Caldas GDA, Grazielle-Silva V, Faustino LP, Teixeira SMR. CRISPR Genome Editing and the Study of Chagas Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1429:111-125. [PMID: 37486519 DOI: 10.1007/978-3-031-33325-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Chagas disease, caused by the protozoan parasite Trypanosoma cruzi, is an illness that affects 6-8 million people worldwide and is responsible for approximately 50,000 deaths per year. Despite intense research efforts on Chagas disease and its causative agent, there is still a lack of effective treatments or strategies for disease control. Although significant progress has been made toward the elucidation of molecular mechanisms involved in host-parasite interactions, particularly immune evasion mechanisms, a deeper understanding of these processes has been hindered by a lack of efficient genetic manipulation protocols. One major challenge is the fact that several parasite virulence factors are encoded by multigene families, which constitute a distinctive feature of the T. cruzi genome. The recent advent of the CRISPR/Cas9 technology represented an enormous breakthrough in the studies involving T. cruzi genetic manipulation compared to previous protocols that are poorly efficient and required a long generation time to develop parasite mutants. Since the first publication of CRISPR gene editing in T. cruzi, in 2014, different groups have used distinct protocols to generated knockout mutants, parasites overexpressing a protein or expressing proteins with sequence tags inserted in the endogenous gene. Importantly, CRISPR gene editing allowed generation of parasite mutants with gene disruption in multi-copy gene families. We described four main strategies used to edit the T. cruzi genome and summarized a large list of studies performed by different groups in the past 7 years that are addressing several mechanisms involved with parasite proliferation, differentiation, and survival strategies within its different hosts.
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Affiliation(s)
| | - Viviane Grazielle-Silva
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Bertotti S, Fleming I, Cámara MDLM, Centeno Cameán C, Carmona SJ, Agüero F, Balouz V, Zahn A, Di Noia JM, Alfonzo JD, Buscaglia CA. Characterization of ADAT2/3 molecules in Trypanosoma cruzi and regulation of mucin gene expression by tRNA editing. Biochem J 2022; 479:561-580. [PMID: 35136964 DOI: 10.1042/bcj20210850] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/28/2022] [Accepted: 02/08/2022] [Indexed: 11/17/2022]
Abstract
Adenosine-to-inosine conversion at position 34 (A34-to-I) of certain tRNAs is essential for expanding their decoding capacity. This reaction is catalyzed by the adenosine deaminase acting on tRNA (ADAT) complex, which in Eukarya is formed by two subunits: ADAT2 and ADAT3. We herein identified and thoroughly characterized the ADAT molecules from the protozoan pathogen Trypanosoma cruzi, the causative agent of Chagas Disease. TcADAT2 and TcADAT3 spontaneously form a catalytically active complex, as shown by expression in engineered bacteria and/or by the increased ex vivo tRNA A-to-I deamination activity of T. cruzi epimastigotes overexpressing TcADAT subunits. Importantly, enhanced TcADAT2/3 activity in transgenic parasites caused a shift in their in vivo tRNAThrAGU signature, which correlated with significant changes in the expression of the Thr-rich TcSMUG proteins. To our knowledge, this is the first evidence indicating that T. cruzi tRNA editing can be modulated in vivo, in turn post-transcriptionally changing the expression of specific genes. Our findings suggest tRNA editing/availability as a forcible step in controlling gene expression and driving codon adaptation in T. cruzi. Moreover, we unveil certain differences between parasite and mammalian host tRNA editing and processing, such as cytosine-to-uridine conversion at position 32 of tRNAThrAGU in T. cruzi, that may be exploited for the identification of novel druggable targets of intervention.
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Affiliation(s)
- Santiago Bertotti
- Laboratory of Molecular Biology of Protozoa, Instituto de Investigaciones Biotecnológicas 'Dr Rodolfo Ugalde' (IIBio, Universidad Nacional de San Martín, UNSAM, and Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET), Av. 25 de Mayo y Francia, Campus UNSAM, San Martín (1650), Buenos Aires, Argentina
| | - Ian Fleming
- Department of Microbiology, The Ohio State University, 318 W 12th Ave. (Aronoff Building), Columbus, U.S.A
| | - María de Los Milagros Cámara
- Laboratory of Molecular Biology of Protozoa, Instituto de Investigaciones Biotecnológicas 'Dr Rodolfo Ugalde' (IIBio, Universidad Nacional de San Martín, UNSAM, and Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET), Av. 25 de Mayo y Francia, Campus UNSAM, San Martín (1650), Buenos Aires, Argentina
| | - Camila Centeno Cameán
- Laboratory of Molecular Biology of Protozoa, Instituto de Investigaciones Biotecnológicas 'Dr Rodolfo Ugalde' (IIBio, Universidad Nacional de San Martín, UNSAM, and Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET), Av. 25 de Mayo y Francia, Campus UNSAM, San Martín (1650), Buenos Aires, Argentina
| | - Santiago J Carmona
- Trypanosomatics Laboratory, IIBio (UNSAM and CONICET), Buenos Aires, Argentina
| | - Fernán Agüero
- Trypanosomatics Laboratory, IIBio (UNSAM and CONICET), Buenos Aires, Argentina
| | - Virginia Balouz
- Laboratory of Molecular Biology of Protozoa, Instituto de Investigaciones Biotecnológicas 'Dr Rodolfo Ugalde' (IIBio, Universidad Nacional de San Martín, UNSAM, and Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET), Av. 25 de Mayo y Francia, Campus UNSAM, San Martín (1650), Buenos Aires, Argentina
| | - Astrid Zahn
- Institut de Recherches Cliniques de Montreal (IRCM), Montreal, Quebec, Canada
- Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Javier M Di Noia
- Institut de Recherches Cliniques de Montreal (IRCM), Montreal, Quebec, Canada
- Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Juan D Alfonzo
- Department of Microbiology, The Ohio State University, 318 W 12th Ave. (Aronoff Building), Columbus, U.S.A
| | - Carlos A Buscaglia
- Laboratory of Molecular Biology of Protozoa, Instituto de Investigaciones Biotecnológicas 'Dr Rodolfo Ugalde' (IIBio, Universidad Nacional de San Martín, UNSAM, and Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET), Av. 25 de Mayo y Francia, Campus UNSAM, San Martín (1650), Buenos Aires, Argentina
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