1
|
Lima DA, Gonçalves LO, Reis-Cunha JL, Guimarães PAS, Ruiz JC, Liarte DB, Murta SMF. Transcriptomic analysis of benznidazole-resistant and susceptible Trypanosoma cruzi populations. Parasit Vectors 2023; 16:167. [PMID: 37217925 DOI: 10.1186/s13071-023-05775-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/16/2023] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Chagas disease (CD), caused by the parasite Trypanosoma cruzi, is a serious public health concern in Latin America. Nifurtimox and benznidazole (BZ), the only two drugs currently approved for the treatment of CD, have very low efficacies in the chronic phase of the disease and several toxic side effects. Trypanosoma cruzi strains that are naturally resistant to both drugs have been reported. We performed a comparative transcriptomic analysis of wild-type and BZ-resistant T. cruzi populations using high-throughput RNA sequencing to elucidate the metabolic pathways related to clinical drug resistance and identify promising molecular targets for the development of new drugs for treating CD. METHODS All complementary DNA (cDNA) libraries were constructed from the epimastigote forms of each line, sequenced and analysed using the Prinseq and Trimmomatic tools for the quality analysis, STAR as the aligner for mapping the reads against the reference genome (T. cruzi Dm28c-2018), the Bioconductor package EdgeR for statistical analysis of differential expression and the Python-based library GOATools for the functional enrichment analysis. RESULTS The analytical pipeline with an adjusted P-value of < 0.05 and fold-change > 1.5 identified 1819 transcripts that were differentially expressed (DE) between wild-type and BZ-resistant T. cruzi populations. Of these, 1522 (83.7%) presented functional annotations and 297 (16.2%) were assigned as hypothetical proteins. In total, 1067 transcripts were upregulated and 752 were downregulated in the BZ-resistant T. cruzi population. Functional enrichment analysis of the DE transcripts identified 10 and 111 functional categories enriched for the up- and downregulated transcripts, respectively. Through functional analysis we identified several biological processes potentially associated with the BZ-resistant phenotype: cellular amino acid metabolic processes, translation, proteolysis, protein phosphorylation, RNA modification, DNA repair, generation of precursor metabolites and energy, oxidation-reduction processes, protein folding, purine nucleotide metabolic processes and lipid biosynthetic processes. CONCLUSIONS The transcriptomic profile of T. cruzi revealed a robust set of genes from different metabolic pathways associated with the BZ-resistant phenotype, proving that T. cruzi resistance mechanisms are multifactorial and complex. Biological processes associated with parasite drug resistance include antioxidant defenses and RNA processing. The identified transcripts, such as ascorbate peroxidase (APX) and iron superoxide dismutase (Fe-SOD), provide important information on the resistant phenotype. These DE transcripts can be further evaluated as molecular targets for new drugs against CD.
Collapse
Affiliation(s)
- Davi Alvarenga Lima
- Genômica Funcional de Parasitos, Instituto René Rachou (IRR/Fiocruz Minas), Av. Augusto de Lima 1715, Belo Horizonte, MG, CEP 30190-002, Brazil
| | - Leilane Oliveira Gonçalves
- Informática de Biossistemas, Genômica e Bioengenharia, Instituto René Rachou (IRR/Fiocruz Minas), Belo Horizonte, MG, Brazil
| | | | - Paul Anderson Souza Guimarães
- Informática de Biossistemas, Genômica e Bioengenharia, Instituto René Rachou (IRR/Fiocruz Minas), Belo Horizonte, MG, Brazil
| | - Jeronimo Conceição Ruiz
- Informática de Biossistemas, Genômica e Bioengenharia, Instituto René Rachou (IRR/Fiocruz Minas), Belo Horizonte, MG, Brazil
| | | | - Silvane Maria Fonseca Murta
- Genômica Funcional de Parasitos, Instituto René Rachou (IRR/Fiocruz Minas), Av. Augusto de Lima 1715, Belo Horizonte, MG, CEP 30190-002, Brazil.
| |
Collapse
|
2
|
Avelar GST, Gonçalves LO, Guimarães FG, Guimarães PAS, do Nascimento Rocha LG, Carvalho MGR, de Melo Resende D, Ruiz JC. Diversity and genome mapping assessment of disordered and functional domains in trypanosomatids. J Proteomics 2020; 227:103919. [PMID: 32721629 DOI: 10.1016/j.jprot.2020.103919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 06/27/2020] [Accepted: 07/20/2020] [Indexed: 12/20/2022]
Abstract
The proteins that have structural disorder exemplify a class of proteins which is part of a new frontier in structural biology that demands a new understanding of the paradigm of structure/function correlations. In order to address the location, relative distances and the functional/structural correlation between disordered and conserved domains, consensus disordered predictions were mapped together with CDD domains in Leishmania braziliensis M2904, Leishmania infantum JPCM5, Trypanosoma cruzi CL-Brener Esmeraldo-like, Trypanosoma cruzi Dm28c, Trypanosoma cruzi Sylvio X10, Blechomonas ayalai B08-376 and Paratrypanosoma confusum CUL13 predicted proteomes. Our results depicts the role of protein disorder in key aspects of parasites biology highlighting: a) statistical significant association between genome structural location of protein disordered consensus stretches and functional domains; b) that disordered protein stretches appear in greater percentage at upstream or downstream position of the predicted domain; c) a possible role of structural disorder in several gene expression, control points that includes but are not limited to: i) protein folding; ii) protein transport and degradation; and iii) protein modification. In addition, for values of protein with disorder content greater than 40%, a small percentage of protein binding sites in IDPs/IDRs, a higher hypothetical protein annotation frequency was observed than expected by chance and trypanosomatid multigene families linked with virulence are rich in protein with disorder content. SIGNIFICANCE: T. cruzi and Leishmania spp are the etiological agents of Chagas disease and leishmaniasis, respectively. Currently, no vaccine or effective drug treatment is available against these neglected diseases and the knowledge about the post-transcriptional and post-translational mechanisms of these organisms, which are key for this scenario, remain scarce. This study depicts the potential impact of the proximity between protein structural disorder and functional domains in the post-transcriptional regulation of pathogenic versus human non-pathogenic trypanosomatids. Our results revealed a significant statistical relationship between the genome structural locations of these two variables and disordered regions appearing more frequently at upstream or downstream positions of the CDD locus domain. This flexibility feature would maintain structural accessibility of functional sites for post-translational modifications, shedding light into this important aspect of parasite biology. This hypothesis is corroborated by the functional enrichment analysis of disordered proteins subset that highlight the involvement of this class of proteins in protein folding, protein transport and degradation and protein modification. Furthermore, our results pointed out: a) the impact of protein disorder in the process of genome annotation (proteins tend to be annotated as hypothetical when the disorder content reaches ~40%); b) that trypanosomatid multigenic families linked with virulence have a key protein disorder content.
Collapse
Affiliation(s)
- Grace Santos Tavares Avelar
- Programa de Pós-graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil; Grupo Informática de Biossistemas, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil
| | - Leilane Oliveira Gonçalves
- Programa de Pós-graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil; Grupo Informática de Biossistemas, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil
| | - Frederico Gonçalves Guimarães
- Programa de Pós-graduação em Ciências da Saúde, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil; Grupo Informática de Biossistemas, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil
| | - Paul Anderson Souza Guimarães
- Programa de Pós-graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil; Grupo Informática de Biossistemas, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil
| | - Luiz Gustavo do Nascimento Rocha
- Programa de Pós-graduação em Ciências da Saúde, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil; Grupo Informática de Biossistemas, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil
| | | | - Daniela de Melo Resende
- Programa de Pós-graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil; Programa de Pós-graduação em Ciências da Saúde, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil; Grupo Informática de Biossistemas, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil
| | - Jeronimo Conceição Ruiz
- Programa de Pós-graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil; Programa de Pós-graduação em Ciências da Saúde, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil; Grupo Informática de Biossistemas, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil.
| |
Collapse
|
3
|
Márcia de Oliveira L, Nogueira de Brito R, Anderson Souza Guimarães P, Vitor Mastrângelo Amaro dos Santos R, Gonçalves Diotaiuti L, de Cássia Moreira de Souza R, Conceição Ruiz J. TriatoKey: a web and mobile tool for biodiversity identification of Brazilian triatomine species. Database (Oxford) 2017; 2017:3737831. [PMID: 28605769 PMCID: PMC5467554 DOI: 10.1093/database/bax033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/13/2017] [Accepted: 03/25/2017] [Indexed: 12/04/2022]
Abstract
Triatomines are blood-sucking insects that transmit the causative agent of Chagas disease, Trypanosoma cruzi. Despite being recognized as a difficult task, the correct taxonomic identification of triatomine species is crucial for vector control in Latin America, where the disease is endemic. In this context, we have developed a web and mobile tool based on PostgreSQL database to help healthcare technicians to overcome the difficulties to identify triatomine vectors when the technical expertise is missing. The web and mobile version makes use of real triatomine species pictures and dichotomous key method to support the identification of potential vectors that occur in Brazil. It provides a user example-driven interface with simple language. TriatoKey can also be useful for educational purposes. Database URL http://triatokey.cpqrr.fiocruz.br.
Collapse
Affiliation(s)
- Luciana Márcia de Oliveira
- Grupo Informática de Biossistemas e Genômica - Centro de Pesquisas René Rachou, Fiocruz Minas. Av. Augusto de Lima, 1715, 30190-002 Belo Horizonte MG -Brazil
- Programa de Pós Graduação em Bioinformática - Universidade Federal de Minas Gerais (UFMG), Av. Antônio Carlos 6627 - Pampulha, 31270-901 Belo Horizonte MG -Brazil
- Centro Universitário UNA – Instituto de Ciências Biológicas e da Saúde. Rua Guajajaras, 175 Centro, 30180-100 Belo Horizonte MG -Brazil and
| | - Raissa Nogueira de Brito
- Laboratório de Triatomíneos - Centro de Pesquisas René Rachou, Fiocruz Minas, Av. Augusto de Lima, 1715, 30190-002 Belo Horizonte MG -Brazil
| | - Paul Anderson Souza Guimarães
- Grupo Informática de Biossistemas e Genômica - Centro de Pesquisas René Rachou, Fiocruz Minas. Av. Augusto de Lima, 1715, 30190-002 Belo Horizonte MG -Brazil
- Centro Universitário UNA – Instituto de Ciências Biológicas e da Saúde. Rua Guajajaras, 175 Centro, 30180-100 Belo Horizonte MG -Brazil and
| | | | - Liléia Gonçalves Diotaiuti
- Laboratório de Triatomíneos - Centro de Pesquisas René Rachou, Fiocruz Minas, Av. Augusto de Lima, 1715, 30190-002 Belo Horizonte MG -Brazil
| | - Rita de Cássia Moreira de Souza
- Laboratório de Triatomíneos - Centro de Pesquisas René Rachou, Fiocruz Minas, Av. Augusto de Lima, 1715, 30190-002 Belo Horizonte MG -Brazil
| | - Jeronimo Conceição Ruiz
- Grupo Informática de Biossistemas e Genômica - Centro de Pesquisas René Rachou, Fiocruz Minas. Av. Augusto de Lima, 1715, 30190-002 Belo Horizonte MG -Brazil
| |
Collapse
|