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Prediction of Conserved Peptides of Paracoccidioides for Interferon-γ Release Assay: The First Step in the Development of a Lab-Based Approach for Immunological Assessment during Antifungal Therapy. J Fungi (Basel) 2020; 6:jof6040379. [PMID: 33352628 PMCID: PMC7766394 DOI: 10.3390/jof6040379] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/24/2020] [Accepted: 11/27/2020] [Indexed: 12/13/2022] Open
Abstract
Impaired antigen-specific cell-mediated immunity (CMI) is a primary immunological disturbance observed in individuals that develop paracoccidioidomycosis (PCM) after exposure to Paracoccidioides spp. Restoration of Paracoccidioides-specific CMI is crucial to stop the antifungal treatment and avoid relapses. A convenient and specific laboratory tool to assess antigen specific CMI is required for the appropriate clinical treatment of fungal infections, in order to decrease the time of antifungal therapy. We used an interferon-γ release assay strategy, used in the diagnosis of latent tuberculosis infection, to address our aims in this study. Information on proteins secreted by two well-studied representative strains-Paracoccidioides brasiliensis (Pb18) and P. lutzii (Pb-01)-were explored using PubMed or MEDLINE. From 26 publications, 252 proteins were identified, of which 203 were similar according to the Basic Local Alignment Search Tool. This enabled a selection of conserved peptides using the MEGA software. The SignalP-5.0, TMHMM, IEDB, NetMHC II, and IFNepitope algorithms were used to identify appropriate epitopes. In our study, we predicted antigenic epitopes of Paracoccidioides that could bind to MHC class II and induce IFN-γ secretion. These T cell epitopes can be used in the development of a laboratory tool to monitor the CMI of patients with PCM.
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Dai Y, Su W, Yang C, Song B, Li Y, Fu Y. Development of Novel Polymorphic EST-SSR Markers in Bailinggu (Pleurotus tuoliensis) for Crossbreeding. Genes (Basel) 2017; 8:genes8110325. [PMID: 29149037 PMCID: PMC5704238 DOI: 10.3390/genes8110325] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 10/16/2017] [Accepted: 11/08/2017] [Indexed: 01/02/2023] Open
Abstract
Identification of monokaryons and their mating types and discrimination of hybrid offspring are key steps for the crossbreeding of Pleurotus tuoliensis (Bailinggu). However, conventional crossbreeding methods are troublesome and time consuming. Using RNA-seq technology, we developed new expressed sequence tag-simple sequence repeat (EST-SSR) markers for Bailinggu to easily and rapidly identify monokaryons and their mating types, genetic diversity and hybrid offspring. We identified 1110 potential EST-based SSR loci from a newly-sequenced Bailinggu transcriptome and then randomly selected 100 EST-SSRs for further validation. Results showed that 39, 43 and 34 novel EST-SSR markers successfully identified monokaryons from their parent dikaryons, differentiated two different mating types and discriminated F1 and F2 hybrid offspring, respectively. Furthermore, a total of 86 alleles were detected in 37 monokaryons using 18 highly informative EST-SSRs. The observed number of alleles per locus ranged from three to seven. Cluster analysis revealed that these monokaryons have a relatively high level of genetic diversity. Transfer rates of the EST-SSRs in the monokaryons of closely-related species Pleurotuseryngii var. ferulae and Pleurotus ostreatus were 72% and 64%, respectively. Therefore, our study provides new SSR markers and an efficient method to enhance the crossbreeding of Bailinggu and closely-related species.
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Affiliation(s)
- Yueting Dai
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Wenying Su
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Chentao Yang
- China National GeneBank, Environmental Genomics, Beijing Genomics Institute, Shenzhen 518083, China.
| | - Bing Song
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Yongping Fu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
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Lacerda Pigosso L, Baeza LC, Vieira Tomazett M, Batista Rodrigues Faleiro M, Brianezi Dignani de Moura VM, Melo Bailão A, Borges CL, Alves Parente Rocha J, Rocha Fernandes G, Gauthier GM, Soares CMDA. Paracoccidioides brasiliensis presents metabolic reprogramming and secretes a serine proteinase during murine infection. Virulence 2017; 8:1417-1434. [PMID: 28704618 PMCID: PMC5711425 DOI: 10.1080/21505594.2017.1355660] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Paracoccidoides brasiliensis and Paracoccidioides lutzii, the etiologic agents of paracoccidioidomycosis, cause disease in healthy and immunocompromised persons in Latin America. We developed a method for harvesting P. brasiliensis yeast cells from infected murine lung to facilitate in vivo transcriptional and proteomic profiling. P. brasiliensis harvested at 6 h post-infection were analyzed using RNAseq and LC-MSE. In vivo yeast cells had 594 differentially expressed transcripts and 350 differentially expressed proteins. Integration of transcriptional and proteomic data indicated that early in infection (6 h), P. brasiliensis yeast cells underwent a shift in metabolism from glycolysis to β-oxidation, upregulated detoxifying enzymes to defend against oxidative stress, and repressed cell wall biosynthesis. Bioinformatics and functional analyses also demonstrated that a serine proteinase was upregulated and secreted in vivo. To our knowledge this is the first study depicting transcriptional and proteomic data of P. brasiliensis yeast cells upon 6 h post-infection of mouse lung.
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Affiliation(s)
- Laurine Lacerda Pigosso
- a Laboratório de Biologia Molecular , Instituto de Ciências Biológicas, Universidade Federal de Goiás , Campus Samambaia s/n, Goiânia , Goiás , Brazil
| | - Lilian Cristiane Baeza
- a Laboratório de Biologia Molecular , Instituto de Ciências Biológicas, Universidade Federal de Goiás , Campus Samambaia s/n, Goiânia , Goiás , Brazil
| | - Mariana Vieira Tomazett
- a Laboratório de Biologia Molecular , Instituto de Ciências Biológicas, Universidade Federal de Goiás , Campus Samambaia s/n, Goiânia , Goiás , Brazil
| | - Mariana Batista Rodrigues Faleiro
- b Laboratório de Patologia , Escola de Veterinária e Zootecnia, Universidade Federal de Goiás , Campus Samambaia s/n, Goiânia , Goiás , Brazil
| | | | - Alexandre Melo Bailão
- a Laboratório de Biologia Molecular , Instituto de Ciências Biológicas, Universidade Federal de Goiás , Campus Samambaia s/n, Goiânia , Goiás , Brazil
| | - Clayton Luiz Borges
- a Laboratório de Biologia Molecular , Instituto de Ciências Biológicas, Universidade Federal de Goiás , Campus Samambaia s/n, Goiânia , Goiás , Brazil
| | - Juliana Alves Parente Rocha
- a Laboratório de Biologia Molecular , Instituto de Ciências Biológicas, Universidade Federal de Goiás , Campus Samambaia s/n, Goiânia , Goiás , Brazil
| | | | | | - Celia Maria de Almeida Soares
- a Laboratório de Biologia Molecular , Instituto de Ciências Biológicas, Universidade Federal de Goiás , Campus Samambaia s/n, Goiânia , Goiás , Brazil
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Casaletti L, Lima PS, Oliveira LN, Borges CL, Báo SN, Bailão AM, Soares CMA. Analysis of Paracoccidioides lutzii mitochondria: a proteomic approach. Yeast 2017; 34:179-188. [PMID: 27886402 DOI: 10.1002/yea.3225] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 11/16/2016] [Accepted: 11/20/2016] [Indexed: 01/21/2023] Open
Abstract
The genus Paracoccidioides is composed of thermal dimorphic fungi, causative agents of paracoccidioidomycosis, one of the most frequent systemic mycoses in Latin America. Mitochondria have sophisticated machinery for ATP production, which involves metabolic pathways such as citric acid and glyoxylate cycles, electron transport chain and oxidative phosphorylation. In addition, this organelle performs a variety of functions in the cell, working as an exceptional metabolic signalling centre that contributes to cellular stress responses, as autophagy and apoptosis in eukaryotic organisms. The aim of this work was to perform a descriptive proteomic analysis of mitochondria in Paracoccidioides lutzii yeast cells. After mitochondria fractionation, samples enriched in mitochondrial proteins were digested with trypsin and analysed using a NanoUPLC-MSE system (Waters Corporation, Manchester, UK). Ours results revealed that the established protocol for purification of mitochondria was very effective for P. lutzii, and 298 proteins were identified as primarily mitochondrial, in our analysis. To our knowledge, this is the first compilation of mitochondrial proteins from P. lutzii, to date. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- L Casaletti
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICBII, Campus II, Universidade Federal de Goiás, 74001-970, Goiânia, Goiás, Brazil.,Escola de Engenharia, Pontifícia Universidade Católica de Goiás, 74605-010, Goiânia, Goiás, Brazil
| | - P S Lima
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICBII, Campus II, Universidade Federal de Goiás, 74001-970, Goiânia, Goiás, Brazil
| | - L N Oliveira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICBII, Campus II, Universidade Federal de Goiás, 74001-970, Goiânia, Goiás, Brazil.,Programa de Pós-graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, 70910-900, Brasília, Distrito Federal, Brazil
| | - C L Borges
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICBII, Campus II, Universidade Federal de Goiás, 74001-970, Goiânia, Goiás, Brazil
| | - S N Báo
- Laboratório de Microscopia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, 70910-900, Brasília, Distrito Federal, Brazil
| | - A M Bailão
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICBII, Campus II, Universidade Federal de Goiás, 74001-970, Goiânia, Goiás, Brazil
| | - C M A Soares
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICBII, Campus II, Universidade Federal de Goiás, 74001-970, Goiânia, Goiás, Brazil
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