1
|
Dallastella M, de Oliveira WK, Rodrigues ML, Goldenberg S, Alves LR. The characterization of RNA-binding proteins and RNA metabolism-related proteins in fungal extracellular vesicles. Front Cell Infect Microbiol 2023; 13:1247329. [PMID: 37780856 PMCID: PMC10539620 DOI: 10.3389/fcimb.2023.1247329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 08/23/2023] [Indexed: 10/03/2023] Open
Abstract
RNA-binding proteins (RBPs) are essential for regulating RNA metabolism, stability, and translation within cells. Recent studies have shown that RBPs are not restricted to intracellular functions and can be found in extracellular vesicles (EVs) in different mammalian cells. EVs released by fungi contain a variety of proteins involved in RNA metabolism. These include RNA helicases, which play essential roles in RNA synthesis, folding, and degradation. Aminoacyl-tRNA synthetases, responsible for acetylating tRNA molecules, are also enriched in EVs, suggesting a possible link between these enzymes and tRNA fragments detected in EVs. Proteins with canonical RNA-binding domains interact with proteins and RNA, such as the RNA Recognition Motif (RRM), Zinc finger, and hnRNP K-homology (KH) domains. Polyadenylate-binding protein (PABP) plays a critical role in the regulation of gene expression by binding the poly(A) tail of messenger RNA (mRNA) and facilitating its translation, stability, and localization, making it a key factor in post-transcriptional control of gene expression. The presence of proteins related to the RNA life cycle in EVs from different fungal species suggests a conserved mechanism of EV cargo packing. Various models have been proposed for selecting RNA molecules for release into EVs. Still, the actual loading processes are unknown, and further molecular characterization of these proteins may provide insight into the mechanism of RNA sorting into EVs. This work reviews the current knowledge of RBPs and proteins related to RNA metabolism in EVs derived from distinct fungi species, and presents an analysis of proteomic datasets through GO term and orthology analysis, Our investigation identified orthologous proteins in fungal EVs on different fungal species.
Collapse
Affiliation(s)
- Marianna Dallastella
- Gene Expression Regulation Laboratory, Carlos Chagas Institute (ICC), Oswaldo Cruz Foundation, FIOCRUZ, Curitiba, Brazil
| | - Willian Klassen de Oliveira
- Laboratory for Applied Sciences and Technology in Health, Carlos Chagas Institute, FIOCRUZ PR, Curitiba, Brazil
| | - Marcio L. Rodrigues
- Gene Expression Regulation Laboratory, Carlos Chagas Institute (ICC), Oswaldo Cruz Foundation, FIOCRUZ, Curitiba, Brazil
- Microbiology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Samuel Goldenberg
- Gene Expression Regulation Laboratory, Carlos Chagas Institute (ICC), Oswaldo Cruz Foundation, FIOCRUZ, Curitiba, Brazil
| | - Lysangela R. Alves
- Gene Expression Regulation Laboratory, Carlos Chagas Institute (ICC), Oswaldo Cruz Foundation, FIOCRUZ, Curitiba, Brazil
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center, University Laval, Quebec, QC, Canada
| |
Collapse
|
2
|
Alves LR, Correa A, Guimarães AJ, Rodrigues ML. Editorial: Extracellular vesicles in diseases, host-pathogen interaction and therapeutic applications. Front Cell Infect Microbiol 2022; 12:1010008. [PMID: 36211952 PMCID: PMC9535090 DOI: 10.3389/fcimb.2022.1010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 08/12/2022] [Indexed: 11/27/2022] Open
Affiliation(s)
- Lysangela R. Alves
- Gene Expression Regulation Laboratory, Instituto Carlos Chagas - FIOCRUZ-PR, Curitiba, Brazil
- *Correspondence: Lysangela R. Alves,
| | - Alejandro Correa
- Stem Cells Basic Biology Laboratory, Instituto Carlos Chagas - FIOCRUZ-PR, Curitiba, Brazil
| | - Allan J. Guimarães
- Laboratório de Bioquímica e Imunologia das Micoses, Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Rio de Janeiro, Brazil
| | - Marcio L. Rodrigues
- Gene Expression Regulation Laboratory, Instituto Carlos Chagas - FIOCRUZ-PR, Curitiba, Brazil
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro, Niteroi, Brazil
| |
Collapse
|
3
|
de Oliveira HC, Castelli RF, Reis FCG, Samby K, Nosanchuk JD, Alves LR, Rodrigues ML. Screening of the Pandemic Response Box Reveals an Association between Antifungal Effects of MMV1593537 and the Cell Wall of Cryptococcus neoformans, Cryptococcus deuterogattii, and Candida auris. Microbiol Spectr 2022; 10:e0060122. [PMID: 35471056 PMCID: PMC9241760 DOI: 10.1128/spectrum.00601-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/11/2022] [Indexed: 11/20/2022] Open
Abstract
There is an urgent unmet need for novel antifungals. In this study, we searched for novel antifungal activities in the Pandemic Response Box, a collection of 400 structurally diverse compounds in various phases of drug discovery. We identified five molecules which could control the growth of Cryptococcus neoformans, Cryptococcus deuterogattii, and the emerging global threat Candida auris. After eliminating compounds which demonstrated paradoxical antifungal effects or toxicity to mammalian macrophages, we selected compound MMV1593537 as a nontoxic, fungicidal molecule for further characterization of antifungal activity. Scanning electron microscopy revealed that MMV1593537 affected cellular division in all three pathogens. In Cryptococcus, MMV1593537 caused a reduction in capsular dimensions. Treatment with MMV1593537 resulted in increased detection of cell wall chitooligomers in these three species. Since chitooligomers are products of the enzymatic hydrolysis of chitin, we investigated whether surface chitinase activity was altered in response to MMV1593537 exposure. We observed peaks of enzyme activity in C. neoformans and C. deuterogattii in response to MMV1593537. We did not detect any surface chitinase activity in C. auris. Our results suggest that MMV1593537 is a promising, nontoxic fungicide whose mechanism of action, at least in Cryptococcus spp, requires chitinase-mediated hydrolysis of chitin. IMPORTANCE The development of novel antifungals is a matter of urgency. In this study, we evaluated antifungal activities in a collection of 400 molecules, using highly lethal fungal pathogens as targets. One of these molecules, namely, MMV1593537, was not toxic to host cells and controlled the growth of isolates of Cryptococcus neoformans, C. deuterogattii, C. gattii, Candida auris, C. albicans, C. parapsilosis, and C. krusei. We tested the mechanisms of antifungal action of MMV1593537 in the Cryptococcus and C. auris models and concluded that the compound affects the cell wall, a structure which is essential for fungal life. At least in Cryptococcus, this effect involved chitinase, an enzyme which is required for remodeling the cell wall. Our results suggest that MMV1593537 is a candidate for future antifungal development.
Collapse
Affiliation(s)
| | - Rafael F. Castelli
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil
- Programa de Pós-Graduação em Biologia Parasitária, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Flavia C. G. Reis
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil
- Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - Joshua D. Nosanchuk
- Department of Microbiology and Immunology and Division of Infectious Diseases, Albert Einstein College of Medicine of Yeshiva University, New York, New York, USA
| | - Lysangela R. Alves
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil
| | - Marcio L. Rodrigues
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
4
|
de Oliveira HC, Castelli RF, Alves LR, Nosanchuk JD, Salama EA, Seleem M, Rodrigues ML. Identification of 4 compounds from the Pharmakon library with antifungal activity against Candida auris and species of Cryptococcus. Med Mycol 2022; 60:6586341. [PMID: 35575621 DOI: 10.1093/mmy/myac033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/11/2022] [Accepted: 05/12/2022] [Indexed: 11/14/2022] Open
Abstract
There is an urgent need to develop novel antifungals. In this study, we screened 1600 compounds for antifungal activity against Cryptococcus neoformans and Candida auris. We evaluated 4 promising compounds against 24 additional isolates of C. neoformans, C. auris, Cryptococcus deuterogattii, and Cryptococcus gattii. The 4 compounds, dequalinium chloride (DQC), bleomycin sulfate (BMS), pentamidine isethionate salt (PIS), and clioquinol (CLQ), varied in their efficacy against these pathogens but were generally more effective against cryptococci. The compounds exerted their antifungal effect via multiple mechanisms including interference with the capsule of cryptococci and induction of hyphal-like morphology in C. auris. Our results indicate that DQC, BMS, PIS, and CLQ represent potential prototypes for the future development of antifungals.
Collapse
Affiliation(s)
| | - Rafael F Castelli
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil.,Programa de Pós-Graduação em Biologia Parasitária, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Lysangela R Alves
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil
| | - Joshua D Nosanchuk
- Departments of Medicine (Division of Infectious Diseases) and Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Ehab A Salama
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - Mohamed Seleem
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - Marcio L Rodrigues
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil.,Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
5
|
Abstract
Extracellular vesicles (EVs) are structures released by a variety of cells from all kingdoms of life. EVs are typically involved in communication between tissues and organs, between distinct organisms, or inside microbial communities. The plasticity of these structures is reflected in the range of biological effects they are able to induce or inhibit. The study of fungal EVs is relatively new with the first report in 2007, but investigators have already demonstrated in several model systems that fungal EVs significantly modulate the host immune system and that the immunogenic materials in EV can be harnessed as vaccination platforms. This chapter describes the two main procedures used to isolate EVs from an emerging pathogenic fungus, Candida auris.
Collapse
Affiliation(s)
- Daniel Zamith-Miranda
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Lysangela R Alves
- Instituto Carlos Chagas, Fundacao Oswaldo Cruz (Fiocruz), Curitiba, Brazil, Curitiba, Brazil
| | - Marcio L Rodrigues
- Instituto Carlos Chagas, Fundacao Oswaldo Cruz (Fiocruz), Curitiba, Brazil, Curitiba, Brazil
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leonardo Nimrichter
- Laboratório de Glicobiologia de Eucariotos, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Joshua D Nosanchuk
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA.
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.
| |
Collapse
|
6
|
Munhoz da Rocha IF, Martins ST, Amatuzzi RF, Zamith-Miranda D, Nosanchuk JD, Rodrigues ML, Alves LR. Cellular and Extracellular Vesicle RNA Analysis in the Global Threat Fungus Candida auris. Microbiol Spectr 2021; 9:e0153821. [PMID: 34908466 PMCID: PMC8672890 DOI: 10.1128/spectrum.01538-21] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/03/2021] [Indexed: 12/18/2022] Open
Abstract
Emerging and reemerging pathogens are a worldwide concern, and it is predicted that these microbes will cause severe outbreaks. Candida auris affects people with weakened immune systems, particularly those who are hospitalized or are in health care facilities. Extracellular vesicles (EVs) are lipid bilayer structures released by organisms from all domains of life. EVs can deliver functional molecules to target cells, including proteins and nucleic acids, especially RNA molecules. EVs from several pathogenic fungi species play diverse biological roles related to cell-cell communication and pathogen-host interaction. In this study, we describe a data set which we produced by sequencing the RNA content of EVs from C. auris under normal growth conditions and in the presence of the antifungal caspofungin, a first-line drug to treat this fungus. To generate a more complete data set for future comparative studies, we also sequenced the RNA cellular content of EVs under the same conditions. This data set addresses a previously unexplored area of fungal biology regarding cellular small RNA and EV RNA. Our data will provide a molecular basis for the study of the aspects associated with antifungal treatment, gene expression response, and EV composition in C. auris. These data will also allow the exploration of small RNA content in the fungal kingdom and might serve as an informative basis for studies on the mechanisms by which molecules are directed to fungal EVs. IMPORTANCE Candida auris, a relevant emerging human-pathogenic yeast, is the first fungus to be called a global public health threat by the WHO. This is because of its rapid spread on all inhabited continents, together with its extremely high frequency of drug and multidrug resistance. In our study, we generated a large data set for 3 distinct strains of C. auris and obtained cellular small RNA fraction as well as extracellular vesicle RNA (EV-RNA) during normal growth conditions and after treatment with caspofungin, the first-line drug used to treat C. auris infection.
Collapse
Affiliation(s)
| | - Sharon T. Martins
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, Fiocruz Paraná, Curitiba, Brazil
| | - Rafaela F. Amatuzzi
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, Fiocruz Paraná, Curitiba, Brazil
| | - Daniel Zamith-Miranda
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Joshua D. Nosanchuk
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Marcio L. Rodrigues
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, Fiocruz Paraná, Curitiba, Brazil
- Microbiology Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lysangela R. Alves
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, Fiocruz Paraná, Curitiba, Brazil
| |
Collapse
|
7
|
Oliveira MM, Schemberger MO, Suzukawa AA, Riediger IN, do Carmo Debur M, Becker G, Resende PC, Gräf T, Balsanelli E, de Baura VA, de Souza EM, Pedrosa FO, Alves LR, Blanes L, Nardelli SC, Aguiar AM, Albrecht L, Zanette D, Ávila AR, Morello LG, Marchini FK, Dos Santos HG, Passetti F, Dallagiovanna B, Faoro H. Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. Virol J 2021; 18:222. [PMID: 34789293 PMCID: PMC8596384 DOI: 10.1186/s12985-021-01690-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/01/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND We report a genomic surveillance of SARS-CoV-2 lineages circulating in Paraná, southern Brazil, from March 2020 to April 2021. Our analysis, based on 333 genomes, revealed that the first variants detected in the state of Paraná in March 2020 were the B.1.1.33 and B.1.1.28 variants. The variants B.1.1.28 and B.1.1.33 were predominant throughout 2020 until the introduction of the variant P.2 in August 2020 and a variant of concern (VOC), Gamma (P.1), in January 2021. The VOC Gamma, a ramification of the B.1.1.28 lineage first detected in Manaus (northern Brazil), has grown rapidly since December 2020 and was thought to be responsible for the deadly second wave of COVID-19 throughout Brazil. METHODS The 333 genomic sequences of SARS-CoV-2 from March 2020 to April 2021 were generated as part of the genomic surveillance carried out by Fiocruz in Brazil Genomahcov Fiocruz. SARS-CoV-2 sequencing was performed using representative samples from all geographic areas of Paraná. Phylogenetic analyses were performed using the 333 genomes also included other SARS-CoV-2 genomes from the state of Paraná and other states in Brazil that were deposited in the GISAID. In addition, the time-scaled phylogenetic tree was constructed with up to 3 random sequences of the Gamma variant from each state in Brazil in each month of 2021. In this analysis we also added the sequences identified as the B.1.1.28 lineage of the Amazonas state and and the Gamma-like-II (P.1-like-II) lineage identified in different regions of Brazil. RESULTS Phylogenetic analyses of the SARS-CoV-2 genomes that were previously classified as the VOC Gamma lineage by WHO/PANGO showed that some genomes from February to April 2021 branched in a monophyletic clade and that these samples grouped together with genomes recently described with the lineage Gamma-like-II. Additionally, a new mutation (E661D) in the spike (S) protein has been identified in nearly 10% of the genomes classified as the VOC Gamma from Paraná in March and April 2021.Finally, we analyzed the correlation between the lineage and the Gamma variant frequency, age group (patients younger or older than 60 years old) and the clinical data of 86 cases from the state of Paraná. CONCLUSIONS Our results provided a reliable picture of the evolution of the SARS-CoV-2 pandemic in the state of Paraná characterized by the dominance of the Gamma strain, as well as a high frequencies of the Gamma-like-II lineage and the S:E661D mutation. Epidemiological and genomic surveillance efforts should be continued to unveil the biological relevance of the novel mutations detected in the VOC Gamma in Paraná.
Collapse
Affiliation(s)
- Mauro M Oliveira
- Laboratório de Ciências e Tecnologias Aplicadas Em Saúde, Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Michelle O Schemberger
- Laboratório de Ciências e Tecnologias Aplicadas Em Saúde, Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Andreia A Suzukawa
- Laboratório de Biologia Básica de Células Tronco, Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Irina N Riediger
- Laboratório Central do Estado do Paraná, LACEN, Curitiba, Paraná, Brazil
| | | | - Guilherme Becker
- Laboratório Central do Estado do Paraná, LACEN, Curitiba, Paraná, Brazil
| | - Paola Cristina Resende
- Laboratórios de Vírus Respiratórios e do Sarampo (LVRS), Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tiago Gräf
- Instituto Gonçalo Moniz, FIOCRUZ, Salvador, Bahia, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal Do Paraná, Curitiba, Paraná, Brazil
| | - Valter Antônio de Baura
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal Do Paraná, Curitiba, Paraná, Brazil
| | - Emanuel M de Souza
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal Do Paraná, Curitiba, Paraná, Brazil
| | - Fábio O Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal Do Paraná, Curitiba, Paraná, Brazil
| | - Lysangela R Alves
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Lucas Blanes
- Laboratório de Ciências e Tecnologias Aplicadas Em Saúde, Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Sheila Cristina Nardelli
- Laboratório de Pesquisa em Apicomplexa, Carlos Chagas Institute, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Alessandra M Aguiar
- Laboratório de Biologia Básica de Células Tronco, Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Letusa Albrecht
- Laboratório de Pesquisa em Apicomplexa, Carlos Chagas Institute, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Dalila Zanette
- Laboratório de Ciências e Tecnologias Aplicadas Em Saúde, Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Andréa R Ávila
- Laboratório de Pesquisa em Apicomplexa, Carlos Chagas Institute, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Luis Gustavo Morello
- Laboratório de Ciências e Tecnologias Aplicadas Em Saúde, Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Fabricio K Marchini
- Laboratório de Ciências e Tecnologias Aplicadas Em Saúde, Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil
| | | | - Fabio Passetti
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Bruno Dallagiovanna
- Laboratório de Biologia Básica de Células Tronco, Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Helisson Faoro
- Laboratório de Ciências e Tecnologias Aplicadas Em Saúde, Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil.
| |
Collapse
|
8
|
Zamith-Miranda D, Amatuzzi RF, Munhoz da Rocha IF, Martins ST, Lucena AC, Vieira AZ, Trentin G, Almeida F, Rodrigues ML, Nakayasu ES, Nosanchuk JD, Alves LR. Transcriptional and translational landscape of Candida auris in response to caspofungin. Comput Struct Biotechnol J 2021; 19:5264-5277. [PMID: 34630944 PMCID: PMC8481930 DOI: 10.1016/j.csbj.2021.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 08/30/2021] [Accepted: 09/09/2021] [Indexed: 01/25/2023] Open
Abstract
Candida auris has emerged as a serious worldwide threat by causing opportunistic infections that are frequently resistant to one or more conventional antifungal medications resulting in high mortality rates. Against this backdrop, health warnings around the world have focused efforts on understanding C. auris fungal biology and effective prevention and treatment approaches to combat this fungus. To date, there is little information about the differentially expressed genes when this fungus is treated with conventional antifungals, and caspofungin is a standard echinocandin deployed in the therapy against C. auris. In this work, we treated two distinct strains of C. auris for 24 h with caspofungin, and the cellular responses were evaluated at the morphological, translational and transcriptional levels. We first observed that the echinocandin caused morphological alterations, aggregation of yeast cells, and modifications in the cell wall composition of C. auris. Transcriptomic analysis revealed an upregulation of genes related to the synthesis of the cell wall, ribosome, and cell cycle after exposure to caspofungin. Supporting these findings, the integrated proteomic analysis showed that caspofungin-treated cells were enriched in ribosome-related proteins and cell wall, especially mannoproteins. Altogether, these results provide further insights into the biology of C. auris and expands our understanding regarding the antifungal activity of caspofungin and reveal cellular targets, as the mannose metabolism, that can be further explored for the development of novel antifungals.
Collapse
Affiliation(s)
- Daniel Zamith-Miranda
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rafaela F. Amatuzzi
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, FIOCRUZ PR, Curitiba, Brazil
| | | | - Sharon T. Martins
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, FIOCRUZ PR, Curitiba, Brazil
| | - Aline C.R. Lucena
- Laboratory for Applied Sciences and Technology in Health, Carlos Chagas Institute, FIOCRUZ PR, Curitiba, Brazil
| | - Alexandre Z. Vieira
- Laboratory for Applied Sciences and Technology in Health, Carlos Chagas Institute, FIOCRUZ PR, Curitiba, Brazil
| | - Gabriel Trentin
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Fausto Almeida
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Marcio L. Rodrigues
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, FIOCRUZ PR, Curitiba, Brazil
- Microbiology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | - Joshua D. Nosanchuk
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Lysangela R. Alves
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, FIOCRUZ PR, Curitiba, Brazil
| |
Collapse
|
9
|
Reis FCG, Gimenez B, Jozefowicz LJ, Castelli RF, Martins ST, Alves LR, de Oliveira HC, Rodrigues ML. Analysis of Cryptococcal Extracellular Vesicles: Experimental Approaches for Studying Their Diversity Among Multiple Isolates, Kinetics of Production, Methods of Separation, and Detection in Cultures of Titan Cells. Microbiol Spectr 2021; 9:e0012521. [PMID: 34346749 PMCID: PMC8552642 DOI: 10.1128/spectrum.00125-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/12/2021] [Indexed: 11/20/2022] Open
Abstract
Extracellular vesicles (EVs) produced by members of the Cryptococcus genus are associated with fundamental processes of fungal physiology and virulence. However, several questions about the properties of cryptococcal EVs remain unanswered, mostly because of technical limitations. We recently described a fast and efficient protocol of high-yield EV isolation from solid medium. In this study, we aimed at using the solid medium protocol to address some of the open questions about EVs, including the kinetics of EV production, the diversity of EVs produced by multiple isolates under different culture conditions, the separation of vesicles in a density gradient followed by the recovery of functional EVs, the direct detection of EVs in culture supernatants, and the production of vesicles in solid cultures of Titan cells. Our results indicate that the production of EVs is directly impacted by the culture medium and time of growth, resulting in variable detection of EVs per cell and a peak of EV detection at 24 h of growth. Nanoparticle tracking analysis (NTA) of EV samples revealed that multiple isolates produce vesicles with variable properties, including particles of diverging dimensions. EVs were produced in the solid medium in amounts that were separated on a centrifugation density gradient, resulting in the recovery of functional EVs containing the major cryptococcal capsular antigen. We also optimized the solid medium protocol for induction of the formation of Titan cells, and analyzed the production of EVs by NTA and transmission electron microscopy. This analysis confirmed that EVs were isolated from solid cultures of cryptococcal enlarged cells. With these approaches, we expect to implement simple methods that will facilitate the analysis of EVs produced by fungal cells. IMPORTANCE Fungal extracellular vesicles (EVs) are considered to be important players in the biology of fungal pathogens. However, the limitations in the methodological approaches to studying fungal EVs impair the expansion of knowledge in this field. In the present study, we used the Cryptococcus genus as a model for the study of EVs. We explored the simplification of protocols for EV analysis, which helped us to address some important, but still unanswered, questions about fungal EVs.
Collapse
Affiliation(s)
- Flavia C. G. Reis
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil
- Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fiocruz, Rio de Janeiro, Brazil
| | - Bianca Gimenez
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil
| | | | - Rafael F. Castelli
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil
| | - Sharon T. Martins
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil
| | - Lysangela R. Alves
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil
| | | | - Marcio L. Rodrigues
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
10
|
Rizzo J, Wong SSW, Gazi AD, Moyrand F, Chaze T, Commere P, Novault S, Matondo M, Péhau‐Arnaudet G, Reis FCG, Vos M, Alves LR, May RC, Nimrichter L, Rodrigues ML, Aimanianda V, Janbon G. Cryptococcus extracellular vesicles properties and their use as vaccine platforms. J Extracell Vesicles 2021; 10:e12129. [PMID: 34377375 PMCID: PMC8329992 DOI: 10.1002/jev2.12129] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 07/02/2021] [Accepted: 07/09/2021] [Indexed: 12/12/2022] Open
Abstract
Whereas extracellular vesicle (EV) research has become commonplace in different biomedical fields, this field of research is still in its infancy in mycology. Here we provide a robust set of data regarding the structural and compositional aspects of EVs isolated from the fungal pathogenic species Cryptococcus neoformans, C. deneoformans and C. deuterogattii. Using cutting-edge methodological approaches including cryogenic electron microscopy and cryogenic electron tomography, proteomics, and flow cytometry, we revisited cryptococcal EV features and suggest a new EV structural model, in which the vesicular lipid bilayer is covered by mannoprotein-based fibrillar decoration, bearing the capsule polysaccharide as its outer layer. About 10% of the EV population is devoid of fibrillar decoration, adding another aspect to EV diversity. By analysing EV protein cargo from the three species, we characterized the typical Cryptococcus EV proteome. It contains several membrane-bound protein families, including some Tsh proteins bearing a SUR7/PalI motif. The presence of known protective antigens on the surface of Cryptococcus EVs, resembling the morphology of encapsulated virus structures, suggested their potential as a vaccine. Indeed, mice immunized with EVs obtained from an acapsular C. neoformans mutant strain rendered a strong antibody response in mice and significantly prolonged their survival upon C. neoformans infection.
Collapse
Affiliation(s)
- Juliana Rizzo
- Unité Biologie des ARN des Pathogènes FongiquesDépartement de Mycologie, Institut Pasteur, F‐75015ParisFrance
| | - Sarah Sze Wah Wong
- Unité Mycologie Moléculaire, CNRS UMR2000Département de Mycologie, Institut Pasteur, F‐75015ParisFrance
| | - Anastasia D. Gazi
- Ultrastructural Bio‐Imaging, UTechS UBI, CNRS UMR 3528Département de Biologie cellulaire et infection, Institut Pasteur, F‐75015ParisFrance
| | - Frédérique Moyrand
- Unité Biologie des ARN des Pathogènes FongiquesDépartement de Mycologie, Institut Pasteur, F‐75015ParisFrance
| | - Thibault Chaze
- Plateforme Protéomique, Unité de Spectrométrie de Masse pour la Biologie (MSBio), CNRS UMR 2000Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F‐75015ParisFrance
| | - Pierre‐Henri Commere
- Cytometry and BiomarkersCentre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F‐75015ParisFrance
| | - Sophie Novault
- Cytometry and BiomarkersCentre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F‐75015ParisFrance
| | - Mariette Matondo
- Plateforme Protéomique, Unité de Spectrométrie de Masse pour la Biologie (MSBio), CNRS UMR 2000Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F‐75015ParisFrance
| | - Gérard Péhau‐Arnaudet
- Ultrastructural Bio‐Imaging, UTechS UBI, CNRS UMR 3528Département de Biologie cellulaire et infection, Institut Pasteur, F‐75015ParisFrance
| | - Flavia C. G. Reis
- Instituto Carlos ChagasFundação Oswaldo Cruz (FIOCRUZ)CuritibaBrazil
- Centro de Desenvolvimento Tecnologico em Saude (CDTS‐Fiocruz)São PauloBrazil
| | - Matthijn Vos
- NanoImaging Core FacilityCentre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F‐75015ParisFrance
| | | | - Robin C. May
- Institute of Microbiology and Infection and School of BiosciencesUniversity of BirminghamBirminghamB15 2TTUK
| | - Leonardo Nimrichter
- Instituto de Microbiologia Paulo de Góes (IMPG)Universidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Marcio L. Rodrigues
- Instituto Carlos ChagasFundação Oswaldo Cruz (FIOCRUZ)CuritibaBrazil
- Instituto de Microbiologia Paulo de Góes (IMPG)Universidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Vishukumar Aimanianda
- Unité Mycologie Moléculaire, CNRS UMR2000Département de Mycologie, Institut Pasteur, F‐75015ParisFrance
| | - Guilhem Janbon
- Unité Biologie des ARN des Pathogènes FongiquesDépartement de Mycologie, Institut Pasteur, F‐75015ParisFrance
| |
Collapse
|
11
|
Zamith-Miranda D, Peres da Silva R, Couvillion SP, Bredeweg EL, Burnet MC, Coelho C, Camacho E, Nimrichter L, Puccia R, Almeida IC, Casadevall A, Rodrigues ML, Alves LR, Nosanchuk JD, Nakayasu ES. Omics Approaches for Understanding Biogenesis, Composition and Functions of Fungal Extracellular Vesicles. Front Genet 2021; 12:648524. [PMID: 34012462 PMCID: PMC8126698 DOI: 10.3389/fgene.2021.648524] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/06/2021] [Indexed: 12/13/2022] Open
Abstract
Extracellular vesicles (EVs) are lipid bilayer structures released by organisms from all kingdoms of life. The diverse biogenesis pathways of EVs result in a wide variety of physical properties and functions across different organisms. Fungal EVs were first described in 2007 and different omics approaches have been fundamental to understand their composition, biogenesis, and function. In this review, we discuss the role of omics in elucidating fungal EVs biology. Transcriptomics, proteomics, metabolomics, and lipidomics have each enabled the molecular characterization of fungal EVs, providing evidence that these structures serve a wide array of functions, ranging from key carriers of cell wall biosynthetic machinery to virulence factors. Omics in combination with genetic approaches have been instrumental in determining both biogenesis and cargo loading into EVs. We also discuss how omics technologies are being employed to elucidate the role of EVs in antifungal resistance, disease biomarkers, and their potential use as vaccines. Finally, we review recent advances in analytical technology and multi-omic integration tools, which will help to address key knowledge gaps in EVs biology and translate basic research information into urgently needed clinical applications such as diagnostics, and immuno- and chemotherapies to fungal infections.
Collapse
Affiliation(s)
- Daniel Zamith-Miranda
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States
| | | | - Sneha P. Couvillion
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Erin L. Bredeweg
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Meagan C. Burnet
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Carolina Coelho
- MRC Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
| | - Emma Camacho
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Leonardo Nimrichter
- Laboratório de Glicobiologia de Eucariotos, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rosana Puccia
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina-Universidade Federal de São Paulo, São Paulo, Brazil
| | - Igor C. Almeida
- Department of Biological Sciences, Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, United States
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Marcio L. Rodrigues
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas-FIOCRUZ PR, Curitiba, Brazil
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lysangela R. Alves
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas-FIOCRUZ PR, Curitiba, Brazil
| | - Joshua D. Nosanchuk
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Ernesto S. Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| |
Collapse
|
12
|
Romagnoli BAA, Holetz FB, Alves LR, Goldenberg S. RNA Binding Proteins and Gene Expression Regulation in Trypanosoma cruzi. Front Cell Infect Microbiol 2020; 10:56. [PMID: 32154189 PMCID: PMC7045066 DOI: 10.3389/fcimb.2020.00056] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/03/2020] [Indexed: 01/24/2023] Open
Abstract
The regulation of gene expression in trypanosomatids occurs mainly at the post-transcriptional level. In the case of Trypanosoma cruzi, the characterization of messenger ribonucleoprotein (mRNP) particles has allowed the identification of several classes of RNA binding proteins (RBPs), as well as non-canonical RBPs, associated with mRNA molecules. The protein composition of the mRNPs as well as the localization and functionality of the mRNAs depend on their associated proteins. mRNPs can also be organized into larger complexes forming RNA granules, which function as stress granules or P-bodies depending on the associated proteins. The fate of mRNAs in the cell, and consequently the genes expressed, depends on the set of proteins associated with the messenger molecule. These proteins allow the coordinated expression of mRNAs encoding proteins that are related in function, resulting in the formation of post-transcriptional operons. However, the puzzle posed by the combinatorial association of sets of RBPs with mRNAs and how this relates to the expressed genes remain to be elucidated. One important tool in this endeavor is the use of the CRISPR/CAS system to delete genes encoding RBPs, allowing the evaluation of their effect on the formation of mRNP complexes and associated mRNAs in the different compartments of the translation machinery. Accordingly, we recently established this methodology for T. cruzi and deleted the genes encoding RBPs containing zinc finger domains. In this manuscript, we will discuss the data obtained and the potential of the CRISPR/CAS methodology to unveil the role of RBPs in T. cruzi gene expression regulation.
Collapse
Affiliation(s)
- Bruno A A Romagnoli
- Gene Expression Regulation Laboratory, Institute Carlos Chagas, Curitiba, Brazil
| | - Fabiola B Holetz
- Gene Expression Regulation Laboratory, Institute Carlos Chagas, Curitiba, Brazil
| | - Lysangela R Alves
- Gene Expression Regulation Laboratory, Institute Carlos Chagas, Curitiba, Brazil
| | - Samuel Goldenberg
- Gene Expression Regulation Laboratory, Institute Carlos Chagas, Curitiba, Brazil
| |
Collapse
|
13
|
Herkert PF, Amatuzzi RF, Alves LR, Rodrigues ML. Extracellular Vesicles as Vehicles for the Delivery of Biologically Active Fungal Molecules. Curr Protein Pept Sci 2019; 20:1027-1036. [PMID: 31142247 DOI: 10.2174/1389203720666190529124055] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 03/28/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 11/22/2022]
Abstract
Extracellular vesicles (EVs) are membranous structures surrounded by a lipid bilayer required for the export of fungal proteins, lipids, toxins, nucleic acids, pigments, and polysaccharides. Proteomic studies of the content of fungal EVs revealed the presence of molecules involved in cell metabolism, signal transduction, and virulence, among others. EVs are evolutionarily conserved in all three domains of life and play important roles in cell-cell communication. Recently, the bidirectional transport of EVs was characterized through the demonstration that EVs can be released and captured by fungal cells. In fungi, EVs participate in immunomodulation through the delivery of virulence factors, antigens and allergens, but further studies are necessary to investigate their potential roles as carriers of diagnostic biomarkers and in drug delivery or antifungal resistance transmission. In this review, we discuss the roles of fungal EVs and their cargo in cell-cell communication, host-pathogen interactions, and environmental perception. The functions of EVs as vehicles for transporting fungal proteins and virulence factors are also addressed, as well as their use as biomarkers for the diagnosis of diseases and possible participation in antifungal responses.
Collapse
Affiliation(s)
- Patricia F Herkert
- Instituto Carlos Chagas, Fundacao Oswaldo Cruz (Fiocruz), Curitiba, Brazil.,Instituto Nacional de Ciência e Tecnologia (INCT) de Inovação em Doenças de Populações Negligenciadas, Brazil
| | - Rafaela F Amatuzzi
- Instituto Carlos Chagas, Fundacao Oswaldo Cruz (Fiocruz), Curitiba, Brazil
| | - Lysangela R Alves
- Instituto Carlos Chagas, Fundacao Oswaldo Cruz (Fiocruz), Curitiba, Brazil
| | - Marcio L Rodrigues
- Instituto Carlos Chagas, Fundacao Oswaldo Cruz (Fiocruz), Curitiba, Brazil.,Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
14
|
Peres da Silva R, Longo LGV, Cunha JPCD, Sobreira TJP, Rodrigues ML, Faoro H, Goldenberg S, Alves LR, Puccia R. Comparison of the RNA Content of Extracellular Vesicles Derived from Paracoccidioides brasiliensis and Paracoccidioides lutzii. Cells 2019; 8:cells8070765. [PMID: 31340551 PMCID: PMC6678485 DOI: 10.3390/cells8070765] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/09/2019] [Accepted: 07/13/2019] [Indexed: 12/12/2022] Open
Abstract
Paracoccidioides brasiliensis and P. lutzii cause human paracoccidioidomycosis. We have previously characterized the <200-nt RNA sub-populations contained in fungal extracellular vesicles (EVs) from P. brasiliensis Pb18 and other pathogenic fungi. We have presently used the RNA-seq strategy to compare the <200- and >200-nt RNA fractions contained in EVs isolated from culture supernatants of P. brasiliensis Pb18, Pb3, and P. lutzii Pb01. Shared mRNA sequences were related to protein modification, translation, and DNA metabolism/biogenesis, while those related to transport and oxidation-reduction were exclusive to Pb01. The presence of functional full-length mRNAs was validated by in vitro translation. Among small non-coding (nc)RNA, 15 were common to all samples; small nucleolar (sno)RNAs were enriched in P. brasiliensis EVs, whereas for P. lutzii there were similar proportions of snoRNA, rRNA, and tRNA. Putative exonic sRNAs were highly abundant in Pb18 EVs. We also found sRNA sequences bearing incomplete microRNA structures mapping to exons. RNA-seq data suggest that extracellular fractions containing Pb18 EVs can modulate the transcriptome of murine monocyte-derived dendritic cells in a transwell system. Considering that sRNA classes are involved in transcription/translation modulation, our general results may indicate that differences in virulence among fungal isolates can be related to their distinct EV-RNA content.
Collapse
Affiliation(s)
- Roberta Peres da Silva
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina-Universidade Federal de São Paulo (EPM-UNIFESP), São Paulo 04023-062, Brazil
| | - Larissa G V Longo
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina-Universidade Federal de São Paulo (EPM-UNIFESP), São Paulo 04023-062, Brazil
| | - Julia P C da Cunha
- Laboratório Especial de Ciclo Celular-Center of Toxins, Immune Response and Cell Signaling-Center (CeTICS), Butantan Institute, São Paulo 05503-900, Brazil
| | - Tiago J P Sobreira
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
| | - Marcio L Rodrigues
- Instituto Carlos Chagas-FIOCRUZ PR, Curitiba 81350-010, Brazil
- Instituto de Microbiologia da Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, Brazil
| | - Helisson Faoro
- Instituto Carlos Chagas-FIOCRUZ PR, Curitiba 81350-010, Brazil
| | | | | | - Rosana Puccia
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina-Universidade Federal de São Paulo (EPM-UNIFESP), São Paulo 04023-062, Brazil.
| |
Collapse
|
15
|
Alves LR, Peres da Silva R, Sanchez DA, Zamith-Miranda D, Rodrigues ML, Goldenberg S, Puccia R, Nosanchuk JD. Extracellular Vesicle-Mediated RNA Release in Histoplasma capsulatum. mSphere 2019; 4:e00176-19. [PMID: 30918062 PMCID: PMC6437275 DOI: 10.1128/msphere.00176-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 01/03/2023] Open
Abstract
Eukaryotic cells, including fungi, release extracellular vesicles (EVs). These lipid bilayered compartments play essential roles in cellular communication and pathogenesis. EV composition is complex and includes proteins, glycans, pigments, and RNA. RNAs with putative roles in pathogenesis have been described in EVs produced by fungi. Here we describe the RNA content in EVs produced by the G186AR and G217B strains of Histoplasma capsulatum, an important human-pathogenic fungal pathogen. A total of 124 mRNAs were identified in both strains. In this set of RNA classes, 93 transcripts were enriched in EVs from the G217B strain, whereas 31 were enriched in EVs produced by the G186AR strain. This result suggests that there are important strain-specific properties in the mRNA composition of fungal EVs. We also identified short fragments (25 to 40 nucleotides in length) that were strain specific, with a greater number identified in EVs produced by the G217B strain. Remarkably, the most highly enriched processes were stress responses and translation. Half of these fragments aligned to the reverse strand of the transcript, suggesting the occurrence of microRNA (miRNA)-like molecules in fungal EVs. We also compared the transcriptome profiles of H. capsulatum with the RNA composition of EVs, and no correlation was observed. Taking the results together, our study provided information about the RNA molecules present in H. capsulatum EVs and about the differences in composition between the strains. In addition, we found no correlation between the most highly expressed transcripts in the cell and their presence in the EVs, reinforcing the idea that the RNAs were directed to the EVs by a regulated mechanism.IMPORTANCE Extracellular vesicles (EVs) play important roles in cellular communication and pathogenesis. The RNA molecules in EVs have been implicated in a variety of processes. EV-associated RNA classes have recently been described in pathogenic fungi; however, only a few reports of studies describing the RNAs in fungal EVs are available. Improved knowledge of EV-associated RNA will contribute to the understanding of their role during infection. In this study, we described the RNA content in EVs produced by two isolates of Histoplasma capsulatum Our results add this important pathogen to the current short list of fungal species with the ability to use EVs for the extracellular release of RNA.
Collapse
Affiliation(s)
- Lysangela R Alves
- Instituto Carlos Chagas, Fiocruz, Curitiba, Cidade Industrial de Curitiba, Brazil
| | - Roberta Peres da Silva
- Departamento de Microbiologia, Imunologia e Parasitologia da Escola Paulista de Medicina, Universidade Federal de São Paulo-UNIFESP, São Paulo, Brazil
| | - David A Sanchez
- Departments of Medicine (Division of Infectious Diseases) and Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Daniel Zamith-Miranda
- Departments of Medicine (Division of Infectious Diseases) and Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Marcio L Rodrigues
- Instituto Carlos Chagas, Fiocruz, Curitiba, Cidade Industrial de Curitiba, Brazil
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Samuel Goldenberg
- Instituto Carlos Chagas, Fiocruz, Curitiba, Cidade Industrial de Curitiba, Brazil
| | - Rosana Puccia
- Departamento de Microbiologia, Imunologia e Parasitologia da Escola Paulista de Medicina, Universidade Federal de São Paulo-UNIFESP, São Paulo, Brazil
| | - Joshua D Nosanchuk
- Departments of Medicine (Division of Infectious Diseases) and Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| |
Collapse
|
16
|
Peres da Silva R, Martins SDT, Rizzo J, Dos Reis FCG, Joffe LS, Vainstein M, Kmetzsch L, Oliveira DL, Puccia R, Goldenberg S, Rodrigues ML, Alves LR. Golgi Reassembly and Stacking Protein (GRASP) Participates in Vesicle-Mediated RNA Export in Cryptococcus Neoformans. Genes (Basel) 2018; 9:genes9080400. [PMID: 30096850 PMCID: PMC6115741 DOI: 10.3390/genes9080400] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 07/25/2018] [Accepted: 07/31/2018] [Indexed: 12/31/2022] Open
Abstract
Golgi reassembly and stacking protein (GRASP) is required for polysaccharide secretion and virulence in Cryptococcus neoformans. In fungal species, extracellular vesicles (EVs) participate in the export of polysaccharides, proteins and RNA. In the present work, we investigated if EV-mediated RNA export is functionally connected with GRASP in C. neoformans using a graspΔ mutant. Since GRASP-mediated unconventional secretion involves autophagosome formation in yeast, we included the atg7Δ mutant with defective autophagic mechanisms in our analysis. All fungal strains exported EVs but deletion of GRASP or ATG7 profoundly affected vesicular dimensions. The mRNA content of the graspΔ EVs differed substantially from that of the other two strains. The transcripts associated to the endoplasmic reticulum were highly abundant transcripts in graspΔ EVs. Among non-coding RNAs (ncRNAs), tRNA fragments were the most abundant in both mutant EVs but graspΔ EVs alone concentrated 22 exclusive sequences. In general, our results showed that the EV RNA content from atg7Δ and WT were more related than the RNA content of graspΔ, suggesting that GRASP, but not the autophagy regulator Atg7, is involved in the EV export of RNA. This is a previously unknown function for a key regulator of unconventional secretion in eukaryotic cells.
Collapse
Affiliation(s)
- Roberta Peres da Silva
- Departamento de Microbiologia, Imunologia e Parasitologia da Escola Paulista de Medicina-UNIFESP, São Paulo, SP 04023-062, Brazil.
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK.
| | | | - Juliana Rizzo
- Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-901, Brazil.
| | - Flavia C G Dos Reis
- Instituto Carlos Chagas, Fundação Oswaldo Cruz, Fiocruz-PR, Curitiba, PR 81310-020, Brazil.
| | - Luna S Joffe
- Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz, Rio de Janeiro, RJ 21040-900, Brazil.
| | - Marilene Vainstein
- Centro de Biotecnologia e Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-970, Brazil.
| | - Livia Kmetzsch
- Centro de Biotecnologia e Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-970, Brazil.
| | - Débora L Oliveira
- Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz, Rio de Janeiro, RJ 21040-900, Brazil.
| | - Rosana Puccia
- Departamento de Microbiologia, Imunologia e Parasitologia da Escola Paulista de Medicina-UNIFESP, São Paulo, SP 04023-062, Brazil.
| | - Samuel Goldenberg
- Instituto Carlos Chagas, Fundação Oswaldo Cruz, Fiocruz-PR, Curitiba, PR 81310-020, Brazil.
| | - Marcio L Rodrigues
- Instituto Carlos Chagas, Fundação Oswaldo Cruz, Fiocruz-PR, Curitiba, PR 81310-020, Brazil.
- Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-901, Brazil.
| | - Lysangela R Alves
- Instituto Carlos Chagas, Fundação Oswaldo Cruz, Fiocruz-PR, Curitiba, PR 81310-020, Brazil.
| |
Collapse
|
17
|
Martins SDT, Kuczera D, Lötvall J, Bordignon J, Alves LR. Characterization of Dendritic Cell-Derived Extracellular Vesicles During Dengue Virus Infection. Front Microbiol 2018; 9:1792. [PMID: 30131785 PMCID: PMC6090163 DOI: 10.3389/fmicb.2018.01792] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 07/17/2018] [Indexed: 12/15/2022] Open
Abstract
The dengue virus (DENV), transmitted by Aedes spp. mosquitoes, is one of the most important arboviral infections in the world. Dengue begins as a febrile condition, and in certain patients, it can evolve severe clinical outcomes, such as dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). The reasons why certain patients develop DHF or DSS have not been thoroughly elucidated to date, and both patient and viral factors have been implicated. Previous work has shown that a severe immune dysfunction involving dendritic cells and T cells plays a key role in increasing the disease severity, especially in secondary heterologous infections. Extracellular vesicles (EVs) are membranous particles that are secreted by several cell types involved in homeostatic and pathological processes. Secretion of EVs by infected cells can enhance immune responses or favor viral evasion. In this study, we compare the molecular content of EVs that are secreted by human primary dendritic cells under different conditions: uninfected or infected with DENV3 strains isolated from patients with different infection phenotypes (a severe case involving DSS and a mild case). Human monocyte-derived dendritic cells (mdDCs) were infected with the dengue virus strains DENV3 5532 (severe) or DENV3 290 (mild), and the EVs were isolated. The presence of cup-shaped EVs was confirmed by electron microscopy and immunostaining with CD9, CD81, and CD83. The RNA content from the mdDC-infected cells contained several mRNAs and miRNAs related to immune responses compared to the EVs from mock-infected mdDCs. A number of these RNAs were detected exclusively during infection with DENV3 290 or DENV3 5532. This result suggests that the differential immune modulation of mdDCs by dengue strains can be achieved through the EV pathway. Additionally, we observed an association of EVs with DENV-infectious particles that seem to be protected from antibodies targeting the DENV envelope protein. We also showed that EVs derived from cells treated with IFN alpha have a protective effect against DENV infection in other cells. These results suggested that during DENV infection, the EV pathway could be exploited to favor viral viability, although immune mechanisms to counteract viral infection can also involve DC-derived EVs.
Collapse
Affiliation(s)
- Sharon de T Martins
- Laboratory of Gene Expression Regulation, Carlos Chagas Institute, FIOCRUZ, Curitiba, Brazil
| | - Diogo Kuczera
- Laboratory of Molecular Virology, Carlos Chagas Institute, FIOCRUZ, Curitiba, Brazil
| | - Jan Lötvall
- Krefting Research Centre, University of Gothenburg, Gothenburg, Sweden
| | - Juliano Bordignon
- Laboratory of Molecular Virology, Carlos Chagas Institute, FIOCRUZ, Curitiba, Brazil
| | - Lysangela R Alves
- Laboratory of Gene Expression Regulation, Carlos Chagas Institute, FIOCRUZ, Curitiba, Brazil
| |
Collapse
|
18
|
Wippel HH, Malgarin JS, Martins SDT, Vidal NM, Marcon BH, Miot HT, Marchini FK, Goldenberg S, Alves LR. The Nuclear RNA-binding Protein RBSR1 Interactome in Trypanosoma cruzi. J Eukaryot Microbiol 2018; 66:244-253. [PMID: 29984450 DOI: 10.1111/jeu.12666] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 03/28/2018] [Revised: 07/01/2018] [Accepted: 07/03/2018] [Indexed: 12/18/2022]
Abstract
Trypanosoma cruzi, the etiological agent of Chagas disease, has been widely studied, reflecting both its medical importance and the particular features that make this pathogen an attractive model for basic biological studies. The repression of transcripts by messenger ribonucleoprotein (mRNP) complexes is an important pathway of post-transcriptional regulation in eukaryotes, including T. cruzi. RBSR1 is a serine-arginine (SR)-rich RNA-binding protein (RBP) in T. cruzi that contains one RNA-recognition motif (RRM); this protein has a primarily nuclear localization and is developmentally regulated, not being detected in metacyclic trypomastigotes. RBSR1 interacts with other RBPs, such as UBP1 and UBP2, and the nuclear SR-protein TRRM1. Phylogenetic analysis indicated that RBSR1 is orthologous to the human splicing factor SRSF7, what might indicate its possible involvement in pre-RNA processing. Accordingly, ribonomics data showed the enrichment of snoRNAs and snRNAs in the RBSR1 immunoprecipiatation complex, hence reinforcing the supposition that this protein might be involved in RNA processing in the nucleus.
Collapse
Affiliation(s)
- Helisa H Wippel
- Carlos Chagas Institute, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Curitiba, Paraná, Brazil
| | - Juliane S Malgarin
- Molecular Biology Institute of Paraná, IBMP, Rua Professor Algacyr Munhoz Mader 3775, Curitiba, Paraná, Brazil
| | - Sharon de Toledo Martins
- Carlos Chagas Institute, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Curitiba, Paraná, Brazil
| | - Newton M Vidal
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland, 20894
| | - Bruna H Marcon
- Carlos Chagas Institute, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Curitiba, Paraná, Brazil
| | - Hálisson T Miot
- Carlos Chagas Institute, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Curitiba, Paraná, Brazil
| | - Fabricio K Marchini
- Carlos Chagas Institute, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Curitiba, Paraná, Brazil
| | - Samuel Goldenberg
- Carlos Chagas Institute, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Curitiba, Paraná, Brazil
| | - Lysangela R Alves
- Carlos Chagas Institute, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Curitiba, Paraná, Brazil
| |
Collapse
|
19
|
Romagnoli BAA, Picchi GFA, Hiraiwa PM, Borges BS, Alves LR, Goldenberg S. Improvements in the CRISPR/Cas9 system for high efficiency gene disruption in Trypanosoma cruzi. Acta Trop 2018; 178:190-195. [PMID: 29174293 DOI: 10.1016/j.actatropica.2017.11.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/16/2017] [Accepted: 11/20/2017] [Indexed: 12/27/2022]
Abstract
Chagas disease, caused by the protozoan parasite Trypanosoma cruzi, affects millions of individuals around the world. Although it has been known for more than a century, the study of T. cruzi has been a challenge, particularly due to the scarcity of tools for genome inquiries. Recently, strategies have been described allowing gene disruption in T. cruzi by the CRISPR/Cas9 nuclease system. Although these strategies demonstrated success in deleting some genes, several aspects could be improved to increase the efficiency of the CRISPR/Cas9 system in T. cruzi. Here, we report a strategy, based on adaptations and improvements of the two previously described systems, that results in efficient gene disruption that can be applied to any target, including the study of essential genes.
Collapse
Affiliation(s)
- Bruno A A Romagnoli
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas - FIOCRUZ Paraná, Curitiba, 81350-010, Brazil
| | - Gisele F A Picchi
- Laboratório de Biologia Molecular de Tripanossomatídeos, Instituto Carlos Chagas - FIOCRUZ Paraná, Curitiba, 81350-010, Brazil
| | - Priscila M Hiraiwa
- Flow Cytometry Facility, Instituto Carlos Chagas - FIOCRUZ Paraná, Curitiba, 81350-010, Brazil
| | - Beatriz S Borges
- Microscopy Facility, Instituto Carlos Chagas - FIOCRUZ Paraná, Curitiba, 81350-010, Brazil
| | - Lysangela R Alves
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas - FIOCRUZ Paraná, Curitiba, 81350-010, Brazil.
| | - Samuel Goldenberg
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas - FIOCRUZ Paraná, Curitiba, 81350-010, Brazil.
| |
Collapse
|
20
|
Bonato P, Alves LR, Osaki JH, Rigo LU, Pedrosa FO, Souza EM, Zhang N, Schumacher J, Buck M, Wassem R, Chubatsu LS. The NtrY-NtrX two-component system is involved in controlling nitrate assimilation in Herbaspirillum seropedicae strain SmR1. FEBS J 2016; 283:3919-3930. [PMID: 27634462 DOI: 10.1111/febs.13897] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 04/15/2016] [Revised: 08/15/2016] [Accepted: 09/13/2016] [Indexed: 10/21/2022]
Abstract
Herbaspirillum seropedicae is a diazotrophic β-Proteobacterium found endophytically associated with gramineae (Poaceae or graminaceous plants) such as rice, sorghum and sugar cane. In this work we show that nitrate-dependent growth in this organism is regulated by the master nitrogen regulatory two-component system NtrB-NtrC, and by NtrY-NtrX, which functions to specifically regulate nitrate metabolism. NtrY is a histidine kinase sensor protein predicted to be associated with the membrane and NtrX is the response regulator partner. The ntrYntrX genes are widely distributed in Proteobacteria. In α-Proteobacteria they are frequently located downstream from ntrBC, whereas in β-Proteobacteria these genes are located downstream from genes encoding an RNA methyltransferase and a proline-rich protein with unknown function. The NtrX protein of α-Proteobacteria has an AAA+ domain, absent in those from β-Proteobacteria. An ntrY mutant of H. seropedicae showed the wild-type nitrogen fixation phenotype, but the nitrate-dependent growth was abolished. Gene fusion assays indicated that NtrY is involved in the expression of genes coding for the assimilatory nitrate reductase as well as the nitrate-responsive two-component system NarX-NarL (narK and narX promoters, respectively). The purified NtrX protein was capable of binding the narK and narX promoters, and the binding site at the narX promoter for the NtrX protein was determined by DNA footprinting. In silico analyses revealed similar sequences in other promoter regions of H. seropedicae that are related to nitrate assimilation, supporting the role of the NtrY-NtrX system in regulating nitrate metabolism in H. seropedicae.
Collapse
Affiliation(s)
- Paloma Bonato
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Lysangela R Alves
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Juliana H Osaki
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Liu U Rigo
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Fabio O Pedrosa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Emanuel M Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Nan Zhang
- Department of Life Sciences, Imperial College London, UK
| | | | - Martin Buck
- Department of Life Sciences, Imperial College London, UK
| | - Roseli Wassem
- Department of Genetics, Universidade Federal do Paraná, Curitiba, Brazil
| | - Leda S Chubatsu
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| |
Collapse
|
21
|
Costa NV, Aboujaoude C, Vieira GS, Paiva VV, Moraes Neto RA, Gondim VS, Alves LR, Torres MCL, Antunes RC. Carcass and meat quality traits in Nellore and F1 Nellore-Araguaia crosses. Genet Mol Res 2015; 14:5379-89. [PMID: 26125733 DOI: 10.4238/2015.may.22.7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We evaluated and compared carcass traits and meat quality in Nellore cattle and F1 crosses between Nellore and Araguaia, where 17 individuals were from the Nellore group and 19 were ½ Nellore and ½ Araguaia crosses. All animals belonged to the same birth season and were raised in pasture systems under the same nutritional, environmental, and management conditions. When the animals reached slaughter weight, they were taken to an industrial slaughterhouse where food was not provided for 24 h (free access to water); they were then stunned, bled, the leather was removed, and they were eviscerated. The carcasses were weighed (hot weight), kept in chilled storage for approximately 24 h at 4°C, and weighed again to obtain the chilled carcass weight. Carcass yield, carcass length, carcass width, leg length, thigh perimeter, loin eye area (LEA), retail cuts, cooling loss, pH, fat depth, marbling rate, intramuscular fat, color, and shear force were analyzed and sensory analysis of the meat was conducted. Significant differences (P < 0.05) were observed for the following variables: slaughter weight, hot and chilled carcass weights, carcass and leg lengths, thigh perimeter, LEA, retail cuts, and lightness (L*), where the ½ Nellore ½ Araguaia individuals showed higher means for all of these traits, except leg length and L*. Therefore, crossbreeding between Nellore and Araguaia did not affect the meat's sensory characteristics, but contributed to an improvement in carcass traits, providing an alternative for farmers that aim for good meat quality, with a higher meat percentage.
Collapse
Affiliation(s)
- N V Costa
- Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, MG, Brasil
| | - C Aboujaoude
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual de São Paulo, Jaboticabal, SP, Brasil
| | - G S Vieira
- Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, MG, Brasil
| | - V V Paiva
- Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, MG, Brasil
| | - R A Moraes Neto
- Associação Brasileira dos Criadores da Raça Araguaia, Araçatuba, SP, Brasil
| | - V S Gondim
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual de São Paulo, Jaboticabal, SP, Brasil
| | - L R Alves
- Serviço Nacional de Aprendizagem Rural, Palmas, TO, Brasil
| | - M C L Torres
- Departamento de Engenharia de Alimentos, Universidade Federal de Goiás, Goiânia, GO, Brasil
| | - R C Antunes
- Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, MG, Brasil
| |
Collapse
|
22
|
Peres da Silva R, Puccia R, Rodrigues ML, Oliveira DL, Joffe LS, César GV, Nimrichter L, Goldenberg S, Alves LR. Extracellular vesicle-mediated export of fungal RNA. Sci Rep 2015; 5:7763. [PMID: 25586039 PMCID: PMC5379013 DOI: 10.1038/srep07763] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/12/2014] [Indexed: 02/07/2023] Open
Abstract
Extracellular vesicles (EVs) play an important role in the biology of various organisms, including fungi, in which they are required for the trafficking of molecules across the cell wall. Fungal EVs contain a complex combination of macromolecules, including proteins, lipids and glycans. In this work, we aimed to describe and characterize RNA in EV preparations from the human pathogens Cryptococcus neoformans, Paracoccidiodes brasiliensis and Candida albicans, and from the model yeast Saccharomyces cerevisiae. The EV RNA content consisted mostly of molecules less than 250 nt long and the reads obtained aligned with intergenic and intronic regions or specific positions within the mRNA. We identified 114 ncRNAs, among them, six small nucleolar (snoRNA), two small nuclear (snRNA), two ribosomal (rRNA) and one transfer (tRNA) common to all the species considered, together with 20 sequences with features consistent with miRNAs. We also observed some copurified mRNAs, as suggested by reads covering entire transcripts, including those involved in vesicle-mediated transport and metabolic pathways. We characterized for the first time RNA molecules present in EVs produced by fungi. Our results suggest that RNA-containing vesicles may be determinant for various biological processes, including cell communication and pathogenesis.
Collapse
Affiliation(s)
- Roberta Peres da Silva
- Departamento de Microbiologia, Imunologia e Parasitologia da Escola Paulista de Medicina-UNIFESP, São Paulo, SP, Brazil
| | - Rosana Puccia
- Departamento de Microbiologia, Imunologia e Parasitologia da Escola Paulista de Medicina-UNIFESP, São Paulo, SP, Brazil
| | - Marcio L Rodrigues
- 1] Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil [2] Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Débora L Oliveira
- Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Luna S Joffe
- Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Gabriele V César
- Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Leonardo Nimrichter
- Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Samuel Goldenberg
- Instituto Carlos Chagas, Fundação Oswaldo Cruz, Fiocruz-PR, Curitiba, PR, Brazil
| | - Lysangela R Alves
- Instituto Carlos Chagas, Fundação Oswaldo Cruz, Fiocruz-PR, Curitiba, PR, Brazil
| |
Collapse
|
23
|
Alves LR, Antunes RC, Andrade RB, Storti AA, Reis SLB, Carrazza LG, Osava CF, Costa NV. Effect of the halothane genotype on intramuscular fat deposition in swine. Genet Mol Res 2014; 13:363-70. [PMID: 24535863 DOI: 10.4238/2014.january.21.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Intramuscular fat (IMF) content has been identified as an important factor in determining the quality of pork. Previous studies have suggested that IMF deposition may be associated with the presence of the halothane (HAL) gene. This study aimed to evaluate the effect of the HAL gene on IMF deposition in crossbred pigs of commercial lines, which were killed at a slaughterhouse under official inspection. The genotype of the HAL gene was determined by polymerase chain reaction-restriction fragment length polymorphism analysis. IMF was analyzed from longissimus dorsi samples. Among all animals analyzed, 42.36% were of the HalNN genotype and 57.64% were of the HalNn genotype. The average IMF content of all samples was 2.14%. Variation in IMF between genotypes was evaluated by analysis of variance. No significant difference in IMF deposition, which could be based on the presence of the halothane allele, was observed, at least in heterozygotes.
Collapse
Affiliation(s)
- L R Alves
- Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, MG, Brasil
| | - R C Antunes
- Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, MG, Brasil
| | - R B Andrade
- Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, MG, Brasil
| | - A A Storti
- Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, MG, Brasil
| | - S L B Reis
- Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, MG, Brasil
| | - L G Carrazza
- Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, MG, Brasil
| | - C F Osava
- Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, MG, Brasil
| | - N V Costa
- Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, MG, Brasil
| |
Collapse
|
24
|
Alves LR, Guerra-Slompo EP, de Oliveira AV, Malgarin JS, Goldenberg S, Dallagiovanna B. mRNA localization mechanisms in Trypanosoma cruzi. PLoS One 2013; 8:e81375. [PMID: 24324687 PMCID: PMC3852752 DOI: 10.1371/journal.pone.0081375] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [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: 03/14/2013] [Accepted: 10/13/2013] [Indexed: 01/06/2023] Open
Abstract
Asymmetric mRNA localization is a sophisticated tool for regulating and optimizing protein synthesis and maintaining cell polarity. Molecular mechanisms involved in the regulated localization of transcripts are widespread in higher eukaryotes and fungi, but not in protozoa. Trypanosomes are ancient eukaryotes that branched off early in eukaryote evolution. We hypothesized that these organisms would have basic mechanisms of mRNA localization. FISH assays with probes against transcripts coding for proteins with restricted distributions showed a discrete localization of the mRNAs in the cytoplasm. Moreover, cruzipain mRNA was found inside reservosomes suggesting new unexpected functions for this vacuolar organelle. Individual mRNAs were also mobilized to RNA granules in response to nutritional stress. The cytoplasmic distribution of these transcripts changed with cell differentiation, suggesting that localization mechanisms might be involved in the regulation of stage-specific protein expression. Transfection assays with reporter genes showed that, as in higher eukaryotes, 3'UTRs were responsible for guiding mRNAs to their final location. Our results strongly suggest that Trypanosoma cruzi have a core, basic mechanism of mRNA localization. This kind of controlled mRNA transport is ancient, dating back to early eukaryote evolution.
Collapse
Affiliation(s)
- Lysangela R. Alves
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, Fiocruz-Paraná. Curitiba, Paraná, Brasil
| | - Eloise P. Guerra-Slompo
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, Fiocruz-Paraná. Curitiba, Paraná, Brasil
| | - Arthur V. de Oliveira
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, Fiocruz-Paraná. Curitiba, Paraná, Brasil
| | - Juliane S. Malgarin
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, Fiocruz-Paraná. Curitiba, Paraná, Brasil
| | - Samuel Goldenberg
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, Fiocruz-Paraná. Curitiba, Paraná, Brasil
| | - Bruno Dallagiovanna
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, Fiocruz-Paraná. Curitiba, Paraná, Brasil
- * E-mail:
| |
Collapse
|
25
|
Fonseca-Silva T, Santos CCO, Alves LR, Dias LC, Brito M, De Paula AMB, Guimarães ALS. Detection and quantification of mast cell, vascular endothelial growth factor, and microvessel density in human inflammatory periapical cysts and granulomas. Int Endod J 2012; 45:859-64. [PMID: 22486765 DOI: 10.1111/j.1365-2591.2012.02043.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AIM To identify and quantify mast cell (MC), vascular endothelial growth factor (VEGF) expression and microvessel density (MVD) in human periapical cysts and granulomas. METHODOLOGY Archived samples of cysts (n = 40) and granulomas (n = 28) were sectioned and stained with toluidine blue. MCs were identified and counted. Immunohistochemical reactions were employed to evaluate the tissue expression of VEGF and vessels. MVD was estimated by determining the areas of tissue labelled with CD31 antibody. The data were analysed using the Mann-Whitney test (P < 0.05). RESULTS MCs were observed in the peripheral regions of both lesion types, whilst VEGF and MVD were distributed in the stroma. The presence of MCs was higher in cysts than in granulomas (P < 0.05). VEGF and MVD expression were similar in these lesions. CONCLUSIONS The highest number of MCs was observed in cysts. Moreover, the identification of VEGF and MVD was consistent with the immune mechanisms involved in the lesions.
Collapse
Affiliation(s)
- T Fonseca-Silva
- Department of Dentistry, State University of Montes Claros, Montes Claros, MG, Brazil
| | | | | | | | | | | | | |
Collapse
|
26
|
Pedrosa FO, Monteiro RA, Wassem R, Cruz LM, Ayub RA, Colauto NB, Fernandez MA, Fungaro MHP, Grisard EC, Hungria M, Madeira HMF, Nodari RO, Osaku CA, Petzl-Erler ML, Terenzi H, Vieira LGE, Steffens MBR, Weiss VA, Pereira LFP, Almeida MIM, Alves LR, Marin A, Araujo LM, Balsanelli E, Baura VA, Chubatsu LS, Faoro H, Favetti A, Friedermann G, Glienke C, Karp S, Kava-Cordeiro V, Raittz RT, Ramos HJO, Ribeiro EMSF, Rigo LU, Rocha SN, Schwab S, Silva AG, Souza EM, Tadra-Sfeir MZ, Torres RA, Dabul ANG, Soares MAM, Gasques LS, Gimenes CCT, Valle JS, Ciferri RR, Correa LC, Murace NK, Pamphile JA, Patussi EV, Prioli AJ, Prioli SMA, Rocha CLMSC, Arantes OMN, Furlaneto MC, Godoy LP, Oliveira CEC, Satori D, Vilas-Boas LA, Watanabe MAE, Dambros BP, Guerra MP, Mathioni SM, Santos KL, Steindel M, Vernal J, Barcellos FG, Campo RJ, Chueire LMO, Nicolás MF, Pereira-Ferrari L, Silva JLDC, Gioppo NMR, Margarido VP, Menck-Soares MA, Pinto FGS, Simão RDCG, Takahashi EK, Yates MG, Souza EM. Genome of Herbaspirillum seropedicae strain SmR1, a specialized diazotrophic endophyte of tropical grasses. PLoS Genet 2011; 7:e1002064. [PMID: 21589895 PMCID: PMC3093359 DOI: 10.1371/journal.pgen.1002064] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [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: 01/25/2011] [Accepted: 03/18/2011] [Indexed: 01/28/2023] Open
Abstract
The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazotrophic endophytes and plants are scarcely known. Herbaspirillum seropedicae is an endophytic bacterium capable of colonizing intercellular spaces of grasses such as rice and sugar cane. The genome of H. seropedicae strain SmR1 was sequenced and annotated by The Paraná State Genome Programme--GENOPAR. The genome is composed of a circular chromosome of 5,513,887 bp and contains a total of 4,804 genes. The genome sequence revealed that H. seropedicae is a highly versatile microorganism with capacity to metabolize a wide range of carbon and nitrogen sources and with possession of four distinct terminal oxidases. The genome contains a multitude of protein secretion systems, including type I, type II, type III, type V, and type VI secretion systems, and type IV pili, suggesting a high potential to interact with host plants. H. seropedicae is able to synthesize indole acetic acid as reflected by the four IAA biosynthetic pathways present. A gene coding for ACC deaminase, which may be involved in modulating the associated plant ethylene-signaling pathway, is also present. Genes for hemagglutinins/hemolysins/adhesins were found and may play a role in plant cell surface adhesion. These features may endow H. seropedicae with the ability to establish an endophytic life-style in a large number of plant species.
Collapse
|
27
|
Holetz FB, Alves LR, Probst CM, Dallagiovanna B, Marchini FK, Manque P, Buck G, Krieger MA, Correa A, Goldenberg S. Protein and mRNA content of TcDHH1-containing mRNPs in Trypanosoma cruzi. FEBS J 2010; 277:3415-26. [PMID: 20629747 DOI: 10.1111/j.1742-4658.2010.07747.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In trypanosomatids, the regulation of gene expression occurs mainly at the post-transcriptional level. Previous studies have revealed nontranslated mRNA in the Trypanosoma cruzi cytoplasm. Previously, we have identified and cloned the TcDHH1 protein, a DEAD box RNA helicase. It has been reported that Dhh1 is involved in multiple RNA-related processes in various eukaryotes. It has also been reported to accumulate in stress granules and processing bodies of yeast, animal cells, Trypanosoma brucei and T. cruzi. TcDHH1 is localized to discrete cytoplasmic foci that vary depending on the life cycle status and nutritional conditions. To study the composition of mRNPs containing TcDHH1, we carried out immunoprecipitation assays with anti-TcDHH1 using epimastigote lysates. The protein content of mRNPs was determined by MS and pre-immune serum was used as control. We also carried out a ribonomic approach to identify the mRNAs present within the TcDHH1 immunoprecipitated complexes. For this purpose, competitive microarray hybridizations were performed against negative controls, the nonprecipitated fraction. Our results showed that mRNAs associated with TcDHH1 in the epimastigote stage are those mainly expressed in the other forms of the T. cruzi life cycle. These data suggest that mRNPs containing TcDHH1 are involved in mRNA metabolism, regulating the expression of at least epimastigote-specific genes.
Collapse
|
28
|
Alves LR, Avila AR, Correa A, Holetz FB, Mansur FCB, Manque PA, de Menezes JPB, Buck GA, Krieger MA, Goldenberg S. Proteomic analysis reveals the dynamic association of proteins with translated mRNAs in Trypanosoma cruzi. Gene 2010; 452:72-8. [PMID: 20060445 DOI: 10.1016/j.gene.2009.12.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 11/22/2009] [Accepted: 12/26/2009] [Indexed: 01/09/2023]
Abstract
Gene regulation is mainly post-transcriptional in trypanosomatids. The stability of mRNA and access to polysomes are thought to be tightly regulated, allowing Trypanosoma cruzi to adapt to the different environmental conditions during its life cycle. Post-transcriptional regulation requires the association between mRNAs and certain proteins to form mRNP complexes. We investigated the dynamic association between proteins and mRNAs, using poly(T) beads to isolate and characterize proteins and protein complexes bound to poly-A+ mRNAs. The protein content of these fractions was analyzed by mass spectrometry (LC-MS/MS). We identified 542 protein component of the mRNP complexes associated with mRNAs. Twenty-four of the proteins obtained were present in all fractions, whereas some other proteins were exclusive to a particular fraction: epimastigote polysomal (0.37%) and post-polysomal (2.95%) fractions; stress polysomal (13.8%) and post-polysomal (40.78%) fractions. Several proteins known to be involved in mRNA metabolism were identified, and this was considered important as it made it possible to confirm the reliability of our mRNP isolation approach. This procedure allowed us to have a first insight into the composition and dynamics of mRNPs in T. cruzi.
Collapse
Affiliation(s)
- Lysangela R Alves
- Instituto Carlos Chagas, Laboratório de Regulação da Expressão Gênica, Curitiba, Paraná, Brazil
| | | | | | | | | | | | | | | | | | | |
Collapse
|