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da Silva JP, Meneghini MR, Santos RS, Alves VL, da Cruz Martho KF, Vallim MA, Pascon RC. ATP sulfurylase atypical leucine zipper interacts with Cys3 and calcineurin A in the regulation of sulfur amino acid biosynthesis in Cryptococcus neoformans. Sci Rep 2023; 13:11694. [PMID: 37474559 PMCID: PMC10359356 DOI: 10.1038/s41598-023-37556-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/23/2023] [Indexed: 07/22/2023] Open
Abstract
Fungal pathogens are a major cause of death, especially among immunocompromised patients. Therapies against invasive fungal infections are restricted to a few antifungals; therefore, novel therapies are necessary. Nutritional signaling and regulation are important for pathogen establishment in the host. In Cryptococcus neoformans, the causal agent of fungal meningitis, amino acid uptake and biosynthesis are major aspects of nutritional adaptation. Disruptions in these pathways lead to virulence attenuation in an animal model of infection, especially for sulfur uptake and sulfur amino acid biosynthesis. Deletion of Cys3, the main transcription factor that controls these pathways, is the most deleterious gene knockout in vitro and in vivo, making it an important target for further application. Previously, we demonstrated that Cys3 is part of a protein complex, including calcineurin, which is necessary to maintain high Cys3 protein levels during sulfur uptake and sulfur amino acid biosynthesis. In the current study, other aspects of Cys3 regulation are explored. Two lines of evidence suggest that C. neoformans Cys3 does not interact with the F-box WD40 protein annotated as Met30, indicating another protein mediates Cys3 ubiquitin degradation. However, we found another level of Cys3 regulation, which involves protein interactions between Cys3 and ATP sulfurylase (MET3 gene). We show that an atypical leucine zipper at the N-terminus of ATP sulfurylase is essential for physical interaction with Cys3 and calcineurin. Our data suggests that Cys3 and ATP sulfurylase interact to regulate Cys3 transcriptional activity. This work evidences the complexity involved in the regulation of a transcription factor essential for the sulfur metabolism, which is a biological process important to nutritional adaptation, oxidative stress response, nucleic acid stability, and methylation. This information may be useful in designing novel therapies against fungal infections.
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Affiliation(s)
- Jeyson Pereira da Silva
- Universidade Federal de São Paulo, Campus Diadema, Rua São Nicolau, Diadema, SP, 21009913-030, Brazil
| | - Mariana Reis Meneghini
- Universidade Federal de São Paulo, Campus Diadema, Rua São Nicolau, Diadema, SP, 21009913-030, Brazil
| | - Ronaldo Silva Santos
- Universidade Federal de São Paulo, Campus Diadema, Rua São Nicolau, Diadema, SP, 21009913-030, Brazil
| | - Verônica Lira Alves
- Universidade Federal de São Paulo, Campus Diadema, Rua São Nicolau, Diadema, SP, 21009913-030, Brazil
| | | | - Marcelo Afonso Vallim
- Universidade Federal de São Paulo, Campus Diadema, Rua São Nicolau, Diadema, SP, 21009913-030, Brazil
| | - Renata Castiglioni Pascon
- Universidade Federal de São Paulo, Campus Diadema, Rua São Nicolau, Diadema, SP, 21009913-030, Brazil.
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Roberto TN, Lima RF, Pascon RC, Idnurm A, Vallim MA. Biological functions of the autophagy-related proteins Atg4 and Atg8 in Cryptococcus neoformans. PLoS One 2020; 15:e0230981. [PMID: 32251488 PMCID: PMC7135279 DOI: 10.1371/journal.pone.0230981] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/12/2020] [Indexed: 11/28/2022] Open
Abstract
Autophagy is a mechanism responsible for intracellular degradation and recycling of macromolecules and organelles, essential for cell survival in adverse conditions. More than 40 autophagy-related (ATG) genes have been identified and characterized in fungi, among them ATG4 and ATG8. ATG4 encodes a cysteine protease (Atg4) that plays an important role in autophagy by initially processing Atg8 at its C-terminus region. Atg8 is a ubiquitin-like protein essential for the synthesis of the double-layer membrane that constitutes the autophagosome vesicle, responsible for delivering the cargo from the cytoplasm to the vacuole lumen. The contributions of Atg-related proteins in the pathogenic yeast in the genus Cryptococcus remain to be explored, to elucidate the molecular basis of the autophagy pathway. In this context, we aimed to investigate the role of autophagy-related proteins 4 and 8 (Atg4 and Atg8) during autophagy induction and their contribution with non-autophagic events in C. neoformans. We found that Atg4 and Atg8 are conserved proteins and that they interact physically with each other. ATG gene deletions resulted in cells sensitive to nitrogen starvation. ATG4 gene disruption affects Atg8 degradation and its translocation to the vacuole lumen, after autophagy induction. Both atg4 and atg8 mutants are more resistant to oxidative stress, have an impaired growth in the presence of the cell wall-perturbing agent Congo Red, and are sensitive to the proteasome inhibitor bortezomib (BTZ). By that, we conclude that in C. neoformans the autophagy-related proteins Atg4 and Atg8 play an important role in the autophagy pathway; which are required for autophagy regulation, maintenance of amino acid levels and cell adaptation to stressful conditions.
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Affiliation(s)
- Thiago Nunes Roberto
- Departamento de Ciências Biológicas, Universidade Federal de São Paulo, Diadema, São Paulo, Brazil
| | - Ricardo Ferreira Lima
- Departamento de Infectologia, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | | | - Alexander Idnurm
- School of BioSciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Marcelo Afonso Vallim
- Departamento de Ciências Biológicas, Universidade Federal de São Paulo, Diadema, São Paulo, Brazil
- * E-mail:
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Silva NM, de Oliveira AMSA, Pegorin S, Giusti CE, Ferrari VB, Barbosa D, Martins LF, Morais C, Setubal JC, Vasconcellos SP, da Silva AM, de Oliveira JCF, Pascon RC, Viana-Niero C. Characterization of novel hydrocarbon-degrading Gordonia paraffinivorans and Gordonia sihwensis strains isolated from composting. PLoS One 2019; 14:e0215396. [PMID: 30998736 PMCID: PMC6472744 DOI: 10.1371/journal.pone.0215396] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/01/2019] [Indexed: 01/10/2023] Open
Abstract
Hydrocarbons are important environmental pollutants, and the isolation and characterization of new microorganisms with the ability to degrade these compounds are important for effective biodegradation. In this work we isolated and characterized several bacterial isolates from compost, a substrate rich in microbial diversity. The isolates were obtained from selective culture medium containing n-hexadecane, aiming to recover alkane-degraders. Six isolates identified as Gordonia by MALDI-TOF and 16S rRNA sequencing had the ability to degrade n-hexadecane in three days. Two isolates were selected for genomic and functional characterization, Gordonia paraffinivorans (MTZ052) and Gordonia sihwensis (MTZ096). The CG-MS results showed distinct n-hexadecane degradation rates for MTZ052 and MTZ096 (86% and 100% respectively). The genome sequence showed that MTZ052 encodes only one alkane degrading gene cluster, the CYP153 system, while MTZ096 harbors both the Alkane Hydroxylase (AH) and the CYP153 systems. qPCR showed that both gene clusters are induced by the presence of n-hexadecane in the growth medium, suggesting that G. paraffinivorans and G. sihwensis use these systems for degradation. Altogether, our results indicate that these Gordonia isolates have a good potential for biotransformation of hydrocarbons.
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Affiliation(s)
- Natalia Maria Silva
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Stefania Pegorin
- Departamento de Ciências Biológicas, Universidade Federal de São Paulo, Diadema, Brazil
| | - Camila Escandura Giusti
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Vitor Batista Ferrari
- Departamento de Ciências Farmacêuticas da Universidade Federal de São Paulo, Diadema, Brazil
| | - Deibs Barbosa
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Layla Farage Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Carlos Morais
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | - Renata Castiglioni Pascon
- Departamento de Ciências Biológicas, Universidade Federal de São Paulo, Diadema, Brazil
- * E-mail: (RCP); (CVN)
| | - Cristina Viana-Niero
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
- * E-mail: (RCP); (CVN)
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Antunes LP, Martins LF, Pereira RV, Thomas AM, Barbosa D, Lemos LN, Silva GMM, Moura LMS, Epamino GWC, Digiampietri LA, Lombardi KC, Ramos PL, Quaggio RB, de Oliveira JCF, Pascon RC, Cruz JBD, da Silva AM, Setubal JC. Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics. Sci Rep 2016; 6:38915. [PMID: 27941956 PMCID: PMC5150989 DOI: 10.1038/srep38915] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [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: 08/03/2016] [Accepted: 11/14/2016] [Indexed: 12/21/2022] Open
Abstract
Composting is a promising source of new organisms and thermostable enzymes that may be helpful in environmental management and industrial processes. Here we present results of metagenomic- and metatranscriptomic-based analyses of a large composting operation in the São Paulo Zoo Park. This composting exhibits a sustained thermophilic profile (50 °C to 75 °C), which seems to preclude fungal activity. The main novelty of our study is the combination of time-series sampling with shotgun DNA, 16S rRNA gene amplicon, and metatranscriptome high-throughput sequencing, enabling an unprecedented detailed view of microbial community structure, dynamics, and function in this ecosystem. The time-series data showed that the turning procedure has a strong impact on the compost microbiota, restoring to a certain extent the population profile seen at the beginning of the process; and that lignocellulosic biomass deconstruction occurs synergistically and sequentially, with hemicellulose being degraded preferentially to cellulose and lignin. Moreover, our sequencing data allowed near-complete genome reconstruction of five bacterial species previously found in biomass-degrading environments and of a novel biodegrading bacterial species, likely a new genus in the order Bacillales. The data and analyses provided are a rich source for additional investigations of thermophilic composting microbiology.
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Affiliation(s)
| | - Layla Farage Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | - Andrew Maltez Thomas
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | - Deibs Barbosa
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | - Leandro Nascimento Lemos
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | - Gianluca Major Machado Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | - Livia Maria Silva Moura
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | - George Willian Condomitti Epamino
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | | | - Karen Cristina Lombardi
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | - Ronaldo Bento Quaggio
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil.,Biocomplexity Institute of Virginia Tech, Blacksburg, VA, USA
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5
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Semighini CP, von Zeska Kress Fagundes MR, Ferreira JC, Pascon RC, de Souza Goldman MH, Goldman GH. Different roles of the Mre11 complex in the DNA damage response in Aspergillus nidulans. Mol Microbiol 2003; 48:1693-709. [PMID: 12791148 DOI: 10.1046/j.1365-2958.2003.03539.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Mre11-Rad50-Nbs1 protein complex has emerged as a central player in the cellular DNA damage response. Mutations in scaANBS1, which encodes the apparent homologue of human Nbs1 in Aspergillus nidulans, inhibit growth in the presence of the anti-topoisomerase I drug camptothecin. We have used the scaANBS1 cDNA as a bait in a yeast two-hybrid screening and report the identification of the A. nidulans Mre11 homologue (mreA). The inactivated mreA strain was more sensitive to several DNA damaging and oxidative stress agents. Septation in A. nidulans is dependent not only on the uvsBATR gene, but also on the mre11 complex. scaANBS1 and mreA genes are both involved in the DNA replication checkpoint whereas mreA is specifically involved in the intra-S-phase checkpoint. ScaANBS1 also participates in G2-M checkpoint control upon DNA damage caused by MMS. In addition, the scaANBS1 gene is also important for ascospore viability, whereas mreA is required for successful meiosis in A. nidulans. Consistent with this view, the Mre11 complex and the uvsCRAD51 gene are highly expressed at the mRNA level during the sexual development.
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Affiliation(s)
- Camile P Semighini
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Brazil
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6
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Pascon RC, Miller BL. Morphogenesis in Aspergillus nidulans requires Dopey (DopA), a member of a novel family of leucine zipper-like proteins conserved from yeast to humans. Mol Microbiol 2000; 36:1250-64. [PMID: 10931277 DOI: 10.1046/j.1365-2958.2000.01950.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DopA is the founding member of a novel protein family required for correct cell morphology and spatiotemporal organization of multicellular structures in the filamentous fungus Aspergillus nidulans. DopA homologues from Saccharomyces cerevisiae (Dop1), Candida albicans, Caenorhabditis elegans, Rattus norvegicus and Homo sapiens have been identified from genome sequencing projects. S. cerevisiae DOP1 is essential for viability and, like DopA, affects cellular morphogenesis. dopA encodes a large protein (207 kDa) containing several putative domains, including three leucine zipper-like domains. Strains with either the temperature-sensitive dopA1(ts) allele, which alters one of the leucine zippers, or the null deltadopA allele, had abnormal morphology of the vegetative hyphae, delayed and asynchronous initiation of asexual development, aberrant morphogenesis of the conidiophore and an early block in the sexual cycle. The expression patterns of key transcriptional regulators of the asexual and sexual cycle (brlA, abaA and steA) are altered in a deltadopA background, suggesting that DopA functions upstream in the developmental pathway. Double mutant analysis showed that dopA interacts genetically with constitutively active and inactive forms of A. nidulans Aras to modulate hyphal morphogenesis and asexual development.
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Affiliation(s)
- R C Pascon
- Department of Microbiology, Molecular Biology and Biochemistry, University of Idaho, Moscow 83844, USA
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Fungaro MH, Rech E, Muhlen GS, Vainstein MH, Pascon RC, de Queiroz MV, Pizzirani-Kleiner AA, de Azevedo JL. Transformation of Aspergillus nidulans by microprojectile bombardment on intact conidia. FEMS Microbiol Lett 1995; 125:293-7. [PMID: 7875577 DOI: 10.1111/j.1574-6968.1995.tb07371.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
This paper describes transformation of intact conidia of Aspergillus nidulans, auxotrophic for arginine, by using the biolistic process. The plasmid employed was pFB39, carrying the argB gene. The transformation frequency obtained was 81 transformants/microgram of DNA. Classical genetics and molecular analysis were conducted to analyse transformants and to determine in which chromosome integration took place.
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Affiliation(s)
- M H Fungaro
- Departamento de Genética, Escola Superior de Agricultura, Luiz de Queiroz, Universidade de São Paulo, Brazil
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