1
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Dang TTV, Maufrais C, Colin J, Moyrand F, Mouyna I, Coppée JY, Onyishi CU, Lipecka J, Guerrera IC, May RC, Janbon G. Alternative TSS use is widespread in Cryptococcus fungi in response to environmental cues and regulated genome-wide by the transcription factor Tur1. PLoS Biol 2024; 22:e3002724. [PMID: 39052688 DOI: 10.1371/journal.pbio.3002724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/06/2024] [Accepted: 06/28/2024] [Indexed: 07/27/2024] Open
Abstract
Alternative transcription start site (TSS) usage regulation has been identified as a major means of gene expression regulation in metazoans. However, in fungi, its impact remains elusive as its study has thus far been restricted to model yeasts. Here, we first re-analyzed TSS-seq data to define genuine TSS clusters in 2 species of pathogenic Cryptococcus. We identified 2 types of TSS clusters associated with specific DNA sequence motifs. Our analysis also revealed that alternative TSS usage regulation in response to environmental cues is widespread in Cryptococcus, altering gene expression and protein targeting. Importantly, we performed a forward genetic screen to identify a unique transcription factor (TF) named Tur1, which regulates alternative TSS (altTSS) usage genome-wide when cells switch from exponential phase to stationary phase. ChiP-Seq and DamID-Seq analyses suggest that at some loci, the role of Tur1 might be direct. Tur1 has been previously shown to be essential for virulence in C. neoformans. We demonstrated here that a tur1Δ mutant strain is more sensitive to superoxide stress and phagocytosed more efficiently by macrophages than the wild-type (WT) strain.
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Affiliation(s)
- Thi Tuong Vi Dang
- Université Paris Cité, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Paris, France
| | - Corinne Maufrais
- Université Paris Cité, Institut Pasteur, HUB Bioinformatique et Biostatistique, C3BI, USR 3756 IP CNRS, Paris, France
| | - Jessie Colin
- Université Paris Cité, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Paris, France
- Ecole Pratique des Hautes Etudes, PSL Research University, Paris, France
| | - Frédérique Moyrand
- Université Paris Cité, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Paris, France
| | - Isabelle Mouyna
- Université Paris Cité, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Paris, France
| | - Jean-Yves Coppée
- Université Paris Cité, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Paris, France
| | - Chinaemerem U Onyishi
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Joanna Lipecka
- Université Paris Cité, SFR Necker INSERM US24/CNRS UAR3633, Proteomics Platform, Paris, France
| | - Ida Chiara Guerrera
- Université Paris Cité, SFR Necker INSERM US24/CNRS UAR3633, Proteomics Platform, Paris, France
| | - Robin C May
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Guilhem Janbon
- Université Paris Cité, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Paris, France
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2
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Kadooka C, Tanaka Y, Hira D, Oka T. Identification of a putative α-galactoside β-(1 → 3)-galactosyltransferase involved in the biosynthesis of galactomannan side chain of glucuronoxylomannogalactan in Cryptococcus neoformans. Front Microbiol 2024; 15:1390371. [PMID: 38841067 PMCID: PMC11150766 DOI: 10.3389/fmicb.2024.1390371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/07/2024] [Indexed: 06/07/2024] Open
Abstract
The cell surface of Cryptococcus neoformans is covered by a thick capsular polysaccharide. The capsule is the most important virulence factor of C. neoformans; however, the complete mechanism of its biosynthesis is unknown. The capsule is composed of glucuronoxylomannan (GXM) and glucuronoxylomannogalactan (GXMGal). As GXM is the most abundant component of the capsule, many studies have focused on GXM biosynthesis. However, although GXMGal has an important role in virulence, studies on its biosynthesis are scarce. Herein, we have identified a GT31 family β-(1 → 3)-galactosyltransferase Ggt2, which is involved in the biosynthesis of the galactomannan side chain of GXMGal. Comparative analysis of GXMGal produced by a ggt2 disruption strain revealed that Ggt2 is a glycosyltransferase that catalyzes the initial reaction in the synthesis of the galactomannan side chain of GXMGal. The ggt2 disruption strain showed a temperature-sensitive phenotype at 37°C, indicating that the galactomannan side chain of GXMGal is important for high-temperature stress tolerance in C. neoformans. Our findings provide insights into complex capsule biosynthesis in C. neoformans.
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Affiliation(s)
- Chihiro Kadooka
- Department of Biotechnology and Life Sciences, Faculty of Biotechnology and Life Sciences, Sojo University, Kumamoto, Japan
| | - Yutaka Tanaka
- Division of Infection and Host Defense, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Daisuke Hira
- Department of Biotechnology and Life Sciences, Faculty of Biotechnology and Life Sciences, Sojo University, Kumamoto, Japan
| | - Takuji Oka
- Department of Biotechnology and Life Sciences, Faculty of Biotechnology and Life Sciences, Sojo University, Kumamoto, Japan
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3
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Rizzo J, Trottier A, Moyrand F, Coppée JY, Maufrais C, Zimbres ACG, Dang TTV, Alanio A, Desnos-Ollivier M, Mouyna I, Péhau-Arnaude G, Commere PH, Novault S, Ene IV, Nimrichter L, Rodrigues ML, Janbon G. Coregulation of extracellular vesicle production and fluconazole susceptibility in Cryptococcus neoformans. mBio 2023; 14:e0087023. [PMID: 37310732 PMCID: PMC10470540 DOI: 10.1128/mbio.00870-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 04/17/2023] [Indexed: 06/14/2023] Open
Abstract
Resistance to fluconazole (FLC), the most widely used antifungal drug, is typically achieved by altering the azole drug target and/or drug efflux pumps. Recent reports have suggested a link between vesicular trafficking and antifungal resistance. Here, we identified novel Cryptococcus neoformans regulators of extracellular vesicle (EV) biogenesis that impact FLC resistance. In particular, the transcription factor Hap2 does not affect the expression of the drug target or efflux pumps, yet it impacts the cellular sterol profile. Subinhibitory FLC concentrations also downregulate EV production. Moreover, in vitro spontaneous FLC-resistant colonies showed altered EV production, and the acquisition of FLC resistance was associated with decreased EV production in clinical isolates. Finally, the reversion of FLC resistance was associated with increased EV production. These data suggest a model in which fungal cells can regulate EV production in place of regulating the drug target gene expression as a first line of defense against antifungal assault in this fungal pathogen. IMPORTANCE Extracellular vesicles (EVs) are membrane-enveloped particles that are released by cells into the extracellular space. Fungal EVs can mediate community interactions and biofilm formation, but their functions remain poorly understood. Here, we report the identification of the first regulators of EV production in the major fungal pathogen Cryptococcus neoformans. Surprisingly, we uncover a novel role of EVs in modulating antifungal drug resistance. Disruption of EV production was associated with altered lipid composition and changes in fluconazole susceptibility. Spontaneous azole-resistant mutants were deficient in EV production, while loss of resistance restored initial EV production levels. These findings were recapitulated in C. neoformans clinical isolates, indicating that azole resistance and EV production are coregulated in diverse strains. Our study reveals a new mechanism of drug resistance in which cells adapt to azole stress by modulating EV production.
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Affiliation(s)
- Juliana Rizzo
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Adèle Trottier
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
| | - Frédérique Moyrand
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
| | - Jean-Yves Coppée
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
| | - Corinne Maufrais
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
- Institut Pasteur, Université Paris Cité, USR 3756 IP CNRS, HUB Bioinformatique et Biostatistique, Paris, France
| | - Ana Claudia G. Zimbres
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thi Tuong Vi Dang
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
| | - Alexandre Alanio
- Institut Pasteur, Université Paris Cité, Centre National de Référence Mycoses Invasives et Antifongiques, Groupe de recherche Mycologie Translationnelle, Département de Mycologie, Paris, France
- Laboratoire de parasitologie-mycologie, AP-HP, Hôpital Saint-Louis, Paris, France
| | - Marie Desnos-Ollivier
- Institut Pasteur, Université Paris Cité, Centre National de Référence Mycoses Invasives et Antifongiques, Groupe de recherche Mycologie Translationnelle, Département de Mycologie, Paris, France
| | - Isabelle Mouyna
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
| | - Gérard Péhau-Arnaude
- Institut Pasteur, Université Paris Cité, Plateforme de Bio-Imagerie Ultrastructurale, Paris, France
| | - Pierre-Henri Commere
- Institut Pasteur, Université Paris Cité, Cytometry and Biomarkers, Paris, France
| | - Sophie Novault
- Institut Pasteur, Université Paris Cité, Cytometry and Biomarkers, Paris, France
| | - Iuliana V. Ene
- Institut Pasteur, Université Paris Cité, Fungal Heterogeneity Group, Paris, France
| | - Leonardo Nimrichter
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcio L. Rodrigues
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Curitiba, Brazil
| | - Guilhem Janbon
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
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4
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Snelders E, Moyrand F, Sturny-Leclère A, Vernel-Pauillac F, Volant S, Janbon G, Alanio A. The role of glycosylphosphatidylinositol (gpi) anchored proteins in Cryptococcus neoformans. Microbes Infect 2022; 24:105016. [DOI: 10.1016/j.micinf.2022.105016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/25/2022] [Accepted: 05/20/2022] [Indexed: 10/31/2022]
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Abstract
Systemic cryptococcosis is fatal without treatment. Globally, this disease kills 180,000 of the 225,000 infected people each year, even with the use of antifungal therapies. Currently, there is no vaccine to prevent cryptococcosis. Previously, we discovered that Znf2, a morphogenesis regulator that directs Cryptococcus yeast-to-hyphal transition, profoundly affects cryptococcal interaction with the host-overexpression of ZNF2 drives filamentous growth, attenuates cryptococcal virulence, and elicits protective host immune responses. Importantly, immunization with cryptococcal cells overexpressing ZNF2, either in live or heat-inactivated form, offers significant protection to the host from a subsequent challenge by the otherwise lethal wild-type H99 strain. We hypothesize that cellular components enriched in ZNF2oe cells are immunoprotective. Here, we discovered that serum from protected animals vaccinated with inactivated ZNF2oe cells recognizes cryptococcal antigens that reside within the capsule. Consistently, capsule is required for immunoprotection offered by ZNF2oe cells. Interestingly, the serum from protective animals recognizes antigens in both wild-type yeast cells and ZNF2oe cells, with higher abundance in the latter. Consequently, even the heat-inactivated wild-type cells become immunoprotective with an increased vaccination dose. We also found that disruption of a chromatin remodeling factor Brf1, which is important for initiation of filamentation by Znf2, reduces the antigen level in ZNF2oe cells. Deletion of BRF1 drastically reduces the protective effect of ZNF2oe cells in both live and heat-killed forms even though the ZNF2oebrf1Δ strain itself is avirulent. Collectively, our findings underscore the importance of identifying the subset of cryptococcal surface factors that are beneficial in host protection. IMPORTANCE Cryptococcosis claims close to 200,000 lives annually. There is no vaccine clinically available for this fungal disease. Many avirulent mutant strains do not provide protection against cryptococcosis. We previously discovered that hyphal ZNF2oe strains elicit protective host immune responses both in the live and heat-inactivated forms. Here we seek to understand the mechanism underlying the host protection provided by ZNF2oe cells. We discovered increased accumulation of antigens located within the caspusle of ZNF2oe cells and consequently the requirement of the capsule for ZNF2oe strain-elicited host protection. Furthermore, genetically blocking the ability of ZNF2oe cells to grow in the hyphal form significantly reduces antigen accumulation and impairs the ability of ZNF2oe strain to provide host protection. Our findings highlight the importance of identifying the Znf2-regulated capsular surface factors that are fundamental in host protection.
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6
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Gröhs Ferrareze PA, Maufrais C, Silva Araujo Streit R, Priest SJ, Cuomo CA, Heitman J, Staats CC, Janbon G. Application of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi loss. G3-GENES GENOMES GENETICS 2021; 11:6080769. [PMID: 33585873 PMCID: PMC8022950 DOI: 10.1093/g3journal/jkaa070] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/24/2020] [Indexed: 12/15/2022]
Abstract
Evaluating the quality of a de novo annotation of a complex fungal genome based on RNA-seq data remains a challenge. In this study, we sequentially optimized a Cufflinks-CodingQuary-based bioinformatics pipeline fed with RNA-seq data using the manually annotated model pathogenic yeasts Cryptococcus neoformans and Cryptococcus deneoformans as test cases. Our results show that the quality of the annotation is sensitive to the quantity of RNA-seq data used and that the best quality is obtained with 5–10 million reads per RNA-seq replicate. We also showed that the number of introns predicted is an excellent a priori indicator of the quality of the final de novo annotation. We then used this pipeline to annotate the genome of the RNAi-deficient species Cryptococcus deuterogattii strain R265 using RNA-seq data. Dynamic transcriptome analysis revealed that intron retention is more prominent in C. deuterogattii than in the other RNAi-proficient species C. neoformans and C. deneoformans. In contrast, we observed that antisense transcription was not higher in C. deuterogattii than in the two other Cryptococcus species. Comparative gene content analysis identified 21 clusters enriched in transcription factors and transporters that have been lost. Interestingly, analysis of the subtelomeric regions in these three annotated species identified a similar gene enrichment, reminiscent of the structure of primary metabolic clusters. Our data suggest that there is active exchange between subtelomeric regions, and that other chromosomal regions might participate in adaptive diversification of Cryptococcus metabolite assimilation potential.
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Affiliation(s)
- Patrícia Aline Gröhs Ferrareze
- Département de Mycologie, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, F-75015 Paris, France.,Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 15005, Brazil
| | - Corinne Maufrais
- Département de Mycologie, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, F-75015 Paris, France.,Département Biologie Computationnelle, Institut Pasteur, HUB Bioinformatique et Biostatistique, C3BI, USR 3756 IP CNRS, F-75015 Paris, France
| | - Rodrigo Silva Araujo Streit
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 15005, Brazil
| | - Shelby J Priest
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Charley Christian Staats
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 15005, Brazil
| | - Guilhem Janbon
- Département de Mycologie, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, F-75015 Paris, France
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7
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Wallace EWJ, Maufrais C, Sales-Lee J, Tuck LR, de Oliveira L, Feuerbach F, Moyrand F, Natarajan P, Madhani HD, Janbon G. Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom. Nucleic Acids Res 2020; 48:2312-2331. [PMID: 32020195 PMCID: PMC7049704 DOI: 10.1093/nar/gkaa060] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 01/13/2020] [Accepted: 01/20/2020] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic protein synthesis generally initiates at a start codon defined by an AUG and its surrounding Kozak sequence context, but the quantitative importance of this context in different species is unclear. We tested this concept in two pathogenic Cryptococcus yeast species by genome-wide mapping of translation and of mRNA 5' and 3' ends. We observed thousands of AUG-initiated upstream open reading frames (uORFs) that are a major contributor to translation repression. uORF use depends on the Kozak sequence context of its start codon, and uORFs with strong contexts promote nonsense-mediated mRNA decay. Transcript leaders in Cryptococcus and other fungi are substantially longer and more AUG-dense than in Saccharomyces. Numerous Cryptococcus mRNAs encode predicted dual-localized proteins, including many aminoacyl-tRNA synthetases, in which a leaky AUG start codon is followed by a strong Kozak context in-frame AUG, separated by mitochondrial-targeting sequence. Analysis of other fungal species shows that such dual-localization is also predicted to be common in the ascomycete mould, Neurospora crassa. Kozak-controlled regulation is correlated with insertions in translational initiation factors in fidelity-determining regions that contact the initiator tRNA. Thus, start codon context is a signal that quantitatively programs both the expression and the structures of proteins in diverse fungi.
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Affiliation(s)
- Edward W J Wallace
- Institute for Cell Biology and SynthSys, School of Biological Sciences, University of Edinburgh, UK
| | - Corinne Maufrais
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015 Paris, France
- Institut Pasteur, HUB Bioinformatique et Biostatistique, C3BI, USR 3756 IP CNRS, F-75015 Paris, France
| | - Jade Sales-Lee
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Laura R Tuck
- Institute for Cell Biology and SynthSys, School of Biological Sciences, University of Edinburgh, UK
| | - Luciana de Oliveira
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015 Paris, France
| | - Frank Feuerbach
- Institut Pasteur, Unité Génétique des Interactions Macromoléculaire, Département Génome et Génétique, F-75015 Paris, France
| | - Frédérique Moyrand
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015 Paris, France
| | - Prashanthi Natarajan
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Guilhem Janbon
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015 Paris, France
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8
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Bastos RW, Freitas GJC, Carneiro HCS, Oliveira LVN, Gouveia-Eufrasio L, Santos APN, Moyrand F, Maufrais C, Janbon G, Santos DA. From the environment to the host: How non-azole agrochemical exposure affects the antifungal susceptibility and virulence of Cryptococcus gattii. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 681:516-523. [PMID: 31121401 DOI: 10.1016/j.scitotenv.2019.05.094] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/07/2019] [Accepted: 05/07/2019] [Indexed: 06/09/2023]
Abstract
Agrochemicals such as the non-azoles, used to improve crop productivity, poses severe undesirable effects on the environment and human health. In addition, they induce cross-resistance (CR) with clinical drugs in pathogenic fungi. However, till date emphasis has been given to the role of azoles on the induction of CR. Herein, we analyzed the effect of a non-azole agrochemical, pyraclostrobin (PCT), on the antifungal susceptibility and virulence of the human and animal pathogens Cryptococcus gattii and C. neoformans. We determined the minimum inhibitory concentration (MIC) of fluconazole (FLC), itraconazole, ravuconazole, amphotericin B, and PCT on colonies: (i) that were not exposed to PCT (non-adapted-NA-cultures), (ii) were exposed at the maximum concentration of PCT (adapted-A-cultures) and (iii) the adapted colonies after cultivation 10 times in PCT-free media (10 passages-10p-cultures). Our results showed that exposure to PCT induced both temporary and permanent CR to clinical azoles in a temperature-dependent manner. With the objective to understand the mechanism of induction of CR through non-azoles, the transcriptomes of NA and 10p cells from C. gattii R265 were analyzed. The transcriptomic analysis showed that expression of the efflux-pump genes (AFR1 and MDR1) and PCT target was higher in resistant 10p cells than that in NA. Moreover, the virulence of 10p cells was reduced as compared to NA cells in mice, as observed by the differential gene expression analysis of genes related to ion-metabolism. Additionally, we observed that FLC could not increase the survival rate of mice infected with 10p cells, confirming the occurrence of permanent CR in vivo. The findings of the present study demonstrate that the non-azole agrochemical PCT can induce permanent CR to clinical antifungals through increased expression of efflux pump genes in resistant cells and that such phenomenon also manifests in vivo.
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Affiliation(s)
- Rafael Wesley Bastos
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Gustavo José Cota Freitas
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Hellem Cristina Silva Carneiro
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Lorena Vívien Neves Oliveira
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ludmila Gouveia-Eufrasio
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Anderson Philip Nonato Santos
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | | | - Guilhem Janbon
- Département de Mycologie, Institut Pasteur, Paris, France
| | - Daniel Assis Santos
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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9
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Rokas A, Wisecaver JH, Lind AL. The birth, evolution and death of metabolic gene clusters in fungi. Nat Rev Microbiol 2019; 16:731-744. [PMID: 30194403 DOI: 10.1038/s41579-018-0075-3] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Fungi contain a remarkable diversity of both primary and secondary metabolic pathways involved in ecologically specialized or accessory functions. Genes in these pathways are frequently physically linked on fungal chromosomes, forming metabolic gene clusters (MGCs). In this Review, we describe the diversity in the structure and content of fungal MGCs, their population-level and species-level variation, the evolutionary mechanisms that underlie their formation, maintenance and decay, and their ecological and evolutionary impact on fungal populations. We also discuss MGCs from other eukaryotes and the reasons for their preponderance in fungi. Improved knowledge of the evolutionary life cycle of MGCs will advance our understanding of the ecology of specialized metabolism and of the interplay between the lifestyle of an organism and genome architecture.
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Affiliation(s)
- Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA. .,Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Jennifer H Wisecaver
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.,Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Abigail L Lind
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA.,Gladstone Institutes, San Francisco, CA, USA
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10
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Hommel B, Sturny-Leclère A, Volant S, Veluppillai N, Duchateau M, Yu CH, Hourdel V, Varet H, Matondo M, Perfect JR, Casadevall A, Dromer F, Alanio A. Cryptococcus neoformans resists to drastic conditions by switching to viable but non-culturable cell phenotype. PLoS Pathog 2019; 15:e1007945. [PMID: 31356623 PMCID: PMC6687208 DOI: 10.1371/journal.ppat.1007945] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 08/08/2019] [Accepted: 06/27/2019] [Indexed: 01/22/2023] Open
Abstract
Metabolically quiescent pathogens can persist in a viable non-replicating state for months or even years. For certain infectious diseases, such as tuberculosis, cryptococcosis, histoplasmosis, latent infection is a corollary of this dormant state, which has the risk for reactivation and clinical disease. During murine cryptococcosis and macrophage uptake, stress and host immunity induce Cryptococcus neoformans heterogeneity with the generation of a sub-population of yeasts that manifests a phenotype compatible with dormancy (low stress response, latency of growth). In this subpopulation, mitochondrial transcriptional activity is regulated and this phenotype has been considered as a hallmark of quiescence in stem cells. Based on these findings, we worked to reproduce this phenotype in vitro and then standardize the experimental conditions to consistently generate this dormancy in C. neoformans. We found that incubation of stationary phase yeasts (STAT) in nutriment limited conditions and hypoxia for 8 days (8D-HYPOx) was able to produced cells that mimic the phenotype obtained in vivo. In these conditions, mortality and/or apoptosis occurred in less than 5% of the yeasts compared to 30-40% of apoptotic or dead yeasts upon incubation in normoxia (8D-NORMOx). Yeasts in 8D-HYPOx harbored a lower stress response, delayed growth and less that 1% of culturability on agar plates, suggesting that these yeasts are viable but non culturable cells (VBNC). These VBNC were able to reactivate in the presence of pantothenic acid, a vitamin that is known to be involved in quorum sensing and a precursor of acetyl-CoA. Global metabolism of 8D-HYPOx cells showed some specific requirements and was globally shut down compared to 8D-NORMOx and STAT conditions. Mitochondrial analyses showed that the mitochondrial mass increased with mitochondria mostly depolarized in 8D-HYPOx compared to 8D-NORMox, with increased expression of mitochondrial genes. Proteomic and transcriptomic analyses of 8D-HYPOx revealed that the number of secreted proteins and transcripts detected also decreased compared to 8D-NORMOx and STAT, and the proteome, secretome and transcriptome harbored specific profiles that are engaged as soon as four days of incubation. Importantly, acetyl-CoA and the fatty acid pathway involving mitochondria are required for the generation and viability maintenance of VBNC. Altogether, these data show that we were able to generate for the first time VBNC phenotype in C. neoformans. This VBNC state is associated with a specific metabolism that should be further studied to understand dormancy/quiescence in this yeast.
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Affiliation(s)
- Benjamin Hommel
- Institut Pasteur, CNRS, Molecular Mycology Unit, UMR2000, Paris, France
- Laboratoire de Parasitologie-Mycologie, Hôpital Saint-Louis, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | | | - Stevenn Volant
- Institut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS, Paris, France
| | | | - Magalie Duchateau
- Institut Pasteur, Unité de spectrométrie de masse et Protéomique, Paris, France
| | - Chen-Hsin Yu
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Véronique Hourdel
- Institut Pasteur, Unité de spectrométrie de masse et Protéomique, Paris, France
| | - Hugo Varet
- Institut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS, Paris, France
- Institut Pasteur - Transcriptome and Epigenome Platform - Biomics Pole - C2RT, Paris, France
| | - Mariette Matondo
- Institut Pasteur, Unité de spectrométrie de masse et Protéomique, Paris, France
| | - John R. Perfect
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Françoise Dromer
- Institut Pasteur, CNRS, Molecular Mycology Unit, UMR2000, Paris, France
| | - Alexandre Alanio
- Institut Pasteur, CNRS, Molecular Mycology Unit, UMR2000, Paris, France
- Laboratoire de Parasitologie-Mycologie, Hôpital Saint-Louis, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- * E-mail:
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11
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Wang ZA, Li LX, Doering TL. Unraveling synthesis of the cryptococcal cell wall and capsule. Glycobiology 2019; 28:719-730. [PMID: 29648596 DOI: 10.1093/glycob/cwy030] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 03/28/2018] [Indexed: 11/15/2022] Open
Abstract
Fungal pathogens cause devastating infections in millions of individuals each year, representing a huge but underappreciated burden on human health. One of these, the opportunistic fungus Cryptococcus neoformans, kills hundreds of thousands of patients annually, disproportionately affecting people in resource-limited areas. This yeast is distinguished from other pathogenic fungi by a polysaccharide capsule that is displayed on the cell surface. The capsule consists of two complex polysaccharide polymers: a mannan substituted with xylose and glucuronic acid, and a galactan with galactomannan side chains that bear variable amounts of glucuronic acid and xylose. The cell wall, with which the capsule is associated, is a matrix of alpha and beta glucans, chitin, chitosan, and mannoproteins. In this review, we focus on synthesis of the wall and capsule, both of which are critical for the ability of this microbe to cause disease and are distinct from structures found in either model yeasts or the mammals afflicted by this infection. Significant research effort over the last few decades has been applied to defining the synthetic machinery of these two structures, including nucleotide sugar metabolism and transport, glycosyltransferase activities, polysaccharide export, and assembly and association of structural elements. Discoveries in this area have elucidated fundamental biology and may lead to novel targets for antifungal therapy. In this review, we summarize the progress made in this challenging and fascinating area, and outline future research questions.
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Affiliation(s)
- Zhuo A Wang
- Department of Molecular Microbiology, Washington University School of Medicine, 660 South Euclid Avenue, Saint Louis, MO, USA
| | - Lucy X Li
- Department of Molecular Microbiology, Washington University School of Medicine, 660 South Euclid Avenue, Saint Louis, MO, USA
| | - Tamara L Doering
- Department of Molecular Microbiology, Washington University School of Medicine, 660 South Euclid Avenue, Saint Louis, MO, USA
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12
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Gonzalez-Hilarion S, Paulet D, Lee KT, Hon CC, Lechat P, Mogensen E, Moyrand F, Proux C, Barboux R, Bussotti G, Hwang J, Coppée JY, Bahn YS, Janbon G. Intron retention-dependent gene regulation in Cryptococcus neoformans. Sci Rep 2016; 6:32252. [PMID: 27577684 PMCID: PMC5006051 DOI: 10.1038/srep32252] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/03/2016] [Indexed: 01/28/2023] Open
Abstract
The biological impact of alternative splicing is poorly understood in fungi, although recent studies have shown that these microorganisms are usually intron-rich. In this study, we re-annotated the genome of C. neoformans var. neoformans using RNA-Seq data. Comparison with C. neoformans var. grubii revealed that more than 99% of ORF-introns are in the same exact position in the two varieties whereas UTR-introns are much less evolutionary conserved. We also confirmed that alternative splicing is very common in C. neoformans, affecting nearly all expressed genes. We also observed specific regulation of alternative splicing by environmental cues in this yeast. However, alternative splicing does not appear to be an efficient method to diversify the C. neoformans proteome. Instead, our data suggest the existence of an intron retention-dependent mechanism of gene expression regulation that is not dependent on NMD. This regulatory process represents an additional layer of gene expression regulation in fungi and provides a mechanism to tune gene expression levels in response to any environmental modification.
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Affiliation(s)
- Sara Gonzalez-Hilarion
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015, Paris, France
| | - Damien Paulet
- Institut Pasteur, Plate-forme transcriptome et Epigénome, Département Génomes et Génétique, F-75015, Paris, France
| | - Kyung-Tae Lee
- Department of Biotechnology, College of Life and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Chung-Chau Hon
- RIKEN Center for Life Science Technologies, Yokohama Institute, Division of Genomic Technology, Yokohama, 230-0045, Japan
| | - Pierre Lechat
- Institut Pasteur, HUB Bioinformatique et Biostatistique, C3BI, USR 3756 IP CNRS, F-75015, Paris, France
| | - Estelle Mogensen
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015, Paris, France
| | - Frédérique Moyrand
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015, Paris, France
| | - Caroline Proux
- Institut Pasteur, Plate-forme transcriptome et Epigénome, Département Génomes et Génétique, F-75015, Paris, France
| | - Rony Barboux
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015, Paris, France
| | - Giovanni Bussotti
- Institut Pasteur, HUB Bioinformatique et Biostatistique, C3BI, USR 3756 IP CNRS, F-75015, Paris, France
| | - Jungwook Hwang
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, Korea
| | - Jean-Yves Coppée
- Institut Pasteur, Plate-forme transcriptome et Epigénome, Département Génomes et Génétique, F-75015, Paris, France
| | - Yong-Sun Bahn
- Department of Biotechnology, College of Life and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Guilhem Janbon
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015, Paris, France
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13
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Li LX, Ashikov A, Liu H, Griffith CL, Bakker H, Doering TL. Cryptococcus neoformans UGT1 encodes a UDP-Galactose/UDP-GalNAc transporter. Glycobiology 2016; 27:87-98. [PMID: 27496760 DOI: 10.1093/glycob/cww078] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/22/2016] [Accepted: 07/27/2016] [Indexed: 12/30/2022] Open
Abstract
Cryptococcus neoformans, an opportunistic fungal pathogen, produces a glycan capsule to evade the immune system during infection. This definitive virulence factor is composed mainly of complex polysaccharides, which are made in the secretory pathway by reactions that utilize activated nucleotide sugar precursors. Although the pathways that synthesize these precursors are known, the identity and the regulation of the nucleotide sugar transporters (NSTs) responsible for importing them into luminal organelles remain elusive. The UDP-galactose transporter, Ugt1, was initially identified by homology to known UGTs and glycan composition analysis of ugt1Δ mutants. However, sequence is an unreliable predictor of NST substrate specificity, cells may express multiple NSTs with overlapping specificities, and NSTs may transport multiple substrates. Determining NST activity thus requires biochemical demonstration of function. We showed that Ugt1 transports both UDP-galactose and UDP-N-acetylgalactosamine in vitro. Deletion of UGT1 resulted in growth and mating defects along with altered capsule and cellular morphology. The mutant was also phagocytosed more readily by macrophages than wild-type cells and cleared more quickly in vivo and in vitro, suggesting a mechanism for the lack of virulence observed in mouse models of infection.
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Affiliation(s)
- Lucy X Li
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Angel Ashikov
- Department of Cellular Chemistry, Hannover Medical School, D-30625 Hannover, Germany
| | - Hong Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Cara L Griffith
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Hans Bakker
- Department of Cellular Chemistry, Hannover Medical School, D-30625 Hannover, Germany
| | - Tamara L Doering
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
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14
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Hayes JB, Sircy LM, Heusinkveld LE, Ding W, Leander RN, McClelland EE, Nelson DE. Modulation of Macrophage Inflammatory Nuclear Factor κB (NF-κB) Signaling by Intracellular Cryptococcus neoformans. J Biol Chem 2016; 291:15614-27. [PMID: 27231343 DOI: 10.1074/jbc.m116.738187] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Indexed: 01/29/2023] Open
Abstract
Cryptococcus neoformans (Cn) is a common facultative intracellular pathogen that can cause life-threatening fungal meningitis in immunocompromised individuals. Shortly after infection, Cn is detectable as both extra- and intracellular yeast particles, with Cn being capable of establishing long-lasting latent infections within host macrophages. Although recent studies have shown that shed capsular polysaccharides and intact extracellular Cn can compromise macrophage function through modulation of NF-κB signaling, it is currently unclear whether intracellular Cn also affects NF-κB signaling. Utilizing live cell imaging and computational modeling, we find that extra- and intracellular Cn support distinct modes of NF-κB signaling in cultured murine macrophages. Specifically, in RAW 264.7 murine macrophages treated with extracellular glucuronoxylomannan (GXM), the major Cn capsular polysaccharide, LPS-induced nuclear translocation of p65 is inhibited, whereas in cells with intracellular Cn, LPS-induced nuclear translocation of p65 is both amplified and sustained. Mathematical simulations and quantification of nascent protein expression indicate that this is a possible consequence of Cn-induced "translational interference," impeding IκBα resynthesis. We also show that long term Cn infection induces stable nuclear localization of p65 and IκBα proteins in the absence of additional pro-inflammatory stimuli. In this case, nuclear localization of p65 is not accompanied by TNFα or inducible NOS (iNOS) expression. These results demonstrate that capsular polysaccharides and intact intracellular yeast manipulate NF-κB via multiple distinct mechanisms and provide new insights into how Cn might modulate cellular signaling at different stages of an infection.
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Affiliation(s)
| | | | | | - Wandi Ding
- Mathematical Sciences, Middle Tennessee State University, Murfreesboro, Tennessee 37130
| | - Rachel N Leander
- Mathematical Sciences, Middle Tennessee State University, Murfreesboro, Tennessee 37130
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15
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Kwon-Chung KJ, Fraser JA, Doering TL, Wang Z, Janbon G, Idnurm A, Bahn YS. Cryptococcus neoformans and Cryptococcus gattii, the etiologic agents of cryptococcosis. Cold Spring Harb Perspect Med 2014; 4:a019760. [PMID: 24985132 PMCID: PMC4066639 DOI: 10.1101/cshperspect.a019760] [Citation(s) in RCA: 323] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cryptococcus neoformans and Cryptococcus gattii are the two etiologic agents of cryptococcosis. They belong to the phylum Basidiomycota and can be readily distinguished from other pathogenic yeasts such as Candida by the presence of a polysaccharide capsule, formation of melanin, and urease activity, which all function as virulence determinants. Infection proceeds via inhalation and subsequent dissemination to the central nervous system to cause meningoencephalitis. The most common risk for cryptococcosis caused by C. neoformans is AIDS, whereas infections caused by C. gattii are more often reported in immunocompetent patients with undefined risk than in the immunocompromised. There have been many chapters, reviews, and books written on C. neoformans. The topics we focus on in this article include species description, pathogenesis, life cycle, capsule, and stress response, which serve to highlight the specializations in virulence that have occurred in this unique encapsulated melanin-forming yeast that causes global deaths estimated at more than 600,000 annually.
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Affiliation(s)
- Kyung J Kwon-Chung
- Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - James A Fraser
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Tamara L Doering
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Zhou Wang
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Guilhem Janbon
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, 75015 Paris, France
| | - Alexander Idnurm
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri, Kansas City, Missouri 64110
| | - Yong-Sun Bahn
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
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16
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Janbon G, Ormerod KL, Paulet D, Byrnes EJ, Yadav V, Chatterjee G, Mullapudi N, Hon CC, Billmyre RB, Brunel F, Bahn YS, Chen W, Chen Y, Chow EWL, Coppée JY, Floyd-Averette A, Gaillardin C, Gerik KJ, Goldberg J, Gonzalez-Hilarion S, Gujja S, Hamlin JL, Hsueh YP, Ianiri G, Jones S, Kodira CD, Kozubowski L, Lam W, Marra M, Mesner LD, Mieczkowski PA, Moyrand F, Nielsen K, Proux C, Rossignol T, Schein JE, Sun S, Wollschlaeger C, Wood IA, Zeng Q, Neuvéglise C, Newlon CS, Perfect JR, Lodge JK, Idnurm A, Stajich JE, Kronstad JW, Sanyal K, Heitman J, Fraser JA, Cuomo CA, Dietrich FS. Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation. PLoS Genet 2014; 10:e1004261. [PMID: 24743168 PMCID: PMC3990503 DOI: 10.1371/journal.pgen.1004261] [Citation(s) in RCA: 276] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 02/07/2014] [Indexed: 02/07/2023] Open
Abstract
Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. It occurs as two serotypes (A and D) representing two varieties (i.e. grubii and neoformans, respectively). Here, we sequenced the genome and performed an RNA-Seq-based analysis of the C. neoformans var. grubii transcriptome structure. We determined the chromosomal locations, analyzed the sequence/structural features of the centromeres, and identified origins of replication. The genome was annotated based on automated and manual curation. More than 40,000 introns populating more than 99% of the expressed genes were identified. Although most of these introns are located in the coding DNA sequences (CDS), over 2,000 introns in the untranslated regions (UTRs) were also identified. Poly(A)-containing reads were employed to locate the polyadenylation sites of more than 80% of the genes. Examination of the sequences around these sites revealed a new poly(A)-site-associated motif (AUGHAH). In addition, 1,197 miscRNAs were identified. These miscRNAs can be spliced and/or polyadenylated, but do not appear to have obvious coding capacities. Finally, this genome sequence enabled a comparative analysis of strain H99 variants obtained after laboratory passage. The spectrum of mutations identified provides insights into the genetics underlying the micro-evolution of a laboratory strain, and identifies mutations involved in stress responses, mating efficiency, and virulence. Cryptococcus neoformans var. grubii is a major human pathogen responsible for deadly meningoencephalitis in immunocompromised patients. Here, we report the sequencing and annotation of its genome. Evidence for extensive intron splicing, antisense transcription, non-coding RNAs, and alternative polyadenylation indicates the potential for highly intricate regulation of gene expression in this opportunistic pathogen. In addition, detailed molecular, genetic, and genomic studies were performed to characterize structural features of the genome, including centromeres and origins of replication. Finally, the phenotypic and genome re-sequencing analysis of a collection of isolates of the reference H99 strain resulting from laboratory passage revealed that microevolutionary processes during in vitro culturing of pathogenic fungi can impact virulence.
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Affiliation(s)
- Guilhem Janbon
- Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France
- INRA, USC2019, Paris, France
- * E-mail: (GJ); (JH); (CAC); (FSD)
| | - Kate L. Ormerod
- University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Queensland, Australia
| | - Damien Paulet
- Institut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, Paris, France
| | - Edmond J. Byrnes
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
| | - Vikas Yadav
- Jawaharlal Nehru Centre for Advanced Scientific Research, Molecular Biology and Genetics Unit, Bangalore, India
| | - Gautam Chatterjee
- Jawaharlal Nehru Centre for Advanced Scientific Research, Molecular Biology and Genetics Unit, Bangalore, India
| | | | - Chung-Chau Hon
- Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Département Biologie Cellulaire et Infection, Paris, France
| | - R. Blake Billmyre
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
| | | | - Yong-Sun Bahn
- Yonsei University, Center for Fungal Pathogenesis, Department of Biotechnology, Seoul, Republic of Korea
| | - Weidong Chen
- Rutgers New Jersey Medical School, Department of Microbiology and Molecular Genetics, Newark, New Jersey, United States of America
| | - Yuan Chen
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
| | - Eve W. L. Chow
- University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Queensland, Australia
| | - Jean-Yves Coppée
- Institut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, Paris, France
| | - Anna Floyd-Averette
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
| | | | - Kimberly J. Gerik
- Washington University School of Medicine, Department of Molecular Microbiology, St. Louis, Missouri, United States of America
| | - Jonathan Goldberg
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Sara Gonzalez-Hilarion
- Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France
- INRA, USC2019, Paris, France
| | - Sharvari Gujja
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Joyce L. Hamlin
- University of Virginia, Department of Biochemistry and Molecular Genetics, Charlottesville, Virginia, United States of America
| | - Yen-Ping Hsueh
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
- California Institute of Technology, Division of Biology, Pasadena, California, United States of America
| | - Giuseppe Ianiri
- University of Missouri-Kansas City, School of Biological Sciences, Division of Cell Biology and Biophysics, Kansas City, Missouri, United States of America
| | - Steven Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Chinnappa D. Kodira
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Lukasz Kozubowski
- Clemson University, Department of Genetics and Biochemistry, Clemson, South Carolina, United States of America
| | - Woei Lam
- Washington University School of Medicine, Department of Molecular Microbiology, St. Louis, Missouri, United States of America
| | - Marco Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Larry D. Mesner
- University of Virginia, Department of Biochemistry and Molecular Genetics, Charlottesville, Virginia, United States of America
| | - Piotr A. Mieczkowski
- University of North Carolina, Department of Genetics, Chapel Hill, North Carolina, United States of America
| | - Frédérique Moyrand
- Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France
- INRA, USC2019, Paris, France
| | - Kirsten Nielsen
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
- University of Minnesota, Microbiology Department, Minneapolis, Minnesota, United States of America
| | - Caroline Proux
- Institut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, Paris, France
| | | | - Jacqueline E. Schein
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Sheng Sun
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
| | - Carolin Wollschlaeger
- Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France
- INRA, USC2019, Paris, France
| | - Ian A. Wood
- University of Queensland, School of Mathematics and Physics, Brisbane, Queensland, Australia
| | - Qiandong Zeng
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | - Carol S. Newlon
- Rutgers New Jersey Medical School, Department of Microbiology and Molecular Genetics, Newark, New Jersey, United States of America
| | - John R. Perfect
- Duke University Medical Center, Duke Department of Medicine and Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
| | - Jennifer K. Lodge
- Washington University School of Medicine, Department of Molecular Microbiology, St. Louis, Missouri, United States of America
| | - Alexander Idnurm
- University of Missouri-Kansas City, School of Biological Sciences, Division of Cell Biology and Biophysics, Kansas City, Missouri, United States of America
| | - Jason E. Stajich
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
- University of California, Department of Plant Pathology & Microbiology, Riverside, California, United States of America
| | - James W. Kronstad
- Michael Smith Laboratories, Department of Microbiology and Immunology, Vancouver, British Columbia, Canada
| | - Kaustuv Sanyal
- Jawaharlal Nehru Centre for Advanced Scientific Research, Molecular Biology and Genetics Unit, Bangalore, India
| | - Joseph Heitman
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
- * E-mail: (GJ); (JH); (CAC); (FSD)
| | - James A. Fraser
- University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Queensland, Australia
| | - Christina A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (GJ); (JH); (CAC); (FSD)
| | - Fred S. Dietrich
- Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
- * E-mail: (GJ); (JH); (CAC); (FSD)
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17
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Dalrymple SA, Ko J, Sheoran I, Kaminskyj SGW, Sanders DAR. Elucidation of substrate specificity in Aspergillus nidulans UDP-galactose-4-epimerase. PLoS One 2013; 8:e76803. [PMID: 24116166 PMCID: PMC3792076 DOI: 10.1371/journal.pone.0076803] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 08/27/2013] [Indexed: 11/18/2022] Open
Abstract
The frequency of invasive fungal infections has rapidly increased in recent years. Current clinical treatments are experiencing decreased potency due to severe host toxicity and the emergence of fungal drug resistance. As such, new targets and their corresponding synthetic pathways need to be explored for drug development purposes. In this context, galactofuranose residues, which are employed in fungal cell wall construction, but are notably absent in animals, represent an appealing target. Herein we present the structural and biochemical characterization of UDP-galactose-4-epimerase from Aspergillus nidulans which produces the precursor UDP-galactopyranose required for galactofuranose synthesis. Examination of the structural model revealed both NAD+ and UDP-glucopyranose were bound within the active site cleft in a near identical fashion to that found in the Human epimerase. Mutational studies on the conserved catalytic motif support a similar mechanism to that established for the Human counterpart is likely operational within the A. nidulans epimerase. While the Km and kcat for the enzyme were determined to be 0.11 mM and 12.8 s-1, respectively, a single point mutation, namely L320C, activated the enzyme towards larger N-acetylated substrates. Docking studies designed to probe active site affinity corroborate the experimentally determined activity profiles and support the kinetic inhibition results.
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Affiliation(s)
- Sean A. Dalrymple
- Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - John Ko
- Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Inder Sheoran
- Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | | | - David A. R. Sanders
- Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- * E-mail:
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Griffiths EJ, Hu G, Fries B, Caza M, Wang J, Gsponer J, Gates-Hollingsworth MA, Kozel TR, De Repentigny L, Kronstad JW. A defect in ATP-citrate lyase links acetyl-CoA production, virulence factor elaboration and virulence in Cryptococcus neoformans. Mol Microbiol 2012; 86:1404-23. [PMID: 23078142 DOI: 10.1111/mmi.12065] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2012] [Indexed: 01/25/2023]
Abstract
The interaction of Cryptococcus neoformans with phagocytic cells of the innate immune system is a key step in disseminated disease leading to meningoencephalitis in immunocompromised individuals. Transcriptional profiling of cryptococcal cells harvested from cell culture medium or from macrophages found differential expression of metabolic and other functions during fungal adaptation to the intracellular environment. We focused on the ACL1 gene for ATP-citrate lyase, which converts citrate to acetyl-CoA, because this gene showed elevated transcript levels in macrophages and because of the importance of acetyl-CoA as a central metabolite. Mutants lacking ACL1 showed delayed growth on medium containing glucose, reduced cellular levels of acetyl-CoA, defective production of virulence factors, increased susceptibility to the antifungal drug fluconazole and decreased survival within macrophages. Importantly, acl1 mutants were unable to cause disease in a murine inhalation model, a phenotype that was more extreme than other mutants with defects in acetyl-CoA production (e.g. an acetyl-CoA synthetase mutant). Loss of virulence is likely due to perturbation of critical physiological interconnections between virulence factor expression and metabolism in C. neoformans. Phylogenetic analysis and structural modelling of cryptococcal Acl1 identified three indels unique to fungal protein sequences; these differences may provide opportunities for the development of pathogen-specific inhibitors.
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Affiliation(s)
- Emma J Griffiths
- The Michael Smith Laboratories, Department of Microbiology and Immunology, Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
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Abstract
The human fungal pathogen Cryptococcus neoformans is characterized by its ability to induce a distinct polysaccharide capsule in response to a number of host-specific environmental stimuli. The induction of capsule is a complex biological process encompassing regulation at multiple steps, including the biosynthesis, transport, and maintenance of the polysaccharide at the cell surface. By precisely regulating the composition of its cell surface and secreted polysaccharides, C. neoformans has developed intricate ways to establish chronic infection and dormancy in the human host. The plasticity of the capsule structure in response to various host conditions also underscores the complex relationship between host and parasite. Much of this precise regulation of capsule is achieved through the transcriptional responses of multiple conserved signaling pathways that have been coopted to regulate this C. neoformans-specific virulence-associated phenotype. This review focuses on specific host stimuli that trigger the activation of the signal transduction cascades and on the downstream transcriptional responses that are required for robust encapsulation around the cell.
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Abstract
The pathogenic fungus Cryptococcus neoformans exhibits a striking propensity to cause central nervous system (CNS) disease in people with HIV/AIDS. Given that cryptococcal infections are generally initiated by pulmonary colonization, dissemination requires that the fungus withstand phagocytic killing, cross the alveolar-capillary interface in the lung, survive in the circulatory system and breach the blood-brain barrier. We know little about the molecular mechanisms underlying dissemination, but there is a rapidly growing list of mutants that fail to cause CNS disease. These mutants reveal a remarkable diversity of functions and therefore illustrate the complexity of the cryptococcal-host interaction. The challenge now is to extend the analysis of these mutants to acquire a detailed understanding of each step in dissemination.
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Sen M, Shah B, Rakshit S, Singh V, Padmanabhan B, Ponnusamy M, Pari K, Vishwakarma R, Nandi D, Sadhale PP. UDP-glucose 4, 6-dehydratase activity plays an important role in maintaining cell wall integrity and virulence of Candida albicans. PLoS Pathog 2011; 7:e1002384. [PMID: 22114559 PMCID: PMC3219719 DOI: 10.1371/journal.ppat.1002384] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 10/01/2011] [Indexed: 11/18/2022] Open
Abstract
Candida albicans, a human fungal pathogen, undergoes morphogenetic changes that are associated with virulence. We report here that GAL102 in C. albicans encodes a homolog of dTDP-glucose 4,6-dehydratase, an enzyme that affects cell wall properties as well as virulence of many pathogenic bacteria. We found that GAL102 deletion leads to greater sensitivity to antifungal drugs and cell wall destabilizing agents like Calcofluor white and Congo red. The mutant also formed biofilms consisting mainly of hyphal cells that show less turgor. The NMR analysis of cell wall mannans of gal102 deletion strain revealed that a major constituent of mannan is missing and the phosphomannan component known to affect virulence is greatly reduced. We also observed that there was a substantial reduction in the expression of genes involved in biofilm formation but increase in the expression of genes encoding glycosylphosphatidylinositol-anchored proteins in the mutant. These, along with altered mannosylation of cell wall proteins together might be responsible for multiple phenotypes displayed by the mutant. Finally, the mutant was unable to grow in the presence of resident peritoneal macrophages and elicited a weak pro-inflammatory cytokine response in vitro. Similarly, this mutant elicited a poor serum pro-inflammatory cytokine response as judged by IFNγ and TNFα levels and showed reduced virulence in a mouse model of systemic candidiasis. Importantly, an Ala substitution for a conserved Lys residue in the active site motif YXXXK, that abrogates the enzyme activity also showed reduced virulence and increased filamentation similar to the gal102 deletion strain. Since inactivating the enzyme encoded by GAL102 makes the cells sensitive to antifungal drugs and reduces its virulence, it can serve as a potential drug target in combination therapies for C. albicans and related pathogens.
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Affiliation(s)
- Manimala Sen
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Bhavin Shah
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Srabanti Rakshit
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Vijender Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Bhavna Padmanabhan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | | | | | | | - Dipankar Nandi
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Parag P. Sadhale
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- * E-mail:
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22
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Vandeputte P, Ischer F, Sanglard D, Coste AT. In vivo systematic analysis of Candida albicans Zn2-Cys6 transcription factors mutants for mice organ colonization. PLoS One 2011; 6:e26962. [PMID: 22073120 PMCID: PMC3205040 DOI: 10.1371/journal.pone.0026962] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 10/07/2011] [Indexed: 12/23/2022] Open
Abstract
The incidence of fungal infections in immuno-compromised patients increased considerably over the last 30 years. New treatments are therefore needed against pathogenic fungi. With Candida albicans as a model, study of host-fungal pathogen interactions might reveal new sources of therapies. Transcription factors (TF) are of interest since they integrate signals from the host environment and participate in an adapted microbial response. TFs of the Zn2-Cys6 class are specific to fungi and are important regulators of fungal metabolism. This work analyzed the importance of the C. albicans Zn2-Cys6 TF for mice kidney colonization. For this purpose, 77 Zn2-Cys6 TF mutants were screened in a systemic mice model of infection by pools of 10 mutants. We developed a simple barcoding strategy to specifically detect each mutant DNA from mice kidney by quantitative PCR. Among the 77 TF mutant strains tested, eight showed a decreased colonization including mutants for orf19.3405, orf19.255, orf19.5133, RGT1, UGA3, orf19.6182, SEF1 and orf19.2646, and four an increased colonization including mutants for orf19.4166, ZFU2, orf19.1685 and UPC2 as compared to the isogenic wild type strain. Our approach was validated by comparable results obtained with the same animal model using a single mutant and the revertant for an ORF (orf19.2646) with still unknown functions. In an attempt to identify putative involvement of such TFs in already known C. albicans virulence mechanisms, we determined their in vitro susceptibility to pH, heat and oxidative stresses, as well as ability to produce hyphae and invade agar. A poor correlation was found between in vitro and in vivo assays, thus suggesting that TFs needed for mice kidney colonization may involve still unknown mechanisms. This large-scale analysis of mice organ colonization by C. albicans can now be extended to other mutant libraries since our in vivo screening strategy can be adapted to any preexisting mutants.
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Affiliation(s)
- Patrick Vandeputte
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - Françoise Ischer
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - Dominique Sanglard
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - Alix T. Coste
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
- * E-mail:
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Roles of the Aspergillus nidulans UDP-galactofuranose transporter, UgtA in hyphal morphogenesis, cell wall architecture, conidiation, and drug sensitivity. Fungal Genet Biol 2011; 48:896-903. [PMID: 21693196 DOI: 10.1016/j.fgb.2011.06.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 06/01/2011] [Accepted: 06/03/2011] [Indexed: 01/28/2023]
Abstract
Galactofuranose (Galf) is the 5-member-ring form of galactose found in the walls of fungi including Aspergillus, but not in mammals. UDP-galactofuranose mutase (UgmA, ANID_3112.1) generates UDP-Galf from UDP-galactopyranose (6-member ring form). UgmA-GFP is cytoplasmic, so the UDP-Galf residues it produces must be transported into an endomembrane compartment prior to incorporation into cell wall components. ANID_3113.1 (which we call UgtA) was identified as being likely to encode the A. nidulans UDP-Galf transporter, based on its high amino acid sequence identity with A. fumigatus GlfB. The ugtAΔ phenotype resembled that of ugmAΔ, which had compact colonies, wide, highly branched hyphae, and reduced sporulation. Like ugmAΔ, the ugtAΔ hyphal walls were threefold thicker than wild type strains (but different in appearance in TEM), and accumulated exogenous material in liquid culture. AfglfB restored wild type growth in the ugtAΔ strain, showing that these genes have homologous function. Immunostaining with EBA2 showed that ugtAΔ hyphae and conidiophores lacked Galf, which was restored in the AfglfB-complemented strain. Unlike wild type and ugmAΔ strains, some ugtAΔ metulae produced triplets of phialides, rather than pairs. Compared to wild type strains, spore production for ugtAΔ was reduced to 1%, and spore germination was reduced to half. UgtA-GFP had a punctate distribution in hyphae, phialides, and young spores. Notably, the ugtAΔ strain was significantly more sensitive than wild type to Caspofungin, which inhibits beta-glucan synthesis, suggesting that drugs that could be developed to target UgtA function would be useful in combination antifungal therapy.
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Quantifying the importance of galactofuranose in Aspergillus nidulans hyphal wall surface organization by atomic force microscopy. EUKARYOTIC CELL 2011; 10:646-53. [PMID: 21335527 DOI: 10.1128/ec.00304-10] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The fungal wall mediates cell-environment interactions. Galactofuranose (Galf), the five-member ring form of galactose, has a relatively low abundance in Aspergillus walls yet is important for fungal growth and fitness. Aspergillus nidulans strains deleted for Galf biosynthesis enzymes UgeA (UDP-glucose-4-epimerase) and UgmA (UDP-galactopyranose mutase) lacked immunolocalizable Galf, had growth and sporulation defects, and had abnormal wall architecture. We used atomic force microscopy and force spectroscopy to image and quantify cell wall viscoelasticity and surface adhesion of ugeAΔ and ugmAΔ strains. We compared the results for ugeAΔ and ugmAΔ strains with the results for a wild-type strain (AAE1) and the ugeB deletion strain, which has wild-type growth and sporulation. Our results suggest that UgeA and UgmA are important for cell wall surface subunit organization and wall viscoelasticity. The ugeAΔ and ugmAΔ strains had significantly larger surface subunits and lower cell wall viscoelastic moduli than those of AAE1 or ugeBΔ hyphae. Double deletion strains (ugeAΔ ugeBΔ and ugeAΔ ugmAΔ) had more-disorganized surface subunits than single deletion strains. Changes in wall surface structure correlated with changes in its viscoelastic modulus for both fixed and living hyphae. Wild-type walls had the largest viscoelastic modulus, while the walls of the double deletion strains had the smallest. The ugmAΔ strain and particularly the ugeAΔ ugmAΔ double deletion strain were more adhesive to hydrophilic surfaces than the wild type, consistent with changes in wall viscoelasticity and surface organization. We propose that Galf is necessary for full maturation of A. nidulans walls during hyphal extension.
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25
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Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi. Proc Natl Acad Sci U S A 2010; 107:10136-41. [PMID: 20479238 PMCID: PMC2890473 DOI: 10.1073/pnas.0914418107] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A notable characteristic of fungal genomes is that genes involved in successive steps of a metabolic pathway are often physically linked or clustered. To investigate how such clusters of functionally related genes are assembled and maintained, we examined the evolution of gene sequences and order in the galactose utilization (GAL) pathway in whole-genome data from 80 diverse fungi. We found that GAL gene clusters originated independently and by different mechanisms in three unrelated yeast lineages. Specifically, the GAL cluster found in Saccharomyces and Candida yeasts originated through the relocation of native unclustered genes, whereas the GAL cluster of Schizosaccharomyces yeasts was acquired through horizontal gene transfer from a Candida yeast. In contrast, the GAL cluster of Cryptococcus yeasts was assembled independently from the Saccharomyces/Candida and Schizosaccharomyces GAL clusters and coexists in the Cryptococcus genome with unclustered GAL paralogs. These independently evolved GAL clusters represent a striking example of analogy at the genomic level. We also found that species with GAL clusters exhibited significantly higher rates of GAL pathway loss than species with unclustered GAL genes. These results suggest that clustering of metabolic genes might facilitate fungal adaptation to changing environments both through the acquisition and loss of metabolic capacities.
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26
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El-Ganiny AM, Sheoran I, Sanders DAR, Kaminskyj SGW. Aspergillus nidulans UDP-glucose-4-epimerase UgeA has multiple roles in wall architecture, hyphal morphogenesis, and asexual development. Fungal Genet Biol 2010; 47:629-35. [PMID: 20211750 DOI: 10.1016/j.fgb.2010.03.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Revised: 02/28/2010] [Accepted: 03/02/2010] [Indexed: 11/16/2022]
Abstract
Aspergillus nidulans UDP-glucose-4-epimerase UgeA interconverts UDP-glucose and UDP-galactose and participates in galactose metabolism. The sugar moiety of UDP-galactose is predominantly found as galactopyranose (Galp, the six-membered ring form), which is the substrate for UDP-galactopyranose mutase (encoded by ugmA) to generate UDP-galactofuranose (Galf, the five-membered ring form) that is found in fungal walls. In A. fumigatus, Galf residues appear to be important for virulence. The A. nidulans ugeA Delta strain is viable, and has defects including wide, slow growing, highly branched hyphae and reduced conidiation that resemble the ugmA Delta strain. As for the ugmA Delta strain, ugeA Delta colonies had substantially reduced sporulation but normal spore viability. Conidia of the ugeA Delta strain could not form colonies on galactose as a sole carbon source, however they produced short, multinucleate germlings suggesting they ceased to grow from starvation. UgeA purified from an expression plasmid had a relative molecular weight of 40.6 kDa, and showed in vitro UDP-glucose-4-epimerase activity. Transmission electron microscope cross-sections of wildtype, ugeA Delta, and ugmA Delta hyphae showed they had similar cytoplasmic contents but the walls of each strain were different in appearance and thickness. Both deletion strains showed increased substrate adhesion. Localization of UgeA-GFP and UgmA-GFP was cytoplasmic, and was similar on glucose and galactose. Neither gene product had a longitudinal polarized distribution. Localization of a UgmA-mRFP in a strain that resembled the ugmA Delta strain was cytoplasmic and lacked a longitudinal polarized distribution. The roles of UgeA in A. nidulans growth and morphogenesis are consistent with the importance of Galf, and are related but not identical to the roles of UgmA.
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Affiliation(s)
- Amira M El-Ganiny
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon SK, Canada
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Doering TL. How sweet it is! Cell wall biogenesis and polysaccharide capsule formation in Cryptococcus neoformans. Annu Rev Microbiol 2009; 63:223-47. [PMID: 19575556 DOI: 10.1146/annurev.micro.62.081307.162753] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cryptococcus neoformans is a pathogenic fungus responsible for severe opportunistic infections. The most prominent feature of this yeast is its elaborate polysaccharide capsule, a complex structure that is required for virulence. The capsule is intimately associated with the cell wall, which underlies the capsule and offers the organism strength and flexibility in potentially hostile environments. Both structures are primarily composed of polysaccharides, offering a glimpse of the tremendous variation inherent in natural carbohydrate structures and their multiple biological functions. The steps in cell wall and capsule biosynthesis and assembly pose fascinating questions of metabolism, enzymology, cell biology, and regulation; the answers have potential application to treatment of a deadly infection. This article reviews current knowledge of cryptococcal cell wall and capsule biosynthesis and outstanding questions for the future.
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Affiliation(s)
- Tamara Lea Doering
- Department of Molecular Microbiology, Washington University Medical School, St. Louis, Missouri, USA.
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Ban Y, Kondo S, Ubi BE, Honda C, Bessho H, Moriguchi T. UDP-sugar biosynthetic pathway: contribution to cyanidin 3-galactoside biosynthesis in apple skin. PLANTA 2009; 230:871-81. [PMID: 19652996 DOI: 10.1007/s00425-009-0993-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Accepted: 07/10/2009] [Indexed: 05/08/2023]
Abstract
UDP-galactose:flavonoid 3-O-galactosyltransferase (UFGalT) is responsible for cyanidin 3-galactoside (cy3-gal) synthesis from cyanidin (cy) and UDP-galactose (UDP-gal) which are, respectively, catalyzed by anthocyanidin synthase (ANS) and UDP-glucose 4-epimerase (UGE). To clarify the contribution of UDP-galactose pathway to cy3-gal accumulation in apple skin, we analyzed the contents of UDP-gal and UDP-glucose (UDP-glu), cy, and, cy3-gal contents along with UGE activity. We confirmed that transcript levels for apple ANS and UDP-glucose: flavonoid 3-O-glucosyltransferase (UFGT) coincided with anthocyanin accumulation in three apple cultivars differing in their skin colors. During fruit development, changes in level of cy coincided with that of cy3-gal, whereas UDP-gal and UGE activity showed no similar trend with cy3-gal. Significant correlation was not observed between the changes in UGE activity and UDP-sugar contents. The effect of temperature and UV-B radiation (different environmental conditions) on the accumulation of UDP-sugars, cy and cy3-gal, and UGE activity were also investigated in a pale-red cultivar. High temperature tended to depress the accumulation of both UDP-sugars and cy concomitant with the decrease in cy3-gal content irrespective of UV-B radiation. Although there was no high inhibition of both cy and UDP-sugars at low-temperature without UV-B, cy3-gal accumulation was highly depressed. UGE activity was highest at low temperature with UV-B, but not much different under other conditions. Most of the parameters under different environmental conditions were significantly correlated with each other. Based on these results, contribution of UDP-sugar biosynthetic pathway to anthocyanin biosynthesis under different environmental conditions as well as during fruit development is discussed.
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Affiliation(s)
- Yusuke Ban
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
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