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Watson RG, Hole CR. Simple growth conditions improve targeted gene deletion in Cryptococcus neoformans. mSphere 2025; 10:e0107024. [PMID: 40172186 PMCID: PMC12039239 DOI: 10.1128/msphere.01070-24] [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: 12/17/2024] [Accepted: 03/04/2025] [Indexed: 04/04/2025] Open
Abstract
Cryptococcus neoformans infections are a significant cause of morbidity and mortality among AIDS patients and the third most common invasive fungal infection in organ transplant recipients. The cryptococcal cell wall is very dynamic and can be modulated depending on growth conditions. It was reported that when C. neoformans is grown in unbuffered yeast nitrogen base (YNB) for 48 hours, the pH of the media drastically drops, and the cells start to shed their cell walls. With this observation, we sought to determine if YNB-grown cells could be used directly for genetic transformation. To test this, we targeted ADE2 using TRACE (transient CRISPR-Cas9 coupled with electroporation) in YNB-grown or competent cells. Deletion of the ADE2 gene results in red-pigmented colonies, allowing visual confirmation of disruption. We were able to successfully delete ADE2 in YNB-grown cells with better efficiency compared to competent cells. Recent studies have shown that gene deletion can be accomplished using short (50 bp) homology arms in place of the normal long arms (~1 kb). However, it was inefficient, leading to more insertions and gene disruption than gene deletions. We tested short homology with YNB-grown cells vs. competent cells and found that gene deletion was significantly improved in YNB-grown cells, at around 60% compared to 6% in competent cells. This was also observed when we deleted LAC1 with the short arms. Altogether, using simple growth conditions, we have greatly improved the speed and efficiency of cryptococcal genetic transformations.IMPORTANCEThe World Health Organization recently ranked C. neoformans as the highest-priority fungal pathogen based on unmet research and development needs and its public health importance. Understanding cryptococcal pathogenicity is key for developing treatments. We found that using simple growth conditions can greatly improve the speed and efficiency of cryptococcal genetic transformations. This finding will advance the field by expanding the ease of cryptococcal genetic manipulations.
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Affiliation(s)
- Rebekah G. Watson
- Department of Clinical Pharmacy and Translational Science, The University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Camaron R. Hole
- Department of Clinical Pharmacy and Translational Science, The University of Tennessee Health Science Center, Memphis, Tennessee, USA
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2
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Viana R, Couceiro D, Newton W, Coutinho L, Dias O, Coelho C, Teixeira MC. Reconstruction and exploitation of a dedicated Genome-Scale Metabolic Model of the human pathogen C. neoformans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.04.02.646762. [PMID: 40291681 PMCID: PMC12026501 DOI: 10.1101/2025.04.02.646762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2025]
Abstract
C. neoformans is notorious for causing severe pulmonary and central nervous system infections, particularly in immunocompromised patients. High mortality rates, associated with its tropism and adaptation to the brain microenvironment and its drug resistance profile, makes this pathogen a public health threat and a World Health Organization (WHO) priority. In this study, we reconstructed GSMM iRV890 for C. neoformans var. grubii , providing a promising platform for the comprehensive understanding of the unique metabolic features of C. neoformans , and subsequently shedding light on its complex tropism for the brain microenvironment and potentially informing the discovery of new drug targets. The GSMM iRV890 model is openly available in the SBML format, and underwent validation using experimental data for nitrogen and carbon assimilation, as well as specific growth and glucose consumption rates. Based on the comparison with GSMMs available for other pathogenic yeasts, unique metabolic features were predicted for C. neoformans , including key pathways shaping the dynamics between C. neoformans and the human host, and underlying its adaptation to the brain environment. Finally, predicted essential genes from the validated model are explored herein as potential novel antifungal drug targets.
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3
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Chadwick BJ, Ristow LC, Blackburn EE, Xie X, Krysan DJ, Lin X. Microevolution of Cryptococcus neoformans in high CO 2 converges on mutations isolated from patients with relapsed cryptococcosis. Cell Rep 2025; 44:115349. [PMID: 39998950 DOI: 10.1016/j.celrep.2025.115349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Revised: 12/19/2024] [Accepted: 02/04/2025] [Indexed: 02/27/2025] Open
Abstract
Cryptococcus neoformans is an environmental fungus that causes an estimated 180,000 deaths annually and transitions from the external environment to the host environment to cause disease. CO2 concentrations in the atmosphere (0.04%) are dramatically lower than in mammalian tissues (5%). Environmental C. neoformans strains that cannot tolerate 5% CO2 are less virulent than CO2-tolerant strains. Microevolution at elevated CO2 generates loss-of-function mutations in the nucleotide binding protein Avc1 that confer CO2 tolerance to CO2-intolerant strains. Mechanistically, Avc1 positively regulates the expression of plasma membrane transporters, including PDR9, a phospholipid floppase that negatively modulates CO2 fitness. Deletion of AVC1 in five CO2-intolerant environmental strains increases competitive fitness in host CO2 and in a mouse infection model. Importantly, strains with similar AVC1 mutations emerge in patients with relapsed cryptococcosis. Therefore, this microevolutionary convergence strongly suggests that adaptation to host CO2 is a significant driver of C. neoformans fitness during infection.
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Affiliation(s)
| | - Laura C Ristow
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Emma E Blackburn
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Xiaofeng Xie
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Damian J Krysan
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA; Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - Xiaorong Lin
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA; Department of Microbiology, University of Georgia, Athens, GA 30602, USA.
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4
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Jacobs E, Dragotakes Q, Kulkarni M, Dziedzic A, Jedlicka A, Hardwick JM, Casadevall A. A method for authenticating the fidelity of Cryptococcus neoformans knockout collections. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.12.03.626716. [PMID: 39677607 PMCID: PMC11642876 DOI: 10.1101/2024.12.03.626716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
Abstract
Gene knockout strain collections are important tools for discovery in microbiology. Cryptococcus neoformans is the only human pathogenic fungus with an available genome-wide deletion collection, and this resource is widely used by the research community. We uncovered mix-ups in the assembly of the commercially available C. neoformans deletion collection of ~6,000 unique strains acquired by our lab. While pursuing the characterization of a gene-of-interest, the corresponding deletion strain from the C. neoformans KO collection displayed several interesting phenotypes associated with virulence. However, RNAseq analysis identified transcripts for the putative knockout gene, and the absence of transcripts for a different knockout strain found in the same plate position in an earlier partial knockout collection, raising the possibility that plates from one collection were substituted for the other. This was supported by determining the size of the nourseothricin (NAT)-resistance cassette used to generate the two separate knockout libraries and was confirmed by RNAseq and genome sequencing. Here we report that our KN99 collection is comprised of mixed plates from two independent KO libraries and present a simple authentication method that other investigators can use to distinguish the identities of these KO collections.
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Affiliation(s)
- Ella Jacobs
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Quigly Dragotakes
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Madhura Kulkarni
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Amanda Dziedzic
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Anne Jedlicka
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - J Marie Hardwick
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Arturo Casadevall
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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5
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Jackson KM, Kono TJY, Betancourt JJ, Wang Y, Kabbale KD, Ding M, Kezh P, Ha G, Yoder JM, Fulton SR, Mukaremera L, Tiffin P, Gusa A, Meya DB, Billmyre RB, Xue C, Nielsen K. Single nucleotide polymorphisms are associated with strain-specific virulence differences among clinical isolates of Cryptococcus neoformans. Nat Commun 2024; 15:10491. [PMID: 39622806 PMCID: PMC11612297 DOI: 10.1038/s41467-024-54729-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 11/18/2024] [Indexed: 12/06/2024] Open
Abstract
Studies across various pathogens highlight the importance of pathogen genetic differences in disease manifestation. In the human fungal pathogen Cryptococcus neoformans, sequence type (ST) associates with patient outcome. We performed a meta-analysis of four genomic studies and identified overlapping gene regions associated with virulence, suggesting the importance of these gene regions in cryptococcal disease in diverse clinical isolates. We explored the relationship between virulence and strain genetic differences using the cryptococcosis mouse model and a closely related library of ST93 clinical isolates. We identified four in vivo virulence phenotypes: hypervirulence, typical virulence with CNS disease, typical virulence with non-CNS disease, and latent disease. Hypervirulent isolates were clade specific and associated with an interferon gamma (IFNγ) dominated immune response. Using a genome wide association study (GWAS), we identified nine genes with polymorphisms associated with IFNγ production, including the inositol sensor ITR4. The itr4Δ mutant recapitulated the hypervirulence phenotype and ITR4 affects expression of two IFNγ associated genes. Finally, we showed that IFNγ production is associated with SNPs that downregulate ITR4 and with SNP accumulation in other IFNγ associated genes. These data highlight the complex role of pathogen genetics in virulence and identify genes associated with hypervirulence and IFNγ in Cryptococcus neoformans.
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Affiliation(s)
- Katrina M Jackson
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Thomas J Y Kono
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
- Institute of Computational Cancer Biology at the University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - Jovany J Betancourt
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Yina Wang
- Public Health Research Institute and Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Kisakye D Kabbale
- Infectious Diseases Institute and School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
- The African Center of Excellence in Bioinformatics and Data Intensive Sciences, Kampala, Uganda
| | - Minna Ding
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Perry Kezh
- Center for One Health Research, Department of Biomedical Sciences and Pathology, Virginia Tech University, Blacksburg, VA, USA
| | - Grace Ha
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - J Marina Yoder
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Sophie R Fulton
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Liliane Mukaremera
- Department of Biosciences, Faculty of Health and Life Sciences, Medical Research Council Centre for Medical Mycology at the University of Exeter, Exeter, UK
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Asiya Gusa
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - David B Meya
- Infectious Diseases Institute and School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
- Division of Infectious Diseases and International Medicine, University of Minnesota, Minneapolis, MN, USA
| | - R Blake Billmyre
- Departments of Pharmaceutical and Biomedical Sciences/Infectious Disease, College of Pharmacy/College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Chaoyang Xue
- Public Health Research Institute and Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Kirsten Nielsen
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA.
- Center for One Health Research, Department of Biomedical Sciences and Pathology, Virginia Tech University, Blacksburg, VA, USA.
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6
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Boucher MJ, Banerjee S, Joshi MB, Wei AL, Huang MY, Lei S, Ciranni M, Condon A, Langen A, Goddard TD, Caradonna I, Goranov AI, Homer CM, Mortensen Y, Petnic S, Reilly MC, Xiong Y, Susa KJ, Pastore VP, Zaro BW, Madhani HD. Phenotypic landscape of a fungal meningitis pathogen reveals its unique biology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.22.619677. [PMID: 39484549 PMCID: PMC11526942 DOI: 10.1101/2024.10.22.619677] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/03/2024]
Abstract
Cryptococcus neoformans is the most common cause of fungal meningitis and the top-ranked W.H.O. priority fungal pathogen. Only distantly related to model fungi, C. neoformans is also a powerful experimental system for exploring conserved eukaryotic mechanisms lost from specialist model yeast lineages. To decipher its biology globally, we constructed 4328 gene deletions and measured-with exceptional precision--the fitness of each mutant under 141 diverse growth-limiting in vitro conditions and during murine infection. We defined functional modules by clustering genes based on their phenotypic signatures. In-depth studies leveraged these data in two ways. First, we defined and investigated new components of key signaling pathways, which revealed animal-like pathways/components not predicted from studies of model yeasts. Second, we identified environmental adaptation mechanisms repurposed to promote mammalian virulence by C. neoformans, which lacks a known animal reservoir. Our work provides an unprecedented resource for deciphering a deadly human pathogen.
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Affiliation(s)
- Michael J Boucher
- Dept. of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Sanjita Banerjee
- Dept. of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Meenakshi B Joshi
- Dept. of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Angela L Wei
- Dept. of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Manning Y Huang
- Dept. of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Susan Lei
- Dept. of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Massimiliano Ciranni
- Department of Informatics, Bioengineering, Robotics and Systems Engineering, University of Genoa, via alla Opera Pia 13, 16145 Genoa, Italy
| | - Andrew Condon
- Dept. of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Andreas Langen
- Dept. of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Thomas D Goddard
- Dept. of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Ippolito Caradonna
- Dept. of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Alexi I Goranov
- Dept. of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Christina M Homer
- Dept. of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Yassaman Mortensen
- Dept. of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Sarah Petnic
- Dept. of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Morgann C Reilly
- Dept. of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Ying Xiong
- Dept. of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Katherine J Susa
- Dept. of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Vito Paolo Pastore
- Department of Informatics, Bioengineering, Robotics and Systems Engineering, University of Genoa, via alla Opera Pia 13, 16145 Genoa, Italy
| | - Balyn W Zaro
- Dept. of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Hiten D Madhani
- Dept. of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
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7
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du Plooy LM, Telzrow CL, Nichols CB, Probst C, Castro-Lopez N, Wormley FL, Alspaugh JA. A fungal ubiquitin ligase and arrestin binding partner contribute to pathogenesis and survival during cellular stress. mBio 2024; 15:e0098124. [PMID: 39235249 PMCID: PMC11481503 DOI: 10.1128/mbio.00981-24] [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: 04/04/2024] [Accepted: 07/29/2024] [Indexed: 09/06/2024] Open
Abstract
Cellular responses to external stress allow microorganisms to adapt to a vast array of environmental conditions, including infection sites. The molecular mechanisms behind these responses are studied to gain insight into microbial pathogenesis, which could lead to new antimicrobial therapies. Here, we explore a role for arrestin protein-mediated ubiquitination in stress response and pathogenesis in the pathogenic fungus Cryptococcus neoformans. In a previous study, we identified four arrestin-like proteins in C. neoformans and found that one of these is required for efficient membrane synthesis, likely by directing interaction between fatty acid synthases and the Rsp5 E3 ubiquitin ligase. Here, we further explore Cn Rsp5 function and determine that this single Ub ligase is absolutely required for pathogenesis and survival in the presence of cellular stress. Additionally, we show that a second arrestin-like protein, Ali2, similarly facilitates interaction between Rsp5 and some of its protein targets. Of the four postulated C. neoformans arrestin-like proteins, Ali2 appears to contribute the most to C. neoformans pathogenesis, likely by directing Rsp5 to pathogenesis-related ubiquitination targets. A proteomics-based differential ubiquitination screen revealed that several known cell surface proteins are ubiquitinated by Rsp5 and a subset also requires Ali2 for their ubiquitination. Rsp5-mediated ubiquitination alters the stability and the localization of these proteins. A loss of Rsp5-mediated ubiquitination results in cell wall defects that increase susceptibility to external stresses. These findings support a model in which arrestin-like proteins guide Rsp5 to ubiquitinate specific target proteins, some of which are required for survival during stress. IMPORTANCE Microbial proteins involved in human infectious diseases often need to be modified by specific chemical additions to be fully functional. Here, we explore the role of a particular protein modification, ubiquitination, in infections due to the human fungal pathogen Cryptococcus neoformans. We identified a complex of proteins responsible for adding ubiquitin groups to fungal proteins, and this complex is required for virulence. These proteins are fungal specific and might be targets for novel anti-infection therapy.
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Affiliation(s)
- Lukas M. du Plooy
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Calla L. Telzrow
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Connie B. Nichols
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Corinna Probst
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Natalia Castro-Lopez
- Department of Biology, University of Texas at San Antonio, San Antonio, Texas, USA
- Department of Biology, Texas Christian University, Fort Worth, Texas, USA
| | - Floyd L. Wormley
- Department of Biology, University of Texas at San Antonio, San Antonio, Texas, USA
- Department of Biology, Texas Christian University, Fort Worth, Texas, USA
| | - J. Andrew Alspaugh
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
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8
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Chadwick BJ, Ristow LC, Xie X, Krysan DJ, Lin X. Discovery of CO 2 tolerance genes associated with virulence in the fungal pathogen Cryptococcus neoformans. Nat Microbiol 2024; 9:2684-2695. [PMID: 39232204 DOI: 10.1038/s41564-024-01792-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 07/23/2024] [Indexed: 09/06/2024]
Abstract
Cryptococcus neoformans is a ubiquitous soil fungus and airborne pathogen that causes over 180,000 deaths each year. Cryptococcus must adapt to host CO2 levels to cause disease, but the genetic basis for this adaptation is unknown. We utilized quantitative trait loci mapping with 374 progeny from a cross between a CO2-tolerant clinical isolate and a CO2-sensitive environmental isolate to identify genetic regions regulating CO2 tolerance. To identify specific quantitative trait genes, we applied fine mapping through bulk segregant analysis of near-isogenic progeny with distinct tolerance levels to CO2. We found that virulence among near-isogenic strains in a murine model of cryptococcosis correlated with CO2 tolerance. Moreover, we discovered that sensitive strains may adapt in vivo to become more CO2 tolerant and more virulent. These findings highlight the underappreciated role of CO2 tolerance and its importance in the ability of an opportunistic environmental pathogen to cause disease.
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Affiliation(s)
| | - Laura C Ristow
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Xiaofeng Xie
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | - Damian J Krysan
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Xiaorong Lin
- Department of Plant Biology, University of Georgia, Athens, GA, USA.
- Department of Microbiology, University of Georgia, Athens, GA, USA.
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Lee CWJ, Brisland A, Qu X, Horianopoulos LC, Hu G, Mayer FL, Kronstad JW. Loss of Opi3 causes a lipid imbalance that influences the virulence traits of Cryptococcus neoformans but not cryptococcosis. Front Cell Infect Microbiol 2024; 14:1448229. [PMID: 39193507 PMCID: PMC11347413 DOI: 10.3389/fcimb.2024.1448229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 07/25/2024] [Indexed: 08/29/2024] Open
Abstract
The basidiomycete fungus Cryptococcus neoformans is a useful model for investigating mechanisms of fungal pathogenesis in mammalian hosts. This pathogen is the causative agent of cryptococcal meningitis in immunocompromised patients and is in the critical priority group of the World Health Organization fungal priority pathogens list. In this study, we employed a mutant lacking the OPI3 gene encoding a methylene-fatty-acyl-phospholipid synthase to characterize the role of phosphatidylcholine (PC) and lipid homeostasis in the virulence of C. neoformans. We first confirmed that OPI3 was required for growth in nutrient limiting conditions, a phenotype that could be rescued with exogenous choline and PC. Additionally, we established that loss of Opi3 and the lack of PC lead to an accumulation of neutral lipids in lipid droplets and alterations in major lipid classes. The growth defect of the opi3Δ mutant was also rescued by sorbitol and polyethylene glycol (PEG), a result consistent with protection of ER function from the stress caused by lipid imbalance. We then examined the impact of Opi3 on virulence and found that the dependence of PC synthesis on Opi3 caused reduced capsule size and this was accompanied by an increase in shed capsule polysaccharide and changes in cell wall composition. Further tests of virulence demonstrated that survival in alveolar macrophages and the ability to cause disease in mice were not impacted by loss of Opi3 despite the choline auxotrophy of the mutant in vitro. Overall, this work establishes the contribution of lipid balance to virulence factor elaboration by C. neoformans and suggests that host choline is sufficient to support proliferation during disease.
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Affiliation(s)
- Christopher W. J. Lee
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Anna Brisland
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Xianya Qu
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Linda C. Horianopoulos
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Guanggan Hu
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - François L. Mayer
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - James W. Kronstad
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
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10
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Francis VI, Liddle C, Camacho E, Kulkarni M, Junior SRS, Harvey JA, Ballou ER, Thomson DD, Brown GD, Hardwick JM, Casadevall A, Witton J, Coelho C. Cryptococcus neoformans rapidly invades the murine brain by sequential breaching of airway and endothelial tissues barriers, followed by engulfment by microglia. mBio 2024; 15:e0307823. [PMID: 38511961 PMCID: PMC11005363 DOI: 10.1128/mbio.03078-23] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/29/2024] [Indexed: 03/22/2024] Open
Abstract
Cryptococcus neoformans causes lethal meningitis and accounts for approximately 10%-15% of AIDS-associated deaths worldwide. There are major gaps in our understanding of how this fungus invades the mammalian brain. To investigate the dynamics of C. neoformans tissue invasion, we mapped fungal localization and host cell interactions in infected brain, lung, and upper airways using mouse models of systemic and airway infection. To enable this, we developed an in situ imaging pipeline capable of measuring large volumes of tissue while preserving anatomical and cellular information by combining thick tissue sections, tissue clarification, and confocal imaging. We confirm high fungal burden in mouse upper airway after nasal inoculation. Yeast in turbinates were frequently titan cells, with faster kinetics than reported in mouse lungs. Importantly, we observed one instance of fungal cells enmeshed in lamina propria of the upper airways, suggesting penetration of airway mucosa as a possible route of tissue invasion and dissemination to the bloodstream. We extend previous literature positing bloodstream dissemination of C. neoformans, by finding viable fungi in the bloodstream of mice a few days after intranasal infection. As early as 24 h post systemic infection, the majority of C. neoformans cells traversed the blood-brain barrier, and were engulfed or in close proximity to microglia. Our work presents a new method for investigating microbial invasion, establishes that C. neoformans can breach multiple tissue barriers within the first days of infection, and demonstrates microglia as the first cells responding to C. neoformans invasion of the brain.IMPORTANCECryptococcal meningitis causes 10%-15% of AIDS-associated deaths globally. Still, brain-specific immunity to cryptococci is a conundrum. By employing innovative imaging, this study reveals what occurs during the first days of infection in brain and in airways. We found that titan cells predominate in upper airways and that cryptococci breach the upper airway mucosa, which implies that, at least in mice, the upper airways are a site for fungal dissemination. This would signify that mucosal immunity of the upper airway needs to be better understood. Importantly, we also show that microglia, the brain-resident macrophages, are the first responders to infection, and microglia clusters are formed surrounding cryptococci. This study opens the field to detailed molecular investigations on airway immune response, how fungus traverses the blood-brain barrier, how microglia respond to infection, and ultimately how microglia monitor the blood-brain barrier to preserve brain function.
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Affiliation(s)
- Vanessa I. Francis
- MRC Centre for Medical Mycology at University of Exeter, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Corin Liddle
- Bioimaging Facility, University of Exeter, Exeter, United Kingdom
| | - Emma Camacho
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Madhura Kulkarni
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | - Jamie A. Harvey
- MRC Centre for Medical Mycology at University of Exeter, University of Exeter, Exeter, United Kingdom
| | - Elizabeth R. Ballou
- MRC Centre for Medical Mycology at University of Exeter, University of Exeter, Exeter, United Kingdom
| | - Darren D. Thomson
- MRC Centre for Medical Mycology at University of Exeter, University of Exeter, Exeter, United Kingdom
| | - Gordon D. Brown
- MRC Centre for Medical Mycology at University of Exeter, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - J. Marie Hardwick
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Arturo Casadevall
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jonathan Witton
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Carolina Coelho
- MRC Centre for Medical Mycology at University of Exeter, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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11
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Boodwa-Ko D, Doering TL. A Quick reCAP: Discovering Cryptococcus neoformans Capsule Mutants. J Fungi (Basel) 2024; 10:114. [PMID: 38392786 PMCID: PMC10889740 DOI: 10.3390/jof10020114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/24/2024] Open
Abstract
Cryptococcus neoformans is an opportunistic fungal pathogen that can cause severe meningoencephalitis in immunocompromised hosts and is a leading cause of death in HIV/AIDS patients. This pathogenic yeast is surrounded by a polysaccharide capsule that is critical for virulence and plays important roles in host-pathogen interactions. Understanding capsule biosynthesis is therefore key to defining the biology of C. neoformans and potentially discovering novel therapeutic targets. By exploiting methods to identify mutants deficient in capsule, June Kwon-Chung and other investigators have discovered numerous genes involved in capsule biosynthesis and regulation. Successful approaches have incorporated combinations of techniques including mutagenesis and systematic gene deletion; complementation and genetic screens; morphological examination, physical separation, and antibody binding; and computational modeling based on gene expression analysis. In this review, we discuss these methods and how they have been used to identify capsule mutants.
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Affiliation(s)
| | - Tamara L. Doering
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO 63110, USA;
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12
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Nielson JA, Jezewski AJ, Wellington M, Davis JM. Survival in macrophages induces enhanced virulence in Cryptococcus. mSphere 2024; 9:e0050423. [PMID: 38073033 PMCID: PMC10826345 DOI: 10.1128/msphere.00504-23] [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: 08/31/2023] [Accepted: 10/31/2023] [Indexed: 01/31/2024] Open
Abstract
Cryptococcus is a ubiquitous environmental fungus and frequent colonizer of human lungs. Colonization can lead to diverse outcomes, from clearance to long-term colonization to life-threatening meningoencephalitis. Regardless of the outcome, the process starts with an encounter with phagocytes. Using the zebrafish model of this infection, we have noted that cryptococcal cells first spend time inside macrophages before they become capable of pathogenic replication and dissemination. What "licensing" process takes place during this initial encounter, and how are licensed cryptococcal cells different? To address this, we isolated cryptococcal cells after phagocytosis by cultured macrophages and found these macrophage-experienced cells to be markedly more virulent in both zebrafish and mouse models. Despite producing a thick polysaccharide capsule, they were still subject to phagocytosis by macrophages in the zebrafish. Analysis of antigenic cell wall components in these licensed cells demonstrated that components of mannose and chitin are more available for staining than they are in culture-grown cells or cells with capsule production induced in vitro. Cryptococcus is capable of exiting or transferring between macrophages in vitro, raising the likelihood that this fungus alternates between intracellular and extracellular life during growth in the lungs. Our results raise the possibility that intracellular life has its advantages over time, and phagocytosis-induced alteration in mannose and chitin exposure is one way that makes subsequent rounds of phagocytosis more beneficial to the fungus.IMPORTANCECryptococcosis begins in the lungs and can ultimately travel through the bloodstream to cause devastating infection in the central nervous system. In the zebrafish model, small amounts of cryptococcus inoculated into the bloodstream are initially phagocytosed and become far more capable of dissemination after they exit macrophages. Similarly, survival in the mouse lung produces cryptococcal cell types with enhanced dissemination. In this study, we have evaluated how phagocytosis changes the properties of Cryptococcus during pathogenesis. Macrophage-experienced cells (MECs) become "licensed" for enhanced virulence. They out-disseminate culture-grown cells in the fish and out-compete non-MECs in the mouse lung. Analysis of their cell surface demonstrates that MECs have increased availability of cell wall components mannose and chitin substances involved in provoking phagocytosis. These findings suggest how Cryptococcus might tune its cell surface to induce but survive repeated phagocytosis during early pathogenesis in the lung.
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Affiliation(s)
- Jacquelyn A. Nielson
- Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Andrew J. Jezewski
- Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Melanie Wellington
- Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - J. Muse Davis
- Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
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13
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Francis VI, Liddle C, Camacho E, Kulkarni M, Junior SRS, Harvey JA, Ballou ER, Thomson DD, Hardwick JM, Casadevall A, Witton J, Coelho C. Cryptococcus neoformans rapidly invades the murine brain by sequential breaching of airway and endothelial tissues barriers, followed by engulfment by microglia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.564824. [PMID: 38014111 PMCID: PMC10680653 DOI: 10.1101/2023.11.13.564824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The fungus Cryptococcus neoformans causes lethal meningitis in humans with weakened immune systems and is estimated to account for 10-15% of AIDS-associated deaths worldwide. There are major gaps in our understanding of how this environmental fungus evades the immune system and invades the mammalian brain before the onset of overt symptoms. To investigate the dynamics of C. neoformans tissue invasion, we mapped early fungal localisation and host cell interactions at early times in infected brain, lung, and upper airways using mouse models of systemic and airway infection. To enable this, we developed an in situ imaging pipeline capable of measuring large volumes of tissue while preserving anatomical and cellular information by combining thick tissue sections, tissue clarification, and confocal imaging. Made possible by these techniques, we confirm high fungal burden in mouse upper airway turbinates after nasal inoculation. Surprisingly, most yeasts in turbinates were titan cells, indicating this microenvironment enables titan cell formation with faster kinetics than reported in mouse lungs. Importantly, we observed one instance of fungal cells enmeshed in lamina propria of upper airways, suggesting penetration of airway mucosa as a possible route of tissue invasion and dissemination to the bloodstream. We extend previous literature positing bloodstream dissemination of C. neoformans, via imaging C. neoformans within blood vessels of mouse lungs and finding viable fungi in the bloodstream of mice a few days after intranasal infection, suggesting that bloodstream access can occur via lung alveoli. In a model of systemic cryptococcosis, we show that as early as 24 h post infection, majority of C. neoformans cells traversed the blood-brain barrier, and are engulfed or in close proximity to microglia. Our work establishes that C. neoformans can breach multiple tissue barriers within the first days of infection. This work presents a new method for investigating cryptococcal invasion mechanisms and demonstrates microglia as the primary cells responding to C. neoformans invasion.
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Affiliation(s)
- Vanessa I Francis
- MRC Centre for Medical Mycology at University of Exeter, University of Exeter, Exeter, EX4 4QD, UK
- Faculty of Health and Life Sciences, University of Exeter, EX4 4QD, UK
| | - Corin Liddle
- Bioimaging Facility, University of Exeter, Exeter, EX4 4QD, UK
| | - Emma Camacho
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Madhura Kulkarni
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Samuel R S Junior
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jamie A Harvey
- MRC Centre for Medical Mycology at University of Exeter, University of Exeter, Exeter, EX4 4QD, UK
| | - Elizabeth R Ballou
- MRC Centre for Medical Mycology at University of Exeter, University of Exeter, Exeter, EX4 4QD, UK
| | - Darren D Thomson
- MRC Centre for Medical Mycology at University of Exeter, University of Exeter, Exeter, EX4 4QD, UK
| | - J Marie Hardwick
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Arturo Casadevall
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jonathan Witton
- Faculty of Health and Life Sciences, University of Exeter, EX4 4QD, UK
| | - Carolina Coelho
- MRC Centre for Medical Mycology at University of Exeter, University of Exeter, Exeter, EX4 4QD, UK
- Faculty of Health and Life Sciences, University of Exeter, EX4 4QD, UK
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14
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Caza M, Santos DA, Burden E, Brisland A, Hu G, Kronstad JW. Proteasome inhibition as a therapeutic target for the fungal pathogen Cryptococcus neoformans. Microbiol Spectr 2023; 11:e0190423. [PMID: 37750732 PMCID: PMC10580939 DOI: 10.1128/spectrum.01904-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
The current therapeutic challenges for treating fungal diseases demand new approaches and new drugs. A promising strategy involves combination therapy with agents of distinct mechanisms of action to increase fungicidal activity and limit the impact of mutations leading to resistance. In this study, we evaluated the antifungal potential of bortezomib by examining the inhibition of proteasome activity, cell proliferation, and capsule production by Cryptococcus neoformans, the causative agent of fungal meningoencephalitis. Chemical genetic screens with collections of deletion mutants identified potential druggable targets for combination therapy with bortezomib. In vitro assays of combinations of bortezomib with flucytosine, chlorpromazine, bafilomycin A1, copper sulfate, or hydroxyurea revealed antifungal effects against C. neoformans. Furthermore, combination treatment with bortezomib and flucytosine in a murine inhalation model of cryptococcosis resulted in the improvement of neurological functions and reduced fungal replication and dissemination, leading to a delay in disease progression. This study therefore highlights the utility of chemical genetic screens to identify new therapeutic approaches as well as the antifungal potential of proteasome inhibition. IMPORTANCE Fungal diseases of humans are difficult to treat, and there is a clear need for additional antifungal drugs, better diagnostics, effective vaccines, and new approaches to deal with emerging drug resistance. Fungi are challenging to control because they share many common biochemical functions with their mammalian hosts and it is therefore difficult to identify fungal-specific targets for drug development. One approach is to employ existing antifungal drugs in combination with agents that target common cellular processes at levels that are (ideally) not toxic for the host. We pursued this approach in this study by examining the potential of the clinically approved proteasome inhibitor bortezomib to influence the proliferation and virulence of Cryptococcus neoformans. We found that the combination of bortezomib with the anti-cryptococcal drug flucytosine improved the survival of infected mice, thus demonstrating the potential of this strategy for antifungal therapy.
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Affiliation(s)
- Mélissa Caza
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel Assis Santos
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Elizabeth Burden
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anna Brisland
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Guanggan Hu
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - James W. Kronstad
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
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15
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Iyer KR, Li SC, Revie NM, Lou JW, Duncan D, Fallah S, Sanchez H, Skulska I, Ušaj MM, Safizadeh H, Larsen B, Wong C, Aman A, Kiyota T, Yoshimura M, Kimura H, Hirano H, Yoshida M, Osada H, Gingras AC, Andes DR, Shapiro RS, Robbins N, Mazhab-Jafari MT, Whitesell L, Yashiroda Y, Boone C, Cowen LE. Identification of triazenyl indoles as inhibitors of fungal fatty acid biosynthesis with broad-spectrum activity. Cell Chem Biol 2023; 30:795-810.e8. [PMID: 37369212 PMCID: PMC11016341 DOI: 10.1016/j.chembiol.2023.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 04/17/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023]
Abstract
Rising drug resistance among pathogenic fungi, paired with a limited antifungal arsenal, poses an increasing threat to human health. To identify antifungal compounds, we screened the RIKEN natural product depository against representative isolates of four major human fungal pathogens. This screen identified NPD6433, a triazenyl indole with broad-spectrum activity against all screening strains, as well as the filamentous mold Aspergillus fumigatus. Mechanistic studies indicated that NPD6433 targets the enoyl reductase domain of fatty acid synthase 1 (Fas1), covalently inhibiting its flavin mononucleotide-dependent NADPH-oxidation activity and arresting essential fatty acid biosynthesis. Robust Fas1 inhibition kills Candida albicans, while sublethal inhibition impairs diverse virulence traits. At well-tolerated exposures, NPD6433 extended the lifespan of nematodes infected with azole-resistant C. albicans. Overall, identification of NPD6433 provides a tool with which to explore lipid homeostasis as a therapeutic target in pathogenic fungi and reveals a mechanism by which Fas1 function can be inhibited.
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Affiliation(s)
- Kali R Iyer
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Sheena C Li
- Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, ON, Canada; RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Nicole M Revie
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jennifer W Lou
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Dustin Duncan
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Sara Fallah
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Hiram Sanchez
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA; Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, USA
| | - Iwona Skulska
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Mojca Mattiazzi Ušaj
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, ON, Canada
| | - Hamid Safizadeh
- Department of Computer Science and Engineering and Department of Electrical and Computer Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Brett Larsen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Cassandra Wong
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Ahmed Aman
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada; Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Taira Kiyota
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Mami Yoshimura
- RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Hiromi Kimura
- RIKEN Center for Sustainable Resource Science, Wako, Japan
| | | | - Minoru Yoshida
- RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Hiroyuki Osada
- RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - David R Andes
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA; Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, USA
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mohammad T Mazhab-Jafari
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Luke Whitesell
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Yoko Yashiroda
- RIKEN Center for Sustainable Resource Science, Wako, Japan.
| | - Charles Boone
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, ON, Canada; RIKEN Center for Sustainable Resource Science, Wako, Japan.
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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16
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Lee S, Abini-Agbomson S, Perry DS, Goodman A, Rao B, Huang MY, Diedrich JK, Moresco JJ, Yates JR, Armache KJ, Madhani HD. Intrinsic mesoscale properties of a Polycomb protein underpin heterochromatin fidelity. Nat Struct Mol Biol 2023; 30:891-901. [PMID: 37217653 PMCID: PMC11935295 DOI: 10.1038/s41594-023-01000-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/17/2023] [Indexed: 05/24/2023]
Abstract
Little is understood about how the two major types of heterochromatin domains (HP1 and Polycomb) are kept separate. In the yeast Cryptococcus neoformans, the Polycomb-like protein Ccc1 prevents deposition of H3K27me3 at HP1 domains. Here we show that phase separation propensity underpins Ccc1 function. Mutations of the two basic clusters in the intrinsically disordered region or deletion of the coiled-coil dimerization domain alter phase separation behavior of Ccc1 in vitro and have commensurate effects on formation of Ccc1 condensates in vivo, which are enriched for PRC2. Notably, mutations that alter phase separation trigger ectopic H3K27me3 at HP1 domains. Supporting a direct condensate-driven mechanism for fidelity, Ccc1 droplets efficiently concentrate recombinant C. neoformans PRC2 in vitro whereas HP1 droplets do so only weakly. These studies establish a biochemical basis for chromatin regulation in which mesoscale biophysical properties play a key functional role.
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Affiliation(s)
- Sujin Lee
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Stephen Abini-Agbomson
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Daniela S Perry
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Allen Goodman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Beiduo Rao
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Manning Y Huang
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - James J Moresco
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Karim-Jean Armache
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
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17
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Jackson KM, Ding M, Nielsen K. Importance of Clinical Isolates in Cryptococcus neoformans Research. J Fungi (Basel) 2023; 9:364. [PMID: 36983532 PMCID: PMC10056780 DOI: 10.3390/jof9030364] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023] Open
Abstract
The human pathogenic fungus Cryptococcus neoformans is a global health concern. Previous research in the field has focused on studies using reference strains to identify virulence factors, generate mutant libraries, define genomic structures, and perform functional studies. In this review, we discuss the benefits and drawbacks of using reference strains to study C. neoformans, describe how the study of clinical isolates has expanded our understanding of pathogenesis, and highlight how studies using clinical isolates can further develop our understanding of the host-pathogen interaction during C. neoformans infection.
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Affiliation(s)
| | | | - Kirsten Nielsen
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
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18
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Nielson JA, Davis JM. Roles for Microglia in Cryptococcal Brain Dissemination in the Zebrafish Larva. Microbiol Spectr 2023; 11:e0431522. [PMID: 36719205 PMCID: PMC10100726 DOI: 10.1128/spectrum.04315-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/20/2022] [Indexed: 02/01/2023] Open
Abstract
Cryptococcal infection begins in the lungs, but yeast cells subsequently access the bloodstream, from which they can reach the central nervous system (CNS). The resulting meningoencephalitis is the most common presentation and is very difficult to treat. How this fungus interacts with the blood-brain barrier (BBB) and establishes growth in the brain parenchyma remains a central question in fungal pathogenesis. We and others have developed the zebrafish larva as a model host for cryptococcosis and demonstrated that hematogenous CNS infection is replicated in this model. Here, we have used this model to examine the details of BBB crossing and the events immediately before and after. We have observed multiple mechanisms of BBB crossing and found that microglia, the resident phagocytes of the brain, likely have multiple roles. First, microglia either actively transfer yeast cells across the BBB or take up a significant proportion of them immediately after crossing. Second, microglia are capable of clearing individual cryptococcal cells at a developmental stage before adaptive immune cells have emerged. Third, microglia serve to maintain endothelial integrity, preventing other, phagocyte-independent forms of crossing. These proposed microglial functions during infection in the zebrafish larva generate new hypotheses concerning the establishment and control of cryptococcal meningoencephalitis. IMPORTANCE Cryptococcal meningitis is a fungal infection of the brain and a major cause of death in people with uncontrolled HIV. Infection begins in the lungs but can enter the bloodstream and disseminate to the brain. A structure called the blood-brain barrier must be crossed for the fungus to enter and cause meningitis. Learning how Cryptococcus crosses the blood-brain barrier will be crucial to understanding and possibly preventing brain infection. Using the zebrafish larva as a model host, we show that microglia, the resident phagocytes of the brain, potentially play multiple previously unappreciated roles in cryptococcal infection of the brain. These roles include reinforcing the integrity of the blood-brain barrier, clearing cryptococcal cells after they have crossed, and possibly participating directly in crossing via a previously unknown mechanism.
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Affiliation(s)
- Jacquelyn A. Nielson
- Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - J. Muse Davis
- Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, USA
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19
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Sephton-Clark P, Tenor JL, Toffaletti DL, Meyers N, Giamberardino C, Molloy SF, Palmucci JR, Chan A, Chikaonda T, Heyderman R, Hosseinipour M, Kalata N, Kanyama C, Kukacha C, Lupiya D, Mwandumba HC, Harrison T, Bicanic T, Perfect JR, Cuomo CA. Genomic Variation across a Clinical Cryptococcus Population Linked to Disease Outcome. mBio 2022; 13:e0262622. [PMID: 36354332 PMCID: PMC9765290 DOI: 10.1128/mbio.02626-22] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/13/2022] [Indexed: 11/12/2022] Open
Abstract
Cryptococcus neoformans is the causative agent of cryptococcosis, a disease with poor patient outcomes that accounts for approximately 180,000 deaths each year. Patient outcomes may be impacted by the underlying genetics of the infecting isolate; however, our current understanding of how genetic diversity contributes to clinical outcomes is limited. Here, we leverage clinical, in vitro growth and genomic data for 284 C. neoformans isolates to identify clinically relevant pathogen variants within a population of clinical isolates from patients with human immunodeficiency virus (HIV)-associated cryptococcosis in Malawi. Through a genome-wide association study (GWAS) approach, we identify variants associated with the fungal burden and the growth rate. We also find both small and large-scale variation, including aneuploidy, associated with alternate growth phenotypes, which may impact the course of infection. Genes impacted by these variants are involved in transcriptional regulation, signal transduction, glycosylation, sugar transport, and glycolysis. We show that growth within the central nervous system (CNS) is reliant upon glycolysis in an animal model and likely impacts patient mortality, as the CNS yeast burden likely modulates patient outcome. Additionally, we find that genes with roles in sugar transport are enriched in regions under selection in specific lineages of this clinical population. Further, we demonstrate that genomic variants in two genes identified by GWAS impact virulence in animal models. Our approach identifies links between the genetic variation in C. neoformans and clinically relevant phenotypes and animal model pathogenesis, thereby shedding light on specific survival mechanisms within the CNS and identifying the pathways involved in yeast persistence. IMPORTANCE Infection outcomes for cryptococcosis, most commonly caused by C. neoformans, are influenced by host immune responses as well as by host and pathogen genetics. Infecting yeast isolates are genetically diverse; however, we lack a deep understanding of how this diversity impacts patient outcomes. To better understand both clinical isolate diversity and how diversity contributes to infection outcomes, we utilize a large collection of clinical C. neoformans samples that were isolated from patients enrolled in a clinical trial across 3 hospitals in Malawi. By combining whole-genome sequence data, clinical data, and in vitro growth data, we utilize genome-wide association approaches to examine the genetic basis of virulence. Genes with significant associations display virulence attributes in both murine and rabbit models, demonstrating that our approach can identify potential links between genetic variants and patho-biologically significant phenotypes.
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Affiliation(s)
- Poppy Sephton-Clark
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jennifer L. Tenor
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Dena L. Toffaletti
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Nancy Meyers
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Charles Giamberardino
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Síle F. Molloy
- Centre for Global Health, Institute of Infection and Immunity, St George's University of London, London, United Kingdom
- Clinical Academic Group in Infection, St George's University Hospital, London, United Kingdom
| | - Julia R. Palmucci
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Adrienne Chan
- Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Tarsizio Chikaonda
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Robert Heyderman
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Mina Hosseinipour
- UNC Project Malawi, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Newton Kalata
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Cecilia Kanyama
- UNC Project Malawi, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Christopher Kukacha
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Duncan Lupiya
- Tisungane Clinic, Zomba Central Hospital, Zomba, Malawi
| | - Henry C. Mwandumba
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Thomas Harrison
- Centre for Global Health, Institute of Infection and Immunity, St George's University of London, London, United Kingdom
- Clinical Academic Group in Infection, St George's University Hospital, London, United Kingdom
| | - Tihana Bicanic
- Centre for Global Health, Institute of Infection and Immunity, St George's University of London, London, United Kingdom
- Clinical Academic Group in Infection, St George's University Hospital, London, United Kingdom
| | - John R. Perfect
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Christina A. Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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20
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Multiple F-Box Proteins Collectively Regulate Cell Development and Pathogenesis in the Human Pathogen Cryptococcus neoformans. J Fungi (Basel) 2022; 8:jof8121259. [PMID: 36547592 PMCID: PMC9781138 DOI: 10.3390/jof8121259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 11/27/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022] Open
Abstract
The ubiquitin-proteasome system (UPS) mediates intracellular proteins degradation that influences various cellular functions in eukaryotic cells. The UPS is also involved in the development and virulence of pathogenic fungi. F-box proteins, which are part of the SCF (Skp1-Cullin-F-box protein) ligase, are a key component of UPS and are essential for the recognition of specific substrates. In this study, we identified 20 F-box proteins in C. neoformans and obtained deletion mutants for 19 of them. A comprehensive phenotypic analysis of these mutants revealed the diverse function of F-box proteins in stress response, cell size regulation, sexual reproduction, antifungal drug resistance, and fungal virulence in C. neoformans. The importance of three F-box proteins: Fbp4, Fbp8, and Fbp11, in these cellular functions were characterized in detail. This study provides an overall view of the F-box gene family in C. neoformans, which will lead to a better understanding of the function of fungal SCF E3 ligase-mediated UPS in fungal development and pathogenesis.
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21
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Moreira-Walsh B, Ragsdale A, Lam W, Upadhya R, Xu E, Lodge JK, Donlin MJ. Membrane Integrity Contributes to Resistance of Cryptococcus neoformans to the Cell Wall Inhibitor Caspofungin. mSphere 2022; 7:e0013422. [PMID: 35758672 PMCID: PMC9429927 DOI: 10.1128/msphere.00134-22] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/01/2022] [Indexed: 01/20/2023] Open
Abstract
The fungal pathogen Cryptococcus neoformans causes up to 278 000 infections each year globally, resulting in up to 180,000 deaths annually, mostly impacting immunocompromised people. Therapeutic options for C. neoformans infections are very limited. Caspofungin, a member of the echinocandin class of antifungals, is generally well tolerated but clinically ineffective against C. neoformans. We sought to identify biological processes that can be targeted to render the cell more susceptible to echinocandins by screening the available libraries of gene deletion mutants made in the KN99α background for caspofungin sensitivity. We adapted a Candida albicans fungal biofilm assay for the growth characteristics of C. neoformans and systematically screened 4,030 individual gene deletion mutants in triplicate plate assays. We identified 25 strains that showed caspofungin sensitivity. We followed up with a dose dependence assay, and 17 of the 25 were confirmed sensitive, 5 of which were also sensitive in an agar plate assay. We made new deletion mutant strains for four of these genes: CFT1, encoding an iron transporter; ERG4, encoding a sterol desaturase; MYO1, encoding a myosin heavy chain; and YSP2, encoding a sterol transporter. All were more sensitive to membrane stress and showed significantly increased sensitivity to caspofungin at higher temperatures. Surprisingly, none showed any obvious cell wall defects such as would be expected for caspofungin-sensitive strains. Our microscopy analyses suggested that loss of membrane integrity contributed to the caspofungin sensitivity, either by allowing more caspofungin to enter or remain in the cell or by altering the location or orientation of the enzyme target to render it more susceptible to inhibition. IMPORTANCE The intrinsic resistance of Cryptococcus neoformans to the cell wall inhibitor caspofungin limits the available therapies for treating cryptococcal infections. We screened a collection of more than 4,000 gene deletion strains for altered caspofungin sensitivity to identify biological processes that could be targeted to render the cell more susceptible to caspofungin. We identified multiple genes with an effect on caspofungin susceptibility and found that they were associated with altered membrane permeability rather than the expected cell wall defects. This suggests that targeting these genes or other genes affecting membrane permeability is a viable path for developing novel therapies for treating this global fungal pathogen.
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Affiliation(s)
- Brenda Moreira-Walsh
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Abigail Ragsdale
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Woei Lam
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Rajendra Upadhya
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Evan Xu
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Jennifer K. Lodge
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Maureen J. Donlin
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
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22
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Dang EV, Lei S, Radkov A, Volk RF, Zaro BW, Madhani HD. Secreted fungal virulence effector triggers allergic inflammation via TLR4. Nature 2022; 608:161-167. [PMID: 35896747 PMCID: PMC9744105 DOI: 10.1038/s41586-022-05005-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 06/21/2022] [Indexed: 12/14/2022]
Abstract
Invasive fungal pathogens are major causes of human mortality and morbidity1,2. Although numerous secreted effector proteins that reprogram innate immunity to promote virulence have been identified in pathogenic bacteria, so far, there are no examples of analogous secreted effector proteins produced by human fungal pathogens. Cryptococcus neoformans, the most common cause of fungal meningitis and a major pathogen in AIDS, induces a pathogenic type 2 response characterized by pulmonary eosinophilia and alternatively activated macrophages3-8. Here, we identify CPL1 as an effector protein secreted by C. neoformans that drives alternative activation (also known as M2 polarization) of macrophages to enable pulmonary infection in mice. We observed that CPL1-enhanced macrophage polarization requires Toll-like receptor 4, which is best known as a receptor for bacterial endotoxin but is also a poorly understood mediator of allergen-induced type 2 responses9-12. We show that this effect is caused by CPL1 itself and not by contaminating lipopolysaccharide. CPL1 is essential for virulence, drives polarization of interstitial macrophages in vivo, and requires type 2 cytokine signalling for its effect on infectivity. Notably, C. neoformans associates selectively with polarized interstitial macrophages during infection, suggesting a mechanism by which C. neoformans generates its own intracellular replication niche within the host. This work identifies a circuit whereby a secreted effector protein produced by a human fungal pathogen reprograms innate immunity, revealing an unexpected role for Toll-like receptor 4 in promoting the pathogenesis of infectious disease.
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Affiliation(s)
- Eric V. Dang
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, United States of America
| | - Susan Lei
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, United States of America
| | - Atanas Radkov
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, United States of America
| | - Regan F. Volk
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, United States of America,Cardiovascular Research Institute, University of California, San Francisco, CA, United States of America
| | - Balyn W. Zaro
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, United States of America,Cardiovascular Research Institute, University of California, San Francisco, CA, United States of America
| | - Hiten D. Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, United States of America,Chan-Zuckerberg Biohub, San Francisco, CA, United States of America,
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23
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Ke W, Xie Y, Hu Y, Ding H, Fan X, Huang J, Tian X, Zhang B, Xu Y, Liu X, Yang Y, Wang L. A forkhead transcription factor contributes to the regulatory differences of pathogenicity in closely related fungal pathogens. MLIFE 2022; 1:79-91. [PMID: 38818325 PMCID: PMC10989923 DOI: 10.1002/mlf2.12011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/21/2022] [Accepted: 02/10/2022] [Indexed: 06/01/2024]
Abstract
Cryptococcus neoformans and its sister species Cryptococcus deuterogattii are important human fungal pathogens. Despite their phylogenetically close relationship, these two Cryptococcus pathogens are greatly different in their clinical characteristics. However, the determinants underlying the regulatory differences of their pathogenicity remain largely unknown. Here, we show that the forkhead transcription factor Hcm1 promotes infection in C. neoformans but not in C. deuterogattii. Monitoring in vitro and in vivo fitness outcomes of multiple clinical isolates from the two pathogens indicates that Hcm1 mediates pathogenicity in C. neoformans through its key involvement in oxidative stress defense. By comparison, Hcm1 is not critical for antioxidation in C. deuterogattii. Furthermore, we identified SRX1, which encodes the antioxidant sulfiredoxin, as a conserved target of Hcm1 in two Cryptococcus pathogens. Like HCM1, SRX1 had a greater role in antioxidation in C. neoformans than in C. deuterogattii. Significantly, overexpression of SRX1 can largely rescue the defective pathogenicity caused by the absence of Hcm1 in C. neoformans. Conversely, Srx1 is dispensable for virulence in C. deuterogattii. Overall, our findings demonstrate that the difference in the contribution of the antioxidant sulfiredoxin to oxidative stress defense underlies the Hcm1-mediated regulatory differences of pathogenicity in two closely related pathogens.
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Affiliation(s)
- Weixin Ke
- State Key Laboratory of Mycology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Yuyan Xie
- State Key Laboratory of Mycology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Yue Hu
- State Key Laboratory of Mycology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Hao Ding
- State Key Laboratory of Mycology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Xin Fan
- Department of Infectious Diseases and Clinical Microbiology, Beijing Chaoyang HospitalCapital Medical UniversityBeijingChina
| | - Jingjing Huang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Peking Union Medical College Hospital, Peking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Graduate School, Peking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
| | - Xiuyun Tian
- State Key Laboratory of Mycology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Baokun Zhang
- Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Disease, Department of BiotechnologyBeijing Institute of Radiation MedicineBeijingChina
| | - Yingchun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Peking Union Medical College Hospital, Peking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
| | - Xiao Liu
- State Key Laboratory of Mycology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Ying Yang
- Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Disease, Department of BiotechnologyBeijing Institute of Radiation MedicineBeijingChina
| | - Linqi Wang
- State Key Laboratory of Mycology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
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24
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Huang MY, Joshi MB, Boucher MJ, Lee S, Loza LC, Gaylord EA, Doering TL, Madhani HD. Short homology-directed repair using optimized Cas9 in the pathogen Cryptococcus neoformans enables rapid gene deletion and tagging. Genetics 2022; 220:iyab180. [PMID: 34791226 PMCID: PMC8733451 DOI: 10.1093/genetics/iyab180] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/08/2021] [Indexed: 01/07/2023] Open
Abstract
Cryptococcus neoformans, the most common cause of fungal meningitis, is a basidiomycete haploid budding yeast with a complete sexual cycle. Genome modification by homologous recombination is feasible using biolistic transformation and long homology arms, but the method is arduous and unreliable. Recently, multiple groups have reported the use of CRISPR-Cas9 as an alternative to biolistics, but long homology arms are still necessary, limiting the utility of this method. Since the S. pyogenes Cas9 derivatives used in prior studies were not optimized for expression in C. neoformans, we designed, synthesized, and tested a fully C. neoformans-optimized (Cno) Cas9. We found that a Cas9 harboring only common C. neoformans codons and a consensus C. neoformans intron together with a TEF1 promoter and terminator and a nuclear localization signal (Cno CAS9 or "CnoCAS9") reliably enabled genome editing in the widely used KN99α C. neoformans strain. Furthermore, editing was accomplished using donors harboring short (50 bp) homology arms attached to marker DNAs produced with synthetic oligonucleotides and PCR amplification. We also demonstrated that prior stable integration of CnoCAS9 further enhances both transformation and homologous recombination efficiency; importantly, this manipulation does not impact virulence in animals. We also implemented a universal tagging module harboring a codon-optimized fluorescent protein (mNeonGreen) and a tandem Calmodulin Binding Peptide-2X FLAG Tag that allows for both localization and purification studies of proteins for which the corresponding genes are modified by short homology-directed recombination. These tools enable short-homology genome engineering in C. neoformans.
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Affiliation(s)
- Manning Y Huang
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Meenakshi B Joshi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Michael J Boucher
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Sujin Lee
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Liza C Loza
- Department of Molecular Microbiology, Washington University School of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Elizabeth A Gaylord
- Department of Molecular Microbiology, Washington University School of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Tamara L Doering
- Department of Molecular Microbiology, Washington University School of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
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25
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Yu CH, Sephton-Clark P, Tenor JL, Toffaletti DL, Giamberardino C, Haverkamp M, Cuomo CA, Perfect JR. Gene Expression of Diverse Cryptococcus Isolates during Infection of the Human Central Nervous System. mBio 2021; 12:e0231321. [PMID: 34724829 PMCID: PMC8561399 DOI: 10.1128/mbio.02313-21] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022] Open
Abstract
Cryptococcus neoformans is a major human central nervous system (CNS) fungal pathogen causing considerable morbidity and mortality. In this study, we provide the widest view to date of the yeast transcriptome directly from the human subarachnoid space and within cerebrospinal fluid (CSF). We captured yeast transcriptomes from C. neoformans of various genotypes in 31 patients with cryptococcal meningoencephalitis as well as several Cryptococcus gattii infections. Using transcriptome sequencing (RNA-seq) analyses, we compared the in vivo yeast transcriptomes to those from other environmental conditions, including in vitro growth on nutritious media or artificial CSF as well as samples collected from rabbit CSF at two time points. We ranked gene expressions and identified genetic patterns and networks across these diverse isolates that reveal an emphasis on carbon metabolism, fatty acid synthesis, transport, cell wall structure, and stress-related gene functions during growth in CSF. The most highly expressed yeast genes in human CSF included those known to be associated with survival or virulence and highlighted several genes encoding hypothetical proteins. From that group, a gene encoding the CMP1 putative glycoprotein (CNAG_06000) was selected for functional studies. This gene was found to impact the virulence of Cryptococcus in both mice and the CNS rabbit model, in agreement with a recent study also showing a role in virulence. This transcriptional analysis strategy provides a view of regulated yeast genes across genetic backgrounds important for human CNS infection and a relevant resource for the study of cryptococcal genes, pathways, and networks linked to human disease. IMPORTANCE Cryptococcus is the most common fungus causing high-morbidity and -mortality human meningitis. This encapsulated yeast has a unique propensity to travel to the central nervous system to produce disease. In this study, we captured transcriptomes of yeasts directly out of the human cerebrospinal fluid, the most concerning site of infection. By comparing the RNA transcript levels with other conditions, we gained insights into how the basic machinery involved in metabolism and environmental responses enable this fungus to cause disease at this body site. This approach was applied to clinical isolates with diverse genotypes to begin to establish a genotype-agnostic understanding of how the yeast responds to stress. Based on these results, future studies can focus on how these genes and their pathways and networks can be targeted with new therapeutics and possibly classify yeasts with bad infection outcomes.
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Affiliation(s)
- Chen-Hsin Yu
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Poppy Sephton-Clark
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jennifer L. Tenor
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Dena L. Toffaletti
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Charles Giamberardino
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Miriam Haverkamp
- Department of Infection Control and Infectious Diseases, University Hospital RWTH Aachen, Aachen, Germany
| | - Christina A. Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - John R. Perfect
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
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26
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Crunden JL, Diezmann S. Hsp90 interaction networks in fungi-tools and techniques. FEMS Yeast Res 2021; 21:6413543. [PMID: 34718512 PMCID: PMC8599792 DOI: 10.1093/femsyr/foab054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 10/26/2021] [Indexed: 01/01/2023] Open
Abstract
Heat-shock protein 90 (Hsp90) is a central regulator of cellular proteostasis. It stabilizes numerous proteins that are involved in fundamental processes of life, including cell growth, cell-cycle progression and the environmental response. In addition to stabilizing proteins, Hsp90 governs gene expression and controls the release of cryptic genetic variation. Given its central role in evolution and development, it is important to identify proteins and genes that interact with Hsp90. This requires sophisticated genetic and biochemical tools, including extensive mutant collections, suitable epitope tags, proteomics approaches and Hsp90-specific pharmacological inhibitors for chemogenomic screens. These usually only exist in model organisms, such as the yeast Saccharomyces cerevisiae. Yet, the importance of other fungal species, such as Candida albicans and Cryptococcus neoformans, as serious human pathogens accelerated the development of genetic tools to study their virulence and stress response pathways. These tools can also be exploited to map Hsp90 interaction networks. Here, we review tools and techniques for Hsp90 network mapping available in different fungi and provide a summary of existing mapping efforts. Mapping Hsp90 networks in fungal species spanning >500 million years of evolution provides a unique vantage point, allowing tracking of the evolutionary history of eukaryotic Hsp90 networks.
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Affiliation(s)
- Julia L Crunden
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Stephanie Diezmann
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, UK
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27
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Hu G, Horianopoulos L, Sánchez-León E, Caza M, Jung W, Kronstad JW. The monothiol glutaredoxin Grx4 influences thermotolerance, cell wall integrity, and Mpk1 signaling in Cryptococcus neoformans. G3 (BETHESDA, MD.) 2021; 11:jkab322. [PMID: 34542604 PMCID: PMC8527476 DOI: 10.1093/g3journal/jkab322] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/27/2021] [Indexed: 02/07/2023]
Abstract
Monothiol glutaredoxins are important regulators of iron homeostasis that play conserved roles in the sensing and trafficking of iron-sulfur clusters. We previously characterized the role of the monothiol glutaredoxin Grx4 in iron homeostasis, the interaction with the iron regulator Cir1, and virulence in Cryptococcus neoformans. This important fungal pathogen causes cryptococcal meningoencephalitis in immunocompromised individuals worldwide. Here, we demonstrate that Grx4 is required for proliferation at elevated temperatures (both 37°C and 39°C) and under stress conditions. In particular, the grx4Δ mutant was hypersensitive to SDS, calcofluor white (CFW), and caffeine, suggesting that Grx4 is required for membrane and cell wall integrity (CWI). In this context, we found that Grx4 regulated the phosphorylation of the Mpk1 mitogen-activated protein kinase (MAPK) of the CWI pathway in cells grown at elevated temperature or upon treatment with CFW, caffeine, or SDS. The grx4Δ mutant also displayed increased sensitivity to FK506 and cyclosporin A, two inhibitors of the calcineurin pathway, indicating that Grx4 may influence growth at higher temperatures in parallel with calcineurin signaling. Upon thermal stress or calcium treatment, loss of Grx4 also caused partial mis-localization of Crz1, the transcription factor that is a calcineurin substrate. The phenotypes of the grx4Δ, crz1Δ, and cna1Δ (calcineurin) mutants suggest shared contributions to the regulation of temperature, cell wall, and other stresses. In summary, we show that Grx4 is also a key regulator of the responses to a variety of stress conditions in addition to its roles in iron homeostasis in C. neoformans.
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Affiliation(s)
- Guanggan Hu
- Michael Smith Laboratories, Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Linda Horianopoulos
- Michael Smith Laboratories, Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Eddy Sánchez-León
- Michael Smith Laboratories, Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Mélissa Caza
- Michael Smith Laboratories, Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Wonhee Jung
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - James W Kronstad
- Michael Smith Laboratories, Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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28
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Raman Characterization of Fungal DHN and DOPA Melanin Biosynthesis Pathways. J Fungi (Basel) 2021; 7:jof7100841. [PMID: 34682262 PMCID: PMC8540899 DOI: 10.3390/jof7100841] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/02/2021] [Accepted: 10/03/2021] [Indexed: 12/16/2022] Open
Abstract
Fungal melanins represent a resource for important breakthroughs in industry and medicine, but the characterization of their composition, synthesis, and structure is not well understood. Raman spectroscopy is a powerful tool for the elucidation of molecular composition and structure. In this work, we characterize the Raman spectra of wild-type Aspergillus fumigatus and Cryptococcus neoformans and their melanin biosynthetic mutants and provide a rough “map” of the DHN (A. fumigatus) and DOPA (C. neoformans) melanin biosynthetic pathways. We compare this map to the Raman spectral data of Aspergillus nidulans wild-type and melanin biosynthetic mutants obtained from a previous study. We find that the fully polymerized A. nidulans melanin cannot be classified according to the DOPA pathway; nor can it be solely classified according to the DHN pathway, consistent with mutational analysis and chemical inhibition studies. Our approach points the way forward for an increased understanding of, and methodology for, investigating fungal melanins.
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29
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Ballou ER, Cook AG, Wallace EWJ. Repeated Evolution of Inactive Pseudonucleases in a Fungal Branch of the Dis3/RNase II Family of Nucleases. Mol Biol Evol 2021; 38:1837-1846. [PMID: 33313834 PMCID: PMC8097288 DOI: 10.1093/molbev/msaa324] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The RNase II family of 3'-5' exoribonucleases is present in all domains of life, and eukaryotic family members Dis3 and Dis3L2 play essential roles in RNA degradation. Ascomycete yeasts contain both Dis3 and inactive RNase II-like "pseudonucleases." The latter function as RNA-binding proteins that affect cell growth, cytokinesis, and fungal pathogenicity. However, the evolutionary origins of these pseudonucleases are unknown: What sequence of events led to their novel function, and when did these events occur? Here, we show how RNase II pseudonuclease homologs, including Saccharomyces cerevisiae Ssd1, are descended from active Dis3L2 enzymes. During fungal evolution, active site mutations in Dis3L2 homologs have arisen at least four times, in some cases following gene duplication. In contrast, N-terminal cold-shock domains and regulatory features are conserved across diverse dikarya and mucoromycota, suggesting that the nonnuclease function requires these regions. In the basidiomycete pathogenic yeast Cryptococcus neoformans, the single Ssd1/Dis3L2 homolog is required for cytokinesis from polyploid "titan" growth stages. This phenotype of C. neoformans Ssd1/Dis3L2 deletion is consistent with those of inactive fungal pseudonucleases, yet the protein retains an active site sequence signature. We propose that a nuclease-independent function for Dis3L2 arose in an ancestral hyphae-forming fungus. This second function has been conserved across hundreds of millions of years, whereas the RNase activity was lost repeatedly in independent lineages.
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Affiliation(s)
- Elizabeth R Ballou
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Atlanta G Cook
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Edward W J Wallace
- Institute for Cell Biology and SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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30
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Stempinski PR, Zielinski JM, Dbouk NH, Huey ES, McCormack EC, Rubin AM, Chandrasekaran S, Kozubowski L. Genetic contribution to high temperature tolerance in Cryptococcus neoformans. Genetics 2021; 217:1-15. [PMID: 33683363 PMCID: PMC8045695 DOI: 10.1093/genetics/iyaa009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 10/24/2020] [Indexed: 11/12/2022] Open
Abstract
The human fungal pathogen Cryptococcus neoformans relies on a complex signaling network for the adaptation and survival at the host temperature. Protein phosphatase calcineurin is central to proliferation at 37°C but its exact contributions remain ill-defined. To better define genetic contributions to the C. neoformans temperature tolerance, 4031 gene knockouts were screened for genes essential at 37°C and under conditions that keep calcineurin inactive. Identified 83 candidate strains, potentially sensitive to 37°C, were subsequently subject to technologically simple yet robust assay, in which cells are exposed to a temperature gradient. This has resulted in identification of 46 genes contributing to the maximum temperature at which C. neoformans can proliferate (Tmax). The 46 mutants, characterized by a range of Tmax on drug-free media, were further assessed for Tmax under conditions that inhibit calcineurin, which led to identification of several previously uncharacterized knockouts exhibiting synthetic interaction with the inhibition of calcineurin. A mutant that lacked septin Cdc11 was among those with the lowest Tmax and failed to proliferate in the absence of calcineurin activity. To further define connections with calcineurin and the role for septins in high temperature growth, the 46 mutants were tested for cell morphology at 37°C and growth in the presence of agents disrupting cell wall and cell membrane. Mutants sensitive to calcineurin inhibition were tested for synthetic lethal interaction with deletion of the septin-encoding CDC12 and the localization of the septin Cdc3-mCherry. The analysis described here pointed to previously uncharacterized genes that were missed in standard growth assays indicating that the temperature gradient assay is a valuable complementary tool for elucidating the genetic basis of temperature range at which microorganisms proliferate.
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Affiliation(s)
- Piotr R Stempinski
- Department of Genetics & Biochemistry, Eukaryotic Pathogens Innovation Center (EPIC), Clemson University, Clemson, SC 29634, USA
| | - Jessica M Zielinski
- Department of Genetics & Biochemistry, Eukaryotic Pathogens Innovation Center (EPIC), Clemson University, Clemson, SC 29634, USA
| | - Nadir H Dbouk
- Department of Biology, Furman University, Greenville, SC 29613, USA
| | - Elizabeth S Huey
- Department of Genetics & Biochemistry, Eukaryotic Pathogens Innovation Center (EPIC), Clemson University, Clemson, SC 29634, USA
| | - Ellen C McCormack
- Department of Genetics & Biochemistry, Eukaryotic Pathogens Innovation Center (EPIC), Clemson University, Clemson, SC 29634, USA
| | - Alexander M Rubin
- Department of Genetics & Biochemistry, Eukaryotic Pathogens Innovation Center (EPIC), Clemson University, Clemson, SC 29634, USA
| | | | - Lukasz Kozubowski
- Department of Genetics & Biochemistry, Eukaryotic Pathogens Innovation Center (EPIC), Clemson University, Clemson, SC 29634, USA
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Madhani HD. Unbelievable but True: Epigenetics and Chromatin in Fungi. Trends Genet 2020; 37:12-20. [PMID: 33092902 DOI: 10.1016/j.tig.2020.09.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 12/22/2022]
Abstract
Evolutionary innovations in chromatin biology have been recently discovered through the study of fungi. In Saccharomyces cerevisiae, a prion form of a deacetylase complex assembles over subtelomeric domains that produces a heritable gene expression state that enables resistance to stress. In Candida albicans, stress triggers adaptive chromosome destabilization via erasure a centromeric histone H3, CENP-A; a process that cooperates with a newly evolved H2A variant lacking a mitotic phosphorylation site. Finally, in Cryptococcus neoformans, the loss of a cytosine DNA methyltransferase at least 50 million years ago has enabled the Darwinian evolution of methylation patterns over geological timescales. These studies reveal a remarkable genetic and epigenetic evolutionary plasticity of the chromatin fiber, despite the highly conserved structure of the nucleosome.
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Affiliation(s)
- Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA; Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA.
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Perlatti B, Harris G, Nichols CB, Ekanayake DI, Alspaugh JA, Gloer JB, Bills GF. Campafungins: Inhibitors of Candida albicans and Cryptococcus neoformans Hyphal Growth. JOURNAL OF NATURAL PRODUCTS 2020; 83:2718-2726. [PMID: 32881504 PMCID: PMC7530089 DOI: 10.1021/acs.jnatprod.0c00641] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Campafungin A is a polyketide that was recognized in the Candida albicans fitness test due to its antiproliferative and antihyphal activity. Its mode of action was hypothesized to involve inhibition of a cAMP-dependent PKA pathway. The originally proposed structure appeared to require a polyketide assembled in a somewhat unusual fashion. However, structural characterization data were never formally published. This background stimulated a reinvestigation in which campafungin A and three closely related minor constituents were purified from fermentations of a strain of the ascomycete fungus Plenodomus enteroleucus. Labeling studies, along with extensive NMR analysis, enabled assignment of a revised structure consistent with conventional polyketide synthetic machinery. The structure elucidation of campafungin A and new analogues encountered in this study, designated here as campafungins B, C, and D, is presented, along with a proposed biosynthetic route. The antimicrobial spectrum was expanded to methicillin-resistant Staphylococcus aureus, Candida tropicalis, Candida glabrata, Cryptococcus neoformans, Aspergillus fumigatus, and Schizosaccharomyces pombe, with MICs ranging as low as 4-8 μg mL-1 in C. neoformans. Mode-of-action studies employing libraries of C. neoformans mutants indicated that multiple pathways were affected, but mutants in PKA/cAMP pathways were unaffected, indicating that the mode of action was distinct from that observed in C. albicans.
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Affiliation(s)
- Bruno Perlatti
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas 77054, United States
| | - Guy Harris
- Guy Harris Consulting, 464 Fairview Road, Belington, West Virginia 26250, United States
| | - Connie B Nichols
- Departments of Medicine and Molecular Genetics & Microbiology, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Dulamini I Ekanayake
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - J Andrew Alspaugh
- Departments of Medicine and Molecular Genetics & Microbiology, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - James B Gloer
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Gerald F Bills
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas 77054, United States
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Li Z, Kim KS. RELATe enables genome-scale engineering in fungal genomics. SCIENCE ADVANCES 2020; 6:eabb8783. [PMID: 32948588 PMCID: PMC7500931 DOI: 10.1126/sciadv.abb8783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/06/2020] [Indexed: 06/11/2023]
Abstract
CRISPR-Cas9-based screening with single-guide RNA (sgRNA) libraries has emerged as a revolutionary tool for comprehensive analysis of genetic elements. However, genome-scale sgRNA libraries are currently available only in a few model organisms. The traditional approach is to synthesize thousands to tens of thousands of sgRNAs, which is laborious and expensive. We have developed a simple method, RELATe (restriction/ligation coupled with Agrobacterium-mediated transformation), to generate sgRNA libraries from 10 μg of genomic DNA, targeting over 98% of the protein-coding genes in the human fungal pathogen Cryptococcus neoformans Functional screens identified 142 potential C. neoformans genes contributing to blood-brain barrier penetration. We selected two cryptococcal genes, SFP1 and WDR1, for a proof-of-concept demonstration that RELATe-identified genes are relevant to C. neoformans central nervous system infection. Our RELATe method can be used in many other fungal species and is powerful and cost-effective for genome-wide high-throughput screening for elucidating functional genomics.
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Affiliation(s)
- Zhongming Li
- Division of Pediatric Infectious Diseases, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Kwang Sik Kim
- Division of Pediatric Infectious Diseases, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA.
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
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Xue A, Robbins N, Cowen LE. Advances in fungal chemical genomics for the discovery of new antifungal agents. Ann N Y Acad Sci 2020; 1496:5-22. [PMID: 32860238 DOI: 10.1111/nyas.14484] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/09/2020] [Accepted: 08/13/2020] [Indexed: 12/15/2022]
Abstract
Invasive fungal infections have escalated from a rare curiosity to a major cause of human mortality around the globe. This is in part due to a scarcity in the number of antifungal drugs available to combat mycotic disease, making the discovery of novel bioactive compounds and determining their mode of action of utmost importance. The development and application of chemical genomic assays using the model yeast Saccharomyces cerevisiae has provided powerful methods to identify the mechanism of action of diverse molecules in a living cell. Furthermore, complementary assays are continually being developed in fungal pathogens, most notably Candida albicans and Cryptococcus neoformans, to elucidate compound mechanism of action directly in the pathogen of interest. Collectively, the suite of chemical genetic assays that have been developed in multiple fungal species enables the identification of candidate drug target genes, as well as genes involved in buffering drug target pathways, and genes involved in general cellular responses to small molecules. In this review, we examine current yeast chemical genomic assays and highlight how such resources provide powerful tools that can be utilized to bolster the antifungal pipeline.
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Affiliation(s)
- Alice Xue
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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Abstract
The ability for cells to maintain homeostasis in the presence of extracellular stress is essential for their survival. Stress adaptations are especially important for microbial pathogens to respond to rapidly changing conditions, such as those encountered during the transition from the environment to the infected host. Many fungal pathogens have acquired the ability to quickly adapt to changes in extracellular pH to promote their survival in the various microenvironments encountered during a host infection. For example, the fungus-specific Rim/Pal alkaline response pathway has been well characterized in many fungal pathogens, including Cryptococcus neoformans However, alternative mechanisms for sensing and responding to host pH have yet to be extensively studied. Recent observations from a genetic screen suggest that the C. neoformans sterol homeostasis pathway is required for growth at elevated pH. This work explores interactions among mechanisms of membrane homeostasis, alkaline pH tolerance, and Rim pathway activation. We find that the sterol homeostasis pathway is necessary for growth in an alkaline environment and that an elevated pH is sufficient to induce Sre1 activation. This pH-mediated activation of the Sre1 transcription factor is linked to the biosynthesis of ergosterol but is not dependent on Rim pathway signaling, suggesting that these two pathways are responding to alkaline pH independently. Furthermore, we discover that C. neoformans is more susceptible to membrane-targeting antifungals under alkaline conditions, highlighting the impact of microenvironmental pH on the treatment of invasive fungal infections. Together, these findings further connect membrane integrity and composition with the fungal pH response and pathogenesis.IMPORTANCE The work described here further elucidates how microorganisms sense and adapt to changes in their environment to establish infections in the human host. Specifically, we uncover a novel mechanism by which an opportunistic human fungal pathogen, Cryptococcus neoformans, responds to increases in extracellular pH in order to survive and thrive within the relatively alkaline environment of the human lung. This mechanism, which is intimately linked with fungal membrane sterol homeostasis, is independent of the previously well-studied alkaline response Rim pathway. Furthermore, this ergosterol-dependent alkaline pH response is present in Candida albicans, indicating that this mechanism spans diverse fungal species. These results are also relevant for novel antimicrobial drug development as we show that currently used ergosterol-targeting antifungals are more active in alkaline environments.
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36
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Deaguero IG, Huda MN, Rodriguez V, Zicari J, Al-Hilal TA, Badruddoza AZM, Nurunnabi M. Nano-Vesicle Based Anti-Fungal Formulation Shows Higher Stability, Skin Diffusion, Biosafety and Anti-Fungal Efficacy In Vitro. Pharmaceutics 2020; 12:pharmaceutics12060516. [PMID: 32517047 PMCID: PMC7355414 DOI: 10.3390/pharmaceutics12060516] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 01/12/2023] Open
Abstract
Opportunistic fungal infections are responsible for over 1.5 million deaths per year. This has created a need for highly effective antifungal medication to be as potent as possible. In this study, we improved the efficacy of a common over the counter (OTC) antifungal skin medication, miconazole, by encapsulating nano-molecules of the drug in cholesterol/sodium oleate nano-vesicles. These nano-vesicles were characterized to optimize their size, zeta potential, polydispersity index and encapsulation efficiency. Furthermore, these nano-vesicles were compared to a conventional miconazole-based commercially available cream to determine potential improvements via permeation through the stratum corneum, cytotoxicity, and antifungal capabilities. Our results found that the vesicle size was within the nano range (~300 nm), with moderate polydispersity and stability. When compared with the commercially available cream, Actavis, as well as free miconazole, the miconazole nano-vesicle formulation displayed enhanced fungal inhibition by a factor of three or more when compared to free miconazole. Furthermore, with smaller nanoparticle (NP) sizes, higher percentages of miconazole may be delivered, further enhancing the efficacy of miconazole's antifungal capability. Cytotoxicity studies conducted with human dermal fibroblast cells confirm its biosafety and biocompatibility, as cell survival rate was observed to be twofold higher in nano-vesicle formulation than free miconazole. This formulation has the potential to treat fungal infections through increasing the retention time in the skin, improving the treatment approach, and by enhancing the efficacy via the use of nano-vesicles.
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Affiliation(s)
- Isaac G. Deaguero
- Biomedical Engineering Program, School of Engineering, University of Texas at El Paso, TX 79902, USA; (I.G.D.); (M.N.H.); (V.R.); (J.Z.); (T.A.A.-H.)
| | - Md Nurul Huda
- Biomedical Engineering Program, School of Engineering, University of Texas at El Paso, TX 79902, USA; (I.G.D.); (M.N.H.); (V.R.); (J.Z.); (T.A.A.-H.)
| | - Victor Rodriguez
- Biomedical Engineering Program, School of Engineering, University of Texas at El Paso, TX 79902, USA; (I.G.D.); (M.N.H.); (V.R.); (J.Z.); (T.A.A.-H.)
| | - Jade Zicari
- Biomedical Engineering Program, School of Engineering, University of Texas at El Paso, TX 79902, USA; (I.G.D.); (M.N.H.); (V.R.); (J.Z.); (T.A.A.-H.)
| | - Taslim A. Al-Hilal
- Biomedical Engineering Program, School of Engineering, University of Texas at El Paso, TX 79902, USA; (I.G.D.); (M.N.H.); (V.R.); (J.Z.); (T.A.A.-H.)
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Texas at El Paso, TX 79902, USA
| | - Abu Zayed Md Badruddoza
- Department of Chemical and Life Sciences Engineering, Virginia Commonwealth University, Richmond, VA 23284, USA
- Correspondence: (A.Z.M.B.); (M.N.); Tel.: +1-915-747-8335 (M.N.)
| | - Md Nurunnabi
- Biomedical Engineering Program, School of Engineering, University of Texas at El Paso, TX 79902, USA; (I.G.D.); (M.N.H.); (V.R.); (J.Z.); (T.A.A.-H.)
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Texas at El Paso, TX 79902, USA
- Border Biomedical Research Center, University of Texas at El Paso, TX 79902, USA
- Department of Environmental Science and Engineering, University of Texas at El Paso, TX 79902, USA
- Correspondence: (A.Z.M.B.); (M.N.); Tel.: +1-915-747-8335 (M.N.)
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37
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Catania S, Dumesic PA, Pimentel H, Nasif A, Stoddard CI, Burke JE, Diedrich JK, Cook S, Shea T, Geinger E, Lintner R, Yates JR, Hajkova P, Narlikar GJ, Cuomo CA, Pritchard JK, Madhani HD. Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase. Cell 2020; 180:263-277.e20. [PMID: 31955845 PMCID: PMC7197499 DOI: 10.1016/j.cell.2019.12.012] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/09/2019] [Accepted: 12/10/2019] [Indexed: 12/18/2022]
Abstract
Cytosine methylation of DNA is a widespread modification of DNA that plays numerous critical roles. In the yeast Cryptococcus neoformans, CG methylation occurs in transposon-rich repeats and requires the DNA methyltransferase Dnmt5. We show that Dnmt5 displays exquisite maintenance-type specificity in vitro and in vivo and utilizes similar in vivo cofactors as the metazoan maintenance methylase Dnmt1. Remarkably, phylogenetic and functional analysis revealed that the ancestral species lost the gene for a de novo methylase, DnmtX, between 50-150 mya. We examined how methylation has persisted since the ancient loss of DnmtX. Experimental and comparative studies reveal efficient replication of methylation patterns in C. neoformans, rare stochastic methylation loss and gain events, and the action of natural selection. We propose that an epigenome has been propagated for >50 million years through a process analogous to Darwinian evolution of the genome.
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Affiliation(s)
- Sandra Catania
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Phillip A Dumesic
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Harold Pimentel
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Ammar Nasif
- MRC London Institute of Medical Sciences (LMS), Reprogramming and Chromatin Group, Du Cane Road, W12 0NN London, UK; Institute of Clinical Sciences, Imperial College Faculty of Medicine, Du Cane Rd, W12 0NN London, UK
| | - Caitlin I Stoddard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jordan E Burke
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sophie Cook
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Terrance Shea
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Elizabeth Geinger
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Robert Lintner
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Petra Hajkova
- MRC London Institute of Medical Sciences (LMS), Reprogramming and Chromatin Group, Du Cane Road, W12 0NN London, UK; Institute of Clinical Sciences, Imperial College Faculty of Medicine, Du Cane Rd, W12 0NN London, UK
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jonathan K Pritchard
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA.
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Abstract
To survive under unpredictable conditions, all organisms must adapt to stressors by regulating adaptive cellular responses. Arrestin proteins are conserved regulators of adaptive cellular responses in eukaryotes. Studies that have been limited to mammals and model fungi have demonstrated that the disruption of arrestin-regulated pathways is detrimental for viability. The human fungal pathogen Cryptococcus neoformans causes more than 180,000 infection-related deaths annually, especially among immunocompromised patients. In addition to being genetically tractable, C. neoformans has a small arrestin family of four members, lending itself to a comprehensive characterization of its arrestin family. This study serves as a functional analysis of arrestins in a pathogen, particularly in the context of fungal fitness and virulence. We investigate the functions of one arrestin protein, Ali1, and define its novel contributions to cytokinesis. We additionally explore the virulence contributions of the C. neoformans arrestin family and find that they contribute to disease establishment and progression. Arrestins, a structurally specialized and functionally diverse group of proteins, are central regulators of adaptive cellular responses in eukaryotes. Previous studies on fungal arrestins have demonstrated their capacity to modulate diverse cellular processes through their adaptor functions, facilitating the localization and function of other proteins. However, the mechanisms by which arrestin-regulated processes are involved in fungal virulence remain unexplored. We have identified a small family of four arrestins, Ali1, Ali2, Ali3, and Ali4, in the human fungal pathogen Cryptococcus neoformans. Using complementary microscopy, proteomic, and reverse genetics techniques, we have defined a role for Ali1 as a novel contributor to cytokinesis, a fundamental cell cycle-associated process. We observed that Ali1 strongly interacts with proteins involved in lipid synthesis, and that ali1Δ mutant phenotypes are rescued by supplementation with lipid precursors that are used to build cellular membranes. From these data, we hypothesize that Ali1 contributes to cytokinesis by serving as an adaptor protein, facilitating the localization of enzymes that modify the plasma membrane during cell division, specifically the fatty acid synthases Fas1 and Fas2. Finally, we assessed the contributions of the C. neoformans arrestin family to virulence to better understand the mechanisms by which arrestin-regulated adaptive cellular responses influence fungal infection. We observed that the C. neoformans arrestin family contributes to virulence, and that the individual arrestin proteins likely fulfill distinct functions that are important for disease progression.
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Pianalto KM, Billmyre RB, Telzrow CL, Alspaugh JA. Roles for Stress Response and Cell Wall Biosynthesis Pathways in Caspofungin Tolerance in Cryptococcus neoformans. Genetics 2019; 213:213-227. [PMID: 31266771 PMCID: PMC6727808 DOI: 10.1534/genetics.119.302290] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 06/24/2019] [Indexed: 12/14/2022] Open
Abstract
Limited antifungal diversity and availability are growing problems for the treatment of fungal infections in the face of increasing drug resistance. The echinocandins, one of the newest classes of antifungal drugs, inhibit production of a crucial cell wall component. However, these compounds do not effectively inhibit the growth of the opportunistic fungal pathogen Cryptococcus neoformans, despite potent inhibition of the target enzyme in vitro Therefore, we performed a forward genetic screen to identify cellular processes that mediate the relative tolerance of this organism to the echinocandin drug caspofungin. Through these studies, we identified 14 genetic mutants that enhance caspofungin antifungal activity. Rather than directly affecting caspofungin antifungal activity, these mutations seem to prevent the activation of various stress-induced compensatory cellular processes. For example, the pfa4Δ mutant has defects in the palmitoylation and localization of many of its target proteins, including the Ras1 GTPase and the Chs3 chitin synthase, which are both required for caspofungin tolerance. Similarly, we have confirmed the link between caspofungin treatment and calcineurin signaling in this organism, but we suggest a deeper mechanism in which caspofungin tolerance is mediated by multiple pathways downstream of calcineurin function. In summary, we describe here several pathways in C. neoformans that contribute to the complex caspofungin tolerance phenotype in this organism.
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Affiliation(s)
- Kaila M Pianalto
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina 27710
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina 27710
| | - R Blake Billmyre
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Calla L Telzrow
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina 27710
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina 27710
| | - J Andrew Alspaugh
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina 27710
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina 27710
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40
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The regulation of the sulfur amino acid biosynthetic pathway in Cryptococcus neoformans: the relationship of Cys3, Calcineurin, and Gpp2 phosphatases. Sci Rep 2019; 9:11923. [PMID: 31417135 PMCID: PMC6695392 DOI: 10.1038/s41598-019-48433-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 08/01/2019] [Indexed: 01/02/2023] Open
Abstract
Cryptococcosis is a fungal disease caused by C. neoformans. To adapt and survive in diverse ecological niches, including the animal host, this opportunistic pathogen relies on its ability to uptake nutrients, such as carbon, nitrogen, iron, phosphate, sulfur, and amino acids. Genetic circuits play a role in the response to environmental changes, modulating gene expression and adjusting the microbial metabolism to the nutrients available for the best energy usage and survival. We studied the sulfur amino acid biosynthesis and its implications on C. neoformans biology and virulence. CNAG_04798 encodes a BZip protein and was annotated as CYS3, which has been considered an essential gene. However, we demonstrated that CYS3 is not essential, in fact, its knockout led to sulfur amino acids auxotroph. Western blots and fluorescence microscopy indicated that GFP-Cys3, which is expressed from a constitutive promoter, localizes to the nucleus in rich medium (YEPD); the addition of methionine and cysteine as sole nitrogen source (SD-N + Met/Cys) led to reduced nuclear localization and protein degradation. By proteomics, we identified and confirmed physical interaction among Gpp2, Cna1, Cnb1 and GFP-Cys3. Deletion of the calcineurin and GPP2 genes in a GFP-Cys3 background demonstrated that calcineurin is required to maintain Cys3 high protein levels in YEPD and that deletion of GPP2 causes GFP-Cys3 to persist in the presence of sulfur amino acids. Global transcriptional profile of mutant and wild type by RNAseq revealed that Cys3 controls all branches of the sulfur amino acid biosynthesis, and sulfur starvation leads to induction of several amino acid biosynthetic routes. In addition, we found that Cys3 is required for virulence in Galleria mellonella animal model.
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Gerstein AC, Jackson KM, McDonald TR, Wang Y, Lueck BD, Bohjanen S, Smith KD, Akampurira A, Meya DB, Xue C, Boulware DR, Nielsen K. Identification of Pathogen Genomic Differences That Impact Human Immune Response and Disease during Cryptococcus neoformans Infection. mBio 2019; 10:e01440-19. [PMID: 31311883 PMCID: PMC6635531 DOI: 10.1128/mbio.01440-19] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 06/10/2019] [Indexed: 12/18/2022] Open
Abstract
Patient outcomes during infection are due to a complex interplay between the quality of medical care, host immunity factors, and the infecting pathogen's characteristics. To probe the influence of pathogen genotype on human survival, immune response, and other parameters of disease, we examined Cryptococcus neoformans isolates collected during the Cryptococcal Optimal Antiretroviral Therapy (ART) Timing (COAT) Trial in Uganda. We measured human participants' survival, meningitis disease parameters, immunologic phenotypes, and pathogen in vitro growth characteristics. We compared those clinical data to whole-genome sequences from 38 C. neoformans isolates of the most frequently observed sequence type (ST), ST93, in our Ugandan participant population and to sequences from an additional 18 strains of 9 other sequence types representing the known genetic diversity within the Ugandan Cryptococcus clinical isolates. We focused our analyses on 652 polymorphisms that were variable among the ST93 genomes, were not in centromeres or extreme telomeres, and were predicted to have a fitness effect. Logistic regression and principal component analysis identified 40 candidate Cryptococcus genes and 3 hypothetical RNAs associated with human survival, immunologic response, or clinical parameters. We infected mice with 17 available KN99α gene deletion strains for these candidate genes and found that 35% (6/17) directly influenced murine survival. Four of the six gene deletions that impacted murine survival were novel. Such bedside-to-bench translational research identifies important candidate genes for future studies on virulence-associated traits in human Cryptococcus infections.IMPORTANCE Even with the best available care, mortality rates in cryptococcal meningitis range from 20% to 60%. Disease is often due to infection by the fungus Cryptococcus neoformans and involves a complex interaction between the human host and the fungal pathogen. Although previous studies have suggested genetic differences in the pathogen impact human disease, it has proven quite difficult to identify the specific C. neoformans genes that impact the outcome of the human infection. Here, we take advantage of a Ugandan patient cohort infected with closely related C. neoformans strains to examine the role of pathogen genetic variants on several human disease characteristics. Using a pathogen whole-genome sequencing approach, we showed that 40 C. neoformans genes are associated with human disease. Surprisingly, many of these genes are specific to Cryptococcus and have unknown functions. We also show deletion of some of these genes alters disease in a mouse model of infection, confirming their role in disease. These findings are particularly important because they are the first to identify C. neoformans genes associated with human cryptococcal meningitis and lay the foundation for future studies that may lead to new treatment strategies aimed at reducing patient mortality.
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Affiliation(s)
- Aleeza C Gerstein
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Katrina M Jackson
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Tami R McDonald
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Yina Wang
- Public Health Research Institute, Rutgers University, Newark, New Jersey, USA
| | - Benjamin D Lueck
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Sara Bohjanen
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kyle D Smith
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andrew Akampurira
- Infectious Diseases Institute and School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - David B Meya
- Infectious Diseases Institute and School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Chaoyang Xue
- Public Health Research Institute, Rutgers University, Newark, New Jersey, USA
| | - David R Boulware
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kirsten Nielsen
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
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A Non-Dicer RNase III and Four Other Novel Factors Required for RNAi-Mediated Transposon Suppression in the Human Pathogenic Yeast Cryptococcus neoformans. G3-GENES GENOMES GENETICS 2019; 9:2235-2244. [PMID: 31092606 PMCID: PMC6643885 DOI: 10.1534/g3.119.400330] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The human pathogenic yeast Cryptococcus neoformans silences transposable elements using endo-siRNAs and an Argonaute, Ago1. Endo-siRNAs production requires the RNA-dependent RNA polymerase, Rdp1, and two partially redundant Dicer enzymes, Dcr1 and Dcr2, but is independent of histone H3 lysine 9 methylation. We describe here an insertional mutagenesis screen for factors required to suppress the mobilization of the C. neoformans HARBINGER family DNA transposon HAR1. Validation experiments uncovered five novel genes (RDE1-5) required for HAR1 suppression and global production of suppressive endo-siRNAs. The RDE genes do not impact transcript levels, suggesting the endo-siRNAs do not act by impacting target transcript synthesis or turnover. RDE3 encodes a non-Dicer RNase III related to S. cerevisiaeRnt1, RDE4 encodes a predicted terminal nucleotidyltransferase, while RDE5 has no strongly predicted encoded domains. Affinity purification-mass spectrometry studies suggest that Rde3 and Rde5 are physically associated. RDE1 encodes a G-patch protein homologous to the S. cerevisiaeSqs1/Pfa1, a nucleolar protein that directly activates the essential helicase Prp43 during rRNA biogenesis. Rde1 copurifies Rde2, another novel protein obtained in the screen, as well as Ago1, a homolog of Prp43, and numerous predicted nucleolar proteins. We also describe the isolation of conditional alleles of PRP43, which are defective in RNAi. This work reveals unanticipated requirements for a non-Dicer RNase III and presumptive nucleolar factors for endo-siRNA biogenesis and transposon mobilization suppression in C. neoformans.
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Do E, Lee HG, Park M, Cho YJ, Kim DH, Park SH, Eun D, Park T, An S, Jung WH. Antifungal Mechanism of Action of Lauryl Betaine Against Skin-Associated Fungus Malassezia restricta. MYCOBIOLOGY 2019; 47:242-249. [PMID: 31448144 PMCID: PMC6691833 DOI: 10.1080/12298093.2019.1625175] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/21/2019] [Accepted: 05/24/2019] [Indexed: 06/10/2023]
Abstract
Betaine derivatives are considered major ingredients of shampoos and are commonly used as antistatic and viscosity-increasing agents. Several studies have also suggested that betaine derivatives can be used as antimicrobial agents. However, the antifungal activity and mechanism of action of betaine derivatives have not yet been fully understood. In this study, we investigated the antifungal activity of six betaine derivatives against Malassezia restricta, which is the most frequently isolated fungus from the human skin and is implicated in the development of dandruff. We found that, among the six betaine derivatives, lauryl betaine showed the most potent antifungal activity. The mechanism of action of lauryl betaine was studied mainly using another phylogenetically close model fungal organism, Cryptococcus neoformans, because of a lack of available genetic manipulation and functional genomics tools for M. restricta. Our genome-wide reverse genetic screening method using the C. neoformans gene deletion mutant library showed that the mutants with mutations in genes for cell membrane synthesis and integrity, particularly ergosterol synthesis, are highly sensitive to lauryl betaine. Furthermore, transcriptome changes in both C. neoformans and M. restricta cells grown in the presence of lauryl betaine were analyzed and the results indicated that the compound mainly affected cell membrane synthesis, particularly ergosterol synthesis. Overall, our data demonstrated that lauryl betaine influences ergosterol synthesis in C. neoformans and that the compound exerts a similar mechanism of action on M. restricta.
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Affiliation(s)
- Eunsoo Do
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Korea
| | - Hyun Gee Lee
- Safety Research Institute, Amorepacific R&D Center, Yongin, Korea
| | - Minji Park
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Korea
| | | | - Dong Hyeun Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Korea
| | - Se-Ho Park
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Korea
| | - Daekyung Eun
- Safety Research Institute, Amorepacific R&D Center, Yongin, Korea
| | - Taehun Park
- Safety Research Institute, Amorepacific R&D Center, Yongin, Korea
| | - Susun An
- Safety Research Institute, Amorepacific R&D Center, Yongin, Korea
| | - Won Hee Jung
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Korea
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Burke JE, Longhurst AD, Merkurjev D, Sales-Lee J, Rao B, Moresco JJ, Yates JR, Li JJ, Madhani HD. Spliceosome Profiling Visualizes Operations of a Dynamic RNP at Nucleotide Resolution. Cell 2019; 173:1014-1030.e17. [PMID: 29727661 DOI: 10.1016/j.cell.2018.03.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/19/2018] [Accepted: 03/07/2018] [Indexed: 11/28/2022]
Abstract
Tools to understand how the spliceosome functions in vivo have lagged behind advances in the structural biology of the spliceosome. Here, methods are described to globally profile spliceosome-bound pre-mRNA, intermediates, and spliced mRNA at nucleotide resolution. These tools are applied to three yeast species that span 600 million years of evolution. The sensitivity of the approach enables the detection of canonical and non-canonical events, including interrupted, recursive, and nested splicing. This application of statistical modeling uncovers independent roles for the size and position of the intron and the number of introns per transcript in substrate progression through the two catalytic stages. These include species-specific inputs suggestive of spliceosome-transcriptome coevolution. Further investigations reveal the ATP-dependent discard of numerous endogenous substrates after spliceosome assembly in vivo and connect this discard to intron retention, a form of splicing regulation. Spliceosome profiling is a quantitative, generalizable global technology used to investigate an RNP central to eukaryotic gene expression.
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Affiliation(s)
- Jordan E Burke
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Adam D Longhurst
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daria Merkurjev
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jade Sales-Lee
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Beiduo Rao
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James J Moresco
- Department of Molecular Medicine, the Scripps Research Institute, La Jolla, CA, USA
| | - John R Yates
- Department of Molecular Medicine, the Scripps Research Institute, La Jolla, CA, USA
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA.
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45
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Brown HE, Ost KS, Esher SK, Pianalto KM, Saelens JW, Guan Z, Andrew Alspaugh J. Identifying a novel connection between the fungal plasma membrane and pH-sensing. Mol Microbiol 2018; 109:474-493. [PMID: 29885030 PMCID: PMC6173979 DOI: 10.1111/mmi.13998] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2018] [Indexed: 01/11/2023]
Abstract
The mechanisms by which micro-organisms sense and internalize extracellular pH signals are not completely understood. One example of a known external pH-sensing process is the fungal-specific Rim/Pal signal transduction pathway. Fungi, such as the opportunistic pathogen Cryptococcus neoformans, use Rim signaling to sense and respond to changes in environmental pH. Mutations in this pathway result in strains that are attenuated for survival at alkaline pH, and often for survival within the host. Here, we used an insertional mutagenesis screen to identify novel genes required for C. neoformans growth at host pH. We discovered altered alkaline pH growth in several strains with specific defects in plasma membrane composition and maintenance of phospholipid assembly. Among these, loss of function of the Cdc50 lipid flippase regulatory subunit affected the temporal dynamics of Rim pathway activation. We defined distinct and overlapping cellular processes regulated by Rim101 and Cdc50 through analysis of the transcriptome in these mutant strains. We further explored how pH-induced membrane changes affect membrane-bound pH-sensing proteins, specifically the C-terminal domain of the Rra1 protein, an upstream Rim pathway activator and pH sensor. These results suggest both broadly applicable and phylum-specific molecular interactions that drive microbial environmental sensing.
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Affiliation(s)
- Hannah E Brown
- Departments of Molecular Genetics and Microbiology/Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Kyla S Ost
- Departments of Molecular Genetics and Microbiology/Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Shannon K Esher
- Departments of Molecular Genetics and Microbiology/Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Kaila M Pianalto
- Departments of Molecular Genetics and Microbiology/Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Joseph W Saelens
- Departments of Molecular Genetics and Microbiology/Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Ziqiang Guan
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - J Andrew Alspaugh
- Departments of Molecular Genetics and Microbiology/Medicine, Duke University School of Medicine, Durham, NC, USA
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46
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Unintended Side Effects of Transformation Are Very Rare in Cryptococcus neoformans. G3-GENES GENOMES GENETICS 2018; 8:815-822. [PMID: 29305388 PMCID: PMC5844303 DOI: 10.1534/g3.117.300357] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Received wisdom in the field of fungal biology holds that the process of editing a genome by transformation and homologous recombination is inherently mutagenic. However, that belief is based on circumstantial evidence. We provide the first direct measurement of the effects of transformation on a fungal genome by sequencing the genomes of 29 transformants and 30 untransformed controls with high coverage. Contrary to the received wisdom, our results show that transformation of DNA segments flanked by long targeting sequences, followed by homologous recombination and selection for a drug marker, is extremely safe. If a transformation deletes a gene, that may create selective pressure for a few compensatory mutations, but even when we deleted a gene, we found fewer than two point mutations per deletion strain, on average. We also tested these strains for changes in gene expression and found only a few genes that were consistently differentially expressed between the wild type and strains modified by genomic insertion of a drug resistance marker. As part of our report, we provide the assembled genome sequence of the commonly used laboratory strain Cryptococcus neoformans var. grubii strain KN99α.
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47
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Integrated Activity and Genetic Profiling of Secreted Peptidases in Cryptococcus neoformans Reveals an Aspartyl Peptidase Required for Low pH Survival and Virulence. PLoS Pathog 2016; 12:e1006051. [PMID: 27977806 PMCID: PMC5158083 DOI: 10.1371/journal.ppat.1006051] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 11/09/2016] [Indexed: 12/29/2022] Open
Abstract
The opportunistic fungal pathogen Cryptococcus neoformans is a major cause of mortality in immunocompromised individuals, resulting in more than 600,000 deaths per year. Many human fungal pathogens secrete peptidases that influence virulence, but in most cases the substrate specificity and regulation of these enzymes remains poorly understood. The paucity of such information is a roadblock to our understanding of the biological functions of peptidases and whether or not these enzymes are viable therapeutic targets. We report here an unbiased analysis of secreted peptidase activity and specificity in C. neoformans using a mass spectrometry-based substrate profiling strategy and subsequent functional investigations. Our initial studies revealed that global peptidase activity and specificity are dramatically altered by environmental conditions. To uncover the substrate preferences of individual enzymes and interrogate their biological functions, we constructed and profiled a ten-member gene deletion collection of candidate secreted peptidases. Through this deletion approach, we characterized the substrate specificity of three peptidases within the context of the C. neoformans secretome, including an enzyme known to be important for fungal entry into the brain. We selected a previously uncharacterized peptidase, which we term Major aspartyl peptidase 1 (May1), for detailed study due to its substantial contribution to extracellular proteolytic activity. Based on the preference of May1 for proteolysis between hydrophobic amino acids, we screened a focused library of aspartyl peptidase inhibitors and identified four high-affinity antagonists. Finally, we tested may1Δ strains in a mouse model of C. neoformans infection and found that strains lacking this enzyme are significantly attenuated for virulence. Our study reveals the secreted peptidase activity and specificity of an important human fungal pathogen, identifies responsible enzymes through genetic tests of their function, and demonstrates how this information can guide the development of high affinity small molecule inhibitors. Many pathogenic organisms secrete peptidases. The activity of these enzymes often contributes to virulence, making their study crucial for understanding host-pathogen biology and developing therapeutics. In this report, we employed an unbiased, activity-based profiling assay to examine the secreted peptidases of a fungal pathogen, Cryptococcus neoformans, which is responsible for 40% of AIDS-related deaths. We discovered which peptidases are secreted, identified their substrate specificity, and interrogated their biological functions. Through this analysis, we identified a principal enzyme responsible for the extracellular peptidase activity of C. neoformans, May1, and demonstrated its importance for growth in acidic environments. Characterization of its substrate preferences allowed us to identify compounds that are potent substrate-based inhibitors of May1 activity. Finally, we found that the presence of this enzyme promotes virulence in a mouse model of infection. Our comprehensive study reveals the expression, regulation and function of C. neoformans secreted peptidases, including evidence for the role of a novel aspartyl peptidase in virulence.
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48
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Intracellular Action of a Secreted Peptide Required for Fungal Virulence. Cell Host Microbe 2016; 19:849-64. [PMID: 27212659 DOI: 10.1016/j.chom.2016.05.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 12/24/2015] [Accepted: 04/28/2016] [Indexed: 01/02/2023]
Abstract
Quorum sensing (QS) is a bacterial communication mechanism in which secreted signaling molecules impact population function and gene expression. QS-like phenomena have been reported in eukaryotes with largely unknown contributing molecules, functions, and mechanisms. We identify Qsp1, a secreted peptide, as a central signaling molecule that regulates virulence in the fungal pathogen Cryptococcus neoformans. QSP1 is a direct target of three transcription factors required for virulence, and qsp1Δ mutants exhibit attenuated infection, slowed tissue accumulation, and greater control by primary macrophages. Qsp1 mediates autoregulatory signaling that modulates secreted protease activity and promotes cell wall function at high cell densities. Peptide production requires release from a secreted precursor, proQsp1, by a cell-associated protease, Pqp1. Qsp1 sensing requires an oligopeptide transporter, Opt1, and remarkably, cytoplasmic expression of mature Qsp1 complements multiple phenotypes of qsp1Δ. Thus, C. neoformans produces an autoregulatory peptide that matures extracellularly but functions intracellularly to regulate virulence.
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49
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Reinke AW, Troemel ER. The Development of Genetic Modification Techniques in Intracellular Parasites and Potential Applications to Microsporidia. PLoS Pathog 2015; 11:e1005283. [PMID: 26720003 PMCID: PMC4699923 DOI: 10.1371/journal.ppat.1005283] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Aaron W. Reinke
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California-San Diego, San Diego, California, United States of America
| | - Emily R. Troemel
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California-San Diego, San Diego, California, United States of America
- * E-mail:
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50
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Rivera V, Gaviria M, Muñoz-Cadavid C, Cano L, Naranjo T. Validation and clinical application of a molecular method for the identification of Cryptococcus neoformans/Cryptococcus gattii complex DNA in human clinical specimens. Braz J Infect Dis 2015; 19:563-70. [PMID: 26365230 PMCID: PMC9425379 DOI: 10.1016/j.bjid.2015.07.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 07/07/2015] [Accepted: 07/07/2015] [Indexed: 12/26/2022] Open
Abstract
The diagnosis of cryptococcosis is usually performed based on cultures of tissue or body fluids and isolation of the fungus, but this method may require several days. Direct microscopic examination, although rapid, is relatively insensitive. Biochemical and immunodiagnostic rapid tests are also used. However, all of these methods have limitations that may hinder final diagnosis. The increasing incidence of fungal infections has focused attention on tools for rapid and accurate diagnosis using molecular biological techniques. Currently, PCR-based methods, particularly nested, multiplex and real-time PCR, provide both high sensitivity and specificity. In the present study, we evaluated a nested PCR targeting the gene encoding the ITS-1 and ITS-2 regions of rDNA in samples from a cohort of patients diagnosed with cryptococcosis. The results showed that in our hands, this Cryptococcus nested PCR assay has 100% specificity and 100% sensitivity and was able to detect until 2 femtograms of Cryptococcus DNA.
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