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Navarro-Mendoza MI, Pérez-Arques C, Parker J, Xu Z, Kelly S, Heitman J. Alternative ergosterol biosynthetic pathways confer antifungal drug resistance in the human pathogens within the Mucor species complex. mBio 2024; 15:e0166124. [PMID: 38980037 PMCID: PMC11323496 DOI: 10.1128/mbio.01661-24] [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: 06/03/2024] [Accepted: 06/18/2024] [Indexed: 07/10/2024] Open
Abstract
Mucormycoses are emerging fungal infections caused by a variety of heterogeneous species within the Mucorales order. Among the Mucor species complex, Mucor circinelloides is the most frequently isolated pathogen in mucormycosis patients and despite its clinical significance, there is an absence of established genome manipulation techniques to conduct molecular pathogenesis studies. In this study, we generated a spontaneous uracil auxotrophic strain and developed a genetic transformation procedure to analyze molecular mechanisms conferring antifungal drug resistance. With this new model, phenotypic analyses of gene deletion mutants were conducted to define Erg3 and Erg6a as key biosynthetic enzymes in the M. circinelloides ergosterol pathway. Erg3 is a C-5 sterol desaturase involved in growth, sporulation, virulence, and azole susceptibility. In other fungal pathogens, erg3 mutations confer azole resistance because Erg3 catalyzes the production of a toxic diol upon azole exposure. Surprisingly, M. circinelloides produces only trace amounts of this toxic diol and yet, it is still susceptible to posaconazole and isavuconazole due to alterations in membrane sterol composition. These alterations are severely aggravated by erg3Δ mutations, resulting in ergosterol depletion and, consequently, hypersusceptibility to azoles. We also identified Erg6a as the main C-24 sterol methyltransferase, whose activity may be partially rescued by the paralogs Erg6b and Erg6c. Loss of Erg6a function diverts ergosterol synthesis to the production of cholesta-type sterols, resulting in resistance to amphotericin B. Our findings suggest that mutations or epimutations causing loss of Erg6 function may arise during human infections, resulting in antifungal drug resistance to first-line treatments against mucormycosis. IMPORTANCE The Mucor species complex comprises a variety of opportunistic pathogens known to cause mucormycosis, a potentially lethal fungal infection with limited therapeutic options. The only effective first-line treatments against mucormycosis consist of liposomal formulations of amphotericin B and the triazoles posaconazole and isavuconazole, all of which target components within the ergosterol biosynthetic pathway. This study uncovered M. circinelloides Erg3 and Erg6a as key enzymes to produce ergosterol, a vital constituent of fungal membranes. Absence of any of those enzymes leads to decreased ergosterol and consequently, resistance to ergosterol-binding polyenes such as amphotericin B. Particularly, losing Erg6a function poses a higher threat as the ergosterol pathway is channeled into alternative sterols similar to cholesterol, which maintain membrane permeability. As a result, erg6a mutants survive within the host and disseminate the infection, indicating that Erg6a deficiency may arise during human infections and confer resistance to the most effective treatment against mucormycoses.
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Affiliation(s)
- María Isabel Navarro-Mendoza
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Carlos Pérez-Arques
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Josie Parker
- Molecular Biosciences Division, School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Ziyan Xu
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Steven Kelly
- Institute of Life Science, Swansea University Medical School, Swansea, Wales, United Kingdom
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
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2
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Billmyre RB, Craig CJ, Lyon J, Reichardt C, Eickbush MT, Zanders SE. Saturation transposon mutagenesis enables genome-wide identification of genes required for growth and fluconazole resistance in the human fungal pathogen Cryptococcus neoformans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.28.605507. [PMID: 39131341 PMCID: PMC11312461 DOI: 10.1101/2024.07.28.605507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Fungi can cause devastating invasive infections, typically in immunocompromised patients. Treatment is complicated both by the evolutionary similarity between humans and fungi and by the frequent emergence of drug resistance. Studies in fungal pathogens have long been slowed by a lack of high-throughput tools and community resources that are common in model organisms. Here we demonstrate a high-throughput transposon mutagenesis and sequencing (TN-seq) system in Cryptococcus neoformans that enables genome-wide determination of gene essentiality. We employed a random forest machine learning approach to classify the Cryptococcus neoformans genome as essential or nonessential, predicting 1,465 essential genes, including 302 that lack human orthologs. These genes are ideal targets for new antifungal drug development. TN-seq also enables genome-wide measurement of the fitness contribution of genes to phenotypes of interest. As proof of principle, we demonstrate the genome-wide contribution of genes to growth in fluconazole, a clinically used antifungal. We show a novel role for the well-studied RIM101 pathway in fluconazole susceptibility. We also show that 5' insertions of transposons can drive sensitization of essential genes, enabling screenlike assays of both essential and nonessential components of the genome. Using this approach, we demonstrate a role for mitochondrial function in fluconazole sensitivity, such that tuning down many essential mitochondrial genes via 5' insertions can drive resistance to fluconazole. Our assay system will be valuable in future studies of C. neoformans, particularly in examining the consequences of genotypic diversity.
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Affiliation(s)
- R. Blake Billmyre
- Department of Pharmaceutical and Biological Sciences, College of Pharmacy, University of Georgia, GA, United States
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, GA, United States
- Department of Microbiology, Franklin College of Arts and Sciences, University of Georgia, GA, United States
- Department of Genetics, Franklin College of Arts and Sciences, University of Georgia, GA, United States
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | - Joshua Lyon
- Department of Pharmaceutical and Biological Sciences, College of Pharmacy, University of Georgia, GA, United States
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, GA, United States
| | - Claire Reichardt
- Department of Pharmaceutical and Biological Sciences, College of Pharmacy, University of Georgia, GA, United States
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, GA, United States
- Department of Microbiology, Franklin College of Arts and Sciences, University of Georgia, GA, United States
| | | | - Sarah E. Zanders
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Cell Biology and Physiology, University of Kansas Medical Center, KS, United States
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3
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Shi R, Lin X. Illuminating the Cryptococcus neoformans species complex: unveiling intracellular structures with fluorescent-protein-based markers. Genetics 2024; 227:iyae059. [PMID: 38752295 PMCID: PMC11228865 DOI: 10.1093/genetics/iyae059] [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: 01/22/2024] [Accepted: 04/06/2024] [Indexed: 07/09/2024] Open
Abstract
Cryptococcus neoformans is a fungal pathogen of the top critical priority recognized by the World Health Organization. This clinically important fungus also serves as a eukaryotic model organism. A variety of resources have been generated to facilitate investigation of the C. neoformans species complex, including congenic pairs, well-annotated genomes, genetic editing tools, and gene deletion sets. Here, we generated a set of strains with all major organelles fluorescently marked. We tested short organelle-specific targeting sequences and successfully labeled the following organelles by fusing the targeting sequences with a fluorescence protein: the plasma membrane, the nucleus, the peroxisome, and the mitochondrion. We used native cryptococcal Golgi and late endosomal proteins fused with a fluorescent protein to label these two organelles. These fluorescence markers were verified via colocalization using organelle-specific dyes. All the constructs for the fluorescent protein tags were integrated in an intergenic safe haven region. These organelle-marked strains were examined for growth and various phenotypes. We demonstrated that these tagged strains could be employed to track cryptococcal interaction with the host in phagocytosis assays. These strains also allowed us to discover remarkable differences in the dynamics of proteins targeted to different organelles during sexual reproduction. Additionally, we revealed that "dormant" spores transcribed and synthesized their own proteins and trafficked the proteins to the appropriate subcellular compartments, demonstrating that spores are metabolically active. We anticipate that these newly generated fluorescent markers will greatly facilitate further investigation of cryptococcal biology and pathogenesis.
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Affiliation(s)
- Ran Shi
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Xiaorong Lin
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
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4
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Dang TTV, Maufrais C, Colin J, Moyrand F, Mouyna I, Coppée JY, Onyishi CU, Lipecka J, Guerrera IC, May RC, Janbon G. Alternative TSS use is widespread in Cryptococcus fungi in response to environmental cues and regulated genome-wide by the transcription factor Tur1. PLoS Biol 2024; 22:e3002724. [PMID: 39052688 DOI: 10.1371/journal.pbio.3002724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/06/2024] [Accepted: 06/28/2024] [Indexed: 07/27/2024] Open
Abstract
Alternative transcription start site (TSS) usage regulation has been identified as a major means of gene expression regulation in metazoans. However, in fungi, its impact remains elusive as its study has thus far been restricted to model yeasts. Here, we first re-analyzed TSS-seq data to define genuine TSS clusters in 2 species of pathogenic Cryptococcus. We identified 2 types of TSS clusters associated with specific DNA sequence motifs. Our analysis also revealed that alternative TSS usage regulation in response to environmental cues is widespread in Cryptococcus, altering gene expression and protein targeting. Importantly, we performed a forward genetic screen to identify a unique transcription factor (TF) named Tur1, which regulates alternative TSS (altTSS) usage genome-wide when cells switch from exponential phase to stationary phase. ChiP-Seq and DamID-Seq analyses suggest that at some loci, the role of Tur1 might be direct. Tur1 has been previously shown to be essential for virulence in C. neoformans. We demonstrated here that a tur1Δ mutant strain is more sensitive to superoxide stress and phagocytosed more efficiently by macrophages than the wild-type (WT) strain.
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Affiliation(s)
- Thi Tuong Vi Dang
- Université Paris Cité, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Paris, France
| | - Corinne Maufrais
- Université Paris Cité, Institut Pasteur, HUB Bioinformatique et Biostatistique, C3BI, USR 3756 IP CNRS, Paris, France
| | - Jessie Colin
- Université Paris Cité, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Paris, France
- Ecole Pratique des Hautes Etudes, PSL Research University, Paris, France
| | - Frédérique Moyrand
- Université Paris Cité, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Paris, France
| | - Isabelle Mouyna
- Université Paris Cité, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Paris, France
| | - Jean-Yves Coppée
- Université Paris Cité, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Paris, France
| | - Chinaemerem U Onyishi
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Joanna Lipecka
- Université Paris Cité, SFR Necker INSERM US24/CNRS UAR3633, Proteomics Platform, Paris, France
| | - Ida Chiara Guerrera
- Université Paris Cité, SFR Necker INSERM US24/CNRS UAR3633, Proteomics Platform, Paris, France
| | - Robin C May
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Guilhem Janbon
- Université Paris Cité, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Paris, France
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Hughes ES, Tuck LR, He Z, Ballou ER, Wallace EWJ. A trade-off between proliferation and defense in the fungal pathogen Cryptococcus at alkaline pH is controlled by the transcription factor GAT201. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.14.543486. [PMID: 37398450 PMCID: PMC10312749 DOI: 10.1101/2023.06.14.543486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Cryptococcus is a fungal pathogen whose virulence relies on proliferation in and dissemination to host sites, and on synthesis of a defensive yet metabolically costly polysaccharide capsule. Regulatory pathways required for Cryptococcus virulence include a GATA-like transcription factor, Gat201, that regulates Cryptococcal virulence in both capsule-dependent and capsule-independent ways. Here we show that Gat201 is part of a negative regulatory pathway that limits fungal survival at alkaline pH. RNA-seq analysis found strong induction of GAT201 expression within minutes of transfer to RPMI media at alkaline pH. Microscopy, growth curves, and colony forming unit assays show that in RPMI at alkaline pH wild-type Cryptococcus neoformans yeast cells produce capsule but do not bud or maintain viability, while gat201Δ cells make buds and maintain viability, yet fail to produce capsule. GAT201 is required for transcriptional upregulation of a specific set of genes, the majority of which are direct Gat201 targets. Evolutionary analysis shows that Gat201 is in a subfamily of GATA-like transcription factors that is conserved within pathogenic fungi but absent in model yeasts. This work identifies the Gat201 pathway as controlling a trade-off between proliferation and production of defensive capsule. The assays established here will allow characterisation of the mechanisms of action of the Gat201 pathway. Together, our findings urge improved understanding of the regulation of proliferation as a driver of fungal pathogenesis.
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Affiliation(s)
- Elizabeth S Hughes
- Institute for Cell Biology, and Centre for Engineering Biology, School of Biological Sciences, The University of Edinburgh
| | - Laura R Tuck
- Institute for Cell Biology, and Centre for Engineering Biology, School of Biological Sciences, The University of Edinburgh
| | - Zhenzhen He
- Institute for Cell Biology, and Centre for Engineering Biology, School of Biological Sciences, The University of Edinburgh
| | | | - Edward W J Wallace
- Institute for Cell Biology, and Centre for Engineering Biology, School of Biological Sciences, The University of Edinburgh
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6
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Aktar K, Davies T, Leontiou I, Clark I, Spanos C, Wallace E, Tuck L, Jeyaprakash AA, Hardwick KG. Conserved signalling functions for Mps1, Mad1 and Mad2 in the Cryptococcus neoformans spindle checkpoint. PLoS Genet 2024; 20:e1011302. [PMID: 38829899 PMCID: PMC11175454 DOI: 10.1371/journal.pgen.1011302] [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: 08/10/2023] [Revised: 06/13/2024] [Accepted: 05/14/2024] [Indexed: 06/05/2024] Open
Abstract
Cryptococcus neoformans is an opportunistic, human fungal pathogen which undergoes fascinating switches in cell cycle control and ploidy when it encounters stressful environments such as the human lung. Here we carry out a mechanistic analysis of the spindle checkpoint which regulates the metaphase to anaphase transition, focusing on Mps1 kinase and the downstream checkpoint components Mad1 and Mad2. We demonstrate that Cryptococcus mad1Δ or mad2Δ strains are unable to respond to microtubule perturbations, continuing to re-bud and divide, and die as a consequence. Fluorescent tagging of Chromosome 3, using a lacO array and mNeonGreen-lacI fusion protein, demonstrates that mad mutants are unable to maintain sister-chromatid cohesion in the absence of microtubule polymers. Thus, the classic checkpoint functions of the SAC are conserved in Cryptococcus. In interphase, GFP-Mad1 is enriched at the nuclear periphery, and it is recruited to unattached kinetochores in mitosis. Purification of GFP-Mad1 followed by mass spectrometric analysis of associated proteins show that it forms a complex with Mad2 and that it interacts with other checkpoint signalling components (Bub1) and effectors (Cdc20 and APC/C sub-units) in mitosis. We also demonstrate that overexpression of Mps1 kinase is sufficient to arrest Cryptococcus cells in mitosis, and show that this arrest is dependent on both Mad1 and Mad2. We find that a C-terminal fragment of Mad1 is an effective in vitro substrate for Mps1 kinase and map several Mad1 phosphorylation sites. Some sites are highly conserved within the C-terminal Mad1 structure and we demonstrate that mutation of threonine 667 (T667A) leads to loss of checkpoint signalling and abrogation of the GAL-MPS1 arrest. Thus Mps1-dependent phosphorylation of C-terminal Mad1 residues is a critical step in Cryptococcus spindle checkpoint signalling. We conclude that CnMps1 protein kinase, Mad1 and Mad2 proteins have all conserved their important, spindle checkpoint signalling roles helping ensure high fidelity chromosome segregation.
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Affiliation(s)
- Koly Aktar
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Thomas Davies
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Ioanna Leontiou
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Ivan Clark
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Christos Spanos
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Edward Wallace
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Laura Tuck
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - A. Arockia Jeyaprakash
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Gene Center, Department of Biochemistry, Ludwig Maximilians Universitat, Munich, Germany
| | - Kevin G. Hardwick
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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7
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Coelho MA, David-Palma M, Shea T, Bowers K, McGinley-Smith S, Mohammad AW, Gnirke A, Yurkov AM, Nowrousian M, Sun S, Cuomo CA, Heitman J. Comparative genomics of the closely related fungal genera Cryptococcus and Kwoniella reveals karyotype dynamics and suggests evolutionary mechanisms of pathogenesis. PLoS Biol 2024; 22:e3002682. [PMID: 38843310 PMCID: PMC11185503 DOI: 10.1371/journal.pbio.3002682] [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: 01/13/2024] [Revised: 06/18/2024] [Accepted: 05/17/2024] [Indexed: 06/19/2024] Open
Abstract
In exploring the evolutionary trajectories of both pathogenesis and karyotype dynamics in fungi, we conducted a large-scale comparative genomic analysis spanning the Cryptococcus genus, encompassing both global human fungal pathogens and nonpathogenic species, and related species from the sister genus Kwoniella. Chromosome-level genome assemblies were generated for multiple species, covering virtually all known diversity within these genera. Although Cryptococcus and Kwoniella have comparable genome sizes (about 19.2 and 22.9 Mb) and similar gene content, hinting at preadaptive pathogenic potential, our analysis found evidence of gene gain (via horizontal gene transfer) and gene loss in pathogenic Cryptococcus species, which might represent evolutionary signatures of pathogenic development. Genome analysis also revealed a significant variation in chromosome number and structure between the 2 genera. By combining synteny analysis and experimental centromere validation, we found that most Cryptococcus species have 14 chromosomes, whereas most Kwoniella species have fewer (11, 8, 5, or even as few as 3). Reduced chromosome number in Kwoniella is associated with formation of giant chromosomes (up to 18 Mb) through repeated chromosome fusion events, each marked by a pericentric inversion and centromere loss. While similar chromosome inversion-fusion patterns were observed in all Kwoniella species with fewer than 14 chromosomes, no such pattern was detected in Cryptococcus. Instead, Cryptococcus species with less than 14 chromosomes showed reductions primarily through rearrangements associated with the loss of repeat-rich centromeres. Additionally, Cryptococcus genomes exhibited frequent interchromosomal translocations, including intercentromeric recombination facilitated by transposons shared between centromeres. Overall, our findings advance our understanding of genetic changes possibly associated with pathogenicity in Cryptococcus and provide a foundation to elucidate mechanisms of centromere loss and chromosome fusion driving distinct karyotypes in closely related fungal species, including prominent global human pathogens.
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Affiliation(s)
- Marco A. Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Márcia David-Palma
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Terrance Shea
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Katharine Bowers
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Sage McGinley-Smith
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Arman W. Mohammad
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Andrey M. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Minou Nowrousian
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität Bochum, Bochum, Germany
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Christina A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
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8
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Navarro-Mendoza MI, Pérez-Arques C, Parker J, Xu Z, Kelly S, Heitman J. Alternative ergosterol biosynthetic pathways confer antifungal drug resistance in the human pathogens within the Mucor species complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.01.569667. [PMID: 38076934 PMCID: PMC10705545 DOI: 10.1101/2023.12.01.569667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Mucormycoses are emerging fungal infections caused by a variety of heterogeneous species within the Mucorales order. Among the Mucor species complex, Mucor circinelloides is the most frequently isolated pathogen in mucormycosis patients and despite its clinical significance, there is an absence of established genome manipulation techniques to conduct molecular pathogenesis studies. In this study, we generated a spontaneous uracil auxotrophic strain and developed a genetic transformation procedure to analyze molecular mechanisms conferring antifungal drug resistance. With this new model, phenotypic analyses of gene deletion mutants were conducted to define Erg3 and Erg6a as key biosynthetic enzymes in the M. circinelloides ergosterol pathway. Erg3 is a C-5 sterol desaturase involved in growth, sporulation, virulence, and azole susceptibility. In other fungal pathogens, erg3 mutations confer azole resistance because Erg3 catalyzes the production of a toxic diol upon azole exposure. Surprisingly, M. circinelloides produces only trace amounts of this toxic diol and yet, it is still susceptible to posaconazole and isavuconazole due to alterations in membrane sterol composition. These alterations are severely aggravated by erg3Δ mutations, resulting in ergosterol depletion and consequently, hypersusceptibility to azoles. We also identified Erg6a as the main C-24 sterol methyltransferase, whose activity may be partially rescued by the paralogs Erg6b and Erg6c. Loss of Erg6a function diverts ergosterol synthesis to the production of cholesta-type sterols, resulting in resistance to amphotericin B. Our findings suggest that mutations or epimutations causing loss of Erg6 function may arise during human infections, resulting in antifungal drug resistance to first-line treatments against mucormycosis.
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9
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Zhu F, Zhou Z, Ma S, Xu Y, Tan C, Yang H, Zhang P, Qin R, Luo Y, Pan P, Chen J. Design of a cryptococcus neoformans vaccine by subtractive proteomics combined with immunoinformatics. Int Immunopharmacol 2024; 135:112242. [PMID: 38772296 DOI: 10.1016/j.intimp.2024.112242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/22/2024] [Accepted: 05/08/2024] [Indexed: 05/23/2024]
Abstract
The emergence of Cryptococcus neoformans has posed an undeniable burden to many regions worldwide, with its strains mainly entering the lungs through the respiratory tract and spreading throughout the body. Limitations of drug regimens, such as high costs and limited options, have directed our attention toward the promising field of vaccine development. In this study, the subtractive proteomics approach was employed to select target proteins from databases that can accurately cover serotypes A and D of the Cryptococcus neoformans. Further, two multi-epitope vaccines consisting of T and B cell epitopes were demonstrated that they have good structural stability and could bind with immune receptor to induce desired immune responses in silico. After further evaluation, these vaccines show the potential for large-scale production and applicability to the majority of the population of the world. In summary, these two vaccines have been theoretically proven to combat Cryptococcus neoformans infections, awaiting further experimental validation of their actual protective effects.
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Affiliation(s)
- Fei Zhu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China; Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China; Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China; FuRong Laboratory, Changsha 410078, Hunan, China
| | - Ziyou Zhou
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China; Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China; Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China; FuRong Laboratory, Changsha 410078, Hunan, China
| | - Shiyang Ma
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China; Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China; Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China; FuRong Laboratory, Changsha 410078, Hunan, China
| | - Yizhong Xu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China; Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China; Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China; FuRong Laboratory, Changsha 410078, Hunan, China
| | - Caixia Tan
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China; Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hang Yang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China; Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China; Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China; FuRong Laboratory, Changsha 410078, Hunan, China
| | - Peipei Zhang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China; Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China; Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China; FuRong Laboratory, Changsha 410078, Hunan, China
| | - Rongliu Qin
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China; Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China; Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China; FuRong Laboratory, Changsha 410078, Hunan, China
| | - Yuying Luo
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China; Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China; Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China; FuRong Laboratory, Changsha 410078, Hunan, China
| | - Pinhua Pan
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China; Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China; Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China; FuRong Laboratory, Changsha 410078, Hunan, China.
| | - Jie Chen
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China; Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China; Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China; FuRong Laboratory, Changsha 410078, Hunan, China.
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10
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Narayanan A, Reza MH, Sanyal K. Behind the scenes: Centromere-driven genomic innovations in fungal pathogens. PLoS Pathog 2024; 20:e1012080. [PMID: 38547101 PMCID: PMC10977804 DOI: 10.1371/journal.ppat.1012080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024] Open
Affiliation(s)
- Aswathy Narayanan
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Md. Hashim Reza
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
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11
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Hester MM, Carlson D, Lodge JK, Levitz SM, Specht CA. Immune evasion by Cryptococcus gattii in vaccinated mice coinfected with C. neoformans. Front Immunol 2024; 15:1356651. [PMID: 38469300 PMCID: PMC10925662 DOI: 10.3389/fimmu.2024.1356651] [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: 12/15/2023] [Accepted: 02/05/2024] [Indexed: 03/13/2024] Open
Abstract
Cryptococcus neoformans and C. gattii, the etiologic agents of cryptococcosis, cause over 100,000 deaths worldwide every year, yet no cryptococcal vaccine has progressed to clinical trials. In preclinical studies, mice vaccinated with an attenuated strain of C. neoformans deleted of three cryptococcal chitin deacetylases (Cn-cda1Δ2Δ3Δ) were protected against a lethal challenge with C. neoformans strain KN99. While Cn-cda1Δ2Δ3Δ extended the survival of mice infected with C. gattii strain R265 compared to unvaccinated groups, we were unable to demonstrate fungal clearance as robust as that seen following KN99 challenge. In stark contrast to vaccinated mice challenged with KN99, we also found that R265-challenged mice failed to induce the production of protection-associated cytokines and chemokines in the lungs. To investigate deficiencies in the vaccine response to R265 infection, we developed a KN99-R265 coinfection model. In unvaccinated mice, the strains behaved in a manner which mirrored single infections, wherein only KN99 disseminated to the brain and spleen. We expanded the coinfection model to Cn-cda1Δ2Δ3Δ-vaccinated mice. Fungal burden, cytokine production, and immune cell infiltration in the lungs of vaccinated, coinfected mice were indicative of immune evasion by C. gattii R265 as the presence of R265 neither compromised the immunophenotype established in response to KN99 nor inhibited clearance of KN99. Collectively, these data indicate that R265 does not dampen a protective vaccine response, but rather suggest that R265 remains largely undetected by the immune system.
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Affiliation(s)
- Maureen M. Hester
- Department of Medicine, The University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Diana Carlson
- Department of Medicine, The University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Jennifer K. Lodge
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
| | - Stuart M. Levitz
- Department of Medicine, The University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Charles A. Specht
- Department of Medicine, The University of Massachusetts Chan Medical School, Worcester, MA, United States
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12
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O'Meara MJ, Rapala JR, Nichols CB, Alexandre AC, Billmyre RB, Steenwyk JL, Alspaugh JA, O'Meara TR. CryptoCEN: A Co-Expression Network for Cryptococcus neoformans reveals novel proteins involved in DNA damage repair. PLoS Genet 2024; 20:e1011158. [PMID: 38359090 PMCID: PMC10901339 DOI: 10.1371/journal.pgen.1011158] [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: 01/05/2024] [Revised: 02/28/2024] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Elucidating gene function is a major goal in biology, especially among non-model organisms. However, doing so is complicated by the fact that molecular conservation does not always mirror functional conservation, and that complex relationships among genes are responsible for encoding pathways and higher-order biological processes. Co-expression, a promising approach for predicting gene function, relies on the general principal that genes with similar expression patterns across multiple conditions will likely be involved in the same biological process. For Cryptococcus neoformans, a prevalent human fungal pathogen greatly diverged from model yeasts, approximately 60% of the predicted genes in the genome lack functional annotations. Here, we leveraged a large amount of publicly available transcriptomic data to generate a C. neoformans Co-Expression Network (CryptoCEN), successfully recapitulating known protein networks, predicting gene function, and enabling insights into the principles influencing co-expression. With 100% predictive accuracy, we used CryptoCEN to identify 13 new DNA damage response genes, underscoring the utility of guilt-by-association for determining gene function. Overall, co-expression is a powerful tool for uncovering gene function, and decreases the experimental tests needed to identify functions for currently under-annotated genes.
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Affiliation(s)
- Matthew J O'Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jackson R Rapala
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Connie B Nichols
- Departments of Medicine and Molecular Genetics/Microbiology; and Cell Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - A Christina Alexandre
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - R Blake Billmyre
- Departments of Pharmaceutical and Biomedical Sciences/Infectious Disease, College of Pharmacy/College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Jacob L Steenwyk
- Howard Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - J Andrew Alspaugh
- Departments of Medicine and Molecular Genetics/Microbiology; and Cell Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Teresa R O'Meara
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
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13
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Conn BN, Lieberman JA, Chatman P, Cotton K, Essandoh MA, Ebqa’ai M, Nelson TL, Wozniak KL. Antifungal activity of eumelanin-inspired indoylenepheyleneethynylene against Cryptococcus neoformans. Front Microbiol 2024; 14:1339303. [PMID: 38293553 PMCID: PMC10826398 DOI: 10.3389/fmicb.2023.1339303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/19/2023] [Indexed: 02/01/2024] Open
Abstract
Cryptococcus neoformans is an opportunistic fungal pathogen that causes meningitis in >152,000 immunocompromised individuals annually, leading to 112,000 yearly deaths. The four classes of existing antifungal agents target plasma membrane sterols (ergosterol), nucleic acid synthesis, and cell wall synthesis. Existing drugs are not highly effective against Cryptococcus, and antifungal drug resistance is an increasing problem. A novel antimicrobial compound, a eumelanin-inspired indoylenepheyleneethynylene, EIPE-1, was synthesized and has antimicrobial activity against Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MSRA), but not towards Gram-negative organisms. Based on EIPE-1's antibacterial activity, we hypothesized that EIPE-1 could have antifungal activity. For these studies, we tested EIPE-1 against C. neoformans strain H99 and 6 additional cryptococcal clinical isolates. We examined antifungal activity, cytotoxicity, effects on fungal gene expression, and mechanism of action of EIPE-1. Results showed that EIPE-1 has fungicidal effects on seven cryptococcal strains with MICs ranging from 1.56 to 3.125 μg/mL depending on the strain, and it is non-toxic to mammalian cells. We conducted scanning and transmission electron microscopy on the exposed cells to examine structural changes to the organism following EIPE-1 treatment. Cells exposed displayed structural changes to their cell wall and membranes, with internal contents leaking out of the cells. To understand the effect of EIPE-1 on fungal gene expression, RNA sequencing was conducted. Results showed that EIPE-1 affects several processes involved stress response, ergosterol biosynthesis, capsule biosynthesis, and cell wall attachment and remodeling. Therefore, our studies demonstrate that EIPE-1 has antifungal activity against C. neoformans, which affects both cellular structure and gene expression of multiple fungal pathways involved in cell membrane stability and viability.
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Affiliation(s)
- Brittney N. Conn
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Jacob A. Lieberman
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Priscilla Chatman
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Kaitlyn Cotton
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Martha A. Essandoh
- Department of Chemistry, Oklahoma State University, Stillwater, OK, United States
| | - Mohammad Ebqa’ai
- Department of Chemistry, Oklahoma State University, Stillwater, OK, United States
| | - Toby L. Nelson
- Department of Chemistry, Oklahoma State University, Stillwater, OK, United States
| | - Karen L. Wozniak
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
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14
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Coelho MA, David-Palma M, Shea T, Bowers K, McGinley-Smith S, Mohammad AW, Gnirke A, Yurkov AM, Nowrousian M, Sun S, Cuomo CA, Heitman J. Comparative genomics of Cryptococcus and Kwoniella reveals pathogenesis evolution and contrasting karyotype dynamics via intercentromeric recombination or chromosome fusion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.27.573464. [PMID: 38234769 PMCID: PMC10793447 DOI: 10.1101/2023.12.27.573464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
A large-scale comparative genomic analysis was conducted for the global human fungal pathogens within the Cryptococcus genus, compared to non-pathogenic Cryptococcus species, and related species from the sister genus Kwoniella. Chromosome-level genome assemblies were generated for multiple species of both genera, resulting in a dataset encompassing virtually all of their known diversity. Although Cryptococcus and Kwoniella have comparable genome sizes (about 19.2 and 22.9 Mb) and similar gene content, hinting at pre-adaptive pathogenic potential, our analysis found evidence in pathogenic Cryptococcus species of specific examples of gene gain (via horizontal gene transfer) and gene loss, which might represent evolutionary signatures of pathogenic development. Genome analysis also revealed a significant variation in chromosome number and structure between the two genera. By combining synteny analysis and experimental centromere validation, we found that most Cryptococcus species have 14 chromosomes, whereas most Kwoniella species have fewer (11, 8, 5 or even as few as 3). Reduced chromosome number in Kwoniella is associated with formation of giant chromosomes (up to 18 Mb) through repeated chromosome fusion events, each marked by a pericentric inversion and centromere loss. While similar chromosome inversion-fusion patterns were observed in all Kwoniella species with fewer than 14 chromosomes, no such pattern was detected in Cryptococcus. Instead, Cryptococcus species with less than 14 chromosomes, underwent chromosome reductions primarily through rearrangements associated with the loss of repeat-rich centromeres. Additionally, Cryptococcus genomes exhibited frequent interchromosomal translocations, including intercentromeric recombination facilitated by transposons shared between centromeres. Taken together, our findings advance our understanding of genomic changes possibly associated with pathogenicity in Cryptococcus and provide a foundation to elucidate mechanisms of centromere loss and chromosome fusion driving distinct karyotypes in closely related fungal species, including prominent global human pathogens.
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Affiliation(s)
- Marco A. Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Márcia David-Palma
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Terrance Shea
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Katharine Bowers
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | | | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Andrey M. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Minou Nowrousian
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität Bochum, Bochum, Germany
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | | | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
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15
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Brauer VS, Querobino SM, Matos GS, Dasilva D, Del Poeta M. Vaccine Strategies for Cryptococcus neoformans. Methods Mol Biol 2024; 2775:411-422. [PMID: 38758334 DOI: 10.1007/978-1-0716-3722-7_28] [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] [Indexed: 05/18/2024]
Abstract
Cryptococcus neoformans infections are a major worldwide concern as current treatment strategies are becoming less effective in alleviating the infection. The most extreme and fatal cases are those of immunocompromised individuals. Clinical treatments for cryptococcosis are limited to a few classes of approved drugs, and due to a rise in drug resistance, these drugs are becoming less effective. Therefore, it is essential to develop innovative ways to control this infection. Vaccinations have emerged as a safe, viable, and cost-effective solution to treat a number of diseases over the years. Currently, there are no clinically available vaccines to treat cryptococcal infections, but a number of studies have shown promising results in animal models. Here, we present step-by-step experimental protocols using live-attenuated or heat-killed C. neoformans cells as a vaccination strategy in a preventive or in a therapeutic murine model of cryptococcosis.
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Affiliation(s)
| | | | - Gabriel Soares Matos
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA
| | - Deveney Dasilva
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA
| | - Maurizio Del Poeta
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA.
- Institute of Chemical Biology and Drug Discovery (ICB&DD), Stony Brook, NY, USA.
- Division of Infectious Diseases, School of Medicine, Stony Brook University, Stony Brook, NY, USA.
- Veterans Administration Medical Center, Northport, NY, USA.
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16
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Dangarembizi R, Drummond R. Immune-related neurodegeneration in the midbrain causes pulmonary dysfunction in murine cryptococcal IRIS. Trends Neurosci 2023; 46:1003-1004. [PMID: 37806831 DOI: 10.1016/j.tins.2023.09.005] [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: 09/03/2023] [Accepted: 09/22/2023] [Indexed: 10/10/2023]
Abstract
Cryptococcal immune reconstitution inflammatory syndrome (C-IRIS) is a condition that affects immunosuppressed individuals recruited to antiretroviral therapy. In a recent publication, Kawano and colleagues used a mouse model to demonstrate that pulmonary dysfunction, one of the fatal complications of C-IRIS, is caused by T cell-driven neurodegeneration in a vital medullary nucleus of the brain responsible for respiratory control.
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Affiliation(s)
- Rachael Dangarembizi
- Division of Physiological Sciences, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; Neuroscience Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; CMM AFRICA Medical Mycology Research Unit, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
| | - Rebecca Drummond
- Institute of Immunology & Immunotherapy, University of Birmingham, Birmingham, UK
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17
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Sephton-Clark P, Temfack E, Tenor JL, Toffaletti DL, Loyse A, Molloy SF, Perfect JR, Bicanic T, Harrison TS, Lortholary O, Kouanfack C, Cuomo CA. Genetic diversity and microevolution in clinical Cryptococcus isolates from Cameroon. Med Mycol 2023; 61:myad116. [PMID: 37952096 PMCID: PMC10709296 DOI: 10.1093/mmy/myad116] [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: 08/22/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023] Open
Abstract
Cryptococcal meningitis is the second most common cause of death in people living with HIV/AIDS, yet we have a limited understanding of how cryptococcal isolates change over the course of infection. Cryptococcal infections are environmentally acquired, and the genetic diversity of these infecting isolates can also be geographically linked. Here, we employ whole genome sequences for 372 clinical Cryptococcus isolates from 341 patients with HIV-associated cryptococcal meningitis obtained via a large clinical trial, across both Malawi and Cameroon, to enable population genetic comparisons of isolates between countries. We see that isolates from Cameroon are highly clonal, when compared to those from Malawi, with differential rates of disruptive variants in genes with roles in DNA binding and energy use. For a subset of patients (22) from Cameroon, we leverage longitudinal sampling, with samples taken at days 7 and 14 post-enrollment, to interrogate the genetic changes that arise over the course of infection, and the genetic diversity of isolates within patients. We see disruptive variants arising over the course of infection in several genes, including the phagocytosis-regulating transcription factor GAT204. In addition, in 13% of patients sampled longitudinally, we see evidence for mixed infections. This approach identifies geographically linked genetic variation, signatures of microevolution, and evidence for mixed infections across a clinical cohort of patients affected by cryptococcal meningitis in Central Africa.
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Affiliation(s)
- Poppy Sephton-Clark
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Elvis Temfack
- Internal Medicine Unit, Douala General Hospital, Douala, Cameroon
- Institut Pasteur, Molecular Mycology Unit, CNRS UMR 2000, Paris, France
| | - 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
| | - Angela Loyse
- Institute of Infection and Immunity, St George's University of London, London, UK
- Clinical Academic Group in Infection, St George's University Hospital, London, UK
| | - Síle F Molloy
- Institute of Infection and Immunity, St George's University of London, London, UK
| | - John R Perfect
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Tihana Bicanic
- Institute of Infection and Immunity, St George's University of London, London, UK
- Clinical Academic Group in Infection, St George's University Hospital, London, UK
| | - Thomas S Harrison
- Institute of Infection and Immunity, St George's University of London, London, UK
- MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Olivier Lortholary
- Department of Infectious Diseases and Tropical Medicine, Paris Cité University, Necker-Enfants Malades Hospital, AP-HP, IHU Imagine, Paris, France
- Mycology Department and National Reference Center for Invasive Mycoses and Antifungals, Institut Pasteur, Paris, France
| | - Charles Kouanfack
- Department of Public Health, Faculty of Medicine and Pharmaceutical Sciences, University of Dschang, Dschang, Cameroon
- Day Hospital, Hospital Central Yaoundé, Yaoundé, Cameroon
- Research Center for Emerging and Re-emerging Diseases, Cameroon Baptist Convention Health Services (CBCHS), Yaoundé, Cameroon
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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18
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Agustinho DP, Brown HL, Chen G, Gaylord EA, Geddes-McAlister J, Brent MR, Doering TL. Unbiased discovery of natural sequence variants that influence fungal virulence. Cell Host Microbe 2023; 31:1910-1920.e5. [PMID: 37898126 PMCID: PMC10842055 DOI: 10.1016/j.chom.2023.10.002] [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: 05/23/2023] [Revised: 08/18/2023] [Accepted: 10/02/2023] [Indexed: 10/30/2023]
Abstract
Isolates of Cryptococcus neoformans, a fungal pathogen that kills over 112,000 people each year, differ from a 19-Mb reference genome at a few thousand up to almost a million DNA sequence positions. We used bulked segregant analysis and association analysis, genetic methods that require no prior knowledge of sequence function, to address the key question of which naturally occurring sequence variants influence fungal virulence. We identified a region containing such variants, prioritized them, and engineered strains to test our findings in a mouse model of infection. At one locus, we identified a 4-nt variant in the PDE2 gene that occurs in common laboratory strains and severely truncates the encoded phosphodiesterase. The resulting loss of phosphodiesterase activity significantly impacts virulence. Our studies demonstrate a powerful and unbiased strategy for identifying key genomic regions in the absence of prior information and provide significant sequence and strain resources to the community.
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Affiliation(s)
- Daniel Paiva Agustinho
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Holly Leanne Brown
- Department of Computer Science & Engineering, Washington University, St. Louis, MO 63130, USA
| | - Guohua Chen
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Elizabeth Anne Gaylord
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Michael Richard Brent
- Department of Computer Science & Engineering, Washington University, St. Louis, MO 63130, USA; Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Tamara Lea Doering
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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19
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Rizzo J, Trottier A, Moyrand F, Coppée JY, Maufrais C, Zimbres ACG, Dang TTV, Alanio A, Desnos-Ollivier M, Mouyna I, Péhau-Arnaude G, Commere PH, Novault S, Ene IV, Nimrichter L, Rodrigues ML, Janbon G. Coregulation of extracellular vesicle production and fluconazole susceptibility in Cryptococcus neoformans. mBio 2023; 14:e0087023. [PMID: 37310732 PMCID: PMC10470540 DOI: 10.1128/mbio.00870-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 04/17/2023] [Indexed: 06/14/2023] Open
Abstract
Resistance to fluconazole (FLC), the most widely used antifungal drug, is typically achieved by altering the azole drug target and/or drug efflux pumps. Recent reports have suggested a link between vesicular trafficking and antifungal resistance. Here, we identified novel Cryptococcus neoformans regulators of extracellular vesicle (EV) biogenesis that impact FLC resistance. In particular, the transcription factor Hap2 does not affect the expression of the drug target or efflux pumps, yet it impacts the cellular sterol profile. Subinhibitory FLC concentrations also downregulate EV production. Moreover, in vitro spontaneous FLC-resistant colonies showed altered EV production, and the acquisition of FLC resistance was associated with decreased EV production in clinical isolates. Finally, the reversion of FLC resistance was associated with increased EV production. These data suggest a model in which fungal cells can regulate EV production in place of regulating the drug target gene expression as a first line of defense against antifungal assault in this fungal pathogen. IMPORTANCE Extracellular vesicles (EVs) are membrane-enveloped particles that are released by cells into the extracellular space. Fungal EVs can mediate community interactions and biofilm formation, but their functions remain poorly understood. Here, we report the identification of the first regulators of EV production in the major fungal pathogen Cryptococcus neoformans. Surprisingly, we uncover a novel role of EVs in modulating antifungal drug resistance. Disruption of EV production was associated with altered lipid composition and changes in fluconazole susceptibility. Spontaneous azole-resistant mutants were deficient in EV production, while loss of resistance restored initial EV production levels. These findings were recapitulated in C. neoformans clinical isolates, indicating that azole resistance and EV production are coregulated in diverse strains. Our study reveals a new mechanism of drug resistance in which cells adapt to azole stress by modulating EV production.
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Affiliation(s)
- Juliana Rizzo
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Adèle Trottier
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
| | - Frédérique Moyrand
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
| | - Jean-Yves Coppée
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
| | - Corinne Maufrais
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
- Institut Pasteur, Université Paris Cité, USR 3756 IP CNRS, HUB Bioinformatique et Biostatistique, Paris, France
| | - Ana Claudia G. Zimbres
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thi Tuong Vi Dang
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
| | - Alexandre Alanio
- Institut Pasteur, Université Paris Cité, Centre National de Référence Mycoses Invasives et Antifongiques, Groupe de recherche Mycologie Translationnelle, Département de Mycologie, Paris, France
- Laboratoire de parasitologie-mycologie, AP-HP, Hôpital Saint-Louis, Paris, France
| | - Marie Desnos-Ollivier
- Institut Pasteur, Université Paris Cité, Centre National de Référence Mycoses Invasives et Antifongiques, Groupe de recherche Mycologie Translationnelle, Département de Mycologie, Paris, France
| | - Isabelle Mouyna
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
| | - Gérard Péhau-Arnaude
- Institut Pasteur, Université Paris Cité, Plateforme de Bio-Imagerie Ultrastructurale, Paris, France
| | - Pierre-Henri Commere
- Institut Pasteur, Université Paris Cité, Cytometry and Biomarkers, Paris, France
| | - Sophie Novault
- Institut Pasteur, Université Paris Cité, Cytometry and Biomarkers, Paris, France
| | - Iuliana V. Ene
- Institut Pasteur, Université Paris Cité, Fungal Heterogeneity Group, Paris, France
| | - Leonardo Nimrichter
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcio L. Rodrigues
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Curitiba, Brazil
| | - Guilhem Janbon
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
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20
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Cissé OH, Curran S, Folco HD, Liu Y, Bishop L, Wang H, Fischer ER, Davis AS, Babb-Biernacki S, Doyle VP, Richards JK, Hassan SA, Dekker JP, Khil PP, Brenchley JM, Grewal S, Cushion M, Ma L, Kovacs JA. The Host Adapted Fungal Pathogens of Pneumocystis Genus Utilize Genic Regional Centromeres. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.12.540427. [PMID: 37425787 PMCID: PMC10327204 DOI: 10.1101/2023.05.12.540427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Centromeres are genomic regions that coordinate accurate chromosomal segregation during mitosis and meiosis. Yet, despite their essential function, centromeres evolve rapidly across eukaryotes. Centromeres are often the sites of chromosomal breaks which contribute to genome shuffling and promote speciation by inhibiting gene flow. How centromeres form in strongly host-adapted fungal pathogens has yet to be investigated. Here, we characterized the centromere structures in closely related species of mammalian-specific pathogens of the fungal phylum of Ascomycota. Methods allowing reliable continuous culture of Pneumocystis species do not currently exist, precluding genetic manipulation. CENP-A, a variant of histone H3, is the epigenetic marker that defines centromeres in most eukaryotes. Using heterologous complementation, we show that the Pneumocystis CENP-A ortholog is functionally equivalent to CENP-ACnp1 of Schizosaccharomyces pombe. Using organisms from a short-term in vitro culture or infected animal models and ChIP-seq, we identified centromeres in three Pneumocystis species that diverged ~100 million years ago. Each species has a unique short regional centromere (< 10kb) flanked by heterochromatin in 16-17 monocentric chromosomes. They span active genes and lack conserved DNA sequence motifs and repeats. CENP-C, a scaffold protein that links the inner centromere to the kinetochore appears dispensable in one species, suggesting a kinetochore rewiring. Despite the loss of DNA methyltransferases, 5-methylcytosine DNA methylation occurs in these species, though not related to centromere function. These features suggest an epigenetic specification of centromere function.
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Affiliation(s)
- Ousmane H Cissé
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Shelly Curran
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - H Diego Folco
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Yueqin Liu
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Lisa Bishop
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Honghui Wang
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Elizabeth R Fischer
- Microscopy Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - A Sally Davis
- Diagnostic Medicine/Pathobiology, Kansas State University College of Veterinary Medicine, Manhattan, USA
| | - Spenser Babb-Biernacki
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Vinson P Doyle
- Department of Plant Pathology and Crop Physiology, Lousiana State University AgCenter, Baton Rouge, Louisiana, USA
| | - Jonathan K Richards
- Department of Plant Pathology and Crop Physiology, Lousiana State University AgCenter, Baton Rouge, Louisiana, USA
| | - Sergio A Hassan
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - John P Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, National Institute of Allergy, and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Pavel P Khil
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, National Institute of Allergy, and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Jason M Brenchley
- Laboratory of Viral Diseases, National Institute of Allergy, and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Shiv Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Melanie Cushion
- Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Liang Ma
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Joseph A Kovacs
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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21
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Yadav V, Sun S, Heitman J. On the evolution of variation in sexual reproduction through the prism of eukaryotic microbes. Proc Natl Acad Sci U S A 2023; 120:e2219120120. [PMID: 36867686 PMCID: PMC10013875 DOI: 10.1073/pnas.2219120120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/23/2023] [Indexed: 03/05/2023] Open
Abstract
Almost all eukaryotes undergo sexual reproduction to generate diversity and select for fitness in their population pools. Interestingly, the systems by which sex is defined are highly diverse and can even differ between evolutionarily closely related species. While the most commonly known form of sex determination involves males and females in animals, eukaryotic microbes can have as many as thousands of different mating types for the same species. Furthermore, some species have found alternatives to sexual reproduction and prefer to grow clonally and yet undergo infrequent facultative sexual reproduction. These organisms are mainly invertebrates and microbes, but several examples are also present among vertebrates suggesting that alternative modes of sexual reproduction evolved multiple times throughout evolution. In this review, we summarize the sex-determination modes and variants of sexual reproduction found across the eukaryotic tree of life and suggest that eukaryotic microbes provide unique opportunities to study these processes in detail. We propose that understanding variations in modes of sexual reproduction can serve as a foundation to study the evolution of sex and why and how it evolved in the first place.
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Affiliation(s)
- Vikas Yadav
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC27710
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC27710
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC27710
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22
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Genetic Diversity of Human Fungal Pathogens. CURRENT CLINICAL MICROBIOLOGY REPORTS 2023. [DOI: 10.1007/s40588-023-00188-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
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23
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Immunological correlates of protection following vaccination with glucan particles containing Cryptococcus neoformans chitin deacetylases. NPJ Vaccines 2023; 8:6. [PMID: 36732332 PMCID: PMC9892683 DOI: 10.1038/s41541-023-00606-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/23/2023] [Indexed: 02/04/2023] Open
Abstract
Vaccination with glucan particles (GP) containing the Cryptococcus neoformans chitin deacetylases Cda1 and Cda2 protect mice against experimental cryptococcosis. Here, immunological correlates of vaccine-mediated protection were explored. Studies comparing knockout and wild-type mice demonstrated CD4+ T cells are crucial, while B cells and CD8+ T cells are dispensable. Protection was abolished following CD4+ T cell depletion during either vaccination or infection but was retained if CD4+ T cells were only partially depleted. Vaccination elicited systemic and durable antigen-specific immune responses in peripheral blood mononuclear cells (PBMCs), spleens, and lungs. Following vaccination and fungal challenge, robust T-helper (Th) 1 and Th17 responses were observed in the lungs. Protection was abrogated in mice congenitally deficient in interferon (IFN) γ, IFNγ receptor, interleukin (IL)-1β, IL-6, or IL-23. Thus, CD4+ T cells and specific proinflammatory cytokines are required for GP-vaccine-mediated protection. Importantly, retention of protection in the setting of partial CD4+ T depletion suggests a pathway for vaccinating at-risk immunocompromised individuals.
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Genome-wide analysis of heat stress-stimulated transposon mobility in the human fungal pathogen Cryptococcus deneoformans. Proc Natl Acad Sci U S A 2023; 120:e2209831120. [PMID: 36669112 PMCID: PMC9942834 DOI: 10.1073/pnas.2209831120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
We recently reported transposon mutagenesis as a significant driver of spontaneous mutations in the human fungal pathogen Cryptococcus deneoformans during murine infection. Mutations caused by transposable element (TE) insertion into reporter genes were dramatically elevated at high temperatures (37° vs. 30°) in vitro, suggesting that heat stress stimulates TE mobility in the Cryptococcus genome. To explore the genome-wide impact of TE mobilization, we generated transposon accumulation lines by in vitro passage of C. deneoformans strain XL280α for multiple generations at both 30° and at the host-relevant temperature of 37°. Utilizing whole-genome sequencing, we identified native TE copies and mapped multiple de novo TE insertions in these lines. Movements of the T1 DNA transposon occurred at both temperatures with a strong bias for insertion between gene-coding regions. By contrast, the Tcn12 retrotransposon integrated primarily within genes and movement occurred exclusively at 37°. In addition, we observed a dramatic amplification in copy number of the Cnl1 (Cryptococcus neoformans LINE-1) retrotransposon in subtelomeric regions under heat-stress conditions. Comparing TE mutations to other sequence variations detected in passaged lines, the increase in genomic changes at elevated temperatures was primarily due to mobilization of the retroelements Tcn12 and Cnl1. Finally, we found multiple TE movements (T1, Tcn12, and Cnl1) in the genomes of single C. deneoformans isolates recovered from infected mice, providing evidence that mobile elements are likely to facilitate microevolution and rapid adaptation during infection.
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Similar evolutionary trajectories in an environmental Cryptococcus neoformans isolate after human and murine infection. Proc Natl Acad Sci U S A 2023; 120:e2217111120. [PMID: 36603033 PMCID: PMC9926274 DOI: 10.1073/pnas.2217111120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
A pet cockatoo was the suspected source of Cryptococcus neoformans recovered from an immunocompromised patient with cryptococcosis based on molecular analyses available in 2000. Here, we report whole genome sequence analysis of the clinical and cockatoo strains. Both are closely related MATα strains belonging to the VNII lineage, confirming that the human infection likely originated from pet bird exposure. The two strains differ by 61 single nucleotide polymorphisms, including eight nonsynonymous changes involving seven genes. To ascertain whether changes in these genes are selected for during mammalian infection, we passaged the cockatoo strain in mice. Remarkably, isolates obtained from mouse tissue possess a frameshift mutation in one of the seven genes altered in the human sample (LQVO5_000317), a gene predicted to encode an SWI-SNF chromatin-remodeling complex protein. In addition, both cockatoo and patient strains as well as mouse-passaged isolates obtained from brain tissue had a premature stop codon in a homologue of ZFC3 (LQVO5_004463), a predicted single-zinc finger containing protein, which is associated with larger capsules when deleted and reverted to a full-length protein in the mouse-passaged isolates obtained from lung tissue. The patient strain and mouse-passaged isolates show variability in virulence factors, with differences in capsule size, melanization, rates of nonlytic expulsion from macrophages, and amoeba predation resistance. Our results establish that environmental strains undergo genomic and phenotypic changes during mammalian passage, suggesting that animal virulence can be a mechanism for genetic change and that the genomes of clinical isolates may provide a readout of mutations acquired during infection.
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Regulatory basis for reproductive flexibility in a meningitis-causing fungal pathogen. Nat Commun 2022; 13:7938. [PMID: 36566249 PMCID: PMC9790007 DOI: 10.1038/s41467-022-35549-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 12/09/2022] [Indexed: 12/25/2022] Open
Abstract
Pathogenic fungi of the genus Cryptococcus can undergo two sexual cycles, involving either bisexual diploidization (after fusion of haploid cells of different mating type) or unisexual diploidization (by autodiploidization of a single cell). Here, we construct a gene-deletion library for 111 transcription factor genes in Cryptococcus deneoformans, and explore the roles of these regulatory networks in the two reproductive modes. We show that transcription factors crucial for bisexual syngamy induce the expression of known mating determinants as well as other conserved genes of unknown function. Deletion of one of these genes, which we term FMP1, leads to defects in bisexual reproduction in C. deneoformans, its sister species Cryptococcus neoformans, and the ascomycete Neurospora crassa. Furthermore, we show that a recently evolved regulatory cascade mediates pre-meiotic unisexual autodiploidization, supporting that this reproductive process is a recent evolutionary innovation. Our findings indicate that genetic circuits with different evolutionary ages govern hallmark events distinguishing unisexual and bisexual reproduction in Cryptococcus.
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27
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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: 9] [Impact Index Per Article: 4.5] [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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Hester MM, Oliveira LVN, Wang R, Mou Z, Lourenco D, Ostroff GR, Specht CA, Levitz SM. Cross-reactivity between vaccine antigens from the chitin deacetylase protein family improves survival in a mouse model of cryptococcosis. Front Immunol 2022; 13:1015586. [PMID: 36248898 PMCID: PMC9554598 DOI: 10.3389/fimmu.2022.1015586] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 08/31/2022] [Indexed: 12/15/2022] Open
Abstract
Meningitis due to the fungal pathogen Cryptococcus neoformans is estimated to cause nearly 200,000 deaths annually, mostly in resource-limited regions. We previously identified cryptococcal protein antigens which, when delivered in glucan particles, afford vaccine-mediated protection against an otherwise lethal infection. Many of these proteins exhibit significant homology to other similar cryptococcal proteins leading us to hypothesize that protection may be augmented by immunologic cross-reactivity to multiple members of a protein family. To examine the significance of protein cross-reactivity in vaccination, we utilized strains of Cryptococcus that are genetically deficient in select antigens, yet are still lethal in mice. Vaccination with a protein without homologs (e.g., Mep1 and Lhc1) protected against challenge with wild-type Cryptococcus, but not against a deletion strain lacking that protein. Contrastingly, vaccination with a single chitin deacetylase (Cda) protein protected against the corresponding deletion strain, presumably due to host recognition of one or more other family members still expressed in this strain. Vaccination with a single Cda protein induced cross-reactive antibody and interferon-gamma (IFNγ) immune responses to other Cda protein family members. Paradoxically, we saw no evidence of cross-protection within the carboxypeptidase family of proteins. Factors such as in vivo protein expression and the degree of homology across the family could inform the extent to which vaccine-mediated immunity is amplified. Together, these data suggest a role for prioritizing protein families in fungal vaccine design: increasing the number of immune targets generated by a single antigen may improve efficacy while diminishing the risk of vaccine-resistant strains arising from gene mutations.
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Affiliation(s)
- Maureen M. Hester
- Department of Medicine, The University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Lorena V. N. Oliveira
- Department of Medicine, The University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Ruiying Wang
- Department of Medicine, The University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Zhongming Mou
- Department of Medicine, The University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Diana Lourenco
- Department of Medicine, The University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Gary R. Ostroff
- Program in Molecular Medicine, The University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Charles A. Specht
- Department of Medicine, The University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Stuart M. Levitz
- Department of Medicine, The University of Massachusetts Chan Medical School, Worcester, MA, United States
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29
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Jung EH, Park YD, Dragotakes Q, Ramirez LS, Smith DQ, Reis FCG, Dziedzic A, Rodrigues ML, Baker RP, Williamson PR, Jedlicka A, Casadevall A, Coelho C. Cryptococcus neoformans releases proteins during intracellular residence that affect the outcome of the fungal-macrophage interaction. MICROLIFE 2022; 3:uqac015. [PMID: 36247839 PMCID: PMC9552768 DOI: 10.1093/femsml/uqac015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/13/2022] [Indexed: 05/26/2023]
Abstract
Cryptococcus neoformans is a facultative intracellular pathogen that can replicate and disseminate in mammalian macrophages. In this study, we analyzed fungal proteins identified in murine macrophage-like cells after infection with C. neoformans. To accomplish this, we developed a protocol to identify proteins released from cryptococcal cells inside macrophage-like cells; we identified 127 proteins of fungal origin in infected macrophage-like cells. Among the proteins identified was urease, a known virulence factor, and others such as transaldolase and phospholipase D, which have catalytic activities that could contribute to virulence. This method provides a straightforward methodology to study host-pathogen interactions. We chose to study further Yeast Oligomycin Resistance (Yor1), a relatively uncharacterized protein belonging to the large family of ATP binding cassette transporter (ABC transporters). These transporters belong to a large and ancient protein family found in all extant phyla. While ABC transporters have an enormous diversity of functions across varied species, in pathogenic fungi they are better studied as drug efflux pumps. Analysis of C. neoformans yor1Δ strains revealed defects in nonlytic exocytosis, capsule size, and dimensions of extracellular vesicles, when compared to wild-type strains. We detected no difference in growth rates and cell body size. Our results indicate that C. neoformans releases a large suite of proteins during macrophage infection, some of which can modulate fungal virulence and are likely to affect the fungal-macrophage interaction.
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Affiliation(s)
- Eric H Jung
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, United States
| | - Yoon-Dong Park
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Memorial Drive, Bethesda, MD 20814, United States
| | - Quigly Dragotakes
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, United States
| | - Lia S Ramirez
- Department of Molecular and Cell Biology, Johns Hopkins University, 615 North Wolfe Street, Baltimore, MD 21205, United States
| | - Daniel Q Smith
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, United States
| | - Flavia C G Reis
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Rua Professor Algacyr Munhoz Mader, 3775, Curitiba - PR, 81310-020, Brazil
- Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz Av. Brasil 4036. Room 814, Rio de Janeiro - RJ, 21040-361, Brazil
| | - Amanda Dziedzic
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, United States
| | - Marcio L Rodrigues
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Rua Professor Algacyr Munhoz Mader, 3775, Curitiba - PR, 81310-020, Brazil
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro, Rio de Janeiro Cidade Universitária da Universidade Federal do Rio de Janeiro,, Rio de Janeiro - RJ, 21941-902, Brazil
| | - Rosanna P Baker
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, United States
| | - Peter R Williamson
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Memorial Drive, Bethesda, MD 20814, United States
| | - Anne Jedlicka
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, United States
| | - Arturo Casadevall
- Corresponding author: Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, 615 N, Wolfe Street, Room E5132, Baltimore, MD 21205, United States. E-mail:
| | - Carolina Coelho
- Corresponding author: Medical Research Council Centre for Medical Mycology at University of Exeter, College of Health and Medicine, Geoffrey Pope Building, Room 325, University of Exeter, Stocker Road, Exeter EX4 4QD, Devon, United Kingdom. E-mail:
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Wizrah MS, Chua SM, Luo Z, Manik MK, Pan M, Whyte JM, Robertson AA, Kappler U, Kobe B, Fraser JA. AICAR transformylase/IMP cyclohydrolase (ATIC) is essential for de novo purine biosynthesis and infection by Cryptococcus neoformans. J Biol Chem 2022; 298:102453. [PMID: 36063996 PMCID: PMC9525906 DOI: 10.1016/j.jbc.2022.102453] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 01/27/2023] Open
Abstract
The fungal pathogen Cryptococcus neoformans is a leading cause of meningoencephalitis in the immunocompromised. As current antifungal treatments are toxic to the host, costly, limited in their efficacy, and associated with drug resistance, there is an urgent need to identify vulnerabilities in fungal physiology to accelerate antifungal discovery efforts. Rational drug design was pioneered in de novo purine biosynthesis as the end products of the pathway, ATP and GTP, are essential for replication, transcription, and energy metabolism, and the same rationale applies when considering the pathway as an antifungal target. Here, we describe the identification and characterization of C. neoformans 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/5'-inosine monophosphate cyclohydrolase (ATIC), a bifunctional enzyme that catalyzes the final two enzymatic steps in the formation of the first purine base inosine monophosphate. We demonstrate that mutants lacking the ATIC-encoding ADE16 gene are adenine and histidine auxotrophs that are unable to establish an infection in a murine model of virulence. In addition, our assays employing recombinantly expressed and purified C. neoformans ATIC enzyme revealed Km values for its substrates AICAR and 5-formyl-AICAR are 8-fold and 20-fold higher, respectively, than in the human ortholog. Subsequently, we performed crystallographic studies that enabled the determination of the first fungal ATIC protein structure, revealing a key serine-to-tyrosine substitution in the active site, which has the potential to assist the design of fungus-specific inhibitors. Overall, our results validate ATIC as a promising antifungal drug target.
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Affiliation(s)
- Maha S.I. Wizrah
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Sheena M.H. Chua
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Zhenyao Luo
- School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Mohammad K. Manik
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Mengqi Pan
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Jessica M.L. Whyte
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Avril A.B. Robertson
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Ulrike Kappler
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Bostjan Kobe
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - James A. Fraser
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia,For correspondence: James A. Fraser
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Priest SJ, Yadav V, Roth C, Dahlmann TA, Kück U, Magwene PM, Heitman J. Uncontrolled transposition following RNAi loss causes hypermutation and antifungal drug resistance in clinical isolates of Cryptococcus neoformans. Nat Microbiol 2022; 7:1239-1251. [PMID: 35918426 PMCID: PMC10840647 DOI: 10.1038/s41564-022-01183-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 06/23/2022] [Indexed: 02/07/2023]
Abstract
Cryptococcus neoformans infections cause approximately 15% of AIDS-related deaths owing to a combination of limited antifungal therapies and drug resistance. A collection of clinical and environmental C. neoformans isolates were assayed for increased mutation rates via fluctuation analysis, and we identified two hypermutator C. neoformans clinical isolates with increased mutation rates when exposed to the combination of rapamycin and FK506. Sequencing of drug target genes found that Cnl1 transposon insertions conferred the majority of resistance to rapamycin and FK506 and could also independently cause resistance to 5-fluoroorotic acid and the clinically relevant antifungal 5-flucytosine. Whole-genome sequencing revealed both hypermutator genomes harbour a nonsense mutation in the RNA-interference component ZNF3 and hundreds of Cnl1 elements organized into massive subtelomeric arrays on each of the fourteen chromosomes. Quantitative trait locus mapping in 28 progeny derived from a cross between a hypermutator and wild-type identified a locus associated with hypermutation that included znf3. CRISPR editing of the znf3 nonsense mutation abolished hypermutation and restored small-interfering-RNA production. We conclude that hypermutation and drug resistance in these clinical isolates result from RNA-interference loss and accumulation of Cnl1 elements.
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Affiliation(s)
- Shelby J Priest
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Vikas Yadav
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Cullen Roth
- Department of Biology, Duke University, Durham, NC, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC, USA
| | - Tim A Dahlmann
- Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Bochum, Germany
| | - Ulrich Kück
- Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Bochum, Germany
| | | | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA.
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Kassaza K, Wasswa F, Nielsen K, Bazira J. Cryptococcus neoformans Genotypic Diversity and Disease Outcome among HIV Patients in Africa. J Fungi (Basel) 2022; 8:jof8070734. [PMID: 35887489 PMCID: PMC9325144 DOI: 10.3390/jof8070734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/24/2022] [Accepted: 07/06/2022] [Indexed: 11/16/2022] Open
Abstract
Cryptococcal meningoencephalitis, a disease with poor patient outcomes, remains the most prevalent invasive fungal infection worldwide, accounting for approximately 180,000 deaths each year. In several areas of sub-Saharan Africa with the highest HIV prevalence, cryptococcal meningitis is the leading cause of community-acquired meningitis, with a high mortality among HIV-infected individuals. Recent studies show that patient disease outcomes are impacted by the genetics of the infecting isolate. Yet, there is still limited knowledge of how these genotypic variations contribute to clinical disease outcome. Further, it is unclear how the genetic heterogeneity of C. neoformans and the extensive phenotypic variation observed between and within isolates affects infection and disease. In this review, we discuss current knowledge of how various genotypes impact disease progression and patient outcome in HIV-positive populations in sub-Saharan African, a setting with a high burden of cryptococcosis.
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Affiliation(s)
- Kennedy Kassaza
- Department of Microbiology and Parasitology, Mbarara University of Science and Technology, Mbarara P.O. Box 1410, Uganda; (K.K.); (F.W.)
| | - Fredrickson Wasswa
- Department of Microbiology and Parasitology, Mbarara University of Science and Technology, Mbarara P.O. Box 1410, Uganda; (K.K.); (F.W.)
| | - Kirsten Nielsen
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
- Correspondence: (K.N.); (J.B.)
| | - Joel Bazira
- Department of Microbiology and Parasitology, Mbarara University of Science and Technology, Mbarara P.O. Box 1410, Uganda; (K.K.); (F.W.)
- Correspondence: (K.N.); (J.B.)
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Zhou Z, Zhu C, Ip M, Liu M, Zhu Z, Liu R, Li X, Zeng L, Wu W. Molecular Epidemiology and Antifungal Resistance of Cryptococcus neoformans From Human Immunodeficiency Virus-Negative and Human Immunodeficiency Virus-Positive Patients in Eastern China. Front Microbiol 2022; 13:942940. [PMID: 35865921 PMCID: PMC9294546 DOI: 10.3389/fmicb.2022.942940] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022] Open
Abstract
Cryptococcosis is an opportunistic and potentially lethal infection caused by Cryptococcus neoformans and Cryptococcus gattii complex, which affects both immunocompromised and immunocompetent people, and it has become a major public health concern worldwide. In this study, we characterized the molecular epidemiology and antifungal susceptibility of 133 C. neoformans isolates from East China Invasive Fungal Infection Group (ECIFIG), 2017–2020. Isolates were identified to species level by matrix-assisted laser desorption ionization-time of flight mass spectrometry and confirmed by IGS1 sequencing. Whole-genome sequencing (WGS) was conducted on three multidrug-resistant isolates. Among the 133 strains, 61 (45.86%) were isolated from HIV-positive patients and 72 (54.16%) were isolated from HIV-negative patients. In total, C. neoformans var. grubii accounted for 97.74% (130/133), while C. neoformans var. neoformans was rare (2.06%, 3/133). The strains were further classified into nine sequence types (STs) dominated by ST5 (90.23%, 120/133) with low genetic diversity. No association was observed between STs and HIV status. All strains were wild type to voriconazole, while high antifungal minimal inhibitory concentrations (MICs) above the epidemiological cutoff values (ECVs) were observed in C. neoformans strains, and more than half of isolates were non-wild-type to amphotericin B (89.15%, 109/133). Eight isolates were resistant to fluconazole, and eight isolates were non-wild type to 5-fluorocytosine. Furthermore, WGS has verified the novel mutations of FUR1 in 5-fluorocytosine-resistant strains. In one isolate, aneuploidy of chromosome 1 with G484S mutation of ERG11 was observed, inducing high-level resistance (MIC: 32 μg/ml) to fluconazole. In general, our data showed that there was no significant difference between HIV-positive and HIV-negative patients on STs, and we elucidate the resistant mechanisms of C. neoformans from different perspectives. It is important for clinical therapy and drug usage in the future.
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Affiliation(s)
- Ziyi Zhou
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chendi Zhu
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Margaret Ip
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Manjiao Liu
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Zhaoqin Zhu
- Shanghai Public Health Clinical Center, Shanghai, China
| | - Ryon Liu
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Xiaomin Li
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Lingbing Zeng
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
- *Correspondence: Lingbing Zeng,
| | - Wenjuan Wu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Wenjuan Wu,
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Passer AR, Clancey SA, Shea T, David-Palma M, Averette AF, Boekhout T, Porcel BM, Nowrousian M, Cuomo CA, Sun S, Heitman J, Coelho MA. Obligate sexual reproduction of a homothallic fungus closely related to the Cryptococcus pathogenic species complex. eLife 2022; 11:e79114. [PMID: 35713948 PMCID: PMC9296135 DOI: 10.7554/elife.79114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/15/2022] [Indexed: 12/03/2022] Open
Abstract
Fungi are enigmatic organisms that flourish in soil, on decaying plants, or during infection of animals or plants. Growing in myriad forms, from single-celled yeast to multicellular molds and mushrooms, fungi have also evolved a variety of strategies to reproduce. Normally, fungi reproduce in one of two ways: either they reproduce asexually, with one individual producing a new individual identical to itself, or they reproduce sexually, with two individuals of different 'mating types' contributing to produce a new individual. However, individuals of some species exhibit 'homothallism' or self-fertility: these individuals can produce reproductive cells that are universally compatible, and therefore can reproduce sexually with themselves or with any other cell in the population. Homothallism has evolved multiple times throughout the fungal kingdom, suggesting it confers advantage when population numbers are low or mates are hard to find. Yet some homothallic fungi been overlooked compared to heterothallic species, whose mating types have been well characterised. Understanding the genetic basis of homothallism and how it evolved in different species can provide insights into pathogenic species that cause fungal disease. With that in mind, Passer, Clancey et al. explored the genetic basis of homothallism in Cryptococcus depauperatus, a close relative of C. neoformans, a species that causes fungal infections in humans. A combination of genetic sequencing techniques and experiments were applied to analyse, compare, and manipulate C. depauperatus' genome to see how this species evolved self-fertility. Passer, Clancey et al. showed that C. depauperatus evolved the ability to reproduce sexually by itself via a unique evolutionary pathway. The result is a form of homothallism never reported in fungi before. C. depauperatus lost some of the genes that control mating in other species of fungi, and acquired genes from the opposing mating types of a heterothallic ancestor to become self-fertile. Passer, Clancey et al. also found that, unlike other Cryptococcus species that switch between asexual and sexual reproduction, C. depauperatus grows only as long, branching filaments called hyphae, a sexual form. The species reproduces sexually with itself throughout its life cycle and is unable to produce a yeast (asexual) form, in contrast to other closely related species. This work offers new insights into how different modes of sexual reproduction have evolved in fungi. It also provides another interesting case of how genome plasticity and evolutionary pressures can produce similar outcomes, homothallism, via different evolutionary paths. Lastly, assembling the complete genome of C. depauperatus will foster comparative studies between pathogenic and non-pathogenic Cryptococcus species.
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Affiliation(s)
- Andrew Ryan Passer
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Shelly Applen Clancey
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Terrance Shea
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Márcia David-Palma
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Anna Floyd Averette
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity InstituteUtrechtNetherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of AmsterdamAmsterdamNetherlands
| | - Betina M Porcel
- Génomique Métabolique, CNRS, University Evry, Université Paris-SaclayEvryFrance
| | - Minou Nowrousian
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität BochumBochumGermany
| | | | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Marco A Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
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Snelders E, Moyrand F, Sturny-Leclère A, Vernel-Pauillac F, Volant S, Janbon G, Alanio A. The role of glycosylphosphatidylinositol (gpi) anchored proteins in Cryptococcus neoformans. Microbes Infect 2022; 24:105016. [DOI: 10.1016/j.micinf.2022.105016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/25/2022] [Accepted: 05/20/2022] [Indexed: 10/31/2022]
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Homa M, Ibragimova S, Szebenyi C, Nagy G, Zsindely N, Bodai L, Vágvölgyi C, Nagy G, Papp T. Differential Gene Expression of Mucor lusitanicus under Aerobic and Anaerobic Conditions. J Fungi (Basel) 2022; 8:jof8040404. [PMID: 35448635 PMCID: PMC9031258 DOI: 10.3390/jof8040404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 02/04/2023] Open
Abstract
Mucor lusitanicus and some other members of the fungal order Mucorales display the phenomenon of morphological dimorphism. This means that these fungi aerobically produce filamentous hyphae, developing a coenocytic mycelium, but they grow in a multipolar yeast-like form under anaerobiosis. Revealing the molecular mechanism of the reversible yeast-hyphal transition can be interesting for both the biotechnological application and in the understanding of the pathomechanism of mucormycosis. In the present study, transcriptomic analyses were carried out after cultivating the fungus either aerobically or anaerobically revealing significant changes in gene expression under the two conditions. In total, 539 differentially expressed genes (FDR < 0.05, |log2FC| ≥ 3) were identified, including 190 upregulated and 349 downregulated transcripts. Within the metabolism-related genes, carbohydrate metabolism was proven to be especially affected. Anaerobiosis also affected the transcription of transporters: among the 14 up- and 42 downregulated transporters, several putative sugar transporters were detected. Moreover, a considerable number of transcripts related to amino acid transport and metabolism, lipid transport and metabolism, and energy production and conversion were proven to be downregulated when the culture had been transferred into an anaerobic atmosphere.
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Affiliation(s)
- Mónika Homa
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary; (M.H.); (S.I.); (C.S.); (C.V.); (G.N.)
| | - Sandugash Ibragimova
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary; (M.H.); (S.I.); (C.S.); (C.V.); (G.N.)
| | - Csilla Szebenyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary; (M.H.); (S.I.); (C.S.); (C.V.); (G.N.)
| | - Gábor Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary; (G.N.); (L.B.)
| | - Nóra Zsindely
- Department of Genetics, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary;
| | - László Bodai
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary; (G.N.); (L.B.)
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary; (M.H.); (S.I.); (C.S.); (C.V.); (G.N.)
| | - Gábor Nagy
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary; (M.H.); (S.I.); (C.S.); (C.V.); (G.N.)
| | - Tamás Papp
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary; (M.H.); (S.I.); (C.S.); (C.V.); (G.N.)
- Correspondence:
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de Melo Teixeira M, Stajich JE, Sahl JW, Thompson GR, Brem RB, Dubin CA, Blackmon AV, Mead HL, Keim P, Barker BM. A chromosomal-level reference genome of the widely utilized Coccidioides posadasii laboratory strain "Silveira". G3 (BETHESDA, MD.) 2022; 12:jkac031. [PMID: 35137016 PMCID: PMC8982387 DOI: 10.1093/g3journal/jkac031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/29/2021] [Indexed: 12/14/2022]
Abstract
Coccidioidomycosis is a common fungal disease that is endemic to arid and semi-arid regions of both American continents. Coccidioides immitis and Coccidioides posadasii are the etiological agents of the disease, also known as Valley Fever. For several decades, the C. posadasii strain Silveira has been used widely in vaccine studies, is the source strain for production of diagnostic antigens, and is a widely used experimental strain for functional studies. In 2009, the genome was sequenced using Sanger sequencing technology, and a draft assembly and annotation were made available. In this study, the genome of the Silveira strain was sequenced using single molecule real-time sequencing PacBio technology, assembled into chromosomal-level contigs, genotyped, and the genome was reannotated using sophisticated and curated in silico tools. This high-quality genome sequencing effort has improved our understanding of chromosomal structure, gene set annotation, and lays the groundwork for identification of structural variants (e.g. transversions, translocations, and copy number variants), assessment of gene gain and loss, and comparison of transposable elements in future phylogenetic and population genomics studies.
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Affiliation(s)
- Marcus de Melo Teixeira
- Faculty of Medicine, University of Brasília, Brasília 70910-900, Brazil
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Jason E Stajich
- Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, USA
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA 92521, USA
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - George R Thompson
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA 95616, USA
| | - Rachel B Brem
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Claire A Dubin
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Austin V Blackmon
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Heather L Mead
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Bridget M Barker
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
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Identification and characterisation of sPEPs in Cryptococcus neoformans. Fungal Genet Biol 2022; 160:103688. [PMID: 35339703 DOI: 10.1016/j.fgb.2022.103688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/02/2022] [Accepted: 03/21/2022] [Indexed: 11/24/2022]
Abstract
Short open reading frame (sORF)-encoded peptides (sPEPs) have been found across a wide range of genomic locations in a variety of species. To date, their identification, validation, and characterisation in the human fungal pathogen Cryptococcus neoformans has been limited due to a lack of standardised protocols. We have developed an enrichment process that enables sPEP detection within a protein sample from this polysaccharide-encapsulated yeast, and implemented proteogenomics to provide insights into the validity of predicted and hypothetical sORFs annotated in the C. neoformans genome. Novel sORFs were discovered within the 5' and 3' UTRs of known transcripts as well as in "non-coding" RNAs. One novel candidate, dubbed NPB1, that resided in an RNA annotated as "non-coding", was chosen for characterisation. Through the creation of both specific point mutations and a full deletion allele, the function of the new sPEP, Npb1, was shown to resemble that of the bacterial trans-translation protein SmpB.
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Jeon J, Kim KT, Choi J, Cheong K, Ko J, Choi G, Lee H, Lee GW, Park SY, Kim S, Kim ST, Min CW, Kang S, Lee YH. Alternative splicing diversifies the transcriptome and proteome of the rice blast fungus during host infection. RNA Biol 2022; 19:373-385. [PMID: 35311472 PMCID: PMC8942408 DOI: 10.1080/15476286.2022.2043040] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Alternative splicing (AS) contributes to diversifying and regulating cellular responses to environmental conditions and developmental cues by differentially producing multiple mRNA and protein isoforms from a single gene. Previous studies on AS in pathogenic fungi focused on profiling AS isoforms under a limited number of conditions. We analysed AS profiles in the rice blast fungus Magnaporthe oryzae, a global threat to rice production, using high-quality transcriptome data representing its vegetative growth (mycelia) and multiple host infection stages. We identified 4,270 AS isoforms derived from 2,413 genes, including 499 genes presumably regulated by infection-specific AS. AS appears to increase during infection, with 32.7% of the AS isoforms being produced during infection but absent in mycelia. Analysis of the isoforms observed at each infection stage showed that 636 AS isoforms were more abundant than corresponding annotated mRNAs, especially after initial hyphal penetration into host cell. Many such dominant isoforms were predicted to encode regulatory proteins such as transcription factors and phospho-transferases. We also identified the genes encoding distinct proteins via AS and confirmed the translation of some isoforms via a proteomic analysis, suggesting potential AS-mediated neo-functionalization of some genes during infection. Comprehensive profiling of the pattern of genome-wide AS during multiple stages of rice-M. oryzae interaction established a foundational resource that will help investigate the role and regulation of AS during rice infection.
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Affiliation(s)
- Jongbum Jeon
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Korea
- Plant Immunity Research Center, Seoul National University, Seoul, Korea
- Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Ki-Tae Kim
- Department of Agricultural Life Science, Sunchon National University, Suncheon, Korea
| | - Jaeyoung Choi
- Smart Farm Research Center, Korea Institute of Science and Technology, Gangneung, Korea
| | - Kyeongchae Cheong
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Korea
| | - Jaeho Ko
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Gobong Choi
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Korea
| | - Hyunjun Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | | | - Sook-Young Park
- Department of Agricultural Life Science, Sunchon National University, Suncheon, Korea
| | - Seongbeom Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang, Korea
- Life and Energy Convergence Research Institute, Pusan National University, Miryang, Korea
| | - Cheol Woo Min
- Department of Plant Bioscience, Pusan National University, Miryang, Korea
| | - Seogchan Kang
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA USA
| | - Yong-Hwan Lee
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Korea
- Plant Immunity Research Center, Seoul National University, Seoul, Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
- Center for Fungal Genetic Resources, Seoul National University, Seoul, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
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40
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Lineages Derived from Cryptococcus neoformans Type Strain H99 Support a Link between the Capacity to Be Pleomorphic and Virulence. mBio 2022; 13:e0028322. [PMID: 35258331 PMCID: PMC9040854 DOI: 10.1128/mbio.00283-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The pathogenic yeast Cryptococcus neoformans causes nearly 200,000 deaths annually in immunocompromised individuals. Cryptococcus cells can undergo substantial morphological change during mammalian infection, including increased capsule and cell size, the release of shed capsule, and the production of titan (>10 μm), micro (<2 μm)-, and irregular cells. We examined phenotypic variation under conditions designed to simulate in vivo stress in a collection of nine lineages derived from the C. neoformans type strain H99. These lineages are highly genetically similar but have a range of virulence levels. Strains from hypervirulent lineages had a larger average capsule size, greater variation in cell size, and an increased production of microcells and shed capsule. We tested whether disruption of SGF29, which encodes a component of the SAGA histone acetylation complex that has previously been implicated in the hypervirulence of some lineages, also has a role in the production of morphological variants. Deletion of SGF29 in a lineage with intermediate virulence substantially increased its production of microcells and released capsule, consistent with a switch to hypervirulence. We further examined SGF29 in a set of 52 clinical isolates and found loss-of-function mutations were significantly correlated with patient death. Expansion of a TA repeat in the second intron of SGF29 was positively correlated with cell and capsule size, suggesting it also affects Sgf29 function. This study extends the evidence for a link between pleomorphism and virulence in Cryptococcus, with a likely role for epigenetic mechanisms mediated by SAGA-induced histone acetylation.
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Vélez N, Vega-Vela N, Muñoz M, Gómez P, Escandón P, Ramírez JD, Zaragoza O, Monteoliva Diaz L, Parra-Giraldo CM. Deciphering the Association among Pathogenicity, Production and Polymorphisms of Capsule/Melanin in Clinical Isolates of Cryptococcus neoformans var. grubii VNI. J Fungi (Basel) 2022; 8:245. [PMID: 35330247 PMCID: PMC8950468 DOI: 10.3390/jof8030245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/17/2022] [Accepted: 02/21/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Cryptococcus neoformans is an opportunistic fungal pathogen that can cause meningitis in immunocompromised individuals. The objective of this work was to study the relationship between the phenotypes and genotypes of isolates of clinical origin from different cities in Colombia. METHODS Genome classification of 29 clinical isolates of C. neoformans var. grubii was performed using multilocus sequence typing (MLST), and genomic sequencing was used to genotype protein-coding genes. Pathogenicity was assessed in a larval model, and melanin production and capsule size were evaluated in vitro and in vivo. RESULTS Eleven MLST sequence types (STs) were found, the most frequent being ST69 (n = 9), ST2, ST93, and ST377 (each with n = 4). In the 29 isolates, different levels of pigmentation, capsule size and pathogenicity were observed. Isolates classified as highly pathogenic showed a tendency to exhibit larger increases in capsule size. In the analysis of polymorphisms, 48 non-synonymous variants located in the predicted functional domains of 39 genes were found to be associated with capsule size change, melanin, or pathogenicity. CONCLUSIONS No clear patterns were found in the analysis of the phenotype and genotype of Cryptococcus. However, the data suggest that the increase in capsule size is a key variable for the differentiation of pathogenic isolates, regardless of the method used for its induction.
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Affiliation(s)
- Nórida Vélez
- Unidad de Proteómica y Micosis Humanas, Grupo de Enfermedades Infecciosas, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Nelson Vega-Vela
- Unidad de Proteómica y Micosis Humanas, Grupo de Enfermedades Infecciosas, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia
| | - Paola Gómez
- Unidad de Proteómica y Micosis Humanas, Grupo de Enfermedades Infecciosas, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Patricia Escandón
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Oscar Zaragoza
- Mycology Reference Laboratory National Centre for Microbiology, Instituto de Salud Carlos III, 28222 Madrid, Spain
| | - Lucía Monteoliva Diaz
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Claudia-Marcela Parra-Giraldo
- Unidad de Proteómica y Micosis Humanas, Grupo de Enfermedades Infecciosas, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
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42
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Sun S, Roth C, Floyd Averette A, Magwene PM, Heitman J. Epistatic genetic interactions govern morphogenesis during sexual reproduction and infection in a global human fungal pathogen. Proc Natl Acad Sci U S A 2022; 119:e2122293119. [PMID: 35169080 PMCID: PMC8872808 DOI: 10.1073/pnas.2122293119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
Cellular development is orchestrated by evolutionarily conserved signaling pathways, which are often pleiotropic and involve intra- and interpathway epistatic interactions that form intricate, complex regulatory networks. Cryptococcus species are a group of closely related human fungal pathogens that grow as yeasts yet transition to hyphae during sexual reproduction. Additionally, during infection they can form large, polyploid titan cells that evade immunity and develop drug resistance. Multiple known signaling pathways regulate cellular development, yet how these are coordinated and interact with genetic variation is less well understood. Here, we conducted quantitative trait locus (QTL) analyses of a mapping population generated by sexual reproduction of two parents, only one of which is unisexually fertile. We observed transgressive segregation of the unisexual phenotype among progeny, as well as a large-cell phenotype under mating-inducing conditions. These large-cell progeny were found to produce titan cells both in vitro and in infected animals. Two major QTLs and corresponding quantitative trait genes (QTGs) were identified: RIC8 (encoding a guanine-exchange factor) and CNC06490 (encoding a putative Rho-GTPase activator), both involved in G protein signaling. The two QTGs interact epistatically with each other and with the mating-type locus in phenotypic determination. These findings provide insights into the complex genetics of morphogenesis during unisexual reproduction and pathogenic titan cell formation and illustrate how QTL analysis can be applied to identify epistasis between genes. This study shows that phenotypic outcomes are influenced by the genetic background upon which mutations arise, implicating dynamic, complex genotype-to-phenotype landscapes in fungal pathogens and beyond.
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Affiliation(s)
- Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Cullen Roth
- Department of Biology, Duke University, Durham, NC 27708
| | - Anna Floyd Averette
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Paul M Magwene
- Department of Biology, Duke University, Durham, NC 27708
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710;
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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: 19] [Impact Index Per Article: 9.5] [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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44
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Michelotti LA, Sun S, Heitman J, James TY. Clonal evolution in serially passaged Cryptococcus neoformans × deneoformans hybrids reveals a heterogenous landscape of genomic change. Genetics 2022; 220:iyab142. [PMID: 34849836 PMCID: PMC8733418 DOI: 10.1093/genetics/iyab142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/25/2021] [Indexed: 11/14/2022] Open
Abstract
Cryptococcus neoformans × deneoformans hybrids (also known as serotype AD hybrids) are basidiomycete yeasts that are common in a clinical setting. Like many hybrids, the AD hybrids are largely locked at the F1 stage and are mostly unable to undergo normal meiotic reproduction. However, these F1 hybrids, which display a high (∼10%) sequence divergence are known to genetically diversify through mitotic recombination and aneuploidy, and this diversification may be adaptive. In this study, we evolved a single AD hybrid genotype in six diverse environments by serial passaging and then used genome resequencing of evolved clones to determine evolutionary mechanisms of adaptation. The evolved clones generally increased fitness after passaging, accompanied by an average of 3.3 point mutations, 2.9 loss of heterozygosity (LOH) events, and 0.7 trisomic chromosomes per clone. LOH occurred through nondisjunction of chromosomes, crossing over consistent with break-induced replication, and gene conversion, in that order of prevalence. The breakpoints of these recombination events were significantly associated with regions of the genome with lower sequence divergence between the parents and clustered in sub-telomeric regions, notably in regions that had undergone introgression between the two parental species. Parallel evolution was observed, particularly through repeated homozygosity via nondisjunction, yet there was little evidence of environment-specific parallel change for either LOH, aneuploidy, or mutations. These data show that AD hybrids have both a remarkable genomic plasticity and yet are challenged in the ability to recombine through sequence divergence and chromosomal rearrangements, a scenario likely limiting the precision of adaptive evolution to novel environments.
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Affiliation(s)
- Lucas A Michelotti
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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Baker RP, Chrissian C, Stark RE, Casadevall A. Cryptococcus neoformans melanization incorporates multiple catecholamines to produce polytypic melanin. J Biol Chem 2022; 298:101519. [PMID: 34942148 PMCID: PMC8760516 DOI: 10.1016/j.jbc.2021.101519] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 01/08/2023] Open
Abstract
Melanin is a major virulence factor in pathogenic fungi that enhances the ability of fungal cells to resist immune clearance. Cryptococcus neoformans is an important human pathogenic fungus that synthesizes melanin from exogenous tissue catecholamine precursors during infection, but the type of melanin made in cryptococcal meningoencephalitis is unknown. We analyzed the efficacy of various catecholamines found in brain tissue in supporting melanization using animal brain tissue and synthetic catecholamine mixtures reflecting brain tissue proportions. Solid-state NMR spectra of the melanin pigment produced from such mixtures yielded more melanin than expected if only the preferred constituent dopamine had been incorporated, suggesting uptake of additional catecholamines. Probing the biosynthesis of melanin using radiolabeled catecholamines revealed that C. neoformans melanization simultaneously incorporated more than one catecholamine, implying that the pigment was polytypic in nature. Nonetheless, melanin derived from individual or mixed catecholamines had comparable ability to protect C. neoformans against ultraviolet light and oxidants. Our results indicate that melanin produced during infection differs depending on the catecholamine composition of tissue and that melanin pigment synthesized in vivo is likely to accrue from the polymerization of a mixture of precursors. From a practical standpoint, our results strongly suggest that using dopamine as a polymerization precursor is capable of producing melanin pigment comparable to that produced during infection. On a more fundamental level, our findings uncover additional structural complexity for natural cryptococcal melanin by demonstrating that pigment produced during human infection is likely to be composed of polymerized moieties derived from chemically different precursors.
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Affiliation(s)
- Rosanna P Baker
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Christine Chrissian
- Department of Chemistry and Biochemistry, The City College of New York and CUNY Institute for Macromolecular Assemblies, New York, New York, USA
| | - Ruth E Stark
- Department of Chemistry and Biochemistry, The City College of New York and CUNY Institute for Macromolecular Assemblies, New York, New York, USA; Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York, USA; Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA.
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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: 22] [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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Palmieri D, Barone G, Cigliano RA, De Curtis F, Lima G, Castoria R, Ianiri G. Complete genome sequence of the biocontrol yeast Papiliotrema terrestris strain LS28. G3 GENES|GENOMES|GENETICS 2021; 11:6371956. [PMID: 34534326 PMCID: PMC8664472 DOI: 10.1093/g3journal/jkab332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 09/13/2021] [Indexed: 11/24/2022]
Abstract
Papiliotrema terrestris strain LS28 is a biocontrol agent selected for its antagonistic activity against several plant pathogens both in the field and postharvest. The availability of a genome sequencing sets the foundation for the identification of the genetic mechanisms of its antagonistic activity. The genome size is 21.29 Mbp with a G+C content of 58.65%, and genome annotation predicts 8,626 protein-encoding genes. Phylogenetic analysis based on whole-genome data confirms that P. terrestris is a Tremellomycetes more closely related to Papiliotrema flavescens than Papiliotrema laurentii.
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Affiliation(s)
- Davide Palmieri
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100 Campobasso, Italy
| | - Giuseppe Barone
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100 Campobasso, Italy
| | | | - Filippo De Curtis
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100 Campobasso, Italy
| | - Giuseppe Lima
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100 Campobasso, Italy
| | - Raffaello Castoria
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100 Campobasso, Italy
| | - Giuseppe Ianiri
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100 Campobasso, Italy
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Fu C, Davy A, Holmes S, Sun S, Yadav V, Gusa A, Coelho MA, Heitman J. Dynamic genome plasticity during unisexual reproduction in the human fungal pathogen Cryptococcus deneoformans. PLoS Genet 2021; 17:e1009935. [PMID: 34843473 PMCID: PMC8670703 DOI: 10.1371/journal.pgen.1009935] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 12/14/2021] [Accepted: 11/08/2021] [Indexed: 12/30/2022] Open
Abstract
Genome copy number variation occurs during each mitotic and meiotic cycle and it is crucial for organisms to maintain their natural ploidy. Defects in ploidy transitions can lead to chromosome instability, which is a hallmark of cancer. Ploidy in the haploid human fungal pathogen Cryptococcus neoformans is exquisitely orchestrated and ranges from haploid to polyploid during sexual development and under various environmental and host conditions. However, the mechanisms controlling these ploidy transitions are largely unknown. During C. deneoformans (formerly C. neoformans var. neoformans, serotype D) unisexual reproduction, ploidy increases prior to the onset of meiosis, can be independent from cell-cell fusion and nuclear fusion, and likely occurs through an endoreplication pathway. To elucidate the molecular mechanisms underlying this ploidy transition, we identified twenty cell cycle-regulating genes encoding cyclins, cyclin-dependent kinases (CDK), and CDK regulators. We characterized four cyclin genes and two CDK regulator genes that were differentially expressed during unisexual reproduction and contributed to diploidization. To detect ploidy transition events, we generated a ploidy reporter, called NURAT, which can detect copy number increases via double selection for nourseothricin-resistant, uracil-prototrophic cells. Utilizing this ploidy reporter, we showed that ploidy transition from haploid to diploid can be detected during the early phases of unisexual reproduction. Interestingly, selection for the NURAT reporter revealed several instances of segmental aneuploidy of multiple chromosomes, which conferred azole resistance in some isolates. These findings provide further evidence of ploidy plasticity in fungi with significant biological and public health implications. Ploidy is an intrinsic fundamental feature of all eukaryotic organisms, and ploidy variation and maintenance are critical to the organism survival and evolution. Fungi exhibit exquisite plasticity in ploidy variation in adaptation to various environmental stresses. For example, the haploid opportunistic human fungal pathogen C. deneoformans can generate diploid blastospores during unisexual reproduction and also forms polyploid titan cells during host infection; however, the mechanisms underlying these ploidy transitions are largely unknown. In this study, we elucidated the genetic regulatory circuitry governing ploidy duplication during C. deneoformans unisexual reproduction through the identification and characterization of cell cycle regulators that are differentially expressed during unisexual reproduction. We showed that four cyclin and two cyclin-dependent kinase regulator genes function in concert to orchestrate ploidy transition during unisexual reproduction. To trace and track ploidy transition events, we also generated a ploidy reporter and revealed the formation of segmental aneuploidy in addition to diploidization, illustrating the diverse mechanisms of genome plasticity in C. deneoformans.
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Affiliation(s)
- Ci Fu
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Aaliyah Davy
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Simeon Holmes
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Vikas Yadav
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Asiya Gusa
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Marco A. Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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Sales-Lee J, Perry DS, Bowser BA, Diedrich JK, Rao B, Beusch I, Yates JR, Roy SW, Madhani HD. Coupling of spliceosome complexity to intron diversity. Curr Biol 2021; 31:4898-4910.e4. [PMID: 34555349 DOI: 10.1016/j.cub.2021.09.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/17/2021] [Accepted: 09/01/2021] [Indexed: 10/20/2022]
Abstract
We determined that over 40 spliceosomal proteins are conserved between many fungal species and humans but were lost during the evolution of S. cerevisiae, an intron-poor yeast with unusually rigid splicing signals. We analyzed null mutations in a subset of these factors, most of which had not been investigated previously, in the intron-rich yeast Cryptococcus neoformans. We found they govern splicing efficiency of introns with divergent spacing between intron elements. Importantly, most of these factors also suppress usage of weak nearby cryptic/alternative splice sites. Among these, orthologs of GPATCH1 and the helicase DHX35 display correlated functional signatures and copurify with each other as well as components of catalytically active spliceosomes, identifying a conserved G patch/helicase pair that promotes splicing fidelity. We propose that a significant fraction of spliceosomal proteins in humans and most eukaryotes are involved in limiting splicing errors, potentially through kinetic proofreading mechanisms, thereby enabling greater intron diversity.
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Affiliation(s)
- Jade Sales-Lee
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daniela S Perry
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Bradley A Bowser
- Department of Molecular and Cellular Biology, University of California, Merced, Merced, CA 95343, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Beiduo Rao
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Irene Beusch
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Scott W Roy
- Department of Biology, San Francisco State University, San Francisco, CA 94132, 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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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: 2.3] [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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