1
|
Ortiz SC, Hull CM. Biogenesis, germination, and pathogenesis of Cryptococcus spores. Microbiol Mol Biol Rev 2024; 88:e0019623. [PMID: 38440970 PMCID: PMC10966950 DOI: 10.1128/mmbr.00196-23] [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] [Indexed: 03/06/2024] Open
Abstract
SUMMARYSpores are primary infectious propagules for the majority of human fungal pathogens; however, relatively little is known about their fundamental biology. One strategy to address this deficiency has been to develop the basidiospores of Cryptococcus into a model for pathogenic spore biology. Here, we provide an update on the state of the field with a comprehensive review of the data generated from the study of Cryptococcus basidiospores from their formation (sporulation) and differentiation (germination) to their roles in pathogenesis. Importantly, we provide support for the presence of basidiospores in nature, define the key characteristics that distinguish basidiospores from yeast cells, and clarify their likely roles as infectious particles. This review is intended to demonstrate the importance of basidiospores in the field of Cryptococcus research and provide a solid foundation from which researchers who wish to study sexual spores in any fungal system can launch their studies.
Collapse
Affiliation(s)
- Sébastien C. Ortiz
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Christina M. Hull
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Kim J, Lee KT, Lee JS, Shin J, Cui B, Yang K, Choi YS, Choi N, Lee SH, Lee JH, Bahn YS, Cho SW. Fungal brain infection modelled in a human-neurovascular-unit-on-a-chip with a functional blood-brain barrier. Nat Biomed Eng 2021; 5:830-846. [PMID: 34127820 DOI: 10.1038/s41551-021-00743-8] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 04/30/2021] [Indexed: 02/05/2023]
Abstract
The neurovascular unit, which consists of vascular cells surrounded by astrocytic end-feet and neurons, controls cerebral blood flow and the permeability of the blood-brain barrier (BBB) to maintain homeostasis in the neuronal milieu. Studying how some pathogens and drugs can penetrate the human BBB and disrupt neuronal homeostasis requires in vitro microphysiological models of the neurovascular unit. Here we show that the neurotropism of Cryptococcus neoformans-the most common pathogen causing fungal meningitis-and its ability to penetrate the BBB can be modelled by the co-culture of human neural stem cells, brain microvascular endothelial cells and brain vascular pericytes in a human-neurovascular-unit-on-a-chip maintained by a stepwise gravity-driven unidirectional flow and recapitulating the structural and functional features of the BBB. We found that the pathogen forms clusters of cells that penetrate the BBB without altering tight junctions, suggesting a transcytosis-mediated mechanism. The neurovascular-unit-on-a-chip may facilitate the study of the mechanisms of brain infection by pathogens, and the development of drugs for a range of brain diseases.
Collapse
Affiliation(s)
- Jin Kim
- Department of Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Kyung-Tae Lee
- Department of Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Jong Seung Lee
- Department of Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Jisoo Shin
- Department of Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Baofang Cui
- Department of Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Kisuk Yang
- Department of Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Yi Sun Choi
- Department of Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Nakwon Choi
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea.,KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, Republic of Korea.,Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Republic of Korea
| | - Soo Hyun Lee
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea
| | - Jae-Hyun Lee
- Institute for Basic Science (IBS), Center for Nanomedicine, Seoul, Republic of Korea.,Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea
| | - Yong-Sun Bahn
- Department of Biotechnology, Yonsei University, Seoul, Republic of Korea.
| | - Seung-Woo Cho
- Department of Biotechnology, Yonsei University, Seoul, Republic of Korea. .,Institute for Basic Science (IBS), Center for Nanomedicine, Seoul, Republic of Korea. .,Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea.
| |
Collapse
|
4
|
Florez LM, Scheper RWA, Fisher BM, Sutherland PW, Templeton MD, Bowen JK. Reference genes for gene expression analysis in the fungal pathogen Neonectria ditissima and their use demonstrating expression up-regulation of candidate virulence genes. PLoS One 2020; 15:e0238157. [PMID: 33186359 PMCID: PMC7665675 DOI: 10.1371/journal.pone.0238157] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 11/01/2020] [Indexed: 11/18/2022] Open
Abstract
European canker, caused by the necrotrophic fungal phytopathogen Neonectria ditissima, is one of the most damaging apple diseases worldwide. An understanding of the molecular basis of N. ditissima virulence is currently lacking. Identification of genes with an up-regulation of expression during infection, which are therefore probably involved in virulence, is a first step towards this understanding. Reverse transcription quantitative real-time PCR (RT-qPCR) can be used to identify these candidate virulence genes, but relies on the use of reference genes for relative gene expression data normalisation. However, no report that addresses selecting appropriate fungal reference genes for use in the N. ditissima-apple pathosystem has been published to date. In this study, eight N. ditissima genes were selected as candidate RT-qPCR reference genes for gene expression analysis. A subset of the primers (six) designed to amplify regions from these genes were specific for N. ditissima, failing to amplify PCR products with template from other fungal pathogens present in the apple orchard. The efficiency of amplification of these six primer sets was satisfactory, ranging from 81.8 to 107.53%. Analysis of expression stability when a highly pathogenic N. ditissima isolate was cultured under 10 regimes, using the statistical algorithms geNorm, NormFinder and BestKeeper, indicated that actin and myo-inositol-1-phosphate synthase (mips), or their combination, could be utilised as the most suitable reference genes for normalisation of N. ditissima gene expression. As a test case, these reference genes were used to study expression of three candidate virulence genes during a time course of infection. All three, which shared traits with fungal effector genes, had up-regulated expression in planta compared to in vitro with expression peaking between five and six weeks post inoculation (wpi). Thus, these three genes may well be involved in N. ditissima pathogenicity and are priority candidates for further functional characterization.
Collapse
Affiliation(s)
- Liz M. Florez
- Bioprotection, The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Reiny W. A. Scheper
- Bioprotection, The New Zealand Institute for Plant & Food Research Limited, Havelock North, New Zealand
| | - Brent M. Fisher
- Bioprotection, The New Zealand Institute for Plant & Food Research Limited, Havelock North, New Zealand
| | - Paul W. Sutherland
- Food Innovation, The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | - Matthew D. Templeton
- Bioprotection, The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Joanna K. Bowen
- Bioprotection, The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
- * E-mail:
| |
Collapse
|
5
|
Sun S, Coelho MA, David-Palma M, Priest SJ, Heitman J. The Evolution of Sexual Reproduction and the Mating-Type Locus: Links to Pathogenesis of Cryptococcus Human Pathogenic Fungi. Annu Rev Genet 2019; 53:417-444. [PMID: 31537103 PMCID: PMC7025156 DOI: 10.1146/annurev-genet-120116-024755] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cryptococcus species utilize a variety of sexual reproduction mechanisms, which generate genetic diversity, purge deleterious mutations, and contribute to their ability to occupy myriad environmental niches and exhibit a range of pathogenic potential. The bisexual and unisexual cycles of pathogenic Cryptococcus species are stimulated by properties associated with their environmental niches and proceed through well-characterized signaling pathways and corresponding morphological changes. Genes governing mating are encoded by the mating-type (MAT) loci and influence pathogenesis, population dynamics, and lineage divergence in Cryptococcus. MAT has undergone significant evolutionary changes within the Cryptococcus genus, including transition from the ancestral tetrapolar state in nonpathogenic species to a bipolar mating system in pathogenic species, as well as several internal reconfigurations. Owing to the variety of established sexual reproduction mechanisms and the robust characterization of the evolution of mating and MAT in this genus, Cryptococcus species provide key insights into the evolution of sexual reproduction.
Collapse
Affiliation(s)
- Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA;
| | - Marco A Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA;
| | - Márcia David-Palma
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA;
| | - Shelby J Priest
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA;
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA;
| |
Collapse
|
6
|
Chen KH, Liao HL, Bellenger JP, Lutzoni F. Differential gene expression associated with fungal trophic shifts along the senescence gradient of the moss Dicranum scoparium. Environ Microbiol 2019; 21:2273-2289. [PMID: 30900793 DOI: 10.1111/1462-2920.14605] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/19/2019] [Accepted: 03/21/2019] [Indexed: 02/05/2023]
Abstract
Bryophytes harbour microbiomes, including diverse communities of fungi. The molecular mechanisms by which perennial mosses interact with these fungal partners along their senescence gradients are unknown, yet this is an ideal system to study variation in gene expression associated with trophic state transitions. We investigated differentially expressed genes of fungal communities and their host Dicranum scoparium across its naturally occurring senescence gradient using a metatranscriptomic approach. Higher activity of fungal nutrient-related (carbon, nitrogen, phosphorus and sulfur) transporters and Carbohydrate-Active enZyme (CAZy) genes was detected toward the bottom, partially decomposed, layer of the moss. The most prominent variation in the expression levels of fungal nutrient transporters was from inorganic nitrogen-related transporters, whereas the breakdown of organonitrogens was detected as the most enriched gene ontology term for the host D. scoparium, for those transcripts having higher expression in the partially decomposed layer. The abundance of bacterial rRNA transcripts suggested that more living members of Cyanobacteria are associated with the photosynthetic layer of D. scoparium, while members of Rhizobiales are detected throughout the gametophytes. Plant genes for specific fungal-plant communication, including defense responses, were differentially expressed, suggesting that different genetic pathways are involved in plant-microbe crosstalk in photosynthetic tissues compared to partially decomposed tissues.
Collapse
Affiliation(s)
- Ko-Hsuan Chen
- Department of Biology, Duke University, Durham, NC, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, Quincy, FL, USA
| | | | | |
Collapse
|
7
|
Rutherford JC, Bahn YS, van den Berg B, Heitman J, Xue C. Nutrient and Stress Sensing in Pathogenic Yeasts. Front Microbiol 2019; 10:442. [PMID: 30930866 PMCID: PMC6423903 DOI: 10.3389/fmicb.2019.00442] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 02/20/2019] [Indexed: 12/23/2022] Open
Abstract
More than 1.5 million fungal species are estimated to live in vastly different environmental niches. Despite each unique host environment, fungal cells sense certain fundamentally conserved elements, such as nutrients, pheromones and stress, for adaptation to their niches. Sensing these extracellular signals is critical for pathogens to adapt to the hostile host environment and cause disease. Hence, dissecting the complex extracellular signal-sensing mechanisms that aid in this is pivotal and may facilitate the development of new therapeutic approaches to control fungal infections. In this review, we summarize the current knowledge on how two important pathogenic yeasts, Candida albicans and Cryptococcus neoformans, sense nutrient availability, such as carbon sources, amino acids, and ammonium, and different stress signals to regulate their morphogenesis and pathogenicity in comparison with the non-pathogenic model yeast Saccharomyces cerevisiae. The molecular interactions between extracellular signals and their respective sensory systems are described in detail. The potential implication of analyzing nutrient and stress-sensing systems in antifungal drug development is also discussed.
Collapse
Affiliation(s)
- Julian C Rutherford
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Yong-Sun Bahn
- Department of Biotechnology, Yonsei University, Seoul, South Korea
| | - Bert van den Berg
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, United States
| | - Chaoyang Xue
- Public Health Research Institute, Rutgers University, Newark, NJ, United States.,Department of Molecular Genetics, Biochemistry and Microbiology, Rutgers University, Newark, NJ, United States
| |
Collapse
|
8
|
Desjardins CA, Giamberardino C, Sykes SM, Yu CH, Tenor JL, Chen Y, Yang T, Jones AM, Sun S, Haverkamp MR, Heitman J, Litvintseva AP, Perfect JR, Cuomo CA. Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans. Genome Res 2018; 27:1207-1219. [PMID: 28611159 PMCID: PMC5495072 DOI: 10.1101/gr.218727.116] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 05/01/2017] [Indexed: 12/23/2022]
Abstract
Cryptococcus neoformans is an opportunistic fungal pathogen that causes approximately 625,000 deaths per year from nervous system infections. Here, we leveraged a unique, genetically diverse population of C. neoformans from sub-Saharan Africa, commonly isolated from mopane trees, to determine how selective pressures in the environment coincidentally adapted C. neoformans for human virulence. Genome sequencing and phylogenetic analysis of 387 isolates, representing the global VNI and African VNB lineages, highlighted a deep, nonrecombining split in VNB (herein, VNBI and VNBII). VNBII was enriched for clinical samples relative to VNBI, while phenotypic profiling of 183 isolates demonstrated that VNBI isolates were significantly more resistant to oxidative stress and more heavily melanized than VNBII isolates. Lack of melanization in both lineages was associated with loss-of-function mutations in the BZP4 transcription factor. A genome-wide association study across all VNB isolates revealed sequence differences between clinical and environmental isolates in virulence factors and stress response genes. Inositol transporters and catabolism genes, which process sugars present in plants and the human nervous system, were identified as targets of selection in all three lineages. Further phylogenetic and population genomic analyses revealed extensive loss of genetic diversity in VNBI, suggestive of a history of population bottlenecks, along with unique evolutionary trajectories for mating type loci. These data highlight the complex evolutionary interplay between adaptation to natural environments and opportunistic infections, and that selection on specific pathways may predispose isolates to human virulence.
Collapse
Affiliation(s)
| | - Charles Giamberardino
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Sean M Sykes
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Chen-Hsin Yu
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Jennifer L Tenor
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Yuan Chen
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Timothy Yang
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Alexander M Jones
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Miriam R Haverkamp
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Anastasia P Litvintseva
- Mycotic Diseases Branch, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30329, USA
| | - John R Perfect
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Christina A Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| |
Collapse
|
9
|
Role of the inositol pyrophosphate multikinase Kcs1 in Cryptococcus inositol metabolism. Fungal Genet Biol 2018; 113:42-51. [PMID: 29357302 DOI: 10.1016/j.fgb.2018.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 01/08/2018] [Accepted: 01/14/2018] [Indexed: 12/20/2022]
Abstract
Cryptococcus neoformans is the most common cause of deadly fungal meningitis. This fungus has a complex inositol acquisition and utilization system, and our previous studies have shown the importance of inositol utilization in cryptococcal development and virulence. However, how inositol utilization is regulated in this fungus remains unknown. In this study, we found that inositol, irrespective of the presence of glucose in the media, represses the expression of C. neoformans genes involved in inositol pyrophosphate biosynthesis, including the gene encoding inositol hexakisphosphate kinase Kcs1. Kcs1 was recently reported to regulate inositol metabolism in Saccharomyces cerevisiae and to impact virulence in C. neoformans. To examine the potential role of Kcs1 in inositol regulation in C. neoformans, we generated the kcs1Δ mutant and compared its phenotype with the wild type strain. We found that Kcs1 negatively regulates inositol uptake and catabolism in C. neoformans, but, in contrast to Kcs1 function in S. cerevisiae, does not appear to regulate inositol biosynthesis. Together, these results show that Kcs1 functions to fine-tune inositol acquisition to maintain inositol homeostasis in C. neoformans.
Collapse
|
10
|
Lee WD, Fong JJ, Eimes JA, Lim YW. Diversity and abundance of human-pathogenic fungi associated with pigeon faeces in urban environments. Mol Ecol 2017. [DOI: 10.1111/mec.14216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Won Dong Lee
- School of Biological Sciences; Seoul National University; Seoul Korea
- Faculty of Biology; Technion-Israel Institute of Technology; Haifa Israel
| | | | - John A. Eimes
- School of Biological Sciences; Seoul National University; Seoul Korea
- University College; Sungkyunkwan University; Suwon Korea
| | - Young Woon Lim
- School of Biological Sciences; Seoul National University; Seoul Korea
| |
Collapse
|
11
|
Abstract
To respond to the changing environment, cells must be able to sense external conditions. This is important for many processes including growth, mating, the expression of virulence factors, and several other regulatory effects. Nutrient sensing at the plasma membrane is mediated by different classes of membrane proteins that activate downstream signaling pathways: nontransporting receptors, transceptors, classical and nonclassical G-protein-coupled receptors, and the newly defined extracellular mucin receptors. Nontransporting receptors have the same structure as transport proteins, but have lost the capacity to transport while gaining a receptor function. Transceptors are transporters that also function as a receptor, because they can rapidly activate downstream signaling pathways. In this review, we focus on these four types of fungal membrane proteins. We mainly discuss the sensing mechanisms relating to sugars, ammonium, and amino acids. Mechanisms for other nutrients, such as phosphate and sulfate, are discussed briefly. Because the model yeast Saccharomyces cerevisiae has been the most studied, especially regarding these nutrient-sensing systems, each subsection will commence with what is known in this species.
Collapse
|
12
|
Xie N, Ruprich-Robert G, Chapeland-Leclerc F, Coppin E, Lalucque H, Brun S, Debuchy R, Silar P. Inositol-phosphate signaling as mediator for growth and sexual reproduction in Podospora anserina. Dev Biol 2017. [PMID: 28629791 DOI: 10.1016/j.ydbio.2017.06.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The molecular pathways involved in the development of multicellular fruiting bodies in fungi are still not well known. Especially, the interplay between the mycelium, the female tissues and the zygotic tissues of the fruiting bodies is poorly documented. Here, we describe PM154, a new strain of the model ascomycetes Podospora anserina able to mate with itself and that enabled the easy recovery of new mutants affected in fruiting body development. By complete genome sequencing of spod1, one of the new mutants, we identified an inositol phosphate polykinase gene as essential, especially for fruiting body development. A factor present in the wild type and diffusible in mutant hyphae was able to induce the development of the maternal tissues of the fruiting body in spod1, but failed to promote complete development of the zygotic ones. Addition of myo-inositol in the growth medium was able to increase the number of developing fruiting bodies in the wild type, but not in spod1. Overall, the data indicated that inositol and inositol polyphosphates were involved in promoting fruiting body maturation, but also in regulating the number of fruiting bodies that developed after fertilization. The same effect of inositol was seen in two other fungi, Sordaria macrospora and Chaetomium globosum. Key role of the inositol polyphosphate pathway during fruiting body maturation appears thus conserved during the evolution of Sordariales fungi.
Collapse
Affiliation(s)
- Ning Xie
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; Univ Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, 75205 Paris Cedex 13, France
| | - Gwenaël Ruprich-Robert
- Univ Paris Descartes, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, 75205 Paris Cedex 13, France
| | - Florence Chapeland-Leclerc
- Univ Paris Descartes, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, 75205 Paris Cedex 13, France
| | - Evelyne Coppin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Hervé Lalucque
- Univ Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, 75205 Paris Cedex 13, France
| | - Sylvain Brun
- Univ Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, 75205 Paris Cedex 13, France
| | - Robert Debuchy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Philippe Silar
- Univ Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, 75205 Paris Cedex 13, France.
| |
Collapse
|
13
|
Abstract
Fungi in the genus Pneumocystis live in the lungs of mammals, where they can cause a fatal pneumonia (PCP [Pneumocystis pneumonia]) in hosts with compromised immune systems. The absence of a continuous in vitro culture system for any species of Pneumocystis has led to limited understanding of these fungi, especially for the discovery of new therapies. We recently reported that Pneumocystis carinii, Pneumocystis murina, and most significantly, Pneumocystis jirovecii lack both enzymes necessary for myo-inositol biosynthesis but contain genes with homologies to fungal myo-inositol transporters. Since myo-inositol is essential for eukaryotic viability, the primary transporter, ITR1, was functionally and structurally characterized in P. carinii The predicted structure of P. carinii ITR1 (PcITR1) contained 12 transmembrane alpha-helices with intracellular C and N termini, consistent with other inositol transporters. The apparent Km was 0.94 ± 0.08 (mean ± standard deviation), suggesting that myo-inositol transport in P. carinii is likely through a low-affinity, highly selective transport system, as no other sugars or inositol stereoisomers were significant competitive inhibitors. Glucose transport was shown to use a different transport system. The myo-inositol transport was distinct from mammalian transporters, as it was not sodium dependent and was cytochalasin B resistant. Inositol transport in these fungi offers an attractive new drug target because of the reliance of the fungi on its transport, clear differences between the mammalian and fungal transporters, and the ability of the host to both synthesize and transport this critical nutrient, predicting low toxicity of potential inhibitors to the fungal transporter. IMPORTANCE myo-Inositol is a sugarlike nutrient that is essential for life in most organisms. Humans and microbes alike can obtain it by making it, which involves only 2 enzymes, by taking it from the environment by a transport process, or by recycling it from other cellular constituents. Inspection of the genomes of the pathogenic fungi of the genus Pneumocystis showed that these pneumonia-causing parasites could not make myo-inositol, as they lacked the 2 enzymes. Instead, we found evidence of inositol transporters, which would import the sugar from the lungs where the fungi reside. In the present report, we characterized the transport of myo-inositol in the fungus and found that the transporter was highly selective for myo-inositol and did not transport any other molecules. The transport was distinct from that in mammalian cells, and since mammals can both make and transport myo-inositol, while Pneumocystis fungi must transport it, this process offers a potential new drug target.
Collapse
|
14
|
Yang J, Barrila J, Roland KL, Kilbourne J, Ott CM, Forsyth RJ, Nickerson CA. Characterization of the Invasive, Multidrug Resistant Non-typhoidal Salmonella Strain D23580 in a Murine Model of Infection. PLoS Negl Trop Dis 2015; 9:e0003839. [PMID: 26091096 PMCID: PMC4474555 DOI: 10.1371/journal.pntd.0003839] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/18/2015] [Indexed: 01/09/2023] Open
Abstract
A distinct pathovar of Salmonella enterica serovar Typhimurium, ST313, has emerged in sub-Saharan Africa as a major cause of fatal bacteremia in young children and HIV-infected adults. D23580, a multidrug resistant clinical isolate of ST313, was previously shown to have undergone genome reduction in a manner that resembles that of the more human-restricted pathogen, Salmonella enterica serovar Typhi. It has since been shown through tissue distribution studies that D23580 is able to establish an invasive infection in chickens. However, it remains unclear whether ST313 can cause lethal disease in a non-human host following a natural course of infection. Herein we report that D23580 causes lethal and invasive disease in a murine model of infection following peroral challenge. The LD50 of D23580 in female BALB/c mice was 4.7 x 105 CFU. Tissue distribution studies performed 3 and 5 days post-infection confirmed that D23580 was able to more rapidly colonize the spleen, mesenteric lymph nodes and gall bladder in mice when compared to the well-characterized S. Typhimurium strain SL1344. D23580 exhibited enhanced resistance to acid stress relative to SL1344, which may lend towards increased capability to survive passage through the gastrointestinal tract as well as during its intracellular lifecycle. Interestingly, D23580 also displayed higher swimming motility relative to SL1344, S. Typhi strain Ty2, and the ST313 strain A130. Biochemical tests revealed that D23580 shares many similar metabolic features with SL1344, with several notable differences in the Voges-Proskauer and catalase tests, as well alterations in melibiose, and inositol utilization. These results represent the first full duration infection study using an ST313 strain following the entire natural course of disease progression, and serve as a benchmark for ongoing and future studies into the pathogenesis of D23580. A deadly form of non-typhoidal Salmonella has emerged as a major cause of invasive disease in sub-Saharan Africa. Initial genomic profiling of this novel Salmonella sequence type, ST313, indicated that although it is technically classified as S. Typhimurium (a serovar characterized by a broad host range), it may be evolving towards becoming a more human-specific, ‘typhoid-like’ pathogen. However, it was recently demonstrated that ST313 strains were indeed able to establish an invasive and damaging infection in chickens. Despite these important findings, it remains unclear whether ST313 is able to cause lethal disease in a non-human host, since no study has yet followed the entire natural course of disease progression. As such, there are no data available concerning the median lethal dose (LD50) of any ST313 strain. This is an important metric, as the LD50 value will serve as a benchmark for mechanistic studies focused on understanding the relationship between virulence and the phenotypic and molecular genetic attributes associated with ST313 infections. Here we report that D23580 causes lethal disease in BALB/c mice and determined the LD50 following peroral challenge. Phenotypic characterization revealed distinct differences in tissue distribution, acid stress resistance, and biochemical utilization between D23580 and the ‘classic’ Typhimurium strain SL1344.
Collapse
Affiliation(s)
- Jiseon Yang
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Jennifer Barrila
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Kenneth L. Roland
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Jacquelyn Kilbourne
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - C. Mark Ott
- Biomedical Research and Environmental Sciences Division, NASA Johnson Space Center, Houston, Texas, United States of America
| | - Rebecca J. Forsyth
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Cheryl A. Nickerson
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- * E-mail:
| |
Collapse
|
15
|
Finding the sweet spot: how human fungal pathogens acquire and turn the sugar inositol against their hosts. mBio 2015; 6:e00109. [PMID: 25736882 PMCID: PMC4358016 DOI: 10.1128/mbio.00109-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Inositol is an essential nutrient with important structural and signaling functions in eukaryotes. Its role in microbial pathogenesis has been reported in fungi, protozoans, and eubacteria. In a recent article, Porollo et al. [mBio 5(6):e01834-14, 2014, doi:10.1128/mBio.01834-14] demonstrated the importance of inositol metabolism in the development and viability of Pneumocystis species—obligate fungal pathogens that remain unculturable in vitro. To understand their obligate nature, the authors used innovative comparative genomic approaches and discovered that Pneumocystis spp. are inositol auxotrophs due to the lack of inositol biosynthetic enzymes and that inositol insufficiency is a contributing factor preventing fungal growth in vitro. This work is in accord with other studies suggesting that inositol plays a conserved role in microbial pathogenesis. Inositol uptake and metabolism therefore may represent novel antimicrobial drug targets. Using comparative genomics to analyze metabolic pathways offers a powerful tool to gain new insights into nutrient utilization in microbes, especially obligate pathogens.
Collapse
|
16
|
Comparative genomics of pneumocystis species suggests the absence of genes for myo-inositol synthesis and reliance on inositol transport and metabolism. mBio 2014; 5:e01834. [PMID: 25370490 PMCID: PMC4222102 DOI: 10.1128/mbio.01834-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
UNLABELLED In the context of deciphering the metabolic strategies of the obligate pathogenic fungi in the genus Pneumocystis, the genomes of three species (P. carinii, P. murina, and P. jirovecii) were compared among themselves and with the free-living, phylogenetically related fission yeast (Schizosaccharomyces pombe). The underrepresentation of amino acid metabolism pathways compared to those in S. pombe, as well as the incomplete steroid biosynthesis pathway, were confirmed for P. carinii and P. jirovecii and extended to P. murina. All three Pneumocystis species showed overrepresentation of the inositol phosphate metabolism pathway compared to that in the fission yeast. In addition to those known in S. pombe, four genes, encoding inositol-polyphosphate multikinase (EC 2.7.1.151), inositol-pentakisphosphate 2-kinase (EC 2.7.1.158), phosphoinositide 5-phosphatase (EC 3.1.3.36), and inositol-1,4-bisphosphate 1-phosphatase (EC 3.1.3.57), were identified in the two rodent Pneumocystis genomes, P. carinii and P. murina. The P. jirovecii genome appeared to contain three of these genes but lacked phosphoinositide 5-phosphatase. Notably, two genes encoding enzymes essential for myo-inositol synthesis, inositol-1-phosphate synthase (INO1) and inositol monophosphatase (INM1), were absent from all three genomes, suggesting that Pneumocystis species are inositol auxotrophs. In keeping with the need to acquire exogenous inositol, two genes with products homologous to fungal inositol transporters, ITR1 and ITR2, were identified in P. carinii and P. murina, while P. jirovecii contained only the ITR1 homolog. The ITR and inositol metabolism genes in P. murina and P. carinii were expressed during fulminant infection as determined by reverse transcriptase real-time PCR of cDNA from infected lung tissue. Supplementation of in vitro culture with inositol yielded significant improvement of the viability of P. carinii for days 7 through 14. IMPORTANCE Microbes in the genus Pneumocystis are obligate pathogenic fungi that reside in mammalian lungs and cause Pneumocystis pneumonia in hosts with weakened immune systems. These fungal infections are not responsive to standard antifungal therapy. A long-term in vitro culture system is not available for these fungi, impeding the study of their biology and genetics and new drug development. Given that all genomes of the Pneumocystis species analyzed lack the genes for inositol synthesis and contain inositol transporters, Pneumocystis fungi, like S. pombe, appear to be inositol auxotrophs. Inositol is important for the pathogenesis, virulence, and mating processes in Candida albicans and Cryptococcus neoformans, suggesting similar importance within the Pneumocystis species as well. This is the first report to (i) characterize genes in the inositol phosphate metabolism and transport pathways in Pneumocystis species and (ii) identify inositol as a supplement that improved the viability of P. carinii in in vitro culture.
Collapse
|
17
|
Implication of lateral genetic transfer in the emergence of Aeromonas hydrophila isolates of epidemic outbreaks in channel catfish. PLoS One 2013; 8:e80943. [PMID: 24278351 PMCID: PMC3835674 DOI: 10.1371/journal.pone.0080943] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 10/08/2013] [Indexed: 01/29/2023] Open
Abstract
To investigate the molecular basis of the emergence of Aeromonas hydrophila responsible for an epidemic outbreak of motile aeromonad septicemia of catfish in the Southeastern United States, we sequenced 11 A. hydrophila isolates that includes five reference and six recent epidemic isolates. Comparative genomics revealed that recent epidemic A. hydrophila isolates are highly clonal, whereas reference isolates are greatly diverse. We identified 55 epidemic-associated genetic regions with 313 predicted genes that are present in epidemic isolates but absent from reference isolates and 35% of these regions are located within genomic islands, suggesting their acquisition through lateral gene transfer. The epidemic-associated regions encode predicted prophage elements, pathogenicity islands, metabolic islands, fitness islands and genes of unknown functions, and 34 of the genes encoded in these regions were predicted as virulence factors. We found two pilus biogenesis gene clusters encoded within predicted pathogenicity islands. A functional metabolic island that encodes a complete pathway for myo-inositol catabolism was evident by the ability of epidemic A. hydrophila isolates to use myo-inositol as a sole carbon source. Testing of A. hydrophila field isolates found a consistent correlation between myo-inositol utilization as a sole carbon source and the presence of an epidemic-specific genetic marker. All epidemic isolates and one reference isolate shared a novel O-antigen cluster. Altogether we identified four different O-antigen biosynthesis gene clusters within the 11 sequenced A. hydrophila genomes. Our study reveals new insights into the evolutionary changes that have resulted in the emergence of recent epidemic A. hydrophila strains.
Collapse
|
18
|
Hagen F, Ceresini PC, Polacheck I, Ma H, van Nieuwerburgh F, Gabaldón T, Kagan S, Pursall ER, Hoogveld HL, van Iersel LJJ, Klau GW, Kelk SM, Stougie L, Bartlett KH, Voelz K, Pryszcz LP, Castañeda E, Lazera M, Meyer W, Deforce D, Meis JF, May RC, Klaassen CHW, Boekhout T. Ancient dispersal of the human fungal pathogen Cryptococcus gattii from the Amazon rainforest. PLoS One 2013; 8:e71148. [PMID: 23940707 PMCID: PMC3737135 DOI: 10.1371/journal.pone.0071148] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 06/25/2013] [Indexed: 11/19/2022] Open
Abstract
Over the past two decades, several fungal outbreaks have occurred, including the high-profile ‘Vancouver Island’ and ‘Pacific Northwest’ outbreaks, caused by Cryptococcus gattii, which has affected hundreds of otherwise healthy humans and animals. Over the same time period, C. gattii was the cause of several additional case clusters at localities outside of the tropical and subtropical climate zones where the species normally occurs. In every case, the causative agent belongs to a previously rare genotype of C. gattii called AFLP6/VGII, but the origin of the outbreak clades remains enigmatic. Here we used phylogenetic and recombination analyses, based on AFLP and multiple MLST datasets, and coalescence gene genealogy to demonstrate that these outbreaks have arisen from a highly-recombining C. gattii population in the native rainforest of Northern Brazil. Thus the modern virulent C. gattii AFLP6/VGII outbreak lineages derived from mating events in South America and then dispersed to temperate regions where they cause serious infections in humans and animals.
Collapse
Affiliation(s)
- Ferry Hagen
- Department of Yeast and Basidiomycete Research, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Paulo C. Ceresini
- Department of Phytopathology, UNESP - University of São Paulo State, Ilha Solteira Campus, Ilha Solteira, Brazil
| | - Itzhack Polacheck
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Hansong Ma
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Filip van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG) and UPF Doctor Aiguader, Barcelona, Spain
| | - Sarah Kagan
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - E. Rhiannon Pursall
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Hans L. Hoogveld
- Netherlands Institute of Ecology (NIOO-KNAW), Centre for Limnology, Wageningen, The Netherlands
| | | | - Gunnar W. Klau
- Centrum Wiskunde & Informatica (CWI), Amsterdam, The Netherlands
| | - Steven M. Kelk
- Centrum Wiskunde & Informatica (CWI), Amsterdam, The Netherlands
| | - Leen Stougie
- Centrum Wiskunde & Informatica (CWI), Amsterdam, The Netherlands
- Department of Operations Research, VU University, Amsterdam, The Netherlands
| | - Karen H. Bartlett
- School of Environmental Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kerstin Voelz
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Leszek P. Pryszcz
- Centre for Genomic Regulation (CRG) and UPF Doctor Aiguader, Barcelona, Spain
| | - Elizabeth Castañeda
- Instituto Nacional de Salud, Grupo de Microbiología, Zona 6 CAN, Bogotá, Colombia
| | - Marcia Lazera
- Laboratorio de Micologia, Instituto de Pesquisa Clinica Evandro Chagas, Fundaçao Oswaldo Cruz – FIOCRUZ, Rio de Janeiro, Brazil
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Center for Infectious Diseases and Microbiology, Westmead Millennium Institute, Sydney Emerging Disease and Biosecurity Institute, Sydney Medical School – Westmead Hospital, University of Sydney, Westmead, NSW, Australia
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Robin C. May
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Corné H. W. Klaassen
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Teun Boekhout
- Department of Yeast and Basidiomycete Research, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
- Shanghai Key Laboratory of Molecular Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
- Department of Internal Medicine and Infectious Diseases, University Medical Center, Utrecht, The Netherlands
- * E-mail:
| |
Collapse
|
19
|
Gonzalez-Fernandez R, Aloria K, Arizmendi JM, Jorrin-Novo JV. Application of label-free shotgun nUPLC-MS(E) and 2-DE approaches in the study of Botrytis cinerea mycelium. J Proteome Res 2013; 12:3042-56. [PMID: 23627497 DOI: 10.1021/pr3010937] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The phytopathogenic fungus Botrytis cinerea infects more than different 200 plant species and causes substantial losses in numerous crops. The B05.10 and T4 wild-type strain genomes have been recently sequenced, becoming a model system for necrotrophic pathogens, as well as opening up new alternatives in functional genomics, such as proteomics. We analyzed B. cinerea mycelium from these two wild-type strains, introducing label-free shotgun nUPLC-MS(E) methodology to complement the 2-DE-MS-based approach. We assessed the label-free nUPLC-MS(E) methodology for protein identification and quantification using five mycelium protein dilutions. A total of 225 and 170 protein species were identified by nUPLC-MS(E) in the B05.10 and T4 strains, respectively. Moreover, 129 protein species were quantified in both strains. Significant differences in protein abundance were found in 15 more abundant and 16 less abundant protein species in the B05.10 strain compared to the T4 strain. Twenty-nine qualitative and 15 significant quantitative differences were found using 2-DE. The label-free nUPLC-MS(E) was a reliable, reproducible and sensitive method for protein identification and quantification to study the B. cinerea mycelial proteome. Results obtained by gel-based and gel-free complementary approaches allow a deeper characterization of this fungus, as well as the identification of potential virulence factors.
Collapse
Affiliation(s)
- Raquel Gonzalez-Fernandez
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba, Agrifood Campus of International Excellence, ceiA3, 14071-Córdoba, Spain
| | | | | | | |
Collapse
|
20
|
Shepardson KM, Cramer RA. Fungal cell wall dynamics and infection site microenvironments: signal integration and infection outcome. Curr Opin Microbiol 2013; 16:385-90. [PMID: 23597789 DOI: 10.1016/j.mib.2013.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 03/11/2013] [Indexed: 10/27/2022]
Abstract
Upon entrance into the host, fungi encounter a myriad of host effector products and microenvironments that they sense and adapt to for survival. Alterations of the structure and composition of the cell wall is a major fungal adaptation mechanism to evade these environments. Here we discuss recent findings of host-microenvironmental induced fungal cell wall changes, including structure, composition, and protein content, and their effects on host immune responses. A take home message from these recent studies is an emerging understanding of how integration of multiple signals, of both fungal and host responses to dynamic infection site microenvironments, determines outcomes of infection. A challenge moving forward is to further understand these mechanisms and harness them for therapeutic benefit.
Collapse
|
21
|
Xu N, Liu L, Zou W, Liu J, Hua Q, Chen J. Reconstruction and analysis of the genome-scale metabolic network of Candida glabrata. ACTA ACUST UNITED AC 2013; 9:205-16. [DOI: 10.1039/c2mb25311a] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|