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Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species.
Lind AL, Wisecaver JH, Lameiras C, Wiemann P, Palmer JM, Keller NP, Rodrigues F, Goldman GH, Rokas A
(2017) PLoS Biol 15: e2003583
MeSH Terms: Alleles, Aspergillus fumigatus, Biological Evolution, Fungal Proteins, Fungi, Genetic Variation, Genome, Fungal, Genomics, Metabolic Networks and Pathways, Multigene Family, Mutation, Polymorphism, Genetic, Secondary Metabolism
Show Abstract · Added March 21, 2018
Filamentous fungi produce a diverse array of secondary metabolites (SMs) critical for defense, virulence, and communication. The metabolic pathways that produce SMs are found in contiguous gene clusters in fungal genomes, an atypical arrangement for metabolic pathways in other eukaryotes. Comparative studies of filamentous fungal species have shown that SM gene clusters are often either highly divergent or uniquely present in one or a handful of species, hampering efforts to determine the genetic basis and evolutionary drivers of SM gene cluster divergence. Here, we examined SM variation in 66 cosmopolitan strains of a single species, the opportunistic human pathogen Aspergillus fumigatus. Investigation of genome-wide within-species variation revealed 5 general types of variation in SM gene clusters: nonfunctional gene polymorphisms; gene gain and loss polymorphisms; whole cluster gain and loss polymorphisms; allelic polymorphisms, in which different alleles corresponded to distinct, nonhomologous clusters; and location polymorphisms, in which a cluster was found to differ in its genomic location across strains. These polymorphisms affect the function of representative A. fumigatus SM gene clusters, such as those involved in the production of gliotoxin, fumigaclavine, and helvolic acid as well as the function of clusters with undefined products. In addition to enabling the identification of polymorphisms, the detection of which requires extensive genome-wide synteny conservation (e.g., mobile gene clusters and nonhomologous cluster alleles), our approach also implicated multiple underlying genetic drivers, including point mutations, recombination, and genomic deletion and insertion events as well as horizontal gene transfer from distant fungi. Finally, most of the variants that we uncover within A. fumigatus have been previously hypothesized to contribute to SM gene cluster diversity across entire fungal classes and phyla. We suggest that the drivers of genetic diversity operating within a fungal species shown here are sufficient to explain SM cluster macroevolutionary patterns.
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13 MeSH Terms
MybA, a transcription factor involved in conidiation and conidial viability of the human pathogen Aspergillus fumigatus.
Valsecchi I, Sarikaya-Bayram Ö, Wong Sak Hoi J, Muszkieta L, Gibbons J, Prevost MC, Mallet A, Krijnse-Locker J, Ibrahim-Granet O, Mouyna I, Carr P, Bromley M, Aimanianda V, Yu JH, Rokas A, Braus GH, Saveanu C, Bayram Ö, Latgé JP
(2017) Mol Microbiol 105: 880-900
MeSH Terms: Aspergillosis, Aspergillus fumigatus, Cell Wall, Fungal Proteins, Gene Deletion, Gene Expression Regulation, Fungal, Humans, Membrane Proteins, Sequence Deletion, Spores, Fungal, Transcription Factors, Virulence
Show Abstract · Added March 21, 2018
Aspergillus fumigatus, a ubiquitous human fungal pathogen, produces asexual spores (conidia), which are the main mode of propagation, survival and infection of this human pathogen. In this study, we present the molecular characterization of a novel regulator of conidiogenesis and conidial survival called MybA because the predicted protein contains a Myb DNA binding motif. Cellular localization of the MybA::Gfp fusion and immunoprecipitation of the MybA::Gfp or MybA::3xHa protein showed that MybA is localized to the nucleus. RNA sequencing data and a uidA reporter assay indicated that the MybA protein functions upstream of wetA, vosA and velB, the key regulators involved in conidial maturation. The deletion of mybA resulted in a very significant reduction in the number and viability of conidia. As a consequence, the ΔmybA strain has a reduced virulence in an experimental murine model of aspergillosis. RNA-sequencing and biochemical studies of the ΔmybA strain suggested that MybA protein controls the expression of enzymes involved in trehalose biosynthesis as well as other cell wall and membrane-associated proteins and ROS scavenging enzymes. In summary, MybA protein is a new key regulator of conidiogenesis and conidial maturation and survival, and plays a crucial role in propagation and virulence of A. fumigatus.
© 2017 John Wiley & Sons Ltd.
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12 MeSH Terms
Zinc and Manganese Chelation by Neutrophil S100A8/A9 (Calprotectin) Limits Extracellular Aspergillus fumigatus Hyphal Growth and Corneal Infection.
Clark HL, Jhingran A, Sun Y, Vareechon C, de Jesus Carrion S, Skaar EP, Chazin WJ, Calera JA, Hohl TM, Pearlman E
(2016) J Immunol 196: 336-44
MeSH Terms: Adolescent, Adult, Aged, Animals, Aspergillus fumigatus, Biological Transport, Calgranulin A, Calgranulin B, Chelating Agents, Cornea, Disease Models, Animal, Humans, Hyphae, Keratitis, Leukocyte L1 Antigen Complex, Manganese, Mice, Mice, Inbred C57BL, Mice, Knockout, Middle Aged, Neutrophils, Phagocytosis, Pulmonary Aspergillosis, Spores, Fungal, Young Adult, Zinc
Show Abstract · Added February 5, 2016
Calprotectin, a heterodimer of S100A8 and S100A9, is an abundant neutrophil protein that possesses antimicrobial activity primarily because of its ability to chelate zinc and manganese. In the current study, we showed that neutrophils from calprotectin-deficient S100A9(-/-) mice have an impaired ability to inhibit Aspergillus fumigatus hyphal growth in vitro and in infected corneas in a murine model of fungal keratitis; however, the ability to inhibit hyphal growth was restored in S100A9(-/-) mice by injecting recombinant calprotectin. Furthermore, using recombinant calprotectin with mutations in either the Zn and Mn binding sites or the Mn binding site alone, we show that both zinc and manganese binding are necessary for calprotectin's antihyphal activity. In contrast to hyphae, we found no role for neutrophil calprotectin in uptake or killing of intracellular A. fumigatus conidia either in vitro or in a murine model of pulmonary aspergillosis. We also found that an A. fumigatus ∆zafA mutant, which demonstrates deficient zinc transport, exhibits impaired growth in infected corneas and following incubation with neutrophils or calprotectin in vitro as compared with wild-type. Collectively, these studies demonstrate a novel stage-specific susceptibility of A. fumigatus to zinc and manganese chelation by neutrophil-derived calprotectin.
Copyright © 2015 by The American Association of Immunologists, Inc.
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26 MeSH Terms
Structure-Functional Characterization of Cytochrome P450 Sterol 14α-Demethylase (CYP51B) from Aspergillus fumigatus and Molecular Basis for the Development of Antifungal Drugs.
Hargrove TY, Wawrzak Z, Lamb DC, Guengerich FP, Lepesheva GI
(2015) J Biol Chem 290: 23916-34
MeSH Terms: Aspergillus fumigatus, Catalysis, Cytochrome P-450 Enzyme System, Drug Resistance, Fungal, Fungal Proteins, Protein Structure, Tertiary, Structure-Activity Relationship, Voriconazole
Show Abstract · Added March 14, 2018
Aspergillus fumigatus is the opportunistic fungal pathogen that predominantly affects the immunocompromised population and causes 600,000 deaths/year. The cytochrome P450 51 (CYP51) inhibitor voriconazole is currently the drug of choice, yet the treatment efficiency remains low, calling for rational development of more efficient agents. A. fumigatus has two CYP51 genes, CYP51A and CYP51B, which share 59% amino acid sequence identity. CYP51B is expressed constitutively, whereas gene CYP51A is reported to be inducible. We expressed, purified, and characterized A. fumigatus CYP51B, including determination of its substrate preferences, catalytic parameters, inhibition, and x-ray structure in complexes with voriconazole and the experimental inhibitor (R)-N-(1-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl)ethyl)-4-(5-phenyl-1,3,4-oxadiazol-2-yl)benzamide (VNI). The enzyme demethylated its natural substrate eburicol and the plant CYP51 substrate obtusifoliol at steady-state rates of 17 and 16 min(-1), respectively, but did not metabolize lanosterol, and the topical antifungal drug miconazole was the strongest inhibitor that we identified. The x-ray crystal structures displayed high overall similarity of A. fumigatus CYP51B to CYP51 orthologs from other biological kingdoms but revealed phylum-specific differences relevant to enzyme catalysis and inhibition. The complex with voriconazole provides an explanation for the potency of this relatively small molecule, whereas the complex with VNI outlines a direction for further enhancement of the efficiency of this new inhibitory scaffold to treat humans afflicted with filamentous fungal infections.
© 2015 by The American Society for Biochemistry and Molecular Biology, Inc.
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8 MeSH Terms
The fumagillin gene cluster, an example of hundreds of genes under veA control in Aspergillus fumigatus.
Dhingra S, Lind AL, Lin HC, Tang Y, Rokas A, Calvo AM
(2013) PLoS One 8: e77147
MeSH Terms: Aspergillosis, Aspergillus fumigatus, Cyclohexanes, Fatty Acids, Unsaturated, Fungal Proteins, Gene Deletion, Gene Expression Regulation, Fungal, Genes, Fungal, Humans, Multigene Family, Sesquiterpenes
Show Abstract · Added February 19, 2015
Aspergillus fumigatus is the causative agent of invasive aspergillosis, leading to infection-related mortality in immunocompromised patients. We previously showed that the conserved and unique-to-fungi veA gene affects different cell processes such as morphological development, gliotoxin biosynthesis and protease activity, suggesting a global regulatory effect on the genome of this medically relevant fungus. In this study, RNA sequencing analysis revealed that veA controls the expression of hundreds of genes in A. fumigatus, including those comprising more than a dozen known secondary metabolite gene clusters. Chemical analysis confirmed that veA controls the synthesis of other secondary metabolites in this organism in addition to gliotoxin. Among the secondary metabolite gene clusters regulated by veA is the elusive but recently identified gene cluster responsible for the biosynthesis of fumagillin, a meroterpenoid known for its anti-angiogenic activity by binding to human methionine aminopeptidase 2. The fumagillin gene cluster contains a veA-dependent regulatory gene, fumR (Afu8g00420), encoding a putative C6 type transcription factor. Deletion of fumR results in silencing of the gene cluster and elimination of fumagillin biosynthesis. We found expression of fumR to also be dependent on laeA, a gene encoding another component of the fungal velvet complex. The results in this study argue that veA is a global regulator of secondary metabolism in A. fumigatus, and that veA may be a conduit via which chemical development is coupled to morphological development and other cellular processes.
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11 MeSH Terms
The diverse applications of RNA-seq for functional genomic studies in Aspergillus fumigatus.
Rokas A, Gibbons JG, Zhou X, Beauvais A, Latgé JP
(2012) Ann N Y Acad Sci 1273: 25-34
MeSH Terms: Aspergillus fumigatus, Base Sequence, Genes, Fungal, Molecular Sequence Data, RNA, Fungal, Sequence Analysis, RNA, Transcriptome
Show Abstract · Added May 30, 2014
The deep sequencing of an mRNA population, RNA-seq, is a very successful application of next-generation sequencing technologies (NGSTs). RNA-seq takes advantage of two key NGST features: (1) samples can be mixtures of different DNA pieces, and (2) sequencing provides both qualitative and quantitative information about each DNA piece analyzed. We recently used RNA-seq to study the transcriptome of Aspergillus fumigatus, a deadly human fungal pathogen. Analysis of the RNA-seq data indicates that there are likely tens of unannotated and hundreds of novel genes in the A. fumigatus transcriptome, mostly encoding for small proteins. Inspection of transcriptome-wide variation between two isolates reveals thousands of single nucleotide polymorphisms. Finally, comparison of the transcriptome profiles of one isolate in two different growth conditions identified thousands of differentially expressed genes. These results demonstrate the utility and potential of RNA-seq for functional genomics studies in A. fumigatus and other fungal human pathogens.
© 2012 New York Academy of Sciences.
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7 MeSH Terms
The index case for the fungal meningitis outbreak in the United States.
Pettit AC, Kropski JA, Castilho JL, Schmitz JE, Rauch CA, Mobley BC, Wang XJ, Spires SS, Pugh ME
(2012) N Engl J Med 367: 2119-25
MeSH Terms: Aspergillosis, Aspergillus fumigatus, Brain, Cerebellum, Cerebral Infarction, Cerebrospinal Fluid, Diagnosis, Differential, Disease Outbreaks, Drug Contamination, Fatal Outcome, Glucocorticoids, Headache, Humans, Injections, Epidural, Intracranial Hemorrhages, Low Back Pain, Male, Meningitis, Fungal, Middle Aged, Tomography, X-Ray Computed, United States
Show Abstract · Added August 14, 2014
Persistent neutrophilic meningitis presents a diagnostic challenge, because the differential diagnosis is broad and includes atypical infectious causes. We describe a case of persistent neutrophilic meningitis due to Aspergillus fumigatus in an immunocompetent man who had no evidence of sinopulmonary or cutaneous disease. An epidural glucocorticoid injection was identified as a potential route of entry for this organism into the central nervous system, and the case was reported to the state health department.
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21 MeSH Terms
Global transcriptome changes underlying colony growth in the opportunistic human pathogen Aspergillus fumigatus.
Gibbons JG, Beauvais A, Beau R, McGary KL, Latgé JP, Rokas A
(2012) Eukaryot Cell 11: 68-78
MeSH Terms: Aspergillus fumigatus, Biofilms, Cell Wall, Chromosome Mapping, Drug Resistance, Fungal, Fungal Proteins, Gene Expression, Gene Expression Regulation, Fungal, Gene Regulatory Networks, Glycolysis, Metabolic Networks and Pathways, Multigene Family, Protein Biosynthesis, Ribosomes, Transcription Factors, Transcriptome
Show Abstract · Added August 16, 2012
Aspergillus fumigatus is the most common and deadly pulmonary fungal infection worldwide. In the lung, the fungus usually forms a dense colony of filaments embedded in a polymeric extracellular matrix. To identify candidate genes involved in this biofilm (BF) growth, we used RNA-Seq to compare the transcriptomes of BF and liquid plankton (PL) growth. Sequencing and mapping of tens of millions sequence reads against the A. fumigatus transcriptome identified 3,728 differentially regulated genes in the two conditions. Although many of these genes, including the ones coding for transcription factors, stress response, the ribosome, and the translation machinery, likely reflect the different growth demands in the two conditions, our experiment also identified hundreds of candidate genes for the observed differences in morphology and pathobiology between BF and PL. We found an overrepresentation of upregulated genes in transport, secondary metabolism, and cell wall and surface functions. Furthermore, upregulated genes showed significant spatial structure across the A. fumigatus genome; they were more likely to occur in subtelomeric regions and colocalized in 27 genomic neighborhoods, many of which overlapped with known or candidate secondary metabolism gene clusters. We also identified 1,164 genes that were downregulated. This gene set was not spatially structured across the genome and was overrepresented in genes participating in primary metabolic functions, including carbon and amino acid metabolism. These results add valuable insight into the genetics of biofilm formation in A. fumigatus and other filamentous fungi and identify many relevant, in the context of biofilm biology, candidate genes for downstream functional experiments.
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16 MeSH Terms
Eosinophilic pleural effusion complicating allergic bronchopulmonary aspergillosis.
Kirschner AN, Kuhlmann E, Kuzniar TJ
(2011) Respiration 82: 478-81
MeSH Terms: Adult, Anti-Inflammatory Agents, Aspergillosis, Allergic Bronchopulmonary, Aspergillus fumigatus, Asthma, Eosinophils, Humans, Male, Pleural Effusion, Prednisolone, Radiography, Thoracic, Sputum, Tomography, X-Ray Computed
Show Abstract · Added April 12, 2015
Allergic bronchopulmonary aspergillosis (ABPA) is primarily a disease of patients with cystic fibrosis or asthma, who typically present with bronchial obstruction, fever, malaise, and expectoration of mucus plugs. We report a case of a young man with a history of asthma who presented with cough, left-sided pleuritic chest pain and was found to have lobar atelectasis and an eosinophilic, empyematous pleural effusion. Bronchoscopy and sputum cultures grew Aspergillus fumigatus, and testing confirmed strong allergic response to this mold, all consistent with a diagnosis of ABPA. This novel and unique presentation of ABPA expands on the differential diagnosis of eosinophilic pleural effusions.
Copyright © 2011 S. Karger AG, Basel.
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13 MeSH Terms
Molecular cloning of Aspergillus fumigatus CgrA, the ortholog of a conserved fungal nucleolar protein.
Boettner D, Huebner N, Rhodes JC, Askew DS
(2001) Med Mycol 39: 517-21
MeSH Terms: Amino Acid Sequence, Aspergillus fumigatus, Cloning, Molecular, Fungal Proteins, Molecular Sequence Data, Nuclear Proteins, RNA-Binding Proteins
Show Abstract · Added October 31, 2013
In this report we describe the cloning of cgrA, the Aspergillus fumigatus ortholog of the yeast nucleolar protein Cgr1p. The cgrA complementary DNA (cDNA) contains a single open reading frame that would encode a protein of 114 amino acids that has 42% sequence identity to yeast Cgrlp. Heterologous expression of a green fluorescent protein (GFP)-tagged A. fumigatus cgrA gene demonstrated that the CgrA protein could localize to the yeast nucleolus. Moreover, the cgrA cDNA complemented the growth deficiency caused by inducible depletion of intracellular Cgr1p levels in yeast. These results support an orthologous relationship between the CgrA and Cgr1 proteins, and open the way for future studies into the potential value of nucleolar proteins as antifungal targets.
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7 MeSH Terms