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.
Fungal infections are underestimated threats that affect over 1 billion people, and Candida spp., Cryptococcus spp., and Aspergillus spp. are the 3 most fatal fungi. The treatment of these infections ...is performed with a limited arsenal of antifungal drugs, and the class of the azoles is the most used. Although these drugs present low toxicity for the host, there is an emergence of therapeutic failure due to azole resistance. Drug resistance normally develops in patients undergoing azole long-term therapy, when the fungus in contact with the drug can adapt and survive. Conversely, several reports have been showing that resistant isolates are also recovered from patients with no prior history of azole therapy, suggesting that other routes might be driving antifungal resistance. Intriguingly, antifungal resistance also happens in the environment since resistant strains have been isolated from plant materials, soil, decomposing matter, and compost, where important human fungal pathogens live. As the resistant fungi can be isolated from the environment, in places where agrochemicals are extensively used in agriculture and wood industry, the hypothesis that fungicides could be driving and selecting resistance mechanism in nature, before the contact of the fungus with the host, has gained more attention. The effects of fungicide exposure on fungal resistance have been extensively studied in Aspergillus fumigatus and less investigated in other human fungal pathogens. Here, we discuss not only classic and recent studies showing that environmental azole exposure selects cross-resistance to medical azoles in A. fumigatus, but also how this phenomenon affects Candida and Cryptococcus, other 2 important human fungal pathogens found in the environment. We also examine data showing that fungicide exposure can select relevant changes in the morphophysiology and virulence of those pathogens, suggesting that its effect goes beyond the cross-resistance.
About the Authors: Antonis Rokas * E-mail: antonis.rokas@vanderbilt.edu Affiliation: Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America ORCID ...logo http://orcid.org/0000-0002-7248-6551 Matthew E. Mead Affiliation: Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America ORCID logo http://orcid.org/0000-0001-9195-7585 Jacob L. Steenwyk Affiliation: Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America ORCID logo http://orcid.org/0000-0002-8436-595X Nicholas H. Oberlies Affiliation: Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, United States of America ORCID logo http://orcid.org/0000-0002-0354-8464 Gustavo H. Goldman Affiliation: Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil ORCID logo http://orcid.org/0000-0002-2986-350X Introduction Species in the genus Aspergillus are saprophytic filamentous fungi that are most commonly found in soil and litter environments of subtropical and warm temperate latitudes 1. The most severe form of aspergillosis is invasive aspergillosis, which primarily affects individuals with compromised immune systems or preexisting lung conditions 3. Since drugs targeting invasive aspergillosis are not always effective due to our lack of understanding of how they function inside the human host 4 and the evolution of drug resistance 5, 6, infected individuals suffer high morbidity and mortality 7. Addressing this question requires that we consider the fact that pathogenic Aspergillus species are not dependent on their hosts for survival and their pathogenic effects are entirely accidental or opportunistic. ...understanding the evolution of pathogenicity in the genus requires that we understand how variation in the traits that enable Aspergillus species to survive in their natural soil and litter environments has rendered a few of these species capable to establish infections inside human hosts. More broadly, given that the ability to cause human disease has repeatedly evolved across the fungal tree of life, and that the vast majority of human fungal pathogens have non-pathogenic close relatives 22, understanding the evolution of Aspergillus pathogenicity can serve as a model for studying fungal pathogenicity in general.
is a basidiomycetous yeast responsible for hundreds of thousands of deaths a year and is particularly threatening in immunocompromised patients. There are few families of antifungals that are ...available to fight fungal infections, and the unique efficient treatment for the most deadly cerebral forms of cryptococcosis is based on a combination of 5-fluorocytosine and amphotericin B. The toxicities of both compounds are elevated, and more therapeutic options are urgently needed for better management of life-threatening cryptococcosis. The newest class of antifungals, i.e., echinocandins, has initially led to great hope. Unfortunately,
was rapidly confirmed to be naturally resistant to these molecules, notably caspofungin. In this respect, we discuss here the recent key findings of the Panepinto research group published in
(M. C. Kalem et al., mBio 12:e03225-20, 2021, https://doi:10.1128/mBio.03225-20) that provide an unprecedented view of how
regulates caspofungin resistance through a complex posttranscriptional regulation of cell wall biosynthesis genes.
Invasive aspergillosis is a life-threatening mycosis caused by the pathogenic fungus
. The predominant causal species is
, and azole drugs are the treatment of choice. Azole drugs approved for ...clinical use include itraconazole, voriconazole, posaconazole, and the recently added isavuconazole. However, epidemiological research has indicated that the prevalence of azole-resistant
isolates has increased significantly over the last decade. What is worse is that azole-resistant strains are likely to have emerged not only in response to long-term drug treatment but also because of exposure to azole fungicides in the environment. Resistance mechanisms include amino acid substitutions in the target Cyp51A protein, tandem repeat sequence insertions at the
promoter, and overexpression of the ABC transporter Cdr1B. Environmental azole-resistant strains harboring the association of a tandem repeat sequence and punctual mutation of the Cyp51A gene (TR34/L98H and TR46/Y121F/T289A) have become widely disseminated across the world within a short time period. The epidemiological data also suggests that the number of
spp. other than
isolated has risen. Some non-
species intrinsically show low susceptibility to azole drugs, imposing the need for accurate identification, and drug susceptibility testing in most clinical cases. Currently, our knowledge of azole resistance mechanisms in non-
species such as
, and
is limited. In this review, we present recent advances in our understanding of azole resistance mechanisms particularly in
. We then provide an overview of the genome sequences of non-
species, focusing on the proteins related to azole resistance mechanisms.
Summary
It is estimated that fungal infections, caused most commonly by Candida albicans, Aspergillus fumigatus and Cryptococcus neoformans, result in more deaths annually than malaria or ...tuberculosis. It has long been hypothesized the fungal metabolism plays a critical role in virulence though specific nutrient sources utilized by human pathogenic fungi in vivo has remained enigmatic. However, the metabolic utilisation of preferred carbon and nitrogen sources, encountered in a host niche‐dependent manner, is known as carbon catabolite and nitrogen catabolite repression (CCR, NCR), and has been shown to be important for virulence. Several sensory and uptake systems exist, including carbon and nitrogen source‐specific sensors and transporters, that allow scavenging of preferred nutrient sources. Subsequent metabolic utilisation is governed by transcription factors, whose functions and essentiality differ between fungal species. Furthermore, additional factors exist that contribute to the implementation of CCR and NCR. The role of the CCR and NCR‐related factors in virulence varies greatly between fungal species and a substantial gap in knowledge exists regarding specific pathways. Further elucidation of carbon and nitrogen metabolism mechanisms is therefore required in a fungal species‐ and animal model‐specific manner in order to screen for targets that are potential candidates for anti‐fungal drug development.
Fungal infections that result in the death of immunocompromised subjects have risen steadily over the last few years. The metabolic utilisation of preferred carbon and nitrogen sources, encountered in a host niche‐specific manner, has been shown to be an important virulence determinant. Characterisation of preferred nutrient source utilisation, including sensing and uptake, by pathogenic fungi has only been partially characterised, and further species‐specific elucidation is required, in order to uncover targets for anti‐fungal therapies.
Carbon catabolite repression (CCR) is a process that selects the energetically most favorable carbon source in an environment. CCR represses the use of less favorable carbon sources when a better ...source is available. Glucose is the preferential carbon source for most microorganisms because it is rapidly metabolized, generating quick energy for growth. In the filamentous fungus Aspergillus nidulans, CCR is mediated by the transcription factor CreA, a C2H2 finger domain DNA-binding protein. The aim of this work was to investigate the regulation of CreA and characterize its functionally distinct protein domains. CreA depends in part on de novo protein synthesis and is regulated in part by ubiquitination. CreC, the scaffold protein in the CreB-CreC deubiquitination (DUB) complex, is essential for CreA function and stability. Deletion of select protein domains in CreA resulted in persistent nuclear localization and target gene repression. A region in CreA conserved between Aspergillus spp. and Trichoderma reesei was identified as essential for growth on various carbon, nitrogen, and lipid sources. In addition, a role of CreA in amino acid transport and nitrogen assimilation was observed. Taken together, these results indicate previously unidentified functions of this important transcription factor. These novel functions serve as a basis for additional research in fungal carbon metabolism with the potential aim to improve fungal industrial applications.
Fungal pathogens represent a rising threat against immunocompromised patients. By using Aspergillus fumigatus, Briard et al. showed that the cell wall galactosaminogalactan (GAG) triggers macrophage ...inflammasome activation, promoting protective immunity. This provides new insights into the role of GAG in host–pathogen interactions and also perspectives for developing GAG-based anti-inflammatory therapeutics.
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