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Keller, N. P.

Publications and source records attributed to Keller, N. P..

At least 19 recordsLinked to original sources

Inhibitors of spore germination act against diverse human fungal pathogens

Current antifungal drugs often cause severe side effects due to the conservation of molecular targets between fungal and mammalian cells. One way to avoid host toxicity in future antifungals is to leverage molecules with targets involved in processes unique to fungi, such as spore germination. Germination is conserved in several of the most critical fungal pathogens but absent in mammalian cells. In this work we evaluated 191 small molecule inhibitors of Cryptococcus germination for their abilities to inhibit germination of another fungal pathogen, Aspergillus fumigatus, as well as yeast growth of Candida albicans and a pan-resistant isolate of Candida (Candidozyma) auris. The cytotoxicity of these inhibitors towards human hepatocytes and erythrocytes was also assessed. Overall, we identified 101 molecules that were either 1) germination-specific inhibitors in one or both germinating species tested, or 2) inhibitory to both germination and vegetative growth in one or more species tested. The majority of these molecules exhibited minimal toxicity to the human cell types tested. Molecules were scored and ranked for therapeutic potential based on assay data. For two key molecules of interest, predicted binding targets (histone deacetylase and acetyl-CoA carboxylase) were identified computationally. Overall, the inhibitor molecules characterized here showed activity against phylogenetically diverse human fungal pathogens with minimal toxic effects on human cell lines.

microbiology↗

An Aspergillus lncRNA atlas reveals a novel modulator of aflatoxin biosynthesis

Long non-coding RNAs (lncRNAs) represent a significant fraction of the transcriptome and are vital regulators in eukaryotes, yet their functional landscape in fungi remains largely undefined. Here we present a transcriptomic atlas of 8,553 lncRNAs across four evolutionarily and biotechnologically diverse Aspergillus species. We observed marked diversity in the long non-coding repertoire between species, with only 39% shared between at least two species. However, conserved lncRNAs are expressed at significantly higher levels and across more conditions than species-specific ones, revealing a functional hierarchy within the non-coding transcriptome. We also identify subtelomeres and transposable elements as hotspots for lncRNA innovation in Aspergillus, albeit at the cost of reduced expression. Integrating genomic and transcriptomic data, we show that lncRNAs predominantly exhibit distance-dependent cis-coexpression with neighboring genes and, through guilt-by-association, we identify their participation in global modules governing primary and secondary metabolism. This framework enabled the discovery of aflalinc, a species- and condition-specific lncRNA in A. flavus that plays a role in regulating the aflatoxin biosynthetic gene cluster. Crucially, deletion of this lncRNA severely reduced the production of aflatoxin B, a highly potent agent of acute toxicity and driver of hepatocarcinoma, without affecting growth, conidiation, or sclerotia formation. In addition, examination of an independent dataset confirms the strength of the co-expression networks and uncovers stage-specific functions for lincRNAs in the maturation of A. fumigatus biofilms. Together, these findings establish lncRNAs as integral components of fungal biology and demonstrate that they can modulate mycotoxin production and biofilm formation, with broad implications for controlling fungal threats to food safety and human health.

microbiology↗

Endosome motility controls light-responsive reproductive development and secondary metabolite production in Aspergillus

Filamentous fungi, such as Aspergillus species, use microtubule transport to move early endosomes. Other cargos, such as peroxisomes and mRNAs, "hitchhike" on early endosomes to move throughout the long hyphae of these organisms. In Aspergillus nidulans, peroxisomes hitchhike on early endosomes using the endosomal protein PxdA and the peroxisomal protein AcbdA. The HookA adaptor protein links endosomes to microtubule motors. Here, we set out to explore the physiological functions of peroxisome hitchhiking and endosome motility. Aspergillus nidulans has a complex life cycle that includes asexual and sexual reproduction. A. nidulans and other fungi within the Pezizomycotina subphylum are also notable for the vast number of secondary metabolites they produce. Light and other environmental conditions influence developmental decisions and secondary metabolite production. Here, we found that sexual reproduction is favored in the absence of endosome motility, even in the light, which normally promotes asexual reproduction. RNA sequencing of strains lacking PxdA-marked motile early endosomes showed altered expression of genes involved in development. Unexpectedly, we also observed altered expression of genes involved in secondary metabolism in strains lacking endosome motility and peroxisome hitchhiking. Using mass spectrometry, we found that the loss of endosome motility affected the biosynthesis of secondary metabolites, including sterigmatocystin, a carcinogenic mycotoxin that is a food contaminant. Finally, in a pathogenic species, Aspergillus fumigatus, we found that deletion of its pxdA homolog also significantly altered secondary metabolite production. Our work uncovers an unexpected link between organelle motility, developmental decisions in response to light, and secondary metabolite production in filamentous fungi.

cell biology↗

Population-Specific Transcriptomic Shifts Underlie Secondary Metabolic Diversification in Aspergillus flavus and the Domestication of Aspergillus oryzae

The genomic signatures of microbial domestication remain poorly understood within the context of natural population variation. Here, we demonstrate that Aspergillus oryzae, the filamentous fungus used in soy sauce production, shares more recent ancestry with a predominantly northern, largely non-aflatoxigenic population of Aspergillus flavus (population C). Strikingly, A. oryzae isolates also overlap with the recently described, clinically enriched A. flavus population D, suggesting the possibility of multiple domestication events. Although A. oryzae exhibits reduced virulence compared to A. flavus, all isolates tested retained pathogenicity in a zebrafish infection model. At the transcriptomic level, Aspergillus populations are significantly differentiated, with distinct responses to population density, indicating that population-specific transcriptomes adapt differently to ecological conditions. These differences extend beyond gene content and are not always explained by phylogenetic relationships, suggesting that phenotypic diversification occurs through the rapid reorganization of transcriptomic architectures. For example, A. oryzae displays significantly elevated expression of a module enriched for carbohydrate metabolism. Population-specific variation is also evident among secondary metabolite (SM) gene clusters. While A. oryzae shows markedly reduced expression of specific SM genes, particularly those involved in aflatoxin biosynthesis, this trend does not extend across the entire secondary metabolome. Using machine- learning-based gene regulatory network inference, we identified population-specific transcriptomic differences linked to distinct transcription factors, with evidence for both cis- and trans-acting regulatory divergence, but no changes in global regulators such as laeA. Together, these findings provide new insights into the domestication of A. oryzae, its global significance, and the microevolution of fungal secondary metabolic pathways. Significance StatementAspergillus flavus poses a significant threat to global agriculture by infecting crops and producing aflatoxin, a potent carcinogen that undermines food safety and international trade. The species is also a major human pathogen causing invasive fungal infections. Here, we demonstrate that A. flavus populations exhibit not only variations in their capacity to produce toxins but also in the way they regulate gene expression in response to environmental cues. These regulatory differences played a key role in the domestication of Aspergillus oryzae, a non-aflatoxigenic relative that has been safely used in food fermentation for centuries. Notably, while A. oryzae exhibits reduced aflatoxin biosynthetic gene expression, it expresses other secondary metabolite genes and retains limited opportunistic pathogenic potential. By revealing how transcriptomic rewiring drives population-level divergence, this work provides new insights into the evolution of toxin production, with broad implications for microbial domestication, crop protection, and global food security.

microbiology↗

Whole-chromosome duplications drive antimicrobial resistance in Aspergillus fumigatus

Aneuploidy causes genome plasticity and enables adaptive responses that increase stress resistance and facilitate persistence under changing conditions in eukaryotes ranging from fungal pathogens to human cancer cells. Aspergillus fumigatus is a soil-resident mold and the most prevalent etiologic agent of invasive fungal infections globally. Invasive aspergillosis has an alarmingly high mortality rate, and fungal persistence in the infection microenvironment often renders treatments unsuccessful. Treatment failures can result from innate or acquired antifungal drug resistance and from fungal adaptation to other stressors encountered during infection including nutrient limitation, immune cell activity, and changes in pH and oxygen tension. Survival under changing environmental and host conditions therefore necessitates an ability to dynamically adapt to stress. We find that exposure of A. fumigatus to FK506, an antifungal and immunosuppressive Streptomyces natural product that inhibits the master regulatory phosphatase calcineurin, selects for unstable whole-chromosome aneuploidies that alleviate the polarized growth defects caused by calcineurin inhibition. Transcriptomic analysis revealed that Chr7 disomy leads to induction of the normally-silent neosartoricin biosynthetic gene cluster in response to FK506 exposure, and we demonstrate that constitutive genetic induction of this cluster is sufficient to largely recapitulate in a haploid background the response to FK506 in the aneuploid state. We further show that aneuploids undergo extensive metabolic rewiring but do not produce detectable neosartoricin, revealing global and cross-pathway effects resulting from both the aneuploid state and activation of nscR. We also demonstrate that the aneuploid chromosome duplications reduce susceptibility to the clinical antifungal voriconazole, underscoring the utility of aneuploidy as a flexible adaptive strategy. These findings represent a major advance in understanding how aneuploidy transiently alters stress responses and metabolism in the deadly human pathogen A. fumigatus. Highlights- A. fumigatus rapidly gains and loses supernumerary chromosomes in response to the calcineurin inhibitor FK506. - Aneuploidy leads to global transcriptional and metabolic rewiring. - Overexpression of the secondary metabolite gene cluster regulator nscR is sufficient to largely recapitulate the aneuploid response to FK506 in a haploid background. - Chr4, 6, and 7 aneuploidies reduce susceptibility to voriconazole without altering expression of the azole target gene cyp51A.

microbiology↗

Zebrafish larval GPR132b differentially influences wound repair and infection control

GPR132 (G2A), a lipid- and pH-sensing GPCR, has been implicated in both pro- and anti-inflammatory signaling, but its in vivo function in wound repair and infection control remains unknown. Here, we investigated the role of GPR132b, a zebrafish homolog of G2A, in regulating innate immune responses. Using CRISPR-Cas9, we generated gpr132b mutants and found that they exhibit enhanced wound healing following sterile injury but increased susceptibility to Listeria monocytogenes infection, indicating that GPR132b modulates a trade-off between wound repair and antimicrobial defense. The enhanced regrowth phenotype was associated with increased macrophage accumulation at the wound site and reduced basal expression of the pro-inflammatory cytokine tnf-. Macrophage depletion suppressed the enhanced regrowth phenotype, suggesting a functional role for macrophages in GPR132b-mediated repair. Pharmacological inhibition of cyclooxygenase (COX) and 12-lipoxygenase (12-LOX) pathways mimicked the gpr132b mutant phenotype in wild-type larvae, indicating that GPR132b likely responds to lipid-derived signals. Together, our findings reveal that GPR132b acts as a context-dependent regulator of innate immunity, impairing efficient tissue repair in sterile conditions while supporting pathogen resistance during infection. Our results underscore the importance of GPCR-mediated signaling in orchestrating effective responses to tissue injury and infection.

immunology↗

Transposable elements facilitate the unintentional domestication of a cheese-associated Penicillium mold

Previous comparative and experimental evolution studies have suggested how fungi may rapidly adapt to new environments, but direct observation of in situ selection in fungal populations is rare due to challenges with tracking populations over human time scales. We monitored a population of Penicillium solitum over eight years in a cheese cave and documented a phenotypic shift from predominantly green to white strains. Diverse mutations in the alb1 gene, which encodes the first protein in the DHN-melanin biosynthesis pathway, explained the green to white shift. A similar phenotypic shift was recapitulated with an alb1 knockout and experimental evolution in laboratory populations. The most common genetic disruption of the alb1 genomic region was caused by putative transposable element insertions upstream of the gene. White strains had substantial downregulation in global transcription, with genetically distinct white strains possessing divergent shifts in expression of different biological processes. White strains outcompeted green strains in co-culture, but this competitive advantage was only observed in the absence of light, suggesting that loss of melanin is only adaptive in dark conditions. Our results illustrate how fermented food production by humans provides opportunities for relaxed selection of key fungal traits over short time scales. Unintentional domestication of microbes by cheesemakers may provide opportunities to generate new strains for innovation in traditional cheese production.

microbiology↗

A conserved in vivo burn wound infection model for diverse pathogenic fungi.

Secondary fungal infections represent a major complication following thermal injuries. However, the mechanisms of fungal colonization of burn tissue and how the host subsequently responds to fungi within this niche remain unclear. We have previously reported a zebrafish model of thermal injury that recapitulates many of the features of human burn wounds. Here, we characterize host-fungal interaction dynamics within the burn wound niche using two of the most common fungal pathogens isolated from burn injuries, Aspergillus fumigatus and Candida albicans. Both A. fumigatus and C. albicans colonize burned tissue in zebrafish larvae and induce a largely conserved innate immune response following colonization. Using drug-induced cell depletion strategies and transgenic zebrafish lines with impaired innate immune function, we found that macrophages control fungal burden while neutrophils primarily control invasive hyphal growth at the early stages of infection. However, we also found that loss of either immune cell can be compensated by the other at the later stages of infection, and that fish with both macrophage and neutrophil deficiencies show more invasive hyphal growth that is sustained throughout the infection process, suggesting redundancy in their antifungal activities. Finally, we demonstrate that C. albicans strains with increased {beta}(1,3)-glucan exposure are cleared faster from the burn wound, demonstrating a need for shielding this immunogenic cell wall epitope for successful fungal colonization of burn tissue. Together, our findings support the use of zebrafish larvae as a model to study host-fungal interaction dynamics within burn wounds. ImportanceSecondary fungal infections within burn wound injuries are a significant problem that delay wound healing and increase the risk of patient mortality. Currently, little is known about how fungi colonize and infect burn tissue or how the host responds to pathogen presence. In this report, we expand upon an existing thermal injury model using zebrafish larvae to begin to elucidate both the host immune response to fungal burn colonization and fungal mechanisms for persistence within burn tissue. We found that both Aspergillus fumigatus and Candida albicans, common fungal burn wound isolates, successfully colonize burn tissue and are effectively cleared in immunocompetent zebrafish by both macrophages and neutrophils. We also find that C. albicans mutants harboring mutations that impact their ability to evade host immune system recognition are cleared more readily from burn tissue. Collectively, our work highlights the efficacy of using zebrafish to study host-fungal interaction dynamics within burn wounds.

microbiology↗

GATA1-deficient human pluripotent stem cells generate neutrophils with improved antifungal immunity that is mediated by the integrin CD18

Neutrophils are critical for host defense against fungi. However, the short life span and lack of genetic tractability of primary human neutrophils has limited in vitro analysis of neutrophil-fungal interactions. Human induced pluripotent stem cell (iPSC)-derived neutrophils (iNeutrophils) are a genetically tractable alternative to primary human neutrophils. Here, we show that deletion of the transcription factor GATA1 from human iPSCs results in iNeutrophils with improved antifungal activity against Aspergillus fumigatus. GATA1 knockout (KO) iNeutrophils have increased maturation, antifungal pattern recognition receptor expression and more readily execute neutrophil effector functions compared to wild-type iNeutrophils. iNeutrophils also show a shift in their metabolism following stimulation with fungal {beta}-glucan, including an upregulation of the pentose phosphate pathway (PPP), similar to primary human neutrophils in vitro. Furthermore, we show that deletion of the integrin CD18 attenuates the ability of GATA1-KO iNeutrophils to kill A. fumigatus but is not necessary for the upregulation of PPP. Collectively, these findings support iNeutrophils as a robust system to study human neutrophil antifungal immunity and has identified specific roles for CD18 in the defense response. Author SummaryNeutrophils are important first responders to fungal infections, and understanding their antifungal functions is essential to better elucidating disease dynamics. Primary human neutrophils are short lived and do not permit genetic manipulation, limiting their use to study neutrophil-fungal interactions in vitro. Human induced pluripotent stem cell (iPSC)-derived neutrophils (iNeutrophils) are a genetically tractable alternative to primary human neutrophils for in vitro analyses. In this report we show that GATA1-deficient iPSCs generate neutrophils (iNeutrophils) that are more mature than wild-type iNeutrophils and display increased antifungal activity against the human fungal pathogen Aspergillus fumigatus. We also show that GATA1-deficient iNeutrophils have increased expression of antifungal receptors than wild-type cells and shift their metabolism and execute neutrophil antifungal functions at levels comparable to primary human neutrophils. Deletion of the integrin CD18 blocks the ability of GATA1-deficient iNeutrophils to kill and control the growth of A. fumigatus, demonstrating an important role for this integrin in iNeutrophil antifungal activity. Collectively, these findings support the use of iNeutrophils as a model to study neutrophil antifungal immunity.

microbiology↗

Terpenoid balance in Aspergillus nidulans unveiled by heterologous squalene synthase expression

Filamentous fungi produce numerous uncharacterized natural products (NPs) that are often challenging to characterize due to cryptic expression in laboratory conditions. Previously, we have successfully isolated novel NPs by expressing fungal artificial chromosomes (FACs) from a variety of fungal species into Aspergillus nidulans. Here, we demonstrate a new twist to FAC utility wherein heterologous expression of a Pseudogymnoascus destructans FAC in A. nidulans altered endogenous terpene biosynthetic pathways. In contrast to wildtype, the FAC transformant produced increased levels of squalene and aspernidine type compounds, including three new nidulenes (1-2, 5), and lost nearly all ability to synthesize the major A. nidulans characteristic terpene, austinol. Deletion of a squalene synthase gene in the FAC restored wildtype chemical profiles. The altered squalene to farnesyl pyrophosphate ratio leading to synthesis of nidulenes and aspernidines at the expense of farnesyl pyrophosphate derived austinols provides unexpected insight into routes of terpene synthesis in fungi. TeaserReshaping terpenes: Heterologous FAC expression reroutes terpene pathways.

microbiology↗

A network-based model of Aspergillus fumigatus elucidates regulators of development and defensive natural products of an opportunistic pathogen

Aspergillus fumigatus is a notorious pathogenic fungus responsible for various harmful, sometimes lethal, diseases known as aspergilloses. Understanding the gene regulatory networks that specify the expression programs underlying this fungus diverse phenotypes can shed mechanistic insight into its growth, development, and determinants of pathogenicity. We used eighteen RNA-seq datasets (seventeen publicly available and one previously unpublished) of Aspergillus fumigatus to construct a comprehensive gene regulatory network resource. Our resource, named GRAsp (Gene Regulation of Aspergillus fumigatus), was able to recapitulate known regulatory pathways such as response to hypoxia, iron and zinc homeostasis, and secondary metabolite synthesis. Further, GRAsp was experimentally validated in two cases: one in which GRAsp accurately identified an uncharacterized transcription factor negatively regulating the production of the virulence factor gliotoxin and another where GRAsp revealed the bZip protein, AtfA, as required for fungal responses to microbial signals known as lipo-chitooligosaccharides. Our work showcases the strength of using network-based approaches to generate new hypotheses about regulatory relationships in Aspergillus fumigatus. We also unveil an online, user-friendly version of GRAsp available to the Aspergillus research community.

systems biology↗

Mining for a New Class of Fungal Natural Products: The Evolution, Diversity, and Distribution of Isocyanide Synthase Biosynthetic Gene Clusters

The products of non-canonical isocyanide synthase (ICS) biosynthetic gene clusters (BGCs) have notable bioactivities that mediate pathogenesis, microbial competition, and metal-homeostasis through metal-associated chemistry. We sought to enable research into this class of compounds by characterizing the biosynthetic potential and evolutionary history of these BGCs across the Fungal Kingdom. We developed the first genome-mining pipeline to identify ICS BGCs, locating 3,800 ICS BGCs in 3,300 genomes. Genes in these clusters share promoter motifs and are maintained in contiguous groupings by natural selection. ICS BGCs are not evenly distributed across fungi, with evidence of gene-family expansions in several Ascomycete families. We show that the ICS dit1/2 gene cluster family (GCF), which was thought to only exist in yeast, is present in [~]30% of all Ascomycetes, including many filamentous fungi. The evolutionary history of the dit GCF is marked by deep divergences and phylogenetic incompatibilities that raise questions about convergent evolution and suggest selection or horizontal gene transfers have shaped the evolution of this cluster in some yeast and dimorphic fungi. Our results create a roadmap for future research into ICS BGCs. We developed a website (www.isocyanides.fungi.wisc.edu) that facilitates the exploration, filtering, and downloading of all identified fungal ICS BGCs and GCFs.

microbiology↗

Aspergillus fumigatus transcription factor ZfpA regulates hyphal development and alters susceptibility to antifungals and neutrophil killing during infection

Hyphal growth is essential for host colonization during Aspergillus infection. The transcription factor ZfpA regulates A. fumigatus hyphal development including branching, septation, and cell wall composition. However, how ZfpA affects fungal growth and susceptibility to host immunity during infection has not been investigated. Here, we use the larval zebrafish-Aspergillus infection model and primary human neutrophils to probe how ZfpA affects A. fumigatus pathogenesis and response to antifungal drugs in vivo. ZfpA deletion promotes fungal clearance and attenuates virulence in wild-type hosts and this virulence defect is abrogated in neutrophil-deficient zebrafish. ZfpA deletion also increases susceptibility to human neutrophils ex vivo while overexpression impairs fungal killing. Overexpression of ZfpA confers protection against the antifungal caspofungin by increasing chitin synthesis during hyphal development, while ZfpA deletion reduces cell wall chitin and increases caspofungin susceptibility in neutrophil-deficient zebrafish. These findings suggest a protective role for ZfpA activity in resistance to the innate immune response and antifungal treatment during A. fumigatus infection. Author SummaryAspergillus fumigatus is a common environmental fungus that can infect immunocompromised people and cause a life-threatening disease called invasive aspergillosis. An important step during infection is the development of A. fumigatus filaments known as hyphae. A. fumigatus uses hyphae to acquire nutrients and invade host tissues, leading to tissue damage and disseminated infection. In this study we report that a regulator of gene transcription in A. fumigatus called ZfpA is important for hyphal growth during infection. We find that ZfpA activity protects the fungus from being killed by innate immune cells and decreases the efficacy of antifungal drugs during infection by regulating construction of the cell wall, an important protective layer for fungal pathogens. Our study introduces ZfpA as an important genetic regulator of stress tolerance during infection that protects A. fumigatus from the host immune response and antifungal drugs.

microbiology↗

Fungal antibiotics control bacterial community diversity in the cheese rind microbiome

Potent antimicrobial metabolites are produced by filamentous fungi in pure lab cultures, but their ecological functions in nature are often unknown. Using an antibiotic-producing Penicillium isolate and the cheese rind microbial community, we demonstrate that a fungal specialized metabolite can regulate the diversity of bacterial communities. Inactivation of the global regulator, LaeA, resulted in the loss of antibacterial activity in the Penicillium isolate. Cheese rind bacterial communities assembled with the laeA deletion strain had significantly higher bacterial abundances than the wild-type strain. RNA-sequencing and metabolite profiling demonstrated a striking reduction in the expression and production of the natural product pseurotin in the laeA deletion strain. Inactivation of a core gene in the pseurotin biosynthetic cluster restored bacterial community composition, demonstrating the role of pseurotins in mediating bacterial community assembly. Our discovery demonstrates how antibiotic production can drive the assembly of microbiomes and provides an ecological context for widespread fungal specialized metabolites.

microbiology↗

A guidance into the fungal metabolomic abyss: Network analysis for revealing relationships between exogenous compounds and their outputs

AO_SCPLOWBSTRACTC_SCPLOWFungal specialized metabolites include many bioactive compounds with potential applications as pharmaceuticals, agrochemical agents, and industrial chemicals. Exploring and discovering novel fungal metabolites is critical to combat antimicrobial resistance in various fields, including medicine and agriculture. Yet, identifying the conditions or treatments that will trigger the production of specialized metabolites in fungi can be cumbersome since most of these metabolites are not produced under standard culture conditions. Here, we introduce a data-driven algorithm comprising various network analysis routes to characterize the production of known and putative specialized metabolites and unknown analytes triggered by different exogenous compounds. We use bipartite networks to quantify the relationship between the metabolites and the treatments stimulating their production through two routes. The first, called the direct route, determines the production of known and putative specialized metabolites induced by a treatment. The second, called the auxiliary route, is specific for unknown analytes. We demonstrated the two routes by applying chitooligosaccharides and lipids at two different temperatures to the opportunistic human fungal pathogen Aspergillus fumigatus. We used various network centrality measures to rank the treatments based on their ability to trigger a broad range of specialized metabolites. The specialized metabolites were ranked based on their receptivity to various treatments. Altogether, our data-driven techniques can track the influence of any exogenous treatment or abiotic factor on the metabolomic output for targeted metabolite research. This approach can be applied to complement existing LC/MS analyses to overcome bottlenecks in drug discovery and development from fungi. NoticeThis manuscript has been authored by UT-Battelle, LLC, under contract DE-AC05-00OR22725 with the US Department of Energy (DOE). The US government retains and the publisher, by accepting the article for publication, acknowledges that the US government retains a nonexclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for US government purposes. DOE will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan). Author summaryTriggering silent biosynthetic gene clusters in fungi to produce specialized metabolites is a tedious process that requires assessing various environmental conditions, applications of epigenetic modulating agents, or co-cultures with other microbes. We provide a data-driven solution using network analysis, called "direct route", to characterize the production of known and putative specialized metabolites triggered by various exogenous compounds. We also provide a "auxiliary route" to distinguish unique unknown analytes amongst the abundantly produced analytes in response to these treatments. The developed techniques can assist researchers to identify treatments or applications that could positively influence the production of a targeted metabolite or recognize unique unknown analytes that can be further fractionated, characterized, and screened for their biological activities and hence, discover new metabolites.

systems biology↗

Cyclooxygenase production of PGE2 promotes phagocyte control of A. fumigatus hyphal growth in larval zebrafish

Invasive aspergillosis is a common opportunistic infection, causing >50% mortality in infected immunocompromised patients. The specific molecular mechanisms of the innate immune system that prevent pathogenesis of invasive aspergillosis in immunocompetent individuals are not fully understood. Here, we used a zebrafish larva-Aspergillus infection model to identify cyclooxygenase (COX) enzyme signaling as one mechanism that promotes host survival. Larvae exposed to the pan-COX inhibitor indomethacin succumb to infection at a significantly higher rate than control larvae. COX signaling is both macrophage- and neutrophil-mediated. However, indomethacin treatment has no effect on phagocyte recruitment. Instead, COX signaling promotes phagocyte-mediated inhibition of germination and invasive hyphal growth. Protective COX-mediated signaling requires the receptor EP2 and exogenous prostaglandin E2 (PGE2) rescues indomethacin-induced decreased immune control of fungal growth. Collectively, we find that COX signaling activates the PGE2-EP2 pathway to increase control A. fumigatus hyphal growth by phagocytes in zebrafish larvae. Author SummaryInvasive aspergillosis causes mortality in >50% of infected patients. It is caused by a free-living fungus Aspergillus fumigatus which releases thousands of airborne spores. While healthy individuals clear inhaled spores efficiently, in immunocompromised individuals these spores grow into filamentous hyphae and destroy lungs and other tissues causing invasive aspergillosis. The immune mechanisms that control this fungal growth in healthy people are still largely unknown. Here, we used a larval zebrafish model of A. fumigatus infection to determine that cyclooxygenase enzymes, which are the target of non-steroidal anti-inflammatory drugs such as aspirin and ibuprofen, are important to control the fungus. Innate immune cells use cyclooxygenase signaling to prevent hyphal growth and tissue destruction. Our study provides new insights into the mechanisms that immune cells deploy to stop invasive growth of A. fumigatus and inform development of future strategies to combat invasive aspergillosis.

immunology↗

An Interpreted Atlas of Biosynthetic Gene Clusters from 1000 Fungal Genomes

Fungi are prolific producers of natural products, compounds which have had a large societal impact as pharmaceuticals, mycotoxins, and agrochemicals. Despite the availability of over 1000 fungal genomes and several decades of compound discovery efforts from fungi, the biosynthetic gene clusters (BGCs) encoded by these genomes and the associated chemical space have yet to be analyzed systematically. Here we provide detailed annotation and analyses of fungal biosynthetic and chemical space to enable genome mining and discovery of fungal natural products. Using 1037 genomes from species across the fungal kingdom (e.g., Ascomycota, Basidiomycota, and non-Dikarya taxa), 36,399 predicted BGCs were organized into a network of 12,067 gene cluster families (GCFs). Anchoring these GCFs with reference BGCs enabled automated annotation of 2,026 BGCs with predicted metabolite scaffolds. We performed parallel analyses of the chemical repertoire of Fungi, organizing 15,213 fungal compounds into 2,945 molecular families (MFs). The taxonomic landscape of fungal GCFs is largely species-specific, though select families such as the equisetin GCF are present across vast phylogenetic distances with parallel diversifications in the GCF and MF. We compare these fungal datasets with a set of 5,453 bacterial genomes and their BGCs and 9,382 bacterial compounds, revealing dramatic differences between bacterial and fungal biosynthetic logic and chemical space. These genomics and cheminformatics analyses reveal the large extent to which fungal and bacterial sources represent distinct compound reservoirs. With a >10-fold increase in the number of interpreted strains and annotated BGCs, this work better regularizes the biosynthetic potential of fungi for rational compound discovery. Significance StatementFungi represent an underexploited resource for new compounds with applications in the pharmaceutical and agriscience industries. Despite the availability of >1000 fungal genomes, our knowledge of the biosynthetic space encoded by these genomes is limited and ad hoc. We present results from systematically organizing the biosynthetic content of 1037 fungal genomes, providing a resource for data-driven genome mining and large-scale comparison of the genetic and molecular repertoires produced in fungi and compare to those present in bacteria.

biochemistry↗

From iron to antibiotics: Identification of conserved bacterial-fungal interactions across diverse partners

Microbial interactions are major determinants in shaping microbiome structure and function. Although fungi are found across diverse microbiomes, the mechanisms through which fungi interact with other species remain largely uncharacterized. In this work, we explore the diversity of ways in which fungi can impact bacteria by characterizing interaction mechanisms across 16 different bacterial-fungal pairs, involving 8 different fungi and 2 bacteria (Escherichia coli and Pseudomonas psychrophila). Using random barcode transposon-site sequencing (RB-TnSeq), we identified a large number of bacterial genes and pathways important in fungal interaction contexts. Within each interaction, fungal partners elicit both antagonistic and beneficial effects. Using a panel of phylogenetically diverse fungi allowed us to identify interactions that were conserved across all species. Our data show that all fungi modulate the availability of iron and biotin, suggesting that these may represent conserved bacterial-fungal interactions. Several fungi also appear to produce previously uncharacterized antibiotic compounds. Generating a mutant in a master regulator of fungal secondary metabolite production showed that fungal metabolites are key shapers of bacterial fitness profiles during interactions. This work demonstrates a diversity of mechanisms through which fungi are able to interact with bacterial species. In addition to many species-specific effects, there appear to be conserved interaction mechanisms which may be important across microbiomes.

microbiology↗