My journey with fungi: the beauty and complexity of fungal natural products

Once viewed as niche curiosities, fungal natural products (NPs), or secondary metabolites, have become central to some of today's most dynamic areas of research—from drug discovery and fungal pathogenicity to computational biology and the microbiome. This surge of interest stands in sharp contrast to the field I first encountered at the start of my scientific journey. My entry into the world of fungal NPs was humble, sparked by a drive to confront the global challenge of mycotoxin contamination in food and feed, an issue that first captured my attention during my service in the Peace Corps. Thus, it feels only natural to begin the story there. Graduate school was never part of my original plan until service as a Peace Corps volunteer in Lesotho changed my outlook. Living and working there awakened a desire to return to Africa and contribute to international agriculture—particularly in the area of food safety, but it also made clear that an advanced degree would be essential. A Peace Corps office director in Lesotho encouraged me to apply to Cornell and a few other universities known for their strength in international agriculture. Cornell ultimately became the choice, partly because it was within reach of family in Pennsylvania after 3 years in Lesotho, and partly because its Plant Pathology program offered an ideal home for my emerging interests. Entering the Plant Pathology Department, the path led to a PhD and a deepening fascination with fungal biology that would shape an entire career. Graduate school was a time of extraordinary intellectual excitement and enduring friendships, and it was there that my initial curiosity about fungal secondary metabolism began to take shape. Biochemistry and the new possibilities of molecular manipulation of fungi quickly became irresistible, prompting a decision to stay on for a PhD rather than stop with a master's degree. Mentors were central: Gary Bergstrom modeled how to maintain resilience during the challenges of graduate school and to work collaboratively and generously, while Olen Yoder, a pioneer in the molecular biology of filamentous fungi, hammered home the importance of using model systems whenever possible. Although my thesis work itself did not directly focus on fungal secondary metabolites, it unfolded in an environment rich with people who did. Olen Yoder and Gillian Turgeon were advancing the molecular genetics of Cochliobolus spp. (Yang 1996; Baker et al. 2006), grain crop pathogens that produce phytotoxins responsible for leaf blight symptoms. The creativity and rigor of postdoctoral scientists and graduate students from this period at Cornell were to profoundly shape the emerging field of fungal NPs. Among them, Tom Wolpert explored how the host-selective toxin victorin, produced by Cochliobolus victoriae, affected plant health (Wolpert and Macko 1989; Lorang et al. 2012); Lynda Ciuffetti went on to characterize the host-specific toxin Ptr ToxB of Pyrenophora tritici-repentis (Martinez et al. 2001; Ciuffetti et al. 2010); Anne Desjardins was instrumental in characterizing the trichothecene and fumonisin biosynthetic gene clusters (BGCs) (Hohn et al. 1993; Proctor et al. 2003), Corby Kistler elucidated how Fusarium trichothecene mycotoxins are synthesized and compartmentalized within specialized “toxisome” organelles (Chen et al. 2019), and Frances Trail became a leader in the genetics of aflatoxin and Fusarium secondary metabolism (Trail et al. 1995; Gaffoor et al. 2005). It was during my graduate years that my enduring fascination with fungi truly took root. The discussions and collaborations with these colleagues not only in graduate school but through the years provided me with an informal but invaluable second education in fungal NPs. While still in graduate school, a more personal turning point in my interest in fungal NPs came from a seminar by Paul Williams, known for his work on fumonisins, mycotoxins produced by Fusarium species that damage the health of horses, pigs, and other animals and are linked to esophageal and liver cancers in humans (Marasas 2001). Much of his research, in collaboration with Wally Marasas, had been carried out in South Africa, geographically and emotionally close to the villages where my service in Lesotho had taken place. As he spoke, memories surfaced of school meals in Lesotho: maize-based food sometimes visibly moldy or otherwise unappealing, yet eaten because there were no alternatives. That juxtaposition—students’ daily reality and the emerging science of fumonisin toxicity—raised an unsettling question that has never entirely faded: had those children, and perhaps their teachers, been consuming fumonisin-contaminated food all along? Toward the end of my PhD, I began searching for postdoctoral positions and, inspired by Paul Williams’ talk on fumonisins, I focused on laboratories working on mycotoxins. I considered Gary Payne's laboratory in North Carolina, Anne Desjardins’ group at the USDA facility in Peoria, and the laboratory of Ed Cleveland and Deepak Bhatnagar at the USDA Southern Regional Research Center in New Orleans. All would have been excellent choices, but I ultimately chose New Orleans, where I could develop a new skill set in protein purification by working on an enzyme in the aflatoxin biosynthetic pathway. The 1990s was an especially dynamic period in molecular mycotoxicology, as the field was transitioning from classical chemical characterization of mycotoxins to uncovering the underlying biochemistry and genetics controlling their production. During my postdoctoral years in New Orleans, I met one of the most influential mentors in my career, Joan Bennett, then a professor at Tulane. Her parasexual genetic studies suggested that many aflatoxin pathway genes are closely linked in a single chromosomal region (Bennett 1979), work that complemented similar linkage analyses from another aflatoxin pioneer, Ken Papa (Papa 1979). In New Orleans, I succeeded in purifying an aflatoxin pathway O-methyltransferase (Keller et al. 1993), and the resulting purified protein enabled us, in collaboration with Fun Sun Chu at the University of Wisconsin, to obtain an antibody allowing us to clone the corresponding gene from Aspergillus parasiticus (Yu et al. 1993). Around the same time, using a mutant first isolated by Ken Papa, a collaborative effort by Gary Payne's group, Charles Woloshuk and my USDA mentors cloned the gene encoding AflR, the aflatoxin regulatory transcription factor (Payne et al. 1993, Fig. 1); and work by John Linz's group at Michigan State cloned additional aflatoxin pathway genes in A. parasiticus (Chang et al. 1992; Skory et al. 1992). All of these works collectively helped to define the aflatoxin gene cluster and its regulation. The collegial collaboration among our USDA laboratory and the Payne, Linz and Bennett laboratories provided a powerful model of how cooperative interactions can accelerate progress in pathway dissection and regulatory analysis (Chang et al. 1993). Timeline of conceptual and technological advances. AF, aflatoxin; ST, sterigmatocystin; OSMAC, One Strain Many Compounds; BGC, biosynthetic gene cluster; FAC, fungal artificial chromosome; GCF, gene cluster family; RiPP, ribosomally synthesized and post-translationally modified peptide. After 2 years as a postdoc, I moved to Texas A&M University as an assistant professor in the Department of Plant Pathology, recruited by Neil Van Alfen as he expanded the cadre of fungal biologists on the faculty. This transition was transformative, greatly broadening my view of fungal secondary metabolism. Following advice from Olen Yoder to invest in a robust model system, I began collaborating with a new colleague in the Biology Department, Tom Adams, who had trained with Bill Timberlake and was working with the genetic model fungus, Aspergillus nidulans. Because A. nidulans had long served as a premier model filamentous fungus and produces sterigmatocystin, a direct precursor and structural relative of aflatoxin, it offered an ideal platform to explore regulatory mechanisms controlling these toxins. My entry into A. nidulans research revealed how versatile a filamentous fungus could be for dissecting natural product pathways, beyond sterigmatocystin itself. Seminal work in this organism on penicillin biosynthesis and its regulation—for example, Miguel Peñalva's studies on pH regulation of the penicillin gene cluster (Espeso et al. 1993; Suárez and Peñalva 1996) and Axel Brakhage's work on the transcriptional regulator PenR1 (Litzka et al. 1996, 1998) —highlighted the sophisticated control of secondary metabolite gene clusters in A. nidulans. I was also strongly influenced by numerous studies from Herb Arst, Claudio Scazzocchio, Michael Hynes and Joan Kelly on A. nidulans nitrogen and carbon metabolism. These studies further shaped my thinking about global regulatory networks governing secondary metabolism in filamentous fungi. There is no doubt that this species has led the charge in genetically and chemically defining NP in fungi (Caesar et al. 2020; Guo et al. 2025). One of my first goals as an assistant professor was to characterize the sterigmatocystin BGC in A. nidulans. John Linz generously sent our laboratory an A. parasiticus plasmid containing aflatoxin genes his laboratory had cloned. Because the DNA sequences were similar enough, we were able to identify a matching cosmid in the A. nidulans overlapping cosmid library (Brody et al. 1991) containing the gene we first called verA, which was later renamed stcU (Keller et al. 1994, 1995). This cosmid library exemplified the power of early genomic tools in A. nidulans and enabled us to identify a series of cosmids spanning the sterigmatocystin gene cluster, work that we published first in 1995 (Keller and Adams 1995) and then more fully in 1996 in collaboration with Tom Leonard and Tom Adams (Brown et al. 1996). This was simultaneous with characterization of the A. parasiticus aflatoxin gene cluster by Frances Trail, John Linz, and colleagues (Trail et al. 1995) and occurred in parallel with mapping and sequencing efforts that established the aflatoxin pathway cluster in A. parasiticus and Aspergillus flavus (Yu et al. 1995). Together, these studies helped launch intensive efforts in several laboratories, including my own with Tom Adams, to define the specific function of many enzymes in the sterigmatocystin/aflatoxin pathway (Brown et al. 1996; Kelkar et al. 1996, 1997; Keller et al. 2000) and the DNA binding site of the sterigmatocystin pathway-specific Zn(II)2 Cys2 transcription factor AflR (Fernandes et al. 1998). The sterigmatocystin/aflatoxin clusters are now frequently cited examples of conservation and diversification within fungal secondary metabolite gene cluster families (GCFs). Toward the end of my sojourn at Texas A&M, my interests shifted to wanting to find how the sterigmatocystin cluster was regulated beyond AflR. To address this, we carried out a mutagenesis screen in A. nidulans and isolated mutants that no longer produced sterigmatocystin but otherwise displayed largely wild-type growth (Butchko et al. 1999). This work would yield the platform leading to a series of exciting discoveries in NP research fully developed in my next career move. In 2001, I moved my laboratory to UW-Madison. Starting a new laboratory at UW-Madison afforded fresh momentum and allowed for development of new ideas and visions. I immediately set out to identify the alleles uncovered by the mutagenesis study. These genes spanned a wide range of functions including linkage of propionyl-CoA metabolism (Zhang et al. 2004) and beta-oxidation to polyketide biosynthesis (Maggio-Hall et al. 2005). But the most significant discovery from the mutagenesis screen was characterization of LaeA (loss of aflR expression), a protein transcriptionally regulating a multitude of BGCs including sterigmatocystin, penicillin, lovastatin and pigment pathways in Aspergillus (Bok and Keller 2004). This work demonstrated that LaeA acts above individual pathway-specific transcription factors and was coined as a global regulator of NP synthesis in Aspergillus spp., reframing secondary metabolism as subject to shared higher-level control. LaeA is widely recognized as a global regulator of secondary metabolism in all filamentous fungi, primarily positively influencing the expression of numerous BGCs and affecting additional traits, including developmental programs and enzymatic activities. Hence LaeA is a widespread tool for SM discovery in fungi where its overexpression leads to increased secondary metabolite gene transcription and product synthesis (Khan et al. 2020; Zhang et al. 2020; Martín et al. 2026). Moreover, LaeA has been established as a virulence factor in both plant- and human-pathogenic fungi, underscoring its broader importance for fungal biology and host–pathogen interactions (Calvo et al. 2024). However, despite the decades of work on LaeA, the mechanistic basis of LaeA function remains unresolved, whether as a methyltransferase (Patananan et al. 2013) or primarily as a structural component of the velvet complex (described next section). Since the discovery of LaeA, several other global regulators have been described. These include RtfA (Lohmar et al. 2016) and McrA (Oakley et al. 2016), the latter showing an interesting twist as primarily a negative regulator as its deletion upregulates several NPs. In 2008, a collaboration with the Gerhard Braus and Jae-Hyuk Yu laboratories demonstrated that LaeA was a component of the heterotrimeric velvet complex, consisting of VelB, VeA, and LaeA, which links light-responsive development to secondary metabolism in filamentous fungi (Bayram et al. 2008). This complex is broadly conserved among filamentous species and coordinates light-dependent morphogenesis with secondary metabolite production (Yu et al. 2023a, 2023b). Subsequent work from both the Yu and Braus groups have continued to define velvet-associated NP regulation and protein complexes, repeatedly underscoring the tight coupling between fungal development and secondary metabolite synthesis (Sarikaya et al. 2010; Karahoda et al. 2022). Also in this time period our laboratory, in collaboration with the Graessle group in Austria, was the first to link epigenetic processes with NP synthesis (Shwab et al. 2007). We expanded this work with the Clay Wang, Berl Oakley, and Joseph Strauss laboratories to identify CclA, a Bre2 ortholog involved in histone H3 lysine 4 methylation that activated cryptic BGCs (Bok et al. 2009). Subsequent collaborative work with the Strauss laboratory showed that LaeA influences chromatin organization of BGCs, counteracting heterochromatin marks such as H3K9 methylation at cluster promoters to permit transcription (Reyes-Dominguez et al. 2010). This epigenetic view advanced the field by providing a mechanistic explanation for how a single regulator can simultaneously affect many physically clustered genes, moving from descriptive genetics to chromatin-based models of SM control. Recognition that chromatin modifications could switch secondary metabolite clusters from an inactive to an active state fundamentally shifted thinking about how to access fungal biosynthetic potential. Whole-genome sequencing of Aspergillus species beginning around 2005 revealed a surprisingly large repertoire of BGCs compared to the relatively small number of compounds detected under laboratory leading to the now widely of or gene Many such clusters have been activated by genetic manipulation of enzymes and chromatin that with chromatin-based can secondary In deletion of the protein can clusters and their products et al. as a of the complex, by the laboratory and et al. 2022). NP regulatory are not to those involved in epigenetic A in point is the discovery of a regulatory complex the binding protein that coordinates many secondary et al. The challenge of BGCs remains one of the in new to In to epigenetic manipulation and overexpression of global or BGC specific several other have to address this The established Strain Many can in active compounds by of growth et al. include the development of of fungi the most natural product gene clusters are for and allowing production of compounds that otherwise are from such as in A. nidulans and in et al. et al. 2026). These have also been in expression of BGCs from other species such as production of and from the BGC from into et al. The of A. nidulans developed by the and laboratories et al. is widely as a expression et et al. 2026). These an because genetic expression and with fungal turning filamentous fungi into for BGCs from The expression of large BGCs remains a to their regulatory and expression To these our laboratory in collaboration with the and Neil laboratories developed the of artificial fungal DNA that the and expression of entire BGCs as single genetic et al. This the for while gene organization and regulatory for BGC the system, which of cloned sequences and Yu et al. 2023a, or of expression et al. Together, these how access and complex fungal pathways, turning was a into a platform for and new NPs. the genetic artificial and advanced systems the to a new of where entire pathways can be as that many NPs are it is no that BGCs are activated through In our laboratory, we focused on the plant and its with fungi, where we the which development in fungi and entry into fungal et al. In several we showed that and its fungal of and developmental secondary the fungal specific and on the and other or to on the of et al. et al. et al. 2022). of interactions have from the and A by et al. showed that between A. nidulans and the otherwise polyketide and leading to production of and other Subsequent mechanistic work of histone H3 in A. nidulans during with and and chromatin as regulatory that a to of BGCs, directly to epigenetic in the fungus et al. This work to specific chromatin at fungal BGCs and established as a for rather than a has been to of with not in that or between fungi can cryptic et al. of the velvet complex can be involved in et al. et al. 2022). These systems the field by showing that secondary metabolism is not or but can be one pathway activated while another is mapping regulatory and of metabolite studies shifted the focus from to showing that and chemical can BGCs chromatin and pathway-specific and tools have fungal secondary metabolism research by of BGCs responsible for such as identify these clusters and pathways that et al. et al. have how these by entire at the discovery of compounds with including and et al. and 2025). entry into computational BGC discovery came through analysis of which computational tools because of their Although our laboratory in collaboration with laboratory had several BGCs et al. et al. et al. only such BGCs, all in Aspergillus including the et al. a with and et al. BGCs fungal among fungal metabolite and at more than the number of clusters et al. of the first fungal synthesized and post-translationally modified in the was by of in et al. 2026). We were also in a collaboration with the Neil laboratory, to with chemical to a linked for BGCs into on both metabolite production and (Caesar et al. et al. 2024). The strength of these in their of such as in plant and of new drug tools have advanced the of secondary metabolism by biosynthetic pathways to their regulators et al. et al. et al. 2026). example, the of A. et al. enabled of an regulatory controlling biosynthesis in A. et al. 2025). despite all of these a remains between genomic and the natural product repertoire of fungi, as many biosynthetic clusters have yet to yield for that The field of fungal secondary metabolism to as and it to the chemical in fungal was a largely is a more in which BGCs can be linked to chromatin and in of and the of further accelerate this and define the biosynthetic of cryptic the same time, access to rich but fungi is expression and artificial are the reach of fungal genetics into and other that have to These are especially because entire pathways to be and in rather than clusters in their the field is moving beyond the that secondary metabolism is on or of epigenetic and have that biosynthetic is shaped by and The next from these into a that genetic to chemical I to the many who have and inspired my career the and the many postdoctoral and scientists who have to my and have truly shaped my scientific journey. I my to and have been I for with I also my colleagues for their and on this by of