Genome mining of ascomycetous fungi reveals their genetic potential for ergot alkaloid production

Fungal ergot alkaloids: Metabolic pathways, biological functions, and advances in synthetic reprogramming

Ergot alkaloids (EAs) are a class of secondary metabolites produced by fungi. These compounds are predominantly synthesized by Ascomycota, with variations in types and biosynthetic pathways among different fungal species. The EA synthesis has minimal impact on the normal growth and development of most EA-producing fungi, but serves as a virulence factor that influences the biocontrol functions of entomopathogenic fungi and symbiotic fungi in plants. In the medical field, EAs have been widely used for treating neurological disorders such as Parkinson's disease. However, the biosynthetic pathways of EAs are highly complex and significantly influenced by environmental factors, resulting in low yields from field production or chemical synthesis. To address the global demand for EAs, various strategies have been developed to reprogram the biosynthetic pathways in some chassis strains, aiming to simplify the process and increase EA production. This review summarizes the biosynthetic pathways and regulatory mechanisms of EAs in fungi, their biological functions, and recent advances in strategies for synthetic reprogramming.

Structural Similarity, Activity, and Toxicity of Mycotoxins: Combining Insights from Unsupervised and Supervised Machine Learning Algorithms

A large number of mycotoxins and related fungal metabolites have not been assessed in terms of their toxicological impacts. Current methodologies often prioritize specific target families, neglecting the complexity and presence of co-occurring compounds. This work addresses a fundamental question: Can we assess molecular similarity and predict the toxicity of mycotoxins in silico using a defined set of molecular descriptors? We propose a rapid nontarget screening approach for multiple classes of mycotoxins, integrating both unsupervised and supervised machine learning models, alongside molecular and physicochemical descriptors to enhance the understanding of structural similarity, activity, and toxicity. Clustering analyses identify natural clusters corresponding to the known mycotoxin families, indicating that mycotoxins belonging to the same cluster share similar molecular properties. However, topological descriptors play a significant role in distinguishing between acutely toxic and nonacutely toxic compounds. Random forest (RF) and neural networks (NN), combined with molecular descriptors, contribute to improved knowledge and predictive capability regarding mycotoxin toxicity profiles. RF allows the prediction of toxicity using data reflecting mainly structural features and performs well in the presence of descriptors reflecting biological activity. NN models prove to be more sensitive to biological activity descriptors than RF. The use of descriptors encompassing structural complexity and diversity, chirality and symmetry, connectivity, atomic charge, and polarizability, together with descriptors representing lipophilicity, absorption, and permeation of molecules, is crucial for predicting toxicity, facilitating broader toxicological evaluations.

Overproduction of medicinal ergot alkaloids based on a fungal platform

Privileged ergot alkaloids (EAs) produced by the fungal genus Claviceps are used to treat a wide range of diseases. However, their use and research have been hampered by the challenging genetic engineering of Claviceps. Here we systematically refactored and rationally engineered the EA biosynthetic pathway in heterologous host Aspergillus nidulans by using a Fungal-Yeast-Shuttle-Vector protocol. The obtained strains allowed the production of diverse EAs and related intermediates, including prechanoclavine (PCC, 333.8 mg/L), chanoclavine (CC, 241.0 mg/L), agroclavine (AC, 78.7 mg/L), and festuclavine (FC, 99.2 mg/L), etc. This fungal platform also enabled the access to the methyl-oxidized EAs (MOEAs), including elymoclavine (EC), lysergic acid (LA), dihydroelysergol (DHLG), and dihydrolysergic acid (DHLA), by overexpressing a P450 enzyme CloA. Furthermore, by optimizing the P450 electron transfer (ET) pathway and using multi-copy of cloA, the titers of EC and DHLG have been improved by 17.3- and 9.4-fold, respectively. Beyond our demonstration of A. nidulans as a robust platform for EA overproduction, our study offers a proof of concept for engineering the eukaryotic P450s-contained biosynthetic pathways in a filamentous fungal host.

Fungal evolution: cellular, genomic and metabolic complexity

The question of how phenotypic and genomic complexity are inter-related and how they are shaped through evolution is a central question in biology that historically has been approached from the perspective of animals and plants. In recent years, however, fungi have emerged as a promising alternative system to address such questions. Key to their ecological success, fungi present a broad and diverse range of phenotypic traits. Fungal cells can adopt many different shapes, often within a single species, providing them with great adaptive potential. Fungal cellular organizations span from unicellular forms to complex, macroscopic multicellularity, with multiple transitions to higher or lower levels of cellular complexity occurring throughout the evolutionary history of fungi. Similarly, fungal genomes are very diverse in their architecture. Deep changes in genome organization can occur very quickly, and these phenomena are known to mediate rapid adaptations to environmental changes. Finally, the biochemical complexity of fungi is huge, particularly with regard to their secondary metabolites, chemical products that mediate many aspects of fungal biology, including ecological interactions. Herein, we explore how the interplay of these cellular, genomic and metabolic traits mediates the emergence of complex phenotypes, and how this complexity is shaped throughout the evolutionary history of Fungi.

Clavine Alkaloids Gene Clusters of Penicillium and Related Fungi: Evolutionary Combination of Prenyltransferases, Monooxygenases and Dioxygenases

The clavine alkaloids produced by the fungi of the Aspergillaceae and Arthrodermatacea families differ from the ergot alkaloids produced by Claviceps and Neotyphodium. The clavine alkaloids lack the extensive peptide chain modifications that occur in lysergic acid derived ergot alkaloids. Both clavine and ergot alkaloids arise from the condensation of tryptophan and dimethylallylpyrophosphate by the action of the dimethylallyltryptophan synthase. The first five steps of the biosynthetic pathway that convert tryptophan and dimethylallyl-pyrophosphate (DMA-PP) in chanoclavine-1-aldehyde are common to both clavine and ergot alkaloids. The biosynthesis of ergot alkaloids has been extensively studied and is not considered in this article. We focus this review on recent advances in the gene clusters for clavine alkaloids in the species of Penicillium, Aspergillus (Neosartorya), Arthroderma and Trychophyton and the enzymes encoded by them. The final products of the clavine alkaloids pathways derive from the tetracyclic ergoline ring, which is modified by late enzymes, including a reverse type prenyltransferase, P450 monooxygenases and acetyltransferases. In Aspergillus japonicus, a α-ketoglutarate and Fe²⁺-dependent dioxygenase is involved in the cyclization of a festuclavine-like unknown type intermediate into cycloclavine. Related dioxygenases occur in the biosynthetic gene clusters of ergot alkaloids in Claviceps purpurea and also in the clavine clusters in Penicillium species. The final products of the clavine alkaloid pathway in these fungi differ from each other depending on the late biosynthetic enzymes involved. An important difference between clavine and ergot alkaloid pathways is that clavine producers lack the enzyme CloA, a P450 monooxygenase, involved in one of the steps of the conversion of chanoclavine-1-aldehyde into lysergic acid. Bioinformatic analysis of the sequenced genomes of the Aspergillaceae and Arthrodermataceae fungi showed the presence of clavine gene clusters in Arthroderma species, Penicillium roqueforti, Penicillium commune, Penicillium camemberti, Penicillium expansum, Penicillium steckii and Penicillium griseofulvum. Analysis of the gene clusters in several clavine alkaloid producers indicates that there are gene gains, gene losses and gene rearrangements. These findings may be explained by a divergent evolution of the gene clusters of ergot and clavine alkaloids from a common ancestral progenitor six genes cluster although horizontal gene transfer of some specific genes may have occurred more recently.

Ergot Alkaloids of the Family Clavicipitaceae

Ergot alkaloids are highly diverse in structure, exhibit diverse effects on animals, and are produced by diverse fungi in the phylum Ascomycota, including pathogens and mutualistic symbionts of plants. These mycotoxins are best known from the fungal family Clavicipitaceae and are named for the ergot fungi that, through millennia, have contaminated grains and caused mass poisonings, with effects ranging from dry gangrene to convulsions and death. However, they are also useful sources of pharmaceuticals for a variety of medical purposes. More than a half-century of research has brought us extensive knowledge of ergot-alkaloid biosynthetic pathways from common early steps to several taxon-specific branches. Furthermore, a recent flurry of genome sequencing has revealed the genomic processes underlying ergot-alkaloid diversification. In this review, we discuss the evolution of ergot-alkaloid biosynthesis genes and gene clusters, including roles of gene recruitment, duplication and neofunctionalization, as well as gene loss, in diversifying structures of clavines, lysergic acid amides, and complex ergopeptines. Also reviewed are prospects for manipulating ergot-alkaloid profiles to enhance suitability of endophytes for forage grasses.

A bifunctional old yellow enzyme from Penicillium roqueforti is involved in ergot alkaloid biosynthesis

Bifunctional FgaOx3_Pr3catalyses the formation of festuclavine in the presence of EasG or FgaFS and enhances the activity of several chanoclavine-I dehydrogenases tremendously.

Structural characterization of EasH (Aspergillus japonicus) - an oxidase involved in cycloclavine biosynthesis

Aj_EasH is a non-heme iron- and α-keto-glutarate-dependent oxidase that is responsible for an unusual cyclopropyl ring formation in the biosynthesis of the fungal ergot alkaloid cycloclavine. The three dimensional structure of Aj_EasH (2.2 Å resolution) reported here provides insight into the mechanism of this unusual and complex reaction.