Fungal lipid enzymes reveal an ancient story of life on land

Fungi conquered nearly every habitat on Earth, from deep-sea sediments to desert rock and the lungs of mammals, and a new study suggests that a family of oily molecules called sphingolipids helped make that conquest possible. A sweeping evolutionary analysis published in IMA Fungus has mapped the full repertoire of sphingolipid metabolism proteins across the fungal tree of life, and the results point to a striking pattern: the enzymes that build and recycle these membrane lipids expanded and diversified just as fungi were making their move onto land, and again as flowering plants radiated across the planet.

Sphingolipids are a class of lipids built around a sphingoid base rather than the glycerol backbone found in ordinary fats. At their center sit ceramides, molecules composed of a long-chain base linked to a fatty acid through an amide bond. In eukaryotic cells, ceramides and their derivatives are far more than structural padding for the plasma membrane. They participate in growth, survival, differentiation, stress adaptation, and signaling, and their synthesis and breakdown form one of the most intricate metabolic networks in the cell. In fungi, the predominant sphingoid base is phytosphingosine, and the complex sphingolipids built on it, such as glycosyl inositol phosphoceramide, are essential constituents of the outer leaflet of the plasma membrane, where they modulate signal transduction, cell adhesion, and cell cycle progression.

Despite this importance, nearly everything scientists know about fungal sphingolipid metabolism comes from a narrow slice of fungal diversity, the Dikarya, which includes the familiar yeasts, molds, and mushrooms. For the vast majority of fungal lineages, the enzymes involved in ceramide biosynthesis and recycling had never been systematically cataloged. To close that gap, the research team assembled protein sets from 148 early diverging fungi and representatives of 35 classes of Dikarya, downloaded from NCBI in May 2022, and screened them against reference sequences drawn from the UniProt and REACTOME databases. Using domain-based clustering with the CLANS algorithm, followed by domain architecture prediction with Pfam and InterProScan, the researchers identified 34 protein families that they subdivided into 59 subfamilies spanning the full sphingolipid pathway.

The 59 subfamilies fall into three main pathway groups: seven involved in de novo ceramide synthesis, 22 in ceramide recycling, and 30 in cooperating pathways that include fatty acid metabolism, sterol metabolism, glycoprotein modification, and lipid transport. The analysis revealed a fundamental split in how these groups have evolved. Five of the seven de novo synthesis subfamilies and 19 of the 30 cooperating pathway components are conserved across all fungi, reflecting their ancient, housekeeping roles. In contrast, roughly half of the ceramide recycling proteins vary between phyla, suggesting that this arm of the pathway has been a playground for evolutionary experimentation.

None of the fungal phyla possesses all 59 subfamilies, and the diversity varies dramatically across the tree. Glomeromycota and Mucoromycota lead with 44 subfamilies each, followed by Chytridiomycota with 42, Blastocladiomycota with 41, and Mortierellomycota with 40. At the other extreme, Microsporidia, obligate intracellular parasites, retain just 9 subfamilies, preserving only the core de novo ceramide and fatty acid synthesis pathways while losing complex sphingolipid metabolism entirely. This reduction likely represents an adaptation to anaerobic parasitism, in which the parasites rely on host-derived fatty acids and shed the metabolic machinery they no longer need. Similarly reduced repertoires appear in the anaerobic gut fungi of the Neocallimastigomycota and in the parasitic Rozellomycota.

One of the most striking findings concerns the difference between flagellated fungi, which include the Chytridiomycota, Neocallimastigomycota, and Blastocladiomycota, and their non-flagellated relatives. Flagellated fungi show a consistent reduction in the diversity of sphingolipid recycling enzymes, including acid sphingomyelin phosphodiesterase, acid ceramidase, lysosomal acid glucosylceramidase, sphingolipid C9-methyltransferase, and several glycosyltransferases. The researchers interpret this as evidence that these enzymes are not essential in aquatic habitats, where constant water immersion buffers cells against the osmotic fluctuations that terrestrial organisms must endure. Blastocladiomycota, which are motile but have colonized semi-terrestrial niches, emerge as an evolutionary bridge, retaining ancestral fungal traits while also displaying innovations typical of the Dikarya.

The study also uncovered a remarkable temporal signature in the molecular clocks of key enzymes. By constructing maximum likelihood phylogenetic trees with IQ-TREE and calibrating them with least squares dating using established divergence times for the major fungal lineages, the researchers traced when specific gene duplications occurred. Duplications of acid sphingomyelin phosphodiesterase and UDP-glucuronosyltransferase in non-flagellated fungi cluster around 200 to 300 million years ago, close to the estimated period of fungal terrestrialization, which is exemplified by the famous Rhynie chert fossils from Scotland dated to approximately 410 million years ago. In Glomeromycota and Dikarya, however, the divergence of acid sphingomyelin phosphodiesterase coincides instead with the evolutionary radiation of flowering plants around 120 million years ago, suggesting a second wave of sphingolipid innovation tied to the rise of the mycorrhizal partnerships that dominate terrestrial ecosystems today.

The ceramide synthase family, which catalyzes the pivotal acylation step in ceramide production, tells its own evolutionary story. The enzyme is not only conserved across all fungi but has undergone multiple independent expansions in vertebrates and in distinct fungal phyla, including Mortierellomycota, filamentous Dikarya, and Entomophthoromycota. Phylogenetically, ceramide synthases split into an animal-like clade containing all CERS1-6 reference sequences from animals, plants, and flagellated fungi, and separate fungal-specific clades that include the Saccharomyces cerevisiae paralogs LAG1 and LAC1. Some paralogs have been recruited for entirely new purposes, such as the sphingosine N-acyltransferase-like proteins FUM17 and ALT7 found in Gibberella moniliformis and Alternaria alternata, which are implicated in mycotoxin biosynthesis rather than membrane construction.

Beyond the evolutionary narrative, the study carries significant biotechnological and medical implications. Ceramide synthase has recently been identified as a potential antifungal drug target, and its deletion in pathogenic fungi abolishes virulence. Transcriptomic data from the human pathogen Rhizopus delemar reveal that during infection of human airway epithelial cells, the fungus downregulates de novo ceramide synthesis while upregulating enzymes involved in sphingomyelin catabolism and ceramide recycling, suggesting a metabolic shift toward ceramide recovery that supports pathogenicity. Similarly, the oleaginous yeast Yarrowia lipolytica carries multiple copies of acid sphingomyelin phosphodiesterase, potentially linked to its remarkable lipid-producing capacity, a trait of growing interest for industrial biotechnology.

The researchers also examined publicly available transcriptomes to verify that the genes they identified are actually active. In axenic cultures of Mucoromycota and Mortierellomycota, most sphingolipid metabolism genes show expression, with patterns differing between species and environmental conditions. Under anaerobic conditions, the anaerobic gut symbiont Smittium and the parasite Entomophthora muscae show distinct expression profiles, while in the mycorrhizal fungus Rhizophagus irregularis, association with host plants triggers upregulation of specific desaturases and glycosyltransferases. These expression patterns confirm that sphingolipid metabolism is not a static inheritance from deep evolutionary time but a dynamic system that fungi actively tune in response to their surroundings, whether those surroundings are a mammalian lung, a plant root, or the oxygen-poor interior of a herbivore gut.

Subject of Research: Evolutionary diversity of sphingolipid metabolism proteins across the fungal tree of life

Article Title: Evolutionary diversity of sphingolipid metabolism proteins in fungi

Article References: Płecha, M., Sokołowska, B., Barua, D., Bartczak, J., Sobczyk, M., Koperska, D., Kułakowska, A., Komosa, A., & Muszewska, A. (2026). Evolutionary diversity of sphingolipid metabolism proteins in fungi. IMA Fungus, 17, Article e177891. https://doi.org/10.3897/imafungus.17.177891

Image Credits: AI Generated

DOI: 10.3897/imafungus.17.177891

Keywords: sphingolipids, ceramides, fungi, evolution, terrestrialization, membrane lipids, phylogenomics, Dikarya, flagellated fungi, molecular dating, sphingomyelin, glycosyltransferases