In Silico Predictions of Ecological Plasticity Mediated by Protein Family Expansions in Early-Diverging Fungi

Low-complexity regions in fungi display functional groups and are depleted in positively charged amino acids

Reports on the diversity and occurrence of low-complexity regions (LCR) in Eukaryota are limited. Some studies have provided a more extensive characterization of LCR proteins in prokaryotes. There is a growing body of knowledge about a plethora of biological functions attributable to LCRs. However, it is hard to determine to what extent observed phenomena apply to fungi since most studies of fungal LCRs were limited to model yeasts. To fill this gap, we performed a survey of LCRs in proteins across all fungal tree of life branches. We show that the abundance of LCRs and the abundance of proteins with LCRs are positively correlated with proteome size. We observed that most LCRs are present in proteins with protein domains but do not overlap with the domain regions. LCRs are associated with many duplicated protein domains. The quantity of particular amino acids in LCRs deviates from the background frequency with a clear over-representation of amino acids with functional groups and a negative charge. Moreover, we discovered that each lineage of fungi favors distinct LCRs expansions. Early diverging fungal lineages differ in LCR abundance and composition pointing at a different evolutionary trajectory of each fungal group.

Contiguous and complete assemblies of Blastocystis gut microbiome-associated protists reveal evolutionary diversification to host ecology

Blastocystis, an obligate host-associated protist, is the most common microbial eukaryote in the human gut and is widely distributed across vertebrate hosts. The evolutionary transition of Blastocystis from its free-living stramenopile ancestors to a radiation of host-associated organisms is poorly understood. To explore this, we cultured and sequenced eight strains representing the significant phylogenetic diversity of the genus using long-read, short-read, and Hi-C DNA sequencing, alongside gene annotation and RNA sequencing. Comparative genomic analyses revealed significant variation in gene content and genome structure across Blastocystis. Notably, three strains from herbivorous tortoises, phylogenetically distant from human subtypes, have markedly larger genomes with longer introns and intergenic regions, and retain canonical stop codons absent in the human-associated strains. Despite these genetic differences, all eight isolates exhibit gene losses linked to the reduced cellular complexity of Blastocystis, including losses of cilia and flagella genes, microtubule motor genes, and signal transduction genes. Isolates from herbivorous tortoises contained higher numbers of plant carbohydrate-metabolizing enzymes, suggesting that like gut bacteria, these protists ferment plant material in the host gut. We find evidence that some of these carbohydrate-metabolizing enzymes were horizontally acquired from bacteria, indicating that horizontal gene transfer is an ongoing process in Blastocystis that has contributed to host-related adaptation. Together, these results highlight substantial genetic and metabolic diversity within the Blastocystis genus, indicating different lineages of Blastocystis have varied ecological roles in the host gut.

Comparative genomics reveals carbohydrate enzymatic fluctuations and herbivorous adaptations in arthropods

Background

Arthropods represent the largest and most diverse phylum on Earth, playing a pivotal role in the biosphere. One key to their evolutionary success is their ability to feed on plant material. However, their endogenous enzymatic repertoire, which contributes to plant digestion, remains largely unexplored and poorly understood.

Results

We analyzed 815 arthropod proteomes and identified a total of 268,171 carbohydrate-active modules. Our findings revealed a strong correlation between enzymatic content and feeding habits, with herbivorous species possessing significantly higher enzyme levels. We identified widespread carbohydrate-active families across the AA, CBM, GH, and GT classes, and observed a progressive increase in taxa-exclusive families in more recent arthropod lineages. Notably, we highlighted the impact of the transition from ametabolous to holometabolous development on carbohydrate metabolism, as well as the ecological adaptations of different species groups. By reconstructing the ancestral enzymatic profiles of arthropods, we identified significant fluctuations in 10 carbohydrate-active families over time.

Conclusions

Our analysis advances the understanding of the evolutionary mechanisms utilized by the megadiverse phylum Arthropoda. We emphasize the critical role of herbivory as a selective force shaping enzymatic strategies, particularly those involved in carbohydrate metabolism. The distribution and exclusivity of carbohydrate-active families across different arthropod groups provide insights into their evolutionary trajectories and offer a clearer picture of the metabolic pathways that led their ancestors to their present forms.

Genomic Sequencing and Functional Analysis of the Ex-Type Strain of Malbranchea zuffiana

Malbranchea is a genus within the order Onygenales (phylum Ascomycota) that includes predominantly saprobic cosmopolitan species. Despite its ability to produce diverse secondary metabolites, no genomic data for Malbranchea spp. are currently available in databases. Therefore, in this study, we obtained, assembled, and annotated the genomic sequence of the ex-type strain of Malbranchea zuffiana (CBS 219.58). For the genomic sequencing, we employed both the Illumina and PacBio platforms, followed by hybrid assembly using MaSuRCA. Quality assessment of the assembly was performed using QUAST and BUSCO tools. Annotation was conducted using BRAKER2, and functional annotation was completed with InterProScan. The resulting genome was of high quality, with a size of 26.46 Mbp distributed across 38 contigs and a BUSCO completion rate of 95.7%, indicating excellent contiguity and assembly completeness. A total of 8248 protein-encoding genes were predicted, with functional annotations assigned to 73.9% of them. Moreover, 82 genes displayed homology with entries in the Pathogen Host Interactions (PHI) database, while 494 genes exhibited similarity to entries in the Carbohydrate-Active Enzymes (CAZymes) database. Furthermore, 30 biosynthetic gene clusters (BGCs) were identified, suggesting significant potential for the biosynthesis of diverse secondary metabolites. Comparative functional analysis with closely related species unveiled a considerable abundance of domains linked to enzymes involved in keratin degradation, alongside a restricted number of domains associated with enzymes engaged in plant cell wall degradation in all studied species of the Onygenales. This genome-based elucidation not only enhances our comprehension of the biological characteristics of M. zuffiana but also furnishes valuable insights for subsequent investigations concerning Malbranchea species and the order Onygenales.

Fucose as a nutrient ligand for Dikarya and a building block of early diverging lineages

Fucose is a deoxyhexose sugar present and studied in mammals. The process of fucosylation has been the primary focus in studies relating to fucose in animals due to the presence of fucose in Lewis antigens. Very few studies have reported its presence in Fungi, mostly in Mucoromycotina. The constitution of 25% and 12% of this sugar in the carbohydrates of cell wall in the respective Umbelopsis and Mucorales strains boosts the need to bridge the gap of knowledge on fucose metabolism across the fungal tree of life. In the absence of a network map involving fucose proteins, we carried out an in-silico approach to construct the fucose metabolic map in Fungi. We analyzed the taxonomic distribution of 85 protein families in Fungi including diverse early diverging fungal lineages. The expression of fucose-related protein-coding genes proteins was validated with the help of transcriptomic data originating from representatives of early diverging fungi. We found proteins involved in several metabolic activities apart from fucosylation such as synthesis, transport and binding. Most of the identified protein families are shared with Metazoa suggesting an ancestral origin in Opisthokonta. However, the overall complexity of fucose metabolism is greater in Metazoa than in Fungi. Massive gene loss has shaped the evolutionary history of these metabolic pathways, leading to a repeated reduction of these pathways in most yeast-forming lineages. Our results point to a distinctive mode of utilization of fucose among fungi belonging to Dikarya and the early diverging lineages. We speculate that, while Dikarya used fucose as a source of nutrients for metabolism, the early diverging group of fungi depended on fucose as a building block and signaling compound.

Secrets of the fungus-specific potassium channel TOK family

Several families of potassium (K⁺) channels are found in membranes of all eukaryotes, underlining the importance of K⁺ uptake and redistribution within and between cells and organs. Among them, TOK (tandem-pore outward-rectifying K⁺) channels consist of eight transmembrane domains and two pore domains per subunit organized in dimers. These channels were originally studied in yeast, but recent identifications and characterizations in filamentous fungi shed new light on this fungus-specific K⁺ channel family. Although their actual function in vivo is often puzzling, recent works indicate a role in cellular K⁺ homeostasis and even suggest a role in plant-fungus symbioses. This review aims at synthesizing the current knowledge on fungal TOK channels and discussing their potential role in yeasts and filamentous fungi.