Biology subjects

Drula, E.

Publications and source records attributed to Drula, E..

18 recordsLinked to original sources

bioRxiv2026

The coculture of Fomitopsis betulina with Escherichia coli induces a nutritional stress and triggers secondary metabolism pathways.

Basidiomycete fungi are an underexplored source of specialized metabolites with significant biotechnological potential. However, the environmental cues that activate their biosynthetic pathways remain poorly understood. Here, we investigated the response of the wood-decaying fungus Fomitopsis betulina, to nutritional competition using co-cultures with Escherichia coli. On solid medium, F. betulina inhibited the bacterial growth. Using a mass spectrometry-based metabolomics approach, we identified a Sumikis acid derivative, calcium diformate, and sulfuric acid among the compounds enriched within the inhibition zone and hypothesized that these compounds were associated with the acidification of the medium. Although F. betulina has previously been reported to produce the antibacterial compound piptamine, neither piptamine nor related derivatives were detected under our experimental conditions. In liquid medium, the co-culture with E. coli caused the rapid depletion of the available glucose, resulting in the establishment of carbon-starvation conditions and a 44% reduction in fungal biomass. Transcriptomic analyses revealed extensive metabolic reprogramming in response to bacterial competition, including the induction of genes involved in carbon acquisition, nutrient transport, redox homeostasis, and stress adaptation. Notably, a homolog of the Velvet regulatory complex, a central regulator of fungal development and specialized metabolism, was upregulated. The co-culture induced the expression of genes associated with multiple biosynthetic gene clusters, including terpene, polyketide, and fungal RiPP. Taken together, our results demonstrate that bacterial competition acts as a potent trigger of nutritional stress and secondary metabolism in F. betulina. More broadly, fungal-bacterial co-culture represents a promising alternative to extractions to identify high-value added metabolites pathways from basidiomycetes.

microbiology↗

bioRxiv2026

Screening for Polysaccharide Utilization Loci Targeting Marine Polysaccharides

Polysaccharide utilization loci (PULs) have been a goldmine for the characterization of novel carbohydrate active enzymes (CAZymes) and the understanding of their synergistic degradation of complex polysaccharides. We collected PUL predictions containing CAZymes from glycoside hydrolase families GH29, GH50 and GH117, expected to participate in marine polysaccharide breakdown. We explored the evolutionary diversity in these families in terms of sequences and PUL composition, based on sulfatases and CAZymes. From 41 selected PULs, more than 400 putative enzymes were produced, purified and screened on a large collection of carbohydrates. We attributed a function to more than 130 enzymes from five sulfatase subfamilies, 29 known CAZymes families and discovered an activity for 4 families previously of unknown function, including an -L-galactosidase structurally and functionally characterized with mutants. Finally, our detailed analysis of the enzymatic synergies in five PULs, two targeting marine polysaccharides and three targeting eukaryotic polysaccharides, by marine and human gut organisms, highlight the efficiency of our exploratory strategy.

biochemistry↗

bioRxiv2025

Chromosome-scale genome assembly of Xiphinema index uncovers an unparalleled epigenetic toolkit in invertebrates

Nematodes constitute the most speciose animal phylum, occupying an exceptionally broad range of biomes and encompassing free-living microbe-feeders, predators, and notorious plant or animal parasites. However, the limited availability of genome-scale resources for early-branching nematode clades has constrained our understanding of the molecular determinants underlying these multiple evolutionary adaptations. Here, we present the genome of the plant-parasitic nematode Xiphinema index, constituting the first telomere-to-telomere assembly for the order Dorylaimida, an early-branching nematode lineage. Phylogenetic analyses reveal that horizontal gene transfers (HGT) have played a pivotal role in the emergence of plant parasitism in this phylum. Remarkably, we identify the first documented case of a plant-derived HGT in a nematode genome. This gene encodes a predicted secreted parasitic effector, underscoring the diversity of evolutionary events that contributed to the parasitic arsenal. Our results suggest that, beyond bacteria and fungi, plants themselves have provided crucial genes for parasitism that may now be used by the nematodes to manipulate them. Our comparative genomic analyses across more than 70 nematode species further uncover an unprecedented epigenetic toolkit in an invertebrate genome. Indeed, X. index harbors a complete set of canonical DNA methyltransferases, a full-length ATRX chromatin remodeler, and 3D-chromatin architectural CTCF protein coding homolog. Consistent with this repertoire, we detected methylation at CpG genome-wide, which inversely correlates with gene expression and chromatin accessibility. Together, these findings reveal a vertebrate-like epigenetic machinery in an early-branching nematode and call for a fundamental reassessment of the prevailing epigenetic paradigm in nematodes and, more broadly, in animals.

genomics↗

bioRxiv2025

Global mapping of thioredoxin interacting proteins in Neurospora crassa

Thioredoxins (Trx) are essential thiol-oxidoreductases that regulate redox homeostasis by reducing oxidized cysteines in a wide range of target proteins. However, the Trx system and other redox regulation mechanisms remain poorly characterized in saprotrophic filamentous fungi. Here, we identified the components of the Neurospora crassa Trx system and uncovered potential redox-regulated proteins using Trx affinity chromatography. Genome search identified three Trx and a single thioredoxin reductase that we named TRX1, TRX2 TRX3 and TRR. Notably, TRX1 carries a C-terminal disordered extension of unknown function, conserved in two ascomycete taxa (Leotiomycetes and Sordariomycetes). Using recombinant cysteine-to-serine mutants of each Trx, we performed affinity chromatography and identified 1,998 proteins - approximately 19% of the N. crassa proteome. To rank the putative Trx targets, we applied a fold enrichment metric, comparing protein abundance before and after affinity chromatography. The average fold enrichment was four, with values reaching up to 117 for the most enriched protein, a DEAD/DEAH box helicase. Among the top-enriched proteins, we identified homologs of known human and plant Trx targets, like peroxiredoxins, as well as 93 transcription factors and 38 kinases. Additional potential Trx targets encompass, ubiquitination-related enzymes, Fe-S cluster assembly proteins, phospholipases, exonucleases, and chitin synthases. Moreover, components of multiprotein complexes were co-purified, reflecting both direct Trx interactions and indirect co-association. Overall, this study provides a global map of potential redox regulated proteins and Trx targets in N. crassa, laying the ground for future investigations into redox signaling in filamentous fungi.

microbiology↗

bioRxiv2024

Functional carbohydrate-active enzymes acquired by horizontal gene transfer from plants in the whitefly Bemisia tabaci

Carbohydrate-active enzymes (CAZymes) involved in the degradation of plant cell walls and/or the assimilation of plant carbohydrates for energy uptake are widely distributed in microorganisms. In contrast, they are less frequent in animals, although there are exceptions, including examples of CAZymes acquired by horizontal gene transfer (HGT) from bacteria or fungi in several of phytophagous arthropods and plant-parasitic nematodes. Although the whitefly Bemisia tabaci is a major agricultural pest, knowledge of HGT-acquired CAZymes in this phloem-feeding insect of the Hemiptera order (subfamily Aleyrodinae) is still lacking. We performed a comprehensive and accurate detection of HGT candidates in B. tabaci and identified 136 HGT events, 14 of which corresponding to CAZymes. The B. tabaci HGT-acquired CAZymes were not only of bacterial or fungal origin, but some were also acquired from plants. Biochemical analysis revealed that members of the glycoside hydrolase families 17 (GH17) and 152 (GH152) acquired from plants are functional beta-glucanases with different substrate specificities, suggesting distinct roles. These two CAZymes are the first characterized GH17 and GH152 glucanases in an animal. We identified a lower number of HGT events in the related Aleyrodinae Trialeurodes vaporariorum, with only three HGT-acquired CAZymes, including a GH152 glucanase, with phylogenetic analysis suggesting a unique HGT event in the ancestor of the Aleyrodinae. Another GH152 CAZyme, most likely independently acquired from plants, was also identified in two plant cell-feeding insects of the Thysanoptera order, highlighting the importance of plant-acquired CAZymes in the biology of piercing-sucking insects. Significance statementCarbohydrate-active enzymes (CAZymes) are crucial for sugar metabolism. Those involved in plant cell wall degradation are usually absent from animal genomes. In this study, we explored CAZyme repertoires in the genomes of several insects: the phloem-feeding whitefly Bemisia tabaci, a major agricultural pest, and the related greenhouse whitefly Trialeurodes vaporariorum, as well as two Thysanoptera species that feed on plant cell contents. We identified several cases of CAZymes acquired from plant via horizontal gene transfer in the genome of these insects. Notably, we showed that two B. tabaci CAZymes of plant origin function as glucanases with distinct substrate specificities, potentially helping the insect to overcome plant defenses. Overall, these findings enhance our understanding of how the ability to feed on plants evolved in insects.

evolutionary biology↗

bioRxiv2024

Evolutionary history of the main extracellular matrix polysaccharides in brown algae

Brown algae belong to the Stramenopiles phylum and are phylogenetically distant from plants and other multicellular organisms. This independent evolutionary history has shaped brown algae with numerous metabolic characteristics specific to this group, including the synthesis of peculiar polysaccharides contained in their extracellular matrix (ECM). Alginates and fucose-containing sulphated polysaccharides (FCSP), the latter including fucans, are the main components of ECMs. However, the metabolic pathways of these polysaccharides remain poorly described due to a lack of genomic data. An extensive genomic dataset has been recently released for brown algae and their close sister species. We performed an expert annotation of key genes involved in ECM-carbohydrate metabolisms, combined with comparative genomics, phylogenetics analyses, and protein modelling. Our analysis indicates that the gene families involved in both the synthesis and degradation of alginate were acquired by the common ancestor of brown algae and their closest sister species Schizocladia ischiensis, and subsequently expanded in brown algae. The pathway for the biosynthesis of fucans still remains biochemically unresolved and we identify the most likely fucosyltransferase genes that may harbour a fucan synthase activity in brown algae. Our analysis questions the possible occurrence of FCSPs outside brown algae, notably within their closest sister taxon.

evolutionary biology↗

bioRxiv2024

Functional exploration of in vivo and in vitro lignocellulose-fed rumen bacterial microbiomes reveals novel enzymes involved in polysaccharide breakdown

BackgroundPlant cell walls are the main carbon sources for ruminal bacteria, which have evolved to produce sophisticated multi-functional enzyme cocktails in response to the structural diversity of lignocelulloses. Since a large proportion of ruminal bacteria are not yet cultured, we developed a high-throughput activity-based metagenomic approach to gain insight into this enzymatic diversity. ResultsA multi-step screening methodology was implemented to identify metagenomic clones acting on polysaccharides and polyaromatic compounds. This approach was used to explore the functional potential of two different microbial consortia derived from in vivo and in vitro enrichments of the bovine rumen microbiome on wheat straw. One hundred and sixty-eight fosmid clones were isolated from libraries. Five to seven times more {beta}-mannanase and {beta}-glucanase clones, and seven times less xylanase clones were obtained from the in vitro enrichment compared to the in vivo one. The sequencing of 51 fosmids, covering in total 1.4 Gb of metagenomic DNA, enabled the identification of various novel glycoside-hydrolases, esterases and oxidoreductases mostly encoded by unknown bacterial genera. Functional analysis showed that most of the identified xylanases belonged to Firmicutes members that were not enriched in the fermenter, while most cellulases and mannanases originate from Bacteroidetes. ConclusionThese enzymes, that, for most of them, had not been previously identified by in depth-metagenome sequencing, present a high potential for biotechnological applications, as they could be used alone or in cocktails to break down plant cell walls. The relationships established between enzyme function and taxonomy highlight the complementary roles played by ruminal Firmicutes and Bacteroidetes in plant cell wall degradation.

biochemistry↗

bioRxiv2023

Methionine oxidation of Carbohydrate-Active enZymes during white-rot wood decay

White-rot fungi employ secreted carbohydrate-active enzymes (CAZymes) along with reactive oxygen species (ROS), like hydrogen peroxide (H2O2), to degrade lignocellulose in wood. H2O2 serves as a co-substrate for key oxidoreductases during the initial decay phase. While the degradation of lignocellulose by CAZymes is well-documented, the impact of ROS on the oxidation of the secreted proteins remains unclear and the identity of the oxidized proteins is unknown. Methionine (Met) can be oxidized to Met sulfoxide (MetO) or Met sulfone (MetO2) with potential deleterious, antioxidant, or regulatory effects. Other residues, like proline (Pro), can undergo carbonylation. Using the white-rot Pycnoporus cinnabarinus grown on aspen wood, we analyzed the Met content of the secreted proteins and their susceptibility to oxidation combining H 18O with deep shotgun proteomics. Strikingly, their overall Met content was significantly lower (1.4%) compared to intracellular proteins (2.1%), a feature conserved in fungi but not in metazoans or plants. We evidenced that a catalase, widespread in white-rot fungi, protects the secreted proteins from oxidation. Our redox proteomics approach allowed identification of 49 oxidizable Met and 40 oxidizable Pro residues within few secreted proteins, mostly CAZymes. Interestingly, many of them had several oxidized residues localized in hotspots. Some Met, including those in GH7 cellobiohydrolases, were oxidized up to 47%, with a substantial percentage of sulfone (13%). These Met are conserved in fungal homologs, suggesting important functional roles. Our findings reveal that white-rot fungi safeguard their secreted proteins by minimizing their Met content and by scavenging ROS and pinpoint redox-active residues in CAZymes. ImportanceThe study of lignocellulose degradation by fungi is critical for understanding the ecological and industrial implications of wood decay. While carbohydrate-active enzymes (CAZymes) play a well-established role in lignocellulose degradation, the impact of hydrogen peroxide (H2O2) on secreted proteins remains unclear. This study aims at evaluating the effect of H2O2 on secreted proteins, focusing on the oxidation of methionine (Met). Using the model white-rot model Pycnoporus cinnabarinus grown on aspen wood, we showed that fungi protect their secreted proteins from oxidation by reducing their Met content and utilizing a secreted catalase to scavenge exogenous H2O2. The research identified key oxidizable Met within secreted CAZymes. Importantly, some Met like those of GH7 cellobiohydrolases, undergone substantial oxidation levels suggesting important roles in lignocellulose degradation. These findings highlight the adaptive mechanisms employed by white-rot fungi to safeguard their secreted proteins during wood decay and emphasize the importance of these processes in lignocellulose breakdown.

microbiology↗

bioRxiv2022

Genomic innovation and horizontal gene transfer shaped plant colonization and biomass degradation strategies of a globally prevalent fungal pathogen

Members of the fungal genus Armillaria are necrotrophic pathogens with efficient plant biomass-degrading strategies. The genus includes some of the largest terrestrial organisms on Earth, spreading underground and causing tremendous losses in diverse ecosystems. Despite their global importance, the mechanism by which Armillaria evolved pathogenicity in a clade of dominantly non-pathogenic wood-degraders (Agaricales) remains elusive. Here, using new genomic data, we show that Armillaria species, in addition to widespread gene duplications and de novo gene origins, appear to have at least 775 genes that were acquired via 101 horizontal gene transfer (HGT) events, primarily from Ascomycota. Functional and expression data suggest that HGT might have affected plant biomass-degrading and virulence abilities of Armillaria, two pivotal traits in their lifestyle. We further assayed gene expression during root and cambium colonization, and report putative virulence factors, extensive regulation of horizontally acquired and wood-decay related genes as well as novel pathogenicity-induced small secreted proteins (PiSSPs). Two PiSSPs induced necrosis in live plants, suggesting they are potential virulence effectors conserved across Armillaria. Overall, this study details how evolution knitted together horizontally and vertically inherited genes in complex adaptive traits, such as plant biomass degradation and pathogenicity, paving the way for development of infection models for one of the most influential pathogens of temperate forest ecosystems.

genomics↗

bioRxiv2022

Genome evolution and transcriptome plasticity associated with adaptation to monocot and eudicot plants in Colletotrichum fungi

Colletotrichum fungi infect a wide diversity of monocot and eudicot hosts, causing plant diseases on almost all economically important crops worldwide. In addition to its economic impact, Colletotrichum is a suitable model for the study of gene family evolution on a fine scale to uncover events in the genome that are associated with the evolution of biological characters important for host interactions. Here we present the genome sequences of 30 Colletotrichum species, 18 of them newly sequenced, covering the taxonomic diversity within the genus. A time-calibrated tree revealed that the Colletotrichum ancestor diverged in the late Cretaceous around 70 million years ago (mya) in parallel with the diversification of flowering plants. We provide evidence of independent host jumps from eudicots to monocots during the evolution of this pathogen, coinciding with a progressive shrinking of the degradative arsenal and expansions in lineage specific genes. Comparative transcriptomics of four reference species with different evolutionary histories and adapted to different hosts revealed similarity in gene content but differences in the modulation of their transcription profiles. Only a few orthologs show similar expression profiles on different plant cell walls. Combining genome sequences and expression profiles we identified a set of core genes, such as specific transcription factors, involved in plant cell wall degradation in Colletotrichum.Together, these results indicate that the ancestral Colletotrichum were associated with eudicot plants and certain branches progressively adapted to different monocot hosts, reshaping part of the degradative and transcriptional arsenal.

microbiology↗

bioRxiv2022

The soybean rust pathogen Phakopsora pachyrhizi displays transposable element proliferation that correlates with broad host-range adaptation on legumes

Asian soybean rust, caused by Phakopsora pachyrhizi, is one of the worlds most economically damaging agricultural diseases. Despite P. pachyrhizis impact, the exceptional size and complexity of its genome prevented generation of an accurate genome assembly. We simultaneously sequenced three P. pachyrhizi genomes uncovering a genome up to 1.25 Gb comprising two haplotypes with a transposable element (TE) content of ~93%. The proliferation of TEs within the genome occurred in several bursts and correlates with the radiation and speciation of the legumes. We present data of clear de-repression of TEs that mirrors expression of virulence-related candidate effectors. We can see a unique expansion in amino acid metabolism for this fungus. Our data shows that TEs play a dominant role in P. pachyrhizis genome and have a key impact on various processes such as host range adaptation, stress responses and genetic plasticity of the genome.

microbiology↗

bioRxiv2021

Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales

O_LIIn this study, we aim to identify genomic traits of the transitions to the ectomycorrhizal ecology within the Boletales, one of the most diverse lineages of symbiotrophic fungi. C_LIO_LIWe sequenced the genomes and compared the gene repertoires of symbiotrophic Boletales species to their saprotrophic brown-rot relatives. We also reconstructed gene duplication/loss histories along a time-calibrated phylogeny. C_LIO_LIWe showed that the rate of gene duplication is constant along the backbone of Boletales phylogeny with large loss events in lineages leading to several families. The rate of gene family expansion sharply increased in the late Miocene and mostly took place in Boletaceae. C_LIO_LIMost of the ectomycorrhizal Boletales are characterized by a large genome size due to transposable element (TE) expansions and a reduction in the diversity of plant cell wall degrading enzymes (PCWDEs) compared to their brown-rot relatives. However, several species in the Boletaceae, Paxillaceae and Boletinellaceae have kept a substantial set of endoglucanases and LPMOs acting on cellulose/hemicellulose and fungal polysaccharides suggesting that they may partly decompose organic matter by a combined activity of oxidative and hydrolytic enzymes. C_LIO_LIThe present study provides novel insights on our understanding of the mechanisms that influence the evolutionary diversification of boletes and symbiosis evolution. C_LI

genomics↗

bioRxiv2021

Time-resolved secretome analysis of three Colletotrichum species identifies copper radical alcohol oxidases for the production of fatty aldehydes

Copper Radical Alcohol Oxidases (CRO-AlcOx), which have been recently discovered among fungal phytopathogens are attractive for the production of fragrant fatty aldehydes. To investigate the secretion of CRO-AlcOx by natural fungal strains, we undertook time-course analyses of the secretomes of three Colletotrichum species (C. graminicola, C. tabacum and C. destructivum) using proteomics. The addition of a copper-manganese-ethanol mixture to Colletotrichum cultures unexpectedly induced the secretion of up to 400 proteins, 29-52% of which were carbohydrate-active enzymes (CAZymes), including a wide diversity of copper-containing oxidoreductases from the auxiliary activities (AA) class (AA1, AA3, AA5, AA7, AA9, AA11-AA13, AA16). Under these specific conditions, while a CRO-glyoxal oxidase from the AA5_1 subfamily was among the most abundantly secreted proteins, the targeted AA5_2 CRO-AlcOx were secreted at lower levels, suggesting heterologous expression as a more promising strategy for CRO-AlcOx production and utilization. C. tabacum and C. destructivum CRO-AlcOx were expressed in Pichia pastoris and their preference toward both aromatic and aliphatic primary alcohols was assessed. The CRO-AlcOx from C. destructivum was further investigated in applied settings, revealing a full conversion of C6 and C8 alcohols into their corresponding fragrant aldehydes. IMPORTANCEIn the context of the industrial shift toward greener processes, the biocatalytic production of aldehydes is of utmost interest owing to their importance as intermediates in preparative chemistry and for their use as flavors and fragrances ingredients. In the search for new biocatalysts, CRO-AlcOx have the potential to become platform enzymes for the oxidation of alcohols to aldehydes. The use of crude fungal secretomes is often seen has an appealing approach by industries since alleviating various costs pertaining to biocatalysts production. However, the secretion of CRO-AlcOx by natural fungal strains has never been explored. This study showed that Colletotrichum species can secrete a broad diversity of copper-containing enzymes, but only little amount of CRO-AlcOx. Thus, recombinant expression remains the most promising approach. The potential of CRO-AlcOx as biocatalyst for flavor and fragrance applications was confirmed through the production of two new enzymes with activity on fatty alcohols.

biochemistry↗

bioRxiv2021

Secondary metabolism drives ecological breadth in the Xylariaceae

Global, large-scale surveys of phylogenetically diverse plant and lichen hosts have revealed an extremely high richness of endophytes in the Xylariales, one of the largest clades of filamentous fungi and a significant source of novel secondary metabolites (SMs). Endophytes may produce host protective antimicrobial or insecticidal SMs, as well as compounds that facilitate symbiotic establishment through suppression or degradation of host immune response, but the ecological roles of most SMs are unknown. Here we characterized metabolic gene clusters in 96 genomes of endophytes and closely related saprotrophs and pathogens in two clades of Xylariales (Xylariaceae s.l. and Hypoxylaceae). Hundreds of genes appear horizontally transferred to xylarialean fungi from distantly related fungi and bacteria, including numerous genes in secondary metabolite gene clusters (SMGCs). Although all xylarialean genomes contain hyperabundant SMGCs, we show that increased gene duplications, horizontal gene transfers (HGTs), and SMGC content in Xylariaceae s.l. taxa are linked to greater phylogenetic host breadth, larger biogeographic distributions, and increased capacity for lignocellulose decomposition compared to Hypoxylaceae taxa. Overall, our results suggest that xylarialean endophytes capable of dual ecological modes (symbiotic and saprotrophic) experience greater selection to diversify SMGCs to both increase competitiveness within microbial communities and facilitate diverse symbiotic interactions.

genomics↗

bioRxiv2021

Genetic determinants of endophytism in the Arabidopsis root mycobiome

Roots of Arabidopsis thaliana do not engage in symbiotic associations with mycorrhizal fungi but host taxonomically diverse fungal communities that influence health and disease states. We sequenced the genomes of 41 fungal isolates representative of the A. thaliana root mycobiota for comparative analysis with 79 other plant-associated fungi. We report that root mycobiota members evolved from ancestors with diverse lifestyles and retained large repertoires of plant cell wall-degrading enzymes (PCWDEs) and effector-like small secreted proteins. We identified a set of 84 gene families predicting best endophytism, including families encoding PCWDEs acting on xylan (GH10) and cellulose (AA9). These genes also belong to a core transcriptional response induced by phylogenetically-distant mycobiota members in A. thaliana roots. Recolonization experiments with individual fungi indicated that strains with detrimental effects in mono-association with the host not only colonize roots more aggressively than those with beneficial activities but also dominate in natural root samples. We identified and validated the pectin degrading enzyme family PL1_7 as a key component linking aggressiveness of endophytic colonization to plant health.

microbiology↗

bioRxiv2021

Evolutionary priming and transition to the ectomycorrhizal habit in an iconic lineage of mushroom-forming fungi: is preadaptation a requirement?

The ectomycorrhizal symbiosis is an essential guild of many forested ecosystems and has a dynamic evolutionary history across kingdom Fungi, having independently evolved from diverse types of saprotrophic ancestors. In this study, we seek to identify genomic features of the transition to the ectomycorrhizal habit within the Russulaceae, one of the most diverse lineages of ectomycorrhizal fungi. We present comparative analyses of the pangenome and gene repertoires of 21 species across the order Russulales, including a closely related saprotrophic member of Russulaceae. The ectomycorrhizal Russulaceae is inferred to have originated around the Cretaceous-Paleogene extinction event (73.6-60.1 million years ago (MY)). The genomes of the ectomycorrhizal Russulaceae are characterized by a loss of genes for plant cell-wall degrading enzymes (PCWDEs), an expansion of genome size through increased transposable element (TE) content, a reduction in secondary metabolism clusters, and an association of genes coding for certain secreted proteins with TE "nests". The saprotrophic sister group of the ectomycorrhizal Russulaceae, Gloeopeniophorella convolvens, possesses some of these aspects (e.g., loss of some PCWDE and protease orthologs, TE expansion, reduction in secondary metabolism clusters), resulting from an accelerated rate of gene evolution in the shared ancestor of Russulaceae that predates the evolution of the ectomycorrhizal habit. Genomes of Russulaceae possess a high degree of synteny, including a conserved set of terpene secondary metabolite gene clusters. We hypothesize that the evolution of the ectomycorrhizal habit requires premodification of the genome for plant root association followed by an accelerated rate of gene evolution within the secretome for host-defense circumvention and symbiosis establishment.

evolutionary biology↗

bioRxiv2019

The genome of Auriculariopsis ampla sheds light on fruiting body development and wood-decay of bark-inhabiting fungi

The Agaricomycetes are fruiting body forming fungi that produce some of the most efficient enzyme systems to degrade woody plant materials. Despite decades-long interest in the ecological and functional diversity of wood-decay types and in fruiting body development, the evolution of the genetic repertoires of both traits are incompletely known. Here, we sequenced and analyzed the genome of Auriculariopsis ampla, a close relative of the model species Schizophyllum commune. Comparative analyses of wood-decay genes in these and other 29 Agaricomycetes species revealed that the gene family composition of A. ampla and S. commune are transitional between that of white rot species and less efficient wood-degraders (brown rot, ectomycorrhizal). Rich repertoires of suberinase and tannase genes were found in both species, with tannases generally restricted to species that preferentially colonize bark-covered wood. Analyses of fruiting body transcriptomes in both A. ampla and S. commune highlighted a high rate of divergence of developmental gene expression. Several genes with conserved developmental expression were found, nevertheless, including 9 new transcription factors as well as small secreted proteins, some of which may serve as fruiting body-specific effector molecules. Taken together, the genome sequence and developmental transcriptome of Auriculariopsis ampla has highlighted novel aspects of wood-decay diversity and of fruiting body development in mushroom-forming fungi.

evolutionary biology↗

bioRxiv2018

Integrative visual omics of the white-rot fungus Polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw plant biomass.

White-rot fungi are wood decayers able to degrade all polymers from lignocellulosic biomass including cellulose, hemicelluloses, and lignin. The white-rot fungus Polyporus brumalis efficiently breaks down lignin and is regarded as having a high potential for the initial treatment of plant biomass in its conversion to bio-energy. We performed integrative multi-omics analyses by combining data from the fungal genome, transcriptomes, and secretomes. We found the fungus possessed an unexpectedly large set of genes coding for enzymes related to lignin degradation, and that these were highly expressed and massively secreted under solid-state fermentation conditions. The examination of interrelated multi-omics patterns revealed the coordinated regulation of lignin-active peroxidases and H2O2-generating enzymes along with the activation of cellular mechanisms for detoxification, which combined to result in the efficient lignin breakdown by the fungus.\n\nImportancePlant biomass conversion for green chemistry and bio-energy is a current challenge for a modern sustainable bioeconomy. The complex polyaromatic lignin polymers in raw biomass feedstocks (i.e. agriculture and forestry by-products) are major obstacles for biomass conversions. From a biotechnological aspect, these compounds could be a potential source of aromatic platform molecules for bio-based polymers. Here we describe the extraordinary ability of Polyporus brumalis for lignin degradation using its enzymatic arsenal to break down wheat straw, a lignocellulosic substrate that is considered as a biomass feedstock worldwide. We observed unusual expansions of gene families coding for; 1) Class II peroxidases involved in lignin degradation; and 2) GMC oxidoreductases/dehydrogenases involved in generating the hydrogen peroxide required for lignin peroxidase activity. Our findings suggested the fungus massively mobilizes this oxidative machinery during growth on wheat straw. Overall, we identified sets of co-regulated enzymes, which could potentially augment the efficiency of biotechnological plant biomass conversions.

bioengineering↗