Two Horizontally Transferred Xenobiotic Resistance Gene Clusters Associated with Detoxification of Benzoxazolinones by Fusarium Species

Insights into the genomic and functional divergence of NAT gene family to serve microbial secondary metabolism

Microbial NAT enzymes, which employ acyl-CoA to acylate aromatic amines and hydrazines, have been well-studied for their role in xenobiotic metabolism. Some homologues have also been linked to secondary metabolism, but this function of NAT enzymes is not as well-known. For this comparative study, we surveyed sequenced microbial genomes to update the list of formally annotated NAT genes, adding over 4000 new sequences (mainly bacterial, but also archaeal, fungal and protist) and portraying a broad but not universal distribution of NATs in the microbiocosmos. Localization of NAT sequences within microbial gene clusters was not a rare finding, and this association was evident across all main types of biosynthetic gene clusters (BGCs) implicated in secondary metabolism. Interrogation of the MIBiG database for experimentally characterized clusters with NAT genes further supports that secondary metabolism must be a major function for microbial NAT enzymes and should not be overlooked by researchers in the field. We also show that NAT sequences can be associated with bacterial plasmids potentially involved in horizontal gene transfer. Combined, our computational predictions and MIBiG literature findings reveal the extraordinary functional diversification of microbial NAT genes, prompting further research into their role in predicted BGCs with as yet uncharacterized function.

Root uptake of cereal benzoxazinoids grants resistance to root-knot nematode invasion in white clover

Plants synthesize a plethora of chemical defence compounds, which vary between evolutionary lineages. We hypothesize that plants evolved the ability to utilize defence compounds synthesized and released by neighbouring heterospecific plants. In two experiments, we incubated clover (Trifolium repens L.) seedlings with individual benzoxazinoid (BX) compounds (2,4-dihydroxy-1,4-benzoxazin-3-one, 2-hydroxy-1,4-benzoxazin-3-one, benzoxazolinone, and 6-methoxy- benzoxazolin-2-one), a group of bioactive compounds produced by cereals, to allow clover BX uptake. Subsequently, we transplanted the seedlings into soil and quantified BX root and shoot content and invasion of root-knot nematodes in clover roots up to 8 weeks after transplantation. We show that clover root uptake of BXs substantially enhanced clover's resistance against the root-knot nematode Meloidogyne incognita. This effect lasted up to 6 weeks after the clover roots were exposed to the BXs. BXs were absorbed by clover roots, and then translocated to the shoots. As a result of clover metabolization, we detected the parent BXs and a range of their transformation products in the roots and shoots. Based on these novel findings, we envisage that co-cultivation of crop species with complementary and transferable chemical defence systems can add to plant protection.

Endophyte genomes support greater metabolic gene cluster diversity compared with non-endophytes in Trichoderma

Trichoderma is a cosmopolitan genus with diverse lifestyles and nutritional modes, including mycotrophy, saprophytism, and endophytism. Previous research has reported greater metabolic gene repertoires in endophytic fungal species compared to closely-related non-endophytes. However, the extent of this ecological trend and its underlying mechanisms are unclear. Some endophytic fungi may also be mycotrophs and have one or more mycoparasitism mechanisms. Mycotrophic endophytes are prominent in certain genera like Trichoderma, therefore, the mechanisms that enable these fungi to colonize both living plants and fungi may be the result of expanded metabolic gene repertoires. Our objective was to determine what, if any, genomic features are overrepresented in endophytic fungi genomes in order to undercover the genomic underpinning of the fungal endophytic lifestyle. Here we compared metabolic gene cluster and mycoparasitism gene diversity across a dataset of thirty-eight Trichoderma genomes representing the full breadth of environmental Trichoderma's diverse lifestyles and nutritional modes. We generated four new Trichoderma endophyticum genomes to improve the sampling of endophytic isolates from this genus. As predicted, endophytic Trichoderma genomes contained, on average, more total biosynthetic and degradative gene clusters than non-endophytic isolates, suggesting that the ability to create/modify a diversity of metabolites potential is beneficial or necessary to the endophytic fungi. Still, once the phylogenetic signal was taken in consideration, no particular class of metabolic gene cluster was independently associated with the Trichoderma endophytic lifestyle. Several mycoparasitism genes, but no chitinase genes, were associated with endophytic Trichoderma genomes. Most genomic differences between Trichoderma lifestyles and nutritional modes are difficult to disentangle from phylogenetic divergences among species, suggesting that Trichoderma genomes maybe particularly well-equipped for lifestyle plasticity. We also consider the role of endophytism in diversifying secondary metabolism after identifying the horizontal transfer of the ergot alkaloid gene cluster to Trichoderma.

Pseudocercospora fijiensis Conidial Germination Is Dominated by Pathogenicity Factors and Effectors

Conidia play a vital role in the survival and rapid spread of fungi. Many biological processes of conidia, such as adhesion, signal transduction, the regulation of oxidative stress, and autophagy, have been well studied. In contrast, the contribution of pathogenicity factors during the development of conidia in fungal phytopathogens has been poorly investigated. To date, few reports have centered on the pathogenicity functions of fungal phytopathogen conidia. Pseudocercospora fijiensis is a hemibiotrophic fungus and the causal agent of the black Sigatoka disease in bananas and plantains. Here, a conidial transcriptome of P. fijiensis was characterized computationally. Carbohydrates, amino acids, and lipid metabolisms presented the highest number of annotations in Gene Ontology. Common conidial functions were found, but interestingly, pathogenicity factors and effectors were also identified. Upon analysis of the resulting proteins against the Pathogen-Host Interaction (PHI) database, 754 hits were identified. WideEffHunter and EffHunter effector predictors identified 618 effectors, 265 of them were shared with the PHI database. A total of 1107 conidial functions devoted to pathogenesis were found after our analysis. Regarding the conidial effectorome, it was found to comprise 40 canonical and 578 non-canonical effectors. Effectorome characterization revealed that RXLR, LysM, and Y/F/WxC are the largest effector families in the P. fijiensis conidial effectorome. Gene Ontology classification suggests that they are involved in many biological processes and metabolisms, expanding our current knowledge of fungal effectors.

Development and Optimization of Culture Medium for the Production of Glabridin by Aspergillus eucalypticola: An Endophytic Fungus Isolated from Glycyrrhiza glabra L. (Fabaceae)

Glabridin is a well-known active isoflavone found in the root of licorice (Glycyrrhiza glabra L.) that possess a wide range of biological activity. Plant cells, hairy roots, and fungal endophytes cultures are the most important alternative methods for plant resources conservation and sustainable production of natural compounds, which has received much attention in recent decades. In the present study, an efficient culture condition was optimized for the biomass accumulation and glabridin production from fungal endophyte Aspergillus eucalypticola SBU-11AE isolated from licorice root. Type of culture medium, range of pH, and licorice root extract (as an elicitor) were tested. The results showed that the highest and lowest biomass production was observed on PCB medium (6.43 ± 0.32 g/l) and peptone malt (5.85 + 0.11 g/l), respectively. The medium culture PCB was produced the highest level of glabridin (7.26 ± 0.44 mg/l), while the lowest level (4.47 ± 0.02 mg/l) was obtained from the medium peptone malt. The highest biomass (8.51 ± 0.43 g/l) and glabridin (8.30 ± 0.51 mg/l) production were observed from the PCB medium adjusted with pH = 6, while the lowest value of both traits was obtained from the same medium with pH = 7. The highest production of total glabridin (10.85 ± 0.84 mg/l) was also obtained from the culture medium treated with 100 mg/l of the plant root extract. This information can be interestingly used for the commercialization of glabridin production for further industrial applications.

Transcriptomic Response of Fusarium verticillioides to Variably Inhibitory Environmental Isolates of Streptomyces

Fusarium verticillioides is a mycotoxigenic fungus that is a threat to food and feed safety due to its common infection of maize, a global staple crop. A proposed strategy to combat this threat is the use of biological control bacteria that can inhibit the fungus and reduce mycotoxin contamination. In this study, the effect of multiple environmental isolates of Streptomyces on F. verticillioides was examined via transcriptome analysis. The Streptomyces strains ranged from inducing no visible response to dramatic growth inhibition. Transcriptionally, F. verticillioides responded proportionally to strain inhibition with either little to no transcript changes to thousands of genes being differentially expressed. Expression changes in multiple F. verticillioides putative secondary metabolite gene clusters was observed. Interestingly, genes involved in the fusaric acid gene cluster were suppressed by inhibitory strains of Streptomyces. A F. verticillioides beta-lactamase encoding gene (FVEG_13172) was found to be highly induced by specific inhibitory Streptomyces strains and its deletion increased visible response to those strains. This study demonstrates that F. verticillioides does not have an all or nothing response to bacteria it encounters but rather a measured response that is strain specific and proportional to the strength of inhibition.

Bioactive Nitrosylated and Nitrated N-(2-hydroxyphenyl)acetamides and Derived Oligomers: An Alternative Pathway to 2-Amidophenol-Derived Phytotoxic Metabolites

Incubation of Aminobacter aminovorans, Paenibacillus polymyxa, and Arthrobacter MPI764 with the microbial 2-benzoxazolinone (BOA)-degradation-product 2-acetamido-phenol, produced from 2-aminophenol, led to the recently identified N-(2-hydroxy-5-nitrophenyl) acetamide, to the hitherto unknown N-(2-hydroxy-5-nitrosophenyl)acetamide, and to N-(2-hydroxy-3-nitrophenyl)acetamide. As an alternative to the formation of phenoxazinone derived from aminophenol, dimers- and trimers-transformation products have been found. Identification of the compounds was carried out by LC/HRMS and MS/MS and, for the new structure N-(2-hydroxy-5-nitrosophenyl)acetamide, additionally by 1D- and 2D-NMR. Incubation of microorganisms, such as the soil bacteria Pseudomonas laurentiana, Arthrobacter MPI763, the yeast Papiliotrema baii and Pantoea ananatis, and the plants Brassica oleracea var. gongylodes L. (kohlrabi) and Arabidopsis thaliana Col-0, with N-(2-hydroxy-5-nitrophenyl) acetamide, led to its glucoside derivative as a prominent detoxification product; in the case of Pantoea ananatis, this was together with the corresponding glucoside succinic acid ester. In contrast, Actinomucor elegans consortium synthesized 2-acetamido-4-nitrophenyl sulfate. 1 mM bioactive N-(2-hydroxy-5-nitrophenyl) acetamide elicits alterations in the Arabidopsis thaliana expression profile of several genes. The most responsive upregulated gene was pathogen-inducible terpene synthase TPS04. The bioactivity of the compound is rapidly annihilated by glucosylation.

A taxonomically representative strain collection to explore xenobiotic and secondary metabolism in bacteria

Bacteria employ secondary metabolism to combat competitors, and xenobiotic metabolism to survive their chemical environment. This project has aimed to introduce a bacterial collection enabling comprehensive comparative investigations of those functions. The collection comprises 120 strains (Proteobacteria, Actinobacteria and Firmicutes), and was compiled on the basis of the broad taxonomic range of isolates and their postulated biosynthetic and/or xenobiotic detoxification capabilities. The utility of the collection was demonstrated in two ways: first, by performing 5144 co-cultures, recording inhibition between isolates and employing bioinformatics to predict biosynthetic gene clusters in sequenced genomes of species; second, by screening for xenobiotic sensitivity of isolates against 2-benzoxazolinone and 2-aminophenol. The co-culture medium of Bacillus siamensis D9 and Lysinibacillus sphaericus DSM 28^T was further analysed for possible antimicrobial compounds, using liquid chromatography-mass spectrometry (LC-MS), and guided by computational predictions and the literature. Finally, LC-MS analysis demonstrated N-acetylation of 3,4-dichloroaniline (a toxic pesticide residue of concern) by the actinobacterium Tsukamurella paurometabola DSM 20162^T which is highly tolerant of the xenobiotic. Microbial collections enable "pipeline" comparative screening of strains: on the one hand, bacterial co-culture is a promising approach for antibiotic discovery; on the other hand, bioremediation is effective in combating pollution, but requires knowledge of microbial xenobiotic metabolism. The presented outcomes are anticipated to pave the way for studies that may identify bacterial strains and/or metabolites of merit in biotechnological applications.

Transcriptomic Responses of Fusarium verticillioides to Lactam and Lactone Xenobiotics

The important cereal crops of maize, rye, and wheat constitutively produce precursors to 2-benzoxazolinone, a phytochemical having antifungal effects towards many Fusarium species. However, Fusarium verticillioides can tolerate 2-benzoxazolinone by converting it into non-toxic metabolites through the synergism of two previously identified gene clusters, FDB1 and FDB2. Inspired by the induction of these two clusters upon exposure to 2-benzoxazolinone, RNA sequencing experiments were carried out by challenging F. verticillioides individually with 2-benzoxazolinone and three related chemical compounds, 2-oxindole, 2-coumaranone, and chlorzoxazone. These compounds all contain lactam and/or lactone moieties, and transcriptional analysis provided inferences regarding the degradation of such lactams and lactones. Besides induction of FDB1 and FDB2 gene clusters, four additional clusters were identified as induced by 2-benzoxazolinone exposure, including a cluster thought to be responsible for biosynthesis of pyridoxine (vitamin B6), a known antioxidant providing tolerance to reactive oxygen species. Three putative gene clusters were identified as induced by challenging F. verticillioides with 2-oxindole, two with 2-coumaranone, and two with chlorzoxazone. Interestingly, 2-benzoxazolinone and 2-oxindole each induced two specific gene clusters with similar composition of enzymatic functions. Exposure to 2-coumranone elicited the expression of the fusaric acid biosynthetic gene cluster. Another gene cluster that may encode enzymes responsible for degrading intermediate catabolic metabolites with carboxylic ester bonds was induced by 2-benzoxazolinone, 2-oxindole, and chlorzoxazone. Also, the induction of a dehalogenase encoding gene during chlorzoxazone exposure suggested its role in the removal of the chlorine atom. Together, this work identifies genes and putative gene clusters responsive to the 2-benzoxazolinone-like compounds with metabolic inferences. Potential targets for future functional analyses are discussed.

Transcriptional Profiles of a Foliar Fungal Endophyte (Pestalotiopsis, Ascomycota) and Its Bacterial Symbiont (Luteibacter, Gammaproteobacteria) Reveal Sulfur Exchange and Growth Regulation during Early Phases of Symbiotic Interaction

Symbiosis with bacteria is widespread among eukaryotes, including fungi. Bacteria that live within fungal mycelia (endohyphal bacteria) occur in many plant-associated fungi, including diverse Mucoromycota and Dikarya. Pestalotiopsis sp. strain 9143 is a filamentous ascomycete isolated originally as a foliar endophyte of Platycladus orientalis (Cupressaceae). It is infected naturally with the endohyphal bacterium Luteibacter sp. strain 9143, which influences auxin and enzyme production by its fungal host. Previous studies have used transcriptomics to examine similar symbioses between endohyphal bacteria and root-associated fungi such as arbuscular mycorrhizal fungi and plant pathogens. However, currently there are no gene expression studies of endohyphal bacteria of Ascomycota, the most species-rich fungal phylum. To begin to understand such symbioses, we developed methods for assessing gene expression by Pestalotiopsis sp. and Luteibacter sp. when grown in coculture and when each was grown axenically. Our assays showed that the density of Luteibacter sp. in coculture was greater than in axenic culture, but the opposite was true for Pestalotiopsis sp. Dual-transcriptome sequencing (RNA-seq) data demonstrate that growing in coculture modulates developmental and metabolic processes in both the fungus and bacterium, potentially through changes in the balance of organic sulfur via methionine acquisition. Our analyses also suggest an unexpected, potential role of the bacterial type VI secretion system in symbiosis establishment, expanding current understanding of the scope and dynamics of fungal-bacterial symbioses.

IMPORTANCE Interactions between microbes and their hosts have important outcomes for host and environmental health. Foliar fungal endophytes that infect healthy plants can harbor facultative endosymbionts called endohyphal bacteria, which can influence the outcome of plant-fungus interactions. These bacterial-fungal interactions can be influential but are poorly understood, particularly from a transcriptome perspective. Here, we report on a comparative, dual-RNA-seq study examining the gene expression patterns of a foliar fungal endophyte and a facultative endohyphal bacterium when cultured together versus separately. Our findings support a role for the fungus in providing organic sulfur to the bacterium, potentially through methionine acquisition, and the potential involvement of a bacterial type VI secretion system in symbiosis establishment. This work adds to the growing body of literature characterizing endohyphal bacterial-fungal interactions, with a focus on a model facultative bacterial-fungal symbiosis in two species-rich lineages, the Ascomycota and Proteobacteria.

Biotransformation ability of endophytic fungi: from species evolution to industrial applications

Abstract

Increased understanding of the interactions between endophytic fungi and plants has led to the discovery of a new generation of chemical compounds and processes between endophytic fungi and plants. Due to the long-term co-evolution between fungal endophytes and host plants, endophytes have evolved special biotransformation abilities, which can have critical consequences on plant metabolic processes and their composition. Biotransformation or bioconversion can impact the synthesis and decomposition of hormones, sugars, amino acids, vitamins, lipids, proteins, and various secondary metabolites, including flavonoids, polysaccharides, and terpenes. Endophytic fungi produce enzymes and various bioactive secondary metabolites with industrial value and can degrade or sequester inorganic and organic small molecules and macromolecules (e.g., toxins, pollutants, heavy metals). These fungi also have the ability to cause highly selective catalytic conversion of high-value compounds in an environmentally friendly manner, which can be important for the production/innovation of bioactive molecules, food and nutrition, agriculture, and environment. This work mainly summarized recent research progress in this field, providing a reference for further research and application of fungal endophytes.

Key points

•The industrial value of degradation of endophytes was summarized.

• The commercial value for the pharmaceutical industry is reviewed.

Graphical abstract

A β-lactamase gene of Fusarium oxysporum alters the rhizosphere microbiota of soybean

The rhizosphere is a multitrophic environment, and for soilborne pathogens such as Fusarium oxysporum, microbial competition in the rhizosphere is inevitable before reaching and infecting roots. This study established a tritrophic interaction among the plant growth-promoting rhizobacterium Burkholderia ambifaria, F. oxysporum and Glycine max (soybean) to study the effects of F. oxysporum genes on shaping the soybean microbiota. Although B. ambifaria inhibited mycelial growth and increased bacterial propagation in the presence of F. oxysporum, F. oxysporum still managed to infect soybean in the presence of B. ambifaria. RNA-Seq identified a putative F. oxysporum secretory β-lactamase-coding gene, FOXG_18438 (abbreviated as Fo18438), that is upregulated during soybean infection in the presence of B. ambifaria. The ∆Fo18438 mutants displayed reduced mycelial growth towards B. ambifaria, and the complementation of full Fo18438 and the Fo18438 β-lactamase domain restored mycelial growth. Using the F. oxysporum wild type, ∆Fo18438 mutants and complemented strains with full Fo18438, Fo18438 β-lactamase domain or Fo18438 RTA1-like domain for soil inoculation, 16S rRNA amplicon sequencing revealed that the abundance of a Burkholderia operational taxonomic unit (OTU) was increased in the rhizosphere microbiota infested by the strains with Fo18438 β-lactamase domain. Non-metric multidimensional scaling and PICRUSt2 functional analysis revealed differential abundance for the bacterial β-lactam-related functions when contrasting the genotypes of F. oxysporum. These results indicated that the Fo18438 β-lactamase domain provides F. oxysporum with the advantage of growing into the soybean rhizosphere, where β-lactam antibiosis is involved in microbial competition. Accordingly, this study highlights the capability of an F. oxysporum gene for altering the soybean rhizosphere and taproot microbiota.

Disarming the Host: Detoxification of Plant Defense Compounds During Fungal Necrotrophy

While fungal biotrophs are dependent on successfully suppressing/subverting host defenses during their interaction with live cells, necrotrophs, due to their lifestyle are often confronted with a suite of toxic metabolites. These include an assortment of plant defense compounds (PDCs) which can demonstrate broad antifungal activity. These PDCs can be either constitutively present in plant tissue or induced in response to infection, but are nevertheless an important obstacle which needs to be overcome for successful pathogenesis. Fungal necrotrophs have developed a number of strategies to achieve this goal, from the direct detoxification of these compounds through enzymatic catalysis and modification, to the active transport of various PDCs to achieve toxin sequestration and efflux. Studies have shown across multiple pathogens that the efficient detoxification of host PDCs is both critical for successful infection and often a determinant factor in pathogen host range. Here, we provide a broad and comparative overview of the various mechanisms for PDC detoxification which have been identified in both fungal necrotrophs and fungal pathogens which depend on detoxification during a necrotrophic phase of infection. Furthermore, the effect that these mechanisms have on fungal host range, metabolism, and disease control will be discussed.

Pyrrocidine, a molecular off switch for fumonisin biosynthesis

Sarocladium zeae is a fungal endophyte of maize and can be found co-inhabiting a single seed with Fusarium verticillioides, a major mycotoxigenic food safety threat. S. zeae produces pyrrocidines A and B that inhibit the growth of F. verticillioides and may limit its spread within the seed to locations lacking S. zeae. Although coinhabiting single seeds, the fungi are generally segregated in separate tissues. To understand F. verticillioides' protective physiological response to pyrrocidines we sequenced the F. verticillioides transcriptome upon exposure to purified pyrrocidine A or B at sub-inhibitory concentrations. Through this work we identified a F. verticillioides locus FvABC3 (FVEG_11089) encoding a transporter critical for resistance to pyrrocidine. We also identified FvZBD1 (FVEG_00314), a gene directly adjacent to the fumonisin biosynthetic gene cluster that was induced several thousand-fold in response to pyrrocidines. FvZBD1 is postulated to act as a genetic repressor of fumonisin production since deletion of the gene resulted in orders of magnitude increase in fumonisin. Further, pyrrocidine acts, likely through FvZBD1, to shut off fumonisin biosynthesis. This suggests that S. zeae is able to hack the secondary metabolic program of a competitor fungus, perhaps as preemptive self-protection, in this case impacting a mycotoxin of central concern for food safety.

Lysosomes, Autophagy, and Hormesis in Cell Physiology, Pathology, and Age-Related Disease

Autophagy has been strongly linked with hormesis, however, it is only relatively recently that the mechanistic basis underlying this association has begun to emerge. Lysosomal autophagy is a group of processes that degrade proteins, protein aggregates, membranes, organelles, segregated regions of cytoplasm, and even parts of the nucleus in eukaryotic cells. These degradative processes are evolutionarily very ancient and provide a survival capability for cells that are stressed or injured. Autophagy and autophagic dysfunction have been linked with many aspects of cell physiology and pathology in disease processes; and there is now intense interest in identifying various therapeutic strategies involving its regulation. The main regulatory pathway for augmented autophagy is the mechanistic target of rapamycin (mTOR) cell signaling, although other pathways can be involved, such as 5'-adenosine monophosphate-activated protein kinase. Mechanistic target of rapamycin is a key player in the many highly interconnected intracellular signaling pathways and is responsible for the control of cell growth among other processes. Inhibition of mTOR (specifically dephosphorylation of mTOR complex 1) triggers augmented autophagy and the search is on the find inhibitors that can induce hormetic responses that may be suitable for treating many diseases, including many cancers, type 2 diabetes, and age-related neurodegenerative conditions.

Allelopathic Plants: Models for Studying Plant-Interkingdom Interactions

Allelopathy is a biochemical interaction between plants in which a donor plant releases secondary metabolites, allelochemicals, that are detrimental to the growth of its neighbours. Traditionally considered as bilateral interactions between two plants, allelopathy has recently emerged as a cross-kingdom process that can influence and be modulated by the other organisms in the plant's environment. Here, we review the current knowledge on plant-interkingdom interactions, with a particular focus on benzoxazinoids. We highlight how allelochemical-producing plants influence not only their plant neighbours but also insects, fungi, and bacteria that live on or around them. We discuss challenges that need to be overcome to study chemical plant-interkingdom interactions, and we propose experimental approaches to address how biotic and chemical processes impact plant health.

The Trichoderma viride F-00612 consortium tolerates 2-amino-3H-phenoxazin-3-one and degrades nitrated benzo[d]oxazol-2(3H)-one

Numerous allelopathic plant secondary metabolites impact plant–microorganism interactions by injuring plant-associated beneficial bacteria and fungi. Fungi belonging to the genus Trichoderma positively influence crops, including benzoxazinone-containing maize. However, benzoxazinones and their downstream metabolites such as benzoxazolinone and phenoxazinones are often fungitoxic. Specimen Trichoderma viride F-00612 was found to be insensitive to 100-µM phenoxazinone and 500-µM benzoxazolinone. Screening of 46 additional specimens of ascomycetes revealed insensitivity to phenoxazinones among fungi that cause disease in benzoxazinone-producing cereal crops, whereas many other ascomycetes were highly sensitive. In contrast, most of the screened fungi were insensitive to benzoxazolinone. T. viride F-00612 was associated with bacteria and, thus, existed as a consortium. By contrast, Enterobacter species and Acinetobacter calcoaceticus were prominent in the original specimen, and Bacillus species predominated after antibiotic application. Prolonged cultivation of T. viride F-00612 in liquid medium and on Czapek agar in the presence of < 100 µM phenoxazinone and < 500 µM benzoxazolinone resulted in a massive loss of bacteria accompanied by impacted fungal growth in the presence of phenoxazinone. The original consortium was actively involved in implementing metabolic sequences for the degradation and detoxification of nitrated benzoxazolinone derivatives. The 2-aminophenol was rapidly converted into acetamidophenol, but benzoxazolinone, methoxylated benzoxazolinone, and picolinic acid remained unchanged. Excluding phenoxazinone, none of the tested compounds markedly impaired fungal growth in liquid culture. In conclusion, members of the T. viride F-00612 consortium may contribute to the ability to manage benzoxazinone downstream products and facilitate BOA-6-OH degradation via nitration.

The Transcriptional Profile of Trichophyton rubrum Co-Cultured with Human Keratinocytes Shows New Insights about Gene Modulation by Terbinafine

The dermatophyte Trichophyton rubrum is the main causative agent of dermatophytoses worldwide. Although a superficial mycosis, its incidence has been increasing especially among diabetic and immunocompromised patients. Terbinafine is commonly used for the treatment of infections caused by dermatophytes. However, cases of resistance of T. rubrum to this allylamine were reported even with the efficacy of this drug. The present study is the first to evaluate the effect of terbinafine using a co-culture model of T. rubrum and human keratinocytes, mimicking a fungus-host interaction, in conjunction with RNA-seq technique. Our data showed the repression of several genes involved in the ergosterol biosynthesis cascade and the induction of genes encoding major facilitator superfamily (MFS)- and ATP-binding cassette superfamily (ABC)-type membrane transporter which may be involved in T. rubrum mechanisms of resistance to this drug. We observed that some genes reported in the scientific literature as candidates of new antifungal targets were also modulated. In addition, we found the modulation of several genes that are hypothetical in T. rubrum but that possess known orthologs in other dermatophytes. Taken together, the results indicate that terbinafine can act on various targets related to the physiology of T. rubrum other than its main target of ergosterol biosynthetic pathway.

Transcriptomes of the interaction between Fusarium verticillioides and a Streptomyces strain reveal the fungal defense strategy under the pressure of a potential biocontrol agent

The actinobacteria Streptomyces sp. AV05 appears to be a potential biocontrol agent (BCA) against mycotoxigenic fungi. It was found to significantly inhibit F. verticillioides growth and mycotoxin production during their co-cultivation. F. verticillioides growth was durably affected while the decrease of the toxin production levels was reversible, suggesting different BCA actions. The study of both transcriptomes brought useful information on the microbial interaction. RNA-seq data indicated that the dual interaction modified genetic expression of both microorganisms as 18.5 % of the genes were differentially expressed for the fungus against 3.8 % for the actinobacteria. Fungal differentially expressed genes (DEGs) were equally up and down regulated while bacterial ones were mainly upregulated. We especially focused the analysis of DEGs on fungal defense reaction to bacterial attack. For example, if this potential BCA implements a strategy of antibiosis with the over expression of 'siderophore-interacting protein' linked to the production of bacteriocins, the fungus in a state of stress is able to adapt its metabolism by up-regulation of amidase. It could correspond to the induction of resistance gene clusters and suggest a detoxification process. Moreover fumonisins-related pathway appears underexpressed in the presence of Streptomyces that explain the reduction of fumonisin accumulation observed.

Deletion of the benzoxazinoid detoxification gene NAT1 in Fusarium graminearum reduces deoxynivalenol in spring wheat

Benzoxazinoid (Bx) metabolites produced by wheat and other members of the Poaceae have activity against Fusarium sp. that cause cereal diseases including Fusarium head blight (FHB) on wheat and barley. Certain Bx metabolites can be detoxified by Fusarium sp. with the arylamine N-acetyltransferase NAT1. Investigation of this pathway may reveal strategies for increasing FHB resistance, such as selection for higher levels of Bx metabolites within existing germplasm and/or engineering fungal susceptibility via host induced silencing of NAT1. We assessed the reactions of fifteen wheat cultivars or breeding lines adapted to the Northwestern United States to infection with F. graminearum Δnat1 mutants that should be sensitive to Bx metabolites. Significant differences were noted in disease severity and deoxynivalenol (DON) among the cultivars 21 d after inoculation with either mutant or wildtype (PH1) strains. Mutant vs. wildtype strains did not result in significant variation for infection severity (as measured by % infected florets), but inoculation with Δnat1 mutants vs. wildtype resulted in significantly lower DON concentrations in mature kernels (p < 0.0001). Of the cultivars tested, HRS3419 was the most resistant cultivar to PH1 (severity = 62%, DON = 45 ppm) and Δnat1 mutants (severity = 61%, DON = 30 ppm). The cultivar most susceptible to infection was Kelse with PH1 (severity = 100%, DON = 292 ppm) and Δnat1 mutants (severity = 100%, DON = 158 ppm). We hypothesized that sub-lethal Bx metabolite levels may suppress DON production in F. graminearum Δnat1 mutants. In vitro assays of Bx metabolites BOA, MBOA, and DIMBOA at 30 μM did not affect growth, but did reduce DON production by Δnat1 and PH1. Although the levels of Bx metabolites are likely too low in the wheat cultivars we tested to suppress FHB, higher levels of Bx metabolites may contribute towards reductions in DON and FHB.

Multiple independent origins for a subtelomeric locus associated with growth rate in Fusarium circinatum

Fusarium is a diverse assemblage that includes a large number of species of considerable medical and agricultural importance. Not surprisingly, whole genome sequences for many Fusarium species have been published or are in the process of being determined, the availability of which is invaluable for deciphering the genetic basis of key phenotypic traits. Here we investigated the distribution, genic composition, and evolutionary history of a locus potentially determining growth rate in the pitch canker pathogen F. circinatum. We found that the genomic region underlying this locus is highly conserved amongst F. circinatum and its close relatives, except for the presence of a 12 000 base pair insertion in all of the examined isolates of F. circinatum. This insertion encodes for five genes and our phylogenetic analyses revealed that each was most likely acquired through horizontal gene transfer from polyphyletic origins. Our data further showed that this region is located in a region low in G+C content and enriched for repetitive sequences and transposable elements, which is situated near the telomere of Chromosome 3 of F. circinatum. As have been shown for other fungi, these findings thus suggest that the emergence of the unique 12 000 bp region in F. circinatum is linked to the dynamic evolutionary processes associated with subtelomeres that, in turn, have been implicated in the ecological adaptation of fungal pathogens.

Fusarium verticillioides: Advancements in Understanding the Toxicity, Virulence, and Niche Adaptations of a Model Mycotoxigenic Pathogen of Maize

The importance of understanding the biology of the mycotoxigenic fungus Fusarium verticillioides and its various microbial and plant host interactions is critical given its threat to maize, one of the world's most valuable food crops. Disease outbreaks and mycotoxin contamination of grain threaten economic returns and have grave implications for human and animal health and food security. Furthermore, F. verticillioides is a member of a genus of significant phytopathogens and, thus, data regarding its host association, biosynthesis of secondary metabolites, and other metabolic (degradative) capabilities are consequential to both basic and applied research efforts across multiple pathosystems. Notorious among its secondary metabolites are the fumonisin mycotoxins, which cause severe animal diseases and are implicated in human disease. Additionally, studies of these mycotoxins have led to new understandings of F. verticillioides plant pathogenicity and provide tools for research into cellular processes and host-pathogen interaction strategies. This review presents current knowledge regarding several significant lines of F. verticillioides research, including facets of toxin production, virulence, and novel fitness strategies exhibited by this fungus across rhizosphere and plant environments.

Specialized plant biochemistry drives gene clustering in fungi

The fitness and evolution of prokaryotes and eukaryotes are affected by the organization of their genomes. In particular, the physical clustering of genes can coordinate gene expression and can prevent the breakup of co-adapted alleles. Although clustering may thus result from selection for phenotype optimization and persistence, the impact of environmental selection pressures on eukaryotic genome organization has rarely been systematically explored. Here, we investigated the organization of fungal genes involved in the degradation of phenylpropanoids, a class of plant-produced secondary metabolites that mediate many ecological interactions between plants and fungi. Using a novel gene cluster detection method, we identified 1110 gene clusters and many conserved combinations of clusters in a diverse set of fungi. We demonstrate that congruence in genome organization over small spatial scales is often associated with similarities in ecological lifestyle. Additionally, we find that while clusters are often structured as independent modules with little overlap in content, certain gene families merge multiple modules into a common network, suggesting they are important components of phenylpropanoid degradation strategies. Together, our results suggest that phenylpropanoids have repeatedly selected for gene clustering in fungi, and highlight the interplay between genome organization and ecological evolution in this ancient eukaryotic lineage.

Fungal Gene Cluster Diversity and Evolution

Metabolic gene clusters (MGCs) have provided some of the earliest glimpses at the biochemical machinery of yeast and filamentous fungi. MGCs encode diverse genetic mechanisms for nutrient acquisition and the synthesis/degradation of essential and adaptive metabolites. Beyond encoding the enzymes performing these discrete anabolic or catabolic processes, MGCs may encode a range of mechanisms that enable their persistence as genetic consortia; these include enzymatic mechanisms to protect their host fungi from their inherent toxicities, and integrated regulatory machinery. This modular, self-contained nature of MGCs contributes to the metabolic and ecological adaptability of fungi. The phylogenetic and ecological patterns of MGC distribution reflect the broad diversity of fungal life cycles and nutritional modes. While the origins of most gene clusters are enigmatic, MGCs are thought to be born into a genome through gene duplication, relocation, or horizontal transfer, and analyzing the death and decay of gene clusters provides clues about the mechanisms selecting for their assembly. Gene clustering may provide inherent fitness advantages through metabolic efficiency and specialization, but experimental evidence for this is currently limited. The identification and characterization of gene clusters will continue to be powerful tools for elucidating fungal metabolism as well as understanding the physiology and ecology of fungi.

Fungal Lactamases: Their Occurrence and Function

Fungi are absorptive feeders and thus must colonize and ramify through their substrate to survive. In so doing they are in competition, particularly in the soil, with myriad microbes. These microbes use xenobiotic compounds as offensive weapons to compete for nutrition, and fungi must be sufficiently resistant to these xenobiotics. One prominent mechanism of xenobiotic resistance is through production of corresponding degrading enzymes. As typical examples, bacterial β-lactamases are well known for their ability to degrade and consequently confer resistance to β-lactam antibiotics, a serious emerging problem in health care. We have identified many fungal genes that putatively encode proteins exhibiting a high degree of similarity to β-lactamases. However, fungal cell walls are structurally different from the bacterial peptidoglycan target of β-lactams. This raises the question, why do fungi have lactamases and what are their functions? Previously, we identified and characterized one Fusarium verticillioides lactamase encoding gene (FVEG_08291) that confers resistance to the benzoxazinoid phytoanticipins produced by maize, wheat, and rye. Since benzoxazinoids are γ-lactams with five-membered rings rather than the four-membered β-lactams, we refer to the predicted enzymes simply as lactamases, rather than β-lactamases. An overview of fungal genomes suggests a strong positive correlation between environmental niche complexity and the number of fungal lactamase encoding genes, with soil-borne fungi showing dramatic amplification of lactamase encoding genes compared to those fungi found in less biologically complex environments. Remarkably, Fusarium species frequently possess large (>40) numbers of these genes. We hypothesize that many fungal hydrolytic lactamases are responsible for the degradation of plant or microbial xenobiotic lactam compounds. Alignment of protein sequences revealed two conserved patterns resembling bacterial β-lactamases, specifically those possessing PFAM domains PF00753 or PF00144. Structural predictions of F. verticillioides lactamases also suggested similar catalytic mechanisms to those of their bacterial counterparts. Overall, we present the first in-depth analysis of lactamases in fungi, and discuss their potential relevance to fitness and resistance to antimicrobials in the environment.