AoStuA, an APSES transcription factor, regulates the conidiation, trap formation, stress resistance and pathogenicity of the nematode-trapping fungus Arthrobotrys oligospora

Identification of a transcription factor AoMsn2 of the Hog1 signaling pathway contributes to fungal growth, development and pathogenicity in Arthrobotrys oligospora

INTRODUCTION

Arthrobotrys oligospora has been utilized as a model strain to study the interaction between fungi and nematodes owing to its ability to capture nematodes by developing specialized traps. A previous study showed that high-osmolarity glycerol (Hog1) signaling regulates the osmoregulation and nematocidal activity of A. oligospora. However, the function of downstream transcription factors of the Hog1 signaling in the nematode-trapping (NT) fungi remains unclear.

OBJECTIVE

This study aimed to investigate the functions and potential regulatory network of AoMsn2, a downstream transcription factor of the Hog1 signaling pathway in A. oligospora.

METHODS

The function of AoMsn2 was characterized using targeted gene deletion, phenotypic experiments, real-time quantitative PCR, RNA sequencing, untargeted metabolomics, and yeast two-hybrid analysis.

RESULTS

Loss of Aomsn2 significantly enlarged and swollen the hyphae, with an increase in septa and a significant decrease in nuclei. In particular, spore yield, spore germination rate, traps, and nematode predation efficiency were remarkably decreased in the mutants. Phenotypic and transcriptomic analyses revealed that AoMsn2 is essential for fatty acid metabolism and autophagic pathways. Additionally, untargeted metabolomic analysis identified an important function of AoMsn2 in the modulation of secondary metabolites. Furtherly, we analyzed the protein interaction network of AoMsn2 based on the Kyoto Encyclopedia of Genes and Genomes pathway map and the online website STRING. Finally, Hog1 and six putative targeted proteins of AoMsn2 were identified by Y2H analysis.

CONCLUSION

Our study reveals that AoMsn2 plays crucial roles in the growth, conidiation, trap development, fatty acid metabolism, and secondary metabolism, as well as establishes a broad basis for understanding the regulatory mechanisms of trap morphogenesis and environmental adaptation in NT fungi.

The APSES transcription factor CfSwi6 is required for growth, cell wall integrity, and pathogenicity of Ceratocystis fimbriata

Cell wall integrity (CWI) is crucial for the growth, development, and host invasion of pathogenic fungi. The APSES transcription factor Swi6 in fungi plays a role in mediating cell wall integrity through the mitogen-activated protein kinase (MAPK) signaling pathway. Ceratocystis fimbriata is a notorious pathogenic fungus responsible for causing black rot in sweet potatoes. In this study, an orthologous APSES transcription factor Swi6 (CfSwi6) downstream of the CWI regulatory pathway in C. fimbriata was characterized. Deletion of CfSWI6 leads to impaired hyphal development, conidiation, and compromised cell wall integrity, resulting in a significant reduction in virulence. Transcriptome analysis revealed the involvement of CfSWI6 in various pathways, including the MAPK pathway, DNA synthesis and stress response. ChIP-seq data provided predictions of potential target genes regulated by CfSwi6. Through yeast one-hybrid, we confirmed the direct binding of CfSwi6 to the promoter of the chitin synthetase gene. In summary, these findings indicated that CfSwi6 plays an important role in the growth, development, and pathogenicity of C. fimbriata. This study provides new insights into the pathogenic mechanism of C. fimbriata in sweet potato and inspires potential strategies to control sweet potato black rot.

AoRab7A interacts with AoVps35 and AoVps41 to regulate vacuole assembly, trap formation, conidiation, and functions of proteasomes and ribosomes in Arthrobotrys oligospora

Rab GTPases regulate vesicle trafficking in organisms and play crucial roles in growth and development. Arthrobotrys oligospora is a ubiquitous nematode-trapping (NT) fungus, it can form elaborate traps to capture nematodes. Our previous study found that deletion of Aorab7A abolished the trap formation and sporulation. Here, we investigated the regulatory mechanism of AoRab7A using transcriptomic, biochemical, and phenotypic comparisons. Transcriptome analysis, yeast library screening, and yeast two-hybrid assay identified two vacuolar protein sorting (Vps) proteins, AoVps41 and AoVps35, as putative targets of AoRab7A. The deletion of Aovps41 and Aovps35 caused considerable defects in multiple phenotypic traits, such as conidiation and trap formation. We further found a close connection between AoRab7A and Vps proteins in vesicle-vacuole fusion, which triggered vacuolar fragmentation. Further transcriptome analysis showed that AoRab7A and AoVps35 play essential roles in many cellular processes and components including proteasomes, autophagy, fatty acid degradation, and ribosomes in A. oligospora. Furthermore, we verified that AoRab7A, AoVps41, and AoVps35 are involved in ribosome and proteasome functions. The absence of these proteins inhibited the biosynthesis of nascent proteins and enhanced ubiquitination. Our findings suggest that AoRab7A interacts with AoVps41 and AoVps35 to mediate vacuolar fusion and influence lipid droplet accumulation, autophagy, and stress response. These proteins are especially required for the conidiation and trap development of A. oligospora.

Functional Study of cAMP-Dependent Protein Kinase A in Penicillium oxalicum

Signaling pathways play a crucial role in regulating cellulase production. The pathway mediated by signaling proteins plays a crucial role in understanding how cellulase expression is regulated. In this study, using affinity purification of ClrB, we have identified sixteen proteins that potentially interact with ClrB. One of the proteins, the catalytic subunit of cAMP-dependent protein kinase A (PoPKA-C), is an important component of the cAMP/PKA signaling pathway. Knocking out PoPKA-C resulted in significant decreases in the growth, glucose utilization, and cellulose hydrolysis ability of the mutant strain. Furthermore, the cellulase activity and gene transcription levels were significantly reduced in the ΔPoPKA-C mutant, while the expression activity of CreA, a transcriptional regulator of carbon metabolism repression, was notably increased. Additionally, deletion of PoPKA-C also led to earlier timing of conidia production. The expression levels of key transcription factor genes stuA and brlA, which are involved in the production of the conidia, showed significant enhancement in the ΔPoPKA-C mutant. These findings highlight the involvement of PoPKA-C in mycelial development, conidiation, and the regulation of cellulase expression. The functional analysis of PoPKA-C provides insights into the mechanism of the cAMP/PKA signaling pathway in cellulase expression in filamentous fungi and has significant implications for the development of high-yielding cellulase strains.

The Alternaria alternata StuA transcription factor interacting with the pH-responsive regulator PacC for the biosynthesis of host-selective toxin and virulence in citrus

IMPORTANCE

In this study, we used Alternaria alternata as a biological model to report the role of StuA in phytopathogenic fungi. Our findings indicated that StuA is required for Alternaria citri toxin (ACT) biosynthesis and fungal virulence. In addition, StuA physically interacts with PacC. Disruption of stuA or pacC led to decreased expression of seven toxin biosynthetic genes (ACCT) and toxin production. PacC could recognize and bind to the promoter regions of ACTT6 and ACTTR. Our results revealed a previously unrecognized (StuA-PacC)→ACTTR module for the biosynthesis of ACT in A. alternata, which also provides a framework for the study of StuA in other fungi.

Key processes required for the different stages of fungal carnivory by a nematode-trapping fungus

Nutritional deprivation triggers a switch from a saprotrophic to predatory lifestyle in soil-dwelling nematode-trapping fungi (NTF). In particular, the NTF Arthrobotrys oligospora secretes food and sex cues to lure nematodes to its mycelium and is triggered to develop specialized trapping devices. Captured nematodes are then invaded and digested by the fungus, thus serving as a food source. In this study, we examined the transcriptomic response of A. oligospora across the stages of sensing, trap development, and digestion upon exposure to the model nematode Caenorhabditis elegans. A. oligospora enacts a dynamic transcriptomic response, especially of protein secretion-related genes, in the presence of prey. Two-thirds of the predicted secretome of A. oligospora was up-regulated in the presence of C. elegans at all time points examined, and among these secreted proteins, 38.5% are predicted to be effector proteins. Furthermore, functional studies disrupting the t-SNARE protein Sso2 resulted in impaired ability to capture nematodes. Additionally, genes of the DUF3129 family, which are expanded in the genomes of several NTF, were highly up-regulated upon nematode exposure. We observed the accumulation of highly expressed DUF3129 proteins in trap cells, leading us to name members of this gene family as Trap Enriched Proteins (TEPs). Gene deletion of the most highly expressed TEP gene, TEP1, impairs the function of traps and prevents the fungus from capturing prey efficiently. In late stages of predation, we observed up-regulation of a variety of proteases, including metalloproteases. Following penetration of nematodes, these metalloproteases facilitate hyphal growth required for colonization of prey. These findings provide insights into the biology of the predatory lifestyle switch in a carnivorous fungus and provide frameworks for other fungal-nematode predator-prey systems.

PdStuA Is a Key Transcription Factor Controlling Sporulation, Hydrophobicity, and Stress Tolerance in Penicillium digitatum

Penicillium digitatum has become one of the main pathogens in citrus due to its high spore production and easy spread. In this study, the function of the APSES transcription factor StuA in P. digitatum was characterized, and the results indicated that it was involved in conidium and conidiophore development. No conidiophores were observed in the mycelium of the ∆PdStuA mutant that had grown for two days, while an abnormal conidiophore was found after another two days of incubation, and only small thin phialides as well as a very small number of spores were formed at the top of the hyphae. Moreover, it was observed that the ∆PdStuA mutant showed various defects, such as reduced hydrophobicity and decreased tolerance to cell wall inhibitors and H2O2. Compared to the original P. digitatum, the colony diameter of the ∆PdStuA mutant was not significantly affected, but the growth of aerial hyphae was obviously induced. In in vivo experiments, the spore production of the ∆PdStuA mutant grown on citrus fruit was remarkably decreased; however, there was no significant difference in the lesion diameter between the mutant and original strain. It could be inferred that less spore production might result in reduced spread in citrus, thereby reducing the green mold infection in citrus fruit during storage. This study provided a gene, PdStuA, which played key role in the sporulation of P. digitatum, and the results might provide a reference for the molecular mechanisms of sporulation in P. digitatum.

Fus3 regulates asexual development and trap morphogenesis in the nematode-trapping fungus Arthrobotrys oligospora

Mitogen-activated protein kinase (MAPK) Fus3 is an essential regulator of cell differentiation and virulence in fungal pathogens of plants and animals. However, the function and regulatory mechanism of MAPK signaling in nematode-trapping (NT) fungi remain largely unknown. NT fungi can specialize in the formation of "traps", an important indicator of transition from a saprophytic to a predatory lifestyle. Here, we characterized an orthologous Fus3 in a typical NT fungus Arthrobotrys oligospora using multi-phenotypic analysis and multi-omics approaches. Our results showed that Fus3 plays an important role in asexual growth and development, conidiation, stress response, DNA damage, autophagy, and secondary metabolism. Importantly, Fus3 plays an indispensable role in hyphal fusion, trap morphogenesis, and nematode predation. Moreover, we constructed the regulatory networks of Fus3 by means of transcriptomic and yeast two-hybrid techniques. This study provides insights into the mechanism of MAPK signaling in asexual development and pathogenicity of NT fungi.

AoMae1 Regulates Hyphal Fusion, Lipid Droplet Accumulation, Conidiation, and Trap Formation in Arthrobotrys oligospora

Malate dehydrogenase (MDH) is a key enzyme in the tricarboxylic acid (TCA) cycle and is essential for energy balance, growth, and tolerance to cold and salt stresses in plants. However, the role of MDH in filamentous fungi is still largely unknown. In this study, we characterized an ortholog of MDH (AoMae1) in a representative nematode-trapping (NT) fungus Arthrobotrys oligospora via gene disruption, phenotypic analysis, and nontargeted metabolomics. We found that the loss of Aomae1 led to a weakening of MDH activity and ATP content, a remarkable decrease in conidia yield, and a considerable increase in the number of traps and mycelial loops. In addition, the absence of Aomae1 also caused an obvious reduction in the number of septa and nuclei. In particular, AoMae1 regulates hyphal fusion under low nutrient conditions but not in nutrient-rich conditions, and the volumes and sizes of the lipid droplets dynamically changed during trap formation and nematode predation. AoMae1 is also involved in the regulation of secondary metabolites such as arthrobotrisins. These results suggest that Aomae1 has an important role in hyphal fusion, sporulation, energy production, trap formation, and pathogenicity in A. oligospora. Our results enhance the understanding of the crucial role that enzymes involved in the TCA cycle play in the growth, development, and pathogenicity of NT fungi.

The MADS-box transcription factor AoRlmA is involved in the regulation of mycelium development, conidiation, cell-wall integrity, stress response, and trap formation of Arthrobotrys oligospora

The maintenance of cell-wall integrity (CWI) is important for mycelial growth, development, and pathogenicity in fungi. Arthrobotrys oligospora is a typical nematode-trapping (NT) fungus which can capture nematodes by producing adhesive networks. In this study, we characterized an orthologous MADS-box transcription factor RlmA (AoRlmA) downstream of the CWI regulatory pathway in A. oligospora. The deletion of AorlmA caused a reduction in mycelial growth, the number of nuclei, conidiation, and trap formation, as well as increased sensitivity to cell-wall synthesis-disrupting agents, osmotic agents, and oxidants; accordingly, the transcript levels of genes associated with sporulation, cell-wall biosynthesis, and DNA damage response were downregulated in the ΔAorlmA mutant. Furthermore, the absence of AorlmA resulted in a reduction in autophagy and endocytosis. Transcriptome analysis showed that differentially expressed genes in the absence of AorlmA were involved in membrane components, the oxidation-reduction process, transmembrane transport, metabolic processes, cellular components, organelles, cellular response to stress, and DNA damage response. In addition, metabolomic analysis showed that AoRlmA was involved in the regulation of secondary metabolites of A. oligospora. To summarize, our results highlighted the important roles of transcription factor RlmA in mycelial growth, conidiation, CWI, trap formation, stress response, autophagy, endocytosis, and secondary metabolism regulation in A. oligospora, providing a basis for elucidating the regulatory mechanism of the mycelial growth and development, pathogenicity, and stress response of NT fungi.

Recent Advances in Life History Transition with Nematode-Trapping Fungus Arthrobotrys oligospora and Its Application in Sustainable Agriculture

Parasitic nematodes cause great annual loss in the agricultural industry globally. Arthrobotrys oligospora is the most prevalent and common nematode-trapping fungus (NTF) in the environment and the candidate for the control of plant- and animal-parasitic nematodes. A. oligospora is also the first recognized and intensively studied NTF species. This review highlights the recent research advances of A. oligospora as a model to study the biological signals of the switch from saprophytism to predation and their sophisticated mechanisms for interacting with their invertebrate hosts, which is of vital importance for improving the engineering of this species as an effective biocontrol fungus. The application of A. oligospora in industry and agriculture, especially as biological control agents for sustainable purposes, was summarized, and we discussed the increasing role of A. oligospora in studying its sexual morph and genetic transformation in complementing biological control research.

AoSte12 Is Required for Mycelial Development, Conidiation, Trap Morphogenesis, and Secondary Metabolism by Regulating Hyphal Fusion in Nematode-Trapping Fungus Arthrobotrys oligospora

Nematode-trapping (NT) fungi are a unique group of carnivorous microorganisms that can capture and digest nematodes by producing ingenious trapping devices (traps). Arthrobotrys oligospora, a representative NT fungus, can develop adhesive three-dimensional networks for nematode predation. Hyphal fusion is indispensable for the trap formation of A. oligospora. Here, we characterized an orthologous Ste12 protein (AoSte12) in A. oligospora via gene disruption, DNA affinity purification sequencing (DAP-Seq), and multi-omics approaches. The disruption of the Aoste12 gene caused an increase in hyphal fusion and resulted in defects in mycelial growth, conidiation, trap morphology, and stress resistance, as well as reducing the number of nuclei and lipid droplet accumulation. Moreover, transcriptome and DAP-Seq analysis revealed that AoSte12 was involved in cellular processes associated with growth, cell fusion, the tricarboxylic acid cycle, vesicles, actin filaments, and lipid metabolism. In addition, combining metabolome with transcriptome and DAP-Seq analysis indicated that AoSte12 was involved in the mitogen-activated protein kinase signaling pathway, lipid metabolism, and secondary metabolites. A yeast two-hybrid assay revealed that AoSte12 can interact with diverse proteins, such as the MAK-2 orthologue protein Fus3, the vacuolar sorting protein Pep3, and UDP-glycosyltransferase. Our results suggest that AoSte12 plays an indispensable role in hyphal fusion and thus regulates sporulation and trap morphogenesis. These results provide deep insights into the connection between hyphal fusion and trap formation in NT fungi. IMPORTANCE Nematode-trapping (NT) fungi are an important natural enemy of nematodes and can capture their prey by producing traps. Hyphal anastomosis and fusion are important for mycelial growth and the colony morphological development of filamentous fungi and are also crucial for the trap morphogenesis of NT fungi. Arthrobotrys oligospora can form complex three-dimensional networks (traps) when sensing the presence of nematodes. This study revealed that AoSte12 is indispensable for hyphal fusion and that it regulates mycelial growth, conidiation, trap morphogenesis, stress resistance, the number of nuclei, and lipid droplet accumulation in A. oligospora. In addition, DNA affinity purification sequencing, transcriptome, and metabolome analyses further revealed that AoSte12 is involved in the mitogen-activated protein kinase pathway, lipid metabolism, and secondary metabolism. Overall, these findings expand the important role of AoSte12 in NT fungus A. oligospora and provide a broad foundation for elucidating the regulatory mechanism of trap development and the lifestyle transitions of pathogenic fungi.

Tools and basic procedures of gene manipulation in nematode-trapping fungi

Nematode-trapping fungi (NTF) are the majority of carnivorous microbes to capture nematodes through diverse and sophisticated trapping organs derived from hyphae. They can adopt carnivorous lifestyles in addition to saprophytism to obtain extra-nutrition from nematodes. As a special group of fungi, the NTF are not only excellent model organism for studying lifestyle transition of fungi but also natural resources of exploring biological control of nematodes. However, the carnivorous mechanism of NTF remains poorly understood. Nowadays, the omics studies of NTF have provided numerous genes and pathways that are associated with the phenotypes of carnivorous traits, which need molecular tools to verify. Here, we review the development and progress of gene manipulation tools in NTF, including methodology and strategy of transformation, random gene mutagenesis methods and target gene mutagenesis methods. The principle and practical approach for each method was summarized and discussed, and the basic operational flow for each tool was described. This paper offers a clear reference and instruction for researchers who work on NTF as well as other group of fungi.

SNARE Protein AoSec22 Orchestrates Mycelial Growth, Vacuole Assembly, Trap Formation, Stress Response, and Secondary Metabolism in Arthrobotrys oligospora

Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) facilitate intracellular vesicle trafficking and membrane fusion in eukaryotes and play a vital role in fungal growth, development, and pathogenicity. However, the functions of SNAREs are still largely unknown in nematode-trapping fungi. Arthrobotrys oligospora is a representative species of nematode-trapping fungi that can produce adhesive networks (traps) for nematode predation. In this study, we characterized AoSec22 in A. oligospora, a homolog of the yeast SNARE protein Sec22. Deletion of Aosec22 resulted in remarkable reductions in mycelial growth, the number of nuclei, conidia yield, and trap formation, especially for traps that failed to develop mature three-dimensional networks. Further, absence of Aosec22 impaired fatty acid utilization, autophagy, and stress tolerance; in addition, the vacuoles became small and fragmented in the hyphal cells of the ∆Aosec22 mutant, and large vacuoles failed to form. The reduced sporulation capacity correlated with the transcriptional repression of several sporulation-related genes, and the impaired accumulation of lipid droplets is in line with the transcriptional repression of several genes involved in fatty acid oxidation. Moreover, absence of Aosec22 remarkably impaired secondary metabolism, resulting in 4717 and 1230 compounds upregulated and downregulated in the ∆Aosec22 mutant, respectively. Collectively, our data highlighted that the SNARE protein AoSec22 plays a pleiotropic role in mycelial growth and development, vacuole assembly, lipid metabolism, stress response, and secondary metabolism; in particular, it is required for the proper development of traps in A. oligospora.

The cAMP-PKA signalling pathway regulates hyphal growth, conidiation, trap morphogenesis, stress tolerance, and autophagy in Arthrobotrys oligospora

The cyclic adenosine monophosphate-protein kinase A (cAMP-PKA) signalling pathway is evolutionarily conserved in eukaryotes and plays a crucial role in defending against external environmental challenges, which can modulate the cellular response to external stimuli. Arthrobotrys oligospora is a typical nematode-trapping fungus that specializes in adhesive networks to kill nematodes. To elucidate the biological roles of the cAMP-PKA signalling pathway, we characterized the orthologous adenylate cyclase AoAcy, a regulatory subunit (AoPkaR), and two catalytic subunits (AoPkaC1 and AoPkaC2) of PKA in A. oligospora by gene disruption, transcriptome, and metabolome analyses. Deletion of Aoacy significantly reduced the levels of cAMP and arthrobotrisins. Results revealed that Aoacy, AopkaR, and AopkaC1 were involved in hyphal growth, trap morphogenesis, sporulation, stress resistance, and autophagy. In addition, Aoacy and AopkaC1 were involved in the regulation of mitochondrial morphology, thereby affecting energy metabolism, whereas AopkaC2 affected sporulation, nuclei, and autophagy. Multi-omics results showed that the cAMP-PKA signalling pathway regulated multiple metabolic and cellular processes. Collectively, these data highlight the indispensable role of cAMP-PKA signalling pathway in the growth, development, and pathogenicity of A. oligospora, and provide insights into the regulatory mechanisms of signalling pathways in sporulation, trap formation, and lifestyle transition.

The cAMP-PKA pathway regulates prey sensing and trap morphogenesis in the nematode-trapping fungus Arthrobotrys oligospora

Sensing environmental factors and responding swiftly to them is essential for all living organisms. For instance, predators must act rapidly once prey is sensed. Nematode-trapping fungi (NTF) are predators that use “traps” differentiated from vegetative hyphae to capture, kill, and consume nematodes. These traps undergo drastic and rapid morphological changes upon nematode induction. Multiple signaling hubs have been shown to regulate this remarkable process. Here, we demonstrate that the conserved cAMP-PKA signaling pathway exerts a crucial role in trap morphogenesis of the nematode-trapping fungi Arthrobotrys oligospora. A gene deletion mutant of the PKA catalytic subunit TPK2 proved insensitive toward nematode presence. Moreover, we show that the G protein alpha subunit GPA2 acts upstream of adenylate cyclase, with GPA2 deletion resulting in substantially reduced trap formation, whereas exogenous provision of cAMP rescued the prey-sensing and trap morphogenesis defects of a gpa2 mutant. Thus, we show that cAMP production triggered by G protein signaling and downstream PKA activity are vital for prey-sensing and trap development in A. oligospora, demonstrating that this highly conserved signaling pathway is critical for nematode-trapping fungi and nematode predator–prey interactions.

The role of WSC domain-containing protein encoding gene AOL_s00043g401 in the growth and nematode trapping of Arthrobotrys oligospora

Arthrobotrys oligospora is a model nematode-trapping fungus that has been extensively investigated to understand the interactions between fungi and nematodes. Nematode capture by A. oligospora is a complex process in which recognition of nematodes is generally believed to be mediated by lectins from the fungi. Lectins are a group of carbohydrate-binding proteins that widely exist in microorganisms and contain specific glycosylation recognition domains. In this work, we report the effect of a putative WSC domain-containing protein encoding gene AOL_s00043g401 (g401) on the growth and nematode-trapping of A. oligospora. The g401 gene was knocked out using the homologous recombination approach, and the △g401 mutant strain was then evaluated for its growth rate, conidial yield and germination rate, adaptation to environmental stresses, and nematocidal activity. Interestingly, the deletion of the putative lectin gene g401 had no significant effect on saprophytic growth, conidial yield and germination rate, responses to high salt, surfactant, and strong oxidative environments, as well as nematode-trapping efficiency of A. oligospora. We speculate that this phenomenon might have been caused by an intrinsic genetic compensation of the g401 in this fungus. For instance, more copies of WSC domain encoding genes or PQQ-DH domain encoding genes were found in the genome of A. oligospora. These findings provide further experimental evidence on the effect of lectin-related functional proteins in A. oligospora on nematode capture and will help further analyze their potential roles in the biological control of nematodes in the future.

PKC-SWI6 signaling regulates asexual development, cell wall integrity, stress response, and lifestyle transition in the nematode-trapping fungus Arthrobotrys oligospora

Predatory fungi possess intricate signal transduction systems that regulate their development and support successful infection of the host. Herein, we characterized three components of the cell wall integrity-controlling pathway, namely protein kinase C (AoPKC), SLT2-MAPK (AoSLT2), and SWI6 (AoSWI6), in a representative nematode-trapping fungus Arthrobotrys oligospora, using gene disruption and multi-omics approaches. The phenotypic traits (such as mycelia development, conidiation, stress response, and trap morphogenesis) and metabolic profiles of ΔAopkc and ΔAoswi6 mutants were similar but differed from those of the ΔAoslt2 mutants. Transcriptomic analysis indicated that the genes differentially expressed in the absence of Aoswi6 were involved in DNA replication, repair, and recombination during trap formation. Moreover, the yeast two-hybrid assay showed that AoPKC interacted with AoSWI6, suggesting that in A. oligospora, PKC can directly regulate SWI6, bypassing the SLT2 signaling cascade. Conclusively, our findings deepen our understanding of the regulatory mechanism of asexual development and lifestyle switching in nematode-trapping fungi.

Identification of Three Novel Conidiogenesis-Related Genes in the Nematode-Trapping Fungus Arthrobotrys oligospora

For filamentous fungi, conidiogenesis is the most common reproductive strategy for environmental dispersal, invasion, and proliferation. Understanding the molecular mechanisms controlling conidiation and increasing conidium yield may provide promising applications in commercial development in the future for nematode-trapping fungi. However, the molecular mechanism for regulating conidium production of filamentous fungi is not fully understood. In this study, we characterized three novel conidiogenesis-related genes via gene knockout in A. oligospora. The absence of the genes AoCorA and AoRgsD caused significant increases in conidia production, while the absence of AoXlnR resulted in a decrease in conidiogenesis. Moreover, we characterized the ortholog of AbaA, a well-known conidiogenesis-related gene in Aspergillus nidulans. The deletion of AoAbaA not only completely abolished conidium production but also affected the production of nematode-trapping traps.

The Arf-GAP Proteins AoGcs1 and AoGts1 Regulate Mycelial Development, Endocytosis, and Pathogenicity in Arthrobotrys oligospora

Small GTPases from the ADP-ribosylation factor (Arf) family and their activating proteins (Arf-GAPs) regulate mycelial development, endocytosis, and virulence in fungi. Here, we identified two orthologous Arf-GAP proteins, AoGcs1 and AoGts1, in a typical nematode-trapping fungus Arthrobotrys oligospora. The transcription of Aogcs1 and Aogts1 was highly expressed in the sporulation stage. The deletion of Aogcs1 and Aogts1 caused defects in DNA damage, endocytosis, scavenging of reactive oxygen species, lipid droplet storage, mitochondrial activity, autophagy, serine protease activity, and the response to endoplasmic reticulum stress. The combined effects resulted in slow growth, decreased sporulation capacity, increased susceptibility to chemical stressors and heat shock, and decreased pathogenicity of the mutants compared with the wild-type (WT) strain. Although deletion of Aogcs1 and Aogts1 produced similar phenotfypic traits, their roles varied in conidiation and proteolytic activity. The ΔAogts1 mutant showed a remarkable reduction in conidial yield compared with the WT strain but not in proteolytic activity; in contrast, the ΔAogcs1 mutant showed an increase in proteolytic activity but not in sporulation. In addition, the growth of ΔAogcs1 and ΔAogts1 mutants was promoted by rapamycin, and the ΔAogts1 mutant was sensitive to H-89. Collectively, the ΔAogts1 mutant showed a more remarkable difference compared with the WT strain than the ΔAogcs1 mutant. Our study further illustrates the importance of Arf-GAPs in the growth, development, and pathogenicity of nematode-trapping fungi.

Regulatory Mechanism of Trap Formation in the Nematode-Trapping Fungi

Nematode-trapping (NT) fungi play a significant role in the biological control of plant- parasitic nematodes. NT fungi, as a predator, can differentiate into specialized structures called “traps” to capture, kill, and consume nematodes at a nutrient-deprived condition. Therefore, trap formation is also an important indicator that NT fungi transition from a saprophytic to a predacious lifestyle. With the development of gene knockout and multiple omics such as genomics, transcriptomics, and metabolomics, increasing studies have tried to investigate the regulation mechanism of trap formation in NT fungi. This review summarizes the potential regulatory mechanism of trap formation in NT fungi based on the latest findings in this field. Signaling pathways have been confirmed to play an especially vital role in trap formation based on phenotypes of various mutants and multi-omics analysis, and the involvement of small molecule compounds, woronin body, peroxisome, autophagy, and pH-sensing receptors in the formation of traps are also discussed. In addition, we also highlight the research focus for elucidating the mechanism underlying trap formation of NT fungi in the future.

Functional Analysis of Two Affinity cAMP Phosphodiesterases in the Nematode-Trapping Fungus Arthrobotrys oligospora

Phosphodiesterases are essential regulators of cyclic nucleotide signaling with diverse physiological functions. Two phosphodiesterases, PdeH and PdeL, have been identified from yeast and filamentous fungi. Here, the orthologs of PdeH and PdeL were characterized in a typical nematode-trapping fungus Arthrobotrys oligospora by gene disruption and phenotypic comparison. Deletion of AopdeH caused serious defects in mycelial growth, conidiation, stress response, trap formation, and nematicidal efficiency compared to the wild-type strain. In contrast, these phenotypes have no significant difference in the absence of AopdeL. In addition, deletion of AopdeH and AopdeL resulted in a remarkable increase in cAMP level during vegetative growth and trap formation, and the number of autophagosomes was decreased in ΔAopdeH and ΔAopdeL mutants, whereas their volumes considerably increased. Moreover, metabolomic analyses revealed that many metabolites were downregulated in ΔAopdeH mutant compared to their expression in the wild-type strain. Our results indicate that AoPdeH plays a crucial role in mycelial growth, conidiation, stress response, secondary metabolism, and trap formation. In contrast, AoPdeL only plays a minor role in hyphal and conidial morphology, autophagy, and trap formation in A. oligospora. This work expands the roles of phosphodiesterases and deepens the understanding of the regulation of trap formation in nematode-trapping fungi.

AoSsk1, a Response Regulator Required for Mycelial Growth and Development, Stress Responses, Trap Formation, and the Secondary Metabolism in Arthrobotrys oligospora

Ssk1, a response regulator of the two-component signaling system, plays an important role in the cellular response to hyperosmotic stress in fungi. Herein, an ortholog of ssk1 (Aossk1) was characterized in the nematode-trapping fungus Arthrobotrys oligospora using gene disruption and multi-phenotypic comparison. The deletion of Aossk1 resulted in defective growth, deformed and swollen hyphal cells, an increased hyphal septum, and a shrunken nucleus. Compared to the wild-type (WT) strain, the number of autophagosomes and lipid droplets in the hyphal cells of the ΔAossk1 mutant decreased, whereas their volumes considerably increased. Aossk1 disruption caused a 95% reduction in conidial yield and remarkable defects in tolerance to osmotic and oxidative stress. Meanwhile, the transcript levels of several sporulation-related genes were significantly decreased in the ΔAossk1 mutant compared to the WT strain, including abaA, brlA, flbC, fluG, and rodA. Moreover, the loss of Aossk1 resulted in a remarkable increase in trap formation and predation efficiency. In addition, many metabolites were markedly downregulated in the ΔAossk1 mutant compared to the WT strain. Our results highlight that AoSsk1 is a crucial regulator of asexual development, stress responses, the secondary metabolism, and pathogenicity, and can be useful in probing the regulatory mechanism underlying the trap formation and lifestyle switching of nematode-trapping fungi.

Aolatg1 and Aolatg13 Regulate Autophagy and Play Different Roles in Conidiation, Trap Formation, and Pathogenicity in the Nematode-Trapping Fungus Arthrobotrys oligospora

Autophagy is a conserved cellular recycling and trafficking pathway in eukaryotes that plays an important role in cell growth, development, and pathogenicity. Atg1 and Atg13 form the Atg1–Atg13 complex, which is essential for autophagy in yeast. Here, we characterized the roles of the Aolatg1 and Aolatg13 genes encoding these autophagy-related proteins in the nematode-trapping fungus Arthrobotrys oligospora. Investigation of the autophagy process by using the AoAtg8-GFP fusion protein showed that autophagosomes accumulated inside vacuoles in the wild-type (WT) A. oligospora strain, whereas in the two mutant strains with deletions of Aolatg1 or Aolatg13, GFP signals were observed outside vacuoles. Similar results were observed by using transmission electron microscopy. Furthermore, deletion of Aolatg1 caused severe defects in mycelial growth, conidiation, conidial germination, trap formation, and nematode predation. In addition, transcripts of several sporulation-related genes were significantly downregulated in the ΔAolatg1 mutant. In contrast, except for the altered resistance to several chemical stressors, no obvious differences were observed in phenotypic traits between the WT and ΔAolatg13 mutant strains. The gene ontology analysis of the transcription profiles of the WT and ΔAolatg1 mutant strains showed that the set of differentially expressed genes was highly enriched in genes relevant to membrane and cellular components. The Kyoto Encyclopedia of Genes and Genomes analysis indicated that differentially expressed genes were highly enriched in those related to metabolic pathways, autophagy and autophagy-related processes, including ubiquitin-mediated proteolysis and SNARE interaction in vesicular transport, which were enriched during trap formation. These results indicate that Aolatg1 and Aolatg13 play crucial roles in the autophagy process in A. oligospora. Aolatg1 is also involved in the regulation of asexual growth, trap formation, and pathogenicity. Our results highlight the importance of Aolatg1 in the growth and development of A. oligospora, and provide a basis for elucidating the role of autophagy in the trap formation and pathogenicity of nematode-trapping fungi.

Transcriptomic Analysis Reveals That Rho GTPases Regulate Trap Development and Lifestyle Transition of the Nematode-Trapping Fungus Arthrobotrys oligospora

Nematode-trapping (NT) fungi can form unique infection structures (traps) to capture and kill free-living nematodes and, thus, can play a potential role in the biocontrol of nematodes. Arthrobotrys oligospora is a representative species of NT fungi. Here, we performed a time course transcriptome sequencing (RNA-seq) analysis of transcriptomes to understand the global gene expression levels of A. oligospora during trap formation and predation. We identified 5,752 unique differentially expressed genes, among which the rac gene was significantly upregulated. Alternative splicing events occurred in 2,012 genes, including the rac and rho2 gene. Furthermore, we characterized three Rho GTPases (Rho2, Rac, and Cdc42) in A. oligospora using gene disruption and multiphenotypic analysis. Our analyses showed that AoRac and AoCdc42 play an important role in mycelium growth, lipid accumulation, DNA damage, sporulation, trap formation, pathogenicity, and stress response in A. oligospora. AoCdc42 and AoRac specifically interacted with components of the Nox complex, thus regulating the production of reactive oxygen species. Moreover, the transcript levels of several genes associated with protein kinase A, mitogen-activated protein kinase, and p21-activated kinase were also altered in the mutants, suggesting that Rho GTPases might function upstream from these kinases. This study highlights the important role of Rho GTPases in A. oligospora and provides insights into the regulatory mechanisms of signaling pathways in the trap morphogenesis and lifestyle transition of NT fungi. IMPORTANCE Nematode-trapping (NT) fungi are widely distributed in terrestrial and aquatic ecosystems. Their broad adaptability and flexible lifestyles make them ideal agents for controlling pathogenic nematodes. Arthrobotrys oligospora is a model species employed for understanding the interaction between fungi and nematodes. Here, we revealed that alternative splicing events play a crucial role in the trap development and lifestyle transition in A. oligospora. Furthermore, Rho GTPases exert differential effects on the growth, development, and pathogenicity of A. oligospora. In particular, AoRac is required for sporulation and trap morphogenesis. In addition, our analysis showed that Rho GTPases regulate the production of reactive oxygen species and function upstream from several kinases. Collectively, these results expand our understanding of gene expression and alternative splicing events in A. oligospora and the important roles of Rho GTPases in NT fungi, thereby providing a foundation for exploring their potential application in the biocontrol of pathogenic nematodes.

Functional analysis of seven regulators of G protein signaling (RGSs) in the nematode-trapping fungus Arthrobotrys oligospora

Regulators of G protein signaling (RGSs) are proteins that negatively regulate G protein signal transduction. In this study, seven putative RGSs were characterized in the nematode-trapping (NT) fungus, Arthrobotrys oligospora. Deleting Rgs genes significantly increased intracellular cAMP levels, and caused defects in mycelia growth, stress resistance, conidiation, trap formation, and nematocidal activity. In particular, the ΔAoFlbA mutant was unable to produce conidia and traps. Transcriptomic analysis showed that amino acid metabolic and biosynthetic processes were significantly enriched in the ΔAoFlbA mutant compared to WT. Interestingly, Gas1 family genes are significantly expanded in A. oligospora and other NT fungi that produce adhesive traps, and are differentially expressed during trap formation in A. oligospora. Disruption of two Gas1 genes resulted in defective conidiation, trap formation, and pathogenicity. Our results indicate that RGSs play pleiotropic roles in regulating A. oligospora mycelial growth, development, and pathogenicity. Further, AoFlbA is a prominent member and required for conidiation and trap formation, possibly by regulating amino acid metabolism and biosynthesis. Our results provide a basis for elucidating the signaling mechanism of vegetative growth, lifestyle transition, and pathogenicity in NT fungi.

Phospholipase C (AoPLC2) regulates mycelial development, trap morphogenesis, and pathogenicity of the nematode-trapping fungus Arthrobotrys oligospora

AIMS

Phospholipase C (PLC) is a hydrolase involved in signal transduction in eukaryotic cells. This study aimed to understand the function of PLC in the nematode-trapping fungus Arthrobotrys oligospora.

METHODS AND RESULTS

Orthologous PLC (AoPLC2) of A. oligospora was functionally analysed using gene disruption and multi-phenotypic analysis. Disrupting Aoplc2 caused a deformation of partial hyphal cells (about 10%) and conidia (about 50%), decreased the number of nuclei in both conidia and hyphal cells, and increased the accumulation of lipid droplets. Meanwhile, the sporulation-related genes fluG and abaA were downregulated in ΔAoplc2 mutants than in the wild-type strain. Moreover, ΔAoplc2 mutants were more sensitive to osmotic stressors. Importantly, the number of traps, electron-dense bodies in traps, and nematicidal activity of ΔAoplc2 mutants were reduced, and the shape of the traps was deformed. In addition, AoPLC2 was involved in the biosynthesis of secondary metabolites in A. oligospora.

CONCLUSIONS

AoPLC2 plays an important role in the development of hyphae, spores, and cell nuclei, responses to stress, formation of traps, and predation of nematodes in A. oligospora.

SIGNIFICANCE AND IMPACT OF STUDY

This study reveals the various functions of phospholipase C and elucidates the regulation of trap morphogenesis in nematode-trapping fungi.

Ric8 acts as a regulator of G-protein signalling required for nematode-trapping lifecycle of Arthrobotrys oligospora

Resistance to inhibitors of cholinesterase 8 (Ric8) is a conserved guanine nucleotide exchange factor that is involved in the regulation of G-protein signalling in filamentous fungi. Here, we characterized an orthologous Ric8 (AoRic8) in Arthrobotrys oligospora by multi-omics analyses. The Aoric8 deletion (ΔAoric8) mutants lost an ability to produce traps essential for nematode predation, accompanied by a marked reduction in cAMP level. Yeast two-hybrid assay revealed that AoRic8 interacted with G-protein subunit Gα1. Moreover, the mutants were compromised in mycelia growth, conidiation, stress resistance, endocytosis, cellular components and intrahyphal hyphae. Revealed by transcriptomic analysis differentially upregulated genes in the absence of Aoric8 were involved in cell cycle, DNA replication and recombination during trap formation while downregulated genes were primarily involved in organelles, carbohydrate metabolism and amino acid metabolism. Metabolomic analysis showed that many compounds were markedly downregulated in ΔAoric8 mutants versus the wild-type strain. Our results demonstrated a crucial role for AoRic8 in the fungal growth, environmental adaption and nematode predation through control of cell cycle, organelle and secondary metabolism by G-protein signalling.

Pleiotropic roles of Ras GTPases in the nematode-trapping fungus Arthrobotrys oligospora identified through multi-omics analyses

The nematode-trapping fungi are ideal agents for controlling pathogenic nematodes. Arthrobotrys oligospora is a representative species of the same, producing traps for nematode predation. Here, three orthologous Ras GTPases (Ras2, Ras3, and Rheb) were characterized in A. oligospora. Our results indicate that they play pleiotropic roles in regulating the mycelial growth, conidiation, stress resistance, and pathogenicity of A. oligospora. Furthermore, deletion of Aoras2 and Aorheb significantly affected the mitochondrial activity, reactive oxygen species levels, lipid storage, and autophagy. Transcriptome analyses of ΔAoras2 mutant revealed that many repressed genes were associated with signal transduction, energy production, and carbohydrate transport and metabolism. Moreover, metabolic profile analyses showed that AoRas2 and AoRheb affect the biosynthesis of secondary metabolites in A. oligospora. Collectively, these findings provide an in-depth insight into the essential roles of Ras GTPases in vegetative growth, development, and pathogenicity and highlight their importance in the lifestyle switch of the nematode-trapping fungi.

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Ras GTPases play a multifunctional role in the lifestyle switch of A. oligospora

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Ras GTPases affect multiple cellular processes, including mitochondrial activity

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AoRas2 plays a key role in regulating global gene expression and nematode predation

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AoRas2 and AoRheb significantly affect the biosynthesis of secondary metabolites

AoBck1 and AoMkk1 Are Necessary to Maintain Cell Wall Integrity, Vegetative Growth, Conidiation, Stress Resistance, and Pathogenicity in the Nematode-Trapping Fungus Arthrobotrys oligospora

The cell wall integrity (CWI) pathway is composed of three mitogen-activated protein kinases (MAPKs), Bck1, Mkk1/2, and Slt2, and is one of the main signaling pathways for fungal pathogenesis, cell wall synthesis, and integrity maintenance. In this study, we characterized orthologs of Saccharomyces cerevisiae Bck1 and Mkk1 in the nematode-trapping (NT) fungus Arthrobotrys oligospora by multiple phenotypic comparison, and the regulation of conidiation and cell wall synthesis was analyzed using real-time PCR (RT-PCR). Both ΔAoBck1 and ΔAoMkk1 mutants showed severe defects in vegetative growth, cell nucleus number, and stress resistance. Both the mutants were unable to produce spores, and the transcription of several genes associated with sporulation and cell wall biosynthesis was markedly downregulated during the conidiation stage. Further, cell walls of the ΔAoBck1 and ΔAoMkk1 mutants were severely damaged, and the Woronin body failed to respond to cellular damage. In particular, the mutants lost the ability to produce mycelial traps for nematode predation. Taken together, AoBck1 and AoMkk1 play a conserved role in mycelial growth and development, CWI, conidiation, multi-stress tolerance, trap formation, and pathogenicity. We highlighted the role of AoBck1 and AoMkk1 in regulating the Woronin body response to cellular damage and cell nucleus development in A. oligospora.

AoATG5 plays pleiotropic roles in vegetative growth, cell nucleus development, conidiation, and virulence in the nematode-trapping fungus Arthrobotrys oligospora

Autophagy is an evolutionarily conserved process in eukaryotes, which is regulated by autophagy-related genes (ATGs). Arthrobotrys oligospora is a representative species of nematode-trapping (NT) fungi that can produce special traps for nematode predation. To elucidate the biological roles of autophagy in NT fungi, we characterized an orthologous Atg protein, AoAtg5, in A. oligospora. We found that AoATG5 deletion causes a significant reduction in vegetative growth and conidiation, and that the transcript levels of several sporulation-related genes were significantly downregulated during sporulation stage. In addition, the cell nuclei were significantly reduced in the ΔAoATG5 mutant, and the transcripts of several genes involved in DNA biosynthesis, repair, and ligation were significantly upregulated. In ΔAoATG5 mutants, the autophagic process was significantly impaired, and trap formation and nematocidal activity were significantly decreased. Comparative transcriptome analysis results showed that AoAtg5 is involved in the regulation of multiple cellular processes, such as autophagy, nitrogen metabolism, DNA biosynthesis and repair, and vesicular transport. In summary, our results suggest that AoAtg5 is essential for autophagy and significantly contributes to vegetative growth, cell nucleus development, sporulation, trap formation, and pathogenicity in A. oligospora, thus providing a basis for future studies focusing on related mechanisms of autophagy in NT fungi.

Methylglyoxal Has Different Impacts on the Fungistatic Roles of Ammonia and Benzaldehyde, and Lactoylglutathione Lyase Is Necessary for the Resistance of Arthrobotrys oligospora to Soil Fungistasis

Biocontrol of root-knot nematode has attracted increasing attention over the past two decades. The inconsistent field performance of biocontrol agents, which is caused by soil fungistasis, often restricts their commercial application. There is still a lack of research on the genes involved in biocontrol fungi response to soil fungistasis, which is important for optimizing practical applications of biocontrol fungi. In this study, the lactoylglutathione lyase-encoding AOL_s00004g335 in the nematophagous fungi Arthrobotrys oligospora was knocked out, and three mutant strains were obtained. The hyphal growth of mutants on the three media was almost the same as that of the wild-type strain, but mutants had slightly higher resistance to NaCl, SDS, and H₂O₂. Methylglyoxal (MG) significantly increased the resistance of A. oligospora to ammonia, but decreased the resistance to benzaldehyde. Furthermore, the resistance of the mutants to soil fungistasis was largely weakened and MG could not increase the resistance of A. oligospora to soil fungistasis. Our results revealed that MG has different effects on the fungistatic roles of ammonia and benzaldehyde and that lactoylglutathione lyase is very important for A. oligospora to resist soil fungistasis.

Polyketide Synthase-Terpenoid Synthase Hybrid Pathway Regulation of Trap Formation through Ammonia Metabolism Controls Soil Colonization of Predominant Nematode-Trapping Fungus

Polyketide synthase-terpenoid synthase (PKS-TPS) hybrid pathways for biosynthesis of unique sesquiterpenyl epoxy-cyclohexenoids (SECs) have been found to be widely distributed in plant pathogenic fungi. However, the natural and ecological functions of these pathways and their metabolites still remain cryptic. In this study, the whole PKS-TPS hybrid pathway in the predominant nematode-trapping fungus Arthrobotrys oligospora was first proposed according to all the intermediates and their derivatives from all the A. oligospora mutants with a deficiency in each gene involved in SEC biosynthesis. Most mutants displayed significantly increased trap formation which was correlated with alteration of the ammonia level. Further analysis revealed that the main metabolites involved in ammonia metabolism were largely increased in most mutants. However, significantly retarded colonization in soil were observed in most mutants compared to the wild-type strain due to significantly decreased antibacterial activities. Our results suggested that A. oligospora used the PKS-TPS hybrid pathway for fungal soil colonization via decreasing fungal nematode-capturing ability. This also provided solid evidence that boosting fungal colonization in soil was the secondary metabolite whose biosynthesis depended on a PKS-TPS hybrid pathway.

The Autophagy-Related Gene Aolatg4 Regulates Hyphal Growth, Sporulation, Autophagosome Formation, and Pathogenicity in Arthrobotrys oligospora

Autophagy plays an important role in cell growth and development. The autophagy-related gene atg4 encodes a cysteine protease, which can cleave the carboxyl terminus of Atg8, thus plays a role in autophagosome formation in yeast and filamentous fungi. Arthrobotrys oligospora is well known for producing special trapping-devices (traps) and capturing nematodes. In this study, two ΔAolatg4 mutants were generated using targeted gene replacement and were used to investigate the biological functions of autophagy in A. oligospora. Autophagic process was observed using the AoAtg8-GFP fusion protein. The mutants showed a defective in hyphal growth and sporulation and were sensitive to chemical stressors, including menadione and Congo red. The spore yield of the ΔAolatg4 mutants was decreased by 88.5% compared to the wild type (WT), and the transcript levels of six sporulation-related genes, such as abaA, fluG, brlA, and wetA, were significantly downregulated during the conidiation stage. Deletion of Aolatg4 also affected the cell nuclei and mycelial septal development in A. oligospora. Importantly, autophagosome formation and the autophagic process were impaired in the ΔAolatg4 mutant. Moreover, the ΔAolatg4 mutant lost its ability to form mature traps. Our results provide novel insights into the roles of autophagy in A. oligospora.

Dynamic Regulation of Peroxisomes and Mitochondria during Fungal Development

Peroxisomes and mitochondria are organelles that perform major functions in the cell and whose activity is very closely associated. In fungi, the function of these organelles is critical for many developmental processes. Recent studies have disclosed that, additionally, fungal development comprises a dynamic regulation of the activity of these organelles, which involves a developmental regulation of organelle assembly, as well as a dynamic modulation of the abundance, distribution, and morphology of these organelles. Furthermore, for many of these processes, the dynamics of peroxisomes and mitochondria are governed by common factors. Notably, intense research has revealed that the process that drives the division of mitochondria and peroxisomes contributes to several developmental processes-including the formation of asexual spores, the differentiation of infective structures by pathogenic fungi, and sexual development-and that these processes rely on selective removal of these organelles via autophagy. Furthermore, evidence has been obtained suggesting a coordinated regulation of organelle assembly and dynamics during development and supporting the existence of regulatory systems controlling fungal development in response to mitochondrial activity. Gathered information underscores an important role for mitochondrial and peroxisome dynamics in fungal development and suggests that this process involves the concerted activity of these organelles.

Two CRISPR/Cas9 Systems Developed in Thermomyces dupontii and Characterization of Key Gene Functions in Thermolide Biosynthesis and Fungal Adaptation

Thermomyces dupontii, a widely distributed thermophilic fungus, is an ideal organism for investigating the mechanism of thermophilic fungal adaptation to diverse environments. However, genetic analysis of this fungus is hindered by a lack of available and efficient gene-manipulating tools. In this study, two different Cas9 proteins from mesophilic and thermophilic bacteria, with in vivo expression of a single guide RNA (sgRNA) under the control of tRNAGly, were successfully adapted for genome editing in T. dupontii We demonstrated the feasibility of applying these two gene editing systems to edit one or two genes in T. dupontii The mesophilic CRISPR/Cas9 system displayed higher editing efficiency (50 to 86%) than the thermophilic CRISPR/Cas9 system (40 to 67%). However, the thermophilic CRISPR/Cas9 system was much less time-consuming than the mesophilic CRISPR/Cas9 system. Combining the CRISPR/Cas9 systems with homologous recombination, a constitutive promoter was precisely knocked in to activate a silent polyketide synthase-nonribosomal peptide synthase (PKS-NRPS) biosynthetic gene, leading to the production of extra metabolites that did not exist in the parental strains. Metabolic analysis of the generated biosynthetic gene mutants suggested that a key biosynthetic pathway existed for the biosynthesis of thermolides in T. dupontii, with the last two steps being different from those in the heterologous host Aspergillus Further analysis suggested that these biosynthetic genes might be involved in fungal mycelial growth, conidiation, and spore germination, as well as in fungal adaptation to osmotic, oxidative, and cell wall-perturbing agents.IMPORTANCE Thermomyces represents a unique ecological taxon in fungi, but a lack of flexible genetic tools has greatly hampered the study of gene function in this taxon. The biosynthesis of potent nematicidal thermolides in T. dupontii remains largely unknown. In this study, mesophilic and thermophilic CRISPR/Cas9 gene editing systems were successfully established for both disrupting and activating genes in T. dupontii In this study, a usable thermophilic CRISPR/Cas9 gene editing system derived from bacteria was constructed in thermophilic fungi. Chemical analysis of the mutants generated by these two gene editing systems identified the key biosynthetic genes and pathway for the biosynthesis of nematocidal thermolides in T. dupontii Phenotype analysis and chemical stress experiments revealed potential roles of secondary metabolites or their biosynthetic genes in fungal development and adaption to chemical stress conditions. These two genomic editing systems will not only accelerate investigations into the biosynthetic mechanisms of unique natural products and functions of cryptic genes in T. dupontii but also offer an example for setting up CRISPR/Cas9 systems in other thermophilic fungi.

The stuA gene controls development, adaptation, stress tolerance, and virulence of the dermatophyte Trichophyton rubrum

The APSES family, comprising of the transcriptional regulators Asm1p, Phd1p, Sok2p, Efg1p, and StuA, is found exclusively in fungi and has been reported to control several cellular processes in these organisms. However, its function in dermatophytes has not yet been completely understood. Here, we generated two null mutant strains by deleting the stuA gene in the dermatophyte Trichophyton rubrum, the most common clinical isolate obtained from human skin and nail mycoses. The functional characterization of the knocked-out strains revealed the involvement of stuA in germination, morphogenesis of conidia and hyphae, pigmentation, stress responses, and virulence. Although the mutant strains could grow under several nutritional conditions, growth on the keratin medium, human nails, and skin was impaired. The co-culture of stuA mutants with human keratinocytes revealed enhanced development. Moreover, a stuA mutant grown on the keratin substrate showed a marked decrease in the transcript numbers of the hydrophobin encoding gene (hypA), suggesting the involvement of stuA in the molecular mechanisms underlying mechanosensing during the fungi-host interaction. In addition, bioinformatics analyses revealed the potential involvement of StuA in different biological processes such as oxidation-reduction, phosphorylation, proteolysis, transcription/translation regulation, and carbohydrate metabolism. Cumulatively, the present study suggested that StuA is a crosstalk mediator of many pathways and is an integral component of the infection process, implying that it could be a potential target for antifungal therapy.

Natural diversity in the predatory behavior facilitates the establishment of a robust model strain for nematode-trapping fungi

Nematode-trapping fungi (NTF) are a group of specialized microbial predators that consume nematodes when food sources are limited. Predation is initiated when conserved nematode ascaroside pheromones are sensed, followed by the development of complex trapping devices. To gain insights into the coevolution of this interkingdom predator-prey relationship, we investigated natural populations of nematodes and NTF that we found to be ubiquitous in soils. Arthrobotrys species were sympatric with various nematode species and behaved as generalist predators. The ability to sense prey among wild isolates of Arthrobotrys oligospora varied greatly, as determined by the number of traps after exposure to Caenorhabditis elegans While some strains were highly sensitive to C. elegans and the nematode pheromone ascarosides, others responded only weakly. Furthermore, strains that were highly sensitive to the nematode prey also developed traps faster. The polymorphic nature of trap formation correlated with competency in prey killing, as well as with the phylogeny of A. oligospora natural strains, calculated after assembly and annotation of the genomes of 20 isolates. A chromosome-level genome assembly and annotation were established for one of the most sensitive wild isolates, and deletion of the only G-protein β-subunit-encoding gene of A. oligospora nearly abolished trap formation. In summary, our study establishes a highly responsive A. oligospora wild isolate as a model strain for the study of fungus-nematode interactions and demonstrates that trap formation is a fitness character in generalist predators of the nematode-trapping fungus family.

The Arf-GAP AoGlo3 regulates conidiation, endocytosis, and pathogenicity in the nematode-trapping fungus Arthrobotrys oligospora

Small GTPases of the ADP-ribosylation factor (Arf) family and their activating proteins (Arf-GAPs) regulate mycelial development and pathogenicity in yeast and filamentous fungi; however, little is known about their roles in nematode-trapping (NT) fungi. In this study, an ortholog of Arf-GAP Glo3 (AoGlo3) in Saccharomyces cerevisiae was characterized in the NT fungus Arthrobotrys oligospora. Deletion of the Aoglo3 gene resulted in growth defects and an increase in hyphal septum. Meanwhile, the sporulation capacity of the ΔAoglo3 mutant was decreased by 98%, and 67.1-71.2% spores became gourd or claviform in shape (from obovoid), which was accompanied by a significant decrease in the spore germination rate. This reduced sporulation capacity correlated with the transcriptional repression of several sporulation-related genes including fluG, rodA, abaA, medA, and lreA. The ΔAoglo3 mutant was also sensitive to several chemical stressors such as Congo red, NaCl, and sorbitol. Additionally, AoGlo3 was found to be involved in endocytosis, and more myelin figures were observed in the ΔAoglo3 mutant than in the wild-type strain, which was consistent with the presence of more autophagosomes observed in the mutant. Importantly, AoGlo3 affected the production of mycelial traps and serine proteases for nematode predation. In summary, AoGlo3 is involved in the regulation of multiple cellular processes such as mycelial growth, conidiation, environmental adaption, endocytosis, and pathogenicity in A. oligospora.

Protein Kinase Ime2 Is Required for Mycelial Growth, Conidiation, Osmoregulation, and Pathogenicity in Nematode-Trapping Fungus Arthrobotrys oligospora

Inducer of meiosis 2 (Ime2), a protein kinase that has been identified in diverse fungal species, functions in the regulation of various cellular processes, such as ascospore formation, pseudohyphal growth, and sexual reproduction. In this study, AoIme2, an ortholog of Saccharomyces cerevisiae Ime2, was characterized in the nematode-trapping fungus Arthrobotrys oligospora. Disruption of the gene Aoime2 caused defective growth, with slower mycelial growth in ΔAoime2 mutants than the wild type (WT) strain, and in the mutants, the number of hyphal septa in mycelia was higher and the number of cell nuclei in mycelia and conidia was considerably lower than in the WT strain. The conidial yields of the ΔAoime2 mutants were decreased by ∼33% relative to the WT strain, and the transcription of several sporulation-related genes, including abaA, fluG, rodA, aspB, velB, and vosA, was markedly downregulated during the conidiation stage. The ΔAoime2 mutants were highly sensitive to the osmotic stressors NaCl and sorbitol, and the cell wall of partial hyphae in the mutants was deformed. Further examination revealed that the cell wall of the traps produced by ΔAoime2 mutants became loose, and that the electron-dense bodies in trap cells were also few than in the WT strain. Moreover, Aoime2 disruption caused a reduction in trap formation and serine-protease production, and most hyphal traps produced by ΔAoime2 mutants did not form an intact hyphal loop; consequently, substantially fewer nematodes were captured by the mutants than by the WT strain. In summary, an Ime2-MAPK is identified here for the first time from a nematode-trapping fungus, and the kinase is shown to be involved in the regulation of mycelial growth and development, conidiation, osmolarity, and pathogenicity in A. oligospora.