Characterization and functional analyses of the chitinase-encoding genes in the nematode-trapping fungus Arthrobotrys oligospora

Expression profiles and characterization of microRNAs responding to chitin in Arthrobotrys oligospora

Extracellular proteases, such as chitinases secreted by Arthrobotrys oligospora (A. oligospora), play a crucial role in the process of nematode infection. However, post-transcriptional regulation of gene expression involving microRNAs (miRNAs) in A. oligospora remains scarcely described. Hereto, transcriptome sequencing was carried out to analyze the expression profiles of chitin-responsive miRNAs in A. oligospora. Based on the RNA-seq data, the differential expression of miRNAs (DEmiRNAs) in response to chitin was screened, identified and characterized in A. oligospora. Meanwhile, the potential target genes were predicted by the online tools miRanda and Targetscan, respectively. Furthermore, the interaction of DEmiRNA with it's target gene was validated by a dual-luciferase reporter assay system. Among 85 novel miRNAs identified, 25 miRNAs displayed significant differences in expression in A. oligospora in response to chitin. Gene Ontology (GO) analysis showed that the potential genes targeted by DEmiRNAs were enriched in the biological processes such as bio-degradation, extracellular components and cell cycle. KEGG analysis revealed that the target genes were mainly involved in Hippo, carbon and riboflavin metabolic pathway. Outstandingly, chitinase AOL_s00004g379, which is involved in the hydrolysis metabolic pathway of chitin, was confirmed to be a target gene of differential miR_70. These findings suggest that chitin-responsive miRNAs are involved in the regulation of cell proliferation, predator hyphae growth and chitinase expression through the mechanisms of post-transcriptional regulation, which provides a new perspective to the molecular mechanisms underlying miRNAs-mediated control of gene expression in A. oligospora.

Chitinases as key virulence factors in microbial pathogens: Understanding their role and potential as therapeutic targets

Chitinases are crucial for the survival of bacterial and fungal pathogens both during host infection and outside the host in the environment. Chitinases facilitate adhesion onto host cells, act as virulence factors during infection, and provide protection from the host immune system, making them crucial factors in the survival of microbial pathogens. Understanding the mechanisms behind chitinase action is beneficial to design novel therapeutics to control microbial infections. This review explores the role of chitinases in the pathogenesis of bacterial, fungal, and viral infections. The mechanisms underlying the action of chitinases of bacterial, fungal, and viral pathogens in host cells are thoroughly reviewed. The evolutionary relationships between chitinases of various bacterial, fungal, and viral pathogens are discussed to determine their involvement in processes, such as adhesion and host immune system modulation. Gaining a better understanding of the distribution and activity of chitinases in these microbial pathogens can help elucidate their role in the invasion and infection of host cells.

Biological Characteristics of Recombinant Arthrobotrys oligospora Chitinase AO-801

Chitinase AO-801 is a hydrolase secreted by Arthrobotrys oligospora during nematode feeding, while its role remained elusive. This study analyzed the molecular characteristics of recombinant chitinase of Arthrobotrys oligospora (reAO-801). AO-801 belongs to the typical glycoside hydrolase 18 family with conserved chitinase sequence and tertiary structure of (α/β)8 triose-phosphate isomerase (TIM) barrel. The molecular weight of reAO-801 was 42 kDa. reAO-801 effectively degraded colloidal and powdered chitin, egg lysate, and stage I larval lysate of Caenorhabditis elegans. The activity of reAO-801 reached its peak at 40˚C and pH values between 4-7. Enzyme activity was inhibited by Zn2+, Ca2+, and Fe3+, whereas Mg2+ and K+ potentiated its activity. In addition, urea, sodium dodecyl sulfate, and 2-mercaptoethanol significantly inhibited enzyme activity. reAO-801 showed complete nematicidal activity against C. elegans stage I larvae. reAO-801 broke down the C. elegans egg shells, causing them to die or die prematurely by hatching the eggs. It also invoked degradation of Haemonchus contortus eggs, resulting in apparent changes in the morphological structure. This study demonstrated the cytotoxic effect of reAO-801, which laid the foundation for further dissecting the mechanism of nematode infestation by A. oligospora.

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.

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.

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.

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.

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.

Chitin Synthesis and Degradation in Fungi: Biology and Enzymes

Chitin is one of the most important carbohydrates of the fungal cell wall, and is synthesized by chitin synthases. Chitin can be degraded by chitinases, which are important virulence factors in pathogenic fungi. Knowledge about the biosynthesis and degradation of chitin, and the enzymes responsible, has accumulated in recent years. In this review, we analyze the amino acid sequences of chitin synthases from several typical fungi. These enzymes can be divided into seven groups. While the different chitin synthases from a single fungus share a low degree of similarity, the same type of chitin synthase from different fungi shows high similarity. The number of chitinase genes in fungi display wide variation, from a single gene in Schizosaccharomyces pombe, to 36 genes in Trichoderma virens. Chitinases from different fungi can be divided into four groups. The functions of chitin synthases and chitinases in several typical fungi are summarized, and the crystal structures of chitinases and chitinase modification are also discussed.

Characterization and functional analysis of calcium/calmodulin-dependent protein kinases (CaMKs) in the nematode-trapping fungus Arthrobotrys oligospora

Ca²⁺/calmodulin-dependent protein kinases (CaMKs) are unique second-messenger molecules that impact almost all cellular processes in eukaryotes. In this study, five genes encoding different CaMKs were characterized in the nematode-trapping fungus Arthrobotrys oligospora. These CaMKs, which were retrieved from the A. oligospora genome according to their orthologs in fungi such as Aspergillus nidulans and Neurospora crassa, were expressed at a low level in vitro during mycelial growth stages. Five deletion mutants corresponding to these CaMKs led to growth defects in different media and increased sensitivity to several environmental stresses, including H₂O₂, menadione, SDS, and Congo red; they also reduced the ability to produce conidia and traps, thus causing a deficiency in nematicidal ability as well. In addition, the transcriptional levels of several typical sporulation-related genes, such as MedA, VelB, and VeA, were down-regulated in all ΔCaMK mutants compared with the wild-type (WT) strain. Moreover, these mutants exhibited hypersensitivity to heat shock and ultraviolet-radiation stresses compared with the WT strain. These results suggest that the five CaMKs in A. oligospora are involved in regulating multiple cellular processes, such as growth, environmental stress tolerance, conidiation, trap formation, and virulence.

MAP kinase Slt2 orthologs play similar roles in conidiation, trap formation, and pathogenicity in two nematode-trapping fungi

Mitogen-activated protein (MAP) kinase Slt2 is a key player in the cell-wall integrity pathway of budding yeast. In this study, we functionally characterized Slt2 orthologs AoSlt2 and MhSlt2 from the nematode-trapping fungi Arthrobotrys oligospora and Monacrosporium haptotylum, respectively. We found that disruption of AoSlt2 and MhSlt2 led to reduced mycelial growth, increased sensitivity to environmental stresses such as sodium dodecyl sulfate, Congo red, and H₂O₂, and an inability to produce conidia and nematode-trapping structures. Real-time polymerase chain reaction-based analyses showed that the transcription of sporulation-related (AbaA, Sep2, and MedA) and cell wall synthesis-related (Chs, Glu, and Gfpa) genes was down-regulated in the mutants compared with the wild-type strains. Moreover, the mutant strains showed reduced extracellular proteolytic activity and decreased transcription of three homologous serine protease-encoding genes. These results show for the first time that MAP kinase Slt2 orthologs play similar roles in regulating mycelial growth, conidiation, trap formation, stress resistance, and pathogenicity in the divergent nematode-trapping fungal species A. oligospora and M. haptotylum.

Taxonomic Resolution of the Nematophagous Fungal Isolate ARF18 via Genome Sequencing

The taxonomically uncharacterized nematophagous fungus ARF18, which parasitizes cysts, juveniles, and adults of the soybean cyst nematode (Heterodera glycines), was proposed as a nematode biological control agent in 1991. A 46.3-Mb draft genome sequence of this fungus is presented, and a tentative taxonomic identification as a novel species of Brachyphoris is proposed.

Random mutagenesis analysis and identification of a novel C2H2-type transcription factor from the nematode-trapping fungus Arthrobotrys oligospora

Arthrobotrys oligospora is a typical nematode-trapping fungus. In this study, 37 transformants of A. oligospora were obtained by REMI (restriction enzyme mediated integration) method and phenotypic properties of nine transformants were analyzed. The nine transformants showed differences in growth, conidiation, trap formation, stress tolerance, and/or pathogenicity among each other and with those of the parental wild-type strain (WT). The insertional sites of the hph cassette were identified in transformants X5 and X13. In X5, the cassette was inserted in the non-coding region between AOL_s00076g273 (76g273) and AOL_s00076g274 (76g274) and the transcription of 76g274, but not 76g273, was enhanced in X5. 76g274p had two conserved domains and was predicted as a nucleoprotein, which we confirmed by its nuclear localization in Saccharomyces cerevisiae using the green fluorescent protein-fused 76g274p. The transcription of 76g274 was stimulated or inhibited by several environmental factors. The sporulation yields of 76g274-deficient mutants were decreased by 70%, and transcription of several sporulation-related genes was severely diminished compared to the WT during the conidiation. In summary, a method for screening mutants was established in A. oligospora and using the method, we identified a novel C₂H₂-type transcription factor that positively regulates the conidiation of A. oligospora.

CAZyme content of Pochonia chlamydosporia reflects that chitin and chitosan modification are involved in nematode parasitism

Pochonia chlamydosporia is a soil fungus with a multitrophic lifestyle combining endophytic and saprophytic behaviors, in addition to a nematophagous activity directed against eggs of root-knot and other plant parasitic nematodes. The carbohydrate-active enzymes encoded by the genome of P. chlamydosporia suggest that the endophytic and saprophytic lifestyles make use of a plant cell wall polysaccharide degradation machinery that can target cellulose, xylan and, to a lesser extent, pectin. This enzymatic machinery is completed by a chitin breakdown system that involves not only chitinases, but also chitin deacetylases and a large number of chitosanases. P. chlamydosporia can degrade and grow on chitin and is particularly efficient on chitosan. The relevance of chitosan breakdown during nematode egg infection is supported by the immunolocalization of chitosan in Meloidogyne javanica eggs infected by P. chlamydosporia and by the fact that the fungus expresses chitosanase and chitin deacetylase genes during egg infection. This suggests that these enzymes are important for the nematophagous activity of the fungus and they are targets for improving the capabilities of P. chlamydosporia as a biocontrol agent in agriculture.

Chitinase from Thermomyces lanuginosus SSBP and its biotechnological applications

Chitinases are ubiquitous class of extracellular enzymes, which have gained attention in the past few years due to their wide biotechnological applications. The effectiveness of conventional insecticides is increasingly compromised by the occurrence of resistance; thus, chitinase offers a potential alternative to the use of chemical fungicides. The thermostable enzymes from thermophilic microorganisms have numerous industrial, medical, environmental and biotechnological applications due to their high stability for temperature and pH. Thermomyces lanuginosus produced a large number of chitinases, of which chitinase I and II are successfully cloned and purified recently. Molecular dynamic simulations revealed that the stability of these enzymes are maintained even at higher temperature. In this review article we have focused on chitinases from different sources, mainly fungal chitinase of T. lanuginosus and its industrial application.

The transcription factor SKN7 regulates conidiation, thermotolerance, apoptotic-like cell death and parasitism in the nematode endoparasitic fungus Hirsutella minnesotensis

The transcription factor SKN7 is a highly conserved protein among fungi and was initially recognized as a response regulator that protects cells from oxidative stress and maintains cell wall integrity in yeast. Orthologs of SKN7 are extensively present in biocontrol agents of plant pathogens, but they had not been functionally characterized. Here, we identified and characterized the transcription factor SKN7 in the nematode endoparasitic fungus Hirsutella minnesotensis. Null mutant lacking HIM-SKN7 (HIM_03620), which was generated by a gene disruption strategy, demonstrated reduced conidiation, increased sensitivity to high temperature, hydrogen peroxide, mannitol and ethanol, and reduced fungal resistance to farnesol. However, over-expression mutant showed increased conidial production, thermotolerance and resistance to farnesol, suggesting that HIM-SKN7 regulates antiapoptotic-like cell death in H. minnesotensis. Moreover, the results showed that in null mutant, H. minnesotensis had decreased endoparasitic ability as compared to wild type and over-expression strain. During the infection process, the relative expression of the HIM-SKN7 gene was significantly induced in the wild type and over-expression strain. The results of the present study advance our understanding of the functions of the SKN7 gene in biocontrol agents, in particular, nematode endoparasitic fungi.

Malate synthase gene AoMls in the nematode-trapping fungus Arthrobotrys oligospora contributes to conidiation, trap formation, and pathogenicity

Malate synthase (Mls), a key enzyme in the glyoxylate cycle, is required for virulence in microbial pathogens. In this study, we identified the AoMls gene from the nematode-trapping fungus Arthobotrys oligospora. The gene contains 4 introns and encodes a polypeptide of 540 amino acids. To characterize the function of AoMls in A. oligospora, we disrupted it by homologous recombination, and the ΔAoMls mutants were confirmed by PCR and Southern blot analyses. The growth rate and colony morphology of the ΔAoMls mutants showed no obvious difference from the wild-type strains on potato dextrose agar (PDA) plate. However, the disruption of gene AoMls led to a significant reduction in conidiation, failure to utilize fatty acids and sodium acetate for growth, and its conidia were unable to germinate on minimal medium supplemented with sodium oleate. In addition, the trap formation was retarded in the ΔAoMls mutants, which only produced immature traps containing one or two rings. Moreover, the nematicidal activity of the ΔAoMls mutants was significantly decreased. Our results suggest that the gene AoMls plays an important role in conidiation, trap formation and pathogenicity of A. oligospora.