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

Transcription Levels of SDR Gene Ao274 in Nematode-Trapping Fungus Arthrobotrys oligospora Regulates Configurations and Oxidation Patterns of Arthrobotrisins and Formation of Trapping Devices

Here, we report hierarchical functions of a putative short-chain dehydrogenase/reductase gene Ao274 for arthrobotrisin biosynthesis in nematode-trapping fungus Arthrobotrys oligospora via an enhanced promoter. Transcriptional analysis revealed that Ao274 exhibited much higher transcriptional levels than all other genes in the arthrobotrisin biosynthetic pathway. We generated four mutants of two types with varying reductions in Ao274 transcription through gene swap experiments. Target isolation and structural elucidation of ten novel intermediates accumulated in the mutants demonstrated that high transcriptional levels are crucial for the hierarchical activity of Ao274, which is responsible for double carbonyl reductions and oxygenations at distinct carbon positions, preferentially acting on carbonyl reduction at C-1, followed by oxygen addition at C-1'. Additionally, variations in Ao274 transcription levels significantly affected conidial formation and trapping device development in A. oligospora. Our findings provide new insights into the chemical and biological functions of short-chain dehydrogenase/reductase family genes regulated by transcriptional levels.

Identification of a chlorosalicylic acid decarboxylase (CsaD) involved in decarboxylation of 3,6-DCSA from an anaerobic dicamba-degrading sludge

3,6-Dichlorosalicylic acid (3,6-DCSA) is the demethylation metabolite of herbicide 3,6-dichloro-2-methoxy benzoic acid (dicamba). Previous studies have shown that anaerobic sludge further transformed 3,6-DCSA through decarboxylation and dechlorination. However, the anaerobe, enzyme, and gene involved in the anaerobic degradation of 3,6-DCSA are still unknown. In this study, an anaerobic sludge that efficiently degraded dicamba was enriched, and a 3,6-DCSA decarboxylase, designated chlorosalicylic acid decarboxylase (CsaD), was partially purified and identified from the anaerobic sludge. Metagenomic analysis showed that the csaD gene was located in a gene cluster of metagenome-assembled genome 8 (MAG8). MAG8 belonged to an uncultured order, OPB41, in the class Coriobacteriia of the phylum Actinobacteria, and its abundance increased approximately once during the enrichment process. CsaD was a non-oxidative decarboxylase in the amidohydrolase 2 family catalyzing the decarboxylation of 3,6-DCSA and 6-chlorosalicylic acid (6-CSA). Its affinity and catalytic efficiency for 3,6-DCSA were significantly higher than those for 6-CSA. This study provides new insights into the anaerobic catabolism of herbicide dicamba.IMPORTANCEDicamba, an important hormone herbicide, easily migrates to anoxic habitats such as sediment, ground water, and deep soil. Thus, the anaerobic catabolism of dicamba is of importance. Anaerobic bacteria or sludge demethylated dicamba to 3,6-DCSA, and in a previous study, based on metabolite identification, it was proposed that 3,6-DCSA be further degraded via two pathways: decarboxylation to 2,5-dichlorophenol, then dechlorination to 3-chlorophenol (3-CP); or dechlorination to 6-CSA, then decarboxylation to 3-CP. However, there was no physiological and genetic validation for the pathway. In this study, CsaD catalyzed the decarboxylation of both 3,6-DCSA and 6-CSA, providing enzyme-level evidence for the anaerobic catabolism of 3,6-DCSA through the two pathways. CsaD was located in MAG8, which belonged to an uncultured anaerobic actinomycetes order, OPB41, indicating that anaerobic actinomycetes in OPB41 was involved in the decarboxylation of 3,6-DCSA. This study provides a basis for understanding the anaerobic catabolism of dicamba and the demethylation product, 3,6-DCSA.

Harnessing in vivo synthesis of bioactive multiarylmethanes in Escherichia coli via oxygen-mediated free radical reaction induced by simple phenols

BACKGROUND

Xanthenes and multi-aryl carbon core containing compounds represent different types of complex and condensed architectures that have impressive wide range of pharmacological, industrial and synthetic applications. Moreover, indoles as building blocks were only found in naturally occurring metabolites with di-aryl carbon cores and in chemically synthesized tri-aryl carbon core containing compounds. Up to date, rare xanthenes with indole bearing multicaryl carbon core have been reported in natural or synthetic products. The underlying mechanism of fluorescein-like arthrocolins with tetra-arylmethyl core were synthesized in an engineered Escherichia coli fed with toluquinol remained unclear.

RESULTS

In this study, the Keio collection of single gene knockout strains of 3901 mutants of E. coli BW25113, together with 14 distinct E. coli strains, was applied to explore the origins of endogenous building blocks and the biogenesis for arthrocolin assemblage. Deficiency in bacterial respiratory and aromatic compound degradation genes ubiX, cydB, sucA and ssuE inhibited the mutant growth fed with toluquinol. Metabolomics of the cultures of 3897 mutants revealed that only disruption of tnaA involving in transforming tryptophan to indole, resulted in absence of arthrocolins. Further media optimization, thermal cell killing and cell free analysis indicated that a non-enzyme reaction was involved in the arthrocolin biosynthesis in E. coli. Evaluation of redox potentials and free radicals suggested that an oxygen-mediated free radical reaction was responsible for arthrocolins formation in E. coli. Regulation of oxygen combined with distinct phenol derivatives as inducer, 31 arylmethyl core containing metabolites including 13 new and 8 biological active, were isolated and characterized. Among them, novel arthrocolins with p-hydroxylbenzene ring from tyrosine were achieved through large scale of aerobic fermentation and elucidated x-ray diffraction analysis. Moreover, most of the known compounds in this study were for the first time synthesized in a microbe instead of chemical synthesis. Through feeding the rat with toluquinol after colonizing the intestines of rat with E. coli, arthrocolins also appeared in the rat blood.

CONCLUSION

Our findings provide a mechanistic insight into in vivo synthesis of complex and condensed arthrocolins induced by simple phenols and exploits a quinol based method to generate endogenous aromatic building blocks, as well as a methylidene unit, for the bacteria-facilitated synthesis of multiarylmethanes.

Rare NRPS Gene Cluster for Desferriferrichrome Biosynthesis Controls the Conflict between Trap Formation and Nematicidal Activity in Arthrobotrys oligospora

The formation of the trapping device induced by nematodes has been assumed as an indicator for a switch from saprophytic to predacious lifestyles for nematode-trapping fungi. However, fungal nematocidal activity is not completely synonymous with fungal trap formation. We found that the predominant nematode-trapping fungus Arthrobotrys oligospora harbored a rare NRPS (Ao415) gene cluster that was mainly distributed in nematode-trapping fungi. The gene Ao415 putatively encodes a protein with a unique domain organization, distinct from other NRPSs in other fungi. Mutation of the two key biosynthetic genes Ao415 and Ao414 combined with nontarget metabolic analysis revealed that the Ao415 gene cluster was responsible for the biosynthesis of a hydroxamate siderophore, desferriferrichrome (1). Lack of desferriferrichrome (1) and its hydroxamate precursor (3) could lead to significantly increased Fe3+ content, which induced fungal trap formation without a nematode inducer. Furthermore, the addition of Fe3+ strongly improved fungal trap formation but deleteriously caused broken traps. The addition of 1 significantly attenuated trap formation but enhanced fungal nematicidal activity. Our findings indicate that iron is a key factor for trap formation and provide a new insight into the underlying mechanism of siderophores in nematode-trapping 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.

Roles of the Fungal-Specific Lysine Biosynthetic Pathway in the Nematode-Trapping Fungus Arthrobotrys oligospora Identified through Metabolomics Analyses

In higher fungi, lysine is biosynthesized via the α-aminoadipate (AAA) pathway, which differs from plants, bacteria, and lower fungi. The differences offer a unique opportunity to develop a molecular regulatory strategy for the biological control of plant parasitic nematodes, based on nematode-trapping fungi. In this study, in the nematode-trapping fungus model Arthrobotrys oligospora, we characterized the core gene in the AAA pathway, encoding α-aminoadipate reductase (Aoaar), via sequence analyses and through comparing the growth, and biochemical and global metabolic profiles of the wild-type and Aoaar knockout strains. Aoaar not only has α-aminoadipic acid reductase activity, which serves fungal L-lysine biosynthesis, but it also is a core gene of the non-ribosomal peptides biosynthetic gene cluster. Compared with WT, the growth rate, conidial production, number of predation rings formed, and nematode feeding rate of the ΔAoaar strain were decreased by 40-60%, 36%, 32%, and 52%, respectively. Amino acid metabolism, the biosynthesis of peptides and analogues, phenylpropanoid and polyketide biosynthesis, and lipid metabolism and carbon metabolism were metabolically reprogrammed in the ΔAoaar strains. The disruption of Aoaar perturbed the biosynthesis of intermediates in the lysine metabolism pathway, then reprogrammed amino acid and amino acid-related secondary metabolism, and finally, it impeded the growth and nematocidal ability of A. oligospora. This study provides an important reference for uncovering the role of amino acid-related primary and secondary metabolism in nematode capture by nematode-trapping fungi, and confirms the feasibility of Aoarr as a molecular target to regulate nematode-trapping fungi to biocontrol nematodes.

The Multifaceted Gene 275 Embedded in the PKS-PTS Gene Cluster Was Involved in the Regulation of Arthrobotrisin Biosynthesis, TCA Cycle, and Septa Formation in Nematode-Trapping Fungus Arthrobotrys oligospora

The predominant nematode-trapping fungus Arthrobotrys oligospora harbors a unique polyketide synthase-prenyltransferase (PKS-PTS) gene cluster AOL_s00215g responsible for the biosynthesis of sesquiterpenyl epoxy-cyclohexenoids (SECs) that are involved in the regulation of fungal growth, adhesive trap formation, antibacterial activity, and soil colonization. However, the function of one rare gene (AOL_s00215g275 (275)) embedded in the cluster has remained cryptic. Here, we constructed two mutants with the disruption of 275 and the overexpression of 275, respectively, and compared their fungal growth, morphology, resistance to chemical stress, nematicidal activity, transcriptomic and metabolic profiles, and infrastructures, together with binding affinity analysis. Both mutants displayed distinct differences in their TCA cycles, SEC biosynthesis, and endocytosis, combined with abnormal mitochondria, vacuoles, septa formation, and decreased nematicidal activity. Our results suggest that gene 275 might function as a separator and as an integrated gene with multiple potential functions related to three distinct genes encoding the retinoic acid induced-1, cortactin, and vacuolar iron transporter 1 proteins in this nematode-trapping fungus. Our unexpected findings provide insight into the intriguing organization and functions of a rare non-biosynthetic gene in a biosynthetic gene cluster.

Modulating Activity Evaluation of Gut Microbiota with Versatile Toluquinol

Gut microbiota have important implications for health by affecting the metabolism of diet and drugs. However, the specific microbial mediators and their mechanisms in modulating specific key intermediate metabolites from fungal origins still remain largely unclear. Toluquinol, as a key versatile precursor metabolite, is commonly distributed in many fungi, including Penicillium species and their strains for food production. The common 17 gut microbes were cultivated and fed with and without toluquinol. Metabolic analysis revealed that four strains, including the predominant Enterococcus species, could metabolize toluquinol and produce different metabolites. Chemical investigation on large-scale cultures led to isolation of four targeted metabolites and their structures were characterized with NMR, MS, and X-ray diffraction analysis, as four toluquinol derivatives (1–4) through O1/O4-acetyl and C5/C6-methylsulfonyl substitutions, respectively. The four metabolites were first synthesized in living organisms. Further experiments suggested that the rare methylsulfonyl groups in 3–4 were donated from solvent DMSO through Fenton’s reaction. Metabolite 1 displayed the strongest inhibitory effect on cancer cells A549, A2780, and G401 with IC₅₀ values at 0.224, 0.204, and 0.597 μM, respectively, while metabolite 3 displayed no effect. Our results suggest that the dominant Enterococcus species could modulate potential precursors of fungal origin and change their biological activity.

Acetylation of Sesquiterpenyl Epoxy-Cyclohexenoids Regulates Fungal Growth, Stress Resistance, Endocytosis, and Pathogenicity of Nematode-Trapping Fungus Arthrobotrys oligospora via Metabolism and Transcription

Sesquiterpenyl epoxy-cyclohexenoids (SECs) that depend on a polyketide synthase-terpenoid synthase (PKS-TPS) pathway are widely distributed in plant pathogenic fungi. However, the biosynthesis and function of the acetylated SECs still remained cryptic. Here, we identified that AOL_s00215g 273 (273) was responsible for the acetylation of SECs in Arthrobotrys oligospora via the construction of Δ273, in which the acetylated SECs were absent and major antibacterial nonacetylated SECs accumulated. Mutant Δ273 displayed increased trap formation, and nematicidal and antibacterial activities but decreased fungal growth and soil colonization. Glutamine, a key precursor for NH₃ as a trap inducer, was highly accumulated, and biologically active phenylpropanoids and antibiotics were highly enriched in Δ273. The decreased endocytosis and increased autophagosomes, with the most upregulated genes involved in maintaining DNA and transcriptional stability and pathways related to coronavirus disease and exosome, suggested that lack of 273 might result in increased virus infection and the acetylation of SECs played a key role in fungal diverse antagonistic ability.

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.