Melanin biosynthesis in the desert-derived Aureobasidium melanogenum XJ5-1 is controlled mainly by the CWI signal pathway via a transcriptional activator Cmr1

NsdD, a GATA-type transcription factor is involved in regulation and biosynthesis of macromolecules melanin, pullulan, and polymalate in Aureobasidium melanogenum

In this study, an NSDD gene, which encoded a GATA-type transcription factor involved in the regulation and biosynthesis of melanin, pullulan, and polymalate (PMA) in Aureobasidium melanogenum, was characterized. After the NSDD gene was completely removed, melanin production by the Δnsd mutants was enhanced, while pullulan and polymalate production was significantly reduced. Transcription levels of the genes involved in melanin biosynthesis were up-regulated while expression levels of the genes responsible for pullulan and PMA biosynthesis were down-regulated in the Δnsdd mutants. In contrast, the complementation of the NSDD gene in the Δnsdd mutants made the overexpressing mutants restore melanin production and transcription levels of the genes responsible for melanin biosynthesis. Inversely, the complementation strains, compared to the wild type strains, showed enhanced pullulan and PMA yields. These results demonstrated that the NsdD was not only a negative regulator for melanin biosynthesis, but also a key positive regulator for pullulan and PMA biosynthesis in A. melanogenum. It was proposed how the same transcriptional factor could play a negative role in melanin biosynthesis and a positive role in pullulan and PMA biosynthesis. This study provided novel insights into the regulatory mechanisms of multiple A. melanogenum metabolites and the possibility for improving its yields of some industrial products through genetic approaches.

Liamocin biosynthesis is induced by an autogenous host acid activation in Aureobasidium melanogenum

It has been known that maximal liamocin production must be carried out at low environmental pH (around 3.0). In this study, it was found that the low pH was mainly caused by the secreted citric acid which is one precursor of acetyl-CoA for liamocin biosynthesis. Determination of citric acid in the culture, deletion, complementation and overexpression of the CEXA gene encoding specific citrate exporter demonstrated that the low pH was indeed caused by the secreted citric acid. Deletion, complementation and overexpression of the ACL gene encoding ATP-citric acid lyase and effects of different initial pHs and added citric acid showed that the low pH in the presence of citric acid was suitable for lysis of intracellular citric acid, liamocin production and expression of the PACC gene encoding the pH signaling transcription factor PacC. This meant that the PACC gene was an acid-expression gene. Deletion, complementation and overexpression of the PACC gene indicated that expression of the key gene cluster GAL1-EST1-PKS1 for liamocin biosynthesis was driven by the pH signaling transcription factor PacC and there was weak nitrogen catabolite repression on liamocin biosynthesis at the low pH. That was why liamocin biosynthesis was induced at a low pH in the presence of citric acid. The mechanisms of the enhanced liamocin biosynthesis by the autogenous host acid activation, together with the pH signaling pathway, were proposed.

Novel chromosomes and genomes provide new insights into evolution and adaptation of the whole genome duplicated yeast-like fungus TN3-1 isolated from natural honey

Aureobasidium melanogenum TN3-1 strain and A. melanogenum P16 strain were isolated from the natural honey and the mangrove ecosystem, respectively. The former can produce much higher pullulan from high concentration of glucose than the latter. In order to know what happened to their genomes, the PacBio sequencing and Hi-C technologies were used to create the first high-quality chromosome-level reference genome assembly of A. melanogenum TN3-1 (51.61 Mb) and A. melanogenum P16 (25.82 Mb) with the contig N50 of 2.19 Mb and 2.26 Mb, respectively. Based on the Hi-C results, a total of 93.33% contigs in the TN3-1 strain and 92.31% contigs in the P16 strain were anchored onto 24 and 12 haploid chromosomes, respectively. The genomes of the TN3-1 strain had two subgenomes A and B. Synteny analysis showed that the genomic contents of the two subgenomes were asymmetric with many structural variations. Intriguingly, the TN3-1 strain was revealed as a recent hybrid/fusion between the ancestor of A. melanogenum CBS105.22/CBS110374 and the ancestor of another unidentified strain of A. melanogenum similar to P16 strain. We estimated that the two ancient progenitors diverged around 18.38 Mya and merged around 10.66-9.98 Mya. It was found that in the TN3-1 strain, telomeres of each chromosome contained high level of long interspersed nuclear elements (LINEs), but had low level of the telomerase encoding gene. Meanwhile, there were high level of transposable elements (TEs) inserted in the chromosomes of the TN3-1 strain. In addition, the positively selected genes of the TN3-1 strain were mainly enriched in the metabolic processes related to harsh environmental adaptability. Most of the stress-related genes were found to be related to the adjacent LTRs, and the glucose derepression was caused by the mutation of the Glc7-2 in the Snf-Mig1 system. All of these could contribute to its genetic instability, genome evolution, high stress resistance, and high pullulan production from glucose.

Influence of Cmr1 in the Regulation of Antioxidant Function Melanin Biosynthesis in Aureobasidium pullulans

We have successfully identified the transcription factor Cmr1 from the fungus Aureobasidium pullulans Hit-lcy3T, which regulates melanin biosynthesis genes. Bioinformatics analysis revealed that the Cmr1 gene encodes a protein of 945 amino acids, containing two Cys₂His₂ zinc finger domains and a Zn(II)₂Cys₆ binuclear cluster domain located at the N-terminus of Cmr1. To investigate the function of the Cmr1 gene, we performed gene knockout and overexpression experiments. Our results showed that Cmr1 is a key regulator of melanin synthesis in Hit-lcy3^T, and its absence caused developmental defects. Conversely, overexpression of Cmr1 significantly increased the number of chlamydospores in Hit-lcy3^T and improved melanin production. RT-qPCR analysis further revealed that overexpression of Cmr1 enhanced the expression of several genes involved in melanin biosynthesis, including Cmr1, PKS, SCD1, and THR1. Melanin extracted from the Hit-lcy3^T was characterized using UV and IR spectroscopy. Furthermore, we assessed the antioxidant properties of Hit-lcy3^T melanin and found that it possesses strong scavenging activity against DPPH·, ABTS·, and OH·, but weaker activity against O₂^-·. These findings suggest that Hit-lcy3^T melanin holds promise for future development as a functional food additive.

Contribution of the Tyrosinase (MoTyr) to Melanin Synthesis, Conidiogenesis, Appressorium Development, and Pathogenicity in Magnaporthe oryzae

Dihydroxynapthalene-(DHN) and L-dihydroxyphenylalanine (L-DOPA) are two types of dominant melanin in fungi. Fungal melanins with versatile functions are frequently associated with pathogenicity and stress tolerance. In rice blast fungus, Magnaporthe oryzae, DHN melanin is essential to maintain the integrity of the infectious structure, appressoria; but the role of the tyrosinase-derived L-DOPA melanin is still unknown. Here, we have genetically and biologically characterized a tyrosinase gene (MoTyr) in M. oryzae. MoTyr encodes a protein of 719 amino acids that contains the typical CuA and CuB domains of tyrosinase. The deletion mutant of MoTyr (ΔMoTyr) was obtained by using a homologous recombination approach. Phenotypic analysis showed that conidiophore stalks and conidia formation was significantly reduced in ΔMoTyr. Under different concentrations of glycerol and PEG, more appressoria collapsed in the mutant strains than in the wild type, suggesting MoTyr is associated with the integrity of the appressorium wall. Melanin measurement confirmed that MoTyr loss resulted in a significant decrease in melanin synthesis. Accordingly, the loss of MoTyr stunted the conidia germination under stress conditions. Importantly, the MoTyr deletion affected both infection and pathogenesis stages. These results suggest that MoTyr, like DHN pigment synthase, plays a key role in conidiophore stalks formation, appressorium integrity, and pathogenesis of M. oryzae, revealing a potential drug target for blast disease control.

Genome-Wide Editing Provides Insights into Role of Unsaturated fatty Acids in Low Temperature Growth of the Psychrotrophic Yeast Metschnikowia bicuspidata var. australis W7-5

In order to know the function of C_18:2 and C_18:3 fatty acids in the cold growth of the psychrotrophic yeast M. bicuspidata var. australis W7-5, the mutant 1 without C_18:2 fatty acid and the mutant 2 without C_18:3 fatty acids were obtained. Only the trace amount of C_18:2 fatty acid in the mutant 1 occurred while no C_18:3 fatty acid in the mutant 2 was detected. The growth rate of only the mutant 1 cultured at 5 ℃ and 25 ℃ was significantly reduced compared with that of the wild-type strain W7-5. But there was no difference between the growth of the mutant 2 and that of the W7-5 strain. These meant that only C_18:2 synthesized by the psychrotrophic yeast played an important role in cell growth at low temperature (5 °C) and high temperature (25 °C). Meanwhile, cell wall in the mutant 1 without C_18:2 fatty acid gown at 5 and 25 °C was also negatively affected, leading to the reduced cell growth rate of the mutant 1 grown at 5 and 25 °C.

A Forward Genetic Screen in Sclerotinia sclerotiorum Revealed the Transcriptional Regulation of Its Sclerotial Melanization Pathway

Most plant fungal pathogens that cause worldwide crop losses are understudied, due to various technical challenges. With the increasing availability of sequenced whole genomes of these non-model fungi, effective genetic analysis methods are highly desirable. Here, we describe a newly developed pipeline, which combines forward genetic screening with high-throughput next-generation sequencing to enable quick gene discovery. We applied this pipeline in the notorious soilborne phytopathogen Sclerotinia sclerotiorum and identified 32 mutants with various developmental and growth deficiencies. Detailed molecular studies of three melanization-deficient mutants provide a proof of concept for the effectiveness of our method. A master transcription factor was found to regulate melanization of sclerotia through the DHN (1,8-dihydroxynaphthalene) melanin biosynthesis pathway. In addition, these mutants revealed that sclerotial melanization is important for sclerotia survival under abiotic stresses, sclerotial surface structure, and sexual reproduction. Foreseeably, this pipeline can be applied to facilitate efficient in-depth studies of other non-model fungal species in the future.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

The signaling pathways involved in metabolic regulation and stress responses of the yeast-like fungi Aureobasidium spp

Aureobasidium spp. can use a wide range of substrates and are widely distributed in different environments, suggesting that they can sense and response to various extracellular signals and be adapted to different environments. It is true that their pullulan, lipid and liamocin biosynthesis and cell growth are regulated by the cAMP-PKA signaling pathway; Polymalate (PMA) and pullulan biosynthesis is controlled by the Ca²⁺ and TORC1 signaling pathways; the HOG1 signaling pathway determines high osmotic tolerance and high pullulan and liamocin biosynthesis; the Snf1/Mig1 pathway controls glucose repression on pullulan and liamocin biosynthesis; DHN-melanin biosynthesis and stress resistance are regulated by the CWI signaling pathway and TORC1 signaling pathway. In addition, the HSF1 pathway may control cell growth of some novel strains of A. melanogenum at 37 °C. However, the detailed molecular mechanisms of high temperature growth and thermotolerance of some novel strains of A. melanogenum and glucose derepression in A. melanogenum TN3-1 are still unclear.

The zinc finger protein StMR1 affects the pathogenicity and melanin synthesis of Setosphaeria turcica and directly regulates the expression of DHN melanin synthesis pathway genes

The infection and colonization of pathogenic fungi are often regulated by transcription factors. In our previous study, the zinc finger protein-encoding gene StMR1 was found to be highly expressed during the infection process of Setosphaeria turcica, the pathogen causing northern corn leaf blight. Evolutionary tree analysis showed that this gene was associated with regulatory factors of melanin synthesis. However, the regulatory mechanism of melanin synthesis and its effect on pathogenicity remain unclear. In this study, the function of StMR1 was analyzed by gene knockout. When the expression level of StMR1 in the mutants was significantly reduced, the colony color became lighter, the mycelia were curved and transparent, and the mutant showed a significant loss of pathogenicity. In addition, compared with wild-type, the accumulation of melanin decreased significantly in △Stmr1. RNA-seq analysis revealed 1,981 differentially expressed genes between the wild-type and knockout mutant, among which 39 genes were involved in melanin metabolism. qPCR revealed that the expression levels of 6 key genes in the melanin synthesis pathway were significantly reduced. ChIP-PCR and yeast one-hybrid assays confirmed that StMR1 directly binds to the promoters of St3HNR, St4HNR, StPKS, and StLAC2 in the DHN melanin synthesis pathway and regulates gene expression. The C2H2-type zinc fingers and Zn(Ⅱ)2Cys6 binuclear cluster in StMR1 was important for the binding to targets.

Dsk2 involves in conidiation, multi-stress tolerance and thermal adaptation in Beauveria bassiana

Dsk2 is a nuclear-enriched ubiquitin-like polyubiquitin-binding protein that regulates protein degradation in yeast but has not been explored yet in filamentous fungi, such as Beauveria bassiana. Here, we report Beauveria bassiana Dsk2 located both in the nucleus and in cytoplasm of hyphal cells. Deletion of Dsk2 resulted in mild growth defect on scant media with various carbon/nitrogen sources and dramatic attenuation in conidiation capability at optimal condition. Compared to the wild-type, ΔDsk2 strains are much more sensitive to high osmotic and oxidative pressure during vegetative growth. Meanwhile, the mutant strains showed an increased chemical tolerance to Congo red and calcofluor white, two cell wall perturbing agents. The transcriptional changes of genes involved in central development, superoxide dismutase and chitin synthesis pathway indicate that Dsk2 acts as a multi-functional regulator in adapting to environmental changes. Importantly, Dsk2 negatively regulated the ability of thermal resistance in B. bassiana, which makes it a potential target gene for constructing engineering anti-thermal strains in the circumstance of global warming. Altogether, our finding highlights novel roles of Dsk2 involved in the asexual cycle, multi-stress tolerance and pest control potential of B. bassiana.

Molecular evolution and regulation of DHN melanin-related gene clusters are closely related to adaptation of different melanin-producing fungi

Many genes responsible for melanin biosynthesis in fungi were physically linked together. The PKS gene clusters in most of the melanin-producing fungi were regulated by the Cmr1. It was found that a close rearrangement of the PKS gene clusters had evolved in most of the melanin-producing fungi and various functions of melanin in them were beneficial to their adaptation to the changing environments. The melanin-producing fungi had undergone at least five large-scale differentiations, making their PKS gene clusters be quickly evolved and the fungi be adapted to different harsh environments. The recent gene losses and expansion were remarkably frequent in the PKS gene clusters, leading to their rapid evolution and adaptation of their hosts to different environments. The PKS gene and the CMR1 gene in them were subject to a strong co-evolution, but the horizontal gene transfer events might have occurred in the genome-duplicated species, Aspergillus and Penicillium.

Correlation between the synthesis of pullulan and melanin in Aureobasidium pullulans

The content of pullulan and melanin in 500 mutants of Aureobasidum pullulans obtained by ultraviolet mutagenesis were examined and statistically analyzed, and a strong positive correlation was found between them. The result was further confirmed by culturing wild type strain As3.3984 in different media. Then we constructed melanin-deletion mutant As-Δalb1 and pullulan-deletion mutant As-Δpul. As-Δalb1 was a melanin-free strain with the yield of pullulan decreased by 41.01%. The supplementation of melanin in the culture of As-Δalb1 increased the production of pullulan. As-Δpul synthesized neither pullulan nor melanin and recovered melanin synthesis by adding pullulan to the medium. The results suggested that high concentration- of pullulan induced morphological transformation and synthesis of melanin, and melanin promoted the synthesis of pullulan. The pullulan biosynthetic genes, upt, pgm, ugp, and pul, were down-regulated, while the negative regulatory gene of pullulan synthesis, creA, was up-regulated by melanin deficiency.

The Genome-Wide Mutation Shows the Importance of Cell Wall Integrity in Growth of the Psychrophilic Yeast Metschnikowia australis W7-5 at Different Temperatures

In this study, it was found that a Cre/loxP system could be successfully used as a tool for editing the genome of the psychrophilic yeast Metschnikowia australis W7-5 isolated from Antarctica. The deletion and over-expression of the TPS1 gene for trehalose biosynthesis, the GSY gene for glycogen biosynthesis, and the GPD1 and GPP genes for glycerol biosynthesis had no influence on cell growth of the mutants and transformants compared to cell growth of their wild-type strain M. australis W7-5, indicating that trehalose, glycogen, and glycerol had no function in growth of the psychrophilic yeast at different temperatures. However, removal of the SLT2 gene encoding the mitogen-activated protein kinase in the cell wall integrity (CWI) signaling pathway and the SWI4 and SWI6 genes encoding the transcriptional activators Swi4/6 had the crucial influence on cell growth of the psychrophilic yeast at the low temperature, especially at 25 °C and expression of the genes related to cell wall and lipid biosynthesis. Therefore, the cell wall could play an important role in growth of the psychrophilic yeast at different temperatures and biosynthesis of cell wall was actively regulated by the CWI signaling pathway. This was the first time to show that the genome of the psychrophilic yeast was successfully edited and the molecular evidences were obtained to elucidate mechanisms of low temperature growth of the psychrophilic yeast from Antarctica.

Efficient Conversion of Cane Molasses into Fructooligosaccharides by a Glucose Derepression Mutant of Aureobasidium melanogenum with High β-Fructofuranosidase Activity

Fructooligosaccharides (FOSs) are excellent food ingredients or feed additives by stimulating probiotics. In this paper, a CREA gene encoding a glucose repressor in the β-fructofuranosidase producer Aureobasidium melanogenum 33 with high-level FOS biosynthesis was disrupted, and glucose repression in disruptant D28 was relieved. The disruptant D28 produced up to 2100 U/mL of β-fructofuranosidase activity, whereas the enzyme activities produced by parent strain 33 and complemented strain C11 were below 600 U/mL. The whole cells of the disruptant D28 was used to convert cane molasses into FOSs, and 0.58 g of FOSs/g of molasses sugar was synthesized from 350 g/L cane molasses sugar within 4 h. Results demonstrated that the industrial waste cane molasses can be efficiently converted into FOSs by the glucose derepression mutant D28 with high β-fructofuranosidase activity. This low-cost and environmentally friendly bioprocess has great potential applications in bioengineering and biotechnology for FOS production.