AtfA-Independent Adaptation to the Toxic Heavy Metal Cadmium in Aspergillus nidulans

Insights into metal tolerance and resistance mechanisms in Trichoderma asperellum unveiled by de novo transcriptome analysis during bioleaching

This study investigates the genetic responses of the fungus Trichoderma asperellum (T. asperellum) during bioleaching of ore and tailing samples, comparing one-step, two-step, and spent media bioleaching processes. HPLC analysis quantified oxalic acid, citric acid, and propionic acids, with oxalic acid identified as the primary organic acid involved in metal bioleaching. Metal analysis revealed differences in recovery between ore and tailing samples and among bioleaching processes. The two-step bioleaching process yielded the highest zinc (>54%) and nickel (>60%) recovery in tailings and ore, respectively. Nickel's efficient recovery in ore bioleaching was attributed to the presence of manganese, while its precipitation as nickel oxalate in tailings hindered recovery. Additional metals such as Co, Mn, Mg, Cu, and As were also successfully recovered. Transcriptomic analyses showed significant upregulation of genes associated with biological processes and cellular components, particularly those related to cell membrane structure and function, indicating T. asperellum's adaptation to environmental stresses during metal bioleaching. These findings enhance our understanding of the diverse mechanisms influencing metal recovery rates in bioleaching processes.

The cadmium tolerance enhancement through regulating glutathione conferred by vacuolar compartmentalization in Aspergillus sydowii

Aspergillus was found to be a vital hyperaccumulation species for heavy metal removal with admirable tolerance capacity. But the potential tolerance mechanism has not been completely studied. This study quantified the amounts of total cadmium (Cd), Cd2+, glutathione (GSH), and reactive oxygen species (ROS) in the protoplasts and vacuoles of mycelium. We modulated GSH synthesis using buthionine sulfoximine (BSO) and 2-oxothiazolidine-4-carboxylic acid (OTC) to investigate the subcellular regulatory mechanisms of GSH in the accumulation of Cd. The results confirmed that GSH plays a crucial role in vacuolar compartmentalization under Cd stress. GSH and GSSG as a redox buffer to keep the cellular redox state in balance and GSH as a metal chelating agent to reduce toxicity. When regulating the decreased GSH content with BSO, and increased GSH content with OTC, the system of Cd-GSH-ROS can change accordingly, this also supported that vacuolar compartmentalization is a detoxification strategy that can modulate the transport and storage of substances inside and outside the vacuole reasonably. Interestingly, GSH tended to be distributed in the cytoplasm, the battleground of redox takes place in the cytoplasm but not in the vacuole. These finding potentially has implications for the understanding of tolerance behavior and detoxification mechanisms of cells. In the future bioremediation of Cd in soil, the efficiency of soil remediation can be improved by developing organisms with high GSH production capacity.

A novel cadmium detoxification pathway in Tri-spine horseshoe crab (Tachypleus tridentatus): A 430-million-years-ago organism

Marine and intertidal heavy metal pollution has been a major concern in recent years. Tachypleus tridentatus has existed on earth for more than 430 million years. It has suffered a sharp decline in population numbers caused by environmental pollution and anthropogenic disturbance for almost 40 years. However, the effects of heavy metal pollution on juvenile T. tridentatus have not been reported. Here we show the mechanism of cadmium (Cd) detoxification in juvenile T. tridentatus using integrated antioxidant indexes and transcriptomic and metabolomic analysis. High Cd²⁺ concentration caused oxidative stress in juvenile T. tridentatus. The hazards increase with increasing Cd²⁺ concentration in juvenile T. tridentatus. Transcriptomics and metabolomics analyses concluded that high Cd²⁺ concentration resulted in the imbalance of glycerophospholipid metabolism in juvenile T. tridentatus to detoxify Cd. Our results offer a rationale for protective measures and further studies of heavy metal stress in T. tridentatus.

Genetic Interaction of Global Regulators AflatfA and AflatfB Mediating Development, Stress Response and Aflatoxins B1 Production in Aspergillus flavus

Aspergillus flavus produces carcinogenic and mutagenic aflatoxins, which cause economic losses and risk of food safety by contaminating grains, food and feed. In this study, we characterized two bZIP transcription factors, AflatfA and AflatfB, and their genetic interaction. Compared to the wild type (WT), AflatfA deletion and AflatfA and AflatfB double deletion both caused retarded vegetative growth of mycelia. Relative to WT, the AflatfA deletion strain (ΔAflatfA) and AflatfA and AflatfB double deletion strain (ΔAflatfAΔAflatfB) produced more sclerotia, whereas the AflatfB deletion strain (ΔAflatfB) produced less sclerotia. After 4 °C preservation and incubation at 50 °C, conidia viability dramatically decreased in the ΔAflatfA and ΔAflatfAΔAflatfB but ΔAflatfB mutants, whereas conidia viability of the ΔAflatfAΔAflatfB strain was higher after storage at 4 °C than in AflatfA mutant. Conidia of ΔAflatfA, ΔAflatfB and ΔAflatfAΔAflatfB strains significantly increased in sensitivity to H2O2 in comparison with WT. Compared to WT, the mycelium of ΔAflatfA and ΔAflatfB strains were more sensitive to H2O2; conversely, the ΔAflatfAΔAflatfB strain showed less sensitivity to H2O2. ΔAflatfA and ΔAflatfAΔAflatfB strains displayed less sensitivity to the osmotic reagents NaCl, KCl and Sorbitol, in comparison with WT and ΔAflatfB strains. When on YES medium and hosts corn and peanut, ΔAflatfA and ΔAflatfAΔAflatfB strains produced less aflatoxin B1 (AFB1) than ΔAflatfB, and the AFB1 yield of ΔAflatfB was higher than that of WT. When WT and mutants were inoculated on corn and peanut, the ΔAflatfA and ΔAflatfAΔAflatfB but not ΔAflatfB mutants produced less conidia than did WT. Taken together, this study reveals that AflatfA controls more cellular processes, and the function of AflatfA is stronger than that of AflatfB when of the same process is regulated, except the response to H2O2, which might result from the effect of AflatfA on the transcriptional level of AflatfB.

Stress Responses Elicited by Glucose Withdrawal in Aspergillus fumigatus

Glucose is a widely used carbon source in laboratory practice to culture Aspergillus fumigatus, however, glucose availability is often low in its “natural habitats”, including the human body. We used a physiological−transcriptomical approach to reveal differences between A. fumigatus Af293 cultures incubated on glucose, glucose and peptone, peptone (carbon limitation), or without any carbon source (carbon starvation). Autolytic cell wall degradation was upregulated by both carbon starvation and limitation. The importance of autolytic cell wall degradation in the adaptation to carbon stress was also highlighted by approximately 12.4% of the A. fumigatus genomes harboring duplication of genes involved in N-acetyl glucosamine utilization. Glucose withdrawal increased redox imbalance, altered both the transcription of antioxidative enzyme genes and oxidative stress tolerance, and downregulated iron acquisition, but upregulated heme protein genes. Transcriptional activity of the Gliotoxin cluster was low in all experiments, while the Fumagillin cluster showed substantial activity both on glucose and under carbon starvation, and the Hexadehydro-astechrome cluster only on glucose. We concluded that glucose withdrawal substantially modified the physiology of A. fumigatus, including processes that contribute to virulence. This may explain the challenge of predicting the in vivo behavior of A. fumigatus based on data from glucose rich cultures.

The Transcription Factor CsAtf1 Negatively Regulates the Cytochrome P450 Gene CsCyp51G1 to Increase Fludioxonil Sensitivity in Colletotrichum siamense

Previous studies have shown that the high-osmolarity glycerol mitogen-activated protein kinase (HOG MAPK) signaling pathway and its downstream transcription factor CsAtf1 are involved in the regulation of fludioxonil sensitivity in C. siamense. However, the downstream target genes of CsAtf1 related to the fludioxonil stress response remain unclear. Here, we performed chromatin immunoprecipitation sequencing (ChIP-Seq) and high-throughput RNA-sequencing (RNA-Seq) to identify genome-wide potential CsAtf1 target genes. A total of 3809 significantly differentially expressed genes were predicted to be directly regulated by CsAtf1, including 24 cytochrome oxidase-related genes. Among them, a cytochrome P450-encoding gene, designated CsCyp51G1, was confirmed to be a target gene, and its transcriptional expression was negatively regulated by CsAtf1, as determined using an electrophoretic mobility shift assay (EMSA), a yeast one-hybrid (Y1H) assay, and quantitative real-time PCR (qRT-PCR). Moreover, the overexpression mutant CsCYP51G1 of C. siamense exhibited increased fludioxonil tolerance, and the CsCYP51G1 deletion mutant exhibited decreased fludioxonil resistance, which revealed that CsCyp51G1 is involved in fludioxonil sensitivity regulation in C. siamense. However, the cellular ergosterol content of the mutants was not consistent with the phenotype of fludioxonil sensitivity, which indicated that CsCyp51G1 regulates fludioxonil sensitivity by affecting factors other than the ergosterol level in C. siamense. In conclusion, our data indicate that the transcription factor CsAtf1 negatively regulates the cytochrome P450 gene CsCyp51G1 to increase fludioxonil sensitivity in C. siamense.

Functional analysis of the bZIP-type transcription factors AtfA and AtfB in Aspergillus nidulans

Transcription factors (TFs) with the basic leucin zipper domain are key elements of the stress response pathways in filamentous fungi. In this study, we functionally characterized the two bZIP type TFs AtfA and AtfB by deletion (Δ) and overexpression (OE) of their encoding genes in all combination: ΔatfA, ΔatfB, ΔatfAΔatfB, ΔatfAatfBOE, ΔatfBatfAOE, atfAOE, atfBOE and atfAOEatfBOE in Aspergillus nidulans. Based on our previous studies, ΔatfA increased the sensitivity of the fungus to oxidative stress mediated by menadione sodium bisulfite (MSB) and tert-butylhydroperoxide (tBOOH), while ΔatfB was not sensitive to any oxidative stress generating agents, namely MSB, tBOOH and diamide at all. Contrarily, the ΔatfB mutant was sensitive to NaCl, but tolerant to sorbitol. Overexpression of atfB was able to compensate the MSB sensitivity of the ΔatfA mutant. Heavy metal stress elicited by CdCl2 reduced diameter of the atfBOE and atfAOEatfBOE mutant colonies to about 50% of control colony, while the cell wall stress generating agent CongoRed increased the tolerance of the ΔatfA mutant. When we tested the heat stress sensitivity of the asexual spores (conidiospores) of the mutants, we found that conidiospores of ΔatfAatfBOE and ΔatfBatfAOE showed nearly 100% tolerance to heat stress. Asexual development was negatively affected by ΔatfA, while atfAOE and atfAOE coupled with ΔatfB increased the number of conidiospores of the fungus approximately 150% compared to the control. Overexpression of atfB led to a 25% reduction in the number of conidiospores, but increased levels of abaA mRNA and size of conidiospores. Sexual fruiting body (cleistothecium) formation was diminished in the ΔatfA and the ΔatfAΔatfB mutants, while relatively elevated in the ΔatfB and the ΔatfBatfAOE mutants. Production of the mycotoxin sterigmatocystin (ST) was decreased to undetectable levels in the ΔatfA mutant, yet ST production was restored in the ΔatfAΔatfB mutant, suggesting that ΔatfB can suppress ST production defect caused by ΔatfA. Levels of ST were also significantly decreased in the ΔatfAatfBOE, ΔatfBatfAOE and atfAOEatfBOE mutants.

Strategies Shaping the Transcription of Carbohydrate-Active Enzyme Genes in Aspergillus nidulans

Understanding the coordinated regulation of the hundreds of carbohydrate-active enzyme (CAZyme) genes occurring in the genomes of fungi has great practical importance. We recorded genome-wide transcriptional changes of Aspergillus nidulans cultivated on glucose, lactose, or arabinogalactan, as well as under carbon-starved conditions. We determined both carbon-stress-specific changes (weak or no carbon source vs. glucose) and carbon-source-specific changes (one type of culture vs. all other cultures). Many CAZyme genes showed carbon-stress-specific and/or carbon-source-specific upregulation on arabinogalactan (138 and 62 genes, respectively). Besides galactosidase and arabinan-degrading enzyme genes, enrichment of cellulolytic, pectinolytic, mannan, and xylan-degrading enzyme genes was observed. Fewer upregulated genes, 81 and 107 carbon stress specific, and 6 and 16 carbon source specific, were found on lactose and in carbon-starved cultures, respectively. They were enriched only in galactosidase and xylosidase genes on lactose and rhamnogalacturonanase genes in both cultures. Some CAZyme genes (29 genes) showed carbon-source-specific upregulation on glucose, and they were enriched in β-1,4-glucanase genes. The behavioral ecological background of these characteristics was evaluated to comprehensively organize our knowledge on CAZyme production, which can lead to developing new strategies to produce enzymes for plant cell wall saccharification.

The impact of bZIP Atf1ortholog global regulators in fungi

Regulation of signal transduction pathways is crucial for the maintenance of cellular homeostasis and organismal development in fungi. Transcription factors are key elements of this regulatory network. The basic-region leucine zipper (bZIP) domain of the bZIP-type transcription factors is responsible for DNA binding while their leucine zipper structural motifs are suitable for dimerization with each other facilitiating the formation of homodimeric or heterodimeric bZIP proteins. This review highlights recent knowledge on the function of fungal orthologs of the Schizosaccharomyces pombe Atf1, Aspergillus nidulans AtfA, and Fusarium verticillioides FvAtfA, bZIP-type transcription factors with a special focus on pathogenic species. We demonstrate that fungal Atf1-AtfA-FvAtfA orthologs play an important role in vegetative growth, sexual and asexual development, stress response, secondary metabolite production, and virulence both in human pathogens, including Aspergillus fumigatus, Mucor circinelloides, Penicillium marneffei, and Cryptococcus neoformans and plant pathogens, like Fusarium ssp., Magnaporthe oryzae, Claviceps purpurea, Botrytis cinerea, and Verticillium dahliae. KEY POINTS: • Atf1 orthologs play crucial role in the growth and development of fungi. • Atf1 orthologs orchestrate environmental stress response of fungi. • Secondary metabolite production and virulence are coordinated by Atf1 orthologs.