Transcriptome analysis reveals gene expression changes of the basidiomycetous yeast Apiotrichum mycotoxinivorans in response to ochratoxin A exposure

Ochratoxin A Degradation and Stress Response Mechanism of Brevundimonas naejangsanensis ML17 Determined by Transcriptomic Analysis

Ochratoxin A (OTA) is a naturally occurring mycotoxin mainly produced by certain species of Aspergillus and Penicillium and is a serious threat to human health and food safety. Previous studies showed that Brevundimonas naejangsanensis ML17 can completely degrade 1 μg/mL of OTA. The aim of this study was to investigate the degradation effect of ML17 at different concentrations of OTA, and specifically, to investigate the mechanism of OTA degradation by ML17. The growth of ML17 was not affected by exposure to 6 μg/mL OTA within 24 h. ML17 could almost completely degrade 12 μg/mL of OTA within 36 h, converting it into the non-toxic OTα and L-phenylalanine. Transcriptomic analysis showed that 275 genes were upregulated, whereas three genes were downregulated in ML17 under the stress of 1 μg/mL OTA. Functional enrichment analysis showed that exposure to OTA enhanced translation, amide and peptide biosynthesis and metabolism, promoted oxidative phosphorylation, and increased ATP production. Further analysis revealed that, when exposed to OTA, ML17 exerted a stress-protective effect by synthesizing large amounts of heat shock proteins, which contributed to the correct folding of proteins. Notably, genes related to antioxidant activity, such as peroxiredoxin, superoxide dismutase, and glutaredoxin 3, were significantly upregulated, indicating that ML17 can resist the toxic effects of OTA through adjusting its metabolic processes, and the enzyme-coding gene0095, having OTA degradation activity, was found to be upregulated. This suggests that ML17 can achieve OTA degradation by regulating its metabolism, upregulating its antioxidant system, and upregulating enzyme-encoding genes with OTA degradation activity. Our work provides a theoretical reference for clarifying the mechanism of OTA degradation by ML17.

Isolation, identification and transcriptome analysis of triadimefon-degrading strain Enterobacter hormaechei TY18

Triadimefon, a type of triazole systemic fungicide, has been extensively used to control various fungal diseases. However, triadimefon could lead to severe environmental pollution, and even threatens human health. To eliminate triadimefon residues, a triadimefon-degrading bacterial strain TY18 was isolated from a long-term polluted site and was identified as Enterobacter hormaechei. Strain TY18 could grow well in a carbon salt medium with triadimefon as the sole nitrogen source, and could efficiently degrade triadimefon. Under triadimefon stress, a total of 430 differentially expressed genes (DEGs), including 197 up-regulated and 233 down-regulated DEGs, were identified in strain TY18 using transcriptome sequencing (RNA-Seq). Functional classification and enrichment analysis revealed that these DEGs were mainly related to amino acid transport and metabolism, carbohydrate transport and metabolism, small molecule and pyrimidine metabolism. Interestingly, the DEGs encoding monooxygenase and hydrolase activity acting on carbon-nitrogen were highly up-regulated, might be mainly responsible for the metabolism in triadimefon. Our findings in this work suggest that strain E. hormaechei TY18 could efficiently degrade triadimefon for the first time. They provide a great potential to manage triadimefon biodegradation in the environment successfully.

Biodegradation Characteristics and Mechanism of Aflatoxin B1 by Bacillus amyloliquefaciens from Enzymatic and Multiomics Perspectives

Aflatoxin B1 (AFB1), a mycotoxin and natural carcinogen, commonly contaminates cereals and animal feeds, posing serious health risks to human and animal. In this study, Bacillus amyloliquefaciens ZG08 isolated from kimchi could effectively remove 80.93% of AFB1 within 72 h at 37 °C and pH 7.0. Metabolome and transcriptome analysis showed that metabolic processes including glycerophospholipid metabolism and amino acid metabolism were most affected in B. amyloliquefaciens ZG08 exposed to AFB1. The adaptation mechanism likely involved activation of the thioredoxin system to restore intracellular redox equilibrium. The key genes, tpx and gldA, overexpressed in Escherichia coli BL21, achieved degradation rates of 60.15% and 47.16% for 100 μg/kg AFB1 under optimal conditions of 37 °C and pH 8.0 and 45 °C and pH 7.0, respectively. The degradation products, identified as AFD1, were less cytotoxic than AFB1 in HepG2 cells. These findings suggest potential strategies for utilizing probiotics and engineered enzymes in AFB1 detoxification.

Biotransformation activities of fungal strain apiotrichum sp. IB-1 to ibuprofen and naproxen

Ibuprofen (IBU) and naproxen (NPX), as widely prescribed non-steroidal anti-inflammatory drugs (NSAIDs), are largely produced and consumed globally, leading to frequent and ubiquitous detection in various aqueous environments. Previously, the microbial transformation of them has been given a little attention, especially with the isolated fungus. A yeast-like Apiotrichum sp. IB-1 has been isolated and identified, which could simultaneously transform IBU (5 mg/L) and NPX (2.5 mg/L) with maximum efficiencies of 95.77% and 88.31%, respectively. For mono-substrate, the transformation efficiency of IB-1 was comparable to that of co-removal conditions, higher than most of isolates so far. IBU was oxidized mainly through hydroxylation (m/z of 221, 253) and NPX was detoxified mainly via demethylation (m/z of 215) as shown by UPLC-MS/MS results. Based on transcriptome analysis, the addition of IBU stimulated the basic metabolism like TCA cycle. The transporters and respiration related genes were also up-regulated accompanied with higher expression of several dehydrogenase, carboxylesterase, dioxygenase and oxidoreductase encoding genes, which may be involved in the transformation of IBU. The main functional genes responsible for IBU and NPX transformation for IB-1 should be similar in view of previous studies, which needs further confirmation. This fungus would be useful for potential bioremediation of NSAIDs pollution and accelerate the discovery of functional oxidative genes and enzymes different from those of bacteria.