Proteomic profiling of Sporotrichum thermophile under the effect of ionic liquids: manifestation of an oxidative stress response

Ligand-Independent Activation of Aryl Hydrocarbon Receptor and Attenuation of Glutamine Levels by Natural Deep Eutectic Solvent

Natural deep eutectic solvents (NADESs) are emerging sustainable alternatives to conventional organic solvents. Beyond their role as laboratory solvents, NADESs are increasingly explored in drug delivery and as therapeutics. Their increasing applications notwithstanding, our understanding of how they interact with biomolecules at multiple levels - metabolome, proteome, and transcriptome - within human cell remain poor. Here, we deploy integrated metabolomics, proteomics, and transcriptomics to probe how NADESs perturb the molecular landscape of human cells. In a human cell line model, we found that an archetypal NADES derived from choline and geranic acid (CAGE) significantly altered the metabolome, proteome, and transcriptome. CAGE upregulated indole-3-lactic acid and 4-hydroxyphenyllactic acid levels, resulting in ligand-independent activation of aryl hydrocarbon receptor to signal the transcription of genes with implications for inflammation, immunomodulation, cell development, and chemical detoxification. Further, treating the cell line with CAGE downregulated glutamine biosynthesis, a nutrient rapidly proliferating cancer cells require. CAGE's ability to attenuate glutamine levels is potentially relevant for cancer treatment. These findings suggest that NADESs, even when derived from natural components like choline, can indirectly modulate cell biology at multiple levels, expanding their applications beyond chemistry to biomedicine and biotechnology.

An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota

Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.