Genome sequence of the fungus Pycnoporus sanguineus, which produces cinnabarinic acid and pH- and thermo- stable laccases

A Review on the Role and Function of Cinnabarinic Acid, a "Forgotten" Metabolite of the Kynurenine Pathway

In the human body, the majority of tryptophan is metabolized through the kynurenine pathway. This consists of several metabolites collectively called the kynurenines and includes, among others, kynurenic acid, L-kynurenine, or quinolinic acid. The wealth of metabolites, as well as the associated molecular targets and biological pathways, bring about a situation wherein even a slight imbalance in the kynurenine levels, both in the periphery and central nervous system, have broad consequences regarding general health. Cinnabarinic acid (CA) is the least known trace kynurenine, and its physiological and pathological roles are not widely understood. Some studies, however, indicate that it might be neuroprotective. Information on its hepatoprotective properties have also emerged, although these are pioneering studies and need to be replicated. Therefore, in this review, I aim to present and critically discuss the current knowledge on CA and its role in physiological and pathological settings to guide future studies.

Effect of fungal pretreatment by Pycnoporus sanguineus and Trichoderma longibrachiatum on the anaerobic digestion of rice straw

Rice straw is composed of complex lignocellulosic biomass, representing a major obstacle in its conversion to bioenergy. The objective of this study was to evaluate the usefulness of less explored fungal strains Trichoderma longibrachiatum (TL) and Pycnoporus sanguineus (PS) in improving hydrolysis and bioavailability of rice straw in anaerobic digestion (AD). The fungal treatment of rice straw for 10 days by PS and TL increased biogas production by 20.79% and 17.85% and reduced soluble chemical oxygen demand (sCOD) by 71.43% and 64.70%, respectively. The AD samples containing fungal-treated rice straw showed higher lignocellulolytic enzyme activities contributing to better process performance. The taxonomic profile of microbial communities in treated samples showed increased diversity that could sustain consistent system performance and exhibit enhanced resilience against pH fluctuations. Metagenomic analysis revealed 60.82% increase in Proteobacteria in PS and 11.58% increase in Bacteroidetes in TL-treated rice straw samples resulting in improved hydrolysis.

Integrated omic profiling of the medicinal mushroom Inonotus obliquus under submerged conditions

BACKGROUND

The Inonotus obliquus mushroom, a wondrous fungus boasting edible and medicinal qualities, has been widely used as a folk medicine and shown to have many potential pharmacological secondary metabolites. The purpose of this study was to supply a global landscape of genome-based integrated omic analysis of the fungus under lab-growth conditions.

RESULTS

This study presented a genome with high accuracy and completeness using the Pacbio Sequel II third-generation sequencing method. The de novo assembled fungal genome was 36.13 Mb, and contained 8352 predicted protein-coding genes, of which 365 carbohydrate-active enzyme (CAZyme)-coding genes and 19 biosynthetic gene clusters (BCGs) for secondary metabolites were identified. Comparative transcriptomic and proteomic analysis revealed a global view of differential metabolic change between seed and fermentation culture, and demonstrated positive correlations between transcription and expression levels of 157 differentially expressed genes involved in the metabolism of amino acids, fatty acids, secondary metabolites, antioxidant and immune responses. Facilitated by the widely targeted metabolomic approach, a total of 307 secondary substances were identified and quantified, with a significant increase in the production of antioxidant polyphenols.

CONCLUSION

This study provided the comprehensive analysis of the fungus Inonotus obliquus, and supplied fundamental information for further screening of promising target metabolites and exploring the link between the genome and metabolites.

Whole-Genome Sequencing and Analysis of the White-Rot Fungus Ceriporia lacerata Reveals Its Phylogenetic Status and the Genetic Basis of Lignocellulose Degradation and Terpenoid Synthesis

Ceriporia lacerata is an endophytic white-rot fungus that has lignocellulolytic and terpenoid-biosynthetic abilities. However, little is known about the genomic architecture of this fungus, even at the genus level. In this study, we present the first de novo genome assembly of C. lacerata (CGMCC No. 10485), based on PacBio long-read and Illumina short-read sequencing. The size of the C. lacerata genome is approximately 36 Mb (N50, 3.4 Mb). It encodes a total of 13,243 genes, with further functional analysis revealing that these genes are primarily involved in primary metabolism and host interactions in this strain's saprophytic lifestyle. Phylogenetic analysis based on ITS demonstrated a primary evolutionary position for C. lacerata, while the phylogenetic analysis based on orthogroup inference and average nucleotide identity revealed high-resolution phylogenetic details in which Ceriporia, Phlebia, Phlebiopsis, and Phanerochaete belong to the same evolutionary clade within the order Polyporales. Annotation of carbohydrate-active enzymes across the genome yielded a total of 806 genes encoding enzymes that decompose lignocellulose, particularly ligninolytic enzymes, lytic polysaccharides monooxygenases, and enzymes involved in the biodegradation of aromatic components. These findings illustrate the strain's adaptation to woody habitats, which requires the degradation of lignin and various polycyclic aromatic hydrocarbons. The terpenoid-production potential of C. lacerata was evaluated by comparing the genes of terpenoid biosynthetic pathways across nine Polyporales species. The shared genes highlight the major part of terpenoid synthesis pathways, especially the mevalonic acid pathway, as well as the main pathways of sesquiterpenoid, monoterpenoid, diterpenoid, and triterpenoid synthesis, while the strain-specific genes illustrate the distinct genetic factors determining the synthesis of structurally diverse terpenoids. This is the first genomic analysis of a species from this genus that we are aware of, and it will help advance functional genome research and resource development of this important fungus for applications in renewable energy, pharmaceuticals, and agriculture.

Improved Foods Using Enzymes from Basidiomycetes

Within the kingdom of fungi, the division Basidiomycota represents more than 30,000 species, some with huge genomes indicating great metabolic potential. The fruiting bodies of many basidiomycetes are appreciated as food (“mushrooms”). Solid-state and submerged cultivation processes have been established for many species. Specifically, xylophilic fungi secrete numerous enzymes but also form smaller metabolites along unique pathways; both groups of compounds may be of interest to the food processing industry. To stimulate further research and not aim at comprehensiveness in the broad field, this review describes some recent progress in fermentation processes and the knowledge of fungal genetics. Processes with potential for food applications based on lipases, esterases, glycosidases, peptidases and oxidoreductases are presented. The formation and degradation of colourants, the degradation of harmful food components, the formation of food ingredients and particularly of volatile and non-volatile flavours serve as examples. In summary, edible basidiomycetes are foods—and catalysts—for food applications and rich donors of genes to construct heterologous cell factories for fermentation processes. Options arise to support the worldwide trend toward greener, more eco-friendly and sustainable processes.

Hybrid Assembly Improves Genome Quality and Completeness of Trametes villosa CCMB561 and Reveals a Huge Potential for Lignocellulose Breakdown

Trametes villosa is a wood-decaying fungus with great potential to be used in the bioconversion of agro-industrial residues and to obtain high-value-added products, such as biofuels. Nonetheless, the lack of high-quality genomic data hampers studies investigating genetic mechanisms and metabolic pathways in T. villosa, hindering its application in industry. Herein, applying a hybrid assembly pipeline using short reads (Illumina HiSeq) and long reads (Oxford Nanopore MinION), we obtained a high-quality genome for the T. villosa CCMB561 and investigated its genetic potential for lignocellulose breakdown. The new genome possesses 143 contigs, N50 of 1,009,271 bp, a total length of 46,748,415 bp, 14,540 protein-coding genes, 22 secondary metabolite gene clusters, and 426 genes encoding Carbohydrate-Active enzymes. Our CAZome annotation and comparative genomic analyses of nine Trametes spp. genomes revealed T. villosa CCMB561 as the species with the highest number of genes encoding lignin-modifying enzymes and a wide array of genes encoding proteins for the breakdown of cellulose, hemicellulose, and pectin. These results bring to light the potential of this isolate to be applied in the bioconversion of lignocellulose and will support future studies on the expression, regulation, and evolution of genes, proteins, and metabolic pathways regarding the bioconversion of lignocellulosic residues.

Anti-malarial drug dihydroartemisinin downregulates the expression levels of CDK1 and CCNB1 in liver cancer

Liver cancer is the third leading cause of cancer-associated mortality worldwide. By the time liver cancer is diagnosed, it is already in the advanced stage. Therefore, novel therapeutic strategies need to be identified to improve the prognosis of patients with liver cancer. In the present study, the profiles of GSE84402, GSE19665 and GSE121248 were used to screen differentially expressed genes (DEGs). Subsequently, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses for DEGs were conducted using the Database for Annotation, Visualization and Integrated Discovery. The protein-protein interaction network was established to screen the hub genes associated with liver cancer. Additionally, the expression levels of hub genes were validated using the Gene Expression Profiling Interactive Analysis and Oncomine databases. In addition, the prognostic value of hub genes in patients with liver cancer was analyzed using Kaplan-Meier Plotter. It was demonstrated that 132 and 246 genes were upregulated and downregulated, respectively, in patients with liver cancer. Among these DEGs, 10 hub genes with high connected node values were identified, which were AURKA, BIRC5, BUB1B, CCNA2, CCNB1, CCNB2, CDC20, CDK1, DLGAP5 and MAD2L1. CDK1 and CCNB1 had the most connection nodes and the highest score and were therefore, the most significantly expressed. In addition, it was demonstrated that high expression levels of CDK1 and CCNB1 were associated with poor overall survival time of patients with liver cancer. Dihydroartemisinin (DHA) is a Food and Drug Administration-approved drug, which is derived from the traditional Chinese medicine Artemisia annua Linn. DHA inhibits cell proliferation in numerous cancer types, including liver cancer. In our previous study, it was revealed that DHA inhibited the proliferation of HepG2215 cells. In the present study, it was further demonstrated that DHA reduced the expression levels of CDK1 and CCNB1 in liver cancer. Overall, CDK1 and CCNB1 were the potential therapeutic targets of liver cancer, and DHA reduced the expression levels of CDK1 and CCNB1, and inhibited the proliferation of liver cancer cells.