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Acetylation is an important modification type of histones, which is dynamically regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs). In this study, the histone acetylation level of Monascus was enhanced through the exogenous addition of the HDACs inhibitor vorinostat, and the regulation effects of histone acetylation on cell growth and secondary metabolism were evaluated. The results demonstrated that the augmentation of histone acetylation level could slightly facilitate sugar consumption, increase biomass weight, and significantly induce noticeable morphological alterations. Furthermore, in the presence of 80 μmol/L vorinostat concentration, there was a significant reduction observed in both extracellular and intracellular Monascus pigments, citrinin productions, with decreases of 35.46%, 63.90%, and 98.33% respectively. RT-qPCR results showed that adding vorinostat resulted in the up-regulation of HAT genes and down-regulation of HDAC genes. Additionally, transcriptome analysis revealed that glycolysis, tricarboxylic acid cycle, fatty acid metabolism, cell membrane anchor-protein related genes, and biosynthetic pathways involved in ergosterol and chitin synthesis were upregulated. Conversely, the electron transport chain and genetic clusters associated with Monascus pigments and citrinin synthesis were down-regulated. These findings underscore the pivotal role of histone acetylation in regulating the cell growth and secondary metabolism of M. purpureus and extend novel perspectives on the potential applications of clinical compounds derived from this process.

Monascus pilosus has been used to produce lipid-lowering drugs rich in monacolin K (MK) for a long period. Genome mining reveals there are still many potential genes worth to be explored in this fungus. Thereby, efficient genetic manipulation tools will greatly accelerate this progress. In this study, we firstly developed the protocol to prepare protoplasts for recipient of CRISPR/Cas9 system. Subsequently, the vector and donor DNA were co-transformed into recipients (10 6 protoplasts/mL) to produce 60–80 transformants for one test. Three genes ( mpclr4 , mpdot1 , and mplig4 ) related to DNA damage response (DDR) were selected to compare the gene replacement frequencies (GRFs) of Agrobacterium tumefaciens -mediated transformation (ATMT) and CRISPR/Cas9 gene editing system (CGES) in M. pilosus MS-1. The results revealed that GRF of CGES was approximately five times greater than that of ATMT, suggesting that CGES was superior to ATMT as a targeting gene editing tool in M. pilosus MS-1. The inactivation of mpclr4 promoted DDR via the non-homologous end-joining (NHEJ) and increased the tolerances to DNA damaging agents. The inactivation of mpdot1 blocked DDR and led to the reduced tolerances to DNA damaging agents. The inactivation of mplig4 mainly blocked the NHEJ pathway and led to obviously reduced tolerances to DNA damaging agents. The submerged fermentation showed that the ability to produce MK in strain Δ mpclr4 was improved by 52.6% compared to the wild type. This study provides an idea for more effective exploration of gene functions in Monascus strains. Key points • A protocol of high-quality protoplasts for CGES has been developed in M. pilosus. • The GRF of CGES was about five times that of ATMT in M. pilosus. • The yield of MK for Δmpclr4 was enhanced by 52.6% compared with the wild type.

Monascus spp. produce several well-known polyketides such as monacolin K, citrinin, and azaphilone pigments. In this study, the azaphilone pigment biosynthetic gene cluster was identified through T-DNA random mutagenesis in Monascus purpureus . The albino mutant W13 bears a T-DNA insertion upstream of a transcriptional regulator gene ( mppR1 ). The transcription of mppR1 and the nearby polyketide synthase gene ( MpPKS5 ) was significantly repressed in the W13 mutant. Targeted inactivation of MpPKS5 also gave rise to an albino mutant, confirming that mppR1 and MpPKS5 belong to an azaphilone pigment biosynthetic gene cluster. This M. purpureus sequence was used to identify the whole biosynthetic gene cluster in the Monascus pilosus genome. MpPKS5 contains SAT/KS/AT/PT/ACP/MT/R domains, and this domain organization is preserved in other azaphilone polyketide synthases. This biosynthetic gene cluster also encodes fatty acid synthase (FAS), which is predicted to assist the synthesis of 3-oxooactanoyl-CoA and 3-oxodecanoyl-CoA. These 3-oxoacyl compounds are proposed to be incorporated into the azaphilone backbone to complete the pigment biosynthesis. A monooxygenase gene (an azaH and tropB homolog) that is located far downstream of the FAS gene is proposed to be involved in pyrone ring formation. A homology search on other fungal genome sequences suggests that this azaphilone pigment gene cluster also exists in the Penicillium marneffei and Talaromyces stipitatus genomes.

Background Species of the genus Monascus are considered to be economically important and have been widely used in the production of yellow and red food colorants. In particular, three Monascus species, namely, M. pilosus , M. purpureus , and M. ruber , are used for food fermentation in the cuisine of East Asian countries such as China, Japan, and Korea. These species have also been utilized in the production of various kinds of natural pigments. However, there is a paucity of information on the genomes and secondary metabolites of these strains. Here, we report the genomic analysis and secondary metabolites produced by M. pilosus NBRC4520, M. purpureus NBRC4478 and M. ruber NBRC4483, which are NBRC standard strains. We believe that this report will lead to a better understanding of red yeast rice food. Results We examined the diversity of secondary metabolite production in three Monascus species ( M. pilosus , M. purpureus , and M. ruber ) at both the metabolome level by LCMS analysis and at the genome level. Specifically, M. pilosus NBRC4520, M. purpureus NBRC4478 and M. ruber NBRC4483 strains were used in this study. Illumina MiSeq 300 bp paired-end sequencing generated 17 million high-quality short reads in each species, corresponding to 200 times the genome size. We measured the pigments and their related metabolites using LCMS analysis. The colors in the liquid media corresponding to the pigments and their related metabolites produced by the three species were very different from each other. The gene clusters for secondary metabolite biosynthesis of the three Monascus species also diverged, confirming that M. pilosus and M. purpureus are chemotaxonomically different. M. ruber has similar biosynthetic and secondary metabolite gene clusters to M. pilosus . The comparison of secondary metabolites produced also revealed divergence in the three species. Conclusions Our findings are important for improving the utilization of Monascus species in the food industry and industrial field. However, in view of food safety, we need to determine if the toxins produced by some Monascus strains exist in the genome or in the metabolome.

In this study, adding mulberry leaf flavonoids (MLFs) during the liquid-state fermentation of Monascus purpureus significantly improved the production of Monascus pigments (MPs). Compared with the control group, the red, yellow, and orange pigment levels increased by 1.69, 1.4, and 1.29 times, respectively. Metabolomic analysis suggested adding rutin, the primary component of MLFs, induced changes in 32 significantly different metabolites. These changes included a significant increase in (S)-2,3,4,5-tetrahydropyridine-2-carboxylate, D-4′-phosphopantothenate, cis-4-hydroxy-D-proline, and L-isoleucine. Enriched Kyoto Encyclopedia of Genes and Genomics (KEGG) metabolic pathways revealed valine, leucine, and isoleucine biosynthesis, and phenylalanine metabolism improvements. These improvements help to activate the pigment synthesis pathway and promote pigment synthesis. These findings offer crucial insights into the impact of MLFs on Monascus purpureus metabolic pathways and suggest potential methods for increasing MP production. Graphical Abstract

Nucleic acid demethylases of α-ketoglutarate-dependent dioxygenase (AlkB) family can reversibly erase methyl adducts from nucleobases, thus dynamically regulating the methylation status of DNA/RNA and playing critical roles in multiple cellular processes. But little is known about AlkB demethylases in filamentous fungi so far. The present study reports that Monascus purpureus genomes contain a total of five MpAlkB genes. The MpAlkB1 gene was disrupted and complemented through homologous recombination strategy to analyze its biological functions in M. purpureus . MpAlkB1 knockout significantly accelerated the growth of strain, increased biomass, promoted sporulation and cleistothecia development, reduced the content of Monascus pigments (Mps), and strongly inhibited citrinin biosynthesis. The downregulated expression of the global regulator gene LaeA , and genes of Mps biosynthesis gene cluster (BGC) or citrinin BGC in MpAlkB1 disruption strain supported the pleiotropic trait changes caused by MpAlkB1 deletion. These results indicate that MpAlkB1-mediated demethylation of nucleic acid plays important roles in regulating the growth and development, and secondary metabolism in Monascus spp.

The genes for Monascus naphthoquinone (monasone) biosynthesis are embedded in and form a composite supercluster with the Monascus azaphilone pigment biosynthetic gene cluster. Early biosynthetic intermediates are shared by the two pathways. Some enzymes encoded by the supercluster play double duty in contributing to both pathways, while others are specific for one or the other pathway. The monasone subcluster is independently regulated and inducible by elicitation with competing microorganisms. This study illustrates genomic and biosynthetic parsimony in fungi and proposes a potential path for the evolution of the mosaic-like azaphilone-naphthoquinone supercluster. The monasone subcluster also encodes a two-tiered self-resistance mechanism that models resistance determinants that may transfer to target microorganisms or emerge in cancer cells in case of naphthoquinone-type cytotoxic agents. Despite the important biological activities of natural product naphthoquinones, the biosynthetic pathways of and resistance mechanisms against such compounds remain poorly understood in fungi. Here, we report that the genes responsible for the biosynthesis of Monascus naphthoquinones (monasones) reside within the gene cluster for Monascus azaphilone pigments (MonAzPs). We elucidate the biosynthetic pathway of monasones by a combination of comparative genome analysis, gene knockouts, heterologous coexpression, and in vivo and in vitro enzymatic reactions to show that this pathway branches from the first polyketide intermediate of MonAzPs. Furthermore, we propose that the monasone subset of biosynthetic genes also encodes a two-tiered resistance strategy in which an inducible monasone-specific exporter expels monasones from the mycelia, while residual intracellular monasones may be rendered nontoxic through a multistep reduction cascade. IMPORTANCE The genes for Monascus naphthoquinone (monasone) biosynthesis are embedded in and form a composite supercluster with the Monascus azaphilone pigment biosynthetic gene cluster. Early biosynthetic intermediates are shared by the two pathways. Some enzymes encoded by the supercluster play double duty in contributing to both pathways, while others are specific for one or the other pathway. The monasone subcluster is independently regulated and inducible by elicitation with competing microorganisms. This study illustrates genomic and biosynthetic parsimony in fungi and proposes a potential path for the evolution of the mosaic-like azaphilone-naphthoquinone supercluster. The monasone subcluster also encodes a two-tiered self-resistance mechanism that models resistance determinants that may transfer to target microorganisms or emerge in cancer cells in case of naphthoquinone-type cytotoxic agents.

Monascus pigments (MPs) as natural food colorants have been widely utilized in food industries in the world, especially in China and Japan. Moreover, MPs possess a range of biological activities, such as anti-mutagenic and anticancer properties, antimicrobial activities, potential anti-obesity activities, and so on. So, in the past two decades, more and more attention has been paid to MPs. Up to now, more than 50 MPs have been identified and studied. However, there have been some reviews about red fermented rice and the secondary metabolites produced by Monascus, but no monograph or review of MPs has been published. This review covers the categories and structures, biosynthetic pathway, production, properties, detection methods, functions, and molecular biology of MPs.

The influence of pH on the biosynthesis of orange Monascus pigments (OMPs) in Monascus ruber M7 was investigated. Under acidic fermentation conditions, pigment mixtures predominantly rich in OMPs were obtained. HPLC analysis revealed the presence of four orange components (O1 – O4) and four yellow components (Y1 – Y4) in the mixtures, and the dominant ones were O1 and O3, which accounted for 56.0% to 75.9% of the total pigments in the pH range 3 – 6. Subsequently, O1 and O3 were identified by LC-DAD-ESI/MS as Rubropunctatin and Monascorubrin, respectively. The yield of OMPs was observed to be inversely dependent on pH. At pH 3, large amounts of OMPs with high purity (79.1%) were accumulated. A real-time quantitative PCR analysis revealed that the expression of genes related to the biosynthesis of OMPs in M. ruber M7 was upregulated at acidic pH as compared to neutral pH, and the variation in the level of expression of these genes with pH was consistent with the production of OMPs. These results indicated that the large accumulation of OMPs under acidic condition involved the acidic pH-induced transcription of genes related to the biosynthesis of OMPs. These results would contribute towards the development of an efficient technology for large-scale production of OMPs.

Monascus-fermented products have been used in food, medicine, and industry dating back over a thousand years in Asian countries. Monascus-fermented products contained several bioactive metabolites such as pigments, polyketide monacolins, dimerumic acid, and γ-aminobutyric acid. Scientific reports showed that Monascus-fermented products proved to be effective for the management of blood cholesterol, diabetes, blood pressure, obesity, Alzheimer’s disease, and prevention of cancer development. This review article describes the beneficial effects about using Monascus-fermented products in human beings and animals.