Genome shuffling improves pigment and other bioactive compound production in Monascus purpureus

Insight into the phylogeny and metabolic divergence of Monascus species (M. pilosus, M. ruber, and M. purpureus) at the genome level

Background

Species of the genus Monascus are economically important and widely used in the production of food colorants and monacolin K. However, they have also been known to produce the mycotoxin citrinin. Currently, taxonomic knowledge of this species at the genome level is insufficient.

Methods

This study presents genomic similarity analyses through the analysis of the average nucleic acid identity of the genomic sequence and the whole genome alignment. Subsequently, the study constructed a pangenome of Monascus by reannotating all the genomes and identifying a total of 9,539 orthologous gene families. Two phylogenetic trees were constructed based on 4,589 single copy orthologous protein sequences and all the 5,565 orthologous proteins, respectively. In addition, carbohydrate active enzymes, secretome, allergic proteins, as well as secondary metabolite gene clusters were compared among the included 15 Monascus strains.

Results

The results clearly revealed a high homology between M. pilosus and M. ruber, and their distant relationship with M. purpureus. Accordingly, all the included 15 Monascus strains should be classified into two distinctly evolutionary clades, namely the M. purpureus clade and the M. pilosus-M. ruber clade. Moreover, gene ontology enrichment showed that the M. pilosus-M. ruber clade had more orthologous genes involved with environmental adaptation than the M. purpureus clade. Compared to Aspergillus oryzae, all the Monascus species had a substantial gene loss of carbohydrate active enzymes. Potential allergenic and fungal virulence factor proteins were also found in the secretome of Monascus. Furthermore, this study identified the pigment synthesis gene clusters present in all included genomes, but with multiple nonessential genes inserted in the gene cluster of M. pilosus and M. ruber compared to M. purpureus. The citrinin gene cluster was found to be intact and highly conserved only among M. purpureus genomes. The monacolin K gene cluster was found only in the genomes of M. pilosus and M. ruber, but the sequence was more conserved in M. ruber.

Conclusion

This study provides a paradigm for phylogenetic analysis of the genus Monascus, and it is believed that this report will lead to a better understanding of these food microorganisms in terms of classification, metabolic differentiation, and safety.

Bacteria as biofactory of pigments: Evolution beyond therapeutics and biotechnological advancements

Bacterial pigments are the wonder molecules of nature that have attracted the attention of industries in recent years. To date, various synthetic pigments have been in use in food, cosmetics, and textile industries that have not only shown a notoriously toxic nature but also posed threat to the ecosystem. Moreover, nutraceuticals, fisheries, and animal husbandry were highly dependent on plant sources for products that aid in disease prevention and improve stock health. In this context, the use of bacterial pigments as new-generation colorants, food fortifiers, and supplements can hold great prospects as low-cost, healthy, and eco-friendly alternatives. The majority of studies on these compounds were restricted to antimicrobial, antioxidant, and anticancer potentials to date. Each of these can be highly beneficial for the development of new-generation drugs, but their other potential niche in various industries that pose health and environmental risks needs to be explored. Recent advances in novel strategies of metabolic engineering, advancements in optimization tools for the fermentation process, and the design of appropriate delivery systems will greatly expand the market of bacterial pigments in industries. This review summarizes the current technologies for enhancing production, recovery, stability, and appreciable use of bacterial pigments in industries apart from therapeutics with proper financial aspects. The toxicity perspectives have been focused to emphasize that these wonder molecules are the need of the hour and their future prospects have been highlighted. Extensive literature has been studied to include the challenges of bacterial pigments from environmental and health risk perspectives.

Comparative Transcriptomic Analysis of Key Genes Involved in Citrinin Biosynthesis in Monascus purpureus

Monascus pigments (MPs) display many beneficial biological activities and have been widely utilized as natural food-grade colorants in the food processing industry. The presence of the mycotoxin citrinin (CIT) seriously restricts the application of MPs, but the gene regulation mechanisms governing CIT biosynthesis remain unclear. We performed a RNA-Seq-based comparative transcriptomic analysis of representative high MPs-producing Monascus purpureus strains with extremely high vs. low CIT yields. In addition, we performed qRT-PCR to detect the expression of genes related to CIT biosynthesis, confirming the reliability of the RNA-Seq data. The results revealed that there were 2518 differentially expressed genes (DEGs; 1141 downregulated and 1377 upregulated in the low CIT producer strain). Many upregulated DEGs were associated with energy metabolism and carbohydrate metabolism, with these changes potentially making more biosynthetic precursors available for MPs biosynthesis. Several potentially interesting genes that encode transcription factors were also identified amongst the DEGs. The transcriptomic results also showed that citB, citD, citE, citC and perhaps MpigI were key candidate genes to limit CIT biosynthesis. Our studies provide useful information on metabolic adaptations to MPs and CIT biosynthesis in M. purpureus, and provide targets for the fermentation industry towards the engineering of safer MPs production.

Optimization of the hongqu starter preparation process for the manufacturing of red mold rice with high gamma-aminobutyric acid production by solid-state fermentation

Red mold rice (RMR) generally contains gamma-aminobutyric acid (GABA), which has several physiological functions. Monascus purpureus M162, with a high GABA production of 15.10 mg/g was generated by atmospheric and room temperature plasma mutation. Furthermore, we conducted a response surface methodology to produce a premium hongqu starter. The results revealed that under optimal conditions, that is, a substrate containing brown rice and bran in a brown rice: bran ratio of 9:1 (wt/wt), an inoculation size of 21.50 mL/100 g, a mixing frequency of one time/9 h, and a cultivation time of 7.20 days, the number of active spores, α-amylase activity, and saccharification power activity was 4.15 × 10⁷ spores/g, 155 U/g, and 3260 U/g in the high-quality starter, respectively. These values were 224.32-fold, 139.64%, and 141.74% higher than those obtained with M. purpureus M162 inoculated into steamed indica rice, respectively, and 153.70-fold, 267.24%, and 151.63% higher than those obtained with the parent strain M. purpureus M1, respectively. The premium hongqu starter of M. purpureus M162 was inoculated into steamed indica rice to produce RMR with 15.93 mg/g of GABA. In conclusion, we proposed a novel strategy for functional RMR production with high GABA concentrations by solid-state fermentation with Monascus spp.

Disruption of the Chitin Biosynthetic Pathway Results in Significant Changes in the Cell Growth Phenotypes and Biosynthesis of Secondary Metabolites of Monascus purpureus

In this study, the gene monascus-5162 from Monascus purpureus LQ-6, identified as chitin synthase gene VI (chs6), was knocked out to disrupt the chitin biosynthetic pathway and regulate the biosynthesis of Monascus pigments (MPs) and citrinin. The results showed that the aerial hyphae on a solid medium were short and sparse after the deletion of chs6 in M. purpureus LQ-6, significantly reducing the germination percentage of active spores to approximately 22%, but the colony diameter was almost unaffected. Additionally, the deletion of chs6 changed the mycelial morphology of M. purpureus LQ-6 during submerged fermentation and increased its sensitivity to environmental factors. MP and citrinin biosynthesis was dramatically inhibited in the recombinant strain. Furthermore, comparative transcriptome analysis revealed that the pathways related to spore development and growth, including the MAPK signaling pathway, chitin biosynthetic pathway, and regulatory factors LaeA and WetA genes, were significantly downregulated in the early phase of fermentation. The mRNA expression levels of genes in the cluster of secondary metabolites were significantly downregulated, especially those related to citrinin biosynthesis. This is the first detailed study to reveal that chs6 plays a vital role in regulating the cell growth and secondary metabolism of the Monascus genus.

Preparation of Monascus-fermented ginkgo seeds: optimization of fermentation parameters and evaluation of bioactivity

In this study, a high monacolin K yield was achieved through solid-state fermentation of Ginkgo biloba seeds. Monascus purpureus suspension made from red yeast rice was used as spore inoculum. Fermentation conditions in solid-state fermentation were optimized using response surface methodology, and the optimal conditions for the maximum monacolin K yield (17.71 ± 1.57 mg/g) were 0.22% ammonium sulfate, 0.34% ammonium chloride, 0.05% magnesium sulfate, fermentation time of 12 days, inoculation volume of 11%, and temperature of 27 °C. The total phenolic content of Monascus-fermented ginkgo seeds attained 9.67 mg GAE/g, 4.88-fold higher than that of unfermented ginkgo seeds. The scavenging abilities of DPPH and ABTS free radicals increased to 9.79 mg TE/g and 13.92 mg TE/g, respectively. These findings highlight the importance of investigating the optimal fermentation conditions for maximum monacolin K yield and the utilization value of ginkgo seed as fermentation substrate for higher bioactivities.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-022-01078-z.

Toward improvements for enhancement the productivity and color value of Monascus pigments: a critical review with recent updates

Monascus pigments are a kind of high-quality natural edible pigments fermented by Monascus filamentous fungi, which have been widely used in food, cosmetics, medicine, textiles, dyes and chemical industries as active functional ingredients. Moreover, Monascus pigments have a good application prospect because of a variety of biological functions such as antibacterial, antioxidation, anti-inflammatory, regulating cholesterol, and anti-cancer. However, the low productivity and color value of pigments restrict their development and application. In this review, we introduced the categories, structures, biosynthesis and functions of Monascus pigments, and summarized the current methods for improving the productivity and color value of pigments, including screening and mutagenesis of strains, optimization of fermentation conditions, immobilized fermentation, mixed fermentation, additives, gene knockout and overexpression technologies, which will help to develop the foundation for the industrial production of Monascus pigments.