Integrated transcriptome and data-independent acquisition proteome analysis of the biosynthesis of Monascus azaphilone pigments and citrinin

Monascus azaphilone pigments (MPs) are widely used functional food additives. However, Monascus may simultaneously produce the mycotoxin citrinin (CIT), compromising MPs safety. Here, we used comparative genome, transcriptome, and quantitative data-independent acquisition mass spectrometry (DIA-MS) proteome analyses to compare three representative Monascus purpureus strains: M3 with high MPs and high CIT titers, M34 with high MPs and low CIT titers, and M69 with low titers of both products. Comparative genomic analysis confirmed high similarity among these strains. Differentially expressed genes (DEGs) and differentially abundant proteins (DAPs) were identified by pairwise comparisons among the strains during peak metabolite production, and selected DEGs and DAPs were verified by reverse transcription quantitative polymerase chain reaction and parallel reaction monitoring. An integrated analysis revealed DEG/DAPs correlating with altered MPs and CIT production, providing insights for strain breeding to engineer safer and more efficient MPs production processes in the food, cosmetics and pharmaceutical industries.