Cell Wall Remodeling and pH Stress Coordinately Regulate Monascus Pigment Biosynthesis Through Transcriptional Reprogramming

Monascus pigments (MPs), natural food colorants produced by <i>Monascus</i> spp., have been traditionally used in China and Southeast Asia. Our prior work demonstrated that altered cell wall architecture in <i>M. purpureus</i> M9 significantly enhances pigment synthesis and secretion, although biosynthetic regulation under combined cell wall stress and acidic conditions remains unexplored. This study employed comparative transcriptomics to investigate coordinated regulation of MP production by pH stress and modified cell wall polysaccharides in wild-type (M9-WT) and UDP-galactopyranose mutase-deficient (M9-KO) strains at pH 5.0 and 3.0. At pH 5.0, <i>MpglfA</i> knockout enhanced MP secretion through cell wall restructuring involving differential expression total 67 genes (DEGs) of primary metabolism. Acidic stress (pH 3.0) significantly increased DEGs (168 up/643 down) in M9-KO versus M9-WT, inducing amino acid/fatty acid degradation pathways that generate MP precursors (acetyl-CoA/propionyl-CoA) and accelerating metabolic transition toward secondary metabolism. Concurrently, M9-KO adopted survival strategies featuring growth suppression and acid stress pathway activation to coordinate osmotic adaptation. Glucan synthase genes exhibited greater pH sensitivity than galactomannan-related genes, while MP biosynthetic genes were transcriptionally repressed in M9-KO under higher acidity. KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment and the series test of cluster confirmed that primary metabolic pathways, particularly nitrogen/carbon metabolism, critically regulate MP biosynthesis. Transcriptomic analysis under limited pH regimes revealed that antagonistic regulators ROX1 and SPT15 mediated pH-responsive transcriptional reprogramming, potentially regulating specific MP biosynthesis (e.g., monascus orange pigments). This work established theoretical foundations for manipulating cell wall composition to enhance MP production efficiency.