Transcriptomics and proteomics insights into carotenoid differentiation in tissue cultured Rehmannia glutinosa root cambial meristematic cells: REG-CMC1 and non-somaclonal REG-CMC2

Plant bioactive compounds, particularly carotenoids, anthocyanins and flavonoids, plays a pivotal role in the pigmentation of plant tissues. In the current study, two distinct cambial meristematic cell (CMC) lines named REG-CMC-1 and REG-CMC-2 were derived from R. glutinosa roots through tissue culture, with significant differences in carotenoid content. REG-CMC-1 showed a significantly higher carotenoid content compared to REG-CMC-2 cell lines. A total of 1.78 mg/g DW (dry weight) of carotenoids were detected from REG-CMC-1 cells, compared to only 0.1 mg/g DW from REG-CMC-2 cells. Comprehensive transcriptomics and proteomics analysis were conducted further to investigate the difference in carotenoid content between two cell lines. Transcriptomics analysis of REG-CMC-1 and REG-CMC-2 cell lines identified 14,773 differentially expressed genes (DEGs) including genes encoding xanthoxin dehydrogenase, zeta-carotene desaturase, zeaxanthin epoxidase and 9-cis-epoxycarotenoid dioxygenase, which may be involved in carotenoid production. Significantly enriched genes were involved in secondary metabolite biosynthesis, plant hormone signaling and stress responses. Proteomics study identified 5,361 unique proteins, of which 1,710 were differentially expressed, with critical categories related to proteolysis, carbohydrate metabolism and phosphorylation highlighting various enzymes critical to carotenoid biosynthesis pathway, including lycopene beta-cyclase and phytoene desaturase. These findings indicate the presence of carotenoid biosynthesis-related components in R. glutinosa root cambial meristematic cells and suggest potential relevance for biotechnological studies of carotenoid production.