Prospective Mapping of Transcriptional Changes Associated with Lipid and Carotenoid Production in Rhodotorula...

The oleaginous yeast Rhodotorula glutinis is a promising industrial host for the simultaneous production of lipids and carotenoids, yet the transcriptional regulation governing carbon flux toward these metabolites is poorly understood. As a foundational step, we performed a comparative transcriptomic analysis on bioreactor cultures under optimized fed-batch conditions with varying carbon-to-nitrogen (C/N) ratios and metal supplementation, comparing a nutrient-replete control (C) with conditions favoring high lipid (HLP) or high carotenoid (HCP) production. This study was designed as a preliminary, in-depth case study using single, well-controlled bioreactor runs per condition, with the goal of generating a comprehensive transcriptional map to identify key candidate genes for future validation. The data delineates two distinct presumptive metabolic strategies. The HLP regime was associated with broad transcriptional downregulation, channeling carbon toward lipogenesis via specific upregulation of the fatty acid synthase complex (FAS1/2, Log₂FC(HLP/HCP) > 2.99) and concerted suppression of β-oxidation genes (Log₂FC < -9.70). Conversely, the HCP condition was characterized by significant upregulation of NADPH-supplying pathways, including the pentose phosphate pathway (e.g., rpiA, Log₂FC(HCP/C) = 11.39) and an NADP⁺-dependent glyceraldehyde-3-phosphate dehydrogenase (gapN, Log₂FC(HCP/C) = 12.24). Notably, a putative beta-carotene hydroxylase (CrtZ) was uniquely sustained in the HCP condition (Log₂FC(HLP/HCP) = -10.65), strongly correlating with torularhodin accumulation and suggesting its novel role in torulene hydroxylation. This exploratory study reveals prospective transcriptional determinants of carbon partitioning in R. glutinis and provides a prioritized genetic blueprint for future hypothesis-driven research with full biological replication.