# Prospective Mapping of Transcriptional Changes Associated with Lipid and Carotenoid Production in Rhodotorula glutinis Using Different Feeding Approaches

## TL;DR

This study maps how the yeast Rhodotorula glutinis directs carbon toward lipid or carotenoid production, identifying key genes and metabolic strategies for industrial applications.

## Contribution

The paper provides a foundational genetic map of transcriptional changes in R. glutinis under different feeding conditions, highlighting novel regulatory mechanisms for lipid and carotenoid production.

## Key findings

- Lipid production is linked to broad transcriptional downregulation and upregulation of fatty acid synthesis genes.
- Carotenoid production correlates with increased NADPH supply and retention of the CrtZ enzyme, possibly involved in torularhodin synthesis.
- The study identifies specific genes and pathways that could be targeted for engineering high-efficiency R. glutinis strains.

## Abstract

The industrial potential of the yeast Rhodotorula glutinis to produce valuable lipids and carotenoids is hampered by an unclear understanding of how it directs carbon toward one product or the other. As a foundational step to decipher this critical regulatory switch, we performed an in-depth comparative transcriptomic case study using optimized bioreactor conditions. Our analysis reveals two distinct and opposing presumptive metabolic strategies: lipid maximization is associated with a broad genetic downregulation and specific upregulation of fat synthesis, while carotenoid production correlates with a boosted cellular NADPH supply and the unique retention of a key enzyme (CrtZ), potentially linked to torularhodin synthesis. This exploratory work provides a foundational genetic map and prioritizes precise molecular targets for future hypothesis-driven engineering of specialized, high-efficiency strains for sustainable bio-oil or high-value pigment production, pending validation with biological replication.

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.