Mining novel cis-regulatory elements from the emergent host Rhodosporidium toruloides using transcriptomic data.

Area of Science:

• Microbial biotechnology
• Synthetic biology
• Industrial microbiology

Background:

• Growing demand for robust microbial cell factories in bioproduction.
• Rhodosporidium toruloides shows promise due to its substrate versatility and stress tolerance.
• Biorefineries require hosts that withstand industrial bioprocess conditions.

Purpose of the Study:

• To investigate the transcriptional responses of Rhodosporidium toruloides under simulated industrial bioprocess conditions.
• To assess R. toruloides suitability as a cell factory for biorefineries.
• To identify key genes and regulatory elements involved in stress response and substrate utilization.

Main Methods:

• RNA sequencing (RNA-seq) was performed on R. toruloides under various stress conditions (high temperature, ethanol) and using sugarcane juice as a substrate.
• Differential gene expression analysis and functional enrichment analysis were conducted on transcriptomic data.
• A bioinformatics workflow was developed for motif discovery to identify transcription factor binding sites.

Main Results:

• Transcriptional profiles revealed yeast responses to high temperature, ethanol stress, and sugarcane juice utilization.
• Key differentially expressed genes and enriched pathways related to stress tolerance and metabolism were identified.
• Novel binding motifs for transcription factors (HAC1, ARG80, RPN4, ADR1, DAL81) were predicted for the first time in R. toruloides.

Conclusions:

• Rhodosporidium toruloides exhibits significant transcriptional adaptation to industrial bioprocess conditions, highlighting its potential as a microbial cell factory.
• The identified transcription factors and regulatory elements provide valuable insights for engineering R. toruloides for enhanced biomaterial production.
• The developed motif discovery method advances the study of gene regulatory networks in biotechnologically important yeasts.