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

Abstract

The demand for robust microbial cell factories that produce valuable biomaterials while resisting stresses imposed by current bioprocesses is rapidly growing. Rhodosporidium toruloides is an emerging host that presents desirable features for bioproduction, since it can grow in a wide range of substrates and tolerate a variety of toxic compounds. To explore R. toruloides suitability for application as a cell factory in biorefineries, we sought to understand the transcriptional responses of this yeast when growing under experimental settings that simulated those used in biofuels-related industries. Thus, we performed RNA sequencing of the oleaginous, carotenogenic yeast in different contexts. The first ones were stress-related: two conditions of high temperature (37 and 42°C) and two ethanol concentrations (2 and 4%), while the other used the inexpensive and abundant sugarcane juice as substrate. Differential expression and functional analysis were implemented using transcriptomic data to select differentially expressed genes and enriched pathways from each set-up. A reproducible bioinformatics workflow was developed for mining new regulatory elements. We then predicted, for the first time in this yeast, binding motifs for several transcription factors, including HAC1, ARG80, RPN4, ADR1, and DAL81. Most putative transcription factors uncovered here were involved in stress responses and found in the yeast genome. Our method for motif discovery provides a new realm of possibilities in studying gene regulatory networks, not only for the emerging host R. toruloides, but for other organisms of biotechnological importance.

Insights into genomics and gene expression of oleaginous yeasts of the genus Rhodoturula

“…They provide a holistic view of cells´ growth and adaptation to changing environments (Figure 3) (Pinu et al, 2019). A variety of -omics studies have been performed on species from the R. glutinis cluster (Bo et al, 2022;Gong et al, 2019;Li et al, 2020;Nora et al, 2023;Tiukova, Brandenburg, et al, 2019;Zhao & Li, 2022;. Most of these studies have focused on R. toruloides and, to a smaller extent, on R. glutinis.…”

Non-canonical d-xylose and l-arabinose metabolism via d-arabitol in the oleaginous yeast Rhodosporidium toruloides

“…Rhodosporidium toruloides ( Rhodotorula toruloides ) is an oleaginous yeast capable of consuming many diverse substrates (including waste office paper, cassava starch, and macroalgae hydrolysate) [ 5 – 7 ]. It is able to tolerate and degrade potential inhibitors in biomass hydrolysates and non-traditional carbon streams (including furfural, 5-HMF, vanillin, syringaldehyde, vanillic acid, levulinic acid, and acetic acid) [ 8 , 9 ], making it a prime candidate for Acetyl-CoA (AcCoA)-derived bioproducts such as lipids and terpenes.…”