Carotenoid Biosynthesis: Genome-Wide Profiling, Pathway Identification in Rhodotorula glutinis X-20, and High-Level Production

Abstract

Rhodotorula glutinis, as a member of the family Sporidiobolaceae, is of great value in the field of biotechnology. However, the evolutionary relationship of R. glutinis X-20 with Rhodosporidiobolus, Sporobolomyces, and Rhodotorula are not well understood, and its metabolic pathways such as carotenoid biosynthesis are not well resolved. Here, genome sequencing and comparative genome techniques were employed to improve the understanding of R. glutinis X-20. Phytoene desaturase (crtI) and 15-cis-phytoene synthase/lycopene beta-cyclase (crtYB), key enzymes in carotenoid pathway from R. glutinis X-20 were more efficiently expressed in S. cerevisiae INVSc1 than in S. cerevisiae CEN.PK2-1C. High yielding engineered strains were obtained by using synthetic biology technology constructing carotenoid pathway in S. cerevisiae and optimizing the precursor supply after fed-batch fermentation with palmitic acid supplementation. Genome sequencing analysis and metabolite identification has enhanced the understanding of evolutionary relationships and metabolic pathways in R. glutinis X-20, while heterologous construction of carotenoid pathway has facilitated its industrial application.

Comparative Genomic Analysis of the Mutant Rhodotorula mucilaginosa JH-R23 Provides Insight into the High-Yield Carotenoid Mechanism

“…In addition, the genome contained numerous genes and gene clusters encoding carotenoid biosynthetic enzymes, such as lycopene cyclase/phytoene synthase (CrtYB), carotenoid oxygenase (CCD1), phytoene desaturase (CrtI), and geranylgeranyl pyrophosphate synthase (CrtE) (Figure 3A). These enzymes collaboratively catalyze the conversion of GGPP into various carotenoids, including lycopene, β-carotene, and torulene [55,56]. S5.…”

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.…”

“…Recently, whole-genome sequencing from R. glutinis strain ZHK was studied as part of a multi-omics approach (Li et al, 2020). Other studies that have published genomic analyses from R. glutinis, and similarly used a combination of short-and long-read sequencing data are (Bo et al, 2022) and paper II. The average GC content and size in the three R. glutinis strains are 67.8% and 22.6 Mbp, respectively.…”

“…However, the studied strains may also not contain some of the missing BUSCO genes or had no significant matches with the selected BUSCO "fungi" profile, independently of the assembly completeness level (paper II). Some other hybrid approaches which reached high numbers of complete BUSCO in high-quality genome assemblies are those from R. glutinis strains ZHK and X-20 with values of 94.4% (Li et al, 2020) and 97.0% (Bo et al, 2022), respectively.…”

“…The number of annotated protein-coding genes in Rhodotorula spp. ranges from 5,625 to 9,464 (7,518 average), strongly impacted by the quality of annotation approaches and reference genomes (Table 1) (Bo et al, 2022;Deligios et al, 2015;Fakankun et al, 2021;Firrincieli et al, 2015;Gan et al, 2017;Li et al, 2020;Morin et al, 2014;Tran et al, 2019; paper I; paper II). The average gene size among available annotated genomes is 2.1 kb (Table 2).…”