Proteomic analyses of the oleaginous and carotenogenic yeast Rhodotorula diobovata across growth phases under nitrogen- and oxygen-limited conditions

Rhodotorula sp. as a promising host for microbial cell factories

Rhodotorula sp. is a red yeast that has emerged as a promising host for microbial cell factories. Under specific conditions, Rhodotorula sp. can accumulate lipids that constitute over 70% of its dry cell weight, underscoring its potential in lipid compound production. Additionally, it can utilize a variety of carbon sources, including glucose, xylose, and volatile fatty acids, and exhibits high tolerance to low-cost carbon sources and industrial by-products, showcasing its excellent performance in industrial processes. Furthermore, the native mevalonate pathway of Rhodotorula sp. enables its efficient synthesis of antioxidant carotenoids and other terpenoids, which are widely applied in the food, pharmaceutical, and cosmetic industries. Due to its excellent accumulation ability of lipophilic compounds, metabolic diversity, and environmental adaptability, this review summarizes recent advances in genetic elements and metabolic engineering technologies for Rhodotorula sp., emphasizing its potential as a chassis cell factory for the production of lipids, carotenoids, and other chemicals. It also highlights key factors influencing commercial fermentation processes and concludes with challenges and solutions for further developing Rhodotorula sp. as microbial chassis.

Sustainable lipid production by oleaginous yeasts: Current outlook and challenges

Yeast lipid has gained prominence as a sustainable energy source and so various oleaginous yeasts are being investigated to create efficient lipogenic platforms. This review aims to assess the various biotechnological strategies for enhanced production of yeast lipids via agro-waste processing and media engineering including multiomic analyses, genetic engineering, random mutagenesis, and laboratory adaptive evolution. The review also emphasizes the role of cutting-edge omics technologies in pinpointing differentially expressed genes and enriched networks crucial for designing advanced metabolic engineering strategies for prominent oleaginous yeast species. The review addresses the challenges and future prospects of a viable lipid production industry that is possible through advancements in current technologies, strain improvement, media optimization and techno-economic and life cycle analyses at lab, pilot and industrial scales. This review comprehensively provides deep insights for enhancement of yeast lipid biosynthesis to reach industrially benchmarked standard of a lipid production platform.

Yeast Proteins: Proteomics, Extraction, Modification, Functional Characterization, and Structure: A Review

Proteins are essential for human tissues and organs, and they require adequate intake for normal physiological functions. With a growing global population, protein demand rises annually. Traditional animal and plant protein sources rely heavily on land and water, making it difficult to meet the increasing demand. The high protein content of yeast and the complete range of amino acids in yeast proteins make it a high-quality source of supplemental protein. Screening of high-protein yeast strains using proteomics is essential to increase the value of yeast protein resources and to promote the yeast protein industry. However, current yeast extraction methods are mainly alkaline solubilization and acid precipitation; therefore, it is necessary to develop more efficient and environmentally friendly techniques. In addition, the functional properties of yeast proteins limit their application in the food industry. To improve these properties, methods must be selected to modify the secondary and tertiary structures of yeast proteins. This paper explores how proteomic analysis can be used to identify nutrient-rich yeast strains, compares the process of preparing yeast proteins, and investigates how modification methods affect the function and structure of yeast proteins. It provides a theoretical basis for solving the problem of inadequate protein intake in China and explores future prospects.

Diversity of Red Yeasts in Various Regions and Environments of Poland and Biotechnological Potential of the Isolated Strains

Due to the growing demand for natural carotenoids, researchers have been searching for strains that are capable of efficient synthesis of these compounds. This study tested 114 red yeast strains collected from various natural environments and food specimens in Poland. The strains were isolated by their ability to produce red or yellow pigments in rich nutrient media. According to potential industrial significance of the carotenoids, both their total production and share of individual carotenoids (β-carotene, γ-carotene, torulene, and torularhodin) were analyzed. The total content of carotenoid pigments in the yeast dry matter ranged from 13.88 to 406.50 µg/g, and the percentages of individual carotenoids highly varied among the strains. Most of the yeast isolates synthesized torulene at the highest amount. Among the studied strains, isolates with a total carotenoid content in biomass greater than 200 µg/g and those containing more than 60% torularhodin were selected for identification (48 strains). The identified strains belonged to six genera: Rhodotorula, Sporidiobolus, Sporobolomyces, Buckleyzyma, Cystofilobasidium, and Erythrobasidium. The largest number of isolates belonged to Rhodotorula babjevae (18), Rhodotorula mucilaginosa (7), Sporidiobolus pararoseus (4), and Rhodotorula glutinis (4).

Carotenoids production by Rhodosporidium paludigenum yeasts: Characterization of chemical composition, antioxidant and antimicrobial properties

The high market potential imposed by natural carotenoids has turned the scientific interest in search for new strains, capable of synthesizing a wide spectrum of these pigments. In this study, Rhodosporidium paludigenum NCYC 2663 and 2664 were investigated for carotenoids production and lipid accumulation utilizing different carbon sources (glucose, fructose, sucrose, mixture of glucose: galactose). Strain R. paludigenum 2663 produced the highest total carotenoids titer (2.21 mg/L) when cultivated on sucrose, together with 4 g/L lipids (30% w/w content) and 7 g/L exopolysaccharides. In the case of R. paludigenum 2664, glucose favored the production of 2.93 mg/L total carotenoids and 1.57 g/L lipids (31.8% w/w content). Analysis of the chemical profile during fermentation revealed that β-carotene was the prominent carotenoid. Strain 2663 co-produced γ-carotene, torulene and torularhodin in lower amounts, whereas 2664 synthesized almost exclusively β-carotene. The produced lipids from strain 2663 were rich in oleic acid, while the presence of linoleic acid was also detected in the lipoic fraction from strain 2664. The obtained carotenoid extracts exhibited antioxidant (IC50 0.14 mg/mL) and high antimicrobial activity, against common bacterial and fungal pathogenic strains. The results of this study are promising for the utilization of biotechnologically produced carotenoids in food applications.

Multi-omics analysis reveals the mechanism of torularhodin accumulation in the mutant Rhodosporidium toruloides A1-15 under nitrogen-limited conditions

A carotenoid production strain Rhodosporidium toruloides NP11 and its mutant strain R. toruloides A1-15 were studied under chemostat nitrogen-limited cultivation. Multi-omics analysis (metabolomics, lipidomics and transcriptomics) was used to investigate the different mechanisms of torularhodin accumulation between NP11 and A1-15. The results showed that the carotenoid synthesis pathway was significantly enhanced in A1-15 compared to NP11 under nitrogen limitation, due to the significant increase of torularhodin. Under nitrogen-limited conditions, higher levels of β-oxidation were present in A1-15 compared to those in NP11, which provided sufficient precursors for carotenoid synthesis. In addition, ROS stress accelerated the intracellular transport of iron ions, promoted the expression of CRTI and CRTY genes, and reduced the transcript levels of FNTB1 and FNTB2 in the bypass pathway, and these factors may be responsible for the regulation of high torularhodin production in A1-15. This study provided insights into the selective production of torularhodin.

Integrative analysis of genomic and metabolomic data reveals key metabolic pathways involved in lipid and carotenoid biosynthesis in oleaginous red yeast Rhodosporidiobolus odoratus XQR

Rhodosporidiobolus odoratus, one of the oleaginous red yeasts, is gaining biotechnological importance for their ability to produce microbial lipids and carotenoids. However, to date, the genomic resource underling lipid and carotenoid biosynthesis in R. odoratus has not been reported. Here, we reported the first genome assembly of R. odoratus using a combination of PacBio and Illumina techniques. The final genome assembly is 23.74 Mb in size, containing 52 scaffolds with a N50 length of 1200,460 bp and a GC content of 56.90%. Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment showed that our assembly contains 94.23% of Basidiomycota universal single-copy orthologs. The genome was predicted to contain 4986 protein-coding genes, 4967 of which were functionally annotated. Metabolomic profiling identified 574 lipids, 3 carotenoids, and 208 volatile organic compounds synthesized by R. odoratus. Integrative analysis of genomics and metabolomics provides insights into the biosynthesis of lipid, carotenoid, and other bioactive compounds in R. odoratus. Collectively, the results presented herein greatly enhance our understanding of R. odoratus in lipids and carotenoids biosynthesis, and thus further accelerate its fundamental molecular investigations and biotechnological applications.