Lipid and carotenoid production by the Rhodosporidium toruloides mutant in cane molasses

Research progress on carotenoid production by Rhodosporidium toruloides

Carotenoids are natural lipophilic pigments, which have been proven to provide significant health benefits to humans, relying on their capacity to efficiently scavenge singlet oxygen and peroxyl radicals as antioxidants. Strains belonging to the genus Rhodosporidium represent a heterogeneous group known for a number of phenotypic traits including accumulation of carotenoids and lipids and tolerance to heavy metals and oxidative stress. As a representative of these yeasts, Rhodosporidium toruloides naturally produces carotenoids with high antioxidant activity and grows on a wide variety of carbon sources. As a result, R. toruloides is a promising host for the efficient production of more value-added lipophilic compound carotenoids, e.g., torulene and torularhodin. This review provides a comprehensive summary of the research progress on carotenoid biosynthesis in R. toruloides, focusing on the understanding of biosynthetic pathways and the regulation of key enzymes and genes involved in the process. Moreover, the relationship between the accumulation of carotenoids and lipid biosynthesis, as well as the stress from diverse abiotic factors, has also been discussed for the first time. Finally, several feasible strategies have been proposed to promote carotenoid production by R. toruloides. It is possible that R. toruloides may become a critical strain in the production of carotenoids or high-value terpenoids by genetic technologies and optimal fermentation processes. KEY POINTS: • Biosynthetic pathway and its regulation of carotenoids in Rhodosporidium toruloides were concluded • Stimulation of abiotic factors for carotenoid biosynthesis in R. toruloides was summarized • Feasible strategies for increasing carotenoid production by R. toruloides were proposed.

Chitosan-coated manganese ferrite nanoparticles enhanced Rhodotorula toruloides carotenoid production

The present study aims to analyze the interaction between Rhodotorula toruloides and magnetic nanoparticles and evaluate their effect on carotenoid production. The manganese ferrite nanoparticles were synthesized without chitosan (MnFe2O4) and chitosan coating (MnFe2O4-CS) by the co-precipitation method assisted by hydrothermal treatment. XRD (X-ray diffraction), Magnetometry, Dynamic Light Scattering (DLS) and FTIR (Fourier-Transform Infrared Spectroscopy), are used to characterize the magnetic nanoparticles. The crystallite size of MnFe2O4 was 16 nm for MnFe2O4 and 20 nm for MnFe2O4-CS. The magnetic saturation of MnFe2O4-CS was lower (39.6 ± 0.6 emu/g) than the same MnFe2O4 nanoparticles (42.7 ± 0.3 emu/g), which was attributed to the chitosan fraction presence. The MnFe2O4-CS FTIR spectra revealed the presence of the characteristic chitosan bands. DLS demonstrated that the average hydrodynamic diameters were 344 nm for MnFe2O4 and 167 nm for MnFe2O4-CS. A kinetic study of cell immobilization performed with their precipitation with a magnet demonstrated that interaction between magnetic nanoparticles and R. toruloides was characterized by an equilibrium time of 2 h. The adsorption isotherm models (Langmuir and Freundlich) were fitted to the experimental values. The trypan blue assay was used for cell viability assessment. The carotenoid production increased to 256.2 ± 6.1 µg/g dry mass at 2.0 mg/mL MnFe2O4-CS. The use of MnFe2O4-CS to stimulate carotenoid yeast production and the magnetic separation of biomass are promising nanobiotechnological alternatives. Magnetic cell immobilization is a perspective technique for obtaining cell metabolites.

The Plasma Membrane H+-ATPase Promoter Driving the Expression of FADX Enables Highly Efficient Production of Punicic Acid in Rhodotorula toruloides Cultivated on Glucose and Crude Glycerol

Punicic acid (PuA) is a conjugated fatty acid with a wide range of nutraceutical properties naturally present in pomegranate seed oil. To meet the rising demand for pomegranate seed oil, a single-cell oil enriched in PuA provides a sustainable biomass-derived alternative. This study describes the production of a PuA-enriched single-cell oil through the engineering of the red yeast Rhodotorula toruloides grown in glucose and a low-cost substrate, crude glycerol. The gene for Punica granatum fatty acid conjugase, PgFADX, was randomly integrated into the genome of R. toruloides without disrupting the carotenoid synthesis. In shake flask studies, the effects of three promoters (PPGI1, PNAR1, and PPMA1) on PuA production were evaluated. PuA titers of 105.77 mg/L and 72.81 mg/L were obtained from engineered cells expressing PgFADX from the PPMA1 promoter cultivated for 72 h in glucose and for 168 h in crude glycerol, respectively. Furthermore, the detailed lipid analysis revealed a high enrichment PuA in the triacylglycerol lipid structures, even without substantial modifications to the metabolic pathways. This report demonstrates the high potential of R. toruloides in the upcycling of a low-cost substrate, crude glycerol, into a value-added product such as PuA. The findings support the feasibility of using engineered R. toruloides for sustainable production of PuA-enriched single-cell oil.

Microbes' role in environmental pollution and remediation: a bioeconomy focus approach

Bioremediation stands as a promising solution amid the escalating challenges posed by environmental pollution. Over the past 25 years, the influx of synthetic chemicals and hazardous contaminants into ecosystems has required innovative approaches for mitigation and restoration. The resilience of these compounds stems from their non-natural existence, distressing both human and environmental health. Microbes take center stage in this scenario, demonstrating their ability of biodegradation to catalyze environmental remediation. Currently, the scientific community supports a straight connection between biorefinery and bioremediation concepts to encourage circular bio/economy practices. This review aimed to give a pre-overview of the state of the art regarding the main microorganisms employed in bioremediation processes and the different bioremediation approaches applied. Moreover, focus has been given to the implementation of bioremediation as a novel approach to agro-industrial waste management, highlighting how it is possible to reduce environmental pollution while still obtaining value-added products with commercial value, meeting the goals of a circular bioeconomy. The main drawbacks and challenges regarding the feasibility of bioremediation were also reported.

Biotechnological approaches for producing natural pigments in yeasts

Pigments are widely used in the food, cosmetic, textile, pharmaceutical, and materials industries. Demand for natural pigments has been increasing due to concerns regarding potential health problems and environmental pollution from synthetic pigments. Microbial production of natural pigments is a promising alternative to chemical synthesis or extraction from natural sources. Here, we discuss yeasts as promising chassis for producing natural pigments with their advantageous traits such as genetic amenability, safety, rapid growth, metabolic diversity, and tolerance. Metabolic engineering strategies and optimizing strategies in downstream process to enhance production of natural pigments are thoroughly reviewed. We discuss the challenges, including expanding the range of natural pigments and improving their feasibility of industrial scale-up, as well as the potential strategies for future development.

β-Carotene production from sugarcane molasses by a newly isolated Rhodotorula toruloides L/24-26-1

Production of carotenoids by yeast fermentation is an advantaged technology due to its easy scaling and safety. Nevertheless, carotenoid production needs an economic culture medium and other efficient yeast stains. The study aims to isolate and identify a yeast strain capable of producing carotenoids using a cost-effective substrate. A new strain was identified as Rhodotorula toruloides L/24-26-1, which can produce carotenoids at different pretreated and unpretreated sugarcane molasses concentrations (40 and 80 g/L). The highest biomass concentration (18.6 ± 0.6 g/L) was reached in the culture using 80 g/L of hydrolyzed molasses. On the other hand, the carotenoid accumulation reached the maximum value using pretreated molasses at 40 g/L (715.4 ± 15.1 µg/g d.w). In this case, the β-carotene was 1.5 times higher than that on the control medium. The yeast growth in molasses was not correlated with carotenoid production. The most outstanding production of The DPPH, ABTS, and FRAP tests demonstrated the antioxidant activity of the obtained carotenogenic extracts. This research demonstrated the R. toruloides L/24-26-1 strain biotechnological potential for carotenoid compounds. The yeast produces carotenoids with antioxidant activity in an inexpensive medium, such as sulfuric acid pretreated and unpretreated molasses.

Strategies for the efficient biosynthesis of β-carotene through microbial fermentation

β-Carotene is an orange fat-soluble compound, which has been widely used in fields such as food, medicine and cosmetics owing to its anticancer, antioxidant and cardiovascular disease prevention properties. Currently, natural β-carotene is mainly extracted from plants and algae, which cannot meet the growing market demand, while chemical synthesis of β-carotene cannot satisfy the pursuit for natural products of consumers. The β-carotene production through microbial fermentation has become a promising alternative owing to its high efficiency and environmental friendliness. With the rapid development of synthetic biology and in-depth study on the synthesis pathway of β-carotene, microbial fermentation has shown promising applications in the β-carotene synthesis. Accordingly, this review aims to summarize the research progress and strategies of natural carotenoid producing strain and metabolic engineering strategies in the heterologous synthesis of β-carotene by engineered microorganisms. Moreover, it also summarizes the adoption of inexpensive carbon sources to synthesize β-carotene as well as proposes new strategies that can further improve the β-carotene production.

Cost-effective production of ergothioneine using Rhodotorula mucilaginosa DL-X01 from molasses and fish bone meal enzymatic hydrolysate

Ergothioneine (EGT) is a high-value natural antioxidant that cannot be synthesized by the human body. This study showed that Rhodotorula mucilaginosa DL-X01 can use untreated molasses and fish bone meal enzymatic hydrolysate as the substrates to synthesize EGT. By optimizing the growth conditions, the EGT yield reached 29.39 mg/L when molasses and fish bone meal (FBM) were added at 60 g/L and 400 g/L respectively. Finally, the EGT yield was increased to 216.25 mg/L by fed-batch fermentation in a 5 L bioreactor. Compared with the fermentation by yeast extract peptone dextrose medium, the feedstock cost of EGT production was reduced by 330.91 % by using molasses and FBM as substrates. These results showed that R. mucilaginosa DL-X01 can produce high-value EGT using two cheap processing by-products, molasses and FBM, which is of great significance for environmental protection and sustainable development.

Generative Artificial Intelligence GPT-4 Accelerates Knowledge Mining and Machine Learning for Synthetic Biology

Knowledge mining from synthetic biology journal articles for machine learning (ML) applications is a labor-intensive process. The development of natural language processing (NLP) tools, such as GPT-4, can accelerate the extraction of published information related to microbial performance under complex strain engineering and bioreactor conditions. As a proof of concept, we proposed prompt engineering for a GPT-4 workflow pipeline to extract knowledge from 176 publications on two oleaginous yeasts (Yarrowia lipolytica and Rhodosporidium toruloides). After human intervention, the pipeline obtained a total of 2037 data instances. The structured data sets and feature selections enabled ML approaches (e.g., a random forest model) to predict Yarrowia fermentation titers with decent accuracy (R2 of 0.86 for unseen test data). Via transfer learning, the trained model could assess the production potential of the engineered nonconventional yeast, R. toruloides, for which there are fewer published reports. This work demonstrated the potential of generative artificial intelligence to streamline information extraction from research articles, thereby facilitating fermentation predictions and biomanufacturing development.

Lignocellulosic biorefineries as a platform for the production of high-value yeast derived pigments - A review

Lignocellulosic byproducts, mainly generated by the agro-industrial sector, have great potential as cost-effective feedstocks for bioprocesses because of their abundant availability and high content of sugar-rich and nutrient-rich elements. This biomass can be employed as a carbon source to produce various molecules using several microorganisms. Yeast strains have shown their capability to metabolize diverse C5 and C6 carbon sources, thereby facilitating their use in the bioprocessing of lignocellulosic biomass. Furthermore, yeasts can produce a wide range of valuable products, including biofuels, enzymes, proteins, and pigments, making them attractive for use in integrated biorefineries. Yeast-derived pigments have versatile applications and are environmentally friendly alternatives to their synthetic counterparts. This review emphasizes the potential of lignocellulosic biomass as a feedstock for producing yeast-derived products with a focus on pigments as valuable molecules. It also proposes a yeast-derived pigment platform utilizing lignocellulosic byproducts and explores its potential integration in biorefineries.

Expanding the genetic toolbox of Rhodotorula toruloides by identification and validation of six novel promoters induced or repressed under nitrogen starvation

BACKGROUND

The non-conventional yeast Rhodotorula toruloides is an emerging host organism in biotechnology by merit of its natural capacity to accumulate high levels of carotenoids and intracellular storage lipids from a variety of carbon sources. While the number of genetic engineering strategies that employ R. toruloides is increasing, the lack of genetic tools available for modification of this yeast is still limiting strain development. For instance, several strong, constitutive R. toruloides promoters have been characterized, but to date, only five inducible promoters have been identified. Although nitrogen-limited cultivation conditions are commonly used to induce lipid accumulation in this yeast, no promoters regulated by nitrogen starvation have been described for R. toruloides.

RESULTS

In this study, we used a combination of genomics and transcriptomics methods to identify novel R. toruloides promoter sequences that are either inducible or repressible by nitrogen starvation. RNA sequencing was used to assess gene expression in the recently isolated strain R. toruloides BOT-A2 during exponential growth and during nitrogen starvation, when cultivated with either glucose or xylose as the carbon source. The genome of BOT-A2 was sequenced using a combination of long- and short-read sequencing and annotated with support of the RNAseq data. Differential expression analysis was used to identify genes with a |log2 fold change|≥ 2 when comparing their expression during nitrogen depletion to that during exponential growth. The promoter regions from 16 of these genes were evaluated for their ability to drive the expression of a fluorescent reporter gene. Three promoters that were clearly upregulated under nitrogen starvation and three that were downregulated were selected and further characterized. One promoter, derived from gene RTBOTA2_003877, was found to function like an on-off switch, as it was only upregulated under full nitrogen depletion and downregulated in the presence of the nitrogen source.

CONCLUSIONS

Six new R. toruloides promoters that were either upregulated or downregulated under nitrogen-starvation were identified. These substantially contribute to the available promoters when engineering this organism and are foreseen to be particularly useful for future engineering strategies requiring specific regulation of target genes in accordance with nitrogen availability.

Diversity investigation of cultivable yeasts associated with honeycombs and identification of a novel Rhodotorula toruloides strain with the robust concomitant production of lipid and carotenoid

Oleaginous yeasts-derived microbial lipids provide a promising alternative feedstock for the biodiesel industry. However, hyperosmotic stress caused by high sugar concentration during fermentation significantly prevents high cell density and productivity. Isolation of new robust osmophilic oleaginous species from specific environment possibly resolves this issue to some extent. In this study, the cultivable yeast composition of honeycombs was investigated. Totally, 11 species of honeycomb-associated cultivable yeast were identified and characterized. Among them, an osmophilic yeast strain, designated as Rhodotorula toruloides C23 was featured with excellent lipogenic and carotenogenic capacity and remarkable cell growth using glucose, xylose or glycerol as feedstock, with simultaneous production of 24.41 g/L of lipids and 15.50 mg/L of carotenoids from 120 g/L glucose in 6.7-L fermentation. Comparative transcriptomic analysis showed that C23 had evolved a dedicated molecular regulation mechanism to maintain their high simultaneous accumulation of intracellular lipids and carotenoids and cell growth under high sugar concentration.

Development and Perspective of Rhodotorula toruloides as an Efficient Cell Factory

Rhodotorula toruloides is receiving significant attention as a novel cell factory because of its high production of lipids and carotenoids, fast growth and high cell density, as well as the ability to utilize a wide variety of substrates. These attractive traits of R. toruloides make it possible to become a low-cost producer that can be engineered for the production of various fuels and chemicals. However, the lack of understanding and genetic engineering tools impedes its metabolic engineering applications. A number of research efforts have been devoted to filling these gaps. This review focuses on recent developments in genetic engineering tools, advances in systems biology for improved understandings, and emerging engineered strains for metabolic engineering applications. Finally, future trends and barriers in developing R. toruloides as a cell factory are also discussed.

Bioconversion of cellulose into bisabolene using Ruminococcus flavefaciens and Rhodosporidium toruloides

In this study, organic acids were demonstrated as a promising carbon source for bisabolene production by the non-conventional yeast, Rhodosporidium toruloides, at microscale with a maximum titre of 1055 ± 7 mg/L. A 125-fold scale-up of the optimal process, enhanced bisabolene titres 2.5-fold to 2606 mg/L. Implementation of a pH controlled organic acid feeding strategy at this scale lead to a further threefold improvement in bisabolene titre to 7758 mg/L, the highest reported microbial titre. Finally, a proof-of-concept sequential bioreactor approach was investigated. Firstly, the cellulolytic bacterium Ruminococcus flavefaciens was employed to ferment cellulose, yielding 4.2 g/L of organic acids. R. toruloides was subsequently cultivated in the resulting supernatant, producing 318 ± 22 mg/L of bisabolene. This highlights the feasibility of a sequential bioprocess for the bioconversion of cellulose, into biojet fuel candidates. Future work will focus on enhancing organic acid yields and the use of real lignocellulosic feedstocks to further enhance bisabolene production.

Sustainable Food Systems: The Case of Functional Compounds towards the Development of Clean Label Food Products

The addition of natural components with functional properties in novel food formulations confers one of the main challenges that the modern food industry is called to face. New EU directives and the global turn to circular economy models are also pressing the agro-industrial sector to adopt cradle-to-cradle approaches for their by-products and waste streams. This review aims to present the concept of “sustainable functional compounds”, emphasizing on some main bioactive compounds that could be recovered or biotechnologically produced from renewable resources. Herein, and in view of their efficient and “greener” production and extraction, emerging technologies, together with their possible advantages or drawbacks, are presented and discussed. Μodern examples of novel, clean label food products that are composed of sustainable functional compounds are summarized. Finally, some action plans towards the establishment of sustainable food systems are suggested.

Enhanced biodiesel and β-carotene production in Rhodotorula pacifica INDKK using sugarcane bagasse and molasses by an integrated biorefinery framework

Dependency on fossil fuels raises an economic and ecological concern that has urged to look for alternative sources of energy. Bio-refinery concept is one of the alternate frameworks for the biomass conversion into biofuel and other value-added by-products. The present work illustrates importance of an oleaginous yeast Rhodotorula pacifica INDKK in an integrated bio-refinery field by utilizing renewable sugars generated from lignocellulosic biomass. The maximum 11.8 g/L lipid titer, 210.4 mg/L β-carotene and 7.1 g animal feed were produced by R. pacifica INDKK in bioreactor containing 5% (v/v) molasses supplemented with enzymatically hydrolyzed and alkali-pretreated sugarcane bagasse hydrolysate (35% v/v). Furthermore, xylooligosaccharides (20.6 g/L), a beneficial prebiotics were also produced from the hemicellulosic fraction separated after alkali pretreatment of bagasse. This novel concept of integrated yeast bio-refinery for concomitant production of biodiesel and multiple value-added products with minimum waste generation is proposed as a sustainable and profitable process.

Harnessing cross-resistance - Sustainable nisin production from low-value food side streams using a Lactococcus lactis mutant with higher nisin-resistance obtained after prolonged chlorhexidine exposure

Nisin has a tendency to associate with the cell wall of the producing strain, which inhibits growth and lowers the ceiling for nisin production. With the premise that resistance to the cationic chlorhexidine could reduce nisin binding, variants with higher tolerance to this compound were isolated. One of the resistant isolates, AT0606, had doubled its resistance to nisin, and produced three times more free nisin, when cultured in shake flasks. Characterization revealed that AT0606 had an overall less negatively charged and thicker cell wall, and these changes appeared to be linked to a defect high-affinity phosphate uptake system, and a mutation inactivating the oleate hydratase. Subsequently, the potential of using AT0606 for cost efficient production of nisin was explored, and it was possible to attain a high titer of 13181 IU/mL using a fermentation substrate based on molasses and a by-product from whey protein hydrolysate production.

Titanium dioxide-mediated fatty acids promoted carotenoid synthesis in Phaffia rhodozyma PR106 analyzed whole genome

Carotenoid, as good colorant and antioxidant, is widely used in the fields of food, medicine and feed. The whole genome of P. rhodozyma PR106 strain with 228.77 mg/L carotenoid (mainly included astaxanthin, β-carotene and lycopene) yield was sequenced, and the genome size was 16.18 Mb, the GC content was 47%. The genetic evolution analysis indicated that PR106 greatly changed in evolution process, and closely related to P. rhodozyma CBS7918. Under 500 mg/L titanium dioxide (TiO₂) stress, carotenoid yield of PR106 was 2.15 times that of the control for 48 h, and was 305.12 mg/L in PR106 to 72 h, interestingly, the yield of oleate, linoleate and α-linolenate also increased significantly among 51 fatty acids by targeted metabolomics analysis. TiO₂ promoted carotenoid synthesis of PR106 by forming astaxanthin esters to reduce the feedback inhibition of carotenoid synthesis. These results provided a theoretical basis for carotenoid production and development using P. rhodozyma.

Rhodotorula toruloides: an ideal microbial cell factory to produce oleochemicals, carotenoids, and other products

Requirement of clean energy sources urges us to find substitutes for fossil fuels. Microorganisms provide an option to produce feedstock for biofuel production by utilizing inexpensive, renewable biomass. Rhodotorula toruloides (Rhodosporidium toruloides), a non-conventional oleaginous yeast, can accumulate intracellular lipids (single cell oil, SCO) more than 70% of its cell dry weight. At present, the SCO-based biodiesel is not a price-competitive fuel to the petroleum diesel. Many efforts are made to cut the cost of SCO by strengthening the performance of genetically modified R. toruloides strains and by valorization of low-cost biomass, including crude glycerol, lignocellulosic hydrolysates, food and agro waste, wastewater, and volatile fatty acids. Besides, optimization of fermentation and SCO recovery processes are carefully studied as well. Recently, new R. toruloides strains are developed via metabolic engineering and synthetic biology methods to produce value-added chemicals, such as sesquiterpenes, fatty acid esters, fatty alcohols, carotenoids, and building block chemicals. This review summarizes recent advances in the main aspects of R. toruloides studies, namely, construction of strains with new traits, valorization of low-cost biomass, process detection and optimization, and product recovery. In general, R. toruloides is a promising microbial cell factory for production of biochemicals.

Carotenoids from fungi and microalgae: A review on their recent production, extraction, and developments

The demand for carotenoids from natural sources obtained by biological extraction methods is increasing with the development of biotechnology and the continued awareness of food safety. Natural plant-derived carotenoids have a relatively high production cost and are affected by the season, while microbial-derived carotenoids are favored due to their natural, high-efficiency, low production cost, and ease of industrialization. This article reviewed the following aspects of natural carotenoids derived from microorganisms: (1) the structures and properties of main carotenoids; (2) fungal and microalgal sources of the main carotenoids; (3) influencing factors and modes of improvement for carotenoids production; (4) efficient extraction methods for carotenoids; and (5) the commercial value of carotenoids. This review provided a reference and guidance for the development of natural carotenoids derived from microorganisms.