Engineering Yarrowia lipolytica to produce advanced biofuels: Current status and perspectives

Transcriptomic profiling of an evolved Yarrowia lipolytica strain: tackling hexanoic acid fermentation to increase lipid production from short-chain fatty acids

BACKGROUND

Short-chain fatty acids (SCFAs) are cost-effective carbon sources for an affordable production of lipids. Hexanoic acid, the acid with the longest carbon chain in the SCFAs pool, is produced in anaerobic fermentation of organic residues and its use is very challenging, even inhibiting oleaginous yeasts growth.

RESULTS

In this investigation, an adaptive laboratory evolution (ALE) was performed to improve Yarrowia lipolytica ACA DC 50109 tolerance to high hexanoic acid concentrations. Following ALE, the transcriptomic analysis revealed several genetic adaptations that improved the assimilation of this carbon source in the evolved strain compared to the wild type (WT). Indeed, the evolved strain presented a high expression of the up-regulated gene YALI0 E16016g, which codes for FAT1 and is related to lipid droplets formation and responsible for mobilizing long-chain acids within the cell. Strikingly, acetic acid and other carbohydrate transporters were over-expressed in the WT strain.

CONCLUSIONS

A more tolerant yeast strain able to attain higher lipid content under the presence of high concentrations of hexanoic acid has been obtained. Results provided novel information regarding the assimilation of hexanoic acid in yeasts.

Biosynthesis Progress of High-Energy-Density Liquid Fuels Derived from Terpenes

High-energy-density liquid fuels (HED fuels) are essential for volume-limited aerospace vehicles and could serve as energetic additives for conventional fuels. Terpene-derived HED biofuel is an important research field for green fuel synthesis. The direct extraction of terpenes from natural plants is environmentally unfriendly and costly. Designing efficient synthetic pathways in microorganisms to achieve high yields of terpenes shows great potential for the application of terpene-derived fuels. This review provides an overview of the current research progress of terpene-derived HED fuels, surveying terpene fuel properties and the current status of biosynthesis. Additionally, we systematically summarize the engineering strategies for biosynthesizing terpenes, including mining and engineering terpene synthases, optimizing metabolic pathways and cell-level optimization, such as the subcellular localization of terpene synthesis and adaptive evolution. This article will be helpful in providing insight into better developing terpene-derived HED fuels.

The Efficacy of Encapsulated Phytase Based on Recombinant Yarrowia lipolytica on Quails' Zootechnic Features and Phosphorus Assimilation

In this study, we used the Manchurian golden breed of quails. We assessed the efficacy of the food additives of the phytase from Obesumbacterium proteus encapsulated in the recombinant Yarrowia lipolytica yeast, which was supplied at a concentration of 500 phytase activity units per kg of the feed. One hundred fifty one-day-old quails were distributed into six treatment groups. The results showed that adding the O. proteus encapsulated phytase to the quails' diets improved live weight, body weight gain, and feed conversion compared to those in the control groups and the groups using a commercial phytase from Aspergillus ficuum. The results obtained during the experiments indicate a high degree of assimilation of phytate-containing feeds if the encapsulated phytase was fed by the quails compared to that in the other groups. We can conclude that the class D encapsulated phytase is an expedient additive to the diets possessing better kinetic features compared to the PhyA and PhyC classes phytases when it acts inside the quail's chyme.

Building Yarrowia lipolytica Cell Factories for Advanced Biomanufacturing: Challenges and Solutions

Microbial cell factories have shown great potential for industrial production with the benefit of being environmentally friendly and sustainable. Yarrowia lipolytica is a promising and superior non-model host for biomanufacturing due to its cumulated advantages compared to model microorganisms, such as high fluxes of metabolic precursors (acetyl-CoA and malonyl-CoA) and its naturally hydrophobic microenvironment. However, although diverse compounds have been synthesized in Y. lipolytica cell factories, most of the relevant studies have not reached the level of industrialization and commercialization due to a number of remaining challenges, including unbalanced metabolic flux, conflict between cell growth and product synthesis, and cytotoxic effects. Here, various metabolic engineering strategies for solving the challenges are summarized, which is developing fast and extremely conducive to rational design and reconstruction of robust Y. lipolytica cell factories for advanced biomanufacturing. Finally, future engineering efforts for enhancing the production efficiency of this platform strain are highlighted.

Universal and unique strategies for the production of polyunsaturated fatty acids in industrial oleaginous microorganisms

Polyunsaturated fatty acids (PUFAs), especially docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA) and arachidonic acid (ARA), are beneficial for reducing blood cholesterol and enhancing memory. Traditional PUFA production relies on extraction from plants and animals, which is unsustainable. Thus, using microorganisms as lipid-producing factories holds promise as an alternative way for PUFA production. Several oleaginous microorganisms have been successfully industrialized to date. These can be divided into universal and specialized hosts according to the products range of biosynthesis. The Yarrowia lipolytica is universal oleaginous host that has been engineered to produce a variety of fatty acids, such as γ-linolenic acid (GLA), EPA, ARA and so on. By contrast, the specialized host are used to produce only certain fatty acids, such as ARA in Mortierella alpina, EPA in Nannochloropsis, and DHA in Thraustochytrids. The metabolic engineering and fermentation strategies for improving PUFA production in universal and specialized hosts are different, which is the subject of this review. In addition, the widely applicable strategies for microbial lipid production that are not specific to individual hosts were also reviewed.

Biodiesel production and properties estimation from food waste and domestic wastewater by Rhodosporidium toruloides

Producing biodiesel from food waste (FW) would benefit both environment and economy. Current study investigated biodiesel production from food waste and domestic wastewater by utilizing the oleaginous yeast Rhodosporidium toruloides under non-sterile condition. The potential of biolipid production from the mixture of effluents of existing local FW treatment facilities and domestic wastewater was firstly evaluated. Then, to increase the nutrient recovery efficiency, FW hydrolysis process by crude enzymes produced from solid FWs by Aspergillus oryzae was introduced and the conditions were further optimized. The optimized hydrolysis process resulted in reducing sugar (RS) yield of 251.81 ± 8.09 mg gdryFW-1 and free amino nitrogen (FAN) yield of 7.70 ± 0.74 mg gdryFW-1 while waste oil with the RS yield of 93.54 ± 0.01 mg gdryFW-1 was easily separated without solvent usage. Compared to the hydrolysate only used, when mixed with domestic wastewater, the results showed obvious enhancement on biomass yield, biolipid yield, and wastewater treatment efficiency. The maximum biolipid yield was 29.80 ± 0.50 mg gdryFW-1 and the estimated quality of biodiesel produced from the biolipid met both EN 14214 and ASTM D6751 standards.

Engineering the Metabolic Landscape of Microorganisms for Lignocellulosic Conversion

Bacteria and yeast are being intensively used to produce biofuels and high-added-value products by using plant biomass derivatives as substrates. The number of microorganisms available for industrial processes is increasing thanks to biotechnological improvements to enhance their productivity and yield through microbial metabolic engineering and laboratory evolution. This is allowing the traditional industrial processes for biofuel production, which included multiple steps, to be improved through the consolidation of single-step processes, reducing the time of the global process, and increasing the yield and operational conditions in terms of the desired products. Engineered microorganisms are now capable of using feedstocks that they were unable to process before their modification, opening broader possibilities for establishing new markets in places where biomass is available. This review discusses metabolic engineering approaches that have been used to improve the microbial processing of biomass to convert the plant feedstock into fuels. Metabolically engineered microorganisms (MEMs) such as bacteria, yeasts, and microalgae are described, highlighting their performance and the biotechnological tools that were used to modify them. Finally, some examples of patents related to the MEMs are mentioned in order to contextualize their current industrial use.

Combining orthogonal plant and non-plant fatty acid biosynthesis pathways for efficient production of microbial oil enriched in nervonic acid in Yarrowia lipolytica

Nervonic acid has proven efficacy in brain development and the prevention of neurodegenerative diseases. Here, an alternative and sustainable strategy for nervonic acid-enriched plant oil production was established. Different β-ketoacyl-CoA synthases and heterologous Δ15 desaturase were co-expressed, combined with the deletion of the β-oxidation pathway to construct orthogonal plant and non-plant nervonic acid biosynthesis pathways in Yarrowia lipolytica. A "block-pull-restrain" strategy was further applied to improve the supply of stearic acid as the precursor of the non-plant pathway. Then, lysophosphatidic acid acyltransferase from Malania oleifera (MoLpaat) was identified, which showed specificity for nervonic acid. Endogenous LPAAT was exchanged by MoLPAAT resulted in 17.10 % nervonic acid accumulation. Finally, lipid metabolism was engineered and cofactor supply was increased to boost the lipid accumulation in a stable null-hyphal strain. The final strain produced 57.84 g/L oils with 23.44 % nervonic acid in fed-batch fermentation, which has the potential to substitute nervonic acid-enriched plant oil.

Reprogramming the fatty acid metabolism of Yarrowia lipolytica to produce the customized omega-6 polyunsaturated fatty acids

Omega-6 polyunsaturated fatty acids (ω6-PUFAs), such as γ-linolenic acid (GLA), dihomo-γ-linolenic acid (DGLA) and arachidonic acid (ARA), are indispensable nutrients for human health. Harnessing the lipogenesis pathway of Yarrowia lipolytica creates a potential platform for producing customized ω6-PUFAs. This study explored the optimal biosynthetic pathways for customized production of ω6-PUFAs in Y. lipolytica via either the Δ6 pathway from Mortierella alpina or the Δ8 pathway from Isochrysis galbana. Subsequently, the proportion of ω6-PUFAs in total fatty acids (TFAs) was effectively increased by bolstering the provision of precursors for fatty acid biosynthesis and carriers for fatty acid desaturation, as well as preventing fatty acid degradation. Finally, the proportions of GLA, DGLA and ARA synthesized by customized strains accounted for 22.58%, 46.65% and 11.30% of TFAs, and the corresponding titers reached 386.59, 832.00 and 191.76 mg/L in shake-flask fermentation, respectively. This work provides valuable insights into the production of functional ω6-PUFAs.

Insights into the Genomic and Phenotypic Landscape of the Oleaginous Yeast Yarrowia lipolytica

Although Yarrowia lipolytica is a model yeast for the study of lipid metabolism, its diversity is poorly known, as studies generally consider only a few standard laboratory strains. To extend our knowledge of this biotechnological workhorse, we investigated the genomic and phenotypic diversity of 56 natural isolates. Y. lipolytica is classified into five clades with no correlation between clade membership and geographic or ecological origin. A low genetic diversity (π = 0.0017) and a pan-genome (6528 genes) barely different from the core genome (6315 genes) suggest Y. lipolytica is a recently evolving species. Large segmental duplications were detected, totaling 892 genes. With three new LTR-retrotransposons of the Gypsy family (Tyl4, Tyl9, and Tyl10), the transposable element content of genomes appeared diversified but still low (from 0.36% to 3.62%). We quantified 34 traits with substantial phenotypic diversity, but genome-wide association studies failed to evidence any associations. Instead, we investigated known genes and found four mutational events leading to XPR2 protease inactivation. Regarding lipid metabolism, most high-impact mutations were found in family-belonging genes, such as ALK or LIP, and therefore had a low phenotypic impact, suggesting that the huge diversity of lipid synthesis and accumulation is multifactorial or due to complex regulations.

Can microbiology help to make aviation more sustainable?

Production of sustainable aviation fuels (SAFs) using microbes still requires huge research efforts to fulfill the needs of aviation, both in the biological utilization of raw materials as well as in the biological processes to convert these materials (oils, sugars, aromatic compounds and others) into SAFs. However, we should also be aware of the microbiology constraints that, in some cases, will not allow us to reach the commercial level and that, by creating false expectations we will harm the credibility of microbiologists. However, in our opinion microbiologists can and should continue to find new avenues for producing SAFs, and for evaluating the advantages and feasibility of their production. This last step will require a close collaboration between researchers and industry.

High-level de novo biosynthesis of cordycepin by systems metabolic engineering in Yarrowia lipolytica

Cordycepin is a nucleoside antibiotic with various biological activities, which has wide applications in the area of cosmetic and medicine industries. However, the current production of cordycepin is costly and time-consuming. To construct the promising cell factory for high-level cordycepin production, firstly, the design and construction of cordycepin biosynthetic pathway were performed in Yarrowia lipolytica. Secondly, the adaptivity between cordycepin biosynthetic pathway and Y. lipolytica was enhanced by enzyme fusion and integration site engineering. Then, the production of cordycepin was improved by the enhancement of adenosine supply. Furthermore, through modular engineering, the production of cordycepin was achieved at 3588.59 mg/L from glucose. Finally, 3249.58 mg/L cordycepin with a yield of 76.46 mg/g total sugar was produced by the engineered strain from the mixtures of glucose and molasses. This research is the first report on the de novo high-level production of cordycepin in the engineered Y. lipolytica.

Valorization of agro-food wastes: Ease of concomitant-enzymes production with application in food and biofuel industries

The novel and greener approach toward the co-production of hydrolytic enzymes in a single-cultivation medium with inexpensive substrates can bring down the production costs. Likewise, the natural and industrial organic biomass/solid are all nutritionally rich substrates waiting for free use in industries such as food, biofuel, etc. Valorization must broaden its applications in industries and households with a step towards a sustainable environment. The biofuel approach can be projected as one of the most promising deputations to meet future energy demands, in reduction of the environmental pollution due to excessive fossil fuel consumption. The present review highlights the multifaceted stature of microbial enzymes in this direction and possible implications mainly in the food industry and biofuel with the global impact of similar bio-based industries. In this review, design scale-up, fermentation cost, energy needs,and agro-food waste management have been meticulously delineated.

Recent advances in biofuel production through metabolic engineering

Rising global energy demands and climate crisis has created an unprecedented need for the bio-based circular economy to ensure sustainable development with the minimized carbon footprint. Along with conventional biofuels such as ethanol, microbes can be used to produce advanced biofuels which are equivalent to traditional fuels in their energy efficiencies and are compatible with already established infrastructure and hence can be directly blended in higher proportions without overhauling of the pre-existing setup. Metabolic engineering is at the frontiers to develop microbial chassis for biofuel bio-foundries to meet the industrial needs for clean energy. This review does a thorough inquiry of recent developments in metabolic engineering for increasing titers, rates, and yields (TRY) of biofuel production by engineered microorganisms.

Advancing Yarrowia lipolytica as a superior biomanufacturing platform by tuning gene expression using promoter engineering

Yarrowia lipolytica is recognized as an excellent non-conventional yeast in the field of biomanufacturing, where it is used as a host to produce oleochemicals, terpenes, organic acids, polyols and recombinant proteins. Consequently, metabolic engineering of this yeast is becoming increasingly popular to advance it as a superior biomanufacturing platform, of which promoters are the most basic elements for tuning gene expression. Endogenous promoters of Yarrowia lipolytica were reviewed, which are the basis for promoter engineering. The engineering strategies, such as hybrid promoter engineering, intron enhancement promoter engineering, and transcription factor-based inducible promoter engineering are described. Additionally, the applications of Yarrowia lipolytica promoter engineering to rationally reconstruct biosynthetic gene clusters and improve the genome-editing efficiency of the CRISPR-Cas systems were reviewed. Finally, research needs and future directions for promoter engineering are also discussed in this review.

Key Enzymes in Fatty Acid Synthesis Pathway for Bioactive Lipids Biosynthesis

Dietary bioactive lipids, one of the three primary nutrients, is not only essential for growth and provides nutrients and energy for life's activities but can also help to guard against disease, such as Alzheimer's and cardiovascular diseases, which further strengthen the immune system and maintain many body functions. Many microorganisms, such as yeast, algae, and marine fungi, have been widely developed for dietary bioactive lipids production. These biosynthetic processes were not limited by the climate and ground, which are also responsible for superiority of shorter periods and high conversion rate. However, the production process was also exposed to the challenges of low stability, concentration, and productivity, which was derived from the limited knowledge about the critical enzyme in the metabolic pathway. Fortunately, the development of enzymatic research methods provides powerful tools to understand the catalytic process, including site-specific mutagenesis, protein dynamic simulation, and metabolic engineering technology. Thus, we review the characteristics of critical desaturase and elongase involved in the fatty acids' synthesis metabolic pathway, which aims to not only provide extensive data for enzyme rational design and modification but also provides a more profound and comprehensive understanding of the dietary bioactive lipids' synthetic process.