Metabolic peculiarities of the citric acid overproduction from glucose in yeasts Yarrowia lipolytica

Novel ternary deep eutectic solvent fractionation for effective utilization of willow

A novel ternary deep eutectic solvent (TDES), consisting of zinc chloride, ethylene glycol and alpha hydroxy carboxylic acids (i.e., glycolic acid, citric acid and malic acid), was first proposed to effectively fractionate and convert willow (Salix matsudana cv. Zhuliu) into fermentable sugar. In particular, the zinc chloride/ethylene glycol/malic acid (ZnCl2/EG/MA) TDES system showed remarkable fractionation performance with 91.66 % xylan and 90.12 % lignin removals at 130 °C for 1.5 h, resulting in 96.01 % glucose yield in the subsequent enzymatic hydrolysis stage. Moreover, the regenerated lignin showed regular nanoparticle morphology and good antioxidant properties. Even after four recycling, the TDES showed 70.16 % of delignification and 83.70 % glucose yield with the TDES pretreated willow. Overall, this study demonstrated an effective solvent fractionation approach to maximize the utilization of total lignocellulose under mild conditions.

Reprogramming Yarrowia lipolytica metabolism for efficient synthesis of itaconic acid from flask to semipilot scale

Itaconic acid is an emerging platform chemical with extensive applications. Itaconic acid is currently produced by Aspergillus terreus through biological fermentation. However, A. terreus is a fungal pathogen that needs additional morphology controls, making itaconic acid production on industrial scale problematic. Here, we reprogrammed the Generally Recognized As Safe (GRAS) yeast Yarrowia lipolytica for competitive itaconic acid production. After preventing carbon sink into lipid accumulation, we evaluated itaconic acid production both inside and outside the mitochondria while fine-tuning its biosynthetic pathway. We then mimicked the regulation of nitrogen limitation in nitrogen-replete conditions by down-regulating NAD+-dependent isocitrate dehydrogenase through weak promoters, RNA interference, or CRISPR interference. Ultimately, we optimized fermentation parameters for fed-batch cultivations and produced itaconic acid titers of 130.1 grams per liter in 1-liter bioreactors and 94.8 grams per liter in a 50-liter bioreactor on semipilot scale. Our findings provide effective approaches to harness the GRAS microorganism Y. lipolytica for competitive industrial-scale production of itaconic acid.

The contribution of microorganisms to sustainable development: towards a green future through synthetic biology and systems biology

Microorganisms, though invisible, they play a pivotal role in influencing both the global economy and societal progress., and job market. This discussion highlights their significant impact on various sectors like food, pharmaceuticals, and chemicals. These versatile microorganisms act as efficient cell factories, producing chemicals from renewable sources and aiding in waste degradation. The historical development of microbial cell factories has relied on a trial-and-error approach, following a cyclic process of design, construction, testing, and refinement. The essay delves into the critical role of microorganisms in sustainable development, highlighting their capacity for sustainable chemical production and waste degradation. The incorporation of microbial technology presents significant opportunities for advancing the United Nations’ Sustainable Development Goals. Microorganisms contribute significantly to sustainable development by influencing the economy, creating jobs, improving food and pharmaceutical production, and advancing chemical manufacturing. Their utilization brings advantages like cleaner production methods, renewable resource utilization, and healthcare contributions. Overall, microorganisms are essential players in sustainable development, offering solutions for a more environmentally friendly and economically viable future.

Citric Acid: Properties, Microbial Production, and Applications in Industries

Citric acid finds broad applications in various industrial sectors, such as the pharmaceutical, food, chemical, and cosmetic industries. The bioproduction of citric acid uses various microorganisms, but the most commonly employed ones are filamentous fungi such as Aspergillus niger and yeast Yarrowia lipolytica. This article presents a literature review on the properties of citric acid, the microorganisms and substrates used, different fermentation techniques, its industrial utilization, and the global citric acid market. This review emphasizes that there is still much to explore, both in terms of production process techniques and emerging new applications of citric acid.

Growth Response of Non-Conventional Yeasts on Sugar-Rich Media: Part 2: Citric Acid Production and Circular-Oriented Valorization of Glucose-Enriched Olive Mill Wastewaters Using Novel Yarrowia lipolytica Strains

The global market for citric acid (CA) is one of the biggest and fastest expanding markets in the food industry. The CA production employing microbial bioprocessing with efficient GRAS strains and renewable waste streams is in line with the European Union binding targets for resource efficiency, sustainable consumption-production, and low-carbon technologies. In this work, the potential of three novel wild-type Yarrowia lipolytica strains (namely LMBF Y-46, LMBF Y-47 and ACA-YC 5033) regarding the production of CA and other valuable metabolites was tested on glucose-based media, and the most promising amongst the screened strains (viz. the strain ACA-YC 5033) was cultured on glucose-based media, in which part of the fermentation water had been replaced by olive-mill wastewaters (OMWs) in a novel approach of simultaneous OMW valorization and bioremediation. In the first part of this study, the mentioned strains were cultured under nitrogen-limited conditions with commercial (low-cost) glucose employed as a sole carbon source in shake-flask cultures at an initial concentration (S0) ≈ of 50 g/L. Variable quantities of secreted citric acid (CA) and intra-cellular compounds (viz. polysaccharides and lipids) were produced. All strains did not accumulate significantly high lipid quantities (i.e., maximum lipid in dry cell weight [DCW] values ≈30% w/w were noted) but produced variable CA quantities. The most promising strain, namely ACA-YC 5033, produced CA up to c. 24 g/L, with a yield of CA produced on glucose consumed (YCA/S) ≈ 0.45 g/g. This strain in stirred tank bioreactor experiments, at remarkably higher S0 concentrations (≈110 g/L) and the same initial nitrogen quantity added into the medium, produced notably higher CA quantities, up to 57 g/L (YCA/S ≈ 0.52 g/g). The potential of the same strain (ACA-YC 5033) to bioremediate OMWs and to produce value-added compounds, i.e., yeast cells, CA, and intra-cellular metabolites, was also assessed; under nitrogen-limited conditions in which OMWs had partially replaced tap water and significant glucose concentrations had been added (S0 ≈ 100 g/L, simultaneous molar ratio C/N ≈ 285 g/g, initial phenolic compounds [Phen0] adjusted to ≈1.0 g/L; these media were similar to the OMWs generated from the traditional press extraction systems) the notable CA quantity of 60.2 g/L with simultaneous YCA/S = 0.66 g/g, was obtained in shake flasks, together with satisfactory phenolic compounds removal (up to 19.5% w/w) and waste decolorization (up to 47.0%). Carbon-limited conditions with Phen0 ≈ 1.0 g/L favored the production of yeast DCW (up to 25.3 g/L), with equally simultaneous interesting phenolic compounds and color removal. The fatty acid profile showed that cellular lipids were highly unsaturated with oleic, linoleic and palmitoleic acids, accounting for more than 80% w/w. This study proposed an interesting approach that could efficiently address the biotreatment of toxic effluents and further convert them into circular-oriented bioproducts.

Growth Response of Non-Conventional Yeasts on Sugar-Rich Media: Part 1: High Production of Lipid by Lipomyces starkeyi and Citric Acid by Yarrowia lipolytica

Sugar-rich waste streams, generated in very high quantities worldwide, constitute an important source of environmental pollution. Their eco-friendly conversions into a plethora of added-value compounds through the use of microbial fermentations is currently a very "hot" scientific topic. The aim of this study, was to assess the potential of single cell oil (SCO), microbial mass and citric acid (CA) production by non-conventional yeast strains growing on expired ("waste") glucose. Six yeast strains (viz. Rhodosporidium toruloides DSM 4444, Rhodotorula glutinis NRRL YB-252, R. toruloides NRRL Y-27012, Yarrowia lipolytica LFMB Y-20, Y. lipolytica ACA-DC 50109 and Lipomyces starkeyi DSM 70296) were initially grown in shake flasks with expired glucose used as substrate under nitrogen limitation, in order to "boost" the cellular metabolism towards the synthesis of SCO and CA, and their growth response was quantitatively evaluated. Initial glucose concentration (Glc₀) was adjusted at c. 50 g/L. Besides Y. lipolytica, all other yeast strains produced noticeable SCO quantities [lipid in dry cell weight (DCW) ranging from 25.3% w/w to 55.1% w/w]. Lipids of all yeasts contained significant quantities of oleic acid, being perfect candidates for the synthesis of 2nd generation biodiesel. The highest DCW production (=13.6 g/L) was obtained by L. starkeyi DSM 70296, while both Y. lipolytica strains did not accumulate noticeable lipid quantities, but produced non-negligible CA amounts. The most promising CA-producing strain, namely Y. lipolytica ACA-DC 50109 was further studied in stirred-tank bioreactor systems, while the very promising DCW- and SCO-producing L. starkeyi DSM 70296 was further studied in shake flasks. Both strains were grown on media presenting higher Glc₀ concentrations and the same initial nitrogen quantity as previously. Indeed, L. starkeyi grown at Glc₀ = 85 g/L, produced DCW_max = 34.0 g/L, that contained lipid =34.1% w/w (thus SCO was =11.6 g/L). The strain ACA-DC 50109 in stirred tank bioreactor with Glc₀ ≈ 105 g/L produced CA up to 46 g/L (yield of CA produced on glucose consumed; Y_CA/Glc ≈ 0.45 g/g). Finally, in fed-batch bioreactor experiment, the significant CA quantity of 82.0 g/L (Y_CA/Glc = 0.50 g/g) was recorded. Concluding, "waste" glucose proved to be a suitable substrate for a number of non-conventional yeast strains. Y. lipolytica ACA-DC 50109 produced significant quantities of CA while L. starkeyi DSM 70296 was a very interesting DCW- and SCO-producing candidate. These strains can be used as potential cell factories amenable to convert glucose-based residues into the mentioned metabolic compounds, that present high importance for food, chemical and biofuel facilities.

Current advances for omics-guided process optimization of microbial manufacturing

Currently, microbial manufacturing is widely used in various fields, such as food, medicine and energy, for its advantages of greenness and sustainable development. Process optimization is the committed step enabling the commercialization of microbial manufacturing products. However, the present optimization processes mainly rely on experience or trial-and-error method ignoring the intrinsic connection between cellular physiological requirement and production performance, so in many cases the productivity of microbial manufacturing could not been fully exploited at economically feasible cost. Recently, the rapid development of omics technologies facilitates the comprehensive analysis of microbial metabolism and fermentation performance from multi-levels of molecules, cells and microenvironment. The use of omics technologies makes the process optimization more explicit, boosting microbial manufacturing performance and bringing significant economic benefits and social value. In this paper, the traditional and omics technologies-guided process optimization of microbial manufacturing are systematically reviewed, and the future trend of process optimization is prospected.

Upgrading Major Waste Streams Derived from the Biodiesel Industry and Olive Mills via Microbial Bioprocessing with Non-Conventional Yarrowia lipolytica Strains

This study reports the development of a bioprocess involving the valorization of biodiesel-derived glycerol as the main carbon source for cell proliferation of Yarrowia lipolytica strains and production of metabolic compounds, i.e., citric acid (Cit), polyols, and other bio-metabolites, the substitution of process tap water with olive mill wastewater (OMW) in batch fermentations, and partial detoxification of OMW (up to 31.1% decolorization). Increasing initial phenolics (Phen) of OMW-glycerol blends led to substantial Cit secretion. Maximum Cit values, varying between 64.1–65.1 g/L, combined with high yield (YCit/S = 0.682–0.690 g Cit/g carbon sources) and productivity (0.335–0.344 g/L/h) were achieved in the presence of Phen = 3 g/L. The notable accumulation of endopolysaccharides (EPs) on the produced biomass was determined when Y. lipolytica LMBF Y-46 (51.9%) and ACA-YC 5033 (61.5%) were cultivated on glycerol-based media. Blending with various amounts of OMW negatively affected EPs and polyols biosynthesis. The ratio of mannitol:arabitol:erythritol was significantly affected (p < 0.05) by the fermentation media. Erythritol was the major polyol in the absence of OMW (53.5–62.32%), while blends of OMW-glycerol (with Phen = 1–3 g/L) promoted mannitol production (54.5–76.6%). Nitrogen-limited conditions did not favor the production of cellular lipids (up to 16.6%). This study addressed sustainable management and resource efficiency enabling the bioconversion of high-organic-load and toxic waste streams into valuable products within a circular bioeconomy approach.

Citric Acid Production by Yarrowia lipolytica NRRL Y-1094: Optimization of pH, Fermentation Time and Glucose Concentration Using Response Surface Methodology

In this study, three Yarrowia lipolytica strains (Y. lipolytica NRRL Y-1094, Y. lipolytica NRRL YB-423 and Y. lipolytica IFP29) were screened for acid-production capacity and the maximum zone-area was formed by Y. lipolytica NRRL Y-1094. The strain was then selected as a potential citric-acid (CA) producer for further studies. The CA production by Y. lipolytica NRRL Y-1094 was optimized using response surface methodology (RSM) and considering three factors, comprising initial pH-value, fermentation time, and initial glucose-concentration. The highest CA-concentration was 30.31 g/L under optimum conditions (pH 5.5, 6 days, and 125 g/L glucose) in shake flasks. It has been reported that this result gives better results than many productions with shake flasks. According to estimated regression-coefficients for CA concentration, the fermentation time had the greatest impact on CA production, followed by the substrate concentration and initial pH-level, respectively. On the other hand, this study is a fundamental step in solving and optimizing the production mechanism of Y. lipolytica NRRL Y-1094, a microorganism that has not yet been used in CA production with a glucose-based medium. The results suggest that future studies can perform higher yields by optimizing other medium constituents and environmental factors.

Citric acid production by a novel autochthonous Candida zeylanoides isolate: optimization of process parameters

In this study, citric acid (CA) production by autochthonous Candida zeylanoides 7.12 was investigated and optimized. Response surface methodology (RSM) was used for the analysis of simultaneous effects of the chosen factors and 2 experiment designs were applied. In the first experimental design, the effects of initial pH value (5.5, 6.0 and 6.5), fermentation time (4, 5 and 6 days) and initial glucose concentration (125, 150 and 175 g/L) on CA production were investigated. Initial pH value was adjusted periodically with NaOH. Results of the statistical analysis showed that the model was found to be not applicable sufficiently to the chosen data. A second experimental design was employed at the same levels of glucose concentration and fermentation time by disabling the pH factor. pH level was kept at 6.5 with CaCO₃. Results of the statistical analysis showed that the fit of the model was good and the lack of fit was not significant (P > 0.05). The highest CA concentration of 11.36 g/L was obtained after 6 days of fermentation with an initial glucose concentration of 125 g/L. The results indicated that initial glucose concentration and fermentation time were important parameters for CA production by C. zeylanoides 7.12 and this strain could be used for future studies.

Modelling of the Citric Acid Production from Crude Glycerol by Wild-Type Yarrowia lipolytica DSM 8218 Using Response Surface Methodology (RSM)

Crude glycerol is the main by-product of the biodiesel manufacturing industry (10% w/w). Its use as a substrate in microbial fermentations is a concrete strategy to efficiently address its market surplus. In this study, the conversion of crude glycerol to citric acid, a key biochemical in the emerging bioeconomy, by a wild-type yeast Yarrowia lipolytica DSM 8218 was modelled using the Response Surface Methodology. The model relates C/N mass ratio and crude glycerol concentration to maximize the citric acid yield in flask scale using two different N sources, yeast extract and ammonium sulphate. Under the optimal conditions (yeast extract, C/N 141, glycerol 33 g/L), the conversion yield was 0.249 g/g. The optimal conditions were used for up-scaling a fed-batch fermentation in a 2 L bioreactor highlighting a metabolic shift from mannitol to citric acid when high stirring rates were applied (800 rpm). In these conditions, a morphic transition from pseudo-mycelial form to round-shaped yeast-like cells was observed too.

Increased Lipid Production in Yarrowia lipolytica from Acetate through Metabolic Engineering and Cosubstrate Fermentation

Bioconversion of acetate, a byproduct generated in industrial processes, into microbial lipids using oleaginous yeasts offers a promising alternative for the economic utilization of acetate-containing waste streams. However, high acetate concentrations will inhibit microbial growth and metabolism. In this study, the acetate utilization capability of Yarrowia lipolytica PO1f was successively improved by overexpressing the key enzyme of acetyl-CoA synthetase (ACS), which resulted in an accumulation of 9.2% microbial lipids from acetate in shake flask fermentation. By further overexpressing the second key enzymes of acetyl-CoA carboxylase (ACC1) and fatty acid synthase (FAS) in Y. lipolytica, the lipid content was increased to 25.7% from acetate. Finally, the maximum OD₆₀₀ of 29.2 and a lipid content of 41.7% were obtained with the engineered strain by the adoption of cosubstrate (glycerol and acetate) fed-batch fermentation, which corresponded to an increase of 68 and 95%, respectively. These results presented a promising strategy for economic and efficient microbial lipid production from the waste acetate.

Emerging technologies for conversion of sustainable algal biomass into value-added products: A state-of-the-art review

Concerns regarding high energy demand and gradual depletion of fossil fuels have attracted the desire of seeking renewable and sustainable alternatives. Similar to but better than the first- and second-generation biomass, algae derived third-generation biorefinery aims to generate value-added products by microbial cell factories and has a great potential due to its abundant, carbohydrate-rich and lignin-lacking properties. However, it is crucial to establish an efficient process with higher competitiveness over the current petroleum industry to effectively utilize algal resources. In this review, we summarize the recent technological advances in maximizing the bioavailability of different algal resources. Following an overview of approaches to enhancing the hydrolytic efficiency, we review prominent opportunities involved in microbial conversion into various value-added products including alcohols, organic acids, biogas and other potential industrial products, and also provide key challenges and trends for future insights into developing biorefineries of marine biomass.

Isocitric Acid Production from Ethanol Industry Waste by Yarrowia lipolytica

There is ever increasing evidence that isocitric acid can be used as a promising compound with powerful antioxidant activity to combat oxidative stress. This work demonstrates the possibility of using waste product from the alcohol industry (so-called ester-aldehyde fraction) for production of isocitric acid by yeasts. The potential producer of isocitric acid from this fraction, Yarrowia lipolytica VKM Y-2373, was selected by screening of various yeast cultures. The selected strain showed sufficient growth and good acid formation in media with growth-limiting concentrations of nitrogen, sulfur, phosphorus, and magnesium. A shortage of Fe2+ and Ca2+ ions suppressed both Y. lipolytica growth and formation of isocitric acid. The preferential synthesis of isocitric acid can be regulated by changing the nature and concentration of nitrogen source, pH of cultivation medium, and concentration of ester-aldehyde fraction. Experiments in this direction allowed us to obtain 65 g/L isocitric acid with a product yield (YICA) of 0.65 g/g in four days of cultivation.

Yarrowia lipolytica Strains and Their Biotechnological Applications: How Natural Biodiversity and Metabolic Engineering Could Contribute to Cell Factories Improvement

Among non-conventional yeasts of industrial interest, the dimorphic oleaginous yeast Yarrowia lipolytica appears as one of the most attractive for a large range of white biotechnology applications, from heterologous proteins secretion to cell factories process development. The past, present and potential applications of wild-type, traditionally improved or genetically modified Yarrowia lipolytica strains will be resumed, together with the wide array of molecular tools now available to genetically engineer and metabolically remodel this yeast. The present review will also provide a detailed description of Yarrowia lipolytica strains and highlight the natural biodiversity of this yeast, a subject little touched upon in most previous reviews. This work intends to fill this gap by retracing the genealogy of the main Yarrowia lipolytica strains of industrial interest, by illustrating the search for new genetic backgrounds and by providing data about the main publicly available strains in yeast collections worldwide. At last, it will focus on exemplifying how advances in engineering tools can leverage a better biotechnological exploitation of the natural biodiversity of Yarrowia lipolytica and of other yeasts from the Yarrowia clade.

Systems-level approaches for understanding and engineering of the oleaginous cell factory Yarrowia lipolytica

Concerns about climate change and the search for renewable energy sources together with the goal of attaining sustainable product manufacturing have boosted the use of microbial platforms to produce fuels and high-value chemicals. In this regard, Yarrowia lipolytica has been known as a promising yeast with potentials in diverse array of biotechnological applications such as being a host for different oleochemicals, organic acid, and recombinant protein production. Having a rapidly increasing number of molecular and genetic tools available, Y. lipolytica has been well studied amongst oleaginous yeasts and metabolic engineering has been used to explore its potentials. More recently, with the advancement in systems biotechnology and the implementation of mathematical modeling and high throughput omics data-driven approaches, in-depth understanding of cellular mechanisms of cell factories have been made possible resulting in enhanced rational strain design. In case of Y. lipolytica, these systems-level studies and the related cutting-edge technologies have recently been initiated which is expected to result in enabling the biotechnology sector to rationally engineer Y. lipolytica-based cell factories with favorable production metrics. In this regard, here, we highlight the current status of systems metabolic engineering research and assess the potential of this yeast for future cell factory design development.

Impact of nitrogen deficiency on succinic acid production by engineered strains of Yarrowia lipolytica

Yarrowia lipolytica strains PGC01003 and PGC202 engineered for succinic acid production were studied and compared to the wild type strain W29. For the first time, these two strains were characterized in a chemically defined medium. Strain growth and organic acid production were investigated in fed-batch mode with glycerol as carbon and energy source. This study evaluated the impact of nitrogen deficiency strategy to redirect carbon flux toward succinic acid synthesis. Strain PGC01003 produced 19 g L^-1 succinic acid with an overall yield of 0.23 g g^-1 and an overall productivity of 0.23 g L^-1 h^-1, while strain PGC202 produced 33 g L^-1 succinic acid with an overall yield of 0.12 g g^-1 and a productivity of 0.57 g L^-1 h^-1. Nitrogen limitation effectively stopped biomass growth and increased succinic acid yield of PGC01003 and PGC202 by 18 % and 62 %, respectively. However, the specific succinic acid production rate was reduced by 77 % and 66 %, respectively.

Citric Acid Production of Yeasts: An Overview

Background

Citric acid, an intermediate product of the Krebs cycle, has a wide usage area in the food industry since it has some functions such as acidulant, flavouring agent, preservative and antioxidant. Although molds are the most commonly used microorganisms in the citric acid production, it is known that there are significant advantages of using yeasts.

Purpose and scope

The microbial citric acid production mechanism needs to be well understood to make production more efficient. In this study, the yeasts used in the production, fermentation types and the factors affecting production were reviewed with studies.

Methodology

Although production of citric acid can be produced by chemical synthesis, the fermentation is preferred because of its low cost and ease of use. More than 90% of citric acid produced in the world is obtained by fermentation.

Results

Yarrowia lipolytica, Candida zeylanoides and Candida oleophila are evaluated for citric acid production with substrates such as molasses, glucose, sucrose and glycerol. On the other hand, there is great interest in developing processes with new substrates and/ or microorganisms.

Conclusion

Although the microbial strain is an important factor, the factors such as carbon, phosphorus and nitrogen sources, aeration, the presence of trace elements and pH are also parameters affecting the production.

Physiological Characterization of a Novel Wild-Type Yarrowia lipolytica Strain Grown on Glycerol: Effects of Cultivation Conditions and Mode on Polyols and Citric Acid Production

A new yeast wild-type Yarrowia lipolytica isolate presented efficient growth on glycerol. During flask cultures, nitrogen limitation led to the secretion of sugar-alcohols as the major metabolites of the process (mannitol, arabitol and erythritol), whereas insignificant quantities of citrate were synthesized. Although in some instances high initial glycerol concentrations were employed (≈150 g/L), remarkable glycerol assimilation and polyol secretion was observed. Total polyols ≈ 52 g/L (conversion yield on glycerol consumed = 0.43 g/g) was recorded in the flask experiments. The sugar-alcohol production bioprocess was successfully simulated with the aid of a modified Velhlust–Aggelis model that fitted very well with the experimental data, while optimized parameter values seemed to be quite consistent. In bioreactor trials, a noticeable metabolic shift towards citric acid production was observed, while simultaneously insignificant polyol quantities were produced. In fed-batch bioreactor experiments, a total citric acid quantity ≈ 102 g/L was recorded—one of the highest in the literature for wild-type Y. lipolytica strains. This metabolic transition was due to higher oxygen saturation into the medium that occurred in the bioreactor experiments compared with the flasks. Cellular lipids produced in the bioreactor trial contained higher concentrations of unsaturated fatty acids compared with those produced in flasks.

Metabolic engineering for increased lipid accumulation in Yarrowia lipolytica - A Review

Current energy security and climate change policies encourage the development and utilization of bioenergy. Oleaginous yeasts provide a particularly attractive platform for the sustainable production of biofuels and industrial chemicals due to their ability to accumulate high amounts of lipids. In particular, microbial lipids in the form of triacylglycerides (TAGs) produced from renewable feedstocks have attracted considerable attention because they can be directly used in the production of biodiesel and oleochemicals analogous to petrochemicals. As an oleaginous yeast that is generally regarded as safe, Yarrowia lipolytica has been extensively studied, with large amounts of data on its lipid metabolism, genetic tools, and genome sequencing and annotation. In this review, we highlight the newest strategies for increasing lipid accumulation using metabolic engineering and summarize the research advances on the overaccumulation of lipids in Y. lipolytica. Finally, perspectives for future engineering approaches are proposed.

Synthetic biology, systems biology, and metabolic engineering of Yarrowia lipolytica toward a sustainable biorefinery platform

Yarrowia lipolytica is an oleaginous yeast that has been substantially engineered for production of oleochemicals and drop-in transportation fuels. The unique acetyl-CoA/malonyl-CoA supply mode along with the versatile carbon-utilization pathways makes this yeast a superior host to upgrade low-value carbons into high-value secondary metabolites and fatty acid-based chemicals. The expanded synthetic biology toolkits enabled us to explore a large portfolio of specialized metabolism beyond fatty acids and lipid-based chemicals. In this review, we will summarize the recent advances in genetic, omics, and computational tool development that enables us to streamline the genetic or genomic modification for Y. lipolytica. We will also summarize various metabolic engineering strategies to harness the endogenous acetyl-CoA/malonyl-CoA/HMG-CoA pathway for production of complex oleochemicals, polyols, terpenes, polyketides, and commodity chemicals. We envision that Y. lipolytica will be an excellent microbial chassis to expand nature's biosynthetic capacity to produce plant secondary metabolites, industrially relevant oleochemicals, agrochemicals, commodity, and specialty chemicals and empower us to build a sustainable biorefinery platform that contributes to the prosperity of a bio-based economy in the future.

Screening various Yarrowia lipolytica strains for citric acid production

Citric acid (CA) productivity by Yarrowia lipolytica dependents on strain type, carbon source, carbon to nitrogen (C/N) molar ratio as well as physicochemical conditions (pH, temperature, oxygen transfer rate, etc.). In the current study, 10 different Y. lipolytica strains were first challenged in shake-flask culture for CA production in a glucose-based media under nitrogen-limited conditions. For the most promising one, strain K57, CA productivity was monitored during culture in batch bioreactor for three initial C/N molar ratio (167, 367, and 567 Cmol/Nmol). The highest CA yield (0.77 g/g glucose), titre (72.3 g/L CA), and productivity (0.04 g/g.h) were found for C/N ratio of 367. However, the highest growth rate was obtained for an initial C/N ratio of 167. From these results, Y. lipolytica strain K57 could be considered to produce CA at higher titre on glucose-based medium in batch bioreactor than others Y. lipolytica strain reported in the literature.

Biodiesel-Derived Glycerol Obtained from Renewable Biomass-A Suitable Substrate for the Growth of Candida zeylanoides Yeast Strain ATCC 20367

Used kitchen oil represents a feasible and renewable biomass to produce green biofuels such as biodiesel. Biodiesel production generates large amounts of by-products such as the crude glycerol fraction, which can be further used biotechnologically as a valuable nutrient for many microorganisms. In this study, we transesterified used kitchen oil with methanol and sodium hydroxide in order to obtain biodiesel and crude glycerol fractions. The crude glycerol fraction consisting of 30% glycerol was integrated into a bioreactor cultivation process as a nutrient source for the growth of Candida zeylanoides ATCC 20367. Cell viability and biomass production were similar to those obtained with batch cultivations on pure glycerol or glucose as the main nutrient substrates. However, the biosynthesis of organic acids (e.g., citric and succinic) was significantly different compared to pure glycerol and glucose used as main carbon sources.

Metabolic engineering in the host Yarrowia lipolytica

The nonconventional, oleaginous yeast, Yarrowia lipolytica is rapidly emerging as a valuable host for the production of a variety of both lipid and nonlipid chemical products. While the unique genetics of this organism pose some challenges, many new metabolic engineering tools have emerged to facilitate improved genetic manipulation in this host. This review establishes a case for Y. lipolytica as a premier metabolic engineering host based on innate metabolic capacity, emerging synthetic tools, and engineering examples. The metabolism underlying the lipid accumulation phenotype of this yeast as well as high flux through acyl-CoA precursors and the TCA cycle provide a favorable metabolic environment for expression of relevant heterologous pathways. These properties allow Y. lipolytica to be successfully engineered for the production of both native and nonnative lipid, organic acid, sugar and acetyl-CoA derived products. Finally, this host has unique metabolic pathways enabling growth on a wide range of carbon sources, including waste products. The expansion of carbon sources, together with the improvement of tools as highlighted here, have allowed this nonconventional organism to act as a cellular factory for valuable chemicals and fuels.

Synthetic Biology Expands the Industrial Potential of Yarrowia lipolytica

The oleaginous yeast Yarrowia lipolytica is quickly emerging as the most popular non-conventional (i.e., non-model organism) yeast in the bioproduction field. With a high propensity for flux through tricarboxylic acid (TCA) cycle intermediates and biological precursors such as acetyl-CoA and malonyl-CoA, this host is especially well suited to meet our industrial chemical production needs. Recent progress in synthetic biology tool development has greatly enhanced our ability to rewire this organism, with advances in genetic component design, CRISPR technologies, and modular cloning strategies. In this review we investigate recent developments in metabolic engineering and describe how the new tools being developed help to realize the full industrial potential of this host. Finally, we conclude with our vision of the developments that will be necessary to enhance future engineering efforts.

A Role of a Newly Identified Isomerase From Yarrowia lipolytica in Erythritol Catabolism

Erythritol is a natural sweetener produced by microorganisms as an osmoprotectant. It belongs to the group of polyols and it can be utilized by the oleaginous yeast Yarrowia lipolytica. Despite the recent identification of the transcription factor of erythritol utilization (EUF1), the metabolic pathway of erythritol catabolism remains unknown. In this study we identified a new gene, YALI0F01628g, involved in erythritol assimilation. In silico analysis showed that YALI0F01628g is a putative isomerase and it is localized in the same region as EUF1. qRT-PCR analysis of Y. lipolytica showed a significant increase in YALI0F01628g expression during growth on erythritol and after overexpression of EUF1. Moreover, the deletion strain ΔF01628 showed significantly impaired erythritol assimilation, whereas synthesis of erythritol remained unchanged. The results showed that YALI0F1628g is involved in erythritol assimilation; thus we named the gene EYI1. Moreover, we suggest the metabolic pathway of erythritol assimilation in yeast Y. lipolytica.