Regulation of amino-acid metabolism controls flux to lipid accumulation in <i>Yarrowia lipolytica</i>

Yarrowia lipolytica is a promising microbial cell factory for the production of lipids to be used as fuels and chemicals, but there are few studies on regulation of its metabolism. Here we performed the first integrated data analysis of Y. lipolytica grown in carbon and nitrogen limited chemostat cultures. We first reconstructed a genome-scale metabolic model and used this for integrative analysis of multilevel omics data. Metabolite profiling and lipidomics was used to quantify the cellular physiology, while regulatory changes were measured using RNAseq. Analysis of the data showed that lipid accumulation in Y. lipolytica does not involve transcriptional regulation of lipid metabolism but is associated with regulation of amino-acid biosynthesis, resulting in redirection of carbon flux during nitrogen limitation from amino acids to lipids. Lipid accumulation in Y. lipolytica at nitrogen limitation is similar to the overflow metabolism observed in many other microorganisms, e.g. ethanol production by Sacchromyces cerevisiae at nitrogen limitation

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

Transcriptomic Analyses during the Transition from Biomass Production to Lipid Accumulation in the Oleaginous Yeast Yarrowia lipolytica

We previously developed a fermentation protocol for lipid accumulation in the oleaginous yeast Y. lipolytica. This process was used to perform transcriptomic time-course analyses to explore gene expression in Y. lipolytica during the transition from biomass production to lipid accumulation. In this experiment, a biomass concentration of 54.6 gCDW/l, with 0.18 g/gCDW lipid was obtained in ca. 32 h, with low citric acid production. A transcriptomic profiling was performed on 11 samples throughout the fermentation. Through statistical analyses, 569 genes were highlighted as differentially expressed at one point during the time course of the experiment. These genes were classified into 9 clusters, according to their expression profiles. The combination of macroscopic and transcriptomic profiles highlighted 4 major steps in the culture: (i) a growth phase, (ii) a transition phase, (iii) an early lipid accumulation phase, characterized by an increase in nitrogen metabolism, together with strong repression of protein production and activity; (iv) a late lipid accumulation phase, characterized by the rerouting of carbon fluxes within cells. This study explores the potential of Y. lipolytica as an alternative oil producer, by identifying, at the transcriptomic level, the genes potentially involved in the metabolism of oleaginous species

Engineering Yarrowia lipolytica for high lipid production

Among potential value-added fuels and chemicals, fatty acid-based chemicals are important due to their wide use in industrial processes and in daily life. Fatty acids produced from microbial systems could provide a sustainable supply to replace the current costly and unsustainable process using plant oil or animal fat. The oleaginous yeast Yarrowia lipolytica naturally possesses moderate lipid production capacity and grows on different kinds of biomass and organic waste. However, fatty acid production from native, un-engineered strains is not economically viable. Therefore, this work develops strategies inspired from synthetic biology and metabolic engineering to expand the engineering potential of Y. lipolytica — helping to establish this organism as a premier platform for industrial-level, high lipid production as well as providing a platform for uncovering novel understanding of lipogenesis. To do so, first, novel synthetic promoters and high expression plasmid were necessary to achieve the ability to tune gene expression levels inside the cell. We developed a hybrid promoter engineering strategy to create a promoter library exhibiting a range of more than 400-fold in terms of mRNA levels as well as engineered plasmids with regulated centromeric function to achieve a 2.7 fold expression range. Next, a rational and evolutionary metabolic engineering approach was coupled with genomic and transcriptomic studies to both engineer and understand underlying lipogenesis in this organism. Through the engineering efforts, we successfully increased the lipid production titer to over 40 g/L in bioreactor as well as identified novel lipogenic enhancers and mechanisms. In addition, we identified and characterized a mutant mga2 protein with superior lipogenesis enhancing capacity, which can regulate fatty acid desaturation and carbon flux inside the cells. Collectively, these studies have facilitated the utilization of Y. lipolytica as an industrially relevant microbial lipid production platform and supplied novel understanding of its lipogenesis process. The methods and concepts developed here can also be adapted to other oleaginous microbes and serve as a template for enabling value-added chemical production in other nonconventional organism.Biochemistr

Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species

Metabolic network reconstructions have become an important tool for probing cellular metabolism in the field of systems biology. They are used as tools for quantitative prediction but also as scaffolds for further knowledge contextualization. The yeast Saccharomyces cerevisiae was one of the first organisms for which a genome-scale metabolic model (GEM) was reconstructed, in 2003, and since then 45 metabolic models have been developed for a wide variety of relevant yeasts species. A systematic evaluation of these models revealed that-despite this long modeling history-the sequential process of tracing model files, setting them up for basic simulation purposes and comparing them across species and even different versions, is still not a generalizable task. These findings call the yeast modeling community to comply to standard practices on model development and sharing in order to make GEMs accessible and useful for a wider public

Synthetic biology tools for engineering Yarrowia lipolytica

The non-conventional oleaginous yeast Yarrowia lipolytica shows great industrial promise. It naturally produces certain compounds of interest but can also artificially generate non-native metabolites, thanks to an engineering process made possible by the significant expansion of a dedicated genetic toolbox. In this review, we present recently developed synthetic biology tools that facilitate the manipulation of Y. lipolytica, including 1) DNA assembly techniques, 2) DNA parts for constructing expression cassettes, 3) genome-editing techniques, and 4) computational tools

Validated Growth Rate-Dependent Regulation of Lipid Metabolism in Yarrowia lipolytica

Given the strong potential of Yarrowia lipolytica to produce lipids for use as renewable fuels and oleochemicals, it is important to gain in-depth understanding of the molecular mechanism underlying its lipid accumulation. As cellular growth rate affects biomass lipid content, we performed a comparative proteomic analysis of Y. lipolytica grown in nitrogen-limited chemostat cultures at different dilution rates. After confirming the correlation between growth rate and lipid accumulation, we were able to identify various cellular functions and biological mechanisms involved in oleaginousness. Inspection of significantly up- and downregulated proteins revealed nonintuitive processes associated with lipid accumulation in this yeast. This included proteins related to endoplasmic reticulum (ER) stress, ER-plasma membrane tether proteins, and arginase. Genetic engineering of selected targets validated that some genes indeed affected lipid accumulation. They were able to increase lipid content and were complementary to other genetic engineering strategies to optimize lipid yield

Exploring the production of high-value compounds in plant Catharanthus roseus hairy roots and yeast Yarrowia lipolytica

This dissertation focuses on studying the production of two categories of high-value compounds in bio organisms. The first group is terpenoid indole alkaloids (TIAs) in plant Catharanthus roseus, and the second group is wax esters, one of fatty acid derivatives. TIAs belong to secondary metabolites in C. roseus and some of them have wide pharmaceutical applications. In particular, vinblastine and vincristine are two TIAs with anticancer properties and have been marked and used in chemotherapeutic reagents. The biggest issue for TIA production is that the content of those secondary metabolites in plant is extremely low. To improve the TIA production, we studied the regulation mechanism of the TIA pathway and explored the feasibility of valuable TIA production in hairy root culture. Compared with the whole plant, plant tissue culture, such as hairy root culture, has many advantages, like fast growth, large-scale cultivation, and ease of genetic engineering. But the biggest issue for hairy root is that the vinblastine and vincristine synthetic pathway is blocked, mainly one of their precursors, vindoline, can not be synthesized in hairy root. To explore whether C. roseus hairy root could produce the intermediates in the vindoline pathway by overexpressing the pathway enzymes, we co-expressed the first two genes, tabersonine 16-hydrolase (T16H) and 16-O-methyltransferase (16OMT) in the vindoline pathway into hairy root. Transcriptional analysis and metabolic profiling were done to compare the difference between the parent hairy root lines and the engineered hairy root lines. For the metabolic profiling, since the standards for those intermediates were not available, we prepared in-house standards by expressing the plant genes in Saccharomyces cerevisiae, fed substrate, and purified TIA compounds from yeast cell culture. Liquid chromatography (LC) coupled with either photodiode array detector (PDA) or mass spectrometry (MS) were applied to isolate and analyze the TIA compounds by their UV-Visible absorption spectra and molecular weights. In addition, fundamental research was done in C. roseus hairy root to study the effects of transcription regulators on the transcript levels and metabolite levels of the TIA pathway. Two of the seven reported transcription activators of the TIA pathway, octadecanoid-responsive Catharanthus AP2-domain 2(ORCA3) and MYB-like DNA-binding protein (BPF1), were overexpessed in hairy root separately, Two of the transcription repressors, G-box binding factors (GBF1 and GBF2), were knocked down by RNA interface in hairy root. And the transcription analysis and metabolic profiling of the transcription regulator-engineered hairy root lines were done to see what were the effects caused by those regulators. Wax esters have a lot of applications in lubricant, skin care products, cosmetics, inking, and coating industries. Currently the main bio source for high-performed wax ester is from the seeds of jojoba. The tight supply makes wax esters high-value compounds. To reduce the production cost, we introduced the wax ester biosynthetic pathway into an oleaginous yeast, Yarrowia lipolytica. The free fatty alcohol, and wax ester were quantified in the engineered Y. lipolytica. To provide more substrate for wax ester synthesis, we knocked out some genes in the substrate competitive pathways, and constructed four strains with different combination of knockout genes. To utilize the most abundant fatty acid types in Y. lipolytica, we compared three fatty acyl-CoA reductases (FAR), the first enzyme in the wax ester pathway, from different species. It was found that those three FARs had different substrate specificity and the wax ester production varied a lot in those strains. To solve the plasmid instability issue, we randomly integrated FAR gene and WS gene into Y. lipolytica genome, and studied the effect of nitrogen limited fermentation on the wax ester production in one of our best strains

Getting Lipids for Biodiesel Production from Oleaginous Fungi

Biomass-based biofuel production represents a pivotal approach to face high energy prices and potential depletion of crude oils reservoirs, to reduce greenhouse gas emissions, and to enhance a sustainable economy (Zinoviev et al., 2010). Microbial lipids can represent a valuable alternative feedstock for biodiesel production, and a potential solution for a bio-based economy.Nowadays, the production of biodiesel is based mostly on plant oils, even though animal fats, and algal oils can also be used. In particular, soybean, rapeseed, and palm oils are adopted as the major feedstock for biodiesel production. They are produced on agricultural land, opening the debate on the impact of the expansion of bioenergy crop cultures, which displace land from food production. Furthermore, their price restricts the large-scale development of biodiesel to some extent. In order to meet the increasing demand of biodiesel production, other oil sources have been explored. Recently, the development of processes to produce single cell oil (SCO) by using heterotrophic oleaginous microorganisms has triggered significant attention (Azocar et al., 2010). These organisms accumulate lipids, mostly consisting of triacylglycerols (TAG), that form the storage fraction of the cell. The occurrence of TAG as reserve compounds is widespread among all eukaryotic organisms such as fungi, plants and animals, whereas it has only rarely been described in bacteria (Meng et al., 2009). In fact, bacteria generally accumulate polyhydroxyalkanoates as storage compound and only few bacterial species, belonging to the actinobacterial genera Mycobacterium, Streptomyces, Rhodococcus and Nocardia produce relevant amounts of lipids (Alvarez & Steinbuchel, 2002).Among heterotrophic microorgansisms, oleaginous fungi, including both molds and yeasts, are increasingly been reported as good TAG producers. This chapter will focus on current knowledge advances in their metabolism, physiology, and in the result achieved in strain improvement, process engineering and raw material exploitation

Unraveling fatty acid transport and activation mechanisms in Yarrowia lipolytica

AbstractFatty acid (FA) transport and activation have been extensively studied in the model yeast species Saccharomyces cerevisiae but have rarely been examined in oleaginous yeasts, such as Yarrowia lipolytica. Because the latter begins to be used in biodiesel production, understanding its FA transport and activation mechanisms is essential. We found that Y. lipolytica has FA transport and activation proteins similar to those of S. cerevisiae (Faa1p, Pxa1p, Pxa2p, Ant1p) but mechanism of FA peroxisomal transport and activation differs greatly with that of S. cerevisiae. While the ScPxa1p/ScPxa2p heterodimer is essential for growth on long-chain FAs, ΔYlpxa1 ΔYlpxa2 is not impaired for growth on FAs. Meanwhile, ScAnt1p and YlAnt1p are both essential for yeast growth on medium-chain FAs, suggesting they function similarly. Interestingly, we found that the ΔYlpxa1 ΔYlpxa2 ΔYlant1 mutant was unable to grow on short-, medium-, or long-chain FAs, suggesting that YlPxa1p, YlPxa2p, and YlAnt1p belong to two different FA degradation pathways. We also found that YlFaa1p is involved in FA storage in lipid bodies and that FA remobilization largely depended on YlFat1p, YlPxa1p and YlPxa2p. This study is the first to comprehensively examine FA intracellular transport and activation in oleaginous yeast