A Yarrowia lipolytica Strain Engineered for Pyomelanin Production

Combinatorial iterative method for metabolic engineering of Yarrowia lipolytica: Application for betanin biosynthesis

Combinatorial library-based metabolic engineering approaches allow lower cost and faster strain development. We developed a genetic toolbox EXPRESSYALI for combinatorial engineering of the oleaginous yeast Yarrowia lipolytica. The toolbox enables consecutive rounds of engineering, where up to three combinatorially assembled gene expression cassettes can be integrated into each yeast clone per round. The cassettes are integrated into distinct intergenic sites or an open reading frame of a target gene if a simultaneous gene knockout is desired. We demonstrate the application of the toolbox by optimizing the Y. lipolytica to produce the red beet color betanin via six consecutive rounds of genome editing and screening. The library size varied between 24 and 360. Library screening was facilitated by automated color-based colony picking. In the first round, betanin pathway genes were integrated, resulting in betanin titer of around 20 mg/L. Through the following five consecutive rounds, additional biosynthetic genes were integrated, and the precursor supply was optimized, resulting in a titer of 70 mg/L. Three beta-glucosidases were deleted to prevent betanin deglycosylation, which led to a betanin titer of 130 mg/L in a small scale and a titer of 1.4 g/L in fed-batch bioreactors. The EXPRESSYALI toolbox can facilitate metabolic engineering efforts in Y. lipolytica (available via AddGene Cat. Nr. 212682-212704, Addgene kit ID # 1000000245).

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.

Sustainable biorefinery approach by utilizing xylose fraction of lignocellulosic biomass

Lignocellulosic biomass (LCB) has been a lucrative feedstock for developing biochemical products due to its rich organic content, low carbon footprint and abundant accessibility. The recalcitrant nature of this feedstock is a foremost bottleneck. It needs suitable pretreatment techniques to achieve a high yield of sugar fractions such as glucose and xylose with low inhibitory components. Cellulosic sugars are commonly used for the bio-manufacturing process, and the xylose sugar, which is predominant in the hemicellulosic fraction, is rejected as most cell factories lack the five‑carbon metabolic pathways. In the present review, more emphasis was placed on the efficient pretreatment techniques developed for disintegrating LCB and enhancing xylose sugars. Further, the transformation of the xylose to value-added products through chemo-catalytic routes was highlighted. In addition, the review also recapitulates the sustainable production of biochemicals by native xylose assimilating microbes and engineering the metabolic pathway to ameliorate biomanufacturing using xylose as the sole carbon source. Overall, this review will give an edge on the bioprocessing of microbial metabolism for the efficient utilization of xylose in the LCB.

Beet red food colourant can be produced more sustainably with engineered Yarrowia lipolytica

Synthetic food colourants are widely used in the food industry, but consumer concerns about safety and sustainability are driving a need for natural food-colour alternatives. Betanin, which is extracted from red beetroots, is a commonly used natural red food colour. However, the betanin content of beetroot is very low (~0.2% wet weight), which means that the extraction of betanin is incredibly wasteful in terms of land use, processing costs and vegetable waste. Here we developed a sustainability-driven biotechnological process for producing red beet betalains, namely, betanin and its isomer isobetanin, by engineering the oleaginous yeast Yarrowia lipolytica. Metabolic engineering and fermentation optimization enabled production of 1,271 ± 141 mg l-1 betanin and 55 ± 7 mg l-1 isobetanin in 51 h using glucose as carbon source in controlled fed-batch fermentations. According to a life cycle assessment, at industrial scale (550 t yr-1), our fermentation process would require significantly less land, energy and resources compared with the traditional extraction of betanin from beetroot crops. Finally, we apply techno-economic assessment to show that betanin production by fermentation could be economically feasible in the existing market conditions.

A DNA assembly toolkit to unlock the CRISPR/Cas9 potential for metabolic engineering

CRISPR/Cas9-based technologies are revolutionising the way we engineer microbial cells. One of the key advantages of CRISPR in strain design is that it enables chromosomal integration of marker-free DNA, eliminating laborious and often inefficient marker recovery procedures. Despite the benefits, assembling CRISPR/Cas9 editing systems is still not a straightforward process, which may prevent its use and applications. In this work, we have identified some of the main limitations of current Cas9 toolkits and designed improvements with the goal of making CRISPR technologies easier to access and implement. These include 1) A system to quickly switch between marker-free and marker-based integration constructs using both a Cre-expressing and standard Escherichia coli strains, 2) the ability to redirect multigene integration cassettes into alternative genomic loci via Golden Gate-based exchange of homology arms, 3) a rapid, simple in-vivo method to assembly guide RNA sequences via recombineering between Cas9-helper plasmids and single oligonucleotides. We combine these methodologies with well-established technologies into a comprehensive toolkit for efficient metabolic engineering using CRISPR/Cas9. As a proof of concept, we developed the YaliCraft toolkit for Yarrowia lipolytica, which is composed of a basic set of 147 plasmids and 7 modules with different purposes. We used the toolkit to generate and characterize a library of 137 promoters and to build a de novo strain synthetizing 373.8 mg/L homogentisic acid.

A DNA assembly toolkit to unlock the CRISPR/Cas9 potential for metabolic engineering

CRISPR/Cas9-based technologies are revolutionising the way we engineer microbial cells. One of the key advantages of CRISPR in strain design is that it enables chromosomal integration of marker-free DNA, eliminating laborious and often inefficient marker recovery procedures. Despite the benefits, assembling CRISPR/Cas9 editing systems is still not a straightforward process, which may prevent its use and applications. In this work, we have identified some of the main limitations of current Cas9 toolkits and designed improvements with the goal of making CRISPR technologies easier to access and implement. These include 1) A system to quickly switch between marker-free and marker-based integration constructs using both a Cre-expressing and standard Escherichia coli strains, 2) the ability to redirect multigene integration cassettes into alternative genomic loci via Golden Gate-based exchange of homology arms, 3) a rapid, simple in-vivo method to assembly guide RNA sequences via recombineering between Cas9-helper plasmids and single oligonucleotides. We combine these methodologies with well-established technologies into a comprehensive toolkit for efficient metabolic engineering using CRISPR/Cas9. As a proof of concept, we generated and characterized a library of 137 promoters and built a de novo Yarrowia lipolytica strain synthetizing 373.8 mg/L homogentisic acid.

Machine Learning Models Using Data Mining for Biomass Production from Yarrowia lipolytica Fermentation

In this paper, a database of biomass production from Yarrowia lipolytica fermentation is prepared and constructed using machine learning and data mining approaches. The database is curated from 15 publications and consists of 301 rows of data with 25 predictors and 1 label. The predictors include inoculum size, temperature, pH, and time, while the label is the corresponding biomass production. The database is then divided into training, validation, and test datasets and analyzed as a supervised machine learning task for regression. Twenty-six regression models are employed and compared for their performance in predicting biomass production. The best-performing model is the Matern 5/2 Gaussian process regression model, which has the lowest root-mean-squared error of 0.75 g/L, the highest R squared of 0.90, and the lowest mean absolute error of 0.52 g/L. The t-test is used to identify the most important predictors, and 14 predictors are sufficient for creating an accurate model. These 14 predictors are fermentation time, peptone, temperature, total Kjeldahl nitrogen, shaking rate, total nitrogen, inoculum size, yeast extract, crude glycerol, glucose, oil and grease, media pH, ammonium sulfate, and olive oil. This research demonstrates the application of machine learning and data mining to estimate biomass production and gives insight into which parameters are essential for Yarrowia lipolytica fermentation.

New insights and advances on pyomelanin production: from microbial synthesis to applications

Pyomelanin is a brown-black phenolic polymer and results from the oxidation of homogentisic acid (HGA) in the L-tyrosine pathway. As part of the research for natural and active ingredients issued from realistic bioprocesses, this work re-evaluates the HGA pigment and makes an updated inventory of its syntheses, microbial pathways, and properties, with tracks and recent advances for its large-scale production. The mechanism of the HGA polymerization is also well documented. In alkaptonuria, pyomelanin formation leads to connective tissue damages and arthritis, most probably due to the ROS issued from HGA oxidation. While UV radiation on human melanin may generate degradation products, pyomelanin is not photodegradable, is hyperthermostable, and has other properties better than the L-Dopa melanin. This review aims to raise awareness about the potential of this pigment for various applications, not only for skin coloring and protection but also for other cells, materials, and as a promising (semi)conductor for bioelectronics and energy.

A comprehensive assessment of Yarrowia lipolytica and its interactions with metals: Current updates and future prospective

The non-conventional yeast Yarrowia lipolytica has been popular as a model system for understanding biological processes such as dimorphism and lipid accumulation. The organism can efficiently utilize hydrophobic substrates (hydrocarbons and triglycerides) thereby rendering it relevant in bioremediation of oil polluted environments. The current review focuses on the interactions of this fungus with metal pollutants and its potential application in bioremediation of metal contaminated locales. This fungus is intrinsically equipped with a variety of physiological and biochemical features that enable it to tide over stress conditions induced by the presence of metals. Production of enzymes such as phosphatases, reductases and superoxide dismutases are worth a special mention. In the presence of metals, levels of inherently produced metal binding proteins (metallothioneins) and the pigment melanin are seen to be elevated. Morphological alterations with respect to biofilm formation and dimorphic transition from yeast to mycelial form are also induced by certain metals. The biomass of Y. lipolytica is inherently important as a biosorbent and cell surface modification, process optimization or whole cell immobilization techniques have aided in improving this capability. In the presence of metals such as mercury, cadmium, copper and uranium, the culture forms nanoparticulate deposits. In addition, on account of its intrinsic reductive ability, Y. lipolytica is being exploited for synthesizing nanoparticles of gold, silver, cadmium and selenium with applications as antimicrobial compounds, location agents for bioimaging and as feed supplements. This versatile organism thus has great potential in interacting with various metals and addressing problems related to their pollutant status.

Identification of Red Pigments Produced by Cheese-Ripening Bacterial Strains of Glutamicibacter arilaitensis Using HPLC

Glutamicibacter arilaitensis is one of the predominant bacterial species involved in the coloration of cheese rinds, especially smear-ripened cheeses. Besides well-known yellow-pigmented carotenoids, this species exhibits an ability to produce red pigments, as the occurrence of pink/red formation was previously found when co-cultured with a fungal strain. In this work, the red pigments synthesized by G. arilaitensis strains grown on cheese-based (curd) solid medium deacidified using Debaryomyces hansenii were identified. The analyses using HPLC equipped with both fluorescence and diode array detectors were performed to characterize the pigments extracted from a dry matter of the medium inoculated with either G. arilaitensis Re117, Po102, or Stp101. Based on the UV–vis absorption spectra, the elution order, and fluorescent property, compared to those of the porphyrin standards, eight metal-free porphyrins, including UPI, UPIII, 7PI, 6PI, 5PI, CPI, CPIII, and MPIX, were indicated as components of the red pigments produced by these G. arilaitensis strains. However, following the chromatographic profiles, the degree of porphyrins formed by each strain was apparently different. Regardless of precise quantitative measurement, the type strains Re117 and Po102 manifested a potential to produce a high amount of CPIII, whereas MPIX was formed by the strains Po102 and Stp101, but exceptionally high by the strain Stp101. The variation in both yield and form of the red pigments synthesized by the cheese-related bacterial G. arilaitensis has not previously been reported; therefore, our results provide the first information on these aspects.