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Yarrowia
Yarrowia
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Yarrowia
Scientific classification
Kingdom:
Fungi
Division:
Ascomycota
Class:
Dipodascomycetes
Order:
Dipodascales
Family:
Incertae sedis
Genus:
Yarrowia

Van der Walt & Arx (1981)[1]
Type species
Yarrowia lipolytica
(Wick., Kurtzman & Herman) Van der Walt & Arx (1980)
Species

Yarrowia bubula
Yarrowia deformans
Yarrowia lipolytica
Yarrowia porcina
Yarrowia yakushimensis
Yarrowia parophonii
Yarrowia galli
Yarrowia oslonensis
Yarrowia alimentaria
Yarrowia hollandica
Yarrowia phangngaensis

Yarrowia is a fungal genus in the family Dipodascaceae. For a while the genus was monotypic, containing the single species Yarrowia lipolytica, a yeast that can use unusual carbon sources, such as hydrocarbons.[2] This has made it of interest for use in industrial microbiology, especially for the production of specialty lipids.[3] Molecular phylogenetics analysis has revealed several other species that have since been added to the genus.[4][5][6]

In January 2019, Yarrowia lipolytica yeast biomass was defined by the European Food Safety Authority as a safe novel food – dried and heat‐killed – with the underlying qualifications that it is widespread in nature, present in the typical environment, may be used as food for people over three years of age (3 grams per day for children under age 10, and 6 grams per day for teens and adults), and may be manufactured as a dietary supplement.[7]

Biology

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Habitat

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Yarrowia lipolytica has been isolated from various locations (e.g. milled corn fiber tailings or Paris sewers[8]). Often these environments contain an excess of lipids, which can be efficiently utilized by Y. lipolytica as a carbon and energy source.[9] This species is strictly aerobic.[10]

Oleaginous yeast

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Single cell state of Yarrowia lipolytica
Single cell state of Yarrowia lipolytica under microscope

The cells of Y. lipolytica have over 20% fat content, placing it in the group of oleaginous yeasts.[10] Most lipids are stored as triacylglycerides (TAGs). This physiological trait makes this species especially interesting for producing lipid derivates. For example, genetic engineering and process optimization allow it to produce high amounts of eicosapentaenoic acid (EPA).[11]

Dimorphism

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Filamentous cell state of Yarrowia lipolytica
Filamentous cell state of Yarrowia lipolytica

Yarrowia lipolytica has dimorphic growth,[10] which means it can grow in two different phenotypes. The usual form of the cells can be described as round and spherical. When exposed to stressful conditions such as temperature, pH, mechanical or osmotic stress,[12] the cell can switch into a filamentous growth form (also see hyphae).

Genome

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The genome of Y. lipolytica consists of around 20.5 Mbp (mega base pairs), encodes for over 7000 genes and is distributed on six chromosomes (named A to F) and the mitochondrial DNA (M). Naturally, there are small differences in the length of the genomes of different strain isolates. Usually hemiascomycetous yeast have a low number of introns, but Y. lipolytica is an exception with about 15% of genes containing introns.[13]

References

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Yarrowia

View on Grokipedia
from Grokipedia
Yarrowia is a of ascomycetous yeasts belonging to the family Dipodascaceae in the order Saccharomycetales, characterized by multilateral budding cells and the capacity to form pseudohyphae and true hyphae, with 13 formally described species exhibiting diverse morphological, physiological, and genetic traits. The genus was established in 1980, named after microbiologist , and initially contained only Yarrowia lipolytica as its , though has since expanded recognition of its . Species within Yarrowia demonstrate significant ecological plasticity, inhabiting varied environments such as products, , , guts, and sites across , , and the . For instance, Y. lipolytica is frequently isolated from lipid-rich substrates like cheese rinds and , where it contributes to cycling through degradation, while species like Y. bubula and Y. divulgata thrive in marine and animal-associated niches with tolerance to high (up to 10% NaCl). Other notable species include Y. deformans, known for thermostable production, and Y. phangngensis, which exhibits high accumulation and growth at elevated temperatures up to 37°C. The genus has garnered substantial interest in due to its oleaginous properties and metabolic versatility, particularly Y. lipolytica, which can accumulate exceeding 20% of its weight and is recognized as (GRAS) by regulatory bodies for food and feed applications. This species serves as a for , enabling efficient production of biofuels, , enzymes (such as lipases and proteases), and nutraceuticals through of its 20.5 Mb . Emerging applications extend to other species, like Y. keelungensis for xylitol synthesis and Y. phangngensis for enhanced lipid bioproduction, underscoring the genus's potential in sustainable industrial processes.

Taxonomy and Classification

Etymology and History

The genus was proposed in 1980 by J.P. van der Walt and J.A. von Arx to classify the ascomycetous previously known as Saccharomycopsis lipolytica or Candida lipolytica, with Yarrowia lipolytica designated as the . The name Yarrowia honors , a at the Centraalbureau voor Schimmelcultures (now Westerdijk ) in the , for his contributions to and identification of novel genera. The species epithet lipolytica derives from its exceptional ability to hydrolyze , a trait first noted in early characterizations of the organism. Y. lipolytica was initially isolated in 1928 by F.C. Harrison from a lipid-rich substrate and described as Mycotorula lipolytica, later transferred to Candida lipolytica in 1942 by Diddens and Lodder. In the , the drew attention in research for its lipolytic activity causing spoilage in cheese and other products, with key isolations and studies reported from dairy environments. The teleomorphic (sexual) state was discovered in 1970 by L.J. Wickerham and colleagues at the Northern Regional Research Laboratory, described as Endomycopsis lipolytica, marking a pivotal shift in understanding its life cycle. By the late 1970s, reclassifications placed it under Saccharomycopsis, setting the stage for the 1980 genus establishment. Taxonomic views evolved significantly in the and , transitioning from a monotypic to recognition of greater diversity through . Early ribosomal DNA sequencing studies in the highlighted Yarrowia's distinct position within the Saccharomycetales, distinct from related genera. Biotechnological interest surged during this period due to investigations into its oleaginous nature and , positioning it as a model for single-cell oil and production. In the , multi-locus phylogenetic analyses expanded the ; for instance, a 2013 study by M. Groenewald and colleagues described the teleomorph of Candida deformans and transferred it to Y. deformans, while introducing Yarrowia yakushimensis. Further work in 2014 delineated new species like Y. porcina and Y. bubula from environmental isolates, using sequence data to resolve cryptic diversity previously lumped under Y. lipolytica.

Species Diversity

The genus Yarrowia currently comprises 13 recognized , primarily oleaginous yeasts that accumulate as a significant portion of their , though specific profiles, tolerances, and substrate assimilation patterns differ among them. These cluster phylogenetically within the Dipodascaceae family, with ongoing phylogenomic analyses refining their boundaries due to recent discoveries and reclassifications. The , Yarrowia lipolytica, originally described as Candida lipolytica in 1928 and transferred to Yarrowia in 1980, was isolated from lipid-rich environments such as products, oils, and processing sites. It is notable for its high accumulation, reaching up to 50% of weight under optimized conditions, with a optimum of 28–30°C and broad assimilation capabilities including alkanes, fats, and various sugars. Other established species include Yarrowia deformans, first noted in 1934 from cheese and human nails, which exhibits lipolytic activity and growth at around 25°C but lower content compared to Y. lipolytica. Yarrowia yakushimensis, described in 2013 as the teleomorph of Candida deformans, shares similar morphological traits and is isolated from natural environments, with moderate oleaginous potential. Yarrowia hollandica, originally Candida hollandica from cow skin in 1973 and reclassified in 2007, tolerates similar temperatures (25–30°C) and shows variable profiles enriched in saturated fatty acids. Yarrowia divulgata, identified in 2013 from animal and marine sources, displays diverse assimilation patterns but limited data, growing optimally at 25–28°C. Yarrowia osloensis, originally described as Candida oslonensis in 2007 from blue-veined cheese, was transferred to Yarrowia and shows growth at 15–30°C with moderate accumulation. More recent additions highlight the genus's ecological breadth. Yarrowia galli, described in 2020 from tissue in , is psychrotolerant with growth up to 25°C and potential for protein degradation, though accumulation is around 20%. Yarrowia brassicae, isolated in 2018 from traditional Chinese (pickled ) and formally described that year, represents a 2020s-era discovery with unique capabilities, no or , and growth up to 30°C, though specific profiles remain understudied. Yarrowia porcina and Yarrowia bubula, both described in 2014 from and sediments, exhibit psychrotrophic optima (15–25°C) and contents up to 20%, with high saturated proportions. Yarrowia alimentaria, noted in 2004 from fermented foods like cheese and , is psychrotolerant (no growth above 30°C) with about 4.5% content dominated by . Yarrowia phangngensis (2015, from seawater, high lipids with C16:0 dominance, up to 37°C tolerance) and Yarrowia keelungensis (2013, from marine microlayers, oil-degrading) further illustrate the genus's to aquatic and lipid-polluted niches. Yarrowia parophonii, described in 2017 from the gut of a beetle in , grows at 20–28°C and exhibits moderate proteolytic activity. These variations underscore the need for continued taxonomic reassessment to account for genomic and physiological diversity.

Phylogenetic Position

Yarrowia belongs to the phylum , subphylum , family Dipodascaceae, and represents an early-branching hemiascomycetous within the Saccharomycetales order. This positioning is supported by multigene phylogenetic analyses that place it distant from more derived yeasts like , highlighting its basal role in the hemiascomycete lineage. The Yarrowia clade comprises all oleaginous species in this group, characterized by their capacity for high lipid accumulation. Its closest relatives are genera such as Cyberlindnera and Dipodascus, also within Dipodascaceae. Genome sizes across Yarrowia species vary modestly, typically around 20 Mb, reflecting conserved genomic architecture in the clade. Phylogenetic resolution relies on molecular markers including the (ITS) region, D1/D2 domains of the 26S rRNA gene, and multi-gene datasets. A 2021 phylogenomic study using these markers reassessed the clade's evolutionary origins, supporting a temperate ancestral rather than strictly marine or tropical associations. Evolutionarily, the clade displays ancestral adaptations in pathways, facilitating efficient utilization of hydrophobic substrates like oils, which are linked to niche exploitation in lipid-rich environments.

Morphology and Growth

Cell Structure

Yarrowia yeast cells exhibit an oval to spherical morphology, typically measuring 3–6 μm in diameter, and display unipolar or bipolar budding patterns in the type species Y. lipolytica, while most species in the genus show multilateral budding. These cells are enclosed by a thick cell wall primarily composed of mannoproteins, chitin, and β-glucans, which provide structural integrity and contribute to environmental stress resistance. The cell wall forms a rigid matrix where β-1,3-D-glucan and β-1,6-D-glucan intertwine with chitin microfibrils, while mannoproteins form an outer fibrillar layer linked via glycosylphosphatidylinositol anchors. Vegetative yeast cells lack the specialized ascospore walls found in sexual spores, consisting instead of a simpler envelope suited to budding reproduction. Internally, the features prominent bodies, particularly in oleaginous strains where these organelles can occupy a significant portion of the cell volume and accumulate up to 40% of the cell dry weight under nutrient-limited conditions. bodies serve as storage sites for neutral like triacylglycerols, synthesized via (ER) networks that facilitate acyl chain assembly and droplet biogenesis. are also conspicuous, playing a key role in β-oxidation by housing enzymes such as oxidases, which proliferate during growth on hydrophobic substrates. Mitochondria, adapted for robust aerobic respiration as a strictly aerobic , contain a compact circular and support high energy demands through efficient electron transport chains. Additional cytoplasmic structures include multivesicular bodies involved in the endosomal sorting and vacuolar degradation pathways, aiding protein trafficking and recycling. The ER forms extensive networks essential for lipid biosynthesis and membrane biogenesis. Cell wall composition exhibits variations with environmental pH, with extreme conditions altering protein expression and potentially increasing content at low pH to enhance rigidity. These structural features in the form underpin the organism's metabolic versatility and its capacity for dimorphic transitions under specific cues. While Y. lipolytica typically shows polar budding, most Yarrowia species exhibit multilateral budding, with variations in cell shape and size across the .

Dimorphic Transitions

Yarrowia lipolytica, the of the , displays dimorphism by alternating between a unicellular form, characterized by , and a filamentous form consisting of pseudohyphae or true septate hyphae. The hyphal structures are typically 3–5 μm in width and can extend to several millimeters in length, with apical cells often exceeding 100 μm. This morphological plasticity allows adaptation to varying environmental conditions. The -to-hyphae transition in Y. lipolytica is triggered by multiple environmental cues. Neutral to alkaline levels, particularly around 6–7, maximize mycelial growth, whereas acidic conditions ( <4) favor the yeast form. Specific carbon sources, such as N-acetylglucosamine in neutral buffers, were previously reported to induce true hypha formation; however, recent studies indicate it can inhibit filamentation under certain conditions. Serum acts as a potent inducer, promoting rapid hyphal development compared to other stimuli. Hydrophobic substrates, including oils like coconut or palm kernel oil rich in lauric and myristic acids, drive the transition, achieving up to 95% mycelium formation by facilitating cell attachment to substrate droplets. Mutants, such as those in the yl-HOG1 gene, impair the filament-to-yeast reversion, locking cells in the hyphal state under certain conditions. Molecular regulation of dimorphism involves signaling pathways responsive to stress and nutrients. The mitogen-activated protein kinase (MAPK) cascade, particularly the high-osmolarity glycerol (HOG) pathway homolog including YlHog1, plays a key role; deletion of YlHOG1 reduces hyphal growth and alters osmotic stress responses. Polyamine metabolism also influences the switch, with elevated ornithine decarboxylase activity and increased intracellular polyamine pools observed in hyphal cells during induction on N-acetylglucosamine-containing media. The hyphal form enhances substrate invasion, particularly for hydrophobic or solid nutrients, improving nutrient acquisition in natural environments. This transition is finely tuned by environmental stresses, such as nutrient availability and pH shifts, underscoring its adaptive significance in ecological and industrial contexts.

Cultural Characteristics

Yarrowia lipolytica exhibits diverse colony morphologies on solid media, typically appearing as smooth, creamy-white, and yeast-like on rich agar such as yeast extract peptone dextrose (YPD), while dimorphic strains may display convoluted or matte surfaces with fuzzy edges due to hyphal outgrowth. Colony texture is influenced by the dimorphic transition, where pseudohyphal or mycelial forms contribute to irregular, wrinkled appearances under certain conditions. Optimal cultivation occurs on YPD or minimal media supplemented with carbon sources like glucose or glycerol, at temperatures around 28°C, under strictly aerobic conditions with no fermentation of sugars observed. The yeast requires oxygenation for growth, thriving in shake flasks or bioreactors where high aeration supports processes like lipid accumulation. Physiological tests confirm lipase-positive activity, enabling efficient degradation of lipids, and assimilation of alkanes and oils as carbon sources, but no assimilation of nitrate. Pseudomycelium formation is evident on cornmeal agar, appearing as off-white growth with pseudohyphae and septate mycelium. Industrial strains, such as W29, tend to produce more uniform yeast-like colonies compared to wild-type isolates, facilitating consistent cultivation for biotechnological applications.

Habitat and Ecology

Natural Environments

Yarrowia species are commonly found in lipid-rich environments, including dairy products such as cheese and milk, as well as meat processing byproducts like sausages. These yeasts thrive in such niches due to their affinity for hydrophobic substrates. Additionally, they are frequently isolated from oily wastes and polluted soils, particularly hydrocarbon-contaminated sites where they contribute to natural remediation processes. The genus exhibits remarkable ecological diversity, with isolates recovered from marine environments and salt marshes, as well as unusual sources like aviation fuel contaminated with kerosene. Yarrowia species have also been isolated from insect guts, such as Y. yakushimensis and Y. parophonii. Certain species, such as Yarrowia brassicae, have been documented in fermented foods, including traditional Chinese pickled cabbage. These varied isolation sources underscore the adaptability of Yarrowia to both aquatic and terrestrial settings worldwide. The isolation history of Yarrowia dates back to the 1940s and 1950s, when strains were first recovered from lipid-rich natural environments during early microbial surveys. Subsequent discoveries in the late 20th century expanded this to extreme sites, including oil spills and contaminated industrial residues. Yarrowia displays a cosmopolitan distribution, with isolates reported from diverse climates including temperate and tropical regions. Although occasionally detected in human-associated sites like the respiratory tract, no Yarrowia species are established as primary human pathogens, with infections limited to rare opportunistic cases in immunocompromised individuals.

Substrate Utilization

Yarrowia species, particularly Y. lipolytica, exhibit a pronounced preference for hydrophobic carbon sources as primary substrates for growth and energy derivation. These include triacylglycerols, which are hydrolyzed extracellularly by lipases such as LIP2, LIP7, and LIP8 to release fatty acids for subsequent uptake and β-oxidation. Alkanes in the C10–C20 range are efficiently assimilated through initial oxidation mediated by cytochrome P450 monooxygenases (e.g., ALK genes), converting them to primary alcohols and then fatty acids. Free fatty acids are directly transported into cells via diffusion or specific transporters and metabolized via peroxisomal and mitochondrial β-oxidation pathways. While these hydrophobic substrates support robust growth, Yarrowia can also utilize hydrophilic alternatives such as glucose (the preferred hexose), glycerol, and acetate, with glycerol enabling particularly rapid proliferation and acetate being converted to acetyl-CoA by acetyl-CoA synthetase. The metabolic versatility of Yarrowia is underscored by its aerobic lifestyle, which precludes ethanol production and favors complete oxidation of substrates for energy. Extracellular lipases facilitate the breakdown of complex oils and fats in the growth medium, enhancing access to otherwise insoluble nutrients. Alkane utilization involves a specialized pathway where cytochrome P450 enzymes, in conjunction with aldehyde dehydrogenases, ensure stepwise conversion to metabolizable forms without accumulation of toxic intermediates. This adaptability positions Yarrowia well in environments rich in oily or waxy materials, such as hydrocarbon-polluted sites. However, Yarrowia displays notable limitations in substrate range, particularly showing poor utilization of complex polysaccharides due to the absence of robust hydrolytic enzymes for starch, cellulose, or hemicellulose. Growth on any substrate requires supplementary nitrogen sources, such as ammonium, to support protein synthesis and cellular proliferation, as nitrogen limitation shifts metabolism toward storage rather than biomass production. Strain-specific variations further influence substrate preferences within Y. lipolytica. For instance, the wild-type strain W29 demonstrates enhanced assimilation of longer-chain alkanes (C15–C20) compared to strains like H222, which favor shorter chains (C10–C14), reflecting differences in P450 enzyme expression and efficiency.

Ecological Roles

Yarrowia species, particularly Y. lipolytica, play a significant role in the biodegradation of hydrocarbons in polluted soils and waters, contributing to natural bioremediation processes such as the cleanup of oil spills. These yeasts efficiently degrade n-alkanes (C11–C19), isoprenoids like pristane and phytane, and aromatic compounds such as naphthalene and phenanthrene through alkane metabolic pathways involving cytochrome P450 monooxygenases for initial oxidation and subsequent β-oxidation, often enhanced by lipase activity and biosurfactant production that improves emulsification and cell adhesion to hydrophobic substrates. For instance, strains like Y. lipolytica IMUFRJ 50682 have demonstrated substantial reduction of crude petroleum components over 120 hours in lab simulations of contaminated environments. In food ecosystems, Yarrowia yeasts exhibit dual roles, contributing to desirable flavor development in fermented products like cheeses and sausages while occasionally causing spoilage defects. Through strong lipolytic and proteolytic activities, Y. lipolytica hydrolyzes fats into volatile compounds such as esters, ketones, and sulfur volatiles (e.g., methanethiol), enhancing aroma and texture in ripening cheeses like Camembert and dry sausages like salami. However, uncontrolled growth can lead to off-flavors, bitter compounds, surface browning, and biogenic amine accumulation (up to 120 mg/kg) in dairy products, particularly fresh lactic curd cheeses and smear-ripened varieties. Yarrowia species participate in symbiotic associations within microbial consortia, facilitating the breakdown of organic waste in lipid-rich environments. Y. lipolytica collaborates with bacteria such as Bacillus spp. and Pseudomonas putida to achieve up to 90–95% degradation of waste fats like butter and olive oil, where the yeast preferentially metabolizes oleic acid and accumulates intracellular lipids (20–24% w/w), complementing bacterial autolysis for efficient nutrient recycling. Additionally, Y. brassicae, isolated from traditional Chinese pickled cabbage, shows potential in fermented food consortia, assimilating glucose, glycerol, and citrate to support pickling processes, though its specific contributions remain understudied. Ecologically, Yarrowia yeasts are non-pathogenic, classified as Generally Recognized as Safe (GRAS) by regulatory bodies, and promote nutrient cycling in lipid-rich niches such as dairy waste, sewage, and oil-polluted sites by converting hydrophobic substrates into biomass and metabolites. Their presence enhances carbon flux and reduces pollutant persistence without posing health risks, as growth is limited above 32°C. Yarrowia species also demonstrate tolerance to extreme conditions, including high salinity up to 12% NaCl, through osmo-protective mechanisms like increased intracellular amino acids (e.g., proline) and proteome adjustments for energy metabolism.

Physiology and Metabolism

Oleaginous Traits

Yarrowia species, including the model Y. lipolytica, are recognized as oleaginous yeasts due to their capacity to accumulate lipids exceeding 20% of their dry cell weight, a defining threshold for oleaginous microorganisms, though profiles vary across the 13 species. In wild-type strains, Y. lipolytica typically amasses 20-50% of its biomass as lipids, primarily stored as triacylglycerols (TAGs) within specialized lipid bodies that serve as intracellular depots. This trait positions Yarrowia as a prominent model for studying lipid biosynthesis in non-conventional yeasts. The biochemical pathways underpinning lipid accumulation in Yarrowia emphasize enhanced fatty acid synthesis, initiated by the ATP-citrate lyase (ACL) pathway, which cleaves citrate to generate acetyl-CoA, the foundational building block for fatty acid elongation and desaturation. NADPH, essential for these reductive processes, is predominantly supplied through the oxidative pentose phosphate pathway, ensuring sufficient reducing power during lipid production. Concurrently, β-oxidation is downregulated under lipid-accumulating conditions, minimizing fatty acid degradation and redirecting carbon flux toward storage lipids. Lipid accumulation is primarily triggered by nutrient imbalances, particularly nitrogen limitation in the presence of excess carbon sources, where carbon-to-nitrogen (C/N) ratios surpass 20, such as 60:1 or higher. This stress halts cellular growth and diverts surplus carbon into lipid synthesis, yielding up to 0.2 g of lipids per gram of glucose consumed in optimized wild-type cultures. Aerobic conditions are crucial, as oxygen supports the respiratory metabolism necessary for high lipid yields. The lipid profile of Yarrowia consists of 40-50% neutral lipids, dominated by TAGs that constitute 80-90% of the neutral fraction, rendering them suitable for biofuel applications due to their similarity to vegetable oils. Variations across strains include elevated levels of polyunsaturated fatty acids (PUFAs), such as linoleic acid (C18:2), in certain isolates, enhancing potential uses in nutraceuticals.

Nutrient Requirements

While nutrient requirements vary across Yarrowia species, detailed studies focus on Y. lipolytica, an oleaginous yeast that exhibits versatile carbon utilization, preferring hydrophobic substrates such as oils and alkanes, though it efficiently assimilates hexoses like glucose at concentrations up to 100 g/L for robust biomass accumulation. Glycerol serves as a favored carbon source, supporting high growth rates, particularly when present at 150 g/L or more in crude forms from industrial wastes. As a strictly aerobic organism, Y. lipolytica mandates adequate oxygen supply, with dissolved oxygen levels exceeding 20% saturation essential to prevent growth inhibition and maintain metabolic efficiency. Nitrogen is critical for protein synthesis and cellular proliferation in Y. lipolytica, typically supplied as inorganic ammonium salts like (NH4)2SO4 at 4-5 g/L or organic forms such as amino acids and yeast extract. Nitrogen limitation, achieved by high carbon-to-nitrogen ratios (e.g., >80:1), redirects toward storage, enhancing oleaginicity without compromising overall viability. Essential minerals include at 1-5 g/L (often as KH2PO4), magnesium at 0.5-1.5 g/L (as MgSO4), and trace elements such as iron and , which support enzymatic functions including lipases. Unlike , Y. lipolytica has no requirement, synthesizing sufficient internally for growth. Optimal growth occurs at 5.5-6.5 within a broader tolerance of 4.5-8.0, with higher values promoting dimorphic transitions to hyphal forms under certain conditions. Temperatures between 20-35°C support proliferation, peaking at 28-30°C, beyond which may alter morphology and productivity.

Reproductive Cycle

The reproductive cycle in Yarrowia species, exemplified by Y. lipolytica, involves both asexual and sexual phases, with variations possible across the . Yarrowia lipolytica reproduces asexually primarily through in its form and fragmentation in its hyphal form, without the production of endospores. In the phase, cells exhibit polar or multipolar , where daughter cells form at specific apical or multilateral sites on the mother cell, often resulting in pseudohyphae when successive buds remain attached after cell separation. In the hyphal phase, asexual propagation occurs via septation and fragmentation of the into arthroconidia—chains of rectangular, uninucleate cells that dissociate and germinate into new cells or hyphae. Sexual reproduction is heterothallic, governed by two nonallelic , MATa and MATb, encoded at distinct chromosomal loci. Haploid cells of opposite mating types fuse to form a , which elongates into dikaryotic hyphae containing unfused nuclei from each parent. subsequently occurs in terminal hyphal cells, yielding a diploid nucleus that undergoes and a mitotic division, culminating in unconjugated each bearing 1–4 smooth, ellipsoidal ascospores. These ascospores are released upon ascus dehiscence and germinate directly into haploid cells under favorable conditions. The reproductive life cycle centers on a dominant haploid stage, where environmental cues trigger dimorphic transitions and to initiate the sexual phase: haploid cells of compatible types → zygote → dikaryotic hyphal growth → and in asci → ascospores → haploid progeny. This cycle is infrequently observed in laboratory cultures due to low natural efficiency (10⁻⁶ to 10⁻⁷), though it can be enhanced to near 10⁻² by nutrient manipulations, such as starvation or use of defined media like yeast extract-malt extract. Most industrial strains of Y. lipolytica are haploid, aligning with the stable haploid dominance in the natural cycle, while the sexual phase remains understudied owing to its rarity and challenges in induction, despite offering opportunities for via recombination. The loci show stable genomic integration without switching, distinguishing Y. lipolytica from related yeasts.

Genetics and Genomics

Genome Organization

The genome of Yarrowia lipolytica typically spans approximately 20 Mb and is organized into six chromosomes. This structure accommodates around 6,400 to 7,800 protein-coding genes, with estimates varying by strain and assembly method; for instance, the reference strain CLIB122 contains 6,485 protein-coding genes. The overall is high at about 49%, contributing to its stability and distinguishing it from lower-GC yeasts like . Key genomic features include a relatively low intron density compared to more complex eukaryotes, with approximately 15% of genes containing s—four times the rate in S. cerevisiae. These s are typically short, averaging 280 , and are enriched in the 5' regions of genes. Repetitive elements constitute a notable portion of the genome, including (LTR) retrotransposons like Ylt1 and LINE elements such as Ylli, which together account for roughly 10% of the sequence and drive structural diversity across strains. Recent assemblies have improved resolution of challenging regions, such as ribosomal DNA () clusters, which are multiple and telomeric; the 2021 hybrid assembly of strain DSM 3286 fully resolved these clusters across its 22.4 Mb genome. Strain-specific variations highlight genomic plasticity relevant to Y. lipolytica's oleaginous . The 2016 assembly of the industrial strain W29/CLIB89 yielded 20.3 Mb across six chromosomes, revealing expansions in lipid biosynthesis pathways compared to S. cerevisiae, including enhanced glycerol utilization and genes. Functional annotation identifies over 20 and genes (16 lipases and 4 esterases), supporting efficient degradation and accumulation. Select strains, like DSM 3286, achieve telomere-to-telomere contiguity in assemblies, enabling precise mapping of subtelomeric repeats and their role in metabolic clusters. These features underpin Y. lipolytica's utility in production, where genomic expansions facilitate high-yield triacylglycerol synthesis under nutrient-limited conditions.

Mating and Sexual Reproduction

Yarrowia lipolytica exhibits a heterothallic mating system characterized by two idiomorphs, MATa and MATb, located on chromosome C. The MATa idiomorph encodes two divergently transcribed genes, MATA1 and MATA2, which produce transcription factors essential for mating-type identity. MATA1 induces sporulation in diploids, while MATA2 represses conjugation; the latter contains an HMG-box DNA-binding domain homologous to those in Saccharomyces cerevisiae mating-type proteins, though with Yarrowia-specific regulatory elements. Similarly, the MATb idiomorph encodes MATB1 and MATB2, which function as transcription factors regulating B-type mating responses and sexual differentiation, featuring unique Y. lipolytica-adapted motifs distinct from but functionally analogous to S. cerevisiae counterparts. Mating initiation relies on a signaling system involving a-factor-like peptides secreted by cells of one to induce responses in the opposite type. These pheromones are detected by G-protein-coupled receptor genes homologous to STE2 (for a-factor reception in MATb cells) and STE3 (for α-factor-like reception in MATa cells) from S. cerevisiae, activating a signaling cascade that promotes arrest, formation, and hyphal fusion between compatible partners. This fusion enables , forming diploids that integrate with the yeast's dimorphic growth by facilitating mating in hyphal forms. Post-karyogamy, diploid cells undergo within specialized ascogenous hyphae under nutrient-limiting conditions, such as starvation, culminating in the formation of asci containing four . Spore viability typically reaches approximately 80%, allowing for reliable tetrad analysis and the generation of maps through controlled crosses between auxotrophic mutants. Evolutionarily, the of Y. lipolytica retains core features conserved across yeasts, including idiomorph-based mating-type switching and pheromone-receptor mechanisms, but shows adaptations for its dimorphic lifestyle, such as enhanced hyphal involvement in fusion events; while predominantly heterothallic, rare homothallic strains capable of self-mating have been isolated, highlighting intraspecific variation.

Genetic Engineering Tools

Genetic engineering of Yarrowia lipolytica relies on efficient transformation methods, primarily electroporation and lithium acetate-based protocols, which enable the introduction of foreign DNA into the yeast cells. Electroporation has been optimized to achieve high transformation efficiencies, with protocols yielding up to 2.1 × 10^4 transformants per microgram of DNA when cells are pretreated with 150 mM lithium acetate for 1 hour prior to pulsing. These methods capitalize on the yeast's native homologous recombination (HR) machinery, which supports integration efficiencies approaching 90% through repression of non-homologous end-joining (NHEJ) components like KU70 and KU80. The compact genome size of approximately 20 Mb further facilitates accurate assembly and verification of engineered constructs. Yarrowia-specific expression vectors, such as the pYL series (e.g., pYL-URA and pYL-ARS), incorporate auxotrophic markers like and LEU2 for selection in mutant strains deficient in uracil or biosynthesis. These plasmids often include autonomously replicating sequences (ARS) for episomal maintenance or integrative elements for stable genomic insertion. Since 2016, CRISPR- systems have been adapted for Y. lipolytica, with initial implementations using codon-optimized Cas9 and single-guide expression cassettes to enable precise targeting and editing without reliance on extensive homology arms. Advanced techniques in Y. lipolytica include transformation-associated recombination (TAR) , which leverages the yeast's HR proficiency for seamless multi-fragment assembly of large pathways, as demonstrated in the integration of polyketide clusters. Optogenetic tools, such as blue light-inducible systems based on the EL222 , have been developed to provide spatiotemporal control over metabolic pathways, allowing light-dependent activation of for dynamic regulation of product synthesis. A comprehensive genetic established in 2017 encompasses a suite of inducible promoters, including the POX2 promoter, which responds to fatty acids and is particularly suited for controlling peroxisomal genes involved in . This supports the creation of strain libraries tailored for , enabling and optimization of oleaginous traits through combinatorial disruptions and overexpression.

Biotechnological Applications

Industrial Production

Yarrowia lipolytica has emerged as a key microbial platform for industrial production of and organic acids, leveraging its oleaginous nature to achieve high yields under optimized conditions. Engineered strains have been developed for the production of omega-3 fatty acids, particularly (EPA), suitable for applications. DuPont's metabolically engineered strains, such as the Gen III HP strain Z5567, produce EPA at levels exceeding 25% of weight (DCW), with over 50% of total comprising EPA, through the introduction of desaturase and elongase genes via the Δ9 pathway. These strains enable the accumulation of triacylglycerols (TAGs) as a primary form, supporting conversion to feedstocks. Additionally, genetic modifications targeting TAG , such as overexpression of diacylglycerol acyltransferases (DGA1, LRO1) and disruption of lipid degradation pathways (e.g., PEX10, POX2), have enhanced overall lipid productivity in strains like those derived from W29. Industrial processes for lipid production typically employ fed-batch fermentation in bioreactors, initiating with a nitrogen-rich growth phase followed by nitrogen limitation to trigger lipid accumulation, often using glucose or waste-derived carbon sources. This approach has yielded lipid titers over 50 g/L, with one engineered strain achieving 54.6 g/L lipids at 45.8% DCW content and a productivity of 2.06 g/L/h in a 5-L bioreactor. Commercial-scale production of omega-3 oils from Y. lipolytica was pioneered by DuPont in the 2010s, resulting in products like New Harvest™ EPA oil for supplements and integration into sustainable aquaculture feeds such as Verlasso salmon; however, New Harvest™ has since been discontinued, demonstrating prior scalability from lab to pilot fermentors. The use of low-cost substrates, such as crude glycerol from biodiesel waste, further improves economics, with fed-batch cultivations reaching over 50% lipid content and biomass yields up to 18.5 g/L, reducing feedstock costs that can account for 60% of production expenses. Beyond , Y. lipolytica serves as an efficient producer of organic acids through and process optimization. The strain DSM 3286 is a well-established producer, capable of yields up to 150 g/L under nitrogen-limited conditions with carbon sources like or glucose, often in repeated-batch modes at 4.5–6.0 and 28–30°C. Mutants derived from similar backgrounds, such as Wratislavia AWG7, have achieved 154 g/L from crude , highlighting the yeast's adaptability to industrial wastes. For , engineering strategies including overexpression of reductive TCA pathway enzymes and disruption of competing routes (e.g., SDH1 promoter ) have enabled titers of 110.7 g/L with a yield of 0.53 g/g in fed-batch without control, positioning Y. lipolytica as a competitive alternative to bacterial producers. These advancements underscore the yeast's versatility in generating high-value bioproducts at scales relevant to chemical .

Food and Pharmaceutical Uses

_Yarrowia lipolytica serves as a starter culture in the production of fermented sausages and cheeses, where its lipolytic activity contributes to flavor development through degradation during ripening. This yeast is naturally associated with environments, enhancing its suitability for these applications. Additionally, Y. lipolytica is utilized to produce (SCP) from agro-industrial wastes, yielding biomass with approximately 50% protein content, which can serve as a sustainable protein source in or . In applications, engineered strains of Y. lipolytica produce such as at levels exceeding 10 mg/g dry cell weight, offering potential as a natural colorant and antioxidant supplement. The yeast also supports (vitamin B2) overproduction, with strains achieving enriched biomass containing up to 5.3 mg/100 g, valuable for fortifying foods to address nutritional deficiencies. For pharmaceutical uses, Y. lipolytica enables high-level secretion of recombinant proteins, such as for enzyme replacement therapy in , with yields reaching approximately 1 g/L in optimized conditions. Its pathways have been engineered to produce human-like N-glycans (e.g., Man5GlcNAc2 or Man8GlcNAc2), facilitating vaccine platforms like virus-like particles for antigens, including those targeting fish nervous necrosis virus. Y. lipolytica holds (GRAS) status from the U.S. FDA for various applications, including production, and has been approved as a by the in 2019, supporting its safe integration into and pharmaceutical products in the EU and US.

Environmental Remediation

Yarrowia lipolytica has emerged as a promising microbial agent for due to its robust metabolic capabilities, particularly in degrading hydrophobic pollutants and tolerating harsh conditions. As an oleaginous , it efficiently assimilates alkanes, fatty acids, and oils through the production of extracellular lipases and biosurfactants, such as glycolipids, which emulsify insoluble substrates and facilitate their uptake and breakdown. This makes it suitable for treating oil-contaminated sites and industrial wastewaters, where it converts recalcitrant compounds into less harmful byproducts like and biomass. In the of hydrocarbons, Y. lipolytica demonstrates high efficiency in degrading n-s and crude components. For instance, wild-type strains can biodegrade up to 45% of n-hexadecane (10 g/L) within 96 hours, while metabolically engineered variants, incorporating alkane hydroxylase genes like AlmA1 and AlkM, achieve 75% degradation under similar conditions by enhancing initial oxidation steps in the alkane assimilation pathway. Co-cultivation with biosurfactant-producing microbes, such as Candida bombicola, further boosts efficiency to over 80% by improving substrate bioavailability through sophorolipid production. These capabilities extend to and remediation of spills, where immobilized cells on alginate gels maintain activity and prevent microbial washout, as observed in geoelectrical monitoring of hydrocarbon-depleted zones. For heavy metal pollution, engineered Y. lipolytica strains have been developed to produce sulfides via CRISPR-Cas9-mediated modifications to the pathway, yielding up to 550 ppm of . This sulfide precipitates metals like , , and lead as insoluble sulfides on the cell surface, achieving over 90% removal from both synthetic and industrial s. Biosurfactants from Y. lipolytica also aid in mobilizing in contaminated soils, with one strain removing 66% of Pb²⁺ and 42% of Cd²⁺ from synthetic while enhancing co-remediation by other microbes. Such approaches highlight its potential in sulfide-mediated , outperforming traditional chemical methods in eco-friendliness. Beyond hydrocarbons and metals, Y. lipolytica contributes to by metabolizing organic pollutants in agro-industrial effluents. In canning wastewater, it reduces by 87.5%, by 44%, and color by 86% over seven days, producing valuable single-cell proteins (46 mg/g ) as a . Its activity hydrolyzes in olive mill wastewaters, significantly lowering loads, while adaptation to saline and high-organic-load environments supports its use in desalination-integrated remediation. These applications underscore Y. lipolytica's versatility in converting waste into resources, though challenges like optimizing strain stability in field conditions remain areas of ongoing .

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