Identification of the UDP-glucosyltransferase gene UGTA1, responsible for the first glucosylation step in the sophorolipid biosynthetic pathway of Candida bombicola ATCC 22214

Microbial biosurfactant hydrogels with tunable rheology for precision 3D printing of soft scaffolds

Bio-based surfactants, derived from microbial fermentation, are appealing biocompatible amphiphiles traditionally employed in depollution, pest control, personal care, cosmetics, and medicine, although their potential in biomedical scaffolds remains largely unexplored due to the limited adaptability of their rheological properties for extrusion-based 3D printing. This work demonstrates that microbial biosurfactants can function as low-molecular-weight gelators with facile, tunable rheological functionalities, enabling their integration into additive-free 3D printing processes. A hydrogel, formed by complexing a single-glucose oleyl lipid surfactant with calcium ions, exhibits shear-thinning behavior, viscoelasticity, yield stress, thixotropic response, and elongational properties, all essential for extrusion-based printing. A comprehensive rheological study reveals that the hydrogel's shear-thinning behavior allows controlled extrusion using conventional methods, while its yield stress ensures structural integrity by resisting capillary and gravitational stresses during deposition. Furthermore, the hydrogel demonstrates rapid stress recovery, enabling it to rebuild yield stress post-extrusion and prevent spreading. It's controlled fragility under stretching and shear ensures that structures can be printed without significant deformation, maintaining high fidelity throughout the process. Beyond its printability, the hydrogel exhibits stimuli-responsive functionality, particularly pH sensitivity, unlocking opportunities for 4D printing applications, where material properties evolve dynamically post-fabrication. This work positions biosurfactant-based hydrogels as a sustainable, high-performance material platform, paving the way for the use of this class of molecules for soft material engineering.

Knockout mutation to enhance sophorolipid production in Starmerella bombicola based on computational structural analysis of fatty acid oxidation enzymes

Sophorolipids (SLs), produced by Starmerella bombicola, consist of a hydrophilic sophorose linked to a hydrophobic ω/ω-1 hydroxyl fatty acid. Fatty acid oxidation competes with the synthesis of SL, particularly under conditions of low content of glucose or high accumulation of fatty acid. While many studies have focused on modifying key enzyme genes within the synthesis pathway of SL, research to identify key genes outside of this pathway, such as those involved in the β- and ω-oxidation of fatty acids, remains limited. This study aimed to prevent ω hydroxyl fatty acids from entering β- and ω-oxidation pathways, thus directing them toward SL synthesis. Key enzymes, SbMFE-2, SbADH1, and SbADH2, were selected for investigation. Gene knockout mutants revealed that the ΔSbADH1 mutant significantly increased SL yield when linoleic acid and oleic acid (C18) was used as the lipid source. No significant differences were observed with lauric acid (C12) as the lipid source. Additionally, computational structural analyses using AlphaFold 3, docking, and molecular dynamics simulations provided insights into the enzyme functions and their substrate preferences, offering a mechanistic explanation for the enhanced SL production in the ΔSbADH1 mutant.

High-throughput screening method for glycolipids based on substrate modification and their efficient biomanufacturing

The development of a high-throughput screening (HTS) method is crucial for boosting microbial synthesis. However, in non-model strains, genetic editing-based HTS is often not feasible. Here, a substrate-modified HTS strategy using Starmerella bombicola PL0120, a sophorolipids (SLs)-producing strain, was designed. First, the medium was optimized to increase the SLs yield to 248 g/L. Then, 2-benzylstearic acid was synthesized, which PL0120 can use to make SLs analogs. Subsequently, by selecting dark-phenotype strains and using 254 nm absorption, a 51.1 % high-yielding SLs strain screening rate was achieved. Among these strains, strain A6 yielded a concentration of 324 g/L. Moreover, this method has been extended to rhamnolipids (RLs). By engineering a microbubble reactor, the yield of RLs was increased to 70.3 g/L. This HTS methodology is instrumental in augmenting the production output of microbial fermentation products, which in turn, facilitates cost-effective biomanufacturing.

Turning the non-pathogenic yeast Starmerella bombicola into a powerful long-chain dicarboxylic acid production host

Bio-based long-chain dicarboxylic acids (LCDAs) are in high demand in the polymer industry. These compounds have diverse applications as building blocks for polymers with distinct features, which lead to a fast-growing global LCDA market. However, bio-based LCDA production is currently limited in Europe as established processes are using the pathogenic yeast, Candida tropicalis. Therefore, this study aimed to establish safe and sustainable LCDA production using an industrially relevant non-pathogenic yeast, Starmerella bombicola. The metabolic network was successfully controlled to channel fatty acids from rapeseed oil into the ω-oxidation for the high production of LCDAs. Importantly, the engineered yeast strain produced 5.5 g/l of total LCDAs in shake flasks. Furthermore, pH optimization of the bioprocess resulted in a significant improvement of the total LCDA titer up to 117.8 g/l. The outcomes strongly demonstrate that S. bombicola can serve as a safe and efficient platform microorganism for industrial LCDA production.

Production and characterization of novel/chimeric sophorose-rhamnose biosurfactants by introducing heterologous rhamnosyltransferase genes into Starmerella bombicola

Glycolipid biosurfactant, sophorolipids (SLs) and rhamnolipids (RLs) can be widely used in agriculture, food and chemical industries. The different physicochemical properties of SLs and RLs, such as hydrophilic lipophilic value (HLB) and critical micelle concentration (CMC), determine they have different application focus. Researchers are still hoping to obtain new glycolipid surfactants with unique surface activities. In this study, we successfully transformed two rhamnosyltransferase genes rhlA and rhlB from Pseudomonas aeruginosa to the sophorolipid-producing Starmerella bombicola CGMGG 1576 to obtain a recombinant strain was SbrhlAB. Two novel components with molecular weight of 554 (C26H50O12) and 536 (C26H48O11) were identified with the ASB C18 column from the fermentation broth of SbrhlAB, the former was a non-acetylated acidic C14:0 glycolipid containing one glucose and one rhamnose, and the latter was an acidic C14:1 glycolipid containing two rhamnoses. With the Venusil MP C18 column, one new glycolipid component was identified as an acidic C18:3 glycolipid with one rhamnose (C24H40O7), which has not been reported before. Our present study demonstrated that novel glycolipids can be synthesized in vivo by reasonable genetic engineering. The results will be helpful to engineer sophorolipid-producing yeast to produce some specific SLs or their derivatives in more rational and controllable way.

Bubbling insights: unveiling the true sophorolipid biosynthetic pathway by Starmerella bombicola

BACKGROUND

The yeast Starmerella bombicola is renowned for its highly efficient sophorolipid production, reaching titers and productivities of (over) 200 g/L and 2 g/(L h), respectively. This inherent efficiency has led to the commercialization of sophorolipids. While the sophorolipid biosynthetic pathway has been elucidated a few years ago, in this study, it is revisited and true key intermediates are revealed.

RESULTS

Recently, Starmerella bombicola strains developed and evaluated in the past were reevaluated unveiling unexpected findings. The AT enzyme encoded in the sophorolipid biosynthetic gene cluster is the only described enzyme known to acetylate sophorolipids, while the SBLE enzyme encoded by the SBLE gene is described to catalyze the conversion of (acetylated) acidic sophorolipids into lactonic sophorolipids. A double knockout of both genes was described to result in the generation of bolaform sophorolipids. However, new experiments performed with respective S. bombicola strains Δsble, Δat Δsble, and ∆at revealed inconsistencies with the current understanding of the SL pathway. It was observed that the ∆sble strain produces mainly bolaform sophorolipids with higher acetylation degrees instead of acidic sophorolipids. Furthermore, the ∆at strain produces predominantly bolaform sophorolipids and lactonic sophorolipids with lower acetylation degrees, while the ∆at ∆sble strain predominantly produces bolaform sophorolipids with lower acetylation degrees. These results indicate that the AT enzyme is not the only enzyme responsible for acetylation of sophorolipids, while the SBLE enzyme performs an intramolecular transesterification reaction on bolaform glycolipids instead of an esterification reaction on acidic sophorolipids. These findings, together with recent in vitro data, led us to revise the sophorolipid biosynthetic pathway.

CONCLUSIONS

Bolaform sophorolipids instead of acidic sophorolipids are the key intermediates in the biosynthetic pathway towards lactonic sophorolipids. Bolaform sophorolipids are found in very small amounts in extracellular S. bombicola wild type broths as they are very efficiently converted into lactonic sophorolipids, while acidic sophorolipids build up as they cannot be converted. Furthermore, acetylation of sophorolipids is not exclusively performed by the AT enzyme encoded in the sophorolipid biosynthetic gene cluster and acetylation of bolaform sophorolipids promotes their transesterification. These findings led to the revision of the industrially relevant sophorolipid biosynthetic pathway.

Revision of the sophorolipid biosynthetic pathway in Starmerella bombicola based on new insights in the substrate profile of its lactone esterase

BACKGROUND

Sophorolipids (SLs) are a class of natural, biodegradable surfactants that found their way as ingredients for environment friendly cleaning products, cosmetics and nanotechnological applications. Large-scale production relies on fermentations using the yeast Starmerella bombicola that naturally produces high titers of SLs from renewable resources. The resulting product is typically an extracellular mixture of acidic and lactonic congeners. Previously, we identified an esterase, termed Starmerella bombicola lactone esterase (SBLE), believed to act as an extracellular reverse lactonase to directly use acidic SLs as substrate.

RESULTS

We here show based on newly available pure substrates, HPLC and mass spectrometric analysis, that the actual substrates of SBLE are in fact bola SLs, revealing that SBLE actually catalyzes an intramolecular transesterification reaction. Bola SLs contain a second sophorose attached to the fatty acyl group that acts as a leaving group during lactonization.

CONCLUSIONS

The biosynthetic function by which the Starmerella bombicola 'lactone esterase' converts acidic SLs into lactonic SLs should be revised to a 'transesterase' where bola SL are the true intermediate. This insights paves the way for alternative engineering strategies to develop designer surfactants.

Updated component analysis method for naturally occurring sophorolipids from Starmerella bombicola

Sophorolipids (SLs) are promising glycolipid biosurfactants as they are easily produced and functional. SLs from microorganisms are comprised of mixtures of multiple derivatives that have different structures and properties, including well-known acidic and lactonic SL (ASLs and LSLs, respectively). In this study, we established a method for analyzing all SL derivatives in the products of Starmerella bombicola, a typical SL-producing yeast. Detailed component analyses of S. bombicola products were carried out using reversed-phase high-performance liquid chromatography and mass spectrometry. Methanol was used as the eluent as it is a good solvent for all SL derivatives. With this approach, it was possible to not only quantify the ratio of the main components of ASL, LSL, and SL glycerides but also confirm trace components such as SL mono-glyceride and bola-form SL (sophorose at both ends); notably, this is the first time these components have been isolated and identified successfully in naturally occurring SLs. In addition, our results revealed a novel SL derivative in which a fatty acid is bonded in series to the ASL, which had not been reported previously. Using the present analysis method, it was possible to easily track compositional changes in the SL components during culture. Our results showed that LSL and ASL are produced initially and that SL glycerides accumulate from the middle stage during the fermentation process. KEY POINTS: • An easy and detailed component analysis method for sophorolipids (SLs) is introduced. • Multiple SL derivatives were identified different from known SLs. • A novel hydrophobic acidic SL was isolated and characterized.

Uncovering the fragmentation and separation characteristics of sophorolipid biosurfactants with LC-MS-ESI

The application of liquid chromatography and mass spectrometry (MS) is a challenging area of research for structural identification of sophorolipids, owing to the large number of possible variations in structure and limited knowledge on the separation and fragmentation characteristics of the variants. The aims of this work was to provide a comprehensive analysis of the expected characteristics and fragmentation patterns of a wide range of sophorolipid biosurfactant congeners, providing a methodology and process alongside freely available data to inform and enable future research of commercial or novel sophorolipids. Samples of acidic and lactonic sophorolipid standards were tested using reverse-phase ultra-high performance liquid chromatography and identified using electrospray ionization MS. 37 sophorolipid variants were identified and compared for their elution order and fragmentation pattern under MS/MS. The retention time of sophorolipids was increased by the presence of lactonization, unsaturation, chain length, and acetylation as hydrophobic interactions with the C18 stationary phase increased. A key finding that acidic forms can elute later than lactonic variants was obtained when the fatty acid length and unsaturation and acetylation are altered, in contradiction to previous literature statements. Fragmentation pathways were determined for lactonic and acidic variants under negative [M-H]- and positive [M+NH4]+ ionization, and unique patterns/pathways were identified to help determine the structural components present. The first publicly available database of chromatograms and MS2 spectra has been made available to aid in the identification of sophorolipid components and provide a reliable dataset to accelerate future research into novel sophorolipids and shorten the time to innovation.

ONE-SENTENCE SUMMARY

This article describes the process and challenges in identifying different structures of eco-friendly biosurfactants, providing a novel database to compare results.

Lyotropic Liquid-Crystalline Phases of Sophorolipid Biosurfactants

Biological amphiphiles derived from natural resources are presently being investigated in the hope that they will someday replace current synthetic surfactants, which are known pollutants of soils and water resources. Sophorolipids constitute one of the main classes of glycosylated biosurfactants that have attracted interest because they are synthesized by non-pathogenic yeasts from glucose and vegetable oils at high titers. In this work, the self-assembly properties of several sophorolipids in water at high concentrations (20-80 wt %), a range so far mostly uncharted, have been investigated by polarized-light microscopy and X-ray scattering. Some of these compounds were found to show lyotropic liquid-crystalline behavior as they display lamellar or hexagonal columnar mesophases. X-ray scattering data shows that the structure of the lamellar phase is almost fully interdigitated, which is likely due to the packing difference between the bulky hydrophilic tails and the more compact aliphatic chains. A tentative representation of the molecular organization of the columnar phase is also given. Moreover, some of these compounds display thermotropic liquid-crystalline behavior, either pure or in aqueous mixtures. In addition, small domains of the lamellar phase can easily be aligned by applying onto them a moderate a.c. electric field, which is a rather unusual feature for lyotropic liquid crystals. Altogether, our work explored the self-assembly liquid-crystalline behavior of sophorolipids at high concentration, which could shed light on the conditions of their potential industrial applications as well as on their biological function.

Sophorolipids bioproduction in the yeast Starmerella bombicola: Current trends and perspectives

Sophorolipids are highly active green surfactants (glycolipid biosurfactants) getting tremendous appreciation worldwide due to their low toxicity, biodegradability, broad spectrum of applications, and significant biotechnological potential. Sophorolipids are mainly produced by an oleaginous budding yeast Starmerella bombicola using low-cost substrates. Therefore, the recent state-of-art literature information about S. bombicola yeast is hereby provided, especially the underlying production pathways, biosynthetic gene cluster, and regulatory enzymes. Moreover, the S. bombicola offers flexibility for regulating the structural diversity of sophorolipids, either genetically or by varying fermentative conditions. The emergence of advanced technologies like 'Omics and CRISPR/Cas have certainly boosted rational engineering research for designing high-performing platform strains. Therefore, currently available genetic engineering tools in S. bombicola were reviewed, thereby opening up exciting new possibilities for improving the overall bioproduction titers, structural variability, and stability of sophorolipids. Finally, some technical perspectives to address the current challenges were discussed.

Elucidation of the Natural Function of Sophorolipids Produced by Starmerella bombicola

The yeast Starmerella bombicola distinguishes itself from other yeasts by its potential of producing copious amounts of the secondary metabolites sophorolipids (SLs): these are glycolipid biosurfactants composed out of a(n) (acetylated) sophorose moiety and a lipid tail. Although SLs are the subject of numerous research papers and have been commercialized, e.g., in eco-friendly cleaning solutions, the natural function of SLs still remains elusive. This research article investigates several hypotheses for why S. bombicola invests that much energy in the production of SLs, and we conclude that the main natural function of SLs in S. bombicola is niche protection: (1) the extracellular storage of an energy-rich, yet metabolically less accessible carbon source that can be utilized by S. bombicola upon conditions of starvation with (2) antimicrobial properties. In this way, S. bombicola creates a dual advantage in competition with other microorganisms. Additionally, SLs can expedite growth on rapeseed oil, composed of triacylglycerols which are hydrophobic substrates present in the yeasts’ environment, for a non-SL producing strain (Δcyp52M1). It was also found that—at least under lab conditions—SLs do not provide protection against high osmotic pressure prevalent in sugar-rich environments such as honey or nectar present in the natural habitat of S. bombicola.

Identification of Four Secreted Aspartic Protease-Like Proteins Associated With Sophorolipids Synthesis in Starmerella bombicola CGMCC 1576

The non-pathogenic yeast Starmerella bombicola CGMCC 1576 is an efficient producer of sophorolipids (SLs). The lactonic SLs are mainly produced with yeast extract, and the acidic SLs are mainly produced with ammonium sulfate. Naturally produced SLs are a mixture of various lactonic and acidic SLs. Usually, the SL mixture is not well separated technically, and the separation cost is relatively high. In order to reduce the cost of separation, four secreted aspartic protease-like proteins were identified through proteomic analysis of fermentation broth of S. bombicola under different nitrogen source conditions. The coding genes of the four proteins, namely, sapl1, sapl2, sapl3, and sapl4, are of high sequence similarity (above 55%) and included in a gene cluster. The expression of the four genes was significantly upregulated on (NH₄)₂SO₄ compared with that on yeast extract. The four genes were deleted together to generate a strain Δsapl. The titer of SLs in Δsapl reached 60.71 g/L after 5 days of fermentation using (NH₄)₂SO₄ as the nitrogen source and increased by 90% compared with the wild-type strain. The concentration of acidic SLs was 55.84 g/L, accounting for 92% of the total SLs. The yield of SLs from glucose (g/g) by Δsapl was 0.78, much higher than that by wild-type strain (0.47). However, no increase of SLs production was observed in Δsapl under yeast extract condition. Compared with that of the wild-type strain, the expression levels of the key genes for SLs synthesis were all upregulated to varying degrees in Δsapl under (NH₄)₂SO₄ conditions, and particularly, the expression level of ugta1 encoding UDP glucosyltransferase was upregulated by 14.3-fold. The results suggest that the sapl gene cluster is negatively involved in the production of SLs in the case of (NH₄)₂SO₄ by restraining the expression of the key genes involved in SLs synthesis. The Δsapl strain is an excellent producer of high-titer and high-yield acidic SLs.

Glycolipid Biosurfactant Production from Waste Cooking Oils by Yeast: Review of Substrates, Producers and Products

Biosurfactants are a microbially synthesized alternative to synthetic surfactants, one of the most important bulk chemicals. Some yeast species are proven to be exceptional biosurfactant producers, while others are emerging producers. A set of factors affects the type, amount, and properties of the biosurfactant produced, as well as the environmental impact and costs of biosurfactant’s production. Exploring waste cooking oil as a substrate for biosurfactants’ production serves as an effective cost-cutting strategy, yet it has some limitations. This review explores the existing knowledge on utilizing waste cooking oil as a feedstock to produce glycolipid biosurfactants by yeast. The review focuses specifically on the differences created by using raw cooking oil or waste cooking oil as the substrate on the ability of various yeast species to synthesize sophorolipids, rhamnolipids, mannosylerythritol lipids, and other glycolipids and the substrate’s impact on the composition, properties, and limitations in the application of biosurfactants.

From bumblebee to bioeconomy: Recent developments and perspectives for sophorolipid biosynthesis

Sophorolipids are biobased compounds produced by the genera Starmerella and Pseudohyphozyma that gain exponential interest from academic and industrial stakeholders due to their mild and environmental friendly characteristics. Currently, industrially relevant sophorolipid volumetric productivities are reached up to 3.7 g∙L^-1∙h^-1 and sophorolipids are used in the personal care and cleaning industry at small scale. Moreover, applications in crop protection, food, biohydrometallurgy and medical fields are being extensively researched. The research and development of sophorolipids is at a crucial stage. Therefore, this work presents an overview of the state-of-the-art on sophorolipid research and their applications, while providing a critical assessment of scientific techniques and standardisation in reporting. In this review, the genuine sophorolipid producing organisms and the natural role of sophorolipids are discussed. Subsequently, an evaluation is made of innovations in production processes and the relevance of in-situ product recovery for process performance is discussed. Furthermore, a critical assessment of application research and its future perspectives are portrayed with a focus on the self-assembly of sophorolipid molecules. Following, genetic engineering strategies that affect the sophorolipid physiochemical properties are summarised. Finally, the impact of sophorolipids on the bioeconomy are uncovered, along with relevant future perspectives.

Advances in sophorolipid-producing strain performance improvement and fermentation optimization technology

Sophorolipids (SLs), currently one of the most promising biosurfactants, are secondary metabolites produced by many non-pathogenic yeasts, among which Candida bombicola ATCC 22214 is the main sophorolipid-producing strain. SLs have gained much attention since they exhibit anti-tumor, anti-bacterial, anti-inflammatory, and other beneficial biological activities. In addition, as biosurfactants, SLs have a low toxicity level and are easily degradable without polluting the environment. However, the production cost of SLs remains high, which hinders the industrialization process of SL production. This paper describes SL structure and the metabolic pathway of SL synthesis firstly. Furthermore, we analyze factors that contribute to the higher production cost of SLs and summarize current research status on the advancement of SL production based on two aspects: (1) the improvement of strain performance and (2) the optimization of fermentation process. Further prospects of lowering the cost of SL production are also discussed in order to achieve larger-scale SL production with a high yield at a low cost. KEY POINTS: • Review of advances in strain performance improvement and fermentation optimization. • High-throughput screening and metabolic engineering for high-performance strains. • Low-cost substrates and semi-continuous strategies for efficient SL production.

Identification and characterization of a protein Bro1 essential for sophorolipids synthesis in Starmerella bombicola

Sophorolipids (SLs) are surface-active molecules produced by the non-pathogenic yeast Starmerella bombicola CGMCC 1576. Several genes involved in the synthesis of SLs have been identified. However, the regulation mechanism of the synthesis pathway for SLs has not been investigated. We recently discovered a protein in S. bombicola, which is structurally related to Yarrowia lipolytica YlBro1. To identify the function of the protein SbBro1 in S. bombicola, the deletion, overexpression, and complementary mutant strains were constructed. We found that the deletion mutant no longer produced SLs. Transcriptome analysis indicated that the expression levels of the key enzyme genes of SLs biosynthetic pathway were significantly down-regulated in the Δbro1, especially the expression level of cyp52m1 encoding the first rate-limiting enzyme in SL synthesis pathway was down-regulated 13-folds and the expression of fatty acid β-oxidation-related enzymes was also down-regulated. This study can give insight into the regulation of SL synthesis.

Primary and Secondary Hydration Forces between Interdigitated Membranes Composed of Bolaform Microbial Glucolipids

To better understand lipid membranes in living organisms, the study of intermolecular forces using the osmotic pressure technique applied to model lipid membranes has constituted the ground knowledge in the field of biophysics since four decades. However, the study of intermolecular forces in lipid systems other than phospholipids, like glycolipids, has gained a certain interest only recently. Even in this case, the work generally focuses on the study of membrane glycolipids, but little is known on new forms of non-membrane functional compounds, like microbial bolaform glycolipids. This work explores, through the osmotic stress method involving an adiabatic humidity chamber coupled to neutron diffraction, the short-range (<2 nm) intermolecular forces of membranes entirely composed of interdigitated glucolipids. Experiments are performed at pH 6 when the glucolipid is partially negatively charged and for which we explore the effect of low (16 mM) and high (100 mM) ionic strength. We find that this system is characterized by primary and secondary hydration regimes insensitive and sensitive to ionic strength, respectively, and with typical decay lengths of λ_H1 = 0.37 ± 0.12 nm and λ_H2 = 1.97 ± 0.78 nm.

Production of long-chain hydroxy fatty acids by Starmerella bombicola

To decrease our dependency for the diminishing source of fossils resources, bio-based alternatives are being explored for the synthesis of commodity and high-value molecules. One example in this ecological initiative is the microbial production of the biosurfactant sophorolipids by the yeast Starmerella bombicola. Sophorolipids are surface-active molecules mainly used as household and laundry detergents. Because S. bombicola is able to produce high titers of sophorolipids, the yeast is also used to increase the portfolio of lipophilic compounds through strain engineering. Here, the one-step microbial production of hydroxy fatty acids by S. bombicola was accomplished by the selective blockage of three catabolic pathways through metabolic engineering. Successful production of 17.39 g/l (ω-1) linked hydroxy fatty acids was obtained by the successive blockage of the sophorolipid biosynthesis, the β-oxidation and the ω-oxidation pathways. Minor contamination of dicarboxylic acids and fatty aldehydes were successfully removed using flash chromatography. This way, S. bombicola was further expanded into a flexible production platform of economical relevant compounds in the chemical, food and cosmetic industries.

Taxonomic Distribution of Cytochrome P450 Monooxygenases (CYPs) among the Budding Yeasts (Sub-Phylum Saccharomycotina)

Cytochrome P450 monooxygenases (CYPs) are ubiquitous throughout the tree of life and play diverse roles in metabolism including the synthesis of secondary metabolites as well as the degradation of recalcitrant organic substrates. The genomes of budding yeasts (phylum Ascomycota, sub-phylum Saccharomycotina) typically contain fewer families of CYPs than filamentous fungi. There are currently five CYP families among budding yeasts with known function while at least another six CYP families with unknown function (“orphan CYPs”) have been described. The current study surveyed the genomes of 372 species of budding yeasts for CYP-encoding genes in order to determine the taxonomic distribution of individual CYP families across the sub-phylum as well as to identify novel CYP families. Families CYP51 and CYP61 (represented by the ergosterol biosynthetic genes ERG11 and ERG5, respectively) were essentially ubiquitous among the budding yeasts while families CYP52 (alkane/fatty acid hydroxylases), CYP56 (N-formyl-l-tyrosine oxidase) displayed several instances of gene loss at the genus or family level. Phylogenetic analysis suggested that the three orphan families CYP5217, CYP5223 and CYP5252 diverged from a common ancestor gene following the origin of the budding yeast sub-phylum. The genomic survey also identified eight CYP families that had not previously been reported in budding yeasts.

Elucidation of secondary alcohol metabolism in Starmerella bombicola and contribution of primary alcohol oxidase FAO1

The yeast Starmerella bombicola NBRC10243 is an excellent producer of sophorolipids, which are among the most useful biosurfactants. The primary alcoholic metabolic pathway of S. bombicola has been elucidated using alcohol oxidase FAO1, but the secondary alcohol metabolic pathway remains unknown. Although the FAO1 mutant was unable to grow with secondary alcohols and seemed to be involved in the secondary alcohol metabolism pathway of S. bombicola, it had very low activity toward secondary alcohols. By analyzing the products of secondary alcohol metabolism, alkyl polyglucosides hydroxylated at the ω position in the alkyl chain of the secondary alcohol were observed in the FAO1 mutant, but not in the wild-type yeast. In the double mutant of FAO1 and UGTA1, accumulation of 1,13-tetradecandiol and 2,13-tetradecandiol was observed. The above results indicated that hydroxylation occurred first at the ω and ω-1 positions in the secondary alcohol metabolism of S. bombicola, followed by primary alcohol oxidation.

Enhanced production of β-glucosides by in-situ UDP-glucose regeneration

Glycosyltransferase (GT)-mediated methodology is recognized as one of the most practical approaches for large-scale production of glycosides. However, GT enzymes require a sugar nucleotide as donor substrate that must be generated in situ for preparative applications by recycling of the nucleotide moiety, e.g. by sucrose synthase (SUS). Three plant GT genes CaUGT2, VvGT14a, and VvGT15c and the fungal SbUGTA1 were successfully co-expressed with GmSUS from soybean in Escherichia coli BL21 and W cells. In vitro, the crude protein extracts prepared from four GT genes and GmSUS co-expressing cells were able to convert several small molecules to the corresponding glucosides, when sucrose and UDP were supplied. In addition, GmSUS was able to enhance the glucosylation efficiency and reduced the amount of supplying UDP-glucose. In the biotransformation system, co-expression of VvGT15c with GmSUS also improved the glucosylation of geraniol and enhanced the resistance of the cells against the toxic terpenol. GT-EcW and GTSUS-EcW cells tolerated up to 2mM geraniol and converted more than 99% of the substrate into the glucoside at production rates exceeding 40μgml(-1)h(-1). The results confirm that co-expression of SUS allows in situ regeneration of UDP-sugars and avoids product inhibition by UDP.

Genome-Wide Transcriptional Excavation of Dipsacus asperoides Unmasked both Cryptic Asperosaponin Biosynthetic Genes and SSR Markers

BACKGROUND

Dipsacus asperoides is a traditional Chinese medicinal crop. The root is generally used as a medicine and is frequently prescribed by Chinese doctors for the treatment of back pain, limb paralysis, flutter trauma, tendon injuries, and fractures. With the rapid development of bioinformatics, research has been focused on this species at the gene or molecular level. For purpose of fleshing out genome information about D. asperoides, in this paper we conducted transcriptome analysis of this species.

PRINCIPAL FINDINGS

To date, many genes encoding enzymes involved in the biosynthesis of triterpenoid saponins in D.asperoides have not been elucidated. Illumina paired-end sequencing was employed to probe D. asperoides's various enzymes associated with the relevant mesostate. A total of 30, 832,805 clean reads and de novo spliced 43,243 unigenes were obtained. Of all unigenes, only 8.27% (3578) were successfully annotated in total of seven public databases: Nr, Nt, Swiss-Prot, GO, KOG, KEGG, and Pfam, which might be attributed to the poor studies on D. asperoides. The candidate genes encoding enzymes involved in triterpenoid saponin biosynthesis were identified and experimentally verified by reverse transcription qPCR, encompassing nine cytochrome P450s and 17 UDP-glucosyltransferases. Specifically, unearthly putative genes involved in the glycosylation of hederagenin were acquired. Simultaneously, 4490 SSRs from 43,243 examined sequences were determined via bioinformatics analysis.

CONCLUSION

This study represents the first report on the use of the Illumina sequence platform on this crop at the transcriptome level. Our findings of candidate genes encoding enzymes involved in Dipsacus saponin VI biosynthes is provide novel information in efforts to further understand the triterpenoid metabolic pathway on this species. The initial genetics resources in this study will contribute significantly to the genetic breeding program of D. asperoides, and are beneficial for clinical diagnosis and treatment.

Cloning, characterization, and heterologous expression of a novel glucosyltransferase gene from sophorolipid-producing Candida bombicola

Candida bombicola is well-studied for the production of a biosurfactant, the sophorolipids. In this paper, the cloning of a glucosyltransferase gene using polymerase-chain-reaction (PCR) technique is described. Degenerative primer-pairs were first designed based on the highly conserved amino-acid sequences of several selected yeast glucosyltransferases. Using these primers, an amplified sequence (amplicon) of 700 base-pair from C. bombicola was obtained and subsequently sequenced. Based on the sequence of this amplicon, additional target-specific PCR primers were designed for use in subsequent rounds of 3'- and 5'-extension using DNA walking technique to eventually obtain a C. bombicola genomic sequence containing an open-reading-frame putatively identified as a glucosyltransferase (gtf-1). The gene was subcloned in Saccharomyces cerevisiae for expression and functional characterization. Quantitative RT-PCR confirmed the expression of gtf-1 in the recombinant S. cerevisiae. In vitro assay with the sonicated cells of the recombinant yeast confirms the presence of glucosylation activity on sterol and hydroxy fatty acid substrates. This study reports for the first time the cloning and characterization of a broad-specificity lipid glucosylation gene from C. bombicola, and the functional activity of its gene product.

Biosurfactant gene clusters in eukaryotes: regulation and biotechnological potential

Biosurfactants (BSs) are a class of secondary metabolites representing a wide variety of structures that can be produced from renewable feedstock by a wide variety of micro-organisms. They have (potential) applications in the medical world, personal care sector, mining processes, food industry, cosmetics, crop protection, pharmaceuticals, bio-remediation, household detergents, paper and pulp industry, textiles, paint industries, etc. Especially glycolipid BSs like sophorolipids (SLs), rhamnolipids (RLs), mannosylerythritol lipids (MELs) and cellobioselipids (CBLs) have been described to provide significant opportunities to (partially) replace chemical surfactants. The major two factors currently limiting the penetration of BSs into the market are firstly the limited structural variety and secondly the rather high production price linked with the productivity. One of the keys to resolve the above mentioned bottlenecks can be found in the genetic engineering of natural producers. This could not only result in more efficient (economical) recombinant producers, but also in a diversification of the spectrum of available BSs as such resolving both limiting factors at once. Unraveling the genetics behind the biosynthesis of these interesting biological compounds is indispensable for the tinkering, fine tuning and rearrangement of these biological pathways with the aim of obtaining higher yields and a more extensive structural variety. Therefore, this review focuses on recent developments in the investigation of the biosynthesis, genetics and regulation of some important members of the family of the eukaryotic glycolipid BSs (MELs, CBLs and SLs). Moreover, recent biotechnological achievements and the industrial potential of engineered strains are discussed.

Expression and characterization of CYP52 genes involved in the biosynthesis of sophorolipid and alkane metabolism from Starmerella bombicola

Three cytochrome P450 monooxygenase CYP52 gene family members were isolated from the sophorolipid-producing yeast Starmerella bombicola (former Candida bombicola), namely, CYP52E3, CYP52M1, and CYP52N1, and their open reading frames were cloned into the pYES2 vector for expression in Saccharomyces cerevisiae. The functions of the recombinant proteins were analyzed with a variety of alkane and fatty acid substrates using microsome proteins or a whole-cell system. CYP52M1 was found to oxidize C16 to C20 fatty acids preferentially. It converted oleic acid (C18:1) more efficiently than stearic acid (C18:0) and linoleic acid (C18:2) and much more effectively than α-linolenic acid (C18:3). No products were detected when C10 to C12 fatty acids were used as the substrates. Moreover, CYP52M1 hydroxylated fatty acids at their ω- and ω-1 positions. CYP52N1 oxidized C14 to C20 saturated and unsaturated fatty acids and preferentially oxidized palmitic acid, oleic acid, and linoleic acid. It only catalyzed ω-hydroxylation of fatty acids. Minor ω-hydroxylation activity against myristic acid, palmitic acid, palmitoleic acid, and oleic acid was shown for CYP52E3. Furthermore, the three P450s were coassayed with glucosyltransferase UGTA1. UGTA1 glycosylated all hydroxyl fatty acids generated by CYP52E3, CYP52M1, and CYP52N1. The transformation efficiency of fatty acids into glucolipids by CYP52M1/UGTA1 was much higher than those by CYP52N1/UGTA1 and CYP52E3/UGTA1. Taken together, CYP52M1 is demonstrated to be involved in the biosynthesis of sophorolipid, whereas CYP52E3 and CYP52N1 might be involved in alkane metabolism in S. bombicola but downstream of the initial oxidation steps.