Elucidation of the Natural Function of Sophorolipids Produced by Starmerella bombicola

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.

Distinct fungal microbiomes of two Thai commercial stingless bee species, Lepidotrigona terminata and Tetragonula pagdeni suggest a possible niche separation in a shared habitat

Stingless bees, a social corbiculate bee member, play a crucial role in providing pollination services. Despite their importance, the structure of their microbiome, particularly the fungal communities, remains poorly understood. This study presents an initial characterization of the fungal community associated with two Thai commercial stingless bee species, Lepidotrigona terminata (Smith) and Tetragonula pagdeni (Schwarz) from Chiang Mai, Thailand. Utilizing ITS amplicon sequencing, we identified distinct fungal microbiomes in these two species. Notably, fungi from the phyla Ascomycota, Basidiomycota, Mucoromycota, Mortierellomycota, and Rozellomycota were present. The most dominant genera, which varied significantly between species, included Candida and Starmerella. Additionally, several key enzymes associated with energy metabolism, structural strength, and host defense reactions, such as adenosine triphosphatase, alcohol dehydrogenase, β-glucosidase, chitinase, and peptidylprolyl isomerase, were predicted. Our findings not only augment the limited knowledge of the fungal microbiome in Thai commercial stingless bees but also provide insights for their sustainable management through understanding their microbiome.

Tuning the antimicrobial activity of microbial glycolipid biosurfactants through chemical modification

Sophorolipids, glycolipid biosurfactants derived from microorganisms such as Starmerella bombicola, possess distinctive surface-active and bioactive properties, holding potential applications in cosmetics, pharmaceuticals and bioremediation. However, the limited structural variability in wild-type sophorolipids restricts their properties and applications. To address this, metabolic engineering efforts have allowed to create a portfolio of molecules. In this study, we went one step further by chemically modifying microbially produced sophorosides, produced by an engineered S. bombicola. Twenty-four new sophoroside derivatives were synthesized, including sophoroside amines with varying alkyl chain lengths (ethyl to octadecyl) on the nitrogen atom and their corresponding quaternary ammonium salts. Additionally, six different microbially produced glycolipid biosurfactants were hydrogenated to achieve fully saturated lipid tails. These derivatives, along with microbially produced glycolipids and three benchmark biosurfactants (di-rhamnolipids, alkyl polyglucosides, cocamidopropyl betaine), were assessed for antimicrobial activity against bacteria (Bacillus subtilis, Staphylococcus aureus, Listeria monocytogenes, Escherichia coli, Pseudomonas aeruginosa) and yeast (Candida albicans). Results indicated that microbially produced glycolipids, such as bola sophorosides, acidic sophorolipids and acidic glucolipids exhibit selective antimicrobial activity against the test organisms. Conversely, lactonic sophorolipids, sophoroside amines and quaternary ammonium salts display a broad antimicrobial activity. N-octyl, N-dodecyl and N-octadecyl derivatives exhibit the lowest minimal inhibitory concentrations, ranging from 0.014 to 20.0 mg mL-1. This study demonstrates the potential synergy of thoughtful biotechnology and targeted chemistry to precisely tailor glycolipid biosurfactants to meet specific requirements across applications.

The wild solitary bees Andrena vaga, Anthophora plumipes, Colletes cunicularius, and Osmia cornuta microbiota are host specific and dominated by endosymbionts and environmental microorganisms

We characterized the microbial communities of the crop, midgut, hindgut, and ovaries of the wild solitary bees Andrena vaga, Anthophora plumipes, Colletes cunicularius, and Osmia cornuta through 16S rRNA gene and ITS2 amplicon sequencing and a large-scale isolation campaign. The bacterial communities of these bees were dominated by endosymbionts of the genera Wolbachia and Spiroplasma. Bacterial and yeast genera representing the remaining predominant taxa were linked to an environmental origin. While only a single sampling site was examined for Andrena vaga, Anthophora plumipes, and Colletes cunicularius, and two sampling sites for Osmia cornuta, the microbiota appeared to be host specific: bacterial, but not fungal, communities generally differed between the analyzed bee species, gut compartments and ovaries. This may suggest a selective process determined by floral and host traits. Many of the gut symbionts identified in the present study are characterized by metabolic versatility. Whether they exert similar functionalities within the bee gut and thus functional redundancy remains to be elucidated.

Microbiota and pathogens in an invasive bee: Megachile sculpturalis from native and invaded regions

The present study aimed to characterise the bacterial, fungal and parasite gut community of the invasive bee Megachile sculpturalis sampled from native (Japan) and invaded (USA and France) regions via 16S rRNA and ITS2 amplicon sequencing and PCR detection of bee microparasites. The bacterial and fungal gut microbiota communities in bees from invaded regions were highly similar and differed strongly from those obtained in Japan. Core amplicon sequence variants (ASVs) within each population represented environmental micro-organisms commonly present in bee-associated niches that likely provide beneficial functions to their host. Although the overall bacterial and fungal communities of the invasive M. sculpturalis in France and the co-foraging native bees Anthidium florentinum and Halictus scabiosae, were significantly different, five out of eight core ASVs were shared suggesting common environmental sources and potential transmission. None of the 46 M. sculpturalis bees analysed harboured known bee pathogens, while microparasite infections were common in A. florentinum, and rare in H. scabiosae. A common shift in the gut microbiota of M. sculpturalis in invaded regions as a response to changed environmental conditions, or a founder effect coupled to population re-establishment in the invaded regions may explain the observed microbial community profiles and the absence of parasites. While the role of pathogen pressure in shaping biological invasions is still debated, the absence of natural enemies may contribute to the invasion success of M. sculpturalis.

Bees just wanna have fungi: a review of bee associations with nonpathogenic fungi

Bee-fungus associations are common, and while most studies focus on entomopathogens, emerging evidence suggests that bees associate with a variety of symbiotic fungi that can influence bee behavior and health. Here, we review nonpathogenic fungal taxa associated with different bee species and bee-related habitats. We synthesize results of studies examining fungal effects on bee behavior, development, survival, and fitness. We find that fungal communities differ across habitats, with some groups restricted mostly to flowers (Metschnikowia), while others are present almost exclusively in stored provisions (Zygosaccharomyces). Starmerella yeasts are found in multiple habitats in association with many bee species. Bee species differ widely in the abundance and identity of fungi hosted. Functional studies suggest that yeasts affect bee foraging, development, and pathogen interactions, though few bee and fungal taxa have been examined in this context. Rarely, fungi are obligately beneficial symbionts of bees, whereas most are facultative bee associates with unknown or ecologically contextual effects. Fungicides can reduce fungal abundance and alter fungal communities associated with bees, potentially disrupting bee-fungi associations. We recommend that future study focus on fungi associated with non-honeybee species and examine multiple bee life stages to document fungal composition, abundance, and mechanistic effects on bees.

Comprehensive metabolomics reveals correlation between sophorolipid biosynthesis and autophagy

Sophorolipids are biobased and biodegradable glycolipid surface-active agents contributing to the shift from petroleum to biobased surfactants, associated with clear environmental benefits. However, their production cost is currently too high to allow commercialisation. Therefore, a continuous sophorolipid production process was evaluated, i.e., a retentostat with an external filtration unit. Despite an initial increase in volumetric productivity, productivity eventually declined to almost 0 g L^-1 h^-1. Following comprehensive metabolomics on supernatant obtained from a standardised retentostat, we hypothesised exhaustion of the N-starvation-induced autophagy as the main mechanism responsible for the decline in bolaform sophorolipid productivity. Thirty-six metabolites that correlate with RNA/protein autophagy and high sophorolipid productivity were putatively identified. In conclusion, our results unveil a plausible cause of this bola sophorolipid productivity decline in an industrially relevant bioreactor set-up, which may thus impact majorly on future yeast biosurfactant regulation studies and the finetuning of bola sophorolipid production processes.

Oleaginous yeasts: Time to rethink the definition?

Oleaginous yeasts are typically defined as those able to accumulate more than 20% of their cell dry weight as lipids or triacylglycerides. Research on these yeasts has increased lately fuelled by an interest to use biotechnology to produce lipids and oleochemicals that can substitute those coming from fossil fuels or offer sustainable alternatives to traditional extractions (e.g., palm oil). Some oleaginous yeasts are attracting attention both in research and industry, with Yarrowia lipolytica one of the best-known and studied ones. Oleaginous yeasts can be found across several clades and different metabolic adaptations have been found, affecting not only fatty acid and neutral lipid synthesis, but also lipid particle stability and degradation. Recently, many novel oleaginous yeasts are being discovered, including oleaginous strains of the traditionally considered non-oleaginous Saccharomyces cerevisiae. In the face of this boom, a closer analysis of the definition of "oleaginous yeast" reveals that this term has instrumental value for biotechnology, while it does not give information about distinct types of yeasts. Having this perspective in mind, we propose to expand the term "oleaginous yeast" to those able to produce either intracellular or extracellular lipids, not limited to triacylglycerides, in at least one growth condition (including ex novo lipid synthesis). Finally, a critical look at Y. lipolytica as a model for oleaginous yeasts shows that the term "oleaginous" should be reserved only for strains and not species and that in the case of Y. lipolytica, it is necessary to distinguish clearly between the lipophilic and oleaginous phenotype.

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.

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.