A multi-omics study to boost continuous bolaform sophorolipid production

Protein production dynamics and physiological adaptation of recombinant Komagataella phaffii at near-zero growth rates

BACKGROUND

Specific productivity (qP) in yeast correlates with growth, typically peaking at intermediate or maximum specific growth rates (μ). Understanding the factors limiting productivity at extremely low μ might reveal decoupling strategies, but knowledge of production dynamics and physiology in such conditions is scarce. Retentostats, a type of continuous cultivation, enable the well-controlled transition to near-zero µ through the combined retention of biomass and limited substrate supply. Recombinant Komagataella phaffii (syn Pichia pastoris) secreting a bivalent single domain antibody (VHH) was cultivated in aerobic, glucose-limited retentostats to investigate recombinant protein production dynamics and broaden our understanding of relevant physiological adaptations at near-zero growth conditions.

RESULTS

By the end of the retentostat cultivation, doubling times of approx. two months were reached, corresponding to µ = 0.00047 h-1. Despite these extremely slow growth rates, the proportion of viable cells remained high, and de novo synthesis and secretion of the VHH were observed. The average qP at the end of the retentostat was estimated at 0.019 mg g-1 h-1. Transcriptomics indicated that genes involved in protein biosynthesis were only moderately downregulated towards zero growth, while secretory pathway genes were mostly regulated in a manner seemingly detrimental to protein secretion. Adaptation to near-zero growth conditions of recombinant K. phaffii resulted in significant changes in the total protein, RNA, DNA and lipid content, and lipidomics revealed a complex adaptation pattern regarding the lipid class composition. The higher abundance of storage lipids as well as storage carbohydrates indicates that the cells are preparing for long-term survival.

CONCLUSIONS

In conclusion, retentostat cultivation proved to be a valuable tool to identify potential engineering targets to decouple growth and protein production and gain important insights into the physiological adaptation of K. phaffii to near-zero growth conditions.

Determining the accuracy and suitability of common analytical techniques for sophorolipid biosurfactants

To determine the performance of a sophorolipid biosurfactant production process, it is important to have accurate and specific analytical techniques in place. Among the most popular are the anthrone assay, gravimetric quantification (hexane:ethyl acetate extraction), and high-performance liquid chromatography (HPLC). The choice of analytical tool varies depending on cost, availability, and ease of use; however, these techniques have never been compared directly against one another. In this work, 75 fermentation broths with varying product/substrate concentrations were comprehensively tested with the 3 techniques and compared. HPLC-ultraviolet detection (198 nm) was capable of quantifying C18:1 subterminal hydroxyl diacetylated lactonic sophorolipid down to a lower limit of 0.3 g/L with low variability (<3.21%). Gravimetric quantification of the broths following liquid:liquid extraction with hexane and ethyl acetate showed some linearity (R2 = .658) when compared to HPLC but could not quantify lower than 11.06 g/L, even when no sophorolipids were detected in the sample, highlighting the non-specificity of the method to co-extract non-sophorolipid components in the final gravimetric measure. The anthrone assay showed no linearity (R2 = .129) and was found to cross-react with media components (rapeseed oil, corn steep liquor, glucose), leading to consistent overestimation of sophorolipid concentration. The appearance of poor biomass separation during sample preparation with centrifugation was noted and resolved with a novel sample preparation method with pure ethanol. Extensive analysis and comparisons of the most common sophorolipid quantification techniques are explored and the limitations/advantages are highlighted. The findings provide a guide for scientists to make an informed decision on the suitable quantification tool that meets their needs, exploring all aspects of the analysis process from harvest, sample preparation, and analysis.

Sophorolipids: A comprehensive review on properties and applications

Sophorolipids are surface-active glycolipids produced by several non-pathogenic yeast species and are widely used as biosurfactants in several industrial applications. Sophorolipids provide a plethora of benefits over chemically synthesized surfactants for certain applications like bioremediation, oil recovery, and pharmaceuticals. They are, for instance less toxic, more benign and environment friendly in nature, biodegradable, freely adsorb to different surfaces, self-assembly in hydrated solutions, robustness for industrial applications etc. These miraculous properties result in valuable physicochemical attributes such as low critical micelle concentrations (CMCs), reduced interfacial surface tension, and capacity to dissolve non-polar components. Moreover, they exhibit a diverse range of physicochemical, functional, and biological attributes due to their unique molecular composition and structure. In this article, we highlight the physico-chemical properties of sophorolipids, how these properties are exploited by the human community for extensive benefits and the conditions which lead to their unique tailor-made structures and how they entail their interfacial behavior. Besides, we discuss the advantages and disadvantages associated with the use of these sophorolipids. We also review their physiological and functional attributes, along with their potential commercial applications, in real-world scenario. Biosurfactants are compared to their man-made equivalents to show the variations in structure-property correlations and possible benefits. Those attempting to manufacture purported natural or green surfactant with innovative and valuable qualities can benefit from an understanding of biosurfactant features structured along the same principles. The uniqueness of this review article is the detailed physico-chemical study of the sophorolipid biosurfactant and how these properties helps in their usage and detailed explicit study of their applications in the current scenario and also covering their pros and cons.

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.