Rational high-throughput screening system for high sophorolipids production in Candida bombicola by co-utilizing glycerol and glucose capacity

Advances in high-throughput screening approaches for biosurfactants: current trends, bottlenecks and perspectives

The market size of biosurfactants (BSs) has been expanding at an extremely fast pace due to their broad application scope. Therefore, the re-construction of cell factories with modified genomic and metabolic profiles for desired industrial performance has been an intriguing aspect. Typical mutagenesis approaches generate huge mutant libraries, whereas a battery of specific, robust, and cost-effective high-throughput screening (HTS) methods is requisite to screen target strains for desired phenotypes. So far, only a few specialized HTS assays have been developed for BSs that were successfully applied to obtain anticipated mutants. The most important milestones to reach, however, continue to be: specificity, sensitivity, throughput, and the potential for automation. Here, we discuss important colorimetric and fluorometric HTS approaches for possible intervention on automated HTS platforms. Moreover, we explain current bottlenecks in developing specialized HTS platforms for screening high-yielding producers and discuss possible perspectives for addressing such challenges.

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.

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.

CRISPR-Cas Technology for Bioengineering Conventional and Non-Conventional Yeasts: Progress and New Challenges

The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (CRISPR-Cas) system has undergone substantial and transformative progress. Simultaneously, a spectrum of derivative technologies has emerged, spanning both conventional and non-conventional yeast strains. Non-conventional yeasts, distinguished by their robust metabolic pathways, formidable resilience against diverse stressors, and distinctive regulatory mechanisms, have emerged as a highly promising alternative for diverse industrial applications. This comprehensive review serves to encapsulate the prevailing gene editing methodologies and their associated applications within the traditional industrial microorganism, Saccharomyces cerevisiae. Additionally, it delineates the current panorama of non-conventional yeast strains, accentuating their latent potential in the realm of industrial and biotechnological utilization. Within this discourse, we also contemplate the potential value these tools offer alongside the attendant challenges they pose.

Development of two devices for high-throughput screening of ethanol-producing microorganisms by real-time CO2 production monitoring

Bioethanol's importance as a renewable energy carrier led to the development of new devices for the high-throughput screening (HTS) of ethanol-producing microorganisms, monitoring ethanol production, and process optimization. This study developed two devices based on measuring CO₂ evolution (an equimolar byproduct of microbial ethanol fermentation) to allow for a fast and robust HTS of ethanol-producing microorganisms for industrial purposes. First, a pH-based system for identifying ethanol producers (Ethanol-HTS) was established in a 96-well plate format where CO₂ emission is captured by a 3D-printed silicone lid and transferred from the fermentation well to a reagent containing bromothymol blue as a pH indicator. Second, a self-made CO₂ flow meter (CFM) was developed as a lab-scale tool for real-time quantification of ethanol production. This CFM contains four chambers to simultaneously apply different fermentation treatments while LCD and serial ports allow fast and easy data transfer. Applying ethanol-HTS with various yeast concentrations and yeast strains displayed different colors, from dark blue to dark and light green, based on the amount of carbonic acid formed. The results of the CFM device revealed a fermentation profile. The curve of CO₂ production flow among six replications showed the same pattern in all batches. The comparison of final ethanol concentrations calculated based on CO₂ flow by the CFM device with the GC analysis showed 3% difference which is not significant. Data validation of both devices demonstrated their applicability for screening novel bioethanol-producer strains, determining carbohydrate fermentation profiles, and monitoring ethanol production in real time.

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.

Developing an understanding of sophorolipid synthesis through application of a central composite design model

A key barrier to market penetration for sophorolipid biosurfactants is the ability to improve productivity and utilize alternative feedstocks to reduce the cost of production. To do this, a suitable screening tool is required that is able to model the interactions between media components and alter conditions to maximize productivity. In the following work, a central composite design is applied to analyse the effects of altering glucose, rapeseed oil, corn steep liquor and ammonium sulphate concentrations on sophorolipid production with Starmerella bombicola ATCC 222144 after 168 h. Sophorolipid production was analysed using standard least squares regression and the findings related to the growth (OD₆₀₀ ) and broth conditions (glucose, glycerol and oil concentration). An optimum media composition was found that was capable of producing 39.5 g l^-1 sophorolipid. Nitrogen and rapeseed oil sources were found to be significant, linked to their role in growth and substrate supply respectively. Glucose did not demonstrate a significant effect on production despite its importance to biosynthesis and its depletion in the broth within 96 h, instead being replaced by glycerol (via triglyceride breakdown) as the hydrophilic carbon source at the point of glucose depletion. A large dataset was obtained, and a regression model with applications towards substrate screening and process optimisation developed.

Cellulase production and efficient saccharification of biomass by a new mutant Trichoderma afroharzianum MEA-12

BACKGROUND

Cellulase plays a key role in converting cellulosic biomass into fermentable sugar to produce chemicals and fuels, which is generally produced by filamentous fungi. However, most of the filamentous fungi obtained by natural breeding have low secretory capacity in cellulase production, which are far from meeting the requirements of industrial production. Random mutagenesis combined with adaptive laboratory evolution (ALE) strategy is an effective method to increase the production of fungal enzymes.

RESULTS

This study obtained a mutant of Trichoderma afroharzianum by exposures to N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), Ethyl Methanesulfonate (EMS), Atmospheric and Room Temperature Plasma (ARTP) and ALE with high sugar stress. The T. afroharzianum mutant MEA-12 produced 0.60, 5.47, 0.31 and 2.17 IU/mL FPase, CMCase, pNPCase and pNPGase, respectively. These levels were 4.33, 6.37, 4.92 and 4.15 times higher than those of the parental strain, respectively. Also, it was found that T. afroharzianum had the same carbon catabolite repression (CCR) effect as other Trichoderma in liquid submerged fermentation. In contrast, the mutant MEA-12 can tolerate the inhibition of glucose (up to 20 mM) without affecting enzyme production under inducing conditions. Interestingly, crude enzyme from MEA-12 showed high enzymatic hydrolysis efficiency against three different biomasses (cornstalk, bamboo and reed), when combined with cellulase from T. reesei Rut-C30. In addition, the factors that improved cellulase production by MEA-12 were clarified.

CONCLUSIONS

Overall, compound mutagenesis combined with ALE effectively increased the production of fungal cellulase. A super-producing mutant MEA-12 was obtained, and its cellulase could hydrolyze common biomasses efficiently, in combination with enzymes derived from model strain T. reesei, which provides a new choice for processing of bioresources in the future.

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.

Target-site directed rational high-throughput screening system for high sophorolipids production by Candida bombicola

In this study we have established a rational and high performance high-throughput screening system to select for a sophorolipids (SLs) high-producing strain of Candida bombicola. Introduction of mutagen combination, relaxation culture and multi-stress significantly improved both mutation and positive mutation rates. A high-performing strain, Ncbio 5, was selected out of 6212 mutants. Final SLs titer, productivity and yield of this strain in 5 L bioreactors were 26.9%, 27.0% and 35.0% higher than in the original strain, respectively. The improved fermentation performance in Ncbio 5 is contributed by the longer production period, higher SLs productivity and more efficient oil utilization. The strategy adopted herein to optimize the high-throughput screening system should be readily extendable to other similar systems.

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.

Mutant breeding of Starmerella bombicola by atmospheric and room-temperature plasma (ARTP) for improved production of specific or total sophorolipids

To enhance specific or total sophorolipids (SLs) production by Starmerella bombicola for specific application, mutant library consisting of 106 mutants from 7 batches was constructed via atmospheric and room-temperature plasma (ARTP). When compared to the wild strain, 11, 36 and 12 mutants performed increases over 30% in lactonic, acidic or total SLs production. Genetic stability investigation showed that 8, 7, and 4 mutants could maintain the improved SLs production capacity. Mutants of A6-9 and A2-8 were selected out for enhanced specific SLs and total SLs production in fed-batch cultivation in flask. Without optimization, A6-9 obtained the highest reported lactonic SLs production of 51.95 g/l and A2-8 performed comparable acidic and total SLs production of 68.75 g/l and 100.33 g/l with all the reported stains. The structural composition of the obtained SLs was analyzed by HPLC and LC/MS, and the results confirmed the enhancement of SLs and certain SL components. These mutants would be important in industrial applications because the production and purification costs of SLs could be greatly reduced. Besides, the acquisition of these mutants also provided materials for the investigation of regulation mechanism of SLs biosynthesis for further genetic engineering of S. bombicola. Furthermore, critical micelle concentration (CMC), minimum surface tension (ST_min) and hydrophilic-lipophilic balance (HLB) of the SLs obtained from the wild and mutant strains were also examined and compared. These results demonstrated the feasibility of obtaining SLs with different properties from different strains and the high efficiency of mutation breeding of S. bombicola by ARTP.

High-Throughput Screening Technology in Industrial Biotechnology

Based on the development of automatic devices and rapid assay methods, various high-throughput screening (HTS) strategies have been established for improving the performance of industrial microorganisms. We discuss the most significant factors that can improve HTS efficiency, including the construction of screening libraries with high diversity and the use of new detection methods to expand the search range and highlight target compounds. We also summarize applications of HTS for enhancing the performance of industrial microorganisms. Current challenges and potential improvements to HTS in industrial biotechnology are discussed in the context of rapid developments in synthetic biology, nanotechnology, and artificial intelligence. Rational integration will be an important driving force for constructing more efficient industrial microorganisms with wider applications in biotechnology.