Identification and characterization of a long-chain fatty acid transporter in the sophorolipid-producing strain Starmerella bombicola

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.

Exploring the genetic expression of Wickerhamomyces anomalus during biosurfactant production from waste cooking oil

AIMS

Biosurfactants are valuable eco-friendly compounds with broad industrial applications, particularly when produced sustainably using yeast and renewable carbon sources. Despite the potential of yeast in biosurfactant synthesis, little is known about the specific gene expression changes underlying this process. This study investigates the genetic response of Wickerhamomyces anomalus CCMA 0358 to biosurfactant production using waste cooking oil (WCO) as a low-cost carbon source.

METHODS AND RESULTS

During a 0-12 h fermentation period, RNA (ribonucleic acid) sequencing revealed 829 differentially expressed genes in W. anomalus grown with WCO, suggesting targeted metabolic adaptations. Pathway analysis showed WCO's significant impact on glycolysis, gluconeogenesis, and lipid biosynthesis. Gene ontology annotations further indicated adaptive responses in ribosome biogenesis and lipid metabolism, which are crucial for the efficient utilization of WCO. Notably, WCO induced the upregulation of very-long-chain fatty acid precursors and adjustments in glycolytic enzyme expression, both essential for biosurfactant production.

CONCLUSIONS

This study reveals, for the first time, the specific genetic pathways and metabolic adjustments that W. anomalus employs to produce biosurfactants from WCO. The increased expression of lipid metabolism enzymes and cell membrane components highlights a tailored adaptive mechanism for lipid-rich waste substrates, positioning W. anomalus as a promising candidate for sustainable biosurfactant 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.

Biocompatibility of Brazilian native yeast-derived sophorolipids and Trichoderma harzianum as plant-growth promoting bioformulations

The replacement of agrochemicals by biomolecules is imperative to mitigate soil contamination and inactivation of its core microbiota. Within this context, this study aimed at the interaction between a biological control agent such as Trichoderma harzianum CCT 2160 (BF-Th) and the biosurfactants (BSs) derived from the native Brazilian yeast Starmerella bombicola UFMG-CM-Y6419. Thereafter, their potential in germination of Oryza sativa L. seeds was tested. Both bioproducts were produced on site and characterized according to their chemical composition by HPLC-MS and GC-MS for BSs and SDS-PAGE gel for BF-Th. The BSs were confirmed to be sophorolipids (SLs) which is a well-studied compound with antimicrobial activity. The biocompatibility was examined by cultivating the fungus with SLs supplementation ranging from 0.1 to 2 g/L in solid and submerged fermentation. In solid state fermentation the supplementation of SLs enhanced spore production, conferring the synergy of both bioproducts. For the germination assays, bioformulations composed of SLs, BF-Th and combined (SLT) were applied in the germination of O. sativa L seeds achieving an improvement of up to 30% in morphological aspects such as root and shoot size as well as the presence of lateral roots. It was hypothesized that SLs were able to regulate phytohormones expression such as auxins and gibberellins during early stage of growth, pointing to their novel plant-growth stimulating properties. Thus, this study has pointed to the potential of hybrid bioformulations composed of biosurfactants and active endophytic fungal spores in order to augment the plant fitness and possibly the control of diseases.

A Cumulative Effect by Multiple-Gene Knockout Strategy Leads to a Significant Increase in the Production of Sophorolipids in Starmerella Bombicola CGMCC 1576

Sophorolipids (SLs), an important biosurfactant produced by S. bombicola, were one of the most potential substitutes for chemical surfactants. Few reports on the transcriptional regulation of SLs synthesis and the engineered strains with high-yield SLs were available. In this study, a Rim9-like protein (Rlp) and three transcription factors (ztf1, leu3, gcl) were mined and analyzed, and a progressive enhancement of SLs production was achieved through cumulative knockouts of three genes. The sophorolipid production of ΔrlpΔleu3Δztf1 reached 97.44 g/L, increased by 50.51% than that of the wild-type strain. Compared with the wild-type strain, the flow of glucose to SLs synthesis pathways was increased, and the synthesis of branched-chain amino acids was reduced in ΔrlpΔleu3Δztf1. The amount of UDP-glucose, the substrate for two glycosyltransferases, also increased, and the expression level of the key genes sble and UGPase for SLs synthesis increased by 2.2 times, respectively. The multiple-gene knockout strategy was proved to be highly effective to construct the engineered strain with high-yield SLs production, and this strain was a superior strain for industrial fermentation of SLs and reduced SLs production costs.

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.

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.

The role of transport proteins in the production of microbial glycolipid biosurfactants

Several microorganisms are currently being used as production platform for glycolipid biosurfactants, providing a greener alternative to chemical biosurfactants. One of the reasons why these processes are commercially competitive is the fact that microbial producers can efficiently export their product to the extracellular environment, reaching high product titers. Glycolipid biosynthetic genes are often found in a dedicated cluster, amidst which genes encoding a dedicated transporter committed to shuttle the glycolipid to the extracellular environment are often found, as is the case for many other secondary metabolites. Knowing this, one can rely on gene clustering features to screen for novel putative transporters, as described and performed in this review. The above strategy proves to be very powerful to identify glycolipid transporters in fungi but is less valid for bacterial systems. Indeed, the genetics of these export systems are currently largely unknown, but some hints are given. Apart from the direct export of the glycolipid, several other transport systems have an indirect effect on glycolipid production. Specific importers dictate which hydrophilic and hydrophobic substrates can be used for production and influence the final yields. In eukaryotes, cellular compartmentalization allows the assembly of glycolipid building blocks in a highly specialized and efficient way. Yet, this requires controlled transport across intracellular membranes. Next to the direct export of glycolipids, the current state of the art regarding this indirect involvement of transporter systems in microbial glycolipid synthesis is summarized in this review. KEY POINTS: • Transporters are directly and indirectly involved in microbial glycolipid synthesis. • Yeast glycolipid transporters are found in their biosynthetic gene cluster. • Hydrophilic and hydrophobic substrate uptake influence microbial glycolipid synthesis.

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.

Enhanced short-chain fatty acids production from waste activated sludge by sophorolipid: Performance, mechanism, and implication

It was found in this study that the presence of sophorolipid (SL) enhanced the production of short-chain fatty acid (SCFA) from anaerobic fermentation of waste activated sludge (WAS). Experimental results showed that with an increase of SL addition from 0 to 0.1 g/g TSS, the maximal SCFA yield increased from 50.5 ± 4.9 to 246.2 ± 7.5 mg COD/g VSS. The presence of SL reduced the surface tension between hydrophobic organics and fermentation liquid, which thereby accelerated the disintegration of WAS and improved the biodegradability of the released organics. SL promoted the carbon/nitrogen ratio of the fermentation system, enhancing the conversion of proteins in WAS. Moreover, SL suppressed severely the activities of methanogens, probably due to the drop of pH caused by SL addition. Amplicon sequencing analyses revealed that SL increased the abundance of hydrolytic microbes such as Bacteroides sp. and Macellibacteroides sp., and SCFA producers (e.g., Acinetobacter sp.).