Production of a human milk oligosaccharide 2'-fucosyllactose by metabolically engineered Saccharomyces cerevisiae

Efficient production of 2'-fucosyllactose in Pichia pastoris through metabolic engineering and constructing an orthogonal energy supply system

2'-fucosyllactose (2'-FL) holds significant role in the infants' nutrition. While microbial production of 2'-FL has predominantly utilized Escherichia coli and Saccharomyces cerevisiae, the potential of Pichia pastoris, renowned for its robust NADPH regeneration capability, remains underexplored. Herein, we systematically engineered the metabolism of P. pastoris to develop an efficient 2'-FL-producing cell factory. We first constructed the de novo biosynthesis pathway for 2'-FL in P. pastoris, achieving an initial titer of 0.143 g/L. By optimizing enzyme selection and solubility of α-1,2-fucosyltransferase (FutC), 2'-FL production was enhanced by nearly ten folds. Subsequently, engineering NADPH supply further increased the 2'-FL production by 170 %. Furthermore, we enhanced energy supply by incorporating an orthogonal energy module based on the methanol dissimilation pathway and increasing GTP availability, resulting in a 32 % improvement in 2'-FL production. Finally, through the optimization of fermentation condition, we realized the production titer of 2'-FL to 3.50 g/L in shake-flask, representing the highest titer in P. pastoris. These findings highlight the potential of P. pastoris as a chassis to produce chemicals by providing abundant NADPH and utilizing methanol as co-substrate to supply sufficient energy.

Intensification of 2'-Fucosyllactose biosynthesis pathway by using a novel fucosyltransferase from Bacillus cereus

Introduction

2'-Fucosyllactose (2'-FL) is an oligosaccharide that can be synthesized in the human body and is known for its health-promoting and prebiotic effects. The biosynthesis of 2'-FL using microorganisms has received attention recently due to its increased application in nutritional and medical infant formulations.

Methods

This work attempts the new application of Bacillus cereus α-1,2-fucosyltransferase (FutCB) in the de novo synthesis of 2'-FL in Escherichia coli (E. coli). Additionally, knocking out the LacZ and WaaF genes alongside overexpression of the key gmd, manB, wcaG, and manC genes enhances the availability of the necessary precursors GDP-L-fucose and lactose for the synthesis of 2'-FL.

Results and discussion

The use of constitutive promoters achieved better control over the production of 2'-FL during fed-batch fermentation. After 64 h of fermentation, the modified E. coli strains produced 121.4 g/L 2'-FL with a yield of 1.90 g/L/h, resulting in an impressive 2'-FL output. These results together indicate the potential of large-scale, high-yield production of 2'-FL and form a basis of much more refinement to be done. The next step will focus on maximum substrate utilization, alteration of gene regulation, and improvement of commercial-scale synthesis.

A review on the expanding biotechnological frontier of Pedobacter

The genus Pedobacter consists of Gram-negative bacteria with a broad geographic distribution, isolated from diverse habitats, including water, soil, plants, wood, rocks and animals. However, characterization efforts have been limited to a small number of species. Likewise, in the context of natural products (NP), only a small fraction of Pedobacter -derived NPs have been characterized so far. In contrast, in silico analysis of the increasing number of available genomes in the databases, suggests a wealth of yet to be discovered compounds. Notable biotechnological applications described so far include the production of heparinases and chondroitinases for therapeutic purposes, phytases and galactosidases as aquaculture feed supplements, alginate lyases for biofuel production, and secondary metabolites such as pedopeptins and isopedopeptins with antimicrobial properties. Further research integrating synthetic biology approaches, holds great promise for unlocking the hidden potential of members of this genus, thus expanding its industrial applications.

Optimization and semi-continuous fermentation of gluco-oligosaccharide production with Weissella cibaria YRK005

In this study, we optimized gluco-oligosaccharide production using Weissella cibaria YRK005 through a semi-continuous fermentation. The Plackett-Burman design identified sucrose and maltose concentrations and fermentation temperature as key factors. Optimization using response surface methodology with a central composite design identified optimal conditions as 14.7% w/v sucrose, 13.5% w/v maltose, and 30 °C, predicting a relative peak area (RPA) of 115.6. Comparative analysis of the anaerobic and aerobic batch fermentation showed higher productivity under the aerobic conditions (25.5 RPA/h) than under the anaerobic conditions (23.7 RPA/h). The aerobic semi-continuous fermentation, with media replenishment every 7 h, achieved 39.2 RPA/h in one-cycle fermentation, exceeding the 27.2 RPA/h in two-cycle fermentation. These results highlight the importance of fermentation conditions in enhancing gluco-oligosaccharide production and suggests that the aerobic semi-continuous fermentation is a promising strategy for industrial applications to increase efficiency and reduce costs.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-024-01703-z.

Metabolic Engineering of Escherichia coli BL21(DE3) for 2'-Fucosyllactose Synthesis in a Higher Productivity

2'-Fucosyllactose (2'-FL) is the most abundant human milk oligosaccharides (HMOs). 2'-FL exhibits great benefits for infant health, such as preventing infantile diarrhea and promoting the growth of intestinal probiotics. The microbial cell factory technique has shown promise for the massive production of 2'-FL. Here, we aimed to construct a recombinant E. coli BL21(DE3) strain for the hyperproduction of 2'-FL. Initially, multicopy genomic integration and expression of the lactose permease gene lacY reduced the formation of byproducts. Furthermore, a more efficient Shine-Dalgarno sequence was used to replace the wild-type sequence in the manC-manB and gmd-wcaG gene clusters, which significantly increased the 2'-FL titer. Based on these results, we overexpressed the sugar efflux transporter SetA and knocked out the pgi gene. This further improved 2'-FL synthesis when glycerol was used as the sole carbon source. Finally, a new α-1,2-fucosyltransferase was identified in Neisseria sp., which exhibited a higher capacity for 2'-FL production. Fed-batch fermentation produced 141.27 g/L 2'-FL in 45 h with a productivity of 3.14 g/L × h. This productivity rate achieved the highest recorded 2'-FL levels, indicating the potential of engineered E. coli BL21 (DE3) strains for use in the industrial production of 2'-FL.

Construction of a Novel Vanillin-Induced Autoregulating Bidirectional Transport System in a Vanillin-Producing E. coli Cell Factory

Vanillin is one of the world's most extensively used flavoring agents with high application value. However, the yield of vanillin biosynthesis remains limited due to the low efficiency of substrate uptake and the inhibitory effect on cell growth caused by vanillin. Here, we screened high-efficiency ferulic acid importer TodX and vanillin exporters PP_0178 and PP_0179 by overexpressing genes encoding candidate transporters in a vanillin-producing engineered Escherichia coli strain VA and further constructed an autoregulatory bidirectional transport system by coexpressing TodX and PP_0178/PP_0179 with a vanillin self-inducible promoter ADH7. Compared with strain VA, strain VA-TodX-PP_0179 can efficiently transport ferulic acid across the cell membrane and convert it to vanillin, which significantly increases the substrate utilization rate efficiency (14.86%) and vanillin titer (51.07%). This study demonstrated that the autoregulatory bidirectional transport system significantly enhances the substrate uptake efficiency while alleviating the vanillin toxicity issue, providing a promising viable route for vanillin biosynthesis.

Enhancing the soluble expression of α-1,2-fucosyltransferase in E. coli using high-throughput flow cytometry screening coupled with a split-GFP

2'-Fucosyllactose (2'-FL), one of the major human milk oligosaccharides, was produced in several engineered microorganisms. However, the low solubility of α-1,2-fucosyltransferase (α1,2-FucT) often becomes a bottleneck to produce maximum amount of 2'-FL in the microorganisms. To overcome this solubility issue, the following studies were conducted to improve the soluble expression of α1,2-FucT. Initially, hydrophobic amino acids in the hydrophilic region of the 6 α-helices were mutated, adhering to the α-helix rule. Subsequently, gfp11 was fused to the C-terminal of futC gene encoding α1,2-FucT (FutC), enabling selection of high-fluorescence mutants through split-GFP. Each mutant library was screened via fluorescence activated cell sorting (FACS) to separate soluble mutants for high-throughput screening. As a result, L80C single mutant and A121D/P124A/L125R triple mutant were found, and a combined quadruple mutant was created. Furthermore, we combined mutations of conserved sequences (Q150H/C151R/Q239S) of FutC, which showed positive effects in the previous studies from our lab, with the above quadruple mutants (L80C/A121D/P124A/L125R). The resulting strain produced approximately 3.4-fold higher 2'-FL titer than that of the wild-type, suggesting that the conserved sequence mutations are an independent subset of the mutations that further improve the solubility of the target protein acquired by random mutagenesis using split-GFP.

Enhancing the Techno-Functional Properties of Lentil Protein Isolate Dispersions Using In-Line High-Shear Rotor-Stator Mixing

In response to global challenges such as climate change and food insecurity, plant proteins have gained interest. Among these, lentils have emerged as a promising source of proteins due to their good nutritional profile and sustainability considerations. However, their widespread use in food products has been impeded by limited solubility. This study aimed to investigate the potential of high-shear mixing, a resource-efficient technique, to enhance lentil protein solubility and its functional properties. Red lentil protein isolate powders were rehydrated and subjected to a semi-continuous in-line high-shear treatment at 10,200 rpm for a timespan ranging from 0 to 15 min. The results highlighted a significant (p < 0.05) increase in solubility from 46.87 to 68.42% after 15 min of shearing and a reduction in particle size as a result of the intense shearing and disruption provided by the rotor and forced passage through the perforations of the stator. The volume-weighted mean diameter decreased from 5.13 to 1.72 µm after 15 min of shearing, also highlighted by the confocal micrographs which confirmed the breakdown of larger particles into smaller and more uniform particles. Rheological analysis indicated consistent Newtonian behaviour across all dispersions, with apparent viscosities ranging from 1.69 to 1.78 mPa.s. Surface hydrophobicity increased significantly (p < 0.05), from 830 to 1245, indicating exposure of otherwise buried hydrophobic groups. Furthermore, colloidal stability of the dispersion was improved, with separation rates decreasing from 71.23 to 24.16%·h-1. The significant enhancements in solubility, particle size reduction, and colloidal stability, highlight the potential of in-line high-shear mixing in improving the functional properties of lentil protein isolates for formulating sustainable food products with enhanced techno-functional properties.

Efficient production of 2'-fucosyllactose in unconventional yeast Yarrowia lipolytica

2'-Fucosyllactose (2'-FL) has great application value as a nutritional component and the whole cell biosynthesis of 2'-FL has become the focus of current research. Yarrowia lipolytica has great potential in oligosaccharide synthesis and large-scale fermentation. In this study, systematic engineering of Y. lipolytica for efficient 2'-FL production was performed. By fusing different protein tags, the synthesis of 2'-FL was optimized and the ubiquitin tag was demonstrated to be the best choice to increase the 2'-FL production. By iterative integration of the related genes, increasing the precursor supply, and promoting NADPH regeneration, the 2'-FL synthesis was further improved. The final 2'-FL titer, 41.10 g/L, was obtained in the strain F5-1. Our work reports the highest 2'-FL production in Y. lipolytica, and demonstrates that Y. lipolytica is an efficient microbial chassis for the synthesis of oligosaccharides.

High-Yield Synthesis of 2'-Fucosyllactose from Glycerol and Glucose in Engineered Escherichia coli

2'-Fucosyllactose (2'-FL) is vital for the growth and development of newborns. In this study, we developed a synthesis pathway for 2'-FL in Escherichia coli BL21 (DE3). Then, we optimized the solubility of α-1,2-fucosyltransferase, thereby enhancing the production yield of 2'-FL. Based on this finding, we further enhanced the expression of guanosine inosine kinase Gsk and knocked out the isocitrate lyase regulator gene iclR. This strategy reduced the formation of byproduct acetate during the metabolic process and alleviated carbon source overflow effects in the strain, resulting in further improvement of the yield of 2'-FL. In a 3 L bioreactor, employing fed-batch fermentation with glycerol and glucose as substrates, the engineered strain BWLAI-RSZL exhibited impressive 2'-FL titers of 121.9 and 111.56 g/L, along with productivity levels of 1.57 and 1.31 g/L/h, respectively. The reported 2'-FL titers reached a groundbreaking level, irrespective of the carbon source employed (glycerol or glucose), highlighting the significant potential for large-scale industrial synthesis of 2'-FL.

Engineering Escherichia coli MG1655 for Highly Efficient Biosynthesis of 2'-Fucosyllactose by De Novo GDP-Fucose Pathway

2'-Fucosyllactose (2'-FL), the most typical human milk oligosaccharide, is used as an additive in premium infant formula. Herein, we constructed two highly effective 2'-FL synthesis producers via a de novo GDP-fucose pathway from engineered Escherichia coli MG1655. First, lacZ and wcaJ, two competitive pathway genes, were disrupted to block the invalid consumption of lactose and GDP-fucose, respectively. Next, the lacY gene was strengthened by switching its native promoter to PJ23119. To enhance the supply of endogenous GDP-fucose, the promoters of gene clusters manC-manB and gmd-fcl were strengthened individually or in combination. Subsequently, chromosomal integration of a constitutive PJ23119 promoter-based BKHT expression cassette (PJ23119-BKHT) was performed in the arsB and recA loci. The most productive plasmid-based and plasmid-free strains produced 76.9 and 50.1 g/L 2'-FL by fed-batch cultivation, respectively. Neither of them generated difucosyl lactose nor 3-fucosyllactose as byproducts.

Prebiotics in New-Born and Children's Health

At present, prebiotics, like probiotics, are receiving more attention as a promising tool for health maintenance. Many studies have recognized the role of prebiotics in preventing and treating various illnesses including metabolic disorders, gastrointestinal disorders, and allergies. Naturally, prebiotics are introduced to the human body in the first few hours of life as the mother breastfeeds the newborn. Prebiotic human milk oligosaccharides (HMOs) are the third largest constituent of human breastmilk. Studies have proven that HMOs modulate an infant's microbial composition and assist in the development of the immune system. Due to some health conditions of the mother or beyond the recommended age for breastfeeding, infants are fed with formula. Few types of prebiotics have been incorporated into formula to yield similar beneficial impacts similar to breastfeeding. Synthetic HMOs have successfully mimicked the bifidogenic effects of breastmilk. However, studies on the effectiveness and safety of consumption of these synthetic HMOs are highly needed before massive commercial production. With the introduction of solid foods after breastfeeding or formula feeding, children are exposed to a range of prebiotics that contribute to further shaping and maturing their gut microbiomes and gastrointestinal function. Therefore, this review evaluates the functional role of prebiotic interventions in improving microbial compositions, allergies, and functional gastrointestinal disorders in children.

Recent Advances in the Biosynthesis of Natural Sugar Substitutes in Yeast

Natural sugar substitutes are safe, stable, and nearly calorie-free. Thus, they are gradually replacing the traditional high-calorie and artificial sweeteners in the food industry. Currently, the majority of natural sugar substitutes are extracted from plants, which often requires high levels of energy and causes environmental pollution. Recently, biosynthesis via engineered microbial cell factories has emerged as a green alternative for producing natural sugar substitutes. In this review, recent advances in the biosynthesis of natural sugar substitutes in yeasts are summarized. The metabolic engineering approaches reported for the biosynthesis of oligosaccharides, sugar alcohols, glycosides, and rare monosaccharides in various yeast strains are described. Meanwhile, some unresolved challenges in the bioproduction of natural sugar substitutes in yeast are discussed to offer guidance for future engineering.

An Overview of Sugar Nucleotide-Dependent Glycosyltransferases for Human Milk Oligosaccharide Synthesis

Human milk oligosaccharides (HMOs) have received increasing attention because of their special effects on infant health and commercial value as the new generation of core components in infant formula. Currently, large-scale production of HMOs is generally based on microbial synthesis using metabolically engineered cell factories. Introduction of the specific glycosyltransferases is essential for the construction of HMO-producing engineered strains in which the HMO-producing glycosyltransferases are generally sugar nucleotide-dependent. Four types of glycosyltransferases have been used for typical glycosylation reactions to synthesize HMOs. Soluble expression, substrate specificity, and regioselectivity are common concerns of these glycosyltransferases in practical applications. Screening of specific glycosyltransferases is an important research topic to solve these problems. Molecular modification has also been performed to enhance the catalytic activity of various HMO-producing glycosyltransferases and to improve the substrate specificity and regioselectivity. In this article, various sugar nucleotide-dependent glycosyltransferases for HMO synthesis were overviewed, common concerns of these glycosyltransferases were described, and the future perspectives of glycosyltransferase-related studies were provided.

De novo biosynthesis of 2'-fucosyllactose in engineered Pichia pastoris

PURPOSE

Pichia pastoris is well known for its ability to produce short and low-immunogenic humanized glycosyl chains onto recombinant glycoproteins, it was thus speculated to be applicable to synthesize oligosaccharides. In this study, generally recognized as safe (GRAS) microorganism Pichia pastoris GS115 was tested for its potential to be used as a new synthetic chassis to produce the most abundant human milk oligosaccharide 2'-fucosyllactose (2'-FL).

METHODS

To enable the de novo synthesis of 2'-FL, lactose transporter lac12, two enzymes of gmd, gmer, and fucosyltransferases futC were integrated into the genome of P. pastoris, under the control of constitutive P_GAP promoter.

RESULTS

The resulting recombinant yeasts yielded up to 0.276 g/L through culture optimization in a 5 L bioreactor.

CONCLUSION

To our knowledge, this is the first report of 2'-FL production in engineered Pichia pastoris. This work is a good starting point to produce 2'-FL using Pichia pastoris as a viable chassis.

Elimination of Byproduct Generation and Enhancement of 2'-Fucosyllactose Synthesis by Expressing a Novel α1,2-Fucosyltransferase in Engineered Escherichia coli

2'-Fucosyllactose (2'-FL) is a kind of fucosylated human milk oligosaccharide (HMO), representing the most abundant oligosaccharide in breast milk. We conducted systematic studies on three canonical α1,2-fucosyltransferases (WbgL, FucT2, and WcfB) to quantify the byproducts in a lacZ- and wcaJ-deleted Escherichia coli BL21(DE3) basic host strain. Further, we screened a highly active α1,2-fucosyltransferase from Helicobacter sp. 11S02629-2 (BKHT), which exhibits high in vivo 2'-FL productivity without the formation of byproducts difucosyl lactose (DFL) and 3-FL. The maximum 2'-FL titer and yield reached 11.13 g/L and 0.98 mol/mol of lactose, respectively, in shake-flask cultivation, both approaching the theoretical maximum value. In a 5 L fed-batch cultivation, the maximum 2'-FL titer reached 94.7 g/L extracellularly with a yield of 0.98 mol of 2'-FL/mol of lactose and productivity of 1.14 g L^-1 h^-1. Our reported 2'-FL yield is the highest from lactose reported to date.

Enhancing lactose recognition of a key enzyme in 2'-fucosyllactose synthesis: α-1,2-fucosyltransferase

BACKGROUND

2'-Fucosyllactose, a representative oligosaccharide in human milk, is an emerging and promising food and pharmaceutical ingredient due to its powerful health benefits, such as participating in immune regulation, regulation of intestinal flora, etc. To enable economically viable production of 2'-fucosyllactose, different biosynthesis strategies using precursors and pathway enzymes have been developed. The α-1,2-fucosyltransferases are an essential part involved in these strategies, but their strict substrate selectivity and unsatisfactory substrate tolerance are one of the key roadblocks limiting biosynthesis.

RESULTS

To tackle this issue, a semi-rational manipulation combining computer-aided designing and screening with biochemical experiments were adopted. The mutant had a 100-fold increase in catalytic efficiency compared to the wild-type. The highest 2'-fucosyllactose yield was up to 0.65 mol mol^-1 lactose with a productivity of 2.56 g mL^-1  h^-1 performed by enzymatic catalysis in vitro. Further analysis revealed that the interactions between the mutant and substrates were reduced. The crucial contributions of wild-type and mutant to substrate recognition ability were closely related to their distinct phylotypes in terms of amino acid preference.

CONCLUSION

It is envisioned that the engineered α-1,2-fucosyltransferase could be harnessed to relieve constraints imposed on the bioproduction of 2'-fucosyllactose and lay a theoretical foundation for elucidating the substrate recognition mechanisms of fucosyltransferases. © 2022 Society of Chemical Industry.

Biosynthesis of human milk oligosaccharides via metabolic engineering approaches: current advances and challenges

Human milk oligosaccharides (HMOs) are structurally complex unconjugated glycans that are the third largest solid component in human milk. HMOs have drawn increasing attention because of their beneficial effects to infant health. Of the more than 200 HMOs, only less than 10 have been used in medical or food industries. Although HMO research has been becoming increasingly intensive and booming, the limited availability of HMOs still cannot meet the demand in health effect research and large-scale application. Therefore, efficient synthetic approaches and strategies for HMO production are urgently needed. The goal of this review is to highlight recent advances in microbial cell factory development for HMO biosynthesis. Key challenges in representative HMO production are also highlighted. The further perspectives in general HMO biosynthesis are discussed.

Directed Evolution of Soluble α-1,2-Fucosyltransferase Using Kanamycin Resistance Protein as a Phenotypic Reporter for Efficient Production of 2'-Fucosyllactose

2'-Fucosyllactose (2'-FL), the most abundant fucosylated oligosaccharide in human milk, has multiple beneficial effects on human health. However, its biosynthesis by metabolically engineered Escherichia coli is often hampered owing to the insolubility and instability of α-1,2-fucosyltransferase (the rate-limiting enzyme). In this study, we aimed to enhance 2'-FL production by increasing the expression of soluble α-1,2-fucosyltransferase from Helicobacter pylori (FucT2). Because structural information regarding FucT2 has not been unveiled, we decided to improve the expression of soluble FucT2 in E. coli via directed evolution using a protein solubility biosensor that links protein solubility to antimicrobial resistance. For such a system to be viable, the activity of kanamycin resistance protein (Kan^R) should be dependent on FucT2 solubility. Kan^R was fused to the C-terminus of mutant libraries of FucT2, which were generated using a combination of error-prone PCR and DNA shuffling. Notably, one round of the directed evolution process, which consisted of mutant library generation and selection based on kanamycin resistance, resulted in a significant increase in the expression level of soluble FucT2. As a result, a batch fermentation with the ΔL M15 pBCGW strain, expressing the FucT2 mutant (F#1-5) isolated from the first round of the directed evolution process, resulted in the production of 0.31 g/l 2'-FL with a yield of 0.22 g 2'-FL/g lactose, showing 1.72- and 1.51-fold increase in the titer and yield, respectively, compared to those of the control strain. The simple and powerful method developed in this study could be applied to enhance the solubility of other unstable enzymes.

Strain engineering and metabolic flux analysis of a probiotic yeast Saccharomyces boulardii for metabolizing L-fucose, a mammalian mucin component

Background

Saccharomyces boulardii is a probiotic yeast that exhibits antimicrobial and anti-toxin activities. Although S. boulardii has been clinically used for decades to treat gastrointestinal disorders, several studies have reported weak or no beneficial effects of S. boulardii administration in some cases. These conflicting results of S. boulardii efficacity may be due to nutrient deficiencies in the intestine that make it difficult for S. boulardii to maintain its metabolic activity.

Results

To enable S. boulardii to overcome any nutritional deficiencies in the intestine, we constructed a S. boulardii strain that could metabolize l-fucose, a major component of mucin in the gut epithelium. The fucU, fucI, fucK, and fucA from Escherichia coli and HXT4 from S. cerevisiae were overexpressed in S. boulardii. The engineered S. boulardii metabolized l-fucose and produced 1,2-propanediol under aerobic and anaerobic conditions. It also produced large amounts of 1,2-propanediol under strict anaerobic conditions. An in silico genome-scale metabolic model analysis was performed to simulate the growth of S. boulardii on l-fucose, and elementary flux modes were calculated to identify critical metabolic reactions for assimilating l-fucose. As a result, we found that the engineered S. boulardii consumes l-fucose via (S)-lactaldehyde-(S)-lactate-pyruvate pathway, which is highly oxygen dependent.

Conclusion

To the best of our knowledge, this is the first study in which S. cerevisiae and S. boulardii strains capable of metabolizing l-fucose have been constructed. This strategy could be used to enhance the metabolic activity of S. boulardii and other probiotic microorganisms in the gut.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01926-x.

Strategies for Enhancing Microbial Production of 2'-Fucosyllactose, the Most Abundant Human Milk Oligosaccharide

Human milk oligosaccharides (HMOs), a group of structurally diverse unconjugated glycans in breast milk, act as important prebiotics and have plenty of unique health effects for growing infants. 2'-Fucosyllactose (2'-FL) is the most abundant HMO, accounting for approximately 30%, among approximately 200 identified HMOs with different structures. 2'-FL can be enzymatically produced by α1,2-fucosyltransferase, using GDP-l-fucose as donor and lactose as acceptor. Metabolic engineering strategies have been widely used for enhancement of GDP-l-fucose supply and microbial production of 2'-FL with high productivity. GDP-l-fucose supply can be enhanced by two main pathways, including de novo and salvage pathways. 2'-FL-producing α1,2-fucosyltransferases have widely been identified from various microorganisms. Metabolic pathways for 2'-FL synthesis can be basically constructed by enhancing GDP-l-fucose supply and introducing α1,2-fucosyltransferase. Various strategies have been attempted to enhance 2'-FL production, such as acceptor enhancement, donor enhancement, and improvement of the functional expression of α1,2-fucosyltransferase. In this review, current progress in GDP-l-fucose synthesis and bacterial α1,2-fucosyltransferases is described in detail, various metabolic engineering strategies for enhancing 2'-FL production are comprehensively reviewed, and future research focuses in biotechnological production of 2'-FL are suggested.

Transporter Engineering in Microbial Cell Factory Boosts Biomanufacturing Capacity

Microbial cell factories (MCFs) are typical and widely used platforms in biomanufacturing for designing and constructing synthesis pathways of target compounds in microorganisms. In MCFs, transporter engineering is especially significant for improving the biomanufacturing efficiency and capacity through enhancing substrate absorption, promoting intracellular mass transfer of intermediate metabolites, and improving transmembrane export of target products. This review discusses the current methods and strategies of mining and characterizing suitable transporters and presents the cases of transporter engineering in the production of various chemicals in MCFs.

Engineered Bacillus subtilis for the de novo production of 2'-fucosyllactose

BACKGROUND

The most abundant human milk oligosaccharide in breast milk, 2'-fucosyllactose (2'-FL), has been approved as an additive to infant formula due to its multifarious nutraceutical and pharmaceutical functions in promoting neonate health. However, the low efficiency of de novo synthesis limits the cost-efficient bioproduction of 2'-FL.

RESULTS

This study achieved 2'-FL de novo synthesis in a generally recognized as safe (GRAS) strain Bacillus subtilis. First, a de novo biosynthetic pathway for 2'-FL was introduced by expressing the manB, manC, gmd, wcaG, and futC genes from Escherichia coli and Helicobacter pylori in B. subtilis, resulting in 2'-FL production of 1.12 g/L. Subsequently, a 2'-FL titer of 2.57 g/L was obtained by reducing the competitive lactose consumption, increasing the regeneration of the cofactor guanosine-5'-triphosphate (GTP), and enhancing the supply of the precursor mannose-6-phosphate (M6P). By replacing the native promoter of endogenous manA gene (encoding M6P isomerase) with a constitutive promoter P7, the 2'-FL titer in shake flask reached 18.27 g/L. The finally engineered strain BS21 could produce 88.3 g/L 2'-FL with a yield of 0.61 g/g lactose in a 3-L bioreactor, without the addition of antibiotics and chemical inducers.

CONCLUSIONS

The efficient de novo synthesis of 2'-FL can be achieved by the engineered B. subtilis, paving the way for the large-scale bioproduction of 2'-FL titer in the future.

Combinatorial metabolic engineering of Escherichia coli for de novo production of 2'-fucosyllactose

2'-Fucosyllactose (2'-FL) is a kind of fucosylated lactose of human milk oligosaccharides (HMOs). In this work, Escherichia coli MG1655 was metabolically engineered to increase 2'-FL production. The 2'-FL titer was raised from 0.0118 to 0.8062 g/L by increasing three gene copies of α1,2-fucosyltransferase (FutC) and by deleting the lon, wcaJ, lacZ, and lacI genes in the competitive pathways. Additionally, the 2'-FL titer was raised to 2.9 g/L by fusing a TrxA tag at the N-terminus of FutC, and then to 3.4 g/L by deleting glutathione reductase (Gor). Finally, the 2'-FL reached 3.3 g/L in the final strain E. coli MG27 through the de novo pathway in shake flask, and reached 10.3 g/L in a 3-L fermentor.

Efficient Bioproduction of Human Milk Alpha-Lactalbumin in Komagataella phaffii

Alpha-lactalbumin (α-LA; the most abundant whey protein in human milk) contributes to infant development, providing bioactive peptides and essential amino acids. Here, Komagataella phaffii (K. phaffii) was selected as the production host. We found that the K. phaffii host X33 was suitable for expressing the target protein, yielding 5.2 mg·L^-1 α-LA. Thereafter, several secretory signal peptides were applied to obtain a higher titer of α-LA. The strain with α-factor secretory signal peptide secreted the highest extracellular titer. Additionally, promoters AOX1, GAP, and GAP(m) were compared and applied. The strain with the promoter AOX1 produced the highest extracellular titer. In addition, coexpressing human protein disulfide isomerase A3 (hPDIA3) increased the titer by 27%. Human α-LA production by the strain X33-pPICZαA-hLALBA-hPDIA3 reached 56.3 mg·L^-1 in a 3 L bioreactor. This is the first report of successful secretory human α-LA expression in K. phaffii and lays foundations for the simulation of human milk for infant formulas and further development of bioengineered milk.

Metabolic engineering for valorization of macroalgae biomass

Marine macroalgae have huge potential as feedstocks for production of a wide spectrum of chemicals used in biofuels, biomaterials, and bioactive compounds. Harnessing macroalgae in these ways could promote wellbeing for people while mitigating climate change and environmental destruction linked to use of fossil fuels. Microorganisms play pivotal roles in converting macroalgae into valuable products, and metabolic engineering technologies have been developed to extend their native capabilities. This review showcases current achievements in engineering the metabolisms of various microbial chassis to convert red, green, and brown macroalgae into bioproducts. Unique features of macroalgae, such as seasonal variation in carbohydrate content and salinity, provide the next challenges to advancing macroalgae-based biorefineries. Three emerging engineering strategies are discussed here: (1) designing dynamic control of metabolic pathways, (2) engineering strains of halophilic (salt-tolerant) microbes, and (3) developing microbial consortia for conversion. This review illuminates opportunities for future research communities by elucidating current approaches to engineering microbes so they can become cell factories for the utilization of macroalgae feedstocks.

Efficient Production of 2'-Fucosyllactose from l-Fucose via Self-Assembling Multienzyme Complexes in Engineered Escherichia coli

2'-Fucosyllactose (2'-FL) has been widely used as a nutritional additive in infant formula due to its multifarious nutraceutical and pharmaceutical functions in neonate health. As such, it is essential to develop an efficient and extensive microbial fermentation platform to cater to the needs of the 2'-FL market. In this study, a spatial synthetic biology strategy was employed to promote 2'-FL biosynthesis in recombinant Escherichia coli. First, the salvage pathway for 2'-FL production from l-fucose and lactose was constructed by introducing a bifunctional enzyme l-fucokinase/GDP-l-fucose pyrophosphorylase (Fkp) derived from Bacteroides fragilis and an α-1,2-fucosyltransferase (FutC) derived from Helicobacter pylori into engineered E. coli BL21(DE3). Next, the endogenous genes involved in the degradation and shunting of the substrate and key intermediate were inactivated to improve the availability of precursors for 2'-FL biosynthesis. Moreover, to further improve the yield and titer of 2'-FL, a short peptide pair (RIAD-RIDD) was used to form self-assembling multienzyme complexes in vivo. The spatial localization of peptides and stoichiometry of enzyme assemblies were subsequently optimized to further improve 2'-FL production. Finally, cofactor regeneration was also considered to alleviate the potential cofactor deficiency and redox flux imbalance in the biocatalysis process. Fed-batch fermentation of the final WLS20 strain accumulated 30.5 g/L extracellular 2'-FL with the yield and productivity of 0.661 mol/mol fucose and 0.48 g/L/h, respectively. This research has demonstrated that the application of spatial synthetic biology and metabolic engineering strategies can dramatically enlarge the titer and yield of 2'-FL biosynthesis in engineered E. coli.

Improved production of 2'-fucosyllactose in engineered Saccharomyces cerevisiae expressing a putative α-1, 2-fucosyltransferase from Bacillus cereus

Background

2′-fucosyllactose (2′-FL) is one of the most abundant oligosaccharides in human milk. It constitutes an authorized functional additive to improve infant nutrition and health in manufactured infant formulations. As a result, a cost-effective method for mass production of 2′-FL is highly desirable.

Results

A microbial cell factory for 2′-FL production was constructed in Saccharomyces cerevisiae by expressing a putative α-1, 2-fucosyltransferase from Bacillus cereus (FutBc) and enhancing the de novo GDP-l-fucose biosynthesis. When enabled lactose uptake, this system produced 2.54 g/L of 2′-FL with a batch flask cultivation using galactose as inducer and carbon source, representing a 1.8-fold increase compared with the commonly used α-1, 2-fucosyltransferase from Helicobacter pylori (FutC). The production of 2′-FL was further increased to 3.45 g/L by fortifying GDP-mannose synthesis. Further deleting gal80 enabled the engineered strain to produce 26.63 g/L of 2′-FL with a yield of 0.85 mol/mol from lactose with sucrose as a carbon source in a fed-batch fermentation.

Conclusion

FutBc combined with the other reported engineering strategies holds great potential for developing commercial scale processes for economic 2′-FL production using a food-grade microbial cell factory.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01657-5.

L-malic acid production from xylose by engineered Saccharomyces cerevisiae

L-malic acid is widely used in the food, chemical, and pharmaceutical industries. Here, we report on production of malic acid from xylose, the second most abundant sugar in lignocellulosic hydrolysates, by engineered Saccharomyces cerevisiae. To enable malic acid production in a xylose-assimilating S. cerevisiae, we overexpressed PYC1 and PYC2, coding for pyruvate carboxylases, a truncated MDH3 coding for malate dehydrogenase, and SpMAE1, coding for a Schizosaccharomyces pombe malate transporter. Additionally, both the ethanol and glycerol-producing pathways were blocked to enhance malic acid production. The resulting strain produced malic acid from both glucose and xylose, but it produced much higher titers of malic acid from xylose than glucose. Interestingly, the engineered strain had higher malic acid yield from lower concentrations (10 g/L) of xylose, with no ethanol production, than from higher xylose concentrations (20 g/L and 40 g/L). As such, a fed-batch culture maintaining xylose concentrations at low levels was conducted and 61.2 g/L of malic acid was produced, with a productivity of 0.32 g/L∙h. These results represent successful engineering of S. cerevisiae for the production of malic acid from xylose, confirming that that xylose offers the efficient production of various biofuels and chemicals by engineered S. cerevisiae. This article is protected by copyright. All rights reserved.

Engineered Microbial Routes for Human Milk Oligosaccharides Synthesis

Human milk oligosaccharides (HMOs) are one of the important ingredients in human milk, which have attracted great interest due to their beneficial effect on the health of newborns. The large-scale production of HMOs has been researched using engineered microbial routes due to the availability, safety, and low cost of host strains. In addition, the development of molecular biology technology and metabolic engineering has promoted the effectiveness of HMOs production. According to current reports, 2'-fucosyllactose (2'-FL), 3-fucosyllactose (3-FL), lacto-N-tetraose (LNT), lacto-N-neotetraose (LNnT), 3'-sialyllactose (3'-SL), 6'-sialyllactose (6'-SL), and some fucosylated HMOs with complex structures have been produced via the engineered microbial route, with 2'-FL having been produced the most. However, due to the uncertainty of metabolic patterns, the selection of host strains has certain limitations. Aside from that, the expression of appropriate glycosyltransferase in microbes is key to the synthesis of different HMOs. Therefore, finding a safe and efficient glycosyltransferase has to be addressed when using engineered microbial pathways. In this review, the latest research on the production of HMOs using engineered microbial routes is reported. The selection of host strains and adapting different metabolic pathways helped researchers designing engineered microbial routes that are more conducive to HMOs production.

Enhanced bioproduction of fucosylated oligosaccharide 3-fucosyllactose in engineered Escherichia coli with an improved de novo pathway

3-fucosyllactose (3-FL) and 2'-fucosyllactose (2'-FL), are two important fucosylated oligosaccharides in human milk. Extensive studies on 2'-FL enabled its official approval for use in infant formula. However, development of 3-FL has been somewhat sluggish due to its low content in human milk and poor yield in enlarged production. Here, an α-1,3-fucosyltransferase mutant was introduced into an engineered Escherichia coli (E. coli) capable of producing GDP-L-fucose, leading to a promising 3-FL titer in a 5.0-L bioreactor. To increase the availability of cofactors (NADPH and GTP) for optimized 3-FL production, zwf, pntAB, and gsk genes were successively overexpressed, finally resulting in a higher 3-FL level with a titer of 35.72 g/L and a yield of 0.82 mol 3-FL/mol lactose. Unexpectedly, the deletion of pfkA gene led to a much lower performance of 3-FL production than the control strain. Still, our strategy achieved the highest 3-FL level in E. coli to date.

Microbial production of human milk oligosaccharide lactodifucotetraose

Human milk oligosaccharides (HMOs) are potent bioactive compounds that modulate neonatal health and are of interest for development as potential drug treatments for adult diseases. The potential of these molecules, their limited access from natural sources, and difficulty in large-scale isolation of individual HMOs for studies and applications have motivated the development of chemical syntheses and in vitro enzymatic catalysis strategies. Whole cell biocatalysts are emerging as alternative self-regulating production platforms that have the potential to reduce the cost for enzymatic synthesis of HMOs. Whole cell biocatalysts for the production of short-chained, linear and small monofucosylated HMOs have been reported but those for fucosylated structures with higher complexity have not been explored. In this study, we established a strategy for producing a difucosylated HMO, lactodifucotetraose (LDFT), from lactose and L-fucose in Escherichia coli. We used two bacterial fucosyltransferases with narrow acceptor selectivity to drive the sequential fucosylation of lactose and intermediate 2'-fucosyllactose (2'-FL) to produce LDFT. Deletion of substrate degradation pathways that decoupled cellular growth from LDFT production, enhanced expression of native substrate transporters and modular induction of the genes in the LDFT biosynthetic pathway allowed complete conversion of lactose into LDFT and minor quantities of the side product 3-fucosyllactose (3-FL). Overall, 5.1 g/L of LDFT was produced from 3 g/L lactose and 3 g/L L-fucose in 24 h. Our results demonstrate promising applications of engineered microbial biosystems for the production of multi-fucosylated HMOs for biochemical studies.

Biotechnological Production of 2'-Fucosyllactose: A Prevalent Fucosylated Human Milk Oligosaccharide

Human milk oligosaccharide (HMO) is a key component of human milk carbohydrates and is closely related to the nutrition and health benefits of breastfeeding in infants. 2'-Fucosyllactose (2'-FL) is the most abundant fucosylated HMO, which has remarkable value in nutrition and medicine, such as suppressing pathogen infection, regulating intestinal flora, and boosting immunity. However, 2'-FL production via the method of extraction or chemical synthesis cannot meet its large demand, and as a result, environmentally friendly and efficient biotechnological approaches, including in vitro enzymatic synthesis and microbial cell factory production, have been developed and applied to its commercialized production. This review introduces, summarizes, and discusses the recent advances in the biotechnological production of 2'-FL. Furthermore, future research directions for the biotechnological production of 2'-FL as well as the strategies to further improve its concentration are highlighted and discussed.

Recent approaches for the quantitative analysis of functional oligosaccharides used in the food industry: A review

Functional oligosaccharides (OS) are diverse groups of carbohydrates that confer several health benefits stemming from their prebiotic activity. Commonly used oligosaccharides, fructooligosaccharides and galactooligosaccharides, are used in a wide range of applications from food ingredients to mimic the prebiotic activity of human milk oligosaccharides (HMOs) in infant formula to sugar and fat replacers in dairy and bakery products. However, while consumption of these compounds is associated with several positive health effects, increased consumption can cause intestinal discomfort and aggravation of intestinal bowel syndrome symptoms. Hence, it is essential to develop rapid and reliable techniques to quantify OS for quality control and proper assessment of their functionality in food and food products. The present review will focus on recent analytical techniques used to quantify OS in different matrices such as food and beverage products.

Pathway Optimization of 2'-Fucosyllactose Production in Engineered Escherichia coli

2'-Fucosyllactose (2'-FL), one of the most valuable oligosaccharides in human milk, is used as an emerging food ingredient in the nutraceutical and food industries due to its numerous health benefits. Herein, the de novo and salvage pathways for GDP-fucose synthesis were engineered and optimized in Escherichia coli BL21 (DE3) to improve the production of 2'-FL. The de novo pathway genes encoding phosphomannomutase (ManB), mannose-1-phosphate guanyltransferase (ManC), GDP-d-mannose-4,6-dehydratase (Gmd), and GDP-l-fucose synthase (WcaG) combined with the gene from the salvage pathway encoding fucose kinase/fucose-1-phosphate guanylyltransferase (Fkp) were reconstructed in two vectors to evaluate the GDP-fucose biosynthesis. Then, the fucT2 gene, encoding α1,2-fucosyltransferase, was introduced into the GDP-fucose-overproducing strains to realize 2'-FL biosynthesis. Furthermore, the genes in bypass pathways, including lacZ, fucI, fucK, and wcaJ, were inactivated to improve 2'-FL production. In addition, the two GDP-fucose synthesis pathways, along with fucT2, were transcriptionally fine-tuned to efficiently increase 2'-FL production. The final metabolically engineered E. coli produced 2.62 and 14.1 g/L in shake-flask and fed-batch cultivations, respectively.

Biological strategies for oligo/polysaccharide synthesis: biocatalyst and microbial cell factory

Oligosaccharides and polysaccharides constitute the principal components of carbohydrates, which are important biomacromolecules that demonstrate considerable bioactivities. However, the variety and structural complexity of oligo/polysaccharides represent a major challenge for biological and structural explorations. To access structurally defined oligo/polysaccharides, biological strategies using glycoenzyme biocatalysts have shown remarkable synthetic potential attributed to their regioselectivity and stereoselectivity that allow mild, structurally controlled reaction without addition of protecting groups necessary in chemical strategies. This review summarizes recent biotechnological approaches of oligo/polysaccharide synthesis, which mainly includes in vitro enzymatic synthesis and cell factory synthesis. We have discussed the important factors involved in the production of nucleotide sugars. Furthermore, the strategies established in the cell factory and enzymatic syntheses are summarized, and we have highlighted concepts like metabolic flux rebuilding and regulation, enzyme engineering, and route design as important strategies. The research challenges and prospects are also outlined and discussed.

Bio-synthesis of food additives and colorants-a growing trend in future food

Food additives and colorants are extensively used in the food industry to improve food quality and safety during processing, storage and packing. Sourcing of these molecules is predominately through three means: extraction from natural sources, chemical synthesis, and bio-production, with the first two being the most utilized. However, growing demands for sustainability, safety and "natural" products have renewed interest in using bio-based production methods. Likewise, the move to more cultured foods and meat alternatives requires the production of new additives and colorants. The production of bio-based food additives and colorants is an interdisciplinary research endeavor and represents a growing trend in future food. To highlight the potential of microbial hosts for food additive and colorant production, we focus on current advances for example molecules based on their utilization stage and bio-production yield as follows: (I) approved and industrially produced with high titers; (II) approved and produced with decent titers (in the g/L range), but requiring further engineering to reduce production costs; (III) approved and produced with very early stage titers (in the mg/L range); and (IV) new/potential candidates that have not been approved but can be sourced through microbes. Promising approaches, as well as current challenges and future directions will also be thoroughly discussed for the bioproduction of these food additives and colorants.

Multi-Path Optimization for Efficient Production of 2'-Fucosyllactose in an Engineered Escherichia coli C41 (DE3) Derivative

2′-fucosyllactose (2′-FL), one of the simplest but most abundant oligosaccharides in human milk, has been demonstrated to have many positive benefits for the healthy development of newborns. However, the high-cost production and limited availability restrict its widespread use in infant nutrition and further research on its potential functions. In this study, on the basis of previous achievements, we developed a powerful cell factory by using a lacZ-mutant Escherichia coli C41 (DE3)ΔZ to ulteriorly increase 2′-FL production by feeding inexpensive glycerol. Initially, we co-expressed the genes for GDP-L-fucose biosynthesis and heterologous α-1,2-fucosyltransferase in C41(DE3)ΔZ through different plasmid-based expression combinations, functionally constructing a preferred route for 2′-FL biosynthesis. To further boost the carbon flux from GDP-L-fucose toward 2′-FL synthesis, deletion of chromosomal genes (wcaJ, nudD, and nudK) involved in the degradation of the precursors GDP-L-fucose and GDP-mannose were performed. Notably, the co-introduction of two heterologous positive regulators, RcsA and RcsB, was confirmed to be more conducive to GDP-L-fucose formation and thus 2′-FL production. Further a genomic integration of an individual copy of α-1,2-fucosyltransferase gene, as well as the preliminary optimization of fermentation conditions enabled the resulting engineered strain to achieve a high titer and yield. By collectively taking into account the intracellular lactose utilization, GDP-L-fucose availability, and fucosylation activity for 2′-FL production, ultimately a highest titer of 2′-FL in our optimized conditions reached 6.86 g/L with a yield of 0.92 mol/mol from lactose in the batch fermentation. Moreover, the feasibility of mass production was demonstrated in a 50-L fed-batch fermentation system in which a maximum titer of 66.80 g/L 2′-FL was achieved with a yield of 0.89 mol 2′-FL/mol lactose and a productivity of approximately 0.95 g/L/h 2′-FL. As a proof of concept, our preliminary 2′-FL production demonstrated a superior production performance, which will provide a promising candidate process for further industrial production.

Recent advances on 2'-fucosyllactose: physiological properties, applications, and production approaches

The trisaccharide, 2'-fucosyllactose (Fucα1-2Galβ1-4Glc; 2'-FL), is the most abundant oligosaccharide in human milk. It has numerous significant biological properties including prebiotics, antibacterial, antiviral, and immunomodulating effects, and has been approved as "generally recognized as safe" (GRAS) by the Food and Drug Administration (FDA) and as a novel food (NF) by the European Food Safety Authority (EFSA). 2'-FL not only serves as a food ingredient added in infant formula, but also as a dietary supplement and medical food material in food bioprocesses. There is considerable commercial interest in 2'-FL for its irreplaceable nutritional applications. This review aims at systematically elaborating key functional properties of 2'-FL as well as its applications. In addition, several approaches for 2'-FL production are described in this review, including chemical, chemo-enzymatical, and cell factory approaches, and the pivotal research results also have been summarized. With the rapid development of metabolic engineering and synthetic biology strategies, using the engineered cell factory for 2'-FL large-scale production might be a promising approach. From an economic and safety point of view, microbial selection for cell factory engineering in 2'-FL bioprocess also should be taken into consideration.