High-Yield Synthesis of Lacto-N-Neotetraose from Glycerol and Glucose in Engineered Escherichia coli

Comprehensive review on human Milk oligosaccharides: Biosynthesis, structure, intestinal health benefits, immune regulation, neuromodulation mechanisms, and applications

This review provides a comprehensive analysis of the biosynthetic pathways of various oligosaccharides in Escherichia coli, structural characteristics, and bioactive mechanisms of human milk oligosaccharides (HMOs), with a particular emphasis on their roles in gut health, immune modulation, and neurodevelopment. HMOs primarily function as prebiotics, facilitating the growth of beneficial bacteria such as Bifidobacterium to maintain microbial homeostasis, with a discussion on the synergistic role of carbohydrate-binding modules (CBMs). In immune modulation, HMOs interact with lectins on immune and epithelial cells, influencing immune responses via pathways such as Toll-like receptors (TLRs). Additionally, HMOs have been linked to enhanced cognitive, motor, and language development in infants, influencing genes such as GABRB2, SLC1A7, GLRA4, and CHRM3. The review also examines commercially available HMO-containing products and highlights future research directions and potential applications in nutrition and healthcare.

Multistep Metabolic Engineering of Escherichia coli for High-Level Ectoine Production

Ectoine is an important natural macromolecule protector that helps extremophiles maintain cellular stability and function under high-salinity conditions. Recently, the development of microbial strains for high-level ectoine production has become an attractive research direction. In this study, we constructed an efficient plasmid-free ectoine-producing strain. We modified the 5'-untranslated region of the ectABC gene cluster from Halomonas elongate to fine-tune the expression of genes ectA, ectB, and ectC. Furthermore, we optimized the carbon flow across the MEP pathway, the TCA cycle, and the aspartic acid metabolic pathway. Subsequently, we blocked the production of byproducts from the aspartic acid metabolic pathway and dynamically regulated the TCA cycle to coordinate the balance between strain growth and production. The final strain was tested in a 5-L fermenter, which reached 118.5 g/L at 114 h of fermentation. The metabolic engineering strategies employed in this study can be used for the biosynthesis of other aspartate derivatives.

Efficient Biosynthesis of Sialyllacto-N-tetraose a by a Metabolically Engineered Escherichia coli BL21(DE3) Strain

Recently, the construction of metabolically engineered strains for the microbial synthesis of human milk oligosaccharides (HMOs) has attracted increasing attention. However, fewer efforts were made in the in vivo biosynthesis of complex HMOs, especially sialylated complex HMOs. In this study, we engineered Escherichia coli BL21(DE3) to efficiently produce sialyllacto-N-tetraose a (LST-a) efficiently. Three sequential glycosylation steps were introduced to construct the LST-a pathway, catalyzed by β1,3-N-acetylglucosaminylation, β1,3-galactosylation, and α2,3-sialylation. Pathway genes for cytidine 5'-monophospho (CMP)-N-acetylneuraminic acid (Neu5Ac) were introduced to support the sialylation donor supply. Production of LST-a was improved by deleting competitive genes of CMP-Neu5Ac synthesis, screening a more efficient α2,3-sialyltransferase, and combinatorial optimization of pathway gene expression. LST-a was finally produced with the titer of 1.235 and 4.85 g/L by shake-flask and fed-batch cultivation, respectively, demonstrating the feasibility of efficient microbial production of complex sialylated HMOs.

Optimization of l-Fucose Biosynthesis in Escherichia coli through Pathway Engineering and Mixed Carbon Source Strategy

This study presents an engineered strain of Escherichia coli specifically designed to enhance the production of l-fucose while minimizing residues of 2'-fucosyllactose. The optimization strategies employed include the selection of key enzymes, optimization of gene copy numbers, and fermentation using mixed carbon sources. The metabolic flux was directed toward l-fucose synthesis by integrating preferred 1,2-fucosyltransferase and α-l-fucosidase into the genome. Furthermore, the gene copy numbers were optimized to enhance enzyme expression, thereby increasing l-fucose production. Additionally, the supply of guanosine 5'-triphosphate was improved, and cofactors were regenerated to better regulate metabolism. Modifications to transporter proteins effectively reduced the accumulation of 2'-fucosyllactose. The implementation of a glucose/glycerol co-fermentation strategy enhanced carbon flux distribution and strain efficiency. The optimized strain achieved a yield of 91.90 g/L of l-fucose in a 5 L bioreactor, representing an 80.01% increase over previous yields, with a productivity of 1.18 g L-1 h-1. This yield is the highest reported for l-fucose, demonstrating its potential for industrial production.

Highly Efficient In Vivo Production of Sialyllacto-N-tetraose C via Screening of Beneficial β1,4-galactosyltransferase and α2,6-sialyltransferase

Biological production of human milk oligosaccharides (HMOs) using metabolically engineered strains is a research hotspot in food biotechnology, but less effort has been made on the biological production of sialylated complex HMOs. Sialyllacto-N-tetraose c is the only monosialylated complex HMO in the top 15 HMOs. In this study, the metabolic pathway of LST c was constructed in Escherichia coli BL21(DE3) by introducing three sequential glycosyltransferases: β1,3-N-acetylglucosaminyltransferase, β1,4-galactosyltransferase, and α2,6-sialyltransferase. The cytidine 5'-monophospho (CMP)-N-acetylneuraminic acid (Neu5Ac) pathway was enhanced to improve LST c production. The β1,4-galactosyltransferase from Helicobacter pylori J99 (HpGalT) and α2,6-sialyltransferase from Vespertiliibacter pulmonis (ED6ST) were screened as a pair of key glycosyltransferases for enhancing LST c production. The final engineered strain could produce 1.718 and 9.745 g/L LST c by shake-flask and fed-batch cultivation, respectively, indicating the feasibility of efficient biosynthesis of complex sialylated HMOs.

Multistrategy Optimization for High-Yield 3-Fucosyllactose Production in Escherichia coli BL21 Star (DE3)

3-Fucosyllactose (3-FL), an essential component of human milk oligosaccharides, is crucial for infant health. However, the extraction of 3-FL from milk presents a significant challenge. In this study, E. coli BL21 Star (DE3) was engineered for 3-FL biosynthesis, and the gene combinations and metabolic pathways were optimized to obtain a high-yield 3-FL production strain. First, the 3-FL production module was integrated into E. coli. Second, an efficient alpha-1,3-fucosyltransferase was screened. Then, different integration sites were used to optimize the precursor synthesis gene cluster and the transferase genes and to screen for transporter proteins and glycerol utilization genes that could enhance 3-FL production. The 3FL05-1 strain yielded a 3-FL titer of 11.26 g/L in shake flasks. Further amplification in a 5 L bioreactor resulted in a 3-FL titer of 60.24 g/L, which represents the highest reported titer to date.

Engineering glycolytic pathway for improved Lacto-N-neotetraose production in pichia pastoris

Lacto-N-neotetraose (LNnT) is a primary solid component of human milk oligosaccharides (HMOs) with various promising health effects for infants. LNnT production by GRAS (generally recognized as safe) microorganisms has attracted considerable attention. However, few studies have emphasized Pichia Pastoris as a cell factory for LNnT's production. Here, we have reported the first-ever synthesis of LNnT employing P. pastoris as the host. Initially, LNnT biosynthetic pathway genes β-1,3-N-acetylglucosaminyltransferase (lgtA) and β-1,4-galactostltransferase (lgtB) along with lactose permease (lac12) and galactose epimerase (gal10) were integrated into the genome of P. pastoris, but only 0.139 g/L LNnT was obtained. Second, the titer of LNnT was improved to 0.162 g/L via up-regulating genes to strengthen the supply of precursors, UDP-GlcNAc (Uridine diphosphate N-acetylglucosamine) and UDP-Gal (Uridine diphosphate galactose), for LNnT biosynthesis. Third, by knocking out critical mediator pfk (6-phosphofructokinase) genes in glycolysis, the major glucose metabolic flux was rewired to the LNnT biosynthesis pathway. As a result, the strain accumulated 0.867 g/L LNnT in YPG medium supplemented with glucose and lactose. Finally, LNnT production was increased to 1.24 g/L in a 3 L bioreactor. The work aimed to explore the potential of P. pastoris as a for LNnT production.

Highly efficient production of lacto-N-tetraose in plasmid-free Escherichia coli through chromosomal integration of multicopy key glycosyltransferase genes

Lacto-N-tetraose (LNT) is a functional human milk oligosaccharide (HMO) commercially added to infant formula. Metabolically engineered strains for efficient production of LNT have been widely constructed. However, most of them rely on the use of plasmids, which might bring metabolic burden and the antibiotic issue. In this study, we attempted to construct a plasmid-free Escherichia coli MG1655 for LNT biosynthesis. Firstly, lacZ gene was disrupted and lacY expression was enhanced to improve the bioavailability of lactose as the initial substrate. Three copies of lgtA (encoding for β1,3-N-acetylglucosaminyltransferase) were integrated into the chromosome, enabling the highly efficient production of lacto-N-triose II (LNTri II) as the direct precursor of LNT. Efficient production of LNT was then optimized by multicopy integration of wbgO (encoding for β1,3-galactosyltransferase), disruption of the competitive pathways, and strengthening of UDP-galactose supply and oligosaccharide efflux. The final titer reached 6.99 and 42.38 g/L in shake-flask and fed-batch cultivation, respectively.

High-Level Production of Nicotinamide Mononucleotide by Engineered Escherichia Coli

Nicotinamide mononucleotide (NMN), a key precursor of NAD+, is a promising nutraceutical due to its excellent efficacy in alleviating aging and disease. The bioproduction of NMN faces challenges related to incomplete metabolic engineering and insufficient metabolic flux. Here, we constructed an NMN synthesis pathway in Escherichia coli BW25113 by deleting the competitive pathway genes and introducing three heterologous genes encoding the key enzymes nicotinamide phosphoribosyltransferase (NAMPT), phosphoribosyl pyrophosphate synthetase and an NMN transporter. Next, the identification of a highly active NAMPT and optimization of gene expression markedly increased the conversion of NAM to NMN, with a titer of 3503.85 mg/L in shake flasks. Furthermore, by facilitating the coutilization of glucose and xylose, more metabolic flux was diverted toward PRPP biosynthesis, resulting in an NMN titer of 15.66 g/L through whole-cell catalysis and 46.66 g/L in a 2-L bioreactor. This represents the highest NMN yield reported to date, exhibiting great potential for initiating sustainable industrial production of NMN.

Efficient Production of 3'-Sialyllactose Using Escherichia coli

3'-Sialyllactose (3'-SL), a key component of human milk oligosaccharides, provides significant health benefits and immune modulation, and is increasingly used in infant formula and dietary supplements. This study presents a novel approach for the efficient biosynthesis of 3'-SL using Escherichia coli BL21star(DE3)ΔlacZ through genomic integration. We first addressed the issue of metabolic competition by deleting crucial genes, nanA, nanK, nanE, and nanT, that are involved in the degradation of N-acetylneuraminic acid. This strategic gene knockout minimized the flux through competing pathways. The engineered Escherichia coli strain was subsequently transformed with the exogenous genes neuBCA and nST, enabling the de novo synthesis of 3'-SL. A modular metabolic engineering strategy was utilized to optimize the expression of key enzymes within the MSU module, enhancing and balancing the carbon flux distribution. Additionally, a cofactor regeneration strategy was implemented to increase CTP availability, which improved cofactor recycling and fine-tuned the metabolic pathway for maximal 3'-SL production. Transport protein screening was incorporated to further increase the extracellular concentration of 3'-SL, resulting in an unprecedented yield of 56.8 g/L in a 5L bioreactor fermentation, setting a new benchmark in the field.

Rational modification of Neisseria meningitidis β1,3-N-acetylglucosaminyltransferase for lacto-N-neotetraose synthesis with reduced long-chain derivatives

Lacto-N-neotetraose (LNnT), as a neutral core structure within human milk oligosaccharides (HMOs), has garnered widespread attention due to its exceptional physiological functions. In the process of LNnT synthesis using cellular factory approaches, substrate promiscuity of glycosyltransferases leads to the production of longer oligosaccharide derivatives. Here, rational modification of β1,3-N-acetylglucosaminyltransferase from Neisseria meningitidis (LgtA) effectively decreased the concentration of long-chain LNnT derivatives. Specifically, the optimal β1,4-galactosyltransferase (β1,4-GalT) was selected from seven known candidates, enabling the efficient synthesis of LNnT in Escherichia coli BL21(DE3). Furthermore, the influence of lactose concentration on the distribution patterns of LNnT and its longer derivatives was investigated. The modification of LgtA was conducted with computational assistance, involving alanine scanning based on molecular docking to identify the substrate binding pocket and implementing large steric hindrance on crucial amino acids to obstruct LNnT entry. The implementation of saturation mutagenesis at positions 223 and 228 of LgtA yielded advantageous mutant variants that did not affect LNnT synthesis while significantly reducing the production of longer oligosaccharide derivatives. The most effective mutant, N223I, reduced the molar ratio of long derivatives by nearly 70 %, showcasing promising prospects for LNnT production with diminished byproducts.

Combinatorial Optimization Strategies for 3-Fucosyllactose Hyperproduction in Escherichia coli

3-Fucosyllactose (3-FL), an important fucosylated human milk oligosaccharide in breast milk, offers numerous health benefits to infants. Previously, we metabolically engineered Escherichia coli BL21(DE3) for the in vivo biosynthesis of 3-FL. In this study, we initially optimized culture conditions to double 3-FL production. Competing pathway genes involved in in vivo guanosine 5'-diphosphate-fucose biosynthesis were subsequently inactivated to redirect fluxes toward 3-FL biosynthesis. Next, three promising transporters were evaluated using plasmid-based or chromosomally integrated expression to maximize extracellular 3-FL production. Additionally, through analysis of α1,3-fucosyltransferase (FutM2) structure, we identified Q126 residues as a highly mutable residue in the active site. After site-saturation mutation, the best-performing mutant, FutM2-Q126A, was obtained. Structural analysis and molecular dynamics simulations revealed that small residue replacement positively influenced helical structure generation. Finally, the best strain BD3-A produced 6.91 and 52.1 g/L of 3-FL in a shake-flask and fed-batch cultivations, respectively, highlighting its potential for large-scale industrial applications.

Improved Enzymatic Production of the Fucosylated Human Milk Oligosaccharide LNFP II with GH29B α-1,3/4-l-Fucosidases

Five GH29B α-1,3/4-l-fucosidases (EC 3.2.1.111) were investigated for their ability to catalyze the formation of the human milk oligosaccharide lacto-N-fucopentaose II (LNFP II) from lacto-N-tetraose (LNT) and 3-fucosyllactose (3FL) via transglycosylation. We studied the effect of pH on transfucosylation and hydrolysis and explored the impact of specific mutations using molecular dynamics simulations. LNFP II yields of 91 and 65% were obtained for the wild-type SpGH29C and CpAfc2 enzymes, respectively, being the highest LNFP II transglycosylation yields reported to date. BbAfcB and BiAfcB are highly hydrolytic enzymes. The results indicate that the effects of pH and buffer systems are enzyme-dependent yet relevant to consider when designing transglycosylation reactions. Replacing Thr284 in BiAfcB with Val resulted in increased transglycosylation yields, while the opposite replacement of Val258 in SpGH29C and Val289 CpAfc2 with Thr decreased the transfucosylation, confirming a role of Thr and Val in controlling the flexibility of the acid/base loop in the enzymes, which in turn affects transglycosylation. The substitution of an Ala residue with His almost abolished secondary hydrolysis in CpAfc2 and BbAfcB. The results are directly applicable in the enhancement of transglycosylation and may have significant implications for manufacturing of LNFP II as a new infant formula ingredient.

Engineering Escherichia coli for Highly Efficient Biosynthesis of Lacto-N-difucohexaose II through De Novo GDP-l-fucose Pathway

Lacto-N-difucohexaose II (LNDFH II) is a typical fucosylated human milk oligosaccharide and can be enzymatically produced from lacto-N-tetraose (LNT) by a specific α1,3/4-fucosyltransferase from Helicobacter pylori DMS 6709, referred to as FucT14. Previously, we constructed an engineered Escherichia coli BL21(DE3) with a single plasmid for highly efficient biosynthesis of LNT. In this study, two additional plasmids harboring the de novo GDP-L-fucose pathway module and FucT14, respectively, were further introduced to construct the strain for successful biosynthesis of LNDFH II. FucT14 was actively expressed, and the engineered strain produced LNDFH II as the major product, lacto-N-fucopentaose (LNFP) V as the minor product, and a trace amount of LNFP II and 3-fucosyllactose as very minor products. Additional expression of the α1,3-fucosyltransferase FutM1 from a Bacteroidaceae bacterium from the gut metagenome could obviously enhance the LNDFH II biosynthesis. After optimization of induction conditions, the maximum titer reached 3.011 g/L by shake-flask cultivation. During the fed-batch cultivation, LNDFH II was highly efficiently produced with the highest titer of 18.062 g/L and the productivity yield of 0.301 g/L·h.

De Novo Biosynthesis of Difucosyllactose by Artificial Pathway Construction and α1,3/4-Fucosyltransferase Rational Design in Escherichia coli

Difucosyllactose (DFL) is a significant and plentiful oligosaccharide found in human breast milk. In this study, an artificial metabolic pathway of DFL was designed, focusing on the de novo biosynthesis of GDP-fucose from only glycerol. This was achieved by engineering Escherichia coli to endogenously overexpress genes manB, manC, gmd, and wcaG and heterologously overexpress a pair of fucosyltransferases to produce DFL from lactose. The introduction of α-1,2-fucosyltransferase from Helicobacter pylori (FucT2) along with α-1,3/4-fucosyltransferase (HP3/4FT) addressed rate-limiting challenges in enzymatic catalysis and allowed for highly efficient conversion of lactose into DFL. Based on these results, molecular modification of HP3/4FT was performed based on computer-assisted screening and structure-based rational design. The best-performing mutant, MH5, containing a combination of five mutated sites (F49K/Y131D/Y197N/E338D/R369A) of HP3/4FT was obtained. The best strain BLC09-58 harboring MH5 yielded 45.81 g/L of extracellular DFL in 5-L fed-batch cultures, which was the highest titer reported to date.