High density fermentation of probiotic E. coli Nissle 1917 towards heparosan production, characterization, and modification

Bioengineered heparin: Advances in production technology

Heparin, a highly sulfated glycosaminoglycan, is considered an indispensable anticoagulant with diverse therapeutic applications and has been a mainstay in medical practice for nearly a century. Its potential extends beyond anticoagulation, showing promise in treating inflammation, cancer, and infectious diseases such as COVID-19. However, its current sourcing from animal tissues poses challenges due to variable structures and adulterations, impacting treatment efficacy and safety. Recent advancements in metabolic engineering and synthetic biology offer alternatives through bioengineered heparin production, albeit with challenges such as controlling molecular weight and sulfonation patterns. This review offers comprehensive insight into recent advancements, encompassing: (i) the metabolic engineering strategies in prokaryotic systems for heparin production; (ii) strides made in the development of bioengineered heparin; and (iii) groundbreaking approaches driving production enhancements in eukaryotic systems. Additionally, it explores the potential of recombinant Chinese hamster ovary cells in heparin synthesis, discussing recent progress, challenges, and future prospects, thereby opening up new avenues in biomedical research.

Advancements in heparosan production through metabolic engineering and improved fermentation

Heparin is one of the most widely used natural drugs, and has been the preferred anticoagulant and antithrombotic agent in the clinical setting for nearly a century. Heparin also shows increasing therapeutic potential for treating inflammation, cancer, and microbial and viral diseases, including COVID-19. With advancements in synthetic biology, heparin production through microbial engineering of heparosan offers a cost-effective and scalable alternative to traditional extraction from animal tissues. Heparosan serves as the starting carbon backbone for the chemoenzymatic synthesis of bioengineered heparin, possessing a chain length that is critically important for the production of heparin-based therapeutics with specific molecular weight (MW) distributions. Recent advancements in metabolic engineering of microbial cell factories have resulted in high-yield heparosan production. This review systematically analyzes the key modules involved in microbial heparosan biosynthesis and the latest metabolic engineering strategies for enhancing production, regulating MW, and optimizing the fermentation scale-up of heparosan. It also discusses future studies, remaining challenges, and prospects in the field.

Minimizing endogenous cryptic plasmids to construct antibiotic-free expression systems for Escherichia coli Nissle 1917

The probiotic bacterium Escherichia coli Nissle 1917 (EcN) holds significant promise for use in clinical and biological industries. However, the reliance on antibiotics to maintain plasmid-borne genes has overshadowed its benefits. In this study, we addressed this issue by engineering the endogenous cryptic plasmids pMUT1 and pMUT2. The non-essential elements were removed to create more stable derivatives pMUT1NR△ and pMUT2HBC△. Synthetic promoters by integrating binding motifs on sigma factors were further constructed and applied for expression of Bacteroides thetaiotaomicron heparinase III and the biosynthesis of ectoine. Compared to traditional antibiotic-dependent expression systems, our newly constructed antibiotic-free expression systems offer considerable advantages for clinical and synthetic biology applications.

Expectations for employing Escherichia coli Nissle 1917 in food science and nutrition

As a promising probiotic strain, Escherichia coli Nissle 1917 (EcN) has been demonstrated to confer beneficial effects on intestinal health, immune function, and pathogen prevention. Additionally, EcN has also been widely studied due to its clear genomic information, tractable gene regulation, and simple growth conditions. This review summarizes the various applications potential of EcN in food science and nutrition, including inflammation prevention, tumor-targeting therapy, antibacterial agents for food, and nutrient production with a focus on specific case studies. Moreover, we highlight the major challenges of employing EcN in food science and nutrition, including regulatory approval, stability during food processing, and consumer acceptance. Finally, we conclude with a discussion on perspectives related to employing EcN in food science and nutrition.

Production of different molecular weight glycosaminoglycans with microbial cell factories

Glycosaminoglycans (GAGs) are naturally occurring acidic polysaccharides with wide applications in pharmaceuticals, cosmetics, and health foods. The diverse biological activities and physiological functions of GAGs are closely associated with their molecular weights and sulfation patterns. Except for the non-sulfated hyaluronan which can be synthesized naturally by group A Streptococcus, all the other GAGs such as heparin and chondroitin sulfate are mainly acquired from animal tissues. Microbial cell factories provide a more effective platform for the production of structurally homogeneous GAGs. Enhancing the production efficiency of polysaccharides, accurately regulating the GAGs molecular weight, and effectively controlling the sulfation degree of GAGs represent the major challenges of developing GAGs microbial cell factories. Several enzymatic, metabolic engineering, and synthetic biology strategies have been developed to tackle these obstacles and push forward the industrialization of biotechnologically produced GAGs. This review summarizes the recent advances in the construction of GAGs synthesis cell factories, regulation of GAG molecular weight, and modification of GAGs chains. Furthermore, the challenges and prospects for future research in this field are also discussed.

Engineering Escherichia coli Nissle 1917 as a microbial chassis for therapeutic and industrial applications

Genetically engineered microbes, especially Escherichia coli, have been widely used in the biosynthesis of proteins and metabolites for medical and industrial applications. As a traditional probiotic with a well-established safety record, E. coli Nissle 1917 (EcN) has recently emerged as a microbial chassis for generating living therapeutics, drug delivery vehicles, and microbial platforms for industrial production. Despite the availability of genetic tools for engineering laboratory E. coli K-12 and B strains, new genetic engineering systems are still greatly needed to expand the application range of EcN. In this review, we have summarized the latest progress in the development of genetic engineering systems in EcN, as well as their applications in the biosynthesis and delivery of valuable small molecules and biomacromolecules of medical and/or industrial interest, followed by a glimpse of how this rapidly growing field will evolve in the future.

Chromosome evolution of Escherichia coli Nissle 1917 for high-level production of heparosan

Heparosan is a crucial-polysaccharide precursor for the chemoenzymatic synthesis of heparin, a widely used anticoagulant drug. Presently, heparosan is mainly extracted with the potential risk of contamination from Escherichia coli strain K5, a pathogenic bacterium causing urinary tract infection. Here, a nonpathogenic probiotic, E. coli strain Nissle 1917 (EcN), was metabolically engineered to carry multiple copies of the 19-kb kps locus and produce heparosan to 9.1 g/L in fed-batch fermentation. Chromosome evolution driven by antibiotics was employed to amplify the kps locus, which governed the synthesis and export of heparosan from EcN at 21 mg L^-1  OD^-1 . The average copy number of kps locus increased from 1 to 24 copies per cell, which produced up to 104 mg L^-1  OD^-1 of heparosan in the shaking flask cultures of engineered strains. The following in-frame deletion of recA stabilized the recombinant duplicates of chromosomal kps locus and the productivity of heparosan in continuous culture for at least 56 generations. Fed-batch fermentation of the engineered strain EcN8 was carried out to bring the yield of heparosan up to 9.1 g/L. Heparosan from the fermentation culture was further purified at a 75% overall recovery. The structure of purified heparosan was characterized and further modified by N-sulfotransferase with 3'-phosphoadenosine-5'-phosphosulfate as the sulfo-donor. The analysis of element composition showed that heparosan was N-sulfated by over 80%. These results indicated that duplicating large DNA cassettes up to 19-kb, followed by high-cell-density fermentation, was promising in the large-scale preparation of chemicals and could be adapted to engineer other industrial-interest bacteria metabolically.

Microbial synthesis of glycosaminoglycans and their oligosaccharides

Compared with chemical synthesis and tissue extraction methods, microbial synthesis of glycosaminoglycans (GAGs) is attractive because of the advantages of eco-friendly processes, production safety, and sustainable development. However, boosting the efficiency of microbial cell factories, precisely regulating GAG molecular weights, and rationally controlling the sulfation degree of GAGs remain challenging. To address these issues, various strategies, including genetic, enzymatic, metabolic, and fermentation engineering, have been developed. In this review, we summarize the recent progress in the construction of efficient GAG-producing microbial cell factories, regulation of the molecular weight of GAGs, and modification of GAG chains. Moreover, future studies, remaining challenges, and potential solutions in this field are discussed.

Development of probiotic E. coli Nissle 1917 for β-alanine production by using protein and metabolic engineering

β-alanine has been used in food and pharmaceutical industries. Although Escherichia coli Nissle 1917 (EcN) is generally considered safe and engineered as living therapeutics, engineering EcN for producing industrial metabolites has rarely been explored. Here, by protein and metabolic engineering, EcN was engineered for producing β-alanine from glucose. First, an aspartate-α-decarboxylase variant ADC_K43Y with improved activity was identified and over-expressed in EcN, promoting the titer of β-alanine from an undetectable level to 0.46 g/L. Second, directing the metabolic flux towards L-aspartate increased the titer of β-alanine to 0.92 g/L. Third, the yield of β-alanine was elevated to 1.19 g/L by blocking conversion of phosphoenolpyruvate to pyruvate, and further increased to 2.14 g/L through optimizing culture medium. Finally, the engineered EcN produced 11.9 g/L β-alanine in fed-batch fermentation. Our work not only shows the potential of EcN as a valuable industrial platform, but also facilitates production of β-alanine via fermentation. KEY POINTS: • Escherichia coli Nissle 1917 (EcN) was engineered as a β-alanine producing cell factory • Identification of a decarboxylase variant ADC_K43Y with improved activity • Directing the metabolic flux to L-ASP and expressing ADC_K43Y elevated the titer of β-alanine to 11.9 g/L.

Heparosan-based self-assembled nanocarrier for zinc(II) phthalocyanine for use in photodynamic cancer therapy

Zinc(II) phthalocyanine (ZnPc) is a promising photosensitizer in photodynamic therapy (PDT) for melanoma treatment. However, the poor solubility of ZnPc limits its application. To overcome this limitation, heparosan (HP)-based nanoparticles were prepared by anchoring the l-lysine-linked α-linolenic acid branch to the carboxylic acid group to produce amphiphilic conjugates named heparosan with an l-lysine-linked α-linolenic acid branch (HLA). HLA conjugates could self-assemble into spherical nanoparticles in aqueous media and encapsulate ZnPc to form HLA-ZnPc nanoparticles. The cellular uptake of ZnPc could be improved by HLA carriers. These nanoparticles presented excellent photodynamic-mediated toxicity against mouse melanoma cells (B16) by markedly upregulating the intracellular reactive oxygen species (ROS) levels while showing no cytotoxicity to either B16 or normal cells (L02 and HK-2 cells) in the dark. Furthermore, HLA-ZnPc displayed excellent stability in both powder and Roswell Park Memorial Institute (RPMI) 1640 medium, indicating its promise for application in drug delivery and PDT. These results revealed a strategy for HP-based enhancement of ZnPc in PDT efficacy.

Expression and characterization of a novel lipase from Bacillus licheniformis NCU CS-5 for application in enhancing fatty acids flavor release for low-fat cheeses

A novel lipase from Bacillus licheniformis NCU CS-5 was expressed in different Escherichia coli cells. The recombinant enzyme achieved a high activity (161.74 U/mL) with protein concentration of 0.27 mg/mL under optimal conditions at the large-scale expression of 12 h. The recombinant lipase showed optimal activity at 40 ℃ and pH 10.0, and maintained more than 80% relative activity after 96 h of incubation at pH 9.0-10.0. This typical alkaline lipase was activated under medium temperature conditions (30 and 45 ℃ for 96 h). The lipase exhibited a degree of adaptability in various organic solvents and metal ions, and showed high specificity towards triglycerides with short and medium chain fatty acids. Among different substrates, the lipase showed the strongest binding affinity towards pNPP (Km = 0.674 mM, Vmax = 950.196 μM/min). In the experiments of its application in enhancing fatty acids flavor release for low-fat cheeses, the lipase was found to hydrolyze cheeses and mainly increase the contents of butyric acid, hexanoic acid, caprylic acid and decanoic acid. The results from NMR and GC provided the possibility of enhancing fatty acids flavor released from low-fat cheeses by the lipolysis method.