Metabolic Engineering of Escherichia coli for Ectoine Production With a Fermentation Strategy of Supplementing the Amino Donor

High Ectoine Production from Lignocellulosic Hydrolysate by Escherichia coli through Metabolic and Fermentation Engineering

Ectoine, a major compatible solute in halophilic micro-organisms, shows great potential in cosmetics and pharmaceuticals areas owing to its water-binding properties and capability to prevent oxidative damage. In this study, the ectABC gene cluster responsible for the ectoine synthesis originated from halophilic bacterium Halomonas venusta was first assembled into Escherichia coli. Subsequently, the crr gene in PTS was knocked out to further drive the metabolic flux from phosphoenolpyruvate to oxaloacetate, resulting in 1.27 g/L of ectoine. Then, the rate-limiting enzyme LysC in the ectoine synthesis pathway was identified and modified. The recombinant E. coli with the further overexpression of feedback-insensitive mutant EclysC* increased the ectoine titer to 2.51 g/L with a yield of 0.37 g/g in shake flasks. After the medium optimization including the carbon and nitrogen source, sodium chloride, and magnesium sulfate concentration, the ectoine titer was improved to 4.55 g/L. 115.15 g/L of ectoine with a yield of 0.23 g/g was obtained in the 5.0 L bioreactor through the optimization of substrate feeding and IPTG supplementation in the fed-batch fermentation. To achieve the cost-effective production of ectoine, lignocellulosic hydrolysate from wheat straw was adopted. 134.08 g/L of ectoine with a yield of 0.33 g/g sugar and a productivity of 3.7 g/L/h was finally produced, representing a relatively high level of ectoine production from renewable resources compared to other studies. This study provides valuable insights into a cost-effective and efficient method for industrial-scale ectoine production.

Microbial Production of Ectoine: A Review

Ectoine is an important natural secondary metabolite widely used in biomedical fields, novel cosmetics development, and the food industry. Due to the increasing market demand for ectoine, more cost-effective production methods are being explored. With the rapid development of synthetic biology and metabolic engineering technologies, the production of ectoine using traditional halophilic bacteria is gradually being replaced by higher-yielding and environmentally friendly nonhalophilic engineered strains. By introducing the ectoine synthesis pathway into model strains and optimizing the fermentation process through various metabolic regulations, high-level production of ectoine can be achieved. This review focuses on strategies for the microbial production of ectoine, including screening of wild strains, mutation breeding, and metabolic engineering of model strains, to elucidate the current research status and provide insights for the industrial production of ectoine.

Metabolic Engineering of Escherichia coli for Efficient Production of Ectoine

Ectoine is a valuable compatible solute with extensive applications in bioengineering, cosmetics, medicine, and the food industry. While certain halophilic bacteria can naturally produce ectoine, as a model organism for biomanufacturing, Escherichia coli offers significant advantages to be engineered for potentially high-level ectoine production. However, complex metabolic flux distributions and byproduct formation present bottlenecks that limit ectoine production in E. coli. In this study, we aimed to enhance ectoine production in E. coli BL21(DE3) through systematic metabolic engineering strategies. We investigated the effects of the ectABC gene cluster sequence, plasmid copy number, and key gene copy number on ectoine synthesis. Using the original ectABC sequence with the high-copy-number plasmid pRSFDuet-1 resulted in the highest level of ectoine production. Knocking out genes encoding homoserine dehydrogenase and diaminopimelate decarboxylase reduced competing pathways, further increasing ectoine yield. Overexpression of aspartate semialdehyde dehydrogenase, aspartate kinase I (thrA*), aspartate aminotransferase, and aspartate ammonia-lyase (aspA) was performed, and optimal gene copy numbers were determined. When the copy numbers of thrA* and aspA were both three, ectoine synthesis improved, reaching 1.91 g/L. Enhancing the oxaloacetate pool by overexpressing phosphoenolpyruvate carboxylase (ppc) or introducing pyruvate carboxylase (pyc) from Corynebacterium glutamicum further increased ectoine production to 4.99 g/L. Balancing NADPH and ATP levels through cofactor engineering contributed to additional production improvements. Combining these strain engineering strategies, we ultimately constructed strain C24, which produced 35.33 g/L ectoine in a 5 L fermenter with a glucose conversion rate of 0.21 g/g. These results demonstrate that targeted metabolic engineering can significantly enhance ectoine production in E. coli, providing a foundation for industrial-scale production.

Metabolic engineering of Bacillus licheniformis DW2 for ectoine production

Ectoine is a high-value protective agent with extensive applications in the fields of fine chemicals and biopharmaceuticals, and it is naturally synthesized by Halomonas in extreme environment, however, the current production level cannot meet the growing market demand. In this study, we aimed to develop an efficient and environmentally friendly ectoine production process using Bacillus licheniformis as the host organism. Through introducing ectoine synthetase gene cluster ectABC from Halomonas elongate, as well as optimizing ectABCHs expression by promoter and 5'-UTR optimization, ectoine titer was increased to 0.55 g/L. Furthermore, subsequent introduction of exogenous phosphoenolpyruvate carboxylase PPCEC and down-regulated expression of phosphoenolpyruvate carboxykinase PCK optimized the carbon flux through C4 anaplerotic pathway, and further benefited ectoine synthesis. Furthermore, the carbon flux towards aspartic acid accumulation was increased through optimization of glyoxylate and TCA cycles, accompanied with introducing lysCT311ICg and asdCg, and blocking by-products pathways, ectoine titer produced by B. licheniformis ECT12 was 2.00 g/L. Moreover, NADPH supply was enhanced by overexpression of exogenous NADH kinase Pos5Sc, and ectoine transportation was improved by introducing compatible solute transporter ProP from Escherichia coli, and the resulting B. licheniformis ECT14 was able to produce 2.60 g/L ectoine. Last but not the least, the ectoine yield of 3.29 g/L was attained in a 5-L fermenter. Taken together, this study not only established B. licheniformis as a framework for sustainable production of ectoine, but also paved the way for achieving the industrial production of ectoine and aspartic acid derivatives in the future.

Multiple Functions of Compatible Solute Ectoine and Strategies for Constructing Overproducers for Biobased Production

Ectoine and its derivative 5-hydroxyectoine are compatible solutes initially found in the hyperhalophilic bacterium Ectothiorhodospira halochloris, which inhabits the desert in Egypt. The habitat of ectoine producers implies the primary function of ectoine as a cytoprotectant against harsh conditions such as high salinity, drought, and high radiation. More extensive and in-depth studies have revealed the multiple functions of ectoine in its native producer bacterial cells and other types of cells and its biomolecular components (such as proteins and DNA) as a general protective agent. Its chemical properties as a bio-based amino acid derivative make it attractive for basic scientific research and related industries, such as the food/agricultural industry, cosmetic manufacturing, biologics, and therapeutic agent preparation. This article first discusses the functions and applications of ectoine and 5-hydroxyectoine. Subsequently, more emphasis was placed on advances in bio-based ectoine and/or 5-hydroxyectoine production. Strategies for developing more robust cell factories for highly efficient ectoine and/or 5-hydroxyectoine production are further discussed. We hope this review will provide a valuable reference for studies on the bio-based production of ectoine and 5-hydroxyectoine.

Thiopseudomonas acetoxidans sp. nov., an aerobic acetic and butyric acids oxidizer isolated from anaerobic fermentation liquid of food waste

A Gram-stain-negative, oxidase-negative, rod-shaped, motile, facultatively anaerobic bacterial strain, designated as CY1220T, was isolated from an anaerobic fermentation liquid of food waste treatment plant. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain CY1220T belongs to the genus Thiopseudomonas, with the highest sequence similarity to Thiopseudomonas alkaliphila B4199T (95.91%), followed by Thiopseudomonas denitrificans X2T (95.56%). The genomic DNA G + C content of strain CY1220T was 48.6 mol%. The average nucleotide identity values and digital DNA-DNA hybridization values between strain CY1220T and the type species of T. alkaliphila and T. denitrificans were in the range of 70.8-71.6% and 19.2-20.0%, respectively, below the thresholds for species delineation. The strain was able to grow utilizing acetic acid and butyric acid (AABA) as the sole carbon source in aerobic conditions. Genomic analysis predicted that the strain could synthesize vitamin B12 and ectoine. The predominant cellular fatty acids were C18:1 ω7c and/or C18:1 ω6c, C16:0, C16:1 ω7c and/or C16:1 ω6c and C12:0. The polar lipids comprised diphosphatidylglycerol, unknown polar lipid, phosphatidylethanolamine, phosphatidylglycerol, and phospholipid. Q-8 (2.1%) and Q-9 (97.9%) were detected as the respiratory quinones. Based on its phenotypic, genotypic and genomic characteristics, strain CY1220T represents a novel species in the genus Thiopseudomonas, for which the name Thiopseudomonas acetoxidans sp. nov. is proposed. The type strain is CY1220T (= GDMCC 1.3503 T = JCM 35747 T).

Comparative genomic analysis of Halomonas campaniensis wild-type and ultraviolet radiation-mutated strains reveal genomic differences associated with increased ectoine production

Ectoine is a natural amino acid derivative and one of the most widely used compatible solutes produced by Halomonas species that affects both cellular growth and osmotic equilibrium. The positive effects of UV mutagenesis on both biomass and ectoine content production in ectoine-producing strains have yet to be reported. In this study, the wild-type H. campaniensis strain XH26 (CCTCCM2019776) was subjected to UV mutagenesis to increase ectoine production. Eight rounds of mutagenesis were used to generate mutated XH26 strains with different UV-irradiation exposure times. Ectoine extract concentrations were then evaluated among all strains using high-performance liquid chromatography analysis, alongside whole genome sequencing with the PacBio RS II platform and comparison of the wild-type strain XH26 and the mutant strain G8-52 genomes. The mutant strain G8-52 (CCTCCM2019777) exhibited the highest cell growth rate and ectoine yields among mutated strains in comparison with strain XH26. Further, ectoine levels in the aforementioned strain significantly increased to 1.51 ± 0.01 g L-1 (0.65 g g-1 of cell dry weight), representing a twofold increase compared to wild-type cells (0.51 ± 0.01 g L-1) when grown in culture medium for ectoine accumulation. Concomitantly, electron microscopy revealed that mutated strain G8-52 cells were obviously shorter than wild-type strain XH26 cells. Moreover, strain G8-52 produced a relatively stable ectoine yield (1.50 g L-1) after 40 days of continuous subculture. Comparative genomics analysis suggested that strain XH26 harbored 24 mutations, including 10 nucleotide insertions, 10 nucleotide deletions, and unique single nucleotide polymorphisms. Notably, the genes orf00723 and orf02403 (lipA) of the wild-type strain mutated to davT and gabD in strain G8-52 that encoded for 4-aminobutyrate-2-oxoglutarate transaminase and NAD-dependent succinate-semialdehyde dehydrogenase, respectively. Consequently, these genes may be involved in increased ectoine yields. These results suggest that continuous multiple rounds of UV mutation represent a successful strategy for increasing ectoine production, and that the mutant strain G8-52 is suitable for large-scale fermentation applications.

Shotgun metagenomics and computational profiling of the plastisphere microbiome: unveiling the potential of enzymatic production and plastic degradation

Plastic pollution is one of the most resilient types of pollution and is considered a global environmental threat, particularly in the marine environment. This study aimed to identify plastic-degrading bacteria from the plastisphere and their pharmaceutical and therapeutic potential. We collected samples from soil and aquatic plastisphere to identify the bacterial communities using shotgun metagenomic sequencing and bioinformatic tools. Results showed that the microbiome comprised 93% bacteria, 0.29% archaea, and 3.87% unidentified microbes. Of these 93% of bacteria, 54% were Proteobacteria, 23.9% were Firmicutes, 13% were Actinobacteria, and 2.1% were other phyla. We found that the plastisphere microbiome was involved in degrading synthetic and polyhydroxy alkanoate (PHA) plastic, biosurfactant production, and can thrive under high temperatures. However, no association existed between thermophiles, synthetic plastic or PHA degraders, and biosurfactant-producing bacterial species except for Pseudomonas. Other plastisphere inhabiting plastic degrading microbes include Streptomyces, Bacillus, Achromobacter, Azospirillum, Bacillus, Brevundimonas, Clostridium, Paenibacillus, Rhodococcus, Serratia, Staphylococcus, Thermobifida, and Thermomonospora. However, the plastisphere microbiome showed potential for producing secondary metabolites that were found to act as anticancer, antitumor, anti-inflammatory, antimicrobial, and enzyme stabilizers. These results revealed that the plastisphere microbiome upholds clinical and environmental significance as it can open future portals in a multi-directional way.

Identification of Antibacterial Components and Modes in the Methanol-Phase Extract from a Herbal Plant Potentilla kleiniana Wight et Arn

The increase in bacterial resistance and the decline in the effectiveness of antimicrobial agents are challenging issues for the control of infectious diseases. Traditional Chinese herbal plants are potential sources of new or alternative medicine. Here, we identified antimicrobial components and action modes of the methanol-phase extract from an edible herb Potentilla kleiniana Wight et Arn, which had a 68.18% inhibition rate against 22 species of common pathogenic bacteria. The extract was purified using preparative high-performance liquid chromatography (Prep-HPLC), and three separated fragments (Fragments 1-3) were obtained. Fragment 1 significantly elevated cell surface hydrophobicity and membrane permeability but reduced membrane fluidity, disrupting the cell integrity of the Gram-negative and Gram-positive pathogens tested (p < 0.05). Sixty-six compounds in Fragment 1 were identified using Ultra-HPLC and mass spectrometry (UHPLC-MS). The identified oxymorphone (6.29%) and rutin (6.29%) were predominant in Fragment 1. Multiple cellular metabolic pathways were altered by Fragment 1, such as the repressed ABC transporters, protein translation, and energy supply in two representative Gram-negative and Gram-positive strains (p < 0.05). Overall, this study demonstrates that Fragment 1 from P. kleiniana Wight et Arn is a promising candidate for antibacterial medicine and food preservatives.

Improved salt tolerance of Synechococcus elongatus PCC 7942 by heterologous synthesis of compatible solute ectoine

Salt stress is one of the essential abiotic stresses for the survival of cyanobacteria. However, the realization of large-scale cultivation of cyanobacteria is inseparable from the utilization of abundant seawater resources. Therefore, research on the regulatory mechanism, as well as the improvement of salt tolerance of cyanobacteria is fundamental. Ectoine, a compatible solute which was found in halophilic microorganisms, has potentiality to confer salt tolerance. Here in this article, the salt tolerance of Synechococcus elongatus PCC 7942 (Syn7942) was significantly improved via expressing the ectoine biosynthetic pathway, reaching an increased final OD₇₅₀ by 20% under 300 mM NaCl and 80% under 400 mM NaCl than that of wild-type (WT), respectively. Encouragingly, the engineered strain could even survive under 500 mM NaCl which was lethal to WT. In addition, by introducing the ectoine synthetic pathway into the sucrose-deficient strain, the salt tolerance of the obtained strain Syn7942/Δsps-ect was restored to the level of WT under 300 mM NaCl stress, demonstrating that ectoine could substitute for sucrose to combat against salt stress in Syn7942. In order to study the difference in the regulation of mechanism on the salt adaptation process after replacing sucrose with ectoine, transcriptomic analysis was performed for Syn7942/Δsps-ect and WT. The differentially expressed gene analysis successfully identified 19 up-regulated genes and 39 down-regulated genes in Syn7942/Δsps-ect compared with WT under salt stress condition. The results also showed that the global regulation of Syn7942/Δsps-ect and WT had certain differences in the process of salt adaptation, in which Syn7942/Δsps-ect reduced the demand for the intensity of sulfur metabolism in this process. This study provides a valuable reference for further salt tolerance engineering in cyanobacteria.

Improved Productivity of Streptomyces mobaraensis Transglutaminase by Regulating Zymogen Activation

Streptomyces mobaraensis transglutaminase (TGase) is extracellularly expressed as a zymogen and then activated by TGase-activating protease (TAP). In this study, we reported the strategy for improving TGase production via the regulation of TAP activity in S. mobaraensis. First, we analyzed the effects of three inorganic nitrogen sources on TGase production. With 30 mM nitrogen content, the time to the peak of TGase activity induced by (NH₄)₂SO₄ or NH₄Cl was 72 h, 12 h earlier than that of the fermentation without adding NH₄⁺. SDS-PAGE analysis indicated that NH₄⁺ accelerated the TGase activation in S. mobaraensis. Then, we examined the effect of NH₄⁺ on TAP biosynthesis using a TGase-deficient S. mobaraensis strain. It showed that NH₄⁺ enhanced the TAP activity at the early stage of the fermentation, which was dependent on the concentration and time of NH₄⁺ addition. Last, the yield and productivity of S. mobaraensis TGase were increased by 1.18-fold and 2.1-fold, respectively, when optimal NH₄⁺ addition (60 mM and 12 h) was used. The fermentation period was shortened from 84 to 48 h. The NH₄⁺ addition also increased the storage stability of crude enzyme at room temperature. These findings will benefit the TGase production and its activation mechanism in S. mobaraensis.