Engineering Escherichia coli for l-homoserine production

Adjustment of the main biosynthesis modules to enhance the production of l-homoserine in Escherichia coli W3110

l-homoserine is an important platform compound of many valuable products. Construction of microbial cell factory for l-homoserine production from glucose has attracted a great deal of attention. In this study, l-homoserine biosynthesis pathway was divided into three modules, the glucose uptake and upstream pathway, the downstream pathway, and the energy supply module. Metabolomics of the chassis strain HS indicated that the supply of ATP was inadequate, therefore, the energy supply module was firstly modified. By balancing the ATP supply module, the l-homoserine production increased by 66% to 12.55 g/L. Further, the results indicated that the upstream pathway was blocked, and increasing the culture temperature to 37°C could solve this problem and the l-homoserine production reached 21.38 g/L. Then, the downstream synthesis pathways were further strengthened to balance the fluxes, and the l-homoserine production reached the highest reported level of 32.55 g/L in shake flasks. Finally, fed-batch fermentation in a 5-L bioreactor was conducted, and l-homoserine production could reach to 119.96 g/L after 92 h cultivation, with the yield of 0.41 g/g glucose and productivity of 1.31 g/L/h. The study provides a well research foundation for l-homoserine production by microbial fermentation with the capacity for industrial application.

Metabolic engineering strategies for L-Homoserine production in Escherichia coli

L-Homoserine, serves as a non-essential precursor for the essential amino acids derived from L-aspartate in both animals and humans. It finds widespread applications across the food, cosmetics, pharmaceutical, and animal feed industries. Microbial fermentation, primarily utilizing Escherichia coli, is the dominant approach for L-Homoserine production. However, despite recent advancements in fermentative processes employing E. coli strains, low production efficiency remains a significant barrier to its commercial viability. This review explores the biosynthesis, secretion, and regulatory mechanisms of L-Homoserine in E. coli while assessing various metabolic engineering strategies aimed at improving production efficiency.

Antibiotic-Free High-Level l-Methionine Production in Engineered Escherichia coli

l-Methionine, a valuable sulfur-containing amino acid, holds great significance as a feed additive, nutraceutical, pharmaceutical, or even in the cosmetic industry. However, achieving efficient microbial production of l-methionine remains challenging due to its complex biosynthetic pathway and plasmid loss during fermentation. Herein, l-methionine biosynthesis was improved by enhancing succinyl-CoA supply, introducing a direct-sulfurylation pathway, and weakening the l-threonine branched pathway. The engineered strain produced 21.55 g/L l-methionine with a yield of 0.14 g/g glucose in a 5 L bioreactor. To eliminate the need for antibiotics and minimize plasmid loss, the hok/sok system was incorporated into the plasmid. The resulting plasmid pAm10 enabled strain M2 thrBA1G to produce 20.39 g/L of l-methionine without antibiotics in 5 L of fed-batch cultivation, a 42.58% increase compared to the control. This study highlights the potential of plasmid-based antibiotic-free fermentation for efficient and cost-effective production of l-methionine, as well as other amino acids or chemicals.

Eliminated high lipid inhibition in the anaerobic digestion of food waste for biomethane production by engineered E. coli with cell surface display lipase

Food waste (FW) with high content of lipid typically inhibits anaerobic digestion (AD) and methane production. In this study, a novel whole-cell catalyst was created to degrade lipid by displaying lipase on the E. coli cells surface to improve FW anaerobic digestion. The methane production rose, going from 25.78 to 161.77 mL/g VS, with a greater VS removal rate of 66.3% compared to CK group (29.6%). Long-chain fatty acids (LCFAs) was similarly reduced from 1733.6 mg/L to 337 mg/L. Microbial community analysis showed the relative abundance of Acinetbacter and Hydrogenophaga were increased from 1.7% to 6.6% and 1.3%-4.9%, respectively for substrates degradation. The methanogenic Methanosarcina increased from 24.7% to 52.3% for methane production. This study provided a potential approach that might be used to lessen lipid inhibition and improve anaerobic digestion of food waste.

Balancing the AspC and AspA Pathways of Escherichia coli by Systematic Metabolic Engineering Strategy for High-Efficient l-Homoserine Production

l-Homoserine is a promising C4 platform compound used in the agricultural, cosmetic, and pharmaceutical industries. Numerous works have been conducted to engineer Escherichia coli to be an excellent l-homoserine producer, but it is still unable to meet the industrial-scale demand. Herein, we successfully engineered a plasmid-free and noninducible E. coli strain with highly efficient l-homoserine production through balancing AspC and AspA synthesis pathways. First, an initial strain was constructed by increasing the accumulation of the precursor oxaloacetate and attenuating the organic acid synthesis pathway. To remodel the carbon flux toward l-aspartate, a balanced route prone to high yield based on TCA intensity regulation was designed. Subsequently, the main synthetic pathway and the cofactor system were strengthened to reinforce the l-homoserine synthesis. Ultimately, under two-stage DO control, strain HSY43 showed 125.07 g/L l-homoserine production in a 5 L fermenter in 60 h, with a yield of 0.62 g/g glucose and a productivity of 2.08 g/L/h. The titer, yield, and productivity surpassed the highest reported levels for plasmid-free strains in the literature. The strategies adopted in this study can be applied to the production of other l-aspartate family amino acids.

Improving Microbial Cell Factory Performance by Engineering SAM Availability

Methylated natural products are widely spread in nature. S-Adenosyl-l-methionine (SAM) is the secondary abundant cofactor and the primary methyl donor, which confer natural products with structural and functional diversification. The increasing demand for SAM-dependent natural products (SdNPs) has motivated the development of microbial cell factories (MCFs) for sustainable and efficient SdNP production. Insufficient and unsustainable SAM availability hinders the improvement of SdNP MCF performance. From the perspective of developing MCF, this review summarized recent understanding of de novo SAM biosynthesis and its regulatory mechanism. SAM is just the methyl mediator but not the original methyl source. Effective and sustainable methyl source supply is critical for efficient SdNP production. We compared and discussed the innate and relatively less explored alternative methyl sources and identified the one involving cheap one-carbon compound as more promising. The SAM biosynthesis is synergistically regulated on multilevels and is tightly connected with ATP and NAD(P)H pools. We also covered the recent advancement of metabolic engineering in improving intracellular SAM availability and SdNP production. Dynamic regulation is a promising strategy to achieve accurate and dynamic fine-tuning of intracellular SAM pool size. Finally, we discussed the design and engineering constraints underlying construction of SAM-responsive genetic circuits and envisioned their future applications in developing SdNP MCFs.

Enhancing tumor-specific recognition of programmable synthetic bacterial consortium for precision therapy of colorectal cancer

Probiotics hold promise as a potential therapy for colorectal cancer (CRC), but encounter obstacles related to tumor specificity, drug penetration, and dosage adjustability. In this study, genetic circuits based on the E. coli Nissle 1917 (EcN) chassis were developed to sense indicators of tumor microenvironment and control the expression of therapeutic payloads. Integration of XOR gate amplify gene switch into EcN biosensors resulted in a 1.8-2.3-fold increase in signal output, as confirmed by mathematical model fitting. Co-culturing programmable EcNs with CRC cells demonstrated a significant reduction in cellular viability ranging from 30% to 50%. This approach was further validated in a mouse subcutaneous tumor model, revealing 47%-52% inhibition of tumor growth upon administration of therapeutic strains. Additionally, in a mouse tumorigenesis model induced by AOM and DSS, the use of synthetic bacterial consortium (SynCon) equipped with multiple sensing modules led to approximately 1.2-fold increased colon length and 2.4-fold decreased polyp count. Gut microbiota analysis suggested that SynCon maintained the abundance of butyrate-producing bacteria Lactobacillaceae NK4A136, whereas reducing the level of gut inflammation-related bacteria Bacteroides. Taken together, engineered EcNs confer the advantage of specific recognition of CRC, while SynCon serves to augment the synergistic effect of this approach.

Advances in Biosynthesis of Non-Canonical Amino Acids (ncAAs) and the Methods of ncAAs Incorporation into Proteins

The functional pool of canonical amino acids (cAAs) has been enriched through the emergence of non-canonical amino acids (ncAAs). NcAAs play a crucial role in the production of various pharmaceuticals. The biosynthesis of ncAAs has emerged as an alternative to traditional chemical synthesis due to its environmental friendliness and high efficiency. The breakthrough genetic code expansion (GCE) technique developed in recent years has allowed the incorporation of ncAAs into target proteins, giving them special functions and biological activities. The biosynthesis of ncAAs and their incorporation into target proteins within a single microbe has become an enticing application of such molecules. Based on that, in this study, we first review the biosynthesis methods for ncAAs and analyze the difficulties related to biosynthesis. We then summarize the GCE methods and analyze their advantages and disadvantages. Further, we review the application progress of ncAAs and anticipate the challenges and future development directions of ncAAs.

Location and Orientation of the Genetic Toxin-Antitoxin Element hok/sok in the Plasmid Affect Expression of Pharmaceutically Significant Proteins in Bacterial Cells

Genetic toxin-antitoxin element hok/sok from the natural Escherichia coli R1 plasmid ensures segregational stability of plasmids. Bacterial cells that have lost all copies of the plasmid encoding the short-lived antitoxin are killed by the stable toxin. When introduced into bacterial expression vectors, the hok/sok element can increase the productive time of recombinant protein biosynthesis by slowing down accumulation of non-producing cells lacking the expression plasmid. In this work, we studied the effects of position and orientation of the hok/sok element in the standard pET28a plasmid with the inducible T7lac promoter and kanamycin resistance gene. It was found that the hok/sok element retained its functional activity regardless of its location and orientation in the plasmid. Bacterial cells retained the hok/sok-containing plasmids after four days of cultivation without antibiotics, while the control plasmid without this element was lost. Using three target proteins - E. coli type II asparaginase (ASN), human growth hormone (HGH), and SARS-CoV-2 virus nucleoprotein (NP) - it was demonstrated that the maximum productivity of bacteria for the cytoplasmic proteins (HGH and NP) was observed only when the hok/sok element was placed upstream of the target gene promoter. In the case of periplasmic protein localization (ASN), the productivity of bacteria during cultivation with the antibiotic decreased for all variants of the hok/sok location. When the bacteria were cultivated without the antibiotic, the productivity was better preserved when the hok/sok element was located upstream of the target gene promoter. The use of the pEHU vector with the upstream location of the hok/sok element allowed to more than double the yield of HGH (produced as inclusion bodies) in the absence of antibiotic and to maintain ASN biosynthesis at the level of at least 10 mg/liter for four days during cultivation without antibiotics. The developed segregation-stabilized plasmid vectors can be used to obtain various recombinant proteins in E. coli cells without the use of antibiotics.