Challenges and opportunities for engineered Escherichia coli as a pivotal chassis toward versatile tyrosine-derived chemicals production

Growing concerns over limited fossil resources and associated environmental problems are motivating the development of sustainable processes for the production of high-volume fuels and high-value-added compounds. The shikimate pathway, an imperative pathway in most microorganisms, is branched with tyrosine as the rate-limiting step precursor of valuable aromatic substances. Such occurrence suggests the shikimate pathway as a promising route in developing microbial cell factories with multiple applications in the nutraceutical, pharmaceutical, and chemical industries. Therefore, an increasing number of studies have focused on this pathway to enable the biotechnological manufacture of pivotal and versatile aromatic products. With advances in genome databases and synthetic biology tools, genetically programmed Escherichia coli strains are gaining immense interest in the sustainable synthesis of chemicals. Engineered E. coli is expected to be the next bio-successor of fossil fuels and plants in commercial aromatics synthesis. This review summarizes successful and applicable genetic and metabolic engineering strategies to generate new chassis and engineer the iterative pathway of the tyrosine route in E. coli, thus addressing the opportunities and current challenges toward the realization of sustainable tyrosine-derived aromatics.

High value ferulic acid biosynthesis using modular design and spent coffee ground in engineered Escherichia coli chassis

Sophisticated genetic engineering enables microbial hosts to derive high-value aromatics in a green manner. Ferulic acid (FA) is one of the noteworthy aromatics due to its potent pharmacokinetic properties. However, the current approaches to FA biosynthesis still decamp from time- and cost-effectiveness. Herein, FA pathway was artificially reconstructed in Escherichia coli using modular designs. Comprehensive screening of E. coli lineages was reckoned for efficient synthesis of p-coumaric acid (pCA) as a precursor and FA eventually. The modular design was further advanced by harboring tyrosine transporter, adapting the heterologous codon, utilizing pCA symporter, and enriching FADH2 cofactor pools via in vivo regeneration. Taken together with simultaneous optimization of culture condition, a remarkable FA yield of 972.6 mg/L with 89.4 % conversion was achieved in 48 h, circumventing the time-consuming issue. Moreover, this study successfully exported inexpensive precursor from spent coffee ground for the first time, paving the economical way of FA biosynthesis.

Prospective and challenges of live bacterial therapeutics from a superhero Escherichia coli Nissle 1917

Escherichia coli Nissle 1917 (EcN), the active component of Mutaflor(R), is a notable probiotic from Gram-negative to treat Crohn's disease and irritable bowel syndrome. Therefore, a comprehensive genomic database maximizes the systemic probiotic assessment to discover EcN's role in human health. Recently, advanced synthetic and genetic tools have opened up a rich area to execute EcN as "living medicines" with controllable functions. Incorporating unique biomarkers allows the engineered EcN to switch genes on and off in response to environmental cues. Since EcN holds promise as a safe nature vehicle, more studies are desired to fully realize a wide range of probiotic potential for disease treatment. This review aims to deliver a historical origin of EcN, discuss the recent promising genetic toolbox in the rational design of probiotics, and pinpoint the clinical translation and evaluation of engineered EcN in vitro and in vivo. The summary of safety concerns, strategies of biotherapeutics development, and the challenges and prospects of engineered EcN is also concluded.

High-level itaconic acid (IA) production using engineered Escherichia coli Lemo21(DE3) toward sustainable biorefinery

Itaconic acid (IA) serves as a prominent building block for polyamides as sustainable material. In vivo IA production is facing the competing side reactions, byproducts accumulation, and long cultivation time. Therefore, the utilization of whole-cell biocatalysts to carry out production from citrate is an alternative approach to sidestep the current limitations. In this study, in vitro reaction of IA was obtained 72.44 g/L by using engineered E. coli Lemo21(DE3) harboring the aconitase (Acn, EC 4.2.1.3) and cis-aconitate decarboxylase (CadA, EC 4.1.1.6) which was cultured in glycerol-based minimal medium. IA productivity enhancement was observed after cold-treating the biocatalysts in - 80 °C for 24 h prior to the reaction, reaching 81.6 g/L. On the other hand, a new seeding strategy in Terrific Broth (TB) as a nutritionally rich medium was employed to maintain the biocatalysts stability up to 30 days. Finally, the highest IA titer of 98.17 g/L was attained using L21::7G chassis, that has a pLemo plasmid and integration of GroELS to the chromosome. The high-level of IA production along with the biocatalyst reutilization enables the economic viability toward a sustainable biorefinery.

Simultaneous carbon dioxide sequestration and utilization for cadaverine production using dual promoters in engineered Escherichia coli strains

Human carbonic anhydrase II (hCAII) is a rapid-acting zinc-metalloenzyme that catalyzes CO₂ hydration reversibly, with encouraging applications in carbon capture, sequestration, and utilization (CCSU). However, biocatalyst durability is a major challenge. Herein, hCAII is emphasized in 4 different Escherichia coli strains and designated under dual promoters from sigma factor 70 (σ⁷⁰) and heat shock protein (HSP70A) to suppress the usage of inducer and stimulate activity in heat environments. As a result, hCAII under high-efficient dual promoters regulation retained high residual activity in CO₂ biomineralization of 68.8 % after 4 cycles at 40 °C. Moreover, co-expression of CA_C9 with lysine decarboxylase (CadA) simultaneously sequestered CO₂ release up to 95.7 % and increased cadaverine titer from 18.0 to 36.7 g/L by using E. coli MG1655. The remnant biomass from cadaverine synthesis sustained converting CO₂ to 57.9 mg-CaCO₃. Thus, the dual promoters design demonstrated the promising potential for CCSU through simultaneous CO₂ utilization and cadaverine synthesis.

Reprogramming T7RNA Polymerase in Escherichia coli Nissle 1917 under Specific Lac Operon for Efficient p-Coumaric Acid Production

Lac operon is the standard regulator used to control the orthogonality of T7RNA polymerase (T7RNAP) and T7 promoter inEscherichia coli BL21(DE3) strain for protein expression. However,E. coliNissle 1917 (EcN), the unique probiotic strain, has seldom been precisely adapted to the T7 system. Herein, we applied bioinformatics analysis on Lac operon from different strains, and it was observed that a weak promoter for LacI repressor existed in EcN. Furthermore, X-gal assay revealed a strong expression of lacZ in EcN. We demonstrated that Lac operon significantly affected the protein expression in the two T7-derived EcN, in which T7RNAP was integrated at lambda (ET7L) and HK022 (ET7H), respectively. Different combinations of replication origin, chaperonin GroELS, inducer, and medium were explored to fine-tune the best strain with tyrosine ammonia-lyase (TAL) for p-coumaric acid (pCA) production, which is one of the essential bioactive compounds for human health. Finally, the highest pCA conversion of 78.8% was achieved using RRtL (plasmid form) under the optimum condition, and a 51.5% conversion was obtained with L::Rt strain which has integrated T7-RtTAL at HK022 of ET7L in the simulated gut environment. The appropriate reprogramming of T7RNAP expedites EcN as an effective and promising cell factory for live bacterial therapeutics in the future.

Enhanced carbon capture and utilization (CCU) using heterologous carbonic anhydrase in Chlamydomonas reinhardtii for lutein and lipid production

Chlamydomonas reinhardtii is a model microalga that has a higher growth rate and produces high levels of lutein and lipids, but biomass production is limited. Carbonic anhydrase (CA) converts atmospheric CO₂ to bicarbonate which is crucial for carbon-concentrating mechanism (CCM) in microalgae and boosts cell density. Therefore, C. reinhardtii harboring the heterologous CA from Mesorhizobium loti (MlCA) and Sulfurihydrogenibium yellowstonense (SyCA) were explored to increase CO₂ capture and utilization (CCU) through different culture devices. Genetically modified C. reinhardtii was able to grow from mixotrophic to autotrophic conditions. Subsequently, biomass, lutein, and lipid were maximized to OD₆₈₀ of 4.56, 21.32 mg/L and 672 mg/L using photo-bioreactor (PBR) with 5% CO₂. Moreover, CO₂ assimilation rate was 2.748 g-CO₂/g-DCW and 2.792 g-CO₂/g-DCW under mixotrophic and autotrophic conditions, respectively. The biomass accumulation correlated with CA activity. In addition, the transcript levels of major genes in metabolic pathways of lutein and lipid were dramatically increased.

Enhanced recombinant Sulfurihydrogenibium yellowstonense carbonic anhydrase activity and thermostability by chaperone GroELS for carbon dioxide biomineralization

Biological carbon fixation is a feasible strategy to reduce atmospheric carbon dioxide levels (CO₂). In this platform, carbonic anhydrase (CA) enzyme is employed to accelerate the sequestration of CO₂. The present work explored the effect of chaperone GroELS and TrxA-tag on improving soluble expression of the recombinant Sulfurihydrogenibium yellowstonense CA which activity and biomineralization capability were taken into consideration. At first, the expression of GroELS using the inducible T7 promoter and constitutive J23100 promoter were investigated. The results indicated that 1.4 folds increment of soluble protein and 100% of CA activity enhancement were achieved with GroELS co-expression driven by J23100 promoter. Furthermore, the involvement of TrxA fusion tag displayed a significant enhancement of soluble protein production which was about 2.67 times higher than that of original SyCA. Besides, co-expression with GroELS intensified the thermostability of SyCA at 60 °C owing to changes in the structural conformation of the protein, which was proved by an in vitro assay. The SyCA was further entrapped and immobilized into polyacrylamide gel (i.e., PAGE-SyCA). The biomineralization capability of the PAGE-SyCA and whole-cell (WC) was compared in a two-column system. After 5 cycles of reuse, PAGE-SyCA maintained 29.8% activity and formed 774 mg of CaCO₃ solids in the B::JG strain. This study presents the recombinant engineering strategies to improve SyCA productivity, activity, thermostability, and effective carbon dioxide conversion.

Genetic design of co-expressed Mesorhizobium loti carbonic anhydrase and chaperone GroELS to enhancing carbon dioxide sequestration

Mesorhizobium loti carbonic anhydrase (MlCA), an intrinsically high catalytic enzyme, has been employed for carbon dioxide capture and sequestration. However, recombinant expression of MlCA in Escherichia coli often forms inclusion bodies. Hence, protein partners such as fusion-tags and molecular chaperones are involved in regarding reduce the harshness of protein folding. TrxA-tag and GroELS have been chosen to co-express with MlCA in E. coli under an inducible T7 promoter or a constitutive J23100 promoter to compare productivity and activity. The results possessed that coupling protein partners effectively increased soluble MlCA up to 2.9-folds under T7 promoter, thus enhancing the CA activity by 120% and achieving a 5.2-folds turnover rate. Besides, it has also shifted the optimum temperature from 40 °C to 50 °C, promoted stability in the broad pH range (4.5 to 9.5) and the presence of various metal ions. Based on the in vitro assay and isothermal titration calorimetry (ITC) analysis, GroELS enhancing CA activity was due to change the intrinsic thermodynamic properties of the enzyme from endothermic to exothermic reaction (i.e., ∆H = 89.8 to -121.8 kJ/mol). Therefore, the collaboration of TrxA-MlCA with GroELS successfully augmented CO₂ biomineralization.