De Novo Biosynthesis of D-p-Hydroxyphenylglycine by a Designed Cofactor Self-Sufficient Route and Co-culture Strategy

Improving the enzymatic activity and stability of N-carbamoyl hydrolase using deep learning approach

BACKGROUND

Optically active D-amino acids are widely used as intermediates in the synthesis of antibiotics, insecticides, and peptide hormones. Currently, the two-enzyme cascade reaction is the most efficient way to produce D-amino acids using enzymes DHdt and DCase, but DCase is susceptible to heat inactivation. Here, to enhance the enzymatic activity and thermal stability of DCase, a rational design software "Feitian" was developed based on kcat prediction using the deep learning approach.

RESULTS

According to empirical design and prediction of "Feitian" software, six single-point mutants with high kcat value were selected and successfully constructed by site-directed mutagenesis. Out of six, three mutants (Q4C, T212S, and A302C) showed higher enzymatic activity than the wild-type. Furthermore, the combined triple-point mutant DCase-M3 (Q4C/T212S/A302C) exhibited a 4.25-fold increase in activity (29.77 ± 4.52 U) and a 2.25-fold increase in thermal stability as compared to the wild-type, respectively. Through the whole-cell reaction, the high titer of D-HPG (2.57 ± 0.43 mM) was produced by the mutant Q4C/T212S/A302C, which was about 2.04-fold of the wild-type. Molecular dynamics simulation results showed that DCase-M3 significantly enhances the rigidity of the catalytic site and thus increases the activity of DCase-M3.

CONCLUSIONS

In this study, an efficient rational design software "Feitian" was successfully developed with a prediction accuracy of about 50% in enzymatic activity. A triple-point mutant DCase-M3 (Q4C/T212S/A302C) with enhanced enzymatic activity and thermostability was successfully obtained, which could be applied to the development of a fully enzymatic process for the industrial production of D-HPG.

Co-Cultivated Enzyme Constraint Metabolic Network Model for Rational Guidance in Constructing Synthetic Consortia to Achieve Optimal Pathway Allocation Prediction

Synthetic consortia have emerged as a promising biosynthetic platform that offers new opportunities for biosynthesis. Genome-scale metabolic network models (GEMs) with complex constraints are extensively utilized to guide the synthesis in monocultures. However, few methods are currently available to guide the rational construction of synthetic consortia for predicting the optimal allocation strategy of synthetic pathways aimed at enhancing product synthesis. A standardized method to construct the co-cultivated Enzyme Constraint metabolic network model (CulECpy) is proposed, which integrates enzyme constraints and modular interaction scale constraints based on the research concept of "independent + global". This method is applied to construct several synthetic consortia models, which encompassed different target products, strains, synthetic pathways, and compositional structures. Analyzing the model, the optimal pathway allocation and initial inoculum ratio that enhance the synthesis of target products by synthetic consortia are predicted and verified. When comparing with the constructed co-culture synthesis system, the normalized root mean square error of all optimal theoretical yield simulations is found to be less than or equal to 0.25. The analyses and verifications demonstrate that the method CulECpy can guide the rational construction of synthetic consortia systems to facilitate biochemical synthesis.

Self-assembly systems to troubleshoot metabolic engineering challenges

Enzyme self-assembly is a technology in which enzyme units can aggregate into ordered macromolecules, assisted by scaffolds. In metabolic engineering, self-assembly strategies have been explored for aggregating multiple enzymes in the same pathway to improve sequential catalytic efficiency, which in turn enables high-level production. The performance of the scaffolds is critical to the formation of an efficient and stable assembly system. This review comprehensively analyzes these scaffolds by exploring how they assemble, and it illustrates how to apply self-assembly strategies for different modules in metabolic engineering. Functional modifications to scaffolds will further promote efficient strategies for production.

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.

Rational Design of Meso-Diaminopimelate Dehydrogenase with Enhanced Reductive Amination Activity for Efficient Production of d-p-Hydroxyphenylglycine

d-p-hydroxyphenylglycine (d-HPG) is an important intermediate in the pharmaceutical industry. In this study, a tri-enzyme cascade for the production of d-HPG from l-HPG was designed. However, the amination activity of Prevotella timonensis meso-diaminopimelate dehydrogenase (PtDAPDH) toward 4-hydroxyphenylglyoxylate (HPGA) was identified as the rate-limiting step. To overcome this issue, the crystal structure of PtDAPDH was solved, and a "binding pocket and conformation remodeling" strategy was developed to improve the catalytic activity toward HPGA. The best variant obtained, PtDAPDHM4, exhibited a catalytic efficiency (kcat/Km) that was 26.75-fold higher than that of the wild type. This improvement was due to the enlarged substrate-binding pocket and enhanced hydrogen bond networks around the active center; meanwhile, the increased number of interdomain residue interactions drove the conformation distribution toward the closed state. Under optimal transformation conditions, PtDAPDHM4 produced 19.8 g/L d-HPG from 40 g/L racemate DL-HPG in a 3 L fermenter within 10 h, with 49.5% conversion and >99% enantiomeric excess. Our study provides an efficient three-enzyme cascade pathway for the industrial production of d-HPG from racemate DL-HPG. IMPORTANCE d-p-hydroxyphenylglycine (d-HPG) is an important intermediate in the synthesis of antimicrobial compounds. d-HPG is mainly produced via chemical and enzymatic approaches, and enzymatic asymmetric amination employing diaminopimelate dehydrogenase (DAPDH) is considered an attractive method. However, the low catalytic activity of DAPDH toward bulky 2-keto acids limits its applications. In this study, we identified a DAPDH from Prevotella timonensis and created a mutant, PtDAPDHM4, which exhibited a catalytic efficiency (kcat/Km) toward 4-hydroxyphenylglyoxylate that was 26.75-fold higher than that of the wild type. The novel strategy developed in this study has practical value for the production of d-HPG from inexpensive racemate DL-HPG.

Microbial production of valuable chemicals by modular co-culture strategy

Nowadays, microbial synthesis has become a common way for producing valuable chemicals. Traditionally, microbial production of valuable chemicals is accomplished by a single strain. For the purpose of increasing the production titer and yield of a recombinant strain, complicated pathways and regulation layers should be fine-tuned, which also brings a heavy metabolic burden to the host. In addition, utilization of various complex and mixed substrates further interferes with the normal growth of the host strain and increases the complexity of strain engineering. As a result, modular co-culture technology, which aims to divide a target complex pathway into separate modules located at different single strains, poses an alternative solution for microbial production. Recently, modular co-culture strategy has been employed for the synthesis of different natural products. Therefore, in this review, various chemicals produced with application of co-cultivation technology are summarized, including co-culture with same species or different species, and regulation of population composition between the co-culture members. In addition, development prospects and challenges of this promising field are also addressed, and possible solution for these issues were also provided.