Recent advances in microbial production of diamines, aminocarboxylic acids, and diacids as potential platform chemicals and bio-based polyamides monomers

Advancing microbial production through artificial intelligence-aided biology

Microbial cell factories (MCFs) have been leveraged to construct sustainable platforms for value-added compound production. To optimize metabolism and reach optimal productivity, synthetic biology has developed various genetic devices to engineer microbial systems by gene editing, high-throughput protein engineering, and dynamic regulation. However, current synthetic biology methodologies still rely heavily on manual design, laborious testing, and exhaustive analysis. The emerging interdisciplinary field of artificial intelligence (AI) and biology has become pivotal in addressing the remaining challenges. AI-aided microbial production harnesses the power of processing, learning, and predicting vast amounts of biological data within seconds, providing outputs with high probability. With well-trained AI models, the conventional Design-Build-Test (DBT) cycle has been transformed into a multidimensional Design-Build-Test-Learn-Predict (DBTLP) workflow, leading to significantly improved operational efficiency and reduced labor consumption. Here, we comprehensively review the main components and recent advances in AI-aided microbial production, focusing on genome annotation, AI-aided protein engineering, artificial functional protein design, and AI-enabled pathway prediction. Finally, we discuss the challenges of integrating novel AI techniques into biology and propose the potential of large language models (LLMs) in advancing microbial production.

Increasing 1,4-Diaminobutane Production in Escherichia coli by Optimization of Cofactor PLP and NADPH Synthesis

1,4-diaminobutane is widely used in the industrial production of polymers, pharmaceuticals, agrochemicals and surfactants. Owing to economic and environmental concerns, there has been a growing interest in using microbes to produce 1,4-diaminobutane. However, there is lack of research on the influence of cofactors pyridoxal phosphate (PLP) and NADPH on the synthesis of 1,4-diaminobutane. PLP serves as a cofactor of ornithine decarboxylase in the synthesis of 1,4-diaminobutane. Additionally, the synthesis of 1 mol 1,4-diaminobutane requires 2 mol NADPH, thus necessitating consideration of NADPH balance in the efficient synthesis of 1,4-diaminobutane by Escherichia coli. The aim of this study was to enhance the synthesis efficiency of 1,4-diaminobutane through increasing production of PLP and NADPH. By optimizing the expression of the genes associated with synthesis of PLP and NADPH in E. coli, cellular PLP and NADPH levels increased, and the yield of 1,4-diaminobutane also increased accordingly. Ultimately, using glucose as the primary carbon source, the yield of 1,4-diaminobutane in the recombinant strain NAP19 reached 272 mg/L·DCW, by increased 79% compared with its chassis strain.

Fine-Tuning Pyridoxal 5'-Phosphate Synthesis in Escherichia coli for Cadaverine Production in Minimal Culture Media

Cadaverine is a critical C5 monomer for the production of polyamides. Pyridoxal 5'-phosphate (PLP), as a crucial cofactor for the key enzyme lysine decarboxylase in the cadaverine biosynthesis pathway, has seen a persistent shortage, leading to limitations in cadaverine production. To address this issue, a dual-pathway strategy was implemented, synergistically enhancing both endogenous and heterologous PLP synthesis modules and resulting in improved PLP synthesis. Subsequently, a growth-stage-dependent molecular switch was introduced to balance the precursor competition between PLP synthesis and cell growth. Additionally, a PLP sensor-based negative feedback circuit was constructed by integrating a newly identified PLP-responsive promoter PygjH and an arabinose-regulated system, dynamically regulating the expression of the PLP synthetic genes and preventing excessive intracellular PLP accumulation. The optimal strain, L18, cultivated in the minimal medium AM1, demonstrated cadaverine production with a titer, yield, and productivity of 64.03 g/L, 0.23 g/g glucose, and 1.33 g/L/h, respectively. This represents the highest titer reported to date in engineered Escherichia coli by fed-batch fermentation in a minimal medium.

Fabrication of a bio-based polymer adsorbent and its application for extraction and determination of glycosides from Huangqi Liuyi decoction

Huangqi Liuyi Decoction, a famous classical Chinese prescription, shows significant curative effect on diabetes and its complications, in which calycosin-7-glucoside, liquiritin and glycyrrhizic acid are the main components that playing these mentioned pharmacological activity, under the synergistic action of various other ingredients in the decoction. However, there are significant differences in the content of active compounds in Chinese medicinal materials, which mainly due to origin, picking seasons, and processing methods. Hence, the accurate content of the glycosides is the prerequisite for ensuring the pharmacological efficacy. Aiming at establishing an efficient extraction and determination method for accurate quantitative analysis of calycosin-7-glucoside, liquiritin and glycyrrhizic acid in Huangqi Liuyi Decoction, an on line solid-phase extraction-high-performance liquid chromatography method was developed, using a homemade bio-based monolithic adsorbent. The bio-based adsorbent was prepared in a stainless steel tube, using bio-monomers of methyleugenol and S-allyl-L-cysteine, which effectively reduced the dependence of the polymer field on non-renewable fossil resources and reduced carbon emissions. Furthermore, the prepared adsorbent owned abundant chemical groups, which can produce interactions of hydrogen bond, dipole-dipole, π-π and hydrophobic force with the target glycosides, thus improving the specific recognition ability of the adsorbent. The experiments were carried out on an LC-3000 HPLC instrument with a six-way valve. Methodology validation indicates that the recovery is in the range of 97.0%-103.4% with the RSD in the range of 1.6%-4.0%, due to the specific selectivity of the bio-based monolithic adsorbent for these three glycosides, and good matrix-removal ability for Huangqi Liuyi decoction. The limit of detection is 0.17, 0.50 and 0.33 μg/mL for calycosin-7-glucoside, liquiritin and glycyrrhizic acid, respectively, and the limit of quantitation is 0.50, 1.50 and 1.00 μg/mL, respectively, with the linear range of 2-200 μg/mL for calycosin-7-glucoside, and 5-500 μg/mL for liquiritin and glycyrrhizic acid. The present work provided a simple and efficient method for the extraction and determination of glycosides in complex medicinal plants.

Base-mediated carboxylation of C-nucleophiles with CO2

Carbon dioxide (CO2) is an available, abundant, and renewable C1 resource, which could be converted into value-added chemicals. Due to its inherent thermodynamic stability and kinetic inertness, it is difficult to realize its efficient utilization. Nevertheless, many elegant strategies for the utilization of CO2 have been developed using Lewis bases, frustrated Lewis pairs, hydroxyl-containing compounds, amino-group-containing compounds or transition metal catalysis. Among them, base-mediated carboxylation of C-nucleophiles is an environmentally friendly strategy for CO2 conversion, which is operationally simple, using low-toxicity bases and economical available promoters, without the use of complex ligands or cocatalysts. This review summarizes related work on the base-mediated carboxylation of C-nucleophiles with CO2, based on the effects of nucleophiles, promoters, additives, and solvents. The types of pronucleophile are categorized as follows: hydrocarbon with C(sp3)-H, C(sp2)-H or C(sp)-H bonds, organosilanes, organotin, organoboron, and N-tosylhydrazones. Typical mechanisms and applications of these carboxylation reactions are also depicted. Moreover, mechanistic comprehension of CO2 activation and conversion at a molecular level aims to further expand the repertoire of carboxylation transformations mediated by bases.

MCF2Chem: A manually curated knowledge base of biosynthetic compound production

BACKGROUND

Microbes have been used as cell factories to synthesize various chemical compounds. Recent advances in synthetic biological technologies have accelerated the increase in the number and capacity of microbial cell factories; the variety and number of synthetic compounds produced via these cell factories have also grown substantially. However, no database is available that provides detailed information on the microbial cell factories and the synthesized compounds.

RESULTS

In this study, we established MCF2Chem, a manually curated knowledge base on the production of biosynthetic compounds using microbial cell factories. It contains 8888 items of production records related to 1231 compounds that were synthesizable by 590 microbial cell factories, including the production data of compounds (titer, yield, productivity, and content), strain culture information (culture medium, carbon source/precursor/substrate), fermentation information (mode, vessel, scale, and condition), and other information (e.g., strain modification method). The database contains statistical analyses data of compounds and microbial species. The data statistics of MCF2Chem showed that bacteria accounted for 60% of the species and that "fatty acids", "terpenoids", and "shikimates and phenylpropanoids" accounted for the top three chemical products. Escherichia coli, Saccharomyces cerevisiae, Yarrowia lipolytica, and Corynebacterium glutamicum synthesized 78% of these chemical compounds. Furthermore, we constructed a system to recommend microbial cell factories suitable for synthesizing target compounds and vice versa by combining MCF2Chem data, additional strain- and compound-related data, the phylogenetic relationships between strains, and compound similarities.

CONCLUSIONS

MCF2Chem provides a user-friendly interface for querying, browsing, and visualizing detailed statistical information on microbial cell factories and their synthesizable compounds. It is publicly available at https://mcf.lifesynther.com . This database may serve as a useful resource for synthetic biologists.

Current advances for omics-guided process optimization of microbial manufacturing

Currently, microbial manufacturing is widely used in various fields, such as food, medicine and energy, for its advantages of greenness and sustainable development. Process optimization is the committed step enabling the commercialization of microbial manufacturing products. However, the present optimization processes mainly rely on experience or trial-and-error method ignoring the intrinsic connection between cellular physiological requirement and production performance, so in many cases the productivity of microbial manufacturing could not been fully exploited at economically feasible cost. Recently, the rapid development of omics technologies facilitates the comprehensive analysis of microbial metabolism and fermentation performance from multi-levels of molecules, cells and microenvironment. The use of omics technologies makes the process optimization more explicit, boosting microbial manufacturing performance and bringing significant economic benefits and social value. In this paper, the traditional and omics technologies-guided process optimization of microbial manufacturing are systematically reviewed, and the future trend of process optimization is prospected.