Module engineering coupled with omics strategies for enhancing D-pantothenate production in Escherichia coli

Elucidating the mechanisms of echinocandin B biosynthesis under fatty acid feeding in Aspergillus nidulans based on genome and transcriptome sequencing

Echinocandin B (ECB), a non-ribosomal lipopeptide synthesized by ascomycete fungi, serves as a first-line therapeutic agent for invasive fungal infections. While the biosynthetic gene clusters of ECB have been identified in several Aspergillus species, the regulatory mechanisms governing its intracellular biosynthesis remain poorly understood, hindering the development of efficient ECB-producing cell factories. To address this issue, we elucidated the mechanisms underlying echinocandin B (ECB) biosynthesis in Aspergillus nidulans ZJB16068 under fatty acid feeding conditions through genome and transcriptome sequencing. The genome of ZJB16068 was sequenced using Oxford Nanopore Technology, yielding a 32.67 Mbp assembly with 11 scaffolds and a GC content of 50.23%. A total of 10,505 protein-coding genes were annotated, revealing 66 secondary metabolite gene clusters. Comparative transcriptomics between ZJB16068 and the reference strain ZJB0817 identified 2,342 differentially expressed genes (DEGs) under fatty acid supplementation. The KEGG analysis of the top 20 DEGs highlighted predominant metabolic pathways, including translation, energy metabolism, cofactor supply and lipid metabolism. We found that the up-regulation of genes related to the fatty acid metabolic pathway, pantothenic acid and CoA synthesis pathway accelerated the synthesis of acetyl-CoA, and the down-regulation of TCA pathway contributed to the throttling of acetyl-CoA. In addition, the genes involved in oxidative phosphorylation are fully upregulated, providing sufficient ATP for ECB synthesis. These pathways synergistically enhance the synthesis of ECB. These findings highlight the critical role of acetyl-CoA synthesis and energy supply in ECB synthesis and provide potential direction for future metabolic engineering aiming at increasing ECB production.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-025-04331-4.

Efficient Synthesis of Vitamin B5 in Escherichia coli by Engineering Ketopantoate Hydroxymethyltransferase and Cofactor Supply

d-pantothenic acid (d-PA), also known as vitamin B5, is an essential precursor of coenzyme A and plays a crucial role in maintaining the physiological functions of organisms. Ketopantoate hydroxymethyltransferase (PanB), encoded by panB gene, serves as a key rate-limiting enzyme in d-PA synthesis. Additionally, the catalytic function of PanB requires the cofactor 5,10-methylenetetrahydrofolate (5,10-CH2-THF). This study aimed to increase d-PA production by engineering ketopantoate hydroxymethyltransferase and cofactor supply. The key transcription factor bhsA that restricts d-PA production was screened and identified through transcription factor engineering applications. Subsequently, PanB was coexpressed with PanC to regulate expression. Furthermore, the highly catalytic mutant PanBMV123I/K124W was generated through Km/Kcat algorithm prediction and enzyme engineering, leading to a 2.5-fold increase in d-PA production. The de novo synthesis pathway of 5,10-CH2-THF was enhanced, whereas its degradation pathway was suppressed to improve cofactor supply. Then, the extracellular transport of d-PA was enhanced by introducing the d-PA transporter PanT from Streptococcus intermedius. The plasmid-free strain DPA23 produced 78.48 g/L of d-PA in a 5-L bioreactor, with a productivity of 2.69 g/L/h after 24 h and a glucose yield of 0.54 g/g. These strategies provided a reference for constructing microbial cell factories for d-PA and its derivatives.

Enhancing D-pantothenate production in Escherichia coli through multiplex combinatorial strategies

D-pantothenate, universally acknowledged as vitamin B5, has garnered considerable interest owing to its crucial functionality in the feed, pharmaceutical, and cosmeceutical sectors. Development of microbial strains for D-pantothenate hyperproducer has emerged as a prominent research direction in recent years. Herein, we converted an engineered Escherichia coli with low yield to a plasmid-free hyperproducer of D-pantothenate using multiplex combinatorial strategies. First, an initial strain was obtained through prolonging the cell lifespan. To promote the accumulation of D-pantothenic acid, the supply of cofactors was adaptively enhanced. Additionally, the heterologous gene panE from Pseudomonas aeruginosa, which encodes ketopantoate reductase (EC 1.1.1.169) catalyzing the synthesis of d-pantoate from α-ketopantoate, was screened and integrated into the chromosome. Subsequently, a strategy of acetate recycling and NOG pathway reconstruction were introduced and successfully to improve the D-pantothenate titer to 5.48 g/L. Additionally, we screened the regulatory factors and optimized its second codon to further increase the DPA yield of the engineered strains to 6.02 g/L in shake flask. The final engineered strain DS6 could efficiently produce 72.40 g/L D-pantothenate, which is 3.18-fold higher than the original strain. This study proposed a novel multiplex combination strategy for developing microbial cell factory of D-pantothenate, which was beneficial for the advancement of efficient D-pantothenate production.

Metabolic engineering of Escherichia coli for enhanced production of D-pantothenic acid

D-pantothenic acid (D-PA) is an essential vitamin that has been widely used in various industries. However, the low productivity caused by slow D-PA production in fermentation hinders its potential applications. In this study, strategies of engineering the synthetic pathway combined with regulating methyl recycle were employed in E. coli to enhance D-PA production. First, a self-induced promoter-mediated dynamic regulation of D-PA degradation pathway was carried out to improve D-PA accumulation. Then, to drive more carbon flux into D-PA synthesis, the key nodes of the R-pantoate pathway which encoded the essential enzyme were integrated into the genome. Subsequently, the further increase in D-PA production was achieved by promoting the regeneration of methyl donor. The strain L11T produced 86.03 g/L D-PA with a productivity of 0.797 g/L/h, which presented the highest D-PA titer and productivity to date. The strategies could be applied to constructing cell factories for producing other bio-based products.

Efficient carbon flux allocation towards D-pantothenic acid production via growth-decoupled strategy in Escherichia coli

For industrial strain construction, rational allocation of carbon flux is of paramount importance especially for decoupling cell growth and chemical productions to get maximum titer, rate, yield (TRY), which become Gordian Knot. Here, a temperature-sensitive switch and genetic circuits was used for effectively decoupling cell growth from D-pantothenic acid (DPA) production, along with systematically metabolic engineering including blocking redundant pathways of pyruvate and enhancing DPA driving force. Afterwards, rapid biomass accumulation only happened during growth stage, and subsequent high-efficient DPA production was initiated with reducing fermentation temperature. Finally, 97.20 g/L DPA and 0.64 g/g glucose conversion rate were achieved in 5-liter fed-batch fermentation. These undisputedly represent a milestone for the biosynthesis of DPA. With using strategies for decoupling cell growth from chemical productions, it would serve as "Alexander's sword" to cut Gordian Knot to get industrial chassis cells with excellent TRY for de novo biosynthesis of valuable chemicals.

Inverse metabolic engineering based on metabonomics for efficient production of hydroxytyrosol by Saccharomyces cerevisiae

Metabolic engineering provides a powerful approach to efficiently produce valuable compounds, with the aid of emerging gene editing tools and diverse metabolic regulation strategies. However, apart from the current known biochemical pathway information, a variety of unclear constraints commonly limited the optimization space of cell phenotype. Hydroxytyrosol is an important phenolic compound that serves various industries with prominent health-beneficial properties. In this study, the inverse metabolic engineering based on metabolome analysis was customized and implemented to disclose the hidden rate-limiting steps and thus to improve hydroxytyrosol production in Saccharomyces cerevisiae (S. cerevisiae). The potential rate-limiting steps involved three modules that were eliminated individually via reinforcing and balancing metabolic flow, optimizing cofactor supply, and weakening the competitive pathways. Ultimately, a 118.53 % improvement in hydroxytyrosol production (639.84 mg/L) was achieved by inverse metabolic engineering.

Development of a vitamin B5 hyperproducer in Escherichia coli by multiple metabolic engineering

Vitamin B5 [D-pantothenic acid (D-PA)] is an essential water-soluble vitamin that is widely used in the food and feed industries. Currently, the relatively low fermentation efficiency limits the industrial application of D-PA. Here, a plasmid-free D-PA hyperproducer was constructed using systematic metabolic engineering strategies. First, pyruvate was enriched by deleting the non-phosphotransferase system, inhibiting pyruvate competitive branches, and dynamically controlling the TCA cycle. Next, the (R)-pantoate pathway was enhanced by screening the rate-limiting enzyme PanBC and regulating the other enzymes of this pathway one by one. Then, to enhance NADPH sustainability, NADPH regeneration was achieved through the novel "PEACES" system by (1) expressing the NAD + kinase gene ppnk from Clostridium glutamicum and the NADP + -dependent gapCcae from Clostridium acetobutyricum and (2) knocking-out the endogenous sthA gene, which interacts with ilvC and panE in the D-PA biosynthesis pathway. Combined with transcriptome analysis, it was found that the membrane proteins OmpC and TolR promoted D-PA efflux by increasing membrane fluidity. Strain PA132 produced a D-PA titer of 83.26 g/L by two-stage fed-batch fermentation, which is the highest D-PA titer reported so far. This work established competitive producers for the industrial production of D-PA and provided an effective strategy for the production of related products.

Multidimensional engineering of Escherichia coli for efficient synthesis of L-tryptophan

Development of microbial cell factory for L-tryptophan (L-trp) production has received widespread attention but still requires extensive efforts due to weak metabolic flux distribution and low yield. Here, the riboswitch-based high-throughput screening (HTS) platform was established to construct a powerful L-trp-producing chassis cell. To facilitate L-trp biosynthesis, gene expression was regulated by promoter and N-terminal coding sequences (NCS) engineering. Modules of degradation, transport and by-product synthesis related to L-trp production were also fine-tuned. Next, a novel transcription factor YihL was excavated to negatively regulate L-trp biosynthesis. Self-regulated promoter-mediated dynamic regulation of branch pathways was performed and cofactor supply was improved for further L-trp biosynthesis. Finally, without extra addition, the yield of strain Trp30 reached 42.5 g/L and 0.178 g/g glucose after 48 h of cultivation in 5-L bioreactor. Overall, strategies described here worked up a promising method combining HTS and multidimensional regulation for developing cell factories for products in interest.

Systematic engineering of Escherichia coli for efficient production of nicotinamide riboside from nicotinamide and 3-cyanopyridine

Nicotinamide riboside (NR), a key biosynthetic precursor of NAD⁺, is receiving increasing attention because of its role. In this study, a whole-cell catalysis method to efficiently synthesize NR was established. First, the performance of 5'-nucleotidase (UshA) from Escherichia coli was confirmed to have high catalytic activity to synthesize NR. Then, the endogenous NR degradation pathway was detected, and the genes (rihA, rihB, and rihC) involved in NR degradation were knocked out, which enabled NR biosynthesis. In addition, the important role of the signal peptide of UshA in NR transport had been confirmed. Subsequently, nitrile hydratase was introduced to achieve the conversion of 3-cyanopyridine to NR. Finally, the NR titer reached 25.6 and 29.8 g/L with nicotinamide and 3-cyanopyridine, respectively, as substrates in a 5-L bioreactor, the efficient biosynthesis of NR in E. coli by using nicotinamide and 3-cyanopyridine.

Tuning an efficient Escherichia coli whole-cell catalyst expressing l-pantolactone dehydrogenase for the biosynthesis of d-(-)-pantolactone

d-(-)-Pantolactone (DPL) is a key intermediate for the production of d-(+)-pantothenate (vitamin B5). Deracemization of d,l-pantolactone (D,L-PL) through oxidizing l-(+)-pantolactone (LPL) to ketopantoyl lactone (KPL) and subsequently reducing KPL to DPL is a promising route for synthesizing DPL. Herein, a newly mined l-pantolactone dehydrogenase from Rhodococcus hoagie (RhoLPLDH) was used for the oxidative dehydrogenation of LPL. To alleviate inclusion bodies formed by membrane-bound RhoLPLDH intracellular expression in E. coli, strategies involving chaperone assistance and decreasing induction temperature were used to achieve RhoLPLDH soluble expression. To enhance its activity, directed evolution and hydrophilicity-based engineering yielded increased catalytic activity and thermostability. 1M LPL was efficiently converted to KPL by engineering strain CM5 co-expressing RhoLPLDH^{L254I/V241I/I156L/F224Q/N164K} and chaperone. A "two stages in one-pot" method was employed in deracemization of 1M D,L-PL with 91.2% yield. These results demonstrated that CM5 catalyst exhibits great potential in enzyme cascade deracemization for the production of DPL.