Improving L-threonine production in Escherichia coli by elimination of transporters ProP and ProVWX

Engineering Escherichia coli for high-yielding 2,5-Dimethylpyrazine synthesis from L-Threonine by reconstructing metabolic pathways and enhancing cofactors regeneration

2,5-Dimethylpyrazine (2,5-DMP) is important pharmaceutical raw material and food flavoring agent. Recently, engineering microbes to produce 2,5-DMP has become an attractive alternative to chemical synthesis approach. In this study, metabolic engineering strategies were used to optimize the modified Escherichia coli BL21 (DE3) strain for efficient synthesis of 2,5-DMP using L-threonine dehydrogenase (EcTDH) from Escherichia coli BL21, NADH oxidase (EhNOX) from Enterococcus hirae, aminoacetone oxidase (ScAAO) from Streptococcus cristatus and L-threonine transporter protein (EcSstT) from Escherichia coli BL21, respectively. We further optimized the reaction conditions for synthesizing 2,5-DMP. In optimized conditions, the modified strain can convert L-threonine to obtain 2,5-DMP with a yield of 2897.30 mg/L. Therefore, the strategies used in this study contribute to the development of high-level cell factories for 2,5-DMP.

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.

Characterization and Application of an Aspartate Dehydrogenase from Achromobacter denitrificans

A novel gene encoding aspartate dehydrogenase (ASPDH) has been discovered in Achromobacter denitrificans. The product of this gene has a strict dependence on NADH and demonstrated significant reductive activity towards not only oxaloacetate (OAA) but also 2-ketobutyric acid. Further enzymatic characterization revealed the kinetic parameters of ASPDH for OAA and 2-ketobutyric acid were as follows: Km values of 4.25 mM and 0.89 mM, Vmax values of 10.67 U mg-1 and 2.10 U mg-1, and Kcat values of 3.70 s-1 and 0.72 s-1, respectively. The enzyme also showed a dependency on metal ions, with EDTA and Cu2+ exerting strong inhibitory effects, while Ca2+ and Fe2+ exhibited pronounced enhancing effects. By utilizing a whole-cell biocatalyst system comprising glucose dehydrogenase (GDH) and ASPDH as a coupled system to replenish cofactors by oxidizing glucose, enabling the effective conversion of 2-ketobutyric acid to L-2-aminobutyric acid (L-2-ABA) with 97.2% yield.

Engineering of increased L-Threonine production in bacteria by combinatorial cloning and machine learning

The goal of this study is to develop a general strategy for bacterial engineering using an integrated synthetic biology and machine learning (ML) approach. This strategy was developed in the context of increasing L-threonine production in Escherichia coli ATCC 21277. A set of 16 genes was initially selected based on metabolic pathway relevance to threonine biosynthesis and used for combinatorial cloning to construct a set of 385 strains to generate training data (i.e., a range of L-threonine titers linked to each of the specific gene combinations). Hybrid (regression/classification) deep learning (DL) models were developed and used to predict additional gene combinations in subsequent rounds of combinatorial cloning for increased L-threonine production based on the training data. As a result, E. coli strains built after just three rounds of iterative combinatorial cloning and model prediction generated higher L-threonine titers (from 2.7 g/L to 8.4 g/L) than those of patented L-threonine strains being used as controls (4-5 g/L). Interesting combinations of genes in L-threonine production included deletions of the tdh, metL, dapA, and dhaM genes as well as overexpression of the pntAB, ppc, and aspC genes. Mechanistic analysis of the metabolic system constraints for the best performing constructs offers ways to improve the models by adjusting weights for specific gene combinations. Graph theory analysis of pairwise gene modifications and corresponding levels of L-threonine production also suggests additional rules that can be incorporated into future ML models.

Phenotype-genotype mapping reveals the betaine-triggered L-arginine overproduction mechanism in Escherichia coli

The production phenotype improvement of industrial microbes is extremely needed and challenging. Environmental factors optimization provides insightful ideas to trigger the superior production phenotype by activating potential genetic determiners. Here, phenotype-genotype mapping was used to dissect the betaine-triggered L-arginine overproduction mechanism and mine beneficial genes for further improving production phenotype. The comparative transcriptomic analysis revealed a novel role for betaine in modulating global gene transcription. Guided by this finding, 4 novel genes (cynX, cynT, pyrB, and rhaB) for L-arginine biosynthesis were identified via reverse engineering. Moreover, the rhaB deletion was demonstrated as a common metabolic engineering strategy to improve ATP pool in E. coli. By combinatorial genes manipulation, the L-arginine titer and yield increased by 17.9% and 28.9% in a 5-L bioreactor without betaine addition. This study revealed the molecular mechanism of gene transcription regulation by betaine and developed a superior L-arginine overproducer that does not require betaine.

Microbial Secondary Metabolites via Fermentation Approaches for Dietary Supplementation Formulations

Food supplementation formulations refer to products that are designed to provide additional nutrients to the diet. Vitamins, dietary fibers, minerals and other functional compounds (such as antioxidants) are concentrated in dietary supplements. Specific amounts of dietary compounds are given to the body through food supplements, and these include as well so-called non-essential compounds such as secondary plant bioactive components or microbial natural products in addition to nutrients in the narrower sense. A significant social challenge represents how to moderately use the natural resources in light of the growing world population. In terms of economic production of (especially natural) bioactive molecules, ways of white biotechnology production with various microorganisms have recently been intensively explored. In the current review other relevant dietary supplements and natural substances (e.g., vitamins, amino acids, antioxidants) used in production of dietary supplements formulations and their microbial natural production via fermentative biotechnological approaches are briefly reviewed. Biotechnology plays a crucial role in optimizing fermentation conditions to maximize the yield and quality of the target compounds. Advantages of microbial production include the ability to use renewable feedstocks, high production yields, and the potential for cost-effective large-scale production. Additionally, it can be more environmentally friendly compared to chemical synthesis, as it reduces the reliance on petrochemicals and minimizes waste generation. Educating consumers about the benefits, safety, and production methods of microbial products in general is crucial. Providing clear and accurate information about the science behind microbial production can help address any concerns or misconceptions consumers may have.

l-Threonine production from whey and fish hydrolysate by E. coli ATCC® 21277TM

In this work production of l-threonine by Escherichia coli ATCC® 21277™ has been studied using a mixture of alternative low-cost substrates, which are recognized to be a major pollution problem. Whey was used as the primary carbon source, whereas Red Tilapia (Oreochromis sp.) viscera hydrolysates constituted the nitrogen source. A Box-Behnken Design was used for optimizing l-threonine and biomass production, using temperature and glucose, whey, and Red Tilapia (Oreochromis sp.) viscera hydrolysate contents as factors. Results indicate that biomass production is affected by the concentration of hydrolysate and temperature. On the other hand, l-threonine production is affected by concentration of whey, hydrolysate, and temperature. In this context, it was possible to maximize l-threonine production, but with a detriment on biomass production. The optimal conditions for biomass and l-threonine maximization (after 24 h) were identified and validated experimentally, resulting in biomass and l-threonine production of 0.767 g/L and 0.406 g/L, respectively. This work has shown the technical feasibility of using whey and Red Tilapia (Oreochromis sp.) viscera hydrolysates for the production of l-threonine by E. coli ATCC® 21277TM. Finally, the complications associated to the use of these low-cost complex substrates for the production of l-threonine by E. coli, suggest that more in detail studies (i.e. at the metabolic level) are required in order to propose strategies to increase the process productivity, before its scale up. This is a first step in our long-term goal of developing a production process for i) dealing with the pollution problems caused by those wastes, and ii) strengthen the milk and fish industries which are important poles of the Colombian economy.

Overexpression of the key genes in the biosynthetic pathways of lipid A and peptidoglycan in Escherichia coli

Gram-negative bacterium Escherichia coli has a tripartite cell envelope with a cytoplasmic membrane, a peptidoglycan layer, and an asymmetric outer membrane containing lipopolysaccharide in its outer leaflet. The biogenesis of peptidoglycan and lipopolysaccharide shares the same substrate UDP-GlcNAc. From UDP-GlcNAc, MurA catalyzes the first reaction for peptidoglycan biosynthesis, while LpxA catalyzes the first reaction for lipopolysaccharide biosynthesis. This study demonstrates that murA overexpression in E. coli MG1655 inhibited the cell growth and increased the cell length, whereas lpxA overexpression in MG1655 neither inhibited the cell growth nor increased the cell length. Further study showed that individual overexpression of the other eight genes encoding the enzymes to catalyze the initial reactions in the biosynthetic pathway of lipopolysaccharide did not inhibit the cell growth. When MG1655/pBad-lpxA, MG1655/pBad-lpxD, and MG1655/pBad-lpxH were transformed with pFW01-thrA*BC-rhtC that contains the key genes for L-threonine biosynthesis and transport, the L-threonine production was increased. The L-threonine production in MG1655/pFW01-thrA*BC-rhtC/pBad-lpxH increased 46.1% as compared to the control MG1655/pFW01-thrA*BC-rhtC/pBad.

Enhancing caffeic acid production in Escherichia coli by engineering the biosynthesis pathway and transporter

Caffeic acid is a phenylpropanoid which is widely used in medical industry. Microbial fermentation provides a green strategy for producing caffeic acid. To improve the capacity for caffeic acid production in Escherichia coli, the competing pathways for l-tyrosine synthesis were knocked out. The biosynthesis pathway of the cofactor FAD and the expression of previously reported polyphenol transporters were enhanced to promote the production of caffeic acid. Transcriptomics analysis was conducted to mine potential transporters that could further enhance the titer of caffeic acid in engineered E. coli. Transcriptomics data of E. coli under caffeic acid and ferulic acid stress showed that 19 transporters were upregulated. Among them, overexpression of ycjP, which was previously identified as a sugar ABC transporter permease, improved the caffeic acid titer to 775.7 mg/L. The caffeic acid titer was further improved to 7922.0 mg/L in a 5-L fermenter, the highest titer achieved by microorganisms.

L-threonine promotes healthspan by expediting ferritin-dependent ferroptosis inhibition in C. elegans

The pathways that impact longevity in the wake of dietary restriction (DR) remain still ill-defined. Most studies have focused on nutrient limitation and perturbations of energy metabolism. We showed that the L-threonine was elevated in Caenorhabditis elegans under DR, and that L-threonine supplementation increased its healthspan. Using metabolic and transcriptomic profiling in worms that were fed with RNAi to induce loss of key candidate mediators. L-threonine supplementation and loss-of-threonine dehydrogenaseincreased the healthspan by attenuating ferroptosis in a ferritin-dependent manner. Transcriptomic analysis showed that FTN-1 encoding ferritin was elevated, implying FTN-1 is an essential mediator of longevity promotion. Organismal ferritin levels were positively correlated with chronological aging and L-threonine supplementation protected against age-associated ferroptosis through the DAF-16 and HSF-1 pathways. Our investigation uncovered the role of a distinct and universal metabolite, L-threonine, in DR-mediated improvement in organismal healthspan, suggesting it could be an effective intervention for preventing senescence progression and age-induced ferroptosis.

Toxicity and inhibition mechanism of gallic acid on physiology and fermentation performance of Escherichia coli

Gallic acid is a natural phenolic acid that has a stress inhibition effect on Escherichia coli. This study by integrates fermentation characteristics and transcriptional analyses to elucidate the physiological mechanism of E. coli 3110 response to gallic acid. Compared with the control (without stress), the cell growth was severely retarded, and irregular cell morphology appeared in the case of high levels of gallic acid stress. The glucose consumption of E. coli was reduced successively with the increase of gallic acid content in the fermentation medium. After 20 h of gallic acid stress, cofactor levels (ATP, NAD+ and NADH) of E. coli 3110 were similarly decreased, indicating a more potent inhibitory effect of gallic acid on E. coli. The transcriptional analysis revealed that gallic acid altered the gene expression profiles related to five notable differentially regulated pathways. The genes related to the two-component system were up-regulated, while the genes associated with ABC-transporter, energy metabolism, carbon metabolism, and fatty acid biosynthesis were down-regulated. This is the first report to comprehensively assess the toxicity of gallic acid on E. coli. This study has implications for the efficient production of phenolic compounds by E. coli and provides new ideas for the study of microbial tolerance to environmental stress and the identification of associated tolerance targets.

Improving CoQ10 productivity by strengthening glucose transmembrane of Rhodobacter sphaeroides

Background

Several Rhodobacter sphaeroides have been widely applied in commercial CoQ₁₀ production, but they have poor glucose use. Strategies for enhancing glucose use have been widely exploited in R. sphaeroides. Nevertheless, little research has focused on the role of glucose transmembrane in the improvement of production.

Results

There are two potential glucose transmembrane pathways in R. sphaeroides ATCC 17023: the fructose specific-phosphotransferase system (PTS^Fru, fruAB) and non-PTS that relied on glucokinase (glk). fruAB mutation revealed two effects on bacterial growth: inhibition at the early cultivation phase (12–24 h) and promotion since 36 h. Glucose metabolism showed a corresponding change in characteristic vs. the growth. For ΔfruAΔfruB, maximum biomass (Bio_max) was increased by 44.39% and the CoQ₁₀ content was 27.08% more than that of the WT. glk mutation caused a significant decrease in growth and glucose metabolism. Over-expressing a galactose:H⁺ symporter (galP) in the ΔfruAΔfruB relieved the inhibition and enhanced the growth further. Finally, a mutant with rapid growth and high CoQ₁₀ titer was constructed (ΔfruAΔfruB/tac::galP_OP) using several glucose metabolism modifications and was verified by fermentation in 1 L fermenters.

Conclusions

The PTS^Fru mutation revealed two effects on bacterial growth: inhibition at the early cultivation phase and promotion later. Additionally, biomass yield to glucose (Y_b/glc) and CoQ₁₀ synthesis can be promoted using fruAB mutation, and glk plays a key role in glucose metabolism. Strengthening glucose transmembrane via non-PTS improves the productivity of CoQ₁₀ fermentation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01695-z.