Enhanced Phenyllactic Acid Production in Escherichia coli Via Oxygen Limitation and Shikimate Pathway Gene Expression

Efficient production of phenyllactic acid in Escherichia coli via metabolic engineering and fermentation optimization strategies

Phenyllactic acid (PhLA), an important natural organic acid, can be used as a biopreservative, monomer of the novel polymeric material poly (phenyllactic acid), and raw material for various medicines. Herein, we achieved a high-level production of PhLA in Escherichia coli through the application of metabolic engineering and fermentation optimization strategies. First, the PhLA biosynthetic pathway was established in E. coli CGSC4510, and the phenylalanine biosynthetic pathway was disrupted to improve the carbon flux toward PhLA biosynthesis. Then, we increased the copy number of the key genes involved in the synthesis of the PhLA precursor phenylpyruvic acid. Concurrently, we disrupted the tryptophan biosynthetic pathway and enhanced the availability of phosphoenolpyruvate and erythrose 4-phosphate, thereby constructing the genetically engineered strain MG-P10. This strain was capable of producing 1.42 ± 0.02 g/L PhLA through shake flask fermentation. Furthermore, after optimizing the dissolved oxygen feedback feeding process and other conditions, the PhLA yield reached 52.89 ± 0.25 g/L in a 6 L fermenter. This study successfully utilized metabolic engineering and fermentation optimization strategies to lay a foundation for efficient PhLA production in E. coli as an industrial application.

Facemask acne attenuation through modulation of indirect microbiome interactions

During the COVID-19 pandemic, facemasks played a pivotal role in preventing person-person droplet transmission of viral particles. However, prolonged facemask wearing causes skin irritations colloquially referred to as 'maskne' (mask + acne), which manifests as acne and contact dermatitis and is mostly caused by pathogenic skin microbes. Previous studies revealed that the putative causal microbes were anaerobic bacteria, but the pathogenesis of facemask-associated skin conditions remains poorly defined. We therefore characterized the role of the facemask-associated skin microbiota in the development of maskne using culture-dependent and -independent methodologies. Metagenomic analysis revealed that the majority of the facemask microbiota were anaerobic bacteria that originated from the skin rather than saliva. Previous work demonstrated direct interaction between pathogenic bacteria and antagonistic strains in the microbiome. We expanded this analysis to include indirect interaction between pathogenic bacteria and other indigenous bacteria classified as either 'pathogen helper (PH)' or 'pathogen inhibitor (PIn)' strains. In vitro screening of bacteria isolated from facemasks identified both strains that antagonized and promoted pathogen growth. These data were validated using a mouse skin infection model, where we observed attenuation of symptoms following pathogen infection. Moreover, the inhibitor of pathogen helper (IPH) strain, which did not directly attenuate pathogen growth in vitro and in vivo, functioned to suppress symptom development and pathogen growth indirectly through PH inhibitory antibacterial products such as phenyl lactic acid. Taken together, our study is the first to define a mechanism by which indirect microbiota interactions under facemasks can control symptoms of maskne by suppressing a skin pathogen.

Enhanced production of itaconic acid from enzymatic hydrolysate of lignocellulosic biomass by recombinant Corynebacteriumglutamicum

Itaconic acid (IA) is a value-added chemical currently produced by Aspergillus terreus from edible glucose and starch but not from inedible lignocellulosic biomass owing to the high sensitivity to fermentation inhibitors present in the hydrolysate of lignocellulosic biomass. To produce IA from lignocellulosic biomass, a gram-positive bacterium, Corynebacterium glutamicum, with a high tolerance to fermentation inhibitors was metabolically engineered to express a fusion protein composed of cis-aconitate decarboxylase from A. terreus responsible for IA formation from cis-aconitate and a maltose-binding protein (malE) from Escherichia coli. The codon-optimized cadA_malE gene was expressed in C. glutamicum ATCC 13032, and the resulting recombinant strain produced IA from glucose. IA concentration increased 4.7-fold by the deletion of the ldh gene encoding lactate dehydrogenase. With the Δldh strain HKC2029, an 18-fold higher IA production was observed from enzymatic hydrolysate of kraft pulp as a model lignocellulosic biomass than from glucose (6.15 and 0.34 g/L, respectively). The enzymatic hydrolysate of kraft pulp contained various potential fermentation inhibitors involved in furan aldehydes, benzaldehydes, benzoic acids, cinnamic acid derivatives, and aliphatic acid. Whereas cinnamic acid derivatives severely inhibited IA production, furan aldehydes, benzoic acids, and aliphatic acid improved IA production at low concentrations. The present study suggests that lignocellulosic hydrolysate contains various potential fermentation inhibitors; however, some of them can serve as enhancers for microbial fermentation likely due to the changing of redox balance in the cell.

Recent development of phenyllactic acid: physicochemical properties, biotechnological production strategies and applications

Phenyllactic acid (PLA) is capable of inhibiting the growth of many microorganisms, showing a broad-spectrum antimicrobial property, which allows it to hold vast applications in the: food, feed, pharmaceutical, and cosmetic industries, especially in the field of food safety. Recently, the production of PLA has garnered considerable attention due to the increasing awareness of food safety from the public. Accordingly, this review mainly updates the recent development for the production of PLA through microbial fermentation and whole-cell catalysis (expression single-, double-, and triple-enzyme) strategies. Firstly, the: physicochemical properties, existing sources, and measurement methods of PLA are systematically covered. Then, the inhibition spectrum of PLA is summarized, and synchronously, the antimicrobial and anti-biofilm mechanisms of PLA on commonly pathogenic microorganisms in foods are described in detail, thereby clarifying the reason for extending the shelf life of foods. Additionally, the factors affecting the production of PLA are summarized from the biosynthesis and catabolism pathway of PLA in microorganisms, as well as external environmental parameters insights. Finally, the downstream treatment process and applications of PLA are discussed and outlined. In the future, clinical data should be supplemented with the metabolic kinetics of PLA in humans and to evaluate animal toxicology, to enable regulatory use of PLA as a food additive. A food-grade host, such as Bacillus subtilis and Lactococcus lactis, should also be developed as a cell vector expressing enzymes for PLA production from a food safety perspective.

Redefining methods for augmenting lactic acid bacteria robustness and phenyllactic acid biocatalysis: Integration valorizes simplicity

The production of phenyllactic acid (PLA) has been reported by several researchers, but so far, no mention has been made of augmented PLA production using an orchestrated assembly of simple techniques integrated to improve lactic acid bacteria (LAB) metabolism for the same. This review summarizes sequentially tailoring LAB growth and metabolism for augmented PLA catalysis through several strategies like monitoring LAB sustenance by choosing appropriate starter PLA-producing LAB strains isolated from natural environments, with desirably fastidious growth rates, properties like acidification, proteolysis, bacteriophage-resistance, aromatic/texturing-features, etc.; entrapping chosen LAB strains in novel cryogels and/or co-cultivating two/more LAB strains to improve their biotransformation potential and promote growth dependency/sustainability; adopting adaptive evolution methods designed to improve LAB strains under selection pressure inducing desired phenotypes tolerant to stress factors like heat, salt, acid, and solvent; monitoring physico-chemical LAB fermentation factors like temperature, pH, dissolved oxygen content, enzymes, and cofactors for PLA biosynthesis; and modulating purification/downstream processes to extract substantial PLA yields. This review paper serves as a comprehensive preliminary guide that can evoke a strategic experimental plan to produce industrial-scale PLA yields using simple techniques orchestrated together in the pursuit of conserving time, effort, and resources.

Simultaneous improvement of the thermostability and activity of lactic dehydrogenase from Lactobacillus rossiae through rational design

d-Phenyllactic acid, is a versatile organic acid with wide application prospects in the food, pharmaceutical and material industries. Wild-type lactate dehydrogenase LrLDH from Lactobacillus rossiae exhibits a high catalytic performance in the production of d-phenyllactic acid from phenylpyruvic acid or sodium phenylpyruvate, but its industrial application is hampered by poor thermostability. Here, computer aided rational design was applied to improve the thermostability of LrLDH. By using HotSpot Wizard 3.0, five hotspot residues (N218, L237, T247, D249 and S301) were identified, after which site-saturation mutagenesis and combined mutagenesis were performed. The double mutant D249A/T247I was screen out as the best variant, with optimum temperature, t_1/2, and T¹⁰₅₀ that were 12 °C, 17.96 min and 19 °C higher than that of wild-type LrLDH, respectively. At the same time, the k_cat/K_m of D249A/T247I was 1.47 s⁻¹ mM⁻¹, which was 3.4 times higher than that of the wild-type enzyme. Thus rational design was successfully applied to simultaneously improve the thermostability and catalytic activity of LrLDH to a significant extent. The results of molecular dynamics simulations and molecular structure analysis could explain the mechanisms for the improved performance of the double mutant. This study shows that computer-aided rational design can greatly improve the thermostability of d-lactate dehydrogenase, offering a reference for the modification of other enzymes.

The d-LDH was engineered using computationally-assisted rational mutagenesis. The two mutants D249A and D249A/T247I showed significantly enhanced thermostability and catalytic activity to sodium phenylpyruvate compared with the wild-type enzyme.

Enhanced production of γ-amino acid 3-amino-4-hydroxybenzoic acid by recombinant Corynebacterium glutamicum under oxygen limitation

Background

Bio-based aromatic compounds are of great interest to the industry, as commercial production of aromatic compounds depends exclusively on the unsustainable use of fossil resources or extraction from plant resources. γ-amino acid 3-amino-4-hydroxybenzoic acid (3,4-AHBA) serves as a precursor for thermostable bioplastics.

Results

Under aerobic conditions, a recombinant Corynebacterium glutamicum strain KT01 expressing griH and griI genes derived from Streptomyces griseus produced 3,4-AHBA with large amounts of amino acids as by-products. The specific productivity of 3,4-AHBA increased with decreasing levels of dissolved oxygen (DO) and was eightfold higher under oxygen limitation (DO = 0 ppm) than under aerobic conditions (DO ≥ 2.6 ppm). Metabolic profiles during 3,4-AHBA production were compared at three different DO levels (0, 2.6, and 5.3 ppm) using the DO-stat method. Results of the metabolome analysis revealed metabolic shifts in both the central metabolic pathway and amino acid metabolism at a DO of < 33% saturated oxygen. Based on this metabolome analysis, metabolic pathways were rationally designed for oxygen limitation. An ldh deletion mutant, with the loss of lactate dehydrogenase, exhibited 3.7-fold higher specific productivity of 3,4-AHBA at DO = 0 ppm as compared to the parent strain KT01 and produced 5.6 g/L 3,4-AHBA in a glucose fed-batch culture.

Conclusions

Our results revealed changes in the metabolic state in response to DO concentration and provided insights into oxygen supply during fermentation and the rational design of metabolic pathways for improved production of related amino acids and their derivatives.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01714-z.

The Protein Interactome of Glycolysis in Escherichia coli

Glycolysis is regulated by numerous mechanisms including allosteric regulation, post-translational modification or protein-protein interactions (PPI). While glycolytic enzymes have been found to interact with hundreds of proteins, the impact of only some of these PPIs on glycolysis is well understood. Here we investigate which of these interactions may affect glycolysis in E. coli and possibly across numerous other bacteria, based on the stoichiometry of interacting protein pairs (from proteomic studies) and their conservation across bacteria. We present a list of 339 protein-protein interactions involving glycolytic enzymes but predict that ~70% of glycolytic interactors are not present in adequate amounts to have a significant impact on glycolysis. Finally, we identify a conserved but uncharacterized subset of interactions that are likely to affect glycolysis and deserve further study.

Dissolved-oxygen feedback control fermentation for enhancing β-carotene in engineered Yarrowia lipolytica

The DO-stat fed-batch fermentation was carried out to explore the volumetric productivity of β-carotene in engineered Yarrowia lipolytica C11 strain. Using DO-stat fed-batch fermentation, we achieved 94 g/L biomass and 2.01 g/L β-carotene. Both biomass and β-carotene were about 1.28-fold higher than that in fed-batch fermentation. The ATP, NADP+/NADPH, and gene expression levels of tHMG, GGS1, carRA, and carB were promoted as compared to that in fed-batch fermentation. As for as the kinetic parameters in DO-stat fed-batch fermentation, μm', Yx/s', and Yp/s' was 0.527, 0.353, and 0.158, respectively. The μm' was elevated 4.66-fold than that in fed-batch fermentation. These data illustrate that more dissolved oxygen increased the biomass. The Yx/s' and Yp/s' were increased 1.15 and 22.57-fold, which suggest that the DO-stat fed-batch fermentation reduced the Crabtree effect and improved the utilization rate of glucose. Therefore, DO-stat fed-batch fermentation is a promising strategy in the industrialized production of β-carotene.

Cecal Butyrate (Not Propionate) Was Connected with Metabolism-Related Chemicals of Mice, Based on the Different Effects of the Two Inonotus obliquus Extracts on Obesity and Their Mechanisms

Obesity is a metabolic disease and causes significant changes in host and gut microbial metabolite levels. However, little research has been done on the relationship between host and gut microbial metabolites. Thus, this study investigated the connection of the chemicals, based on the different effects of two Inonotus obliquus extracts on high-fat-diet-induced mice and their mechanisms. In this study, C57BL6/J mice fed with a high-fat diet were given I. obliquus ethanol extract (IOE) and polysaccharide (IOP). ¹H NMR-based metabolomics, 16S rRNA sequencing, and real-time reverse transcription polymerase chain reaction (RT-PCR) were used to detect metabolites, cecal microbes, and expressions of genes in liver. IOE and IOP effectively improved the obesity of mice, including the adjustment of body weight gain, energy intake, energy efficiency, liver glucose metabolism and triglyceride metabolism, tricarboxylic acid (TCA) cycle, and degradation of three major nutrients (carbohydrate, lipid, and protein). IOE significantly increased cecal propionate based on Bacteroides and Akkermansia, thereby inhibiting energy intake and fat accumulation in mice. IOP remarkably improved the level of cecal butyrate by Lactobacillus and the Bacteroidales S24-7 group, resulting in increased energy consumption, and fat degradation by regulating the TCA cycle of the host. Two extracts containing different bioactive substances of I. obliquus improved obesity in mice through different effects on production of cecal microbial metabolites. Moreover, cecal butyrate (not propionate) was connected with chemicals of mice, including four metabolites of the TCA cycle and other metabolism-related chemicals.

Metabolic engineering of Escherichia coli for production of chemicals derived from the shikimate pathway

The shikimate pathway is indispensable for the biosynthesis of natural products with aromatic moieties. These products have wide current and potential applications in food, cosmetics and medicine, and consequently have great commercial value. However, compounds extracted from various plants or synthesized from petrochemicals no longer satisfy the requirements of contemporary industries. As a result, an increasing number of studies has focused on this pathway to enable the biotechnological manufacture of natural products, especially in E. coli. Furthermore, the development of synthetic biology, systems metabolic engineering and high flux screening techniques has also contributed to improving the biosynthesis of high-value compounds based on the shikimate pathway. Here, we review approaches based on a combination of traditional and new metabolic engineering strategies to increase the metabolic flux of the shikimate pathway. In addition, applications of this optimized pathway to produce aromatic amino acids and a range of natural products is also elaborated. Finally, this review sums up the opportunities and challenges facing this field.

Combination of multi-enzyme expression fine-tuning and co-substrates addition improves phenyllactic acid production with an Escherichia coli whole-cell biocatalyst

The aim of this study was to develop an environmentally safe and efficient method for phenyllactic acid (PLA) production using whole-cell cascade catalysis with l-amino acid deaminase (l-AAD), lactate dehydrogenase (LDH), and formate dehydrogenase (FDH). The PPA titer was low due to relatively low expression of LDH, intermediate accumulation, and lack of cofactors. To address this issue, ribosome binding site regulation, gene duplication, and induction optimization were performed to increased the PLA titer to 43.8 g/L. Then co-substrates (glucose, yeast extract, and glycerol) were used to increase NADH concentration and cell stability, resulting that the PLA titer was increased to 54.0 g/L, which is the highest reported production by biocatalyst. Finally, glucose was replaced with wheat straw hydrolysate as co-substrate to decrease the cost. Notably, the strategies reported herein may be generally applicable to other whole-cell cascade biocatalysts.