Metabolic engineering and fermentation optimization strategies for producing organic acids of the tricarboxylic acid cycle by microbial cell factories

A Green Analytical Method for Differentiating Fresh and Stored Green Teas via Determining Their Tricarboxylic Acid Organic Acids

RATIONALE

TEA IS A POPULAR NONALCOHOLIC BEVERAGE; NEVERTHELESS, SOME TRADERS UTILIZE STORED TEA AS A SUBSTITUTE FOR FRESH TEA, A PRACTICE THAT HAS HAD A NASTY EFFECT ON THE MARKET. THEREBY, IT IS NECESSARY TO DEVELOP AN OBJECTIVE METHOD TO DISTINGUISH BETWEEN FRESH AND STORED TEA SAMPLES.: METHODS: IN THIS WORK, A SIMPLE METHOD HAS BEEN DEVELOPED FOR THE DETERMINATION OF EIGHT ORGANIC ACIDS OF THE TRICARBOXYLIC ACIDS (OTCAS), INCLUDING CITRIC ACID, MALIC ACID, Α-KETOGLUTARIC ACID, CIS-ACONITIC ACID, SUCCINIC ACID, MALONIC ACID, AND FUMARIC ACID, IN 38 TEA SAMPLES. THE EXTRACTION AND PRETREATMENT OF OTCA IN TEA WERE CONDUCTED USING A 0.1% FORMIC ACID SOLUTION AND ACTIVATED CARBON.: RESULTS: THE LOQ (10 S/N) OF THE METHOD IS BETWEEN 0.47 AND 0.9 NG/ML, THE METHOD RSD ≤ 10%, THE SURFACE METHOD IS STABLE AND RELIABLE, AND THE AGREEPREP SCORE, WHICH CORRESPONDS TO THE METHOD'S PERFORMANCE, WAS CALCULATED TO BE 0.59, INDICATING THAT THE METHOD ALIGNS WITH THE PRINCIPLES OF GREEN ANALYTICAL CHEMISTRY. THEN, THESE OTCAS IN 38 TEA SAMPLES WERE SIMULTANEOUSLY DETERMINED BY LC-MS ANALYSIS OF THE EXTRACT.: CONCLUSION: IT IS NOTEWORTHY THAT DISTINCTIVE DIFFERENCES IN THE CONCENTRATION HAVE BEEN OBTAINED FOR MALIC ACID, SUCCINIC ACID, AND Α-KETOGLUTARIC ACID IN THE FRESH TEA VERSUS THE STORED TEA, RESPECTIVELY, INDICATING THAT THESE OTCAS CAN BE SELECTED AS THE POTENTIAL BIOMARKERS FOR THE DIFFERENTIATION OF STORED TEA SAMPLES FROM FRESH ONES.

Metabolic engineering of Corynebacterium glutamicum for highly selective production of 5-hydroxyvaleric acid

The biosynthesis of 5-hydroxyvaleric acid (5-HV) from glucose via the l-lysine degradation pathway cocurrently generates by-products, including l-lysine, 5-aminovaleric acid (5-AVA), and glutaric acid (GTA), which are closely interconnected with the 5-HV biosynthesis pathway. This study focuses on developing a highly selective 5-HV production system in Corynebacterium glutamicum. Initial strategies, such as using sorbitol as a co-substrate, deleting the endogenous GTA biosynthesis pathway, and incorporating a GTA recycling system, were insufficient to achieve selectivity. To address this, a combination of strategies was implemented, including deletion of the endogenous GTA biosynthesis pathway, incorporation of a GTA recycling pathway, removal of the l-lysine exporter gene (lysE), and integration of a l-lysine conversion module. These modifications synergistically enhanced 5-HV selectivity. The final engineered strain, which lacked lysE and gabD2 genes and overexpressed the 5-HV biosynthesis and GTA recycling modules, achieved 88.23 g/L of 5-HV in fed-batch fermentation. By-product levels were significantly reduced to 3.28 g/L of GTA, 1.16 g/L of 5-AVA, and no detectable l-lysine. With this highly selective 5-HV biosynthesis system, δ-valerolactone (DVL) was synthesized via acid treatment of microbially produced 5-HV, achieving a 65% conversion efficiency. This approach presents a more environmentally friendly and sustainable method for producing DVL, a valuable C5 solvent with industrial applications.

Nicotinamide Mononucleotide Production in Metabolically Engineered Saccharomyces cerevisiae

Nicotinamide mononucleotide (NMN) is an essential precursor in the biosynthesis of nicotinamide adenine dinucleotide (NAD+), a critical cofactor in cellular metabolism and energy regulation. With the growing interest in NMN for its antiaging and therapeutic benefits, microbial production systems, particularly Saccharomyces cerevisiae, offer a promising alternative to traditional chemical synthesis. This study explored the optimization of NMN production in S. cerevisiae BY4742 using both constitutive and inducible promoters. Yeast strains were engineered to express human nicotinamide phosphoribosyl transferase (h-NAMPT) and yeast phosphoribosyl pyrophosphate synthetase (PRS5 and PRS2) to enable the direct conversion of nicotinamide (NAM) to NMN. The genes were expressed under the control of GAL1 (inducible) and TEF1 (constitutive) promoters in the plasmids. The results demonstrated that strains with the TEF1 constitutive promoter produced higher levels of intracellular NMN and NAD+ compared with those using the GAL1 inducible promoter. Additionally, fermentation in a rich R-SD medium further enhanced NMN production, with the scTEF2g strain (overexpressing plasmid-based h-NAMPT and PRS5 genes under the TEF1 promoter) achieving 151.71 mg/L NMN, a 3-fold increase in NMN yield compared to the control strain. This is the highest intracellular NMN produced in recombinant yeast from NAM in a flask. This work highlights the importance of gene regulation through promoter selection and culture optimization in maximizing NMN yields, presenting yeast-based systems as a promising platform for NMN production from NAM.

Issatchenkia orientalis as a platform organism for cost-effective production of organic acids

Driven by the urgent need to reduce the reliance on fossil fuels and mitigate environmental impacts, microbial cell factories capable of producing value-added products from renewable resources have gained significant attention over the past few decades. Notably, non-model yeasts with unique physiological characteristics have emerged as promising candidates for industrial applications, particularly for the production of organic acids. Among them, Issatchenkia orientalis stands out for its exceptional natural tolerance to low pH and high osmotic pressure, traits that are critical for overcoming the limitations of conventional microbial organisms. The acid tolerance of I. orientalis enables organic acid production under low pH conditions, bypassing the need for expensive neutral pH control typically required in conventional processes. Organic acids produced by I. orientalis, such as lactic acid, succinic acid, and itaconic acid, are widely used as building blocks for bioplastics, food additives, and pharmaceuticals. This review summarizes the key findings from systems biology studies on I. orientalis over the past two decades, providing insights into its unique metabolic and physiological traits. Advances in genetic tool development for this non-model yeast are also discussed, enabling targeted metabolic engineering to enhance its production capabilities. Additionally, case studies are highlighted to illustrate the potential of I. orientalis as a platform organism. Finally, the remaining challenges and future directions are addressed to further develop I. orientalis into a robust and versatile microbial cell factory for sustainable biomanufacturing.

Engineering Escherichia coli for Anaerobic Succinate Fermentation Using Corn Stover Hydrolysate as a Substrate

Succinic acid is regarded as one of the most important platform chemicals used in materials science, chemistry, and food industrial applications. Currently, the main bottlenecks in the microbial succinate synthesis lie in the low titer, cofactor imbalance, and high production costs. To overcome these challenges, the reductive tricarboxylic acid cycle (TCA) and glucose uptake pathway were enhanced, increasing the titer of succinate to 4.31 g/l, 2.06-fold of the original strain. Furthermore, formate dehydrogenase from Candida boidinii was simultaneously overexpressed to increase the regeneration of NADH which was deficient in succinate synthesis under anaerobic condition. On this basis, the oxygen-responsive biosensor was used to replace the isopropyl-β-d-thiogalactoside (IPTG)-induction system, enabling strain to avoid the utilization of IPTG for succinate production. Using corn stover hydrolysate as the substrate, the optimum strain produced 60.74 g/l succinate in 5 L bioreactor. The engineered strain exhibited high succinate titer using biomass hydrolysate as substrate, significantly reduced the fermentation cost.

Progress on production of malic acid and succinic acid by industrially-important engineered microorganisms

Organic acids are widely used as additives in the food, pharmaceutical, chemical, and plastic industries. Currently, the industrial production methods of organic acids mainly include plant extraction and chemical synthesis. The latter mainly uses petroleum-based compounds as raw materials to synthesize organic acids through a series of chemical reactions. All of these methods have problems such as environmental pollution, high cost, and unsustainability. By contrast, microbial fermentation can effectively utilize a variety of carbon sources. Due to its low production cost, environmental friendliness, and high product purity, microbial fermentation has received increasing attention in recent years. However, the low yield and long fermentation cycle of microbial fermentation limits its industrial application. With the development of genomics, transcriptomics, and other omics technologies, the metabolic pathways of various strains producing organic acids have gradually been elucidated. Based on this, new technologies such as synthetic biology and high-throughput screening have also been extensively studied. This review summarizes the latest research progress in improving organic acid biosynthesis through metabolic engineering, focusing on L-malic acid (L-MA) and succinic acid (SA). Finally, we also discuss the challenges and future prospects of this field. This review has important reference value in the fields of food, pharmaceuticals, and chemicals, providing a theoretical basis for the study of organic acid biosynthesis.

Advancements in metabolic engineering: unlocking the potential of key organic acids for sustainable industrial applications

This review explores the advancements, application potential, and challenges of microbial metabolic engineering strategies for sustainable organic acid production. By integrating gene editing, pathway reconstruction, and dynamic regulation, microbial platforms have achieved enhanced biosynthesis of key organic acids such as pyruvate, lactic acid, and succinic acid. Strategies including by-product pathway knockout, key enzyme overexpression, and improved CO2 fixation have contributed to higher production efficiency. Additionally, utilizing non-food biomass sources, such as lignocellulose, algal feedstocks, and industrial waste, has reduced reliance on conventional carbon sources, supporting sustainability goals. However, challenges remain in substrate inhibition, purification complexity, and metabolic flux imbalances. Addressing these requires omics-driven metabolic optimization, stress-resistant strain development, and biorefinery integration. Future research should focus on system-level design to enhance cost-effectiveness and sustainability, advancing industrial bio-manufacturing of organic acids.

Myceliophthora thermophila as promising fungal cell factories for industrial bioproduction: From rational design to industrial applications

Myceliophthora thermophila stands out as a prominent fungal cell factory, garnering growing interest due to its distinctive traits advantageous. Currently, M. thermophila has been developed as an efficient cell factory, producing a variety of products from various raw materials. In this review, we firstly discuss the potential advantages of M. thermophila as a platform for metabolic engineering and industrial applications, with special emphasis on its physiological characteristics, the development of genetic modification techniques and tools, gene expression and regulation strategies. Then, the latest progress in industrial application of M. thermophila as microbial cell factory was systematically summarized, including biochemical synthesis platform, enzyme expression platform, antibody protein and vaccine production platform, bio-organic fertilizer production platform, and efficient enzyme element library. Finally, the current challenges of M. thermophila as a cell factory and its corresponding strategies are proposed, aiming to achieve green biomanufacturing of multiple products with higher efficiency.

Creation of a eukaryotic multiplexed site-specific inversion system and its application for metabolic engineering

The site-specific recombination system is a versatile tool in genome engineering, enabling controlled DNA inversion or deletion at specific sites to generate genetic diversity. The multiplexed inversion system, which preferentially facilitates inversion at reverse-oriented sites rather than deletion at same-oriented sites, has not been found in eukaryotes. Here, we establish a multiplexed site-specific inversion system, Rci51-5/multi-sfxa101, in yeast. Firstly, we develop a high-throughput screening system based on the on/off transcriptional control of multiple markers by DNA inversion. After two rounds of progressively stringent directed evolution, a mutant Rci51-5 shows an ability of multisite inversion and a ~ 1000-fold increase in total inversion efficiency against the wild-type Rci derived from Salmonella typhimurium. Subsequently, we demonstrate that the Rci51-5/multi-sfxa101 system exhibits significantly lower deletion rate than the Cre/multi-loxP system. Using the synthetic metabolic pathway of β-carotene as an example, we illustrate that the system can effectively facilitate promoter substitution in the metabolic pathway, resulting in a more than 7-fold increase in the yield of β-carotene. In summary, we develop a multiplexed site-specific inversion system in eukaryotes, providing an approach to metabolic engineering and a tool for eukaryotic genome manipulation.

Enhanced degradation of exogenetic citrinin by glycosyltransferases in the oleaginous yeast Saitozyma podzolica zwy-2-3

The contamination by the toxin citrinin (CIT), produced by fungi, has been reported in agricultural foods and is known to be nephrotoxic to humans. In this study, we found that CIT could be effectively degraded by the oleaginous yeast Saitozyma podzolica zwy-2-3. Four genes encoding glycosyltransferases (GTs) in S. podzolica zwy-2-3 (SPGTs) were identified by evolutionary and structural analyses. The overexpression of SPGTs enhanced CIT degradation to 0.56 mg/L/h in S. podzolica zwy-2-3 by increasing ATP and glutathione (GSH) contents to oxidize CIT and scavenge reactive oxygen species (ROS). Besides, SPGTs promoted lipid synthesis by 9.3 % of S. podzolica zwy-2-3 under CIT stress. These results suggest that SPGTs in oleaginous yeast play a pivotal role in enhancing CIT degradation and lipid accumulation. These findings provide a valuable basis for the application of GTs in oleaginous yeast to alleviate CIT contamination in agricultural production, which may contribute to food safety.

Optimization Co-Culture of Monascus purpureus and Saccharomyces cerevisiae on Selenium-Enriched Lentinus edodes for Increased Monacolin K Production

Selenium-enriched Lentinus edodes (SL) is a kind of edible fungi rich in organic selenium and nutrients. Monascus purpureus with high monacolin K (MK) production and Saccharomyces cerevisiae were selected as the fermentation strains. A single-factor experiment and response surface methodology were conducted to optimize the production conditions for MK with higher contents from selenium-enriched Lentinus edodes fermentation (SLF). Furthermore, we investigated the nutritional components, antioxidant capacities, and volatile organic compounds (VOCs) of SLF. The MK content in the fermentation was 2.42 mg/g under optimal fermentation conditions. The organic selenium content of SLF was 7.22 mg/kg, accounting for 98% of the total selenium content. Moreover, the contents of total sugars, proteins, amino acids, reducing sugars, crude fiber, fat, and ash in SLF were increased by 9%, 23%, 23%, 94%, 38%, 44%, and 25%, respectively. The antioxidant test results demonstrated that 1.0 mg/mL of SLF exhibited scavenging capacities of 40%, 70%, and 79% for DPPH, ABTS, and hydroxyl radicals, respectively. Using gas chromatography-ion mobility spectrometry technology, 34 unique VOCs were identified in SLF, with esters, alcohols, and ketones being the main components of its aroma. This study showed that fungal fermentation provides a theoretical reference for enhancing the nutritional value of SL.

Effect of sugar content on characteristic flavour formation of tomato sour soup fermented by Lacticaseibacillus casei H1 based on non-targeted metabolomics analysis

To reveal the formation mechanism of the characteristic flavour of tomato sour soup (TSS), metabolomics based on UHPLC-Q-TOF/MS was used to investigate the effect of sugar addition on TSS metabolomics during fermentation with Lacticaseibacillus casei H1. A total of 254 differentially abundant metabolites were identified in the 10% added-sugar group, which mainly belonged to organic acids and derivatives, fatty acyls, and organic oxygen compounds. Metabolic pathway analysis revealed that alanine aspartate and glutamate metabolism, valine leucine and isoleucine metabolism and butanoate metabolism were the potential pathways for the flavour of TSS formation. Lactic acid, acetic acid, Ala, Glu and Asp significantly contributed to the acidity and umami formation of TSS. This study showed that sugar regulation played an important role in the formation of the characteristic TSS flavour during fermentation, providing important support for understanding the formation mechanism of organic acids as the main characteristic flavour of TSS.

A Fermentation State Marker Rule Design Task in Metabolic Engineering

There are several ways in which mathematical modeling is used in fermentation control, but mechanistic mathematical genome-scale models of metabolism within the cell have not been applied or implemented so far. As part of the metabolic engineering task setting, we propose that metabolite fluxes and/or biomass growth rate be used to search for a fermentation steady state marker rule. During fermentation, the bioreactor control system can automatically detect the desired steady state using a logical marker rule. The marker rule identification can be also integrated with the production growth coupling approach, as presented in this study. A design of strain with marker rule is demonstrated on genome scale metabolic model iML1515 of Escherichia coli MG1655 proposing two gene deletions enabling a measurable marker rule for succinate production using glucose as a substrate. The marker rule example at glucose consumption 10.0 is: IF (specific growth rate μ is above 0.060 h-1, AND CO2 production under 1.0, AND ethanol production above 5.5), THEN succinate production is within the range 8.2-10, where all metabolic fluxes units are mmol ∗ gDW-1 ∗ h-1. An objective function for application in metabolic engineering, including productivity features and rule detecting sensor set characterizing parameters, is proposed. Two-phase approach to implementing marker rules in the cultivation control system is presented to avoid the need for a modeler during production.

Metabolic engineering combined with enzyme engineering for overproduction of ectoine in Escherichia coli

Ectoine, a natural protective agent, is naturally synthesized at low titers by some extreme environment microorganisms that are usually difficult to culture. There is a need for an efficient and eco-friendly ectoine production process. In this study, Escherichia coli BL21(DE3) with the ectABC gene cluster from Halomonas venusta achieved 1.7 g/L ectoine. After optimizing the expression plasmid, 2.1 g/L ectoine was achieved. Besides, the aspartate kinase mutant LysCT311I from Corynebacterium glutamicum and aspartate semialdehyde dehydrogenase from Halomonas elongata were overexpressed to increase precursors supply. Furthermore, the rate-limiting enzyme EctB was semirationally engineered, and the E407D mutation enhanced ectoine production by 13.8 %. To improve acetyl-CoA supply, the non-oxidative glycolysis pathway was introduced. Overall, the optimized strain ECT9-5 produced 67.1 g/L ectoine by fed-batch fermentation with a 0.3 g/g of glucose and the kinetic model resulted in a good fit.

Combinatorial protein engineering and transporter engineering for efficient synthesis of L-Carnosine in Escherichia coli

L-Carnosine has various physiological functions and is widely used in cosmetics, medicine, food additives, and other fields. However, the yield of L-Carnosine obtained by biological methods is far from the level of industrial production. Herein, a cell factory for efficient synthesis of L-Carnosine was constructed based on transporter engineering and protein engineering. Firstly, a dipeptidase (SmpepD) was screened from Serratia marcescens through genome mining to construct a cell factory for synthesizing L-Carnosine. Subsequently, through rationally designed SmPepD, a double mutant T168S/G148D increased the L-Carnosine yield by 41.6% was obtained. Then, yeaS, a gene encoding the exporter of L-histidine, was deleted to further increase the production of L-Carnosine. Finally, L-Carnosine was produced by one-pot biotransformation in a 5 L bioreactor under optimized conditions with a yield of 133.2 mM. This study represented the highest yield of L-Carnosine synthesized in microorganisms and provided a biosynthetic pathway for the industrial production of L-Carnosine.

New insight into the metabolic mechanism of a novel lipid-utilizing and denitrifying bacterium capable of simultaneous removal of nitrogen and grease through transcriptome analysis

Introduction

Issues related to fat, oil, and grease from kitchen waste (KFOG) in lipid-containing wastewater are intensifying globally. We reported a novel denitrifying bacterium Pseudomonas CYCN-C with lipid-utilizing activity and high nitrogen-removal efficiency. The aim of the present study was aim to explore the metabolic mechanism of the simultaneous lipid-utilizing and denitrifying bacterium CYCN-C at transcriptome level.

Methods

We comparatively investigated the cell-growth and nitrogen-removal performances of newly reported Pseudomonas glycinae CYCN-C under defined cultivation conditions. Transcriptome analysis was further used to investigate all pathway genes involved in nitrogen metabolism, lipid degradation and utilization, and cell growth at mRNA levels.

Results

CYCN-C could directly use fat, oil, and grease from kitchen waste (KFOG) as carbon source with TN removal efficiency of 73.5%, significantly higher than that (60.9%) with sodium acetate. The change levels of genes under defined KFOG and sodium acetate were analyzed by transcriptome sequencing. Results showed that genes cyo, CsrA, PHAs, and FumC involved in carbon metabolism under KFOG were significantly upregulated by 6.9, 0.7, 26.0, and 19.0-folds, respectively. The genes lipA, lipB, glpD, and glpK of lipid metabolic pathway were upregulated by 0.6, 0.4, 21.5, and 1.3-folds, respectively. KFOG also improved the denitrification efficiency by inducing the expression of the genes nar, nirB, nirD, and norR of denitrification pathways.

Conclusion

In summary, this work firstly provides valuable insights into the genes expression of lipid-utilizing and denitrifying bacterium, and provides a new approach for sewage treatment with reuse of KFOG wastes.