Microbial Biosynthesis of L-Malic Acid and Related Metabolic Engineering Strategies: Advances and Prospects

Enabling malic acid production from corn-stover hydrolysate in Lipomyces starkeyi via metabolic engineering and bioprocess optimization

BACKGROUND

Lipomyces starkeyi is an oleaginous yeast with a native metabolism well-suited for production of lipids and biofuels from complex lignocellulosic and waste feedstocks. Recent advances in genetic engineering tools have facilitated the development of L. starkeyi into a microbial chassis for biofuel and chemical production. However, the feasibility of redirecting L. starkeyi lipid flux away from lipids and towards other products remains relatively unexplored. Here, we engineer the native metabolism to produce malic acid by introducing the reductive TCA pathway and a C4-dicarboxylic acid transporter to the yeast.

RESULTS

Heterogeneous expression of two genes, the Aspergillus oryzae malate transporter and malate dehydrogenase, enabled L. starkeyi malic acid production. Overexpression of a third gene, the native pyruvate carboxylase, allowed titers to reach approximately 10 g/L during shaking flasks cultivations, with production of malic acid inhibited at pH values less than 4. Corn-stover hydrolysates were found to be well-tolerated, and controlled bioreactor fermentations on the real hydrolysate produced 26.5 g/L of malic acid. Proteomic, transcriptomic and metabolomic data from real and mock hydrolysate fermentations indicated increased levels of a S. cerevisiae hsp9/hsp12 homolog (proteinID: 101453), glutathione dependent formaldehyde dehydrogenases (proteinIDs: 2047, 278215), oxidoreductases, and expression of efflux pumps and permeases during growth on the real hydrolysate. Simultaneously, machine learning based medium optimization improved production dynamics by 18% on mock hydrolysate and revealed lower tolerance to boron (a trace element included in the standard cultivation medium) than other yeasts.

CONCLUSIONS

Together, this work demonstrated the ability to produce organic acids in L. starkeyi with minimal byproducts. The fermentation characterization and omic analyses provide a rich dataset for understanding L. starkeyi physiology and metabolic response to growth in hydrolysates. Identified upregulated genes and proteins provide potential targets for overexpression for improving growth and tolerance to concentrated hydrolysates, as well as valuable information for future L. starkeyi engineering work.

Carbon-conserving bioproduction of malate in an E. coli-based cell-free system

Formate, a biologically accessible form of CO2, has attracted interest as a renewable feedstock for bioproduction. However, approaches are needed to investigate efficient routes for biological formate assimilation due to its toxicity and limited utilization by microorganisms. Cell-free systems hold promise due to their potential for efficient use of carbon and energy sources and compatibility with diverse feedstocks. However, bioproduction using purified cell-free systems is limited by costly enzyme purification, whereas lysate-based systems must overcome loss of flux to background reactions in the cell extract. Here, we engineer an E. coli-based system for an eight-enzyme pathway from DNA and incorporate strategies to regenerate cofactors and minimize loss of flux through background reactions. We produce the industrial di-acid malate from glycine, bicarbonate, and formate by engineering the carbon-conserving reductive TCA and formate assimilation pathways. We show that in situ regeneration of NADH drives metabolic flux towards malate, improving titer by 15-fold. Background reactions can also be reduced 6-fold by diluting the lysate following expression and introducing chemical inhibitors of competing reactions. Together, these results establish a carbon-conserving, lysate-based cell-free platform for malate production, producing 64 μM malate after 8 h. This system conserves 43 % of carbon otherwise lost as CO2 through the TCA cycle and incorporates 0.13 mol CO2 equivalents/mol glycine fed. Finally, techno-economic analysis of cell-free malate production from formate revealed that the high cost of lysate is a key challenge to the economic feasibility of the process, even assuming efficient cofactor recycling. This work demonstrates the capabilities of cell-free expression systems for both the prototyping of carbon-conserving pathways and the sustainable bioproduction of platform chemicals.

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.

Morphological and metabolic changes in Changshan Huyou (Citrus changshan-huyou) following natural tetraploidization

BACKGROUND

Polyploids in citrus are generally used to improve crop varieties. Changshan Huyou (Citrus changshan-huyou) is a native citrus species in China that is highly adaptable and has pharmaceutical value. However, the influence in Changshan Huyou following polyploidization remains unclear. Here we evaluated the adult tetraploid scions of Changshan Huyou with contemporary diploid scions as the control in the phenotypic variations, metabolic alterations of fruits and associated transcriptomic changes.

RESULT

The tetraploid scions had rounder and thicker leaves, larger floral organs and fruits, and satisfactory viability of pollen grains and ovules. The tetraploid fruits accumulated lower levels of soluble solids but similar levels of organic acids. Metabolic profiling of three tissues of fruits revealed that most of 2064 differentially accumulated metabolites (DAMs), including flavonoids, lignans, and coumarins, were downregulated. In contrast, the upregulated DAMs mainly included alkaloids (clausine K and 2-(1-pentenyl)quinoline), amino acids (L-asparagine and L-ornithine), and terpenoids (deacetylnomilin and evodol) in tetraploid peels, as well as, flavonoids (neohesperidin and quercetin-5-O-β-D-glucoside) and organic acids (2-methylsuccinic acid and dimethylmalonic acid) in juice sacs. The upregulated genes were associated with phenylpropanoid biosynthesis, secondary metabolite biosynthesis, and the biosynthesis of various alkaloid pathways. Pearson Correlation Analysis showed that the upregulated genes encoding PEROXIDASE and CYTOCHROME P450 (CYP450) were closely related to the higher accumulation of amino acids and alkaloids in tetraploid peels, and up-regulated neohesperidin and quercetin glucoside were positively associated with FERULATE-5-HYDROXYLASE (F5H), CYP450 81Q32, FLAVONOID 3'-MONOOXYGENASE (F3'H), 4-COUMARATE-CoA LIGASE 1 (4CL1), and UDP-GLUCOSE FLAVONOID 3-O-GLUCOSYLTRANSFERASE (UFOG), as well as, some transcription factors in tetraploid juice sacs.

CONCLUSION

The tetraploid Changshan Huyou investigated here may be used in triploids breeding to produce seedless citrus, and for fruit processing on pharmaceutical purpose due to the alteration of metabolites following polyploidization.

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.

Coprinolide, a novel antifungal tricyclic polyketide with a rare furanone-fused chromene skeleton isolated from the mushroom Coprinus comatus

A search for antifungal compounds from the mushroom Coprinus comatus using a bioassay-guided chromatographic fractionation approach led to the discovery of a novel polyketide harboring a rare 3,3a,9,9a-tetrahydro-1H-furo[3,4-b]chromen-1-one skeleton. The novel compound was named coprinolide. The inhibitory activity and fungicidal potential of coprinolide were evaluated against five economically important plant-pathogenic fungi. Coprinolide showed inhibitory effects on conidial germination and germ tube elongation of all tested fungi. The strongest effect was observed for Colletotrichum orbiculare with half-maximal inhibitory concentrations of 7.1 ppm and 8.2 ppm for conidial germination and germ tube elongation, respectively. Furthermore, coprinolide exhibited fungicidal activity against the tested fungi by inhibiting conidial germination to conidial death as confirmed by fluorescence microscopy using fluorescein diacetate and propidium iodide. These findings showed the potential of the mushroom as a source of a novel bioactive compound with promising agricultural application as an antifungal agent against different plant-pathogenic fungi.

Enhanced lipid accumulation in microalgae Scenedesmus sp. under nitrogen limitation

Microalgae-based biofuel production is cost-effective only in a biorefinery, where valuable co-products offset high costs. Fatty acids produced by photosynthetic microalgae can serve as raw materials for bioenergy and pharmaceuticals. This study aims to understand the metabolic imprints of Scenedesmus sp. CABeR52, to decipher the physiological mechanisms behind lipid accumulation under nitrogen deprivation. Metabolomics profiles were generated using gas chromatography-mass spectrometry (GC-MS) of Scenedesmus sp. CABeR52 subjected to nutrient deprivation. Our initial data sets indicate that deprived cells have an increased accumulation of lipids (278.31 mg.g-1 dcw), 2.0 times higher than the control. The metabolomic profiling unveils a metabolic reprogramming, highlighting the upregulation of key metabolites involved in fatty acid biosynthesis, such as citric acid, succinic acid, and 2-ketoglutaric acid. The accumulation of trehalose, a stress-responsive metabolite, further underscores the microalga's adaptability. Interestingly, we found that a new fatty acid, nervonic acid, was identified in the complex, which has a significant role in brain development. These findings provide valuable insights into the metabolic pathways governing lipid accumulation in Scenedesmus sp., paving the way for its exploitation as a sustainable biofuel feedstock.

Different paths, same destination: Bisphenol A and its substitute induce the conjugative transfer of antibiotic resistance genes

Antibiotic resistance genes are primarily spread through horizontal gene transfer in aquatic environments. Bisphenols, which are widely used in industry, are pervasive contaminants in such environments. This study investigated how environmentally relevant concentrations of bisphenol A and its substitute (bisphenol S, Bisphenol AP and Bisphenol AF) affect the spread of antibiotic resistance genes among Escherichia coli. As a result, bisphenol A and its three substitutes were found to promote the RP4 plasmid-mediated conjugative transfer of antibiotic resistance genes with different promotive efficiency. Particularly, bisphenol A and bisphenol S were found to induce more than double the incidence of conjugation at 0.1 nmol/L concentration. They therefore were selected as model compounds to investigate the involved mechanisms. Surprisingly, both slightly inhibited bacterial activity, but there was no significant increase in cell death. Bisphenols exposure changed the polymeric substances excreted by the bacteria, increased the permeability of their cell membranes, induced the secretion of antioxidant enzymes and generated reactive oxygen species. They also affected the expression of genes related to conjugative transfer by upregulating replication and DNA transfer genes and downregulating global regulatory genes. It should be noted that gene expression levels were higher in the BPS-exposed group than in the BPA-exposed group. The synthesis of bacterial metabolites and functional components was also significantly affected by bisphenols exposure. This research has helped to clarify the potential health risks of bisphenol contamination of aquatic environments.

Spectroscopic Studies of Lanthanide(III) Complexes with L-Malic Acid in Binary Systems

Binary systems of lanthanide ions (La, Nd, Gd, Ho, Tb, and Lu) with L-malic acid in molar ratios of 1:1 and 1:2 were studied. This study was carried out in aqueous solutions, and the composition of the formed complexes was confirmed using computer data analysis. The overall stability constants of the complexes and the equilibrium constants of the reaction were determined. The effect of ligand concentration on the composition of the internal coordination sphere of the central atom was observed. Changes in the coordination sphere of lanthanide ions were confirmed by spectroscopic measurements.

Phosphate limitation enhances malic acid production on nitrogen-rich molasses with Ustilago trichophora

BACKGROUND

An important step in replacing petrochemical products with sustainable, cost-effective alternatives is the use of feedstocks other than, e.g., pure glucose in the fermentative production of platform chemicals. Ustilaginaceae offer the advantages of a wide substrate spectrum and naturally produce a versatile range of value-added compounds under nitrogen limitation. A promising candidate is the dicarboxylic acid malic acid, which may be applied as an acidulant in the food industry, a chelating agent in pharmaceuticals, or in biobased polymer production. However, fermentable residue streams from the food and agricultural industry with high nitrogen content, e.g., sugar beet molasses, are unsuited for processes with Ustilaginaceae, as they result in low product yields due to high biomass and low product formation.

RESULTS

This study uncovers challenges in evaluating complex feedstock applicability for microbial production processes, highlighting the role of secondary substrate limitations, internal storage molecules, and incomplete assimilation of these substrates. A microliter-scale screening method with online monitoring of microbial respiration was developed using malic acid production with Ustilago trichophora on molasses as an application example. Investigation into nitrogen, phosphate, sulphate, and magnesium limitations on a defined minimal medium demonstrated successful malic acid production under nitrogen and phosphate limitation. Furthermore, a reduction of nitrogen and phosphate in the elemental composition of U. trichophora was revealed under the respective secondary substrate limitation. These adaptive changes in combination with the intricate metabolic response hinder mathematical prediction of product formation and make the presented screening methodology for complex feedstocks imperative. In the next step, the screening was transferred to a molasses-based complex medium. It was determined that the organism assimilated only 25% and 50% of the elemental nitrogen and phosphorus present in molasses, respectively. Due to the overall low content of bioavailable phosphorus in molasses, the replacement of the state-of-the-art nitrogen limitation was shown to increase malic acid production by 65%.

CONCLUSION

The identification of phosphate as a superior secondary substrate limitation for enhanced malic acid production opens up new opportunities for the effective utilization of molasses as a more sustainable and cost-effective substrate than, e.g., pure glucose for biobased platform chemical production.

The forced activation of asexual conidiation in Aspergillus niger simplifies bioproduction

Aspergillus niger is an efficient cell factory for organic acids production, particularly l-malic acid, through genetic manipulation. However, the traditional method of collecting A. niger spores for inoculation is labor-intensive and resource-consuming. In our study, we used the CRISPR-Cas9 system to replace the promoter of brlA, a key gene in Aspergillus conidiation, with a xylose-inducible promoter xylP in l-malic acid-producing A. niger strain RG0095, generating strain brlAxylP. When induced with xylose in submerged liquid culture, brlAxylP exhibited significant upregulation of conidiation-related genes. This induction allowed us to easily collect an abundance of brlAxylP spores (>7.1 × 106/mL) in liquid xylose medium. Significantly, the submerged conidiation approach preserves the substantial potential of A. niger as a foundational cellular platform for the biosynthesis of organic acids, including but not limited to l-malic acid. In summary, our study offers a simplified submerged conidiation strategy to streamline the preparation stage and reduce labor and material costs for industrial organic acid production using Aspergillus species.

Untargeted metabolomics reveals intervention effects of wine-processed Schisandra chinensis polysaccharide on Alzheimer's disease mice

Schisandra chinensis (Turcz.) Baill (SC) is a traditional sedative in China, with wide applications for treating various neurological disorders. Its polysaccharide component has been gaining increased attention for its potential in nerve protection. While raw SC is the primary focus of current research, its processed products are primarily utilized as clinical medicines. Notably, limited research exists on the mechanisms underlying the effects of wine-processed Schisandra chinensis polysaccharide (WSCP) in Alzheimer's Disease (AD). Therefore, this study seeks to assess the therapeutic impact of WSCP on AD mice and investigate the underlying mechanisms through biochemical and metabolomics analyses. The results demonstrate that WSCP exerts significant therapeutic effects on AD mice by enhancing learning and memory abilities, mitigating hippocampal neuronal damage, reducing abnormal amyloid-beta (Aβ) deposition, and attenuating hyperphosphorylation of Tau. Biochemical analysis revealed that WSCP can increase SOD content and decrease MDA, IL-6, and TNF-α content in AD mice. Furthermore, serum metabolomic results showed that WSCP intervention can reverse metabolic disorders in AD mice. 43 endogenous metabolites were identified as potential biomarkers for WSCP treatment of AD, and the major metabolic pathways were Ala, Glu and Asp metabolism, TCA cycle. Overall, these findings will provide a basis for further development of WSCP.

Conditional expression of FumA in Aspergillus niger enhances synthesis of L-malic acid

Currently, the L-malic acid titer achieved through Aspergillus niger fermentation reaches 201 g/L, meeting industrial demands satisfactorily. However, the co-presence of structurally similar fumaric acid and succinic acid in fermentation products suggests a theoretical potential for further improvement in L-malic acid production. In the tricarboxylic acid cycle, fumarate reductase mediates the conversion of succinic acid to fumaric acid. Subsequently, fumarase catalyzes the conversion of fumaric acid to L-malic acid. Notably, both enzymatic reactions are reversible. Our investigation revealed that A. niger contains only one mitochondria-located fumarase FumA. Employing CRISPR-Cas9 technology, we performed a replacement of the fumA promoter with a doxycycline-induced promoter Tet. Under non-inducing condition, the conditional strain exhibited increased levels of fumaric acid and succinic acid. It strongly suggests that FumA mainly promotes the flow of fumaric acid to L-malic acid. Furthermore, a promoter PmfsA that is exclusively activated in a fermentation medium by calcium carbonate was identified through RNA-sequencing screening. Utilizing PmfsA to regulate fumA expression led to a 9.0% increase in L-malic acid titer, an 8.75% increase in yield (glucose to L-malic acid), and an 8.86% enhancement in productivity. This research serves as a significant step toward expediting the industrialization of L-malic acid synthesis via biological fermentation. Additionally, it offers valuable insights for the biosynthesis of other organic acids.IMPORTANCEThis study focuses on enhancing L-malic acid synthesis by modifying the tricarboxylic acid cycle within the mitochondria of Aspergillus niger. We emphasize the significant role of fumarase in converting fumaric acid into L-malic acid, enhancing our understanding of metabolic pathways in A. niger. The precise regulation of fumA is highlighted as a key factor in enhancing L-malic acid production. Furthermore, this research introduces a stringent conditional promoter (PmfsA), exclusively activated by CaCO3. The utilization of PmfsA for fumA expression resulted in heightened L-malic acid titers. The progress in metabolic engineering and bioprocess optimization holds promise for expediting industrial L-malic acid synthesis via biological fermentation. Moreover, it carries implications for the biosynthesis of various other organic acids.

Enhancing l-Malic Acid Production in Aspergillus niger via Natural Activation of sthA Gene Expression

The efficient production of l-malic acid using Aspergillus niger requires overcoming challenges in synthesis efficiency and excessive byproduct buildup. This study addresses these hurdles, improving the activity of NADH-dependent malate dehydrogenase (Mdh) in the early stages of the fermentation process. By employing a constitutive promoter to express the Escherichia coli sthA responsible for the transfer of reducing equivalents between NAD(H) and NADP(H) in A. niger, the l-malic acid production was significantly elevated. However, this resulted in conidiation defects of A. niger, limiting industrial viability. To mitigate this, we discovered and utilized the PmfsA promoter, enabling the specific expression of sthA during the fermentation stage. This conditional expression strain showed similar phenotypes to its parent strain while exhibiting exceptional performance in a 5 L fermenter. Notably, it achieved a 65.5% increase in productivity, reduced fermentation cycle by 1.5 days, and lowered succinic acid by 76.2%. This work marks a promising advancement in industrial l-malic acid synthesis via biological fermentation, showcasing the potential of synthetic biology in A. niger for broader applications.

Nanopore analysis of cis-diols in fruits

Natural fruits contain a large variety of cis-diols. However, due to the lack of a high-resolution sensor that can simultaneously identify all cis-diols without a need of complex sample pretreatment, direct and rapid analysis of fruits in a hand-held device has never been previously reported. Nanopore, a versatile single molecule sensor, can be specially engineered to perform this task. A hetero-octameric Mycobacterium smegmatis porin A (MspA) nanopore modified with a sole phenylboronic acid (PBA) adapter is prepared. This engineered MspA accurately recognizes 1,2-diphenols, alditols, α-hydroxy acids and saccharides in prune, grape, lemon, different varieties of kiwifruits and commercial juice products. Assisted with a custom machine learning program, an accuracy of 99.3% is reported and the sample pretreatment is significantly simplified. Enantiomers such as DL-malic acids can also be directly identified, enabling sensing of synthetic food additives. Though demonstrated with fruits, these results suggest wide applications of nanopore in food and drug administration uses.

Unveiling malic acid biorefinery: Comprehensive insights into feedstocks, microbial strains, and metabolic pathways

The over-reliance on fossil fuels and resultant environmental issues necessitate sustainable alternatives. Microbial fermentation of biomass for malic acid production offers a viable, eco-friendly solution, enhancing resource efficiency and minimizing ecological damage. This review covers three core aspects of malic acid biorefining: feedstocks, microbial strains, and metabolic pathways. It emphasizes the significance of utilizing biomass sugars, including the co-fermentation of different sugar types to improve feedstock efficiency. The review discusses microbial strains for malic acid fermentation, addressing challenges related to by-products from biomass breakdown and strategies for overcoming them. It delves into the crucial pathways and enzymes for malic acid production, outlining methods to optimize its metabolism, focusing on enzyme regulation, energy balance, and yield enhancement. These insights contribute to advancing the field of consolidated bioprocessing in malic acid biorefining.

Rewiring metabolic flux to simultaneously improve malate production and eliminate by-product succinate accumulation by Myceliophthora thermophila

Although a high titre of malic acid is achieved by filamentous fungi, by-product succinic acid accumulation leads to a low yield of malic acid and is unfavourable for downstream processing. Herein, we conducted a series of metabolic rewiring strategies in a previously constructed Myceliophthora thermophila to successfully improve malate production and abolish succinic acid accumulation. First, a pyruvate carboxylase CgPYC variant with increased activity was obtained using a high-throughput system and introduced to improve malic acid synthesis. Subsequently, shifting metabolic flux to malate synthesis from mitochondrial metabolism by deleing mitochondrial carriers of pyruvate and malate, led to a 53.7% reduction in succinic acid accumulation. The acceleration of importing cytosolic succinic acid into the mitochondria for consumption further decreased succinic acid formation by 53.3%, to 2.12 g/L. Finally, the importer of succinic acid was discovered and used to eliminate by-product accumulation. In total, malic acid production was increased by 26.5%, relative to the start strain JG424, to 85.23 g/L and 89.02 g/L on glucose and Avicel, respectively, in the flasks. In a 5-L fermenter, the titre of malic acid reached 182.7 g/L using glucose and 115.8 g/L using raw corncob, without any by-product accumulation. This study would accelerate the industrial production of biobased malic acid from renewable plant biomass.

Engineering the reductive tricarboxylic acid pathway in Aureobasidium pullulans for enhanced biosynthesis of poly-L-malic acid

Aureobasidium pullulans produced poly-L-malic acid (PMA) as the main metabolite in fermentation but with relatively low productivity and yield limiting its industrial application. In this study, A. pullulans ZX-10 was engineered to overexpress cytosolic malate dehydrogenase (MDH) and pyruvate carboxylase (PYC) and PMA synthetase (PMS) using a high-copy yeast episomal plasmid with the gpdA promoter from Aspergillus nidulans. Overexpressing endogenous PMS and heterologous MDH and PYC from Aspergillus oryzae respectively increased PMA production by 19 % - 37 % (0.64 - 0.74 g/g vs. 0.54 g/g for wild type) in shake-flask fermentations, demonstrating the importance of the reductive tricarboxylic acid (rTCA) pathway in PMA biosynthesis. A. pullulans co-expressing MDH and PYC produced 96.7 g/L PMA at 0.90 g/L∙h and 0.68 g/g glucose in fed-batch fermentation, which were among the highest yield and productivity reported. The engineered A. pullulans with enhanced rTCA pathway is advantageous and promising for PMA production.

The regulation of key flavor of traditional fermented food by microbial metabolism: A review

The beneficial microorganisms in food are diverse and complex in structure. These beneficial microorganisms can produce different and unique flavors in the process of food fermentation. The unique flavor of these fermented foods is mainly produced by different raw and auxiliary materials, fermentation technology, and the accumulation of flavor substances by dominant microorganisms during fermentation. The succession and metabolic accumulation of microbial flora significantly impacts the distinctive flavor of fermented foods. The investigation of the role of microbial flora changes in the production of flavor substances during fermentation can reveal the potential connection between microbial flora succession and the formation of key flavor compounds. This paper reviewed the evolution of microbial flora structure as food fermented and the key volatile compounds that contribute to flavor in the food system and their potential relationship. Further, it was a certain guiding significance for food industrial production.

Identification of hub genes associated with somatic cell score in dairy cow

CONTEXT

Somatic cell count (SCC) is used as an indicator of udder health. The log transformation of SCC is called somatic cell score (SCS).

AIM

Several QTL and genes have been identified that are associated with SCS. This study aimed to identify the most important genes associated with SCS.

METHODS

This study compiled 168 genes that were reported to be significantly linked to SCS. Pathway analysis and network analysis were used to identify hub genes.

KEY RESULTS

Pathway analysis of these genes identified 73 gene ontology (GO) terms associated with SCS. These GO terms are associated with molecular function, biological processes, and cellular components, and the identified pathways are directly or indirectly linked with the immune system. In this study, a gene network was constructed, and from this network, the 17 hub genes (CD4, CXCL8, TLR4, STAT1, TLR2, CXCL9, CCR2, IGF1, LEP, SPP1, GH1, GHR, VWF, TNFSF11, IL10RA, NOD2, and PDGFRB) associated to SCS were identified. The subnetwork analysis yielded 10 clusters, with cluster 1 containing all identified hub genes (except for the VWF gene).

CONCLUSION

Most hub genes and pathways identified in our study were mainly involved in inflammatory and cytokine responses.

IMPLICATIONS

Result obtained in current study provides knowledge of the genetic basis and biological mechanisms controlling SCS. Therefore, the identified hub genes may be regarded as the main gene for the genomic selection of mastitis resistance.

An enzyme-centric approach for constructing an amperometric l-malate biosensor with a long and programmable linear range

l-Malate is a key flavor enhancer and acidulant in the food and beverage industry, particularly winemaking. Enzyme-based amperometric biosensors offer convenience for monitoring its concentration. However, only a small number of off-the-shelf malate-oxidizing enzymes have been used in previous devices. These typically have linear ranges poorly suited for the l-malate concentrations found in fruit processing and winemaking, making it necessary to use precisely diluted samples. Here, we describe a pipeline of database-mining, gene synthesis, recombinant expression, and spectrophotometric assays to characterize previously untested enzymes for their suitability in biosensors. The pipeline yielded a bespoke biocatalyst-the Ascaris suum malic enzyme carrying mutation R181Q [AsME(R181Q)]. Our first prototype with AsME(R181Q) had an ultra-wide linear range of 50-200 mM l-malate, corresponding to concentrations found in undiluted fruit juices (including grape). Changing the dication from Mg2+ to Mn2+ increased sensitivity five-fold and adding citrate (100 mM) increased it another six-fold, albeit decreasing the linear range to 1-10 mM. To our knowledge, this is the first time an l-malate biosensor with a tuneable combination of sensitivity and linear range has been described. The sensor response was also tested in the presence of various molecules abundant in juices and wines, with ascorbate shown to be a potent interferent. Interference was mitigated by the addition of ascorbate oxidase, allowing for differential measurements on an undiluted, untreated wine sample that corresponded well with commercial l-malate testing kits. Overall, this work demonstrates the power of an enzyme-centric approach for designing electrochemical biosensors with improved operational parameters and novel functionality.

Production of L-Malic Acid by Metabolically Engineered Aspergillus nidulans Based on Efficient CRISPR-Cas9 and Cre-loxP Systems

Aspergillus nidulans has been more extensively characterized than other Aspergillus species considering its morphology, physiology, metabolic pathways, and genetic regulation. As it has a rapid growth rate accompanied by simple nutritional requirements and a high tolerance to extreme cultural conditions, A. nidulans is a promising microbial cell factory to biosynthesize various products in industry. However, it remains unclear for whether it is also a suitable host for synthesizing abundant L-malic acid. In this study, we developed a convenient and efficient double-gene-editing system in A. nidulans strain TN02A7 based on the CRISPR-Cas9 and Cre-loxP systems. Using this gene-editing system, we made a L-malic acid-producing strain, ZQ07, derived from TN02A7, by deleting or overexpressing five genes (encoding Pyc, pyruvate carboxylase; OahA, oxaloacetate acetylhydrolase; MdhC, malate dehydrogenase; DctA, C4-dicarboxylic acid transporter; and CexA, citric acid transporter). The L-malic acid yield in ZQ07 increased to approximately 9.6 times higher (up to 30.7 g/L titer) than that of the original unedited strain TN02A7, in which the production of L-malic acid was originally very low. The findings in this study not only demonstrate that A. nidulans could be used as a potential host for biosynthesizing organic acids, but also provide a highly efficient gene-editing strategy in filamentous fungi.

Integrated fermentative production and downstream processing of L-malic acid by Aspergillus wentii using cassava peel waste

L-malic acid (L-MA) is an industrially significant chemical with enormous potential. The fungal cell factories could be exploited to harvest it on large scales. In our study, Aspergillus wentii strain (MTCC 1901 ^T) was explored for L-MA production. Initially, the L-MA production was carried out using glucose with optimization of parameters influencing product accumulation (pH and CaCO₃). The fermentation resulted in L-MA titer of 37.9 g/L with 0.39 g/g yield. Then, cassava peel waste (CPW) was used for L-MA production by separate hydrolysis and fermentation. Optimized acidic and enzymatic hydrolysis resulted in glucose release of 0.53 and 0.66 g/g CPW, respectively. The strain accumulated 20.9 g/L and 33.1 g/L L-MA with corresponding yields of 0.25 g/g and 0.34 g/g during batch cultivation using acid and enzyme hydrolysate, respectively. Finally, the produced L-MA was separated using an inexpensive solvent extraction method. Among various solvents used, n-butanol exhibited maximum L-MA extraction efficiency (31%).

Recent advances in producing food additive L-malate: Chassis, substrate, pathway, fermentation regulation and application

In addition to being an important intermediate in the TCA cycle, L-malate is also widely used in the chemical and beverage industries. Due to the resulting high demand, numerous studies investigated chemical methods to synthesize L-malate from petrochemical resources, but such approaches are hampered by complex downstream processing and environmental pollution. Accordingly, there is an urgent need to develop microbial methods for environmentally-friendly and economical L-malate biosynthesis. The rapid progress and understanding of DNA manipulation, cell physiology, and cell metabolism can improve industrial L-malate biosynthesis by applying intelligent biochemical strategies and advanced synthetic biology tools. In this paper, we mainly focused on biotechnological approaches for enhancing L-malate synthesis, encompassing the microbial chassis, substrate utilization, synthesis pathway, fermentation regulation, and industrial application. This review emphasizes the application of novel metabolic engineering strategies and synthetic biology tools combined with a deep understanding of microbial physiology to improve industrial L-malate biosynthesis in the future.

Changes of gut microbiota and tricarboxylic acid metabolites may be helpful in early diagnosis of necrotizing enterocolitis: A pilot study

Purpose

We aimed to explore the value of gut microbiota and tricarboxylic acid (TCA) metabolites in early diagnosis of necrotizing enterocolitis (NEC) among infants with abdominal manifestations.

Methods

Thirty-two preterm infants with abdominal manifestations at gestational age ≤ 34 weeks were included in the study and were divided into non-NEC (n = 16) and NEC (n = 16) groups. Faecal samples were collected when the infants were enrolled. The gut microbiota was analysed with high-throughput sequencing, and TCA metabolites were measured with multiple reaction monitoring (MRM) targeted metabolomics. Receiver operating characteristic (ROC) curves were generated to explore the predictive value of the obtained data.

Results

There was no significant difference in alpha diversity or beta diversity between the two groups (p > 0.05). At the phylum level, Proteobacteria increased, and Actinomycetota decreased in the NEC group (p < 0.05). At the genus level, Bifidobacterium and Lactobacillaceae decreased significantly, and at the species level, unclassified Staphylococcus, Lactobacillaceae and Bifidobacterium animalis subsp. lactis decreased in the NEC group (p < 0.05). Further Linear discriminant analysis effect sizes (LEfSe) analysis showed that the change in Proteobacteria at the phylum level and Lactobacillaceae and Bifidobacterium at the genus level scored higher than 4. The concentrations of succinate, L-malic acid and oxaloacetate in the NEC group significantly increased (p < 0.05), and the areas under the ROC curve for these metabolites were 0.6641, 0.7617, and 0.7344, respectively.

Conclusion

Decreased unclassified Staphylococcus, Lactobacillaceae and Bifidobacterium animalis subsp. lactis at the species level as well as the increase in the contents of some TCA metabolites, including succinate, L-malic acid and oxaloacetate, have potential value for the early diagnosis of NEC.

Partial compression increases acidity, but decreases phenolics in jujube fruit: Evidence from targeted metabolomics

Jujube fruit (Ziziphus jujuba Mill.) is extremely susceptible to mechanical injury by extrusion and collision during storage, transportation and processing. In this study, we examined the morphology and endogenous metabolism of jujubes at three developmental stages after applying partial compression (PC) to mimic mechanical injury. Generally, PC did not affect the total soluble solids content, but increased the acidity and decreased the amount of phenolics in the jujube fruit. Targeted metabolomics analysis further confirmed that acid and phenolics content were differentially altered in response to PC. To our knowledge, this is the first study to characterize metabolic variations in ready-to-eat fruit that occur in response to physical damage. The results will provide insight into the understanding the consequences of mechanical injury on fruit nutrition and health benefits.

Microbial cell factories based on filamentous bacteria, yeasts, and fungi

BACKGROUND

Advanced DNA synthesis, biosensor assembly, and genetic circuit development in synthetic biology and metabolic engineering have reinforced the application of filamentous bacteria, yeasts, and fungi as promising chassis cells for chemical production, but their industrial application remains a major challenge that needs to be solved.

RESULTS

As important chassis strains, filamentous microorganisms can synthesize important enzymes, chemicals, and niche pharmaceutical products through microbial fermentation. With the aid of metabolic engineering and synthetic biology, filamentous bacteria, yeasts, and fungi can be developed into efficient microbial cell factories through genome engineering, pathway engineering, tolerance engineering, and microbial engineering. Mutant screening and metabolic engineering can be used in filamentous bacteria, filamentous yeasts (Candida glabrata, Candida utilis), and filamentous fungi (Aspergillus sp., Rhizopus sp.) to greatly increase their capacity for chemical production. This review highlights the potential of using biotechnology to further develop filamentous bacteria, yeasts, and fungi as alternative chassis strains.

CONCLUSIONS

In this review, we recapitulate the recent progress in the application of filamentous bacteria, yeasts, and fungi as microbial cell factories. Furthermore, emphasis on metabolic engineering strategies involved in cellular tolerance, metabolic engineering, and screening are discussed. Finally, we offer an outlook on advanced techniques for the engineering of filamentous bacteria, yeasts, and fungi.

Engineering Escherichia coli for Efficient Aerobic Conversion of Glucose to Malic Acid through the Modified Oxidative TCA Cycle

Malic acid is a versatile building-block chemical that can serve as a precursor of numerous valuable products, including food additives, pharmaceuticals, and biodegradable plastics. Despite the present petrochemical synthesis, malic acid, being an intermediate of the TCA cycle of a variety of living organisms, can also be produced from renewable carbon sources using wild-type and engineered microbial strains. In the current study, Escherichia coli was engineered for efficient aerobic conversion of glucose to malic acid through the modified oxidative TCA cycle resembling that of myco- and cyanobacteria and implying channelling of 2-ketoglutarate towards succinic acid via succinate semialdehyde formation. The formation of succinate semialdehyde was enabled in the core strain MAL 0 (∆ackA-pta, ∆poxB, ∆ldhA, ∆adhE, ∆ptsG, PL-glk, Ptac-galP, ∆aceBAK, ∆glcB) by the expression of Mycobacterium tuberculosis kgd gene. The secretion of malic acid by the strain was ensured, resulting from the deletion of the mdh, maeA, maeB, and mqo genes. The Bacillus subtilis pycA gene was expressed in the strain to allow pyruvate to oxaloacetate conversion. The corresponding recombinant was able to synthesise malic acid from glucose aerobically with a yield of 0.65 mol/mol. The yield was improved by the derepression in the strain of the electron transfer chain and succinate dehydrogenase due to the enforcement of ATP hydrolysis and reached 0.94 mol/mol, amounting to 94% of the theoretical maximum. The implemented strategy offers the potential for the development of highly efficient strains and processes of bio-based malic acid production.

Recent advances in microbial production of L-malic acid

Over the last few decades, increasing concerns regarding fossil fuel depletion and excessive CO2 emissions have led to extensive fundamental studies and industrial trials regarding microbial chemical production. As an additive or precursor, L-malic acid has been shown to exhibit distinctive properties in the food, pharmaceutical, and daily chemical industries. L-malic acid is currently mainly fabricated through a fumarate hydratase-based biocatalytic conversion route, wherein petroleum-derived fumaric acid serves as a substrate. In this review, for the first time, we comprehensively describe the methods of malic acid strain transformation, raw material utilization, malic acid separation, etc., especially recent progress and remaining challenges for industrial applications. First, we summarize the various pathways involved in L-malic acid biosynthesis using different microorganisms. We also discuss several strain engineering strategies for improving the titer, yield, and productivity of L-malic acid. We illustrate the currently available alternatives for reducing production costs and the existing strategies for optimizing the fermentation process. Finally, we summarize the present challenges and future perspectives regarding the development of microbial L-malic acid production. KEY POINTS: • A range of wild-type, mutant, laboratory-evolved, and metabolically engineered strains which could produce L-malic acid were comprehensively described. • Alternative raw materials for reducing production costs and the existing strategies for optimizing the fermentation were sufficiently summarized. • The present challenges and future perspectives regarding the development of microbial L-malic acid production were elaboratively discussed.

Effects of heat stress on growth performance, carcass traits, serum metabolism, and intestinal microflora of meat rabbits

To investigate the effects of heat stress on meat rabbits, we assigned 80 rabbits to the moderate temperature group (24 ± 1°C; Control group) and the continuous high-temperature group (HT group), then monitored the effects using growth performance, carcass characteristics, biochemical assays, UPLC-MS/MS-based metabolomics, and microbiome. The results showed that after continuous high-temperature exposure, the average daily gain, average daily feed intake, and thymus index were significantly decreased (p < 0.05). Contents of HSP70, ALP, and Cortisol in serum were significantly increased, while TP, GLU, T3, and T4 were significantly decreased (p < 0.05). Nine kinds of differential metabolites were screened by serum metabolomics, which can be used as biomarkers of heat stress in meat rabbits. The selected differential metabolites were analyzed by KEGG annotation and enrichment analysis. The results showed that 14 pathways affected by heat stress were identified by KEGG pathway enrichment analysis, including Sphingolipid metabolism, Pyrimidine metabolism, Citrate cycle (TCA cycle)), aminoacyl-tRNA biosynthesis, and so on. The analysis of the effect of heat stress on the cecal microflora of meat rabbits showed that the abundance of cecal Proteus in the HT group was significantly higher than that in the moderate Control group. The number of Candidatus-saccharimonas in the cecum microflora was significantly higher than that in the moderate temperature group (p < 0.05) which may be related to inflammatory diseases in the heat stress group. These findings indicated that the heat-stressed rabbits were in negative energy balance, which affected protein metabolism, and subsequently affected growth performance and carcass characteristics.

Effect of process mode, nitrogen source and temperature on L-malic acid production with Aspergillus oryzae DSM 1863 using acetate as carbon source

Malic acid, mainly used as acidulant and taste enhancer in the food industry, is currently produced from fossil resources. In this study, microbial L-malate production with the filamentous fungus A. oryzae using the carbon source acetate was evaluated. Acetate is for example contained in biomass-derived substrates such as lignocellulosic hydrolysates and condensates of fast pyrolysis, thus avoiding competition with food production. Since research on malic acid synthesis from acetate is limited and reported productivities and yields are low, this work aimed to improve the process. First, different cultivation temperatures were tested. This parameter was found to affect the ratio between malic and succinic acid, which is the major by-product of organic acid production with A. oryzae. At 32°C, the malate share was highest (53.7 ± 1.6%), while it was lowest at 38°C (43.3 ± 1.1%) whereas succinate represented the main product (51.5 ± 1.0%). Besides the temperature, the type of nitrogen source was also found to affect malate synthesis as well as biomass production. In the pre-culture, the biomass concentration was increased by a factor of 3.4–3.9, and germination started earlier with the complex nitrogen sources yeast extract, casein hydrolysate and peptone compared to the defined nitrogen source (NH₄)₂SO₄. Especially with yeast extract, malate synthesis in the main culture was accelerated and the titer obtained after 48 h was about 2.6 times higher than that quantified with (NH₄)₂SO₄. To reduce substrate inhibition in acetate medium, fed-batch and repeated-batch processes were evaluated using (NH₄)₂SO₄ or yeast extract as nitrogen source. In the fed-batch process, the period of malate production was extended, and the maximum product concentration was increased to 11.49 ± 1.84 g/L with (NH₄)₂SO₄ and 12.08 ± 1.25 g/L with yeast extract. In the repeated-batch process, the total acid production was highest within the first 240 h of fermentation, but optimization is required to maintain high production rates in later cycles. The lessons learned in this study will help in the development of further process strategies to maximize malate production using acetate as alternative substrate to the commonly used glucose.

Malic acid: fermentative production and applications

Microbial metabolites have gained lot of industrial interest. These are currently employed in various industries including pharmaceuticals, chemical, textiles, food etc. Organic acids are among the important microbial products. Production of microbial organic acids present numerous advantages like agro-industrial waste may be utilized as substrate, low production cost, natural in origin and production is environment friendly. Malic acid is an organic acid (C4 dicarboxylic acid) that can be produced by microbes. It is also useful in industrial sectors as food, chemicals, and pharmaceuticals etc. Production/extraction of malic acid has been reported from fruits, egg shells, microbes, via chemical synthesis, bio-transformation and from renewable sources. Microbial production of malic acid seems very promising due to various advantages and the approach is environment-friendly. In recent years, researchers have focused on fermentative microbial production of malic acid and possibility of using agro-industrial waste as raw substrates. In current article, malic acid production along with applications has been discussed with recent advances in the area.

Peptide supplementation relieves stress and enhances glycolytic flux in filamentous fungi during organic acid bioproduction

Filamentous fungi occupy a uniquely favorable position in the bioproduction of organic acids. Intracellular stress is the main stimulator in filamentous fungi to produce and accumulate organic acids with high flux. However, stress can affect the physiological activities of filamentous fungi, thereby deteriorating their fermentation performance. Herein, we report that peptide supplementation during Rhizopus oryzae fermentation significantly improved fumaric acid production. Specifically, fumaric acid productivity was elevated by approximately 100%, fermentation duration was shortened from 72 to 36 h, while maintaining the final titer. Furthermore, transcriptome profile analysis and biochemical assays indicated that the overall capabilities of the stress defense systems (enzymatic and nonenzymatic) were significantly improved in R. oryzae. Consequently, glycolytic metabolism was distinctly enhanced, which eventually resulted in improved fumaric acid production and reduced fermentation duration. We expect our findings and efforts to provide essential insights into the optimization of the fermentation performance of filamentous fungi in industrial biotechnology and fermentation engineering.