Metabolic engineering advances and prospects for amino acid production

Recent advances on engineering Escherichia coli and Corynebacterium glutamicum for efficient production of L-threonine and its derivatives

L-threonine, one of the three major amino acids, plays a vital role in various industries such as food, feed, pharmaceuticals, and cosmetics. Currently, the fermentation-based production of L-threonine has evolved into an efficient, cost-effective, and environmentally friendly industrial process. Escherichia coli and Corynebacterium glutamicum, as the industrial workhorses of amino acids production, have long been widely studied due to their well-established genetic backgrounds and powerful molecular tools. This review focuses on recent advances in the microbial production of L-threonine by metabolic engineering. From three key modules, including L-threonine synthesis module, central metabolism module and global regulation module, we provide a comprehensive analysis on the entire metabolic pathway of L-threonine and the global regulation of the production process. Furthermore, we systematically summarize biotransformation methods for producing high-value derivatives of L-threonine, thereby broadening the application scope and market potential of L-threonine. Overall, this review shows many effective strategies for the biosynthesis of L-threonine, and offers guidance for the microbial production of L-aspartate family amino acids and their derivatives.

ALE reveals a surprising link between [Fe-S] cluster formation, tryptophan biosynthesis and the potential regulatory protein TrpP in Corynebacterium glutamicum

BACKGROUND

The establishment of synthetic microbial communities comprising complementary auxotrophic strains requires efficient transport processes for common goods. With external supplementation of the required metabolite, most auxotrophic strains reach wild-type level growth. One exception was the L-trypton auxotrophic strain phaCorynebacterium glutamicum ΔTRP ΔtrpP, which grew 35% slower than the wild type in supplemented defined media. C. glutamicum ΔTRP ΔtrpP lacks the whole L-tryptophan biosynthesis cluster (TRP, cg3359-cg3364) as well as the putative L-tryptophan transporter TrpP (Cg3357). We wanted to explore the role of TrpP in L-tryptophan transport, metabolism or regulation and to elucidate the cause of growth limitation despite supplementation.

RESULTS

Mutants lacking either TRP or trpP revealed that the growth defect was caused solely by trpP deletion, whereas L-tryptophan auxotrophy was caused only by TRP deletion. Notably, not only the deletion but also the overexpression of trpP in an L-tryptophan producer increased the final L-tryptophan titer, arguing against a transport function of TrpP. A transcriptome comparison of C. glutamicum ΔtrpP with the wild type showed alterations in the regulon of WhcA, that contains an [Fe-S] cluster. Through evolution-guided metabolic engineering, we discovered that inactivation of SufR (Cg1765) partially complemented the growth defect caused by ΔtrpP. SufR is the transcriptional repressor of the suf operon (cg1764-cg1759), which encodes the only system of C. glutamicum for iron‒sulfur cluster formation and repair. Finally, we discovered that the combined deletion of trpP and sufR increased L-tryptophan production by almost 3-fold in comparison with the parental strain without the deletions.

CONCLUSIONS

On the basis of our results, we exclude the possibility that TrpP is an L-tryptophan transporter. TrpP presence influences [Fe-S] cluster formation or repair, presumably through a regulatory function via direct interaction with another protein. [Fe-S] cluster availability influences not only certain enzymes but also targets of the WhiB-family regulator WhcA, which is involved in oxidative stress response. The reduced growth of WT ΔtrpP is likely caused by the reduced activity of [Fe-S]-cluster-containing enzymes involved in central metabolism, such as aconitase or succinate: menaquinone oxidoreductase. In summary, we identified a very interesting link between L-tryptophan biosynthesis and iron sulfur cluster formation that is relevant for L-tryptophan production.

CLINICAL TRIAL NUMBER

Not applicable.

Two routes for tyrosol production by metabolic engineering of Corynebacterium glutamicum

BACKGROUND

The phenolic compound tyrosol is widely used in the pharmaceutical industry, owing to its beneficial effects on human health and its use as a precursor for key pharmaceuticals, including β1-receptor blockers. Tyrosol can be found in olive oil, but despite its natural biosynthesis in plants, low extraction efficiencies render microbial production a more viable alternative.

RESULTS

Here, we engineered the L-tyrosine overproducing Corynebacterium glutamicum strain AROM3 for the de novo production of tyrosol. Two routes were established and compared: one via 4-OH-phenylpyruvate as intermediate and the other via tyramine. We initially expected the first route to require heterologous expression of a prephenate dehydrogenase gene, given that C. glutamicum lacks this enzymatic function. However, heterologous expression of ARO10 from Saccharomyces cerevisiae (ARO10Sc), which encodes a phenylpyruvate decarboxylase, was sufficient to establish tyrosol production in strain AROM3. We identified that 4-OH-phenylpyruvate is synthesized from L-tyrosine by native aminotransferases, which is subsequently decarboxylated by Aro10Sc, and reduced to tyrosol by native alcohol dehydrogenases, leading to a titer of 9.4 ± 1.1 mM (1.30 ± 0.15 g/L). We identified the furfural dehydrogenase FudC as major enzyme involved in this pathway, as its gene deletion reduced tyrosol production by 75%. Given the instability of 4-OH-phenylpyruvate, the synthesis of tyrosol via the stable intermediate tyramine was pursued via the second route. Decarboxylation of L-tyrosine followed by oxidative deamination was accomplished by overexpression of the L-tyrosine decarboxylase gene tdc from Levilactobacillus brevis (tdcLb) and the tyramine oxidase gene tyo from Kocuria rhizophila (tyoKr). Using this route, tyrosol production was increased by 44% compared to the route via 4-OH-phenylpyruvate. With a division of labor approach by co-cultivating L-tyrosine producing strains that either express tdcLb or tyoKr, the highest titer of 14.1 ± 0.3 mM (1.95 ± 0.04 g/L) was achieved.

CONCLUSIONS

This study demonstrates the potential of endotoxin-free C. glutamicum as production host for the L-tyrosine-derived product tyrosol. Due to its L-arogenate pathway for L-tyrosine synthesis, the unstable 4-OH-phenylpyruvate could be excluded as intermediate in the Tdc-Tyo pathway, outcompeting the most often utilized production route via phenylpyruvate decarboxylases.

Nonheme Manganese-Catalyzed Oxidative N-Dealkylation of Tertiary Amides: Manganese(IV)-Oxo Aminopyridine Cation Radical Species and Hydride Transfer Mechanism

The development of efficient and practical N-dealkylation reactions stands as a longstanding objective in synthetic chemistry. Inspired by the oxidative N-dealkylation reactions mediated by heme and nonheme metalloenzymes, we disclose a biomimetic oxidative N-dealkylation catalysis that utilizes a nonheme manganese complex bearing anthryl-appended aminopyridine ligand and hydrogen peroxide (H2O2) as the terminal oxidant. A variety of Weinreb amides and cyclic aliphatic amines are efficiently transformed into valuable methyl hydroxamates and ω-amino acids through oxidative C-N bond cleavage. Mechanistic studies, including density functional theory (DFT) calculations, reveal that a manganese(IV)-oxo aminopyridine cation radical species, which is formed via the bromoacetic acid-assisted heterolytic O-O bond cleavage of a presumed manganese(III)-hydroperoxo aminopyridine species and the subsequent intramolecular electron transfer (ET) from the anthryl group of the aminopyridine ligand to the manganese center, is the active intermediate that initiates the oxidative N-dealkylation reactions; this process is reminiscent to the heterolytic O-O bond cleavage of iron(III)-hydroperoxo porphyrin intermediates (Cpd 0) to form iron(IV)-oxo porphyrin π-cation radicals (Cpd I) that are responsible for diverse selective oxidation reactions. Moreover, it is revealed that the oxidative activation of the C-H bond adjacent to the nitrogen atom proceeds via a hydride transfer (HT) mechanism, which involves a concerted asynchronous proton-coupled electron transfer (PCET), followed by an ET process. Thus, this study reports the first instance of catalytic oxidative N-dealkylation of a variety of tertiary amides, such as Weinreb amides and cyclic aliphatic amines, mediated by a Cpd I-like nonheme manganese(IV)-oxo aminopyridine cation radical species via an initial HT pathway.

Novel Reprogramming of Polyketide Synthase for Valerolactam Production

δ-Valerolactam (VL), as an organic compound, is an important precursor chemical for nylon and has a wide range of applications in organic synthesis, pharmaceutical synthesis, polymer materials, and other fields. This study introduces a novel biosynthetic method for producing VL in the engineered strain Escherichia coli BL21 through the reprogramming of polyketide synthases (PKS). Initially, an in vitro multienzyme system was constructed to verify the reliability of the VL synthesis pathway. Subsequently, an optimized biosynthetic pathway was established in E. coli, converting l-aspartate to VL with a yield of 3.66 mg/L in a 250 mL shake flask. Various engineering strategies were then implemented to enhance VL production, including substrate-enzyme affinity modification and multidimensional substrate optimization. These methods resulted in a 3.7-fold increase in VL yield, reaching 13.5 mg/L in shake flask cultures. Further scale-up in a 5 L fed-batch fermenter achieved a VL concentration of 76.2 mg/L. This research provides innovative insights into the optimization of VL production pathways and industrial-scale production.

Biosynthesis of poly(ester amide)s in engineered Escherichia coli

The development of biobased polymers to substitute their current petroleum-based counterparts is crucial for fostering a sustainable plastic industry. Here we report the biosynthesis and characterization of a group of biopolymers, poly(ester amide)s (PEAs), in Escherichia coli. PEAs are biosynthesized by constructing a new-to-nature amino acid polymerization pathway, comprising amino acid activation by β-alanine CoA transferase and subsequent polymerization of amino acyl-CoA by polyhydroxyalkanoate synthase. The engineered E. coli strains harboring this pathway are capable of biosynthesizing various PEAs, each incorporating different amino acid monomers in varying fractions. Examination of the physical, thermal and mechanical properties reveals a dependence of molecular weight on the type of polyhydroxyalkanoate synthase, a decrease in melting temperature and crystallinity as the 3-aminopropionate monomer fraction increases and enhanced elongation at break compared to its polyester analog. The engineered bacterial system will prove beneficial for the biobased production of various PEAs using renewable resources.

Construction of a synthetic metabolic pathway for biosynthesis of threonine from ethylene glycol

Ethylene glycol is a promising substrate for bioprocesses which can be derived from widely abundant CO2 or plastic waste. In this work, we describe the construction of an eight-step synthetic metabolic pathway enabling carbon-conserving biosynthesis of threonine from ethylene glycol. This route extends the previously disclosed synthetic threose-dependent glycolaldehyde assimilation (STEGA) pathway for the synthesis of 2-oxo-4-hydroxybutyrate with three additional reaction steps catalyzed by homoserine transaminase, homoserine kinase, and threonine synthase. We first validated the functionality of the new pathway in an Escherichia coli strain auxotrophic for threonine, which was also employed for discovering a better-performing D-threose dehydrogenase enzyme activity. Subsequently, we transferred the pathway to producer strains and used 13C-tracer experiments to improve threonine biosynthesis starting from glycolaldehyde. Finally, extending the pathway for ethylene glycol assimilation resulted in the production of up to 6.5 mM (or 0.8 g L-1) threonine by optimized E. coli strains at a yield of 0.10 mol mol-1 (corresponding to 20 % of the theoretical yield).

Utilization of Microalgae and Duckweed as Sustainable Protein Sources for Food and Feed: Nutritional Potential and Functional Applications

Aquatic biomass, particularly microalgae and duckweed, presents a promising and sustainable alternative source of plant-based protein and bioactive compounds for food and feed applications. This review highlights the nutritional potential of these aquatic species, focusing on their high protein content, rapid growth rates, and adaptability to nonarable environments. Microalgae, such as Chlorella and Arthrospira spp., and duckweed, such as Lemna minor, are evaluated for their functional food applications, including their roles as protein supplements, bioactive components, antioxidants, and emulsifiers in food formulations. The study also examines their environmental benefits, including wastewater bioremediation, nutrient recycling, and greenhouse gas mitigation, which contribute to a more sustainable agricultural system. Technological advancements in the cultivation, harvesting, and processing of microalgae and duckweed are discussed to enhance their scalability and economic feasibility in food and feed production. The findings suggest that integrating microalgae and duckweed into agricultural and food systems can significantly improve food security, nutritional outcomes, and sustainability. Future research should focus on optimizing cultivation efficiencies, advancing protein extraction techniques, and expanding the applications of aquatic biomass in various food products.

Quantitative analysis of amino acid excretion by Methanothermobacter marburgensis under N2-fixing conditions

Methanogenic archaea (methanogens) possess fascinating metabolic characteristics, such as the ability to fix molecular nitrogen (N2). Methanogens are of biotechnological importance due to the ability to produce methane (CH4) from molecular hydrogen (H2) and carbon dioxide (CO2) and to excrete proteinogenic amino acids. This study focuses on analyzing the link between biological methanogenesis and amino acid excretion under N2-fixing conditions. Among five hydrogenotrophic, autotrophic methanogens, Methanothermobacter marburgensis was prioritized and further cultivated in closed batch cultivation mode under N2-fixing conditions. M. marburgensis was grown on chemically defined minimal medium with different concentrations of ammonium in a H2/CO2/N2 atmosphere. This enabled the quantification of ammonia uptake, N2-fixation, amino acid excretion and the conversion of H2/CO2 to CH4. To quantify N2-fixation rates in a mass balance setting a novel method has been established. The method utilizes the pressure drop below a certain threshold pressure in closed batch cultivation mode - the threshold pressure for N2-fixation (THpN2fix). Using the THpN2fix method, volumetric N2-fixation rates of M. marburgensis as high as 0.91 mmol L-1 h-1 were determined. Excretion of amino acids was found with highest detected values of glutamic acid, alanine, glycine and asparagine. The highest total amino acid excretion of 7.5 µmol L-1 h-1 was detected with H2/CO2/N2 at an ammonium concentration of 40 mmol L-1. This study sheds light on the link between methanogenesis, biological N2-fixation, and proteinogenic amino acid excretion. The concomitant production of amino acids and CH4 could become of biotechnological relevance in an integrated approach coupling biomethanation and N2-fixation in a biorefinery concept.

Screening of high glucose tolerant Escherichia coli for L-valine fermentation by autonomous evolutionary mutation

L-valine holds wide-ranging applications in medicine, food, feed, and various industrial sectors. Escherichia coli, a pivotal strain in industrial L-valine production, features a concise fermentation period and a well-defined genetic background. This study focuses on mismatch repair genes (mutH, mutL, mutS, and recG) and genes associated with mutagenesis (dinB, rpoS, rpoD, and recA), employing a high-glucose adaptive culture in conjunction with metabolic modifications to systematically screen for superior phenotypes. This approach enhances the spontaneous survival rate of stress cells and facilitates the enrichment of positive mutations. Leveraging a multi-fragment seamless recombination technique, we successfully assembled the ilvBN, ilvC, ilvE, and ilvD pathway enzyme genes, transforming E. coli from a non-producer into a proficient L-valine producer capable of generating up to 6.62 g/L. Through a synergistic application of self-evolution engineering and metabolic engineering strategies, the engineered E. coli strain exhibited significantly enhanced tolerance and demonstrated heightened accumulation of L-valine. KEY POINTS: • The innovation centered on mutated genes and mismatch repair genes • By integrating modification with adaptive culture, a superior phenotype was attained • Double plasmids expressing enzymes for L-valine production in E. coli were obtained.

Engineering of L-threonine and L-proline biosensors by directed evolution of transcriptional regulator SerR and application for high-throughput screening

Amino acids are important bio-based products with a multi-billion-dollar market. The development of efficient high-throughput screening technologies utilizing biosensors is essential for the rapid identification of high-performance amino acid producers. However, there remains a pressing need for biosensors that specifically target certain critical amino acids, such as L-threonine and L-proline. In this study, a novel transcriptional regulator-based biosensor for L-threonine and L-proline was successfully developed, inspired by our new finding that SerE can export L-proline in addition to the previously known L-threonine and L-serine. Through directed evolution of SerR (the corresponding transcriptional regulator of SerE), the mutant SerRF104I which can recognize both L-threonine and L-proline as effectors and effectively distinguish strains with varying production levels was identified. Subsequently, the SerRF104I-based biosensor was employed for high-throughput screening of the superior enzyme mutants of L-homoserine dehydrogenase and γ-glutamyl kinase, which are critical enzymes in the biosynthesis of L-threonine and L-proline, respectively. A total of 25 and 13 novel mutants that increased the titers of L-threonine and L-proline by over 10% were successfully identified. Notably, six of the newly identified mutants exhibited similarities to the most effective mutants reported to date, indicating the promising application potential of the SerRF104I-based biosensor. This study illustrates an effective strategy for the development of transcriptional regulator-based biosensors for amino acids and other chemical compounds.

Channel Engineering of a Glutamate Exporter

Mechanosensitive channel MscCG2 is involved in glutamate excretion in most C. glutamicum strains. Improving the excretion efficiency of MscCG2 is beneficial to the production of glutamate. In this study, structure-based rational design was carried out to obtain an improved efflux ability of exporter MscCG2 and its mechanistic advance via two strategies: widening the channel entrance for smoother entry of glutamate and reducing the electronegativity at the entrance of the channels to minimize the rejection of negatively charged glutamate entry. The designed variants were found to enhance glutamate excretion by 2 to 3.3-fold in the early phase and 1.1-fold to 1.5-fold in the late phase of fermentation. The enhanced glutamate excretion was further confirmed by using glutamate toxic analog 4-fluoroglutamate (4-FG) and Glu-Glu peptide uptake and glutamate export assay. Molecular dynamic (MD) simulations revealed that the amino acid substitutions indeed enlarged the channel entrance and reduced the repulsion of glutamate when entering the channel. The finding of this study is important for understanding the underlying structure-function relationship and the mechanism of glutamate secretion to improve glutamate efflux efficiency of glutamate exporter.

Carbon Negative Synthesis of Amino Acids Using a Cell-Free-Based Biocatalyst

Biological systems can directly upgrade carbon dioxide (CO2) into chemicals. The CO2 fixation rate of autotrophic organisms, however, is too slow for industrial utility, and the breadth of engineered metabolic pathways for the synthesis of value-added chemicals is too limited. Biotechnology workhorse organisms with extensively engineered metabolic pathways have recently been engineered for CO2 fixation. Yet, their low carbon fixation rate, compounded by the fact that living organisms split their carbon between cell growth and chemical synthesis, has led to only cell growth with no chemical synthesis achieved to date. Here, we engineer a lysate-based cell-free expression (CFE)-based multienzyme biocatalyst for the carbon negative synthesis of the industrially relevant amino acids glycine and serine from CO2 equivalents─formate and bicarbonate─and ammonia. The formate-to-serine biocatalyst leverages tetrahydrofolate (THF)-dependent formate fixation, reductive glycine synthesis, serine synthesis, and phosphite dehydrogenase-dependent NAD(P)H regeneration to convert 30% of formate into serine and glycine, surpassing the previous 22% conversion using a purified enzyme system. We find that (1) the CFE-based biocatalyst is active even after 200-fold dilution, enabling higher substrate loading and product synthesis without incurring additional cell lysate cost, (2) NAD(P)H regeneration is pivotal to driving forward reactions close to thermodynamic equilibrium, (3) balancing the ratio of the formate-to-serine pathway genes added to the CFE is key to improving amino acid synthesis, and (4) efficient THF recycling enables lowering the loading of this cofactor, reducing the cost of the CFE-based biocatalyst. To our knowledge, this is the first synthesis of amino acids that can capture CO2 equivalents for the carbon negative synthesis of amino acids using a CFE-based biocatalyst. Looking ahead, the CFE-based biocatalyst process could be extended beyond serine to pyruvate, a key intermediate, to access a variety of chemicals from aromatics and terpenes to alcohols and polymers.

Metabolic engineering of Escherichia coli for de novo production of 5-hydroxyvalerate via L-lysine α-oxidase pathway

5-hydroxyvalerate (5-HV) is a crucial C5 platform chemical with versatile applications, yet its efficient production remains a challenge. The Raip, gabT, and yahK genes were integrated into the E. coli LE genome, deleted gabD, and enhanced gabP expression, resulting in the QluMG strain. Additionally, the impact of ethanol and H2O2 on 5-HV production was investigated. Further enhancement was achieved by incorporating an NADPH supplementation system, resulting in the QluMG strain. In the 5 L fermenter, the QluMGD strain produced 21.7 g/L of 5-HV from 50 g/L glucose, with a conversion rate of 43.4 %. The successful integration of the RaiP pathway into the E. coli genome significantly enhanced 5-HV production. The QluMG strain achieved the highest reported yield from glucose in engineered E. coli to date. This study provides a new strategy for the efficient production of 5-HV and other chemicals using 5-HV as a precursor, demonstrating potential for industrial application.

Sustainable production of the drug precursor tyramine by engineered Corynebacterium glutamicum

Tyramine has attracted considerable interest due to recent findings that it is an excellent starting material for the production of high-performance thermoplastics and hydrogels. Furthermore, tyramine is a precursor of a diversity of pharmaceutically relevant compounds, contributing to its growing importance. Given the limitations of chemical synthesis, including lack of selectivity and laborious processes with harsh conditions, the biosynthesis of tyramine by decarboxylation of L-tyrosine represents a promising sustainable alternative. In this study, the de novo production of tyramine from simple nitrogen and sustainable carbon sources was successfully established by metabolic engineering of the L-tyrosine overproducing Corynebacterium glutamicum strain AROM3. A phylogenetic analysis of aromatic-L-amino acid decarboxylases (AADCs) revealed potential candidate enzymes for the decarboxylation of tyramine. The heterologous overexpression of the respective AADC genes resulted in successful tyramine production, with the highest tyramine titer of 1.9 g L-1 obtained for AROM3 overexpressing the tyrosine decarboxylase gene of Levilactobacillus brevis. Further metabolic engineering of this tyramine-producing strain enabled tyramine production from the alternative carbon sources ribose and xylose. Additionally, up-scaling of tyramine production from xylose to a 1.5 L bioreactor batch fermentation was demonstrated to be stable, highlighting the potential for sustainable tyramine production. KEY POINTS: • Phylogenetic analysis revealed candidate l-tyrosine decarboxylases • C. glutamicum was engineered for de novo production of tyramine • Tyramine production from alternative carbon substrates was enabled.

Fine-Regulating the Carbon Flux of l-Isoleucine Producing Corynebacterium glutamicum WM001 for Efficient l-Threonine Production

l-Threonine, an essential amino acid, is widely used in various industries, with an annually growing demand. However, the present Corynebacterium glutamicum strains are difficult to achieve industrialization of l-threonine due to low yield and purity. In this study, we engineered an l-isoleucine-producing C. glutamicum WM001 to efficiently produce l-threonine by finely regulating the carbon flux. First, the threonine dehydratase in WM001 was mutated to lower the level of l-isoleucine production, then the homoserine dehydrogenase and aspartate kinase were mutated to release the feedback inhibition of l-threonine, and the resulting strain TWZ006 produced 14.2 g/L l-threonine. Subsequently, aspartate ammonia-lyase and aspartate transaminase were overexpressed to accumulate the precursor l-aspartate. Next, phosphoenolpyruvate carboxylase, pyruvate carboxylase and pyruvate kinase were overexpressed, and phosphoenolpyruvate carboxykinase, oxaloacetate decarboxylase were inactivated to fine-regulate the carbon flux among oxaloacetate, pyruvate and phosphoenolpyruvate. The resulting strain TWZ017 produced 21.5 g/L l-threonine. Finally, dihydrodipicolinate synthase was mutated with strong allosteric inhibition from l-lysine to significantly decrease byproducts accumulation, l-threonine export was optimized, and the final engineered strain TWZ024/pXTuf-thrE produced 78.3 g/L of l-threonine with the yield of 0.33 g/g glucose and the productivity of 0.82 g/L/h in a 7 L bioreactor. To the best of our knowledge, this represents the highest l-threonine production in C. glutamicum, providing possibilities for industrial-scale production.

Corynebacterium glutamicum pyruvate:quinone oxidoreductase: an enigmatic metabolic enzyme with unusual structural features

Pyruvate:quinone oxidoreductase (PQO) is a flavin-containing peripheral membrane enzyme catalyzing the decarboxylation of pyruvate to acetate and CO2 with quinone as an electron acceptor. Here, we investigate PQO activity in Corynebacterium glutamicum, examine purified PQO, and describe the crystal structure of the native enzyme and a truncated version. The specific PQO activity was highest in stationary phase cells grown in complex medium, lower in cells grown in complex medium containing glucose or acetate, and lowest in cells grown in minimal acetate-medium. A similar pattern with about 30-fold higher specific PQO activities was observed in C. glutamicum with plasmid-bound pqo expression under the control of the tac promoter, indicating that the differences in PQO activity are likely due to post-transcriptional control. Continuous cultivation of C. glutamicum at dilution rates between 0.05 and 0.4 h-1 revealed a negative correlation between PQO activity and growth rate. Kinetic analysis of PQO enzymes purified from cells grown in complex or in minimal acetate-medium revealed substantial differences in specific activity (72.3 vs. 11.9 U·mg protein-1) and turnover number (kcat: 440 vs. 78 s-1, respectively), suggesting post-translational modifications affecting PQO activity. Structural analysis of PQO revealed a homotetrameric arrangement very similar to the Escherichia coli pyruvate oxidase PoxB except for the C-terminal membrane binding domain, which exhibited a conformation markedly different from its PoxB counterpart. A truncated PQO variant lacking 17 C-terminal amino acids showed higher affinity to pyruvate and was independent of detergent activation, highlighting the importance of the C-terminus for enzyme activation and lipid binding.

Mining unique cysteine synthetases and computational study on thoroughly eliminating feedback inhibition through tunnel engineering

L-cysteine is an essential component in pharmaceutical and agricultural industries, and synthetic biology has made strides in developing new metabolic pathways for its production, particularly in archaea with unique O-phosphoserine sulfhydrylases (OPSS) as key enzymes. In this study, we employed database mining to identify a highly catalytic activity OPSS from Acetobacterium sp. (AsOPSS). However, it was observed that the enzymatic activity of AsOPSS suffered significant feedback inhibition from the product L-cysteine, exhibiting an IC50 value of merely 1.2 mM. A semi-rational design combined with tunnel analysis strategy was conducted to engineer AsOPSS. The best variant, AsOPSSA218R was achieved, totally eliminating product inhibition without sacrificing catalytic efficiency. Molecular docking and molecular dynamic simulations indicated that the binding conformation of AsOPSSA218R with L-cys was altered, leading to a reduced affinity between L-cysteine and the active pocket. Tunnel analysis revealed that the AsOPSSA218R variant reshaped the landscape of the tunnel, resulting in the construction of a new tunnel. Furthermore, random acceleration molecular dynamics simulation and umbrella sampling simulation demonstrated that the novel tunnel improved the suitability for product release and effectively separated the interference between the product release and substrate binding processes. Finally, more than 45 mM of L-cysteine was produced in vitro within 2 h using the AsOPSSA218R variant. Our findings emphasize the potential for relieving feedback inhibition by artificially generating new product release channels, while also laying an enzymatic foundation for efficient L-cysteine production.

One-step cloning and targeted duplication of Pantoea ananatis chromosomal fragments

In this study, we describe a novel method for one-step cloning and targeted duplication of P. ananatis chromosomal fragments. According to this method, the chromosomal region of interest is subcloned in vivo via λ Red recombination into the short synthetic non-replicable DNA fragment containing the excisable antibiotic-resistance marker gene and φ80 att-P site. The resulting circular non-replicating DNA molecule was immediately inserted into an alternative chromosomal locus due to φ80-integrase activity. To this end, the specially designed helper plasmid pONI, which can provide both the λ Red recombineering and φ80-integrase-mediated insertion, was constructed. In the described method, PCR amplification of the cloning fragment is unnecessary, making it convenient for manipulation of long-length DNA. Additionally, the possibility of spontaneous mutations occurring is completely precluded. This method was effectively used for the targeted chromosomal integration of additional copies of individual genes and operons up to 16 kb in size.

Reducing Oxidative Stress Levels and Inhibiting Aging by l-Cysteine-Derived Carbon Dots with Highly Efficient Broad-Spectrum UV Absorption

Ultraviolet (UV) exposure causes damage to human skin and mucous membranes, resulting in oxidative stress, and can also lead to inflammation of human skin, skin aging, and even diseases such as squamous cell carcinoma and melanoma of the skin. The main means of protection against UV radiation is physical shielding and the use of sunscreen products. Carbon dots as a novel nanomaterial provide a new option for UV protection. In this article, we introduced sulfhydryl groups to synthesize l-cysteine-derived carbon dots (GLCDs) with UV resistance. GLCDs exhibit high-efficiency and excellent UV absorption, achieving 200-400 nm UV absorption (99% UVC, 97% UVB, and 86% UVA) at a low concentration of 0.5 mg/mL. Meanwhile, GLCDs can reduce apoptosis and UVB-induced oxidative damage, increase collagen type I gene expression, and inhibit skin aging in zebrafish. It also inhibits senescence caused by the senescence inducer 2,2'-azobis(2-methylpropionamidine) dihydrochloride and reduces oxidative damage. The above studies show that GLCDs possess efficient broad-spectrum UV absorption, antiphotoaging, and antiaging capabilities, which will have a broad application prospect in UV protection.

Utilization of orange peel waste for sustainable amino acid production by Corynebacterium glutamicum

Oranges are the most processed fruit in the world-it is therefore apparent that the industrial production of orange juice generates large quantities of orange peel as a by-product. Unfortunately, the management of the orange peel waste leads to economic and environmental problems. Meanwhile, the use of sustainable raw materials for the production of bulk chemicals, such as amino acids, is becoming increasingly attractive. To address both issues, this study focused on the use of orange peel waste as a raw material for media preparation for the production of amino acids by engineered Corynebacterium glutamicum. C. glutamicum grew on pure orange peel hydrolysate (OPH) and growth was enhanced by the addition of a nitrogen source and a pH buffer. Inhibitory effects by the combination of high concentrations of OPH, (NH4)2SO4, and MOPS buffer in the wild-type strain (WT), were overcome in the tyrosine-producing engineered C. glutamicum strain AROM3. Genetic modifications that we identified to allow for improved growth rates under these conditions included the deletions of the vanillin dehydrogenase gene vdh, the ʟ-lactate dehydrogenase gene ldhA and the 19 genes comprising cluster cg2663-cg2686. A growth inhibiting compound present in high concentrations in the OPH is 5-(hydroxymethyl)furfural (HMF). We identified vdh as being primarily responsible for the oxidation of HMF to its acid 5-hydroxymethyl-2-furancarboxylic acid (HMFCA), as the formation of HMFCA was reduced by 97% upon deletion of vdh in C. glutamicum WT. In addition, we showed that growth limitations could be overcome by adjusting the media preparation, using a combination of cheap ammonia water and KOH for pH neutralization after acidic hydrolysis. Overall, we developed a sustainable medium based on orange peel waste for the cultivation of C. glutamicum and demonstrated the successful production of the exemplary amino acids ʟ-arginine, ʟ-lysine, ʟ-serine, ʟ-valine and ʟ-tyrosine.

Engineering of the Lrp/AsnC-type transcriptional regulator DecR as a genetically encoded biosensor for multilevel optimization of L-cysteine biosynthesis pathway in Escherichia coli

L-cysteine is an important sulfur-containing amino acid being difficult to produce by microbial fermentation. Due to the lack of high-throughput screening methods, existing genetically engineered bacteria have been developed by simply optimizing the expression of L-cysteine-related genes one by one. To overcome this limitation, in this study, a biosensor-based approach for multilevel biosynthetic pathway optimization of L-cysteine from the DecR regulator variant of Escherichia coli was applied. Through protein engineering, we obtained the DecRN29Y/C81E/M90Q/M99E variant-based biosensor with improved specificity and an 8.71-fold increase in dynamic range. Using the developed biosensor, we performed high-throughput screening of the constructed promoter and RBS combination library, and successfully obtained the optimized strain, which resulted in a 6.29-fold increase in L-cysteine production. Molecular dynamics (MD) simulations and electrophoretic mobility shift analysis (EMSA) showed that the N29Y/C81E/M90Q/M99E variant had enhanced induction activity. This enhancement may be due to the increased binding of the variant to DNA in the presence of L-cysteine, which enhances transcriptional activation. Overall, our biosensor-based strategy provides a promising approach for optimizing biosynthetic pathways at multiple levels. The successful implementation of this strategy demonstrates its potential for screening improved recombinant strains.

Contributions of the anaplerotic reaction enzymes pyruvate carboxylase and phosphoenolpyruvate carboxylase to l-lysine production in Corynebacterium glutamicum

Anaplerotic reactions catalyzed by pyruvate carboxylase (PC) and phosphoenolpyruvate carboxylase (PEPC) have important roles in the production of l-lysine to replenish oxaloacetic acid (OAA) in Corynebacterium glutamicum. However, the relative contributions of these enzymes to l-lysine production in C. glutamicum are not fully understood. In this study, using a parent strain (P) carrying a feedback inhibition-resistant aspartokinase with the T311I mutation, we constructed a PC gene-deleted mutant strain (PΔPC) and a PEPC gene-deleted mutant strain (PΔPEPC). Although the growth of both mutant strains was comparable to the growth of strain P, the maximum l-lysine production in strains PΔPC and PΔPEPC decreased by 14% and 49%, respectively, indicating that PEPC strongly contributed to OAA supply. l-Lysine production in strain PΔPC slightly decreased during the logarithmic phase, while production during the early stationary phase was comparable to production in strain P. By contrast, strain PΔPEPC produced l-lysine in an amount comparable to the production of strain P during the logarithmic phase; l-lysine production after the early stationary phase was completely stopped in strain PΔPEPC. These results indicate that OAA is supplied by both PC and PEPC during the logarithmic phase, while only PEPC can continuously supply OAA after the logarithmic phase.

Recent Advances in Metabolic Engineering for the Biosynthesis of Phosphoenol Pyruvate-Oxaloacetate-Pyruvate-Derived Amino Acids

The phosphoenol pyruvate-oxaloacetate-pyruvate-derived amino acids (POP-AAs) comprise native intermediates in cellular metabolism, within which the phosphoenol pyruvate-oxaloacetate-pyruvate (POP) node is the switch point among the major metabolic pathways existing in most living organisms. POP-AAs have widespread applications in the nutrition, food, and pharmaceutical industries. These amino acids have been predominantly produced in Escherichia coli and Corynebacterium glutamicum through microbial fermentation. With the rapid increase in market requirements, along with the global food shortage situation, the industrial production capacity of these two bacteria has encountered two bottlenecks: low product conversion efficiency and high cost of raw materials. Aiming to push forward the update and upgrade of engineered strains with higher yield and productivity, this paper presents a comprehensive summarization of the fundamental strategy of metabolic engineering techniques around phosphoenol pyruvate-oxaloacetate-pyruvate node for POP-AA production, including L-tryptophan, L-tyrosine, L-phenylalanine, L-valine, L-lysine, L-threonine, and L-isoleucine. Novel heterologous routes and regulation methods regarding the carbon flux redistribution in the POP node and the formation of amino acids should be taken into consideration to improve POP-AA production to approach maximum theoretical values. Furthermore, an outlook for future strategies of low-cost feedstock and energy utilization for developing amino acid overproducers is proposed.

Toward Synthetic Intrinsically Disordered Polypeptides (IDPs): Controlled Incorporation of Glycine in the Ring-Opening Polymerization of N-Carboxyanhydrides

Intrinsically disordered proteins (IDPs) do not have a well-defined folded structure but instead behave as extended polymer chains in solution. Many IDPs are rich in glycine residues, which create steric barriers to secondary structuring and protein folding. Inspired by this feature, we have studied how the introduction of glycine residues influences the secondary structure of a model polypeptide, poly(l-glutamic acid), a helical polymer. For this purpose, we carried out ring-opening copolymerization with γ-benzyl-l-glutamate and glycine N-carboxyanhydride (NCA) monomers. We aimed to control the glycine distribution within PBLG by adjusting the reactivity ratios of the two NCAs using different reaction conditions (temperature, solvent). The relationship between those conditions, the monomer distributions, and the secondary structure enabled the design of intrinsically disordered polypeptides when a highly gradient microstructure was achieved in DMSO.

Production of L-serine and its derivative L-cysteine from renewable feedstocks using Corynebacterium glutamicum: advances and perspectives

L-serine and its derivative L-cysteine have broad industrial applications, and their direct fermentative production from renewable biomass is gaining increasing attention. Corynebacterium glutamicum is an extensively studied and well-established industrial microorganism, which is a predominant microbial host for producing amino acids. In this review, updated information on the genetics and molecular mechanisms underlying L-serine and L-cysteine production using C. glutamicum is presented, including their synthesis and degradation pathways, and other intracellular processes related to their production, as well as the mechanisms underlying substrate import and product export are also analyzed. Furthermore, metabolic strategies for strain improvement are systematically discussed, and conclusions and future perspectives for bio-based L-serine and L-cysteine production using C. glutamicum are presented. This review can provide a thorough understanding of L-serine and L-cysteine metabolic pathways to facilitate metabolic engineering modifications of C. glutamicum and development of more efficient industrial fermentation processes for L-serine and L-cysteine production.

Reconstruction the feedback regulation of amino acid metabolism to develop a non-auxotrophic L-threonine producing Corynebacterium glutamicum

L-Threonine is an important feed additive with the third largest market size among the amino acids produced by microbial fermentation. The GRAS (generally regarded as safe) industrial workhorse Corynebacterium glutamicum is an attractive chassis for L-threonine production. However, the present L-threonine production in C. glutamicum cannot meet the requirement of industrialization due to the relatively low production level of L-threonine and the accumulation of large amounts of by-products (such as L-lysine, L-isoleucine, and glycine). Herein, to enhance the L-threonine biosynthesis in C. glutamicum, releasing the aspartate kinase (LysC) and homoserine dehydrogenase (Hom) from feedback inhibition by L-lysine and L-threonine, respectively, and overexpressing four flux-control genes were performed. Next, to reduce the formation of by-products L-lysine and L-isoleucine without the cause of an auxotrophic phenotype, the feedback regulation of dihydrodipicolinate synthase (DapA) and threonine dehydratase (IlvA) was strengthened by replacing the native enzymes with heterologous analogues with more sensitive feedback inhibition by L-lysine and L-isoleucine, respectively. The resulting strain maintained the capability of synthesizing enough amounts of L-lysine and L-isoleucine for cell biomass formation but exhibited almost no extracellular accumulation of these two amino acids. To further enhance L-threonine production and reduce the by-product glycine, L-threonine exporter and homoserine kinase were overexpressed. Finally, the rationally engineered non-auxotrophic strain ZcglT9 produced 67.63 g/L (17.2% higher) L-threonine with a productivity of 1.20 g/L/h (108.0% higher) in fed-batch fermentation, along with significantly reduced by-product accumulation, representing the record for L-threonine production in C. glutamicum. In this study, we developed a strategy of reconstructing the feedback regulation of amino acid metabolism and successfully applied this strategy to de novo construct a non-auxotrophic L-threonine producing C. glutamicum. The main end by-products including L-lysine, L-isoleucine, and glycine were almost eliminated in fed-batch fermentation of the engineered C. glutamicum strain. This strategy can also be used for engineering producing strains for other amino acids and derivatives.

Microbial production of branched chain amino acids: Advances and perspectives

Branched-chain amino acids (BCAAs) such as L-valine, L-leucine, and L-isoleucine are widely used in food and feed. To comply with sustainable development goals, commercial production of BCAAs has been completely replaced with microbial fermentation. However, the efficient production of BCAAs by microorganisms remains a serious challenge due to their staggered metabolic networks and cell growth. To overcome these difficulties, systemic metabolic engineering has emerged as an effective and feasible strategy for the biosynthesis of BCAA. This review firstly summarizes the research advances in the microbial synthesis of BCAAs and representative engineering strategies. Second, systematic methods, such as high-throughput screening, adaptive laboratory evolution, and omics analysis, can be used to analyses the synthesis of BCAAs at the whole-cell level and further improve the titer of target chemicals. Finally, new tools and engineering strategies that may increase the production output and development direction of the microbial production of BCAAs are discussed.

Cloning and expression heterologous alanine dehydrogenase genes: Investigation of reductive amination potential of L-alanine dehydrogenases for green synthesis of alanine derivatives

Unnatural amino acids (UAAs) offer significant promise in a wide range of applications, including drug discovery, the custom design of peptides and proteins, and their utility and use as markers for monitoring molecular interactions in biological research. The synthesis of UAAs presents a formidable challenge and can be classified into two primary categories: enzymatic and chemical synthesis. Notably, the enzymatic route, specifically asymmetric synthesis, emerges as a an attractive method for procuring enantiopure UAAs with high efficiency, owing to its streamlined and concise reaction mechanism. The current study investigated the reductive amination activity mechanisms of alanine dehydrogenase (L-AlaDH), sourced from a combination of newly and previously characterized microorganisms. Our principal aim was to evaluate the catalytic efficiency of these L-AlaDH enzymes concerning a range of specific ketoacids and pyruvate to ascertain their capability for facilitating the production of both natural and unnatural amino acids. After the characterization processes, mutation points for TtAlaDH were determined and as a result of the mutations, mutants that could use ketocaproate and ketovalerate more effectively than the wild type were obtained. Among the enzymes studied, MetAlaDH exhibited the highest specific activity against pyruvate, 173 U/mg, and a KM value of 1.3 mM. VlAlaDH displayed the most favourable catalytic efficiency with a rate constant of 170 s-1mM-1. On the other hand, AfAlaDH demonstrated the highest catalytic efficiency against α-ketobutyrate (34.0 s-1mM-1) and α-ketovalerate (2.7 s-1mM-1). Of the enzymes investigated in the study, TtAlaDH exhibited the highest effectiveness among bacterial enzymes in catalyzing ketocaproate with a measured catalytic efficiency of about 0.6 s-1mM-1 and a KM value of approximately 0.3 mM. These findings provide valuable insights into the substrate specificity and catalytic performance of L-AlaDHs, enhancing our understanding of their potential applications in various biocatalytic processes.

Design of a dual-responding genetic circuit for high-throughput identification of L-threonine-overproducing Escherichia coli

L-threonine is a crucial amino acid that is extensively employed in the realms of food, animal feed and pharmaceuticals. Unfortunately, the lack of an appropriate biosensor has hindered the establishment of a robust high-throughput screening (HTS) system for the identification of the desired strains from random mutants. In this study, a dual-responding genetic circuit that capitalizes on the L-threonine inducer-like effect, the L-threonine riboswitch, and a signal amplification system was designed for the purpose of screening L-threonine overproducers. This platform effectively enhanced the performance of the enzyme and facilitated the identification of high L-threonine-producing strains from a random mutant library. Consequently, pathway optimization and directed evolution of the key enzyme enhanced L-threonine production by 4 and 7-fold, respectively. These results demonstrate the potential of biosensor design for dynamic metabolite detection and offer a promising tool for HTS and metabolic regulation for the development of L-threonine-hyperproducing strains.

Efficient L-valine production using systematically metabolic engineered Klebsiella oxytoca

L-Valine, a branched-chain amino acid with diversified applications, is biosynthesized with α-acetolactate as the key precursor. In this study, the metabolic flux in Klebsiella oxytoca PDL-K5, a Risk Group 1 organism producing 2,3-butanediol as the major fermentation product, was rearranged to L-valine production by introducing exogenous L-valine biosynthesis pathway and blocking endogenous 2,3-butanediol generation at the metabolic branch point α-acetolactate. After further enhancing L-valine efflux, strengthening pyruvate polymerization and selecting of key enzymes for L-valine synthesis, a plasmid-free K. oxytoca strain VKO-9 was obtained. Fed-batch fermentation with K. oxytoca VKO-9 in a 7.5 L fermenter generated 122 g/L L-valine with a yield of 0.587 g/g in 56 h. In addition, repeated fed-batch fermentation was conducted to prevent precipitation of L-valine due to oversaturation. The average concentration, yield, and productivity of produced L-valine in three cycles of repeated fed-batch fermentation were 81.3 g/L, 0.599 g/g, and 3.39 g/L/h, respectively.

Engineering serine hydroxymethyltransferases for efficient synthesis of L-serine in Escherichia coli

L-serine is a high-value amino acid widely used in the food, medicine, and cosmetic industries. However, the low yield of L-serine has limited its industrial production. In this study, a cellular factory for efficient synthesis of L-serine was obtained by engineering the serine hydroxymethyltransferases (SHMT). Firstly, after screening the SHMT from Alcanivorax dieselolei by genome mining, a mutant AdSHMTE266M with high thermal stability was identified through rational design. Subsequently, an iterative saturating mutant library was constructed by using coevolutionary analysis, and a mutant AdSHMTE160L/E193Q with enzyme activity 1.35 times higher than AdSHMT was identified. Additionally, the target protein AdSHMTE160L/E193Q/E266M was efficiently overexpressed by improving its mRNA stability. Finally, combining the substrate addition strategy and system optimization, the optimized strain BL21/pET28a-AdSHMTE160L/E193Q/E266M-5'UTR-REP3S16 produced 106.06 g/L L-serine, which is the highest production to date. This study provides new ideas and insights for the engineering design of SHMT and the industrial production of L-serine.

Synergistic application of atmospheric and room temperature plasma mutagenesis and adaptive laboratory evolution improves the tolerance of Escherichia coli to L-cysteine

L-Cysteine production through fermentation stands as a promising technology. However, excessive accumulation of L-cysteine poses a challenge due to the potential to inflict damage on cellular DNA. In this study, we employed a synergistic approach encompassing atmospheric and room temperature plasma mutagenesis (ARTP) and adaptive laboratory evolution (ALE) to improve L-cysteine tolerance in Escherichia coli. ARTP-treated populations obtained substantial enhancement in L-cysteine tolerance by ALE. Whole-genome sequencing, transcription analysis, and reverse engineering, revealed the pivotal role of an effective export mechanism mediated by gene eamB in augmenting L-cysteine resistance. The isolated tolerant strain, 60AP03/pTrc-cysEf , achieved a 2.2-fold increase in L-cysteine titer by overexpressing the critical gene cysEf during batch fermentation, underscoring its enormous potential for L-cysteine production. The production evaluations, supplemented with L-serine, further demonstrated the stability and superiority of tolerant strains in L-cysteine production. Overall, our work highlighted the substantial impact of the combined ARTP and ALE strategy in increasing the tolerance of E. coli to L-cysteine, providing valuable insights into improving L-cysteine overproduction, and further emphasized the potential of biotechnology in industrial production.

Highly Efficient Ru-Based Catalysts for Lactic Acid Conversion to Alanine

The primary objective of this research was to develop efficient solid catalysts that can directly convert the lactic acid (LA) obtained from lignocellulosic biomass into alanine (AL) through a reductive amination process. To achieve this, various catalysts based on ruthenium were synthesized using different carriers such as multi-walled carbon nanotubes (MWCNTs), beta-zeolite, and magnetic nanoparticles (MNPs). Among these catalysts, Ru/MNP demonstrated a remarkable yield of 74.0% for alanine at a temperature of 200 °C. This yield was found to be superior not only to the Ru/CNT (55.7%) and Ru/BEA (6.6%) catalysts but also to most of the previously reported catalysts. The characterization of the catalysts and their catalytic results revealed that metallic ruthenium nanoparticles, which were highly dispersed on the external surface of the magnetic carrier, significantly enhanced the catalyst's ability for dehydrogenation. Additionally, the -NH2 basic sites on the catalyst further facilitated the formation of alanine by promoting the adsorption of acidic reactants. Furthermore, the catalyst could be easily separated using an external magnetic field and exhibited the potential for multiple reuses without any significant loss in its catalytic performance. These practical advantages further enhance its appeal for applications in the reductive amination of lactic acid to alanine.

Challenges and Advances in the Bioproduction of L-Cysteine

L-cysteine is a proteogenic amino acid with many applications in the pharmaceutical, food, animal feed, and cosmetic industries. Due to safety and environmental issues in extracting L-cysteine from animal hair and feathers, the fermentative production of L-cysteine offers an attractive alternative using renewable feedstocks. Strategies to improve microbial production hosts like Pantoea ananatis, Corynebacterium glutamicum, Pseudomonas sp., and Escherichia coli are summarized. Concerning the metabolic engineering strategies, the overexpression of feedback inhibition-insensitive L-serine O-acetyltransferase and weakening the degradation of L-cysteine through the removal of L-cysteine desulfhydrases are crucial adjustments. The overexpression of L-cysteine exporters is vital to overcome the toxicity caused by intracellular accumulating L-cysteine. In addition, we compiled the process engineering aspects for the bioproduction of L-cysteine. Utilizing the energy-efficient sulfur assimilation pathway via thiosulfate, fermenting cheap carbon sources, designing scalable, fed-batch processes with individual feedings of carbon and sulfur sources, and implementing efficient purification techniques are essential for the fermentative production of L-cysteine on an industrial scale.

Genome-based analyses to learn from and about Paenibacillus sonchi genomovar Riograndensis SBR5T

Paenibacillus sonchi genomovar Riograndensis SBR5T is a plant growth-promoting rhizobacterium (PGPR) isolated in the Brazilian state of Rio Grande do Sul from the rhizosphere of Triticum aestivum. It fixes nitrogen, produces siderophores as well as the phytohormone indole-3-acetic acid, solubilizes phosphate and displays antagonist activity against Listeria monocytogenes and Pectobacterium carotovorum. Comprehensive omics analysis and the development of genetic tools are key to characterizing and engineering such non-model microorganisms. Therefore, the complete genome of SBR5T was sequenced, and shown to encode 6,705 proteins, 87 tRNAs, and 27 rRNAs and it enabled a landscape transcriptome analysis that unveiled conserved transcriptional and translational patterns and characterized operon structures and riboswitches. The pangenome of P. sonchi species is open with a stable core pangenome. At the same time, the analysis of genes coding for nitrogenases revealed that the trait of nitrogen fixation is sparse within the Paenibacillaceae family and the presence of Fe-only nitrogenase in the P. sonchi group was exclusive to SBR5T. The development of genetic tools for SBR5T enabled genetic transformation, plasmid construction for constitutive and inducible gene expression, and gene repression using the CRISPRi system. Altogether, the work with P. sonchi can guide the study of non-model bacteria with economic potential.

Enhanced L-serine production by Corynebacterium glutamicum based on novel insights into L-serine exporters

The L-serine exporters ThrE and SerE play important roles in L-serine production by Corynebacterium glutamicum. Deletion of both thrE and serE decreased L-serine titer by 60%, suggesting the existence of other L-serine exporters. A comparative transcriptomics identified NCgl0254 and NCgl0255 as novel L-serine exporters. Further analysis of the contributions of ThrE, SerE, NCgl0254, and NCgl0255 found that SerE was the major L-serine exporter in C. glutamicum and these four L-serine exporters were responsible for 79.7% of L-serine export. Deletion of one L-serine exporter upregulated the transcription levels of the other three, which might be coursed by increased intracellular concentrations of L-serine. Overexpression of NCgl0254 and NCgl0255 increased L-serine titer by 20.8% in C. glutamicum A36, while overexpression of the four L-serine exporters increased L-serine production by 31.9% (41.1 g·L-1 ) in C. glutamicum A36. The identification of novel L-serine exporters in C. glutamicum will help to improve industrial production of L-serine.

Structural and Biochemical Analysis of 3-Dehydroquinate Dehydratase from Corynebacterium glutamicum

Dehydroquinate dehydratase (DHQD) catalyzes the conversion of 3-dehydroquinic acid (DHQ) into 3-dehydroshikimic acid in the mid stage of the shikimate pathway, which is essential for the biosynthesis of aromatic amino acids and folates. Here, we report two the crystal structures of type II DHQD (CgDHQD) derived from Corynebacterium glutamicum, which is a widely used industrial platform organism. We determined the structures for CgDHQDWT with the citrate at a resolution of 1.80Å and CgDHQDR19A with DHQ complexed forms at a resolution of 2.00 Å, respectively. The enzyme forms a homododecamer consisting of four trimers with three interfacial active sites. We identified the DHQ-binding site of CgDHQD and observed an unusual binding mode of citrate inhibitor in the site with a half-opened lid loop. A structural comparison of CgDHQD with a homolog derived from Streptomyces coelicolor revealed differences in the terminal regions, lid loop, and active site. Particularly, CgDHQD, including some Corynebacterium species, possesses a distinctive residue P105, which is not conserved in other DHQDs at the position near the 5-hydroxyl group of DHQ. Replacements of P105 with isoleucine and valine, conserved in other DHQDs, caused an approximately 70% decrease in the activity, but replacement of S103 with threonine (CgDHQDS103T) caused a 10% increase in the activity. Our biochemical studies revealed the importance of key residues and enzyme kinetics for wild type and CgDHQDS103T, explaining the effect of the variation. This structural and biochemical study provides valuable information for understanding the reaction efficiency that varies due to structural differences caused by the unique sequences of CgDHQD.

p-Nitrobenzoate production from glucose by utilizing p-aminobenzoate N-oxygenase: AurF

Nitroaromatic compounds are widely used in industry, but their production is associated with issues such as the hazardousness of the process and low regioselectivity. Here, we successfully demonstrated the production of p-nitrobenzoate (PNBA) from glucose by constructing p-aminobenzoate N-oxygenase AurF-expressing E. coli. We generated this strain, which we named PN-1 by disrupting four genes involved in PNBA degradation: nfsA, nfsB, nemA, and azoR. We then expressed AurF from Streptomyces thioluteus in this strain, which resulted in the production of 945 mg/L PNBA in the presence of 1 g/L p-aminobenzoate. Direct production of PNBA from glucose was achieved by co-expressing the pabA, pabB, and pabC, as well as aurF, resulting in the production of 393 mg/L PNBA from 20 g/L glucose. To improve the PNBA titer, we disrupted genes involved in competing pathways: pheA, tyrA, trpE, pykA, and pykF. The resultant strain PN-4Ap produced 975 mg/L PNBA after 72 h of cultivation. These results highlight the potential of using microorganisms to produce other nitroaromatic compounds.

Genetically encoded ATP and NAD(P)H biosensors: potential tools in metabolic engineering

To date, many metabolic engineering tools and strategies have been developed, including tools for cofactor engineering, which is a common strategy for bioproduct synthesis. Cofactor engineering is used for the regulation of pyridine nucleotides, including NADH/NAD+ and NADPH/NADP+, and adenosine triphosphate/adenosine diphosphate (ATP/ADP), which is crucial for maintaining redox and energy balance. However, the intracellular levels of NADH/NAD+, NADPH/NADP+, and ATP/ADP cannot be monitored in real time using traditional methods. Recently, many biosensors for detecting, monitoring, and regulating the intracellular levels of NADH/NAD+, NADPH/NADP+, and ATP/ADP have been developed. Although cofactor biosensors have been mainly developed for use in mammalian cells, the potential application of cofactor biosensors in metabolic engineering in bacterial and yeast cells has received recent attention. Coupling cofactor biosensors with genetic circuits is a promising strategy in metabolic engineering for optimizing the production of biochemicals. In this review, we focus on the development of biosensors for NADH/NAD+, NADPH/NADP+, and ATP/ADP and the potential application of these biosensors in metabolic engineering. We also provide critical perspectives, identify current research challenges, and provide guidance for future research in this promising field.

Progress advances in the production of bio-sourced methionine and its hydroxyl analogues

The essential sulphur-containing amino acid, methionine, is becoming a mass-commodity product with an annual production that exceeded 1,500,000 tons in 2018. This amino acid is today almost exclusively produced by chemical process from fossil resources. The environmental problems caused by this industrial process, and the expected scarcity of oil resources in the coming years, have recently accelerated the development of bioprocesses for producing methionine from renewable carbon feedstock. After a brief description of the chemical process and the techno-economic context that still justify the production of methionine by petrochemical processes, this review will present the current state of the art of biobased alternatives aiming at a sustainable production of this amino acid and its hydroxyl analogues from renewable carbon feedstock. In particular, this review will focus on three bio-based processes, namely a purely fermentative process based on the metabolic engineering of the natural methionine pathway, a mixed process combining the production of the O-acetyl/O-succinyl homoserine intermediate of this pathway by fermentation followed by an enzyme-based conversion of this intermediate into L-methionine and lately, a hybrid process in which the non-natural chemical synthon, 2,4-dihydroxybutyric acid, obtained by fermentation of sugars is converted by chemo-catalysis into hydroxyl methionine analogues. The industrial potential of these three bioprocesses, as well as the major technical and economic obstacles that remain to be overcome to reach industrial maturity are discussed. This review concludes by bringing up the assets of these bioprocesses to meet the challenge of the "green transition", with the accomplishment of the objective "zero carbon" by 2050 and how they can be part of a model of Bioeconomy enhancing local resources.

Challenges and opportunities for engineered Escherichia coli as a pivotal chassis toward versatile tyrosine-derived chemicals production

Growing concerns over limited fossil resources and associated environmental problems are motivating the development of sustainable processes for the production of high-volume fuels and high-value-added compounds. The shikimate pathway, an imperative pathway in most microorganisms, is branched with tyrosine as the rate-limiting step precursor of valuable aromatic substances. Such occurrence suggests the shikimate pathway as a promising route in developing microbial cell factories with multiple applications in the nutraceutical, pharmaceutical, and chemical industries. Therefore, an increasing number of studies have focused on this pathway to enable the biotechnological manufacture of pivotal and versatile aromatic products. With advances in genome databases and synthetic biology tools, genetically programmed Escherichia coli strains are gaining immense interest in the sustainable synthesis of chemicals. Engineered E. coli is expected to be the next bio-successor of fossil fuels and plants in commercial aromatics synthesis. This review summarizes successful and applicable genetic and metabolic engineering strategies to generate new chassis and engineer the iterative pathway of the tyrosine route in E. coli, thus addressing the opportunities and current challenges toward the realization of sustainable tyrosine-derived aromatics.

Microbial production of L-methionine and its precursors using systems metabolic engineering

L-methionine is an essential amino acid with versatile applications in food, feed, cosmetics and pharmaceuticals. At present, the production of L-methionine mainly relies on chemical synthesis, which conflicts with the concern over serious environmental problems and sustainable development goals. In recent years, microbial production of natural products has been amply rewarded with the emergence and rapid development of system metabolic engineering. However, efficient L-methionine production by microbial fermentation remains a great challenge due to its complicated biosynthetic pathway and strict regulatory mechanism. Additionally, the engineered production of L-methionine precursors, L-homoserine, O-succinyl-L-homoserine (OSH) and O-acetyl-L-homoserine (OAH), has also received widespread attention because they can be catalyzed to L-methionine via a high-efficiently enzymatic reaction in vitro, which is also a promising alternative to chemical route. This review provides a comprehensive overview on the recent advances in the microbial production of L-methionine and its precursors, highlighting the challenges and potential solutions for developing L-methionine microbial cell factories from the perspective of systems metabolic engineering, aiming to offer guidance for future engineering.

Creating Polyploid Escherichia Coli and Its Application in Efficient L-Threonine Production

Prokaryotic genomes are generally organized in haploid. In synthetic biological research, efficient chassis cells must be constructed to produce bio-based products. Here, the essential division of the ftsZ gene to create functional polyploid E. coli is regulated. The artificial polyploid E. coli containing 2-4 chromosomes is confirmed through PCR amplification, terminator localization, and flow cytometry. The polyploid E. coli exhibits a larger cell size, and its low pH tolerance and acetate resistance are stronger than those of haploid E. coli. Transcriptome analysis shows that the genes of the cell's main functional pathways are significantly upregulated in the polyploid E. coli. These advantages of the polyploid E. coli results in the highest reported L-threonine yield (160.3 g L-1 ) in fed-batch fermentation to date. In summary, an easy and convenient method for constructing polyploid E. coli and demonstrated its application in L-threonine production is developed. This work provides a new approach for creating an excellent host strain for biochemical production and studying the evolution of prokaryotes and their chromosome functions.

Lignin-derived carbon nanosheets boost electrochemical reductive amination of pyruvate to alanine

Efficient and sustainable amino acid synthesis is essential for industrial applications. Electrocatalytic reductive amination has emerged as a promising method, but challenges such as undesired side reactions and low efficiency persist. Herein, we demonstrated a lignin-derived catalyst for alanine synthesis. Carbon nanosheets (CNSs) were synthesized from lignin via a template-assisted method and doped with nitrogen and sulfur to boost reductive amination and suppress side reactions. The resulting N,S-co-doped carbon nanosheets (NS-CNSs) exhibited outstanding electrochemical performance. It achieved a maximum alanine Faradaic efficiency of 79.5%, and a yield exceeding 1,199 μmol h-1 cm-2 on NS-CNS, with a selectivity above 99.9%. NS-CNS showed excellent durability during long-term electrolysis. Kinetic studies including control experiments and theoretical calculations provided further insights into the reaction pathway. Moreover, NS-CNS catalysts demonstrated potential in upgrading real-world polylactic acid plastic waste, yielding value-added alanine with a selectivity over 75%.

Microbial synthesis of the plant natural product precursor p-coumaric acid with Corynebacterium glutamicum

BACKGROUND

Phenylpropanoids such as p-coumaric acid represent important precursors for the synthesis of a broad range of plant secondary metabolites including stilbenoids, flavonoids, and lignans, which are of pharmacological interest due to their health-promoting properties. Although extraction from plant material or chemical synthesis is possible, microbial synthesis of p-coumaric acid from glucose has the advantage of being less expensive and more resource efficient. In this study, Corynebacterium glutamicum was engineered for the production of the plant polyphenol precursor p-coumaric acid from glucose.

RESULTS

Heterologous expression of the tyrosine ammonia-lyase encoding gene from Flavobacterium johnsoniae enabled the conversion of endogenously provided tyrosine to p-coumaric acid. Product consumption was avoided by abolishing essential reactions of the phenylpropanoid degradation pathway. Accumulation of anthranilate as a major byproduct was eliminated by reducing the activity of anthranilate synthase through targeted mutagenesis to avoid tryptophan auxotrophy. Subsequently, the carbon flux into the shikimate pathway was increased, phenylalanine biosynthesis was reduced, and phosphoenolpyruvate availability was improved to boost p-coumaric acid accumulation. A maximum titer of 661 mg/L p-coumaric acid (4 mM) in defined mineral medium was reached. Finally, the production strain was utilized in co-cultivations with a C. glutamicum strain previously engineered for the conversion of p-coumaric acid into the polyphenol resveratrol. These co-cultivations enabled the synthesis of 31.2 mg/L (0.14 mM) resveratrol from glucose without any p-coumaric acid supplementation.

CONCLUSIONS

The utilization of a heterologous tyrosine ammonia-lyase in combination with optimization of the shikimate pathway enabled the efficient production of p-coumaric acid with C. glutamicum. Reducing the carbon flux into the phenylalanine and tryptophan branches was the key to success along with the introduction of feedback-resistant enzyme variants.

Extraction and Purification of Highly Active Astaxanthin from Corynebacterium glutamicum Fermentation Broth

The marine carotenoid astaxanthin is one of the strongest natural antioxidants and therefore is used in a broad range of applications such as cosmetics or nutraceuticals. To meet the growing market demand, the natural carotenoid producer Corynebacterium glutamicum has been engineered to produce astaxanthin by heterologous expression of genes from the marine bacterium Fulvimarina pelagi. To exploit this promising source of fermentative and natural astaxanthin, an efficient extraction process using ethanol was established in this study. Appropriate parameters for ethanol extraction were identified by screening ethanol concentration (62.5-97.5% v/v), temperature (30-70 °C) and biomass-to-solvent ratio (3.8-19.0 mgCDW/mLsolvent). The results demonstrated that the optimal extraction conditions were: 90% ethanol, 60 °C, and a biomass-to-solvent ratio of 5.6 mgCDW/mLsolvent. In total, 94% of the cellular astaxanthin was recovered and the oleoresin obtained contained 9.4 mg/g astaxanthin. With respect to other carotenoids, further purification of the oleoresin by column chromatography resulted in pure astaxanthin (100%, HPLC). In addition, a 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay showed similar activities compared to esterified astaxanthin from microalgae and a nine-fold higher antioxidative activity than synthetic astaxanthin.

Transcription factor OxyR regulates sulfane sulfur removal and L-cysteine biosynthesis in Corynebacterium glutamicum

Sulfane sulfur, a collective term for hydrogen polysulfide and organic persulfide, often damages cells at high concentrations. Cells can regulate intracellular sulfane sulfur levels through specific mechanisms, but these mechanisms are unclear in Corynebacterium glutamicum. OxyR is a transcription factor capable of sensing oxidative stress and is also responsive to sulfane sulfur. In this study, we found that OxyR functioned directly in regulating sulfane sulfur in C. glutamicum. OxyR binds to the promoter of katA and nrdH and regulates its expression, as revealed via in vitro electrophoretic mobility shift assay analysis, real-time quantitative PCR, and reporting systems. Overexpression of katA and nrdH reduced intracellular sulfane sulfur levels by over 30% and 20% in C. glutamicum, respectively. RNA-sequencing analysis showed that the lack of OxyR downregulated the expression of sulfur assimilation pathway genes and/or sulfur transcription factors, which may reduce the rate of sulfur assimilation. In addition, OxyR also affected the biosynthesis of L-cysteine in C. glutamicum. OxyR overexpression strain Cg-2 accumulated 183 mg/L of L-cysteine, increased by approximately 30% compared with the control (142 mg/L). In summary, OxyR not only regulated sulfane sulfur levels by controlling the expression of katA and nrdH in C. glutamicum but also facilitated the sulfur assimilation and L-cysteine synthesis pathways, providing a potential target for constructing robust cell factories of sulfur-containing amino acids and their derivatives. IMPORTANCE C. glutamicum is an important industrial microorganism used to produce various amino acids. In the production of sulfur-containing amino acids, cells inevitably accumulate a large amount of sulfane sulfur. However, few studies have focused on sulfane sulfur removal in C. glutamicum. In this study, we not only revealed the regulatory mechanism of OxyR on intracellular sulfane sulfur removal but also explored the effects of OxyR on the sulfur assimilation and L-cysteine synthesis pathways in C. glutamicum. This is the first study on the removal of sulfane sulfur in C. glutamicum. These results contribute to the understanding of sulfur regulatory mechanisms and may aid in the future optimization of C. glutamicum for biosynthesis of sulfur-containing amino acids.

Balancing Redox Homeostasis to Improve l-Cysteine Production in Corynebacterium glutamicum

l-Cysteine is a valuable sulfur-containing amino acid with applications across a wide range of fields. Recently, microbial fermentation has emerged as a method to produce l-cysteine. However, cellular redox stress from high levels of l-cysteine is a bottleneck for achieving efficient production. In this study, we aimed to facilitate l-cysteine biosynthesis by modulating cellular redox homeostasis through the introduction of the natural antioxidant astaxanthin in Corynebacterium glutamicum. To achieve this, we first introduced an exogenous astaxanthin synthesis module in C. glutamicum. Then, an l-cysteine-dependent autonomous bifunctional genetic switch was developed to dynamically regulate the l-cysteine and astaxanthin biosynthesis pathway to maintain cellular redox homeostasis. This regulation system achieved high biosynthesis of astaxanthin, which significantly facilitated l-cysteine production. Finally, engineered strain Cg-10 produced 8.45 g/L l-cysteine and 95 mg/L astaxanthin in a 5 L bioreactor, both of which are the highest reported levels in C. glutamicum.

Combinatorial Metabolic Engineering of Escherichia coli for Enhanced L-Cysteine Production: Insights into Crucial Regulatory Modes and Optimization of Carbon-Sulfur Metabolism and Cofactor Availability

Microbial production of valuable compounds can be enhanced by various metabolic strategies. This study proposed combinatorial metabolic engineering to develop an effective Escherichia coli cell factory dedicated to L-cysteine production. First, the crucial regulatory modes that control L-cysteine levels were investigated to guide metabolic modifications. A two-stage fermentation was achieved by employing multi-copy gene expression, improving the balance between production and growth. Subsequently, carbon flux distribution was further optimized by modifying the C1 unit metabolism and the glycolytic pathway. The modifications of sulfur assimilation demonstrated superior performance of thiosulfate utilization pathways in enhancing L-cysteine titer. Furthermore, the studies focusing on cofactor availability and preference emphasized the vital role of synergistic enhancement of sulfur-carbon metabolism in L-cysteine overproduction. In a 5 L bioreactor, the strain BW15-3/pED accumulated 12.6 g/L of L-cysteine. This work presented an effective metabolic engineering strategy for the development of L-cysteine-producing strains.