Microbial Production of l-Serine from Renewable Feedstocks

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.

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.

One-Pot Synthesis of Useful S-Substituted-l-cysteine Sulfoxides Using Genetically Engineered Escherichia coli

S-Substituted-l-cysteine sulfoxides are valuable compounds that are contained in plants. Particularly, (+)-alliin and its degraded products have gained significant attention because of their human health benefits. However, (+)-alliin production has been limited to extraction from plants and chemical synthesis; both methods have drawbacks in terms of stability and safety. Here, we proposed the enzymatic cascade reaction for synthesizing (+)-alliin from readily available substrates. To achieve a one-pot (+)-alliin production, we constructed Escherichia coli coexpressing the genes encoding tryptophan synthase from Aeromonas hydrophila ssp. hydrophila NBRC 3820 and l-isoleucine hydroxylase from Bacillus thuringiensis 2e2 for the biocatalyst. Deletion of tryptophanase gene in E. coli increased the yield about 2-fold. Under optimized conditions, (+)-alliin accumulation reached 110 mM, which is the highest productivity thus far. Moreover, natural and unnatural S-substituted-l-cysteine sulfoxides were synthesized by applying various thiols to the cascade reaction. These results indicate that the developed bioprocess would enable the supply of diverse S-substituted-l-cysteine sulfoxides.

Rewiring Metabolic Flux in Corynebacterium glutamicum Using a CRISPR/dCpf1-Based Bifunctional Regulation System

Corynebacterium glutamicum, a microorganism classified as generally recognized as safe for use in the industrial production of food raw materials and additives, has encountered challenges in achieving widespread adoption and popularization as microbial cell factories. These obstacles arise from the intricate nature of manipulating metabolic flux through conventional methods, such as gene knockout and enzyme overexpression. To address this challenge, we developed a CRISPR/dCpf1-based bifunctional regulation system to bidirectionally regulate the expression of multiple genes in C. glutamicum. Specifically, through fusing various transcription factors to the C-terminus of dCpf1, the resulting dCpf1-SoxS exhibited both CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) capabilities in C. glutamicum by altering the binding sites of crRNAs. The bifunctional regulation system was used to fine-tune metabolic flux from shikimic acid (SA) and l-serine biosynthesis, resulting in 27-fold and 10-fold increases in SA and l-serine production, respectively, compared to the original strain. These findings highlight the potential of the CRISPR/dCpf1-based bifunctional regulation system in effectively enhancing the yield of target products in C. glutamicum.

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.

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.

Microbial production of vitamin B5: current status and prospects

Vitamin B5, also called D-pantothenic acid (D-PA), is a necessary micronutrient that plays an essential role in maintaining the physiological function of an organism. It is widely used in: food, medicine, feed, cosmetics, and other fields. Currently, the production of D-PA in industry heavily relies on chemical processes and enzymatic catalysis. With an increasing demand on the market, replacing chemical-based production of D-PA with microbial fermentation utilizing renewable resources is necessary. In this review, the physiological role and applications of D-PA were firstly introduced, after which the biosynthesis pathways and enzymes will be summarized. Subsequently, a series of cell factory development strategies for excessive D-PA production are analyzed and discussed. Finally, the prospect of microbial production of D-PA production has been prospected.

Engineering acetylation platform for the total biosynthesis of D-amino acids

Optically pure D-amino acids are key chemicals with various applications. Although the production of specific D-amino acids has been achieved by chemical synthesis or with in vitro enzyme catalysts, it is challenging to convert a simple carbon source into D-amino acids with high efficiency. Here, we design an artificial metabolic pathway by engineering bacteria to heterologously express racemase and N-acetyltransferase to produce N-acetyl-D-amino acids from L-amino acids. This new platform allows the cytotoxicity of D-amino acids to be avoided. The universal potential of this acetylation protection strategy for effectively synthesizing optically pure D-amino acids is demonstrated by testing sixteen amino acid targets. Furthermore, we combine pathway optimization and metabolic engineering in Escherichia coli and achieve practically useful efficiency with four specific examples, including N-acetyl-D-valine, N-acetyl-D-serine, N-acetyl-D-phenylalanine and N-acetyl-D-phenylglycine, with titers reaching 5.65 g/L, 5.25 g/L, 8.025 g/L and 130 mg/L, respectively. This work opens up opportunities for synthesizing D-amino acids directly from simple carbon sources, avoiding costly and unsustainable conventional approaches.

Multi-Level Optimization and Strategies in Microbial Biotransformation of Nature Products

Continuously growing demand for natural products with pharmacological activities has promoted the development of microbial transformation techniques, thereby facilitating the efficient production of natural products and the mining of new active compounds. Furthermore, due to the shortcomings and defects of microbial transformation, it is an important scientific issue of social and economic value to improve and optimize microbial transformation technology in increasing the yield and activity of transformed products. In this review, the aspects regarding the optimization of fermentation and the cross-disciplinary strategy, leading to the microbial transformation of increased levels of the high-efficiency process from natural products of a plant or microbial origin, were discussed. Additionally, due to the increasing craving for targeted and efficient methods for detecting transformed metabolites, analytical methods based on multiomics were also discussed. Such strategies can be well exploited and applied to the production of more efficient and more natural products from microbial resources.

Biodegradation of Pine Processionary Caterpillar Silk Is Mediated by Elastase- and Subtilisin-like Proteases

Pine processionary caterpillar nests are made from raw silk. Fibroin protein is the main component of silk which, in the case of pine processionary caterpillar, has some unusual properties such as a higher resistance to chemical hydrolysis. Isolation of microorganisms naturally present in silk nests led to identification of Bacillus licheniformis and Pseudomonas aeruginosa strains that in a defined minimal medium were able to carry out extensive silk biodegradation. A LasB elastase-like protein from P. aeruginosa was shown to be involved in silk biodegradation. A recombinant form of this protein expressed in Escherichia coli and purified by affinity chromatography was able to efficiently degrade silk in an in vitro assay. However, silk biodegradation by B. licheniformis strain was mediated by a SubC subtilisin-like protease. Homologous expression of a subtilisin Carlsberg encoding gene (subC) allowed faster degradation compared to the biodegradation kinetics of a wildtype B. licheniformis strain. This work led to the identification of new enzymes involved in biodegradation of silk materials, a finding which could lead to possible applications for controlling this pest and perhaps have importance from sanitary and biotechnological points of view.

Bioprocess Engineering, Transcriptome, and Intermediate Metabolite Analysis of L-Serine High-Yielding Escherichia coli W3110

L-serine is widely used in the food, cosmetic, and pharmaceutical industries. However, the complicated metabolic network and regulatory mechanism of L-serine production lead to the suboptimal productivity of the direct fermentation of L-serine and limits its large-scale industrial production. In this study, a high-yield L-serine production Escherichia coli strain was constructed by a series of defined genetic modification methodologies. First, L-serine-mediated feedback inhibition was removed and L-serine biosynthetic pathway genes (serAfr, serC, and serB) associated with phosphoglycerate kinase (pgk) were overexpressed. Second, the L-serine conversion pathway was further examined by introducing a glyA mutation (K229G) and deleting other degrading enzymes based on the deletion of initial sdaA. Finally, the L-serine transport system was rationally engineered to reduce uptake and accelerate L-serine export. The optimally engineered strain produced 35 g/L L-serine with a productivity of 0.98 g/L/h and a yield of 0.42 g/g glucose in a 5-L fermenter, the highest productivity and yield of L-serine from glucose reported to date. Furthermore, transcriptome and intermediate metabolite of the high-yield L-serine production Escherichia coli strain were analyzed. The results demonstrated the regulatory mechanism of L-serine production is delicate, and that combined metabolic and bioprocess engineering strategies for L-serine producing strains can improve the productivity and yield.

Revealing a New Family of D-2-Hydroxyglutarate Dehydrogenases in Escherichia coli and Pantoea ananatis Encoded by ydiJ

In E. coli and P. ananatis, L-serine biosynthesis is initiated by the action of D-3-phosphoglycerate dehydrogenase (SerA), which converts D-3-phosphoglycerate into 3-phosphohydroxypyruvate. SerA can concomitantly catalyze the production of D-2-hydroxyglutarate (D-2-HGA) from 2-ketoglutarate by oxidizing NADH to NAD⁺. Several bacterial D-2-hydroxyglutarate dehydrogenases (D2HGDHs) have recently been identified, which convert D-2-HGA back to 2-ketoglutarate. However, knowledge about the enzymes that can metabolize D-2-HGA is lacking in bacteria belonging to the Enterobacteriaceae family. We found that ydiJ encodes novel D2HGDHs in P. ananatis and E. coli, which were assigned as D2HGDHPa and D2HGDHEc, respectively. Inactivation of ydiJ in P. ananatis and E. coli led to the significant accumulation of D-2-HGA. Recombinant D2HGDHEc and D2HGDHPa were purified to homogeneity and characterized. D2HGDHEc and D2HGDHPa are homotetrameric with a subunit molecular mass of 110 kDa. The pH optimum was 7.5 for D2HGDHPa and 8.0 for D2HGDHEc. The Km for D-2-HGA was 208 μM for D2HGDHPa and 83 μM for D2HGDHEc. The enzymes have strict substrate specificity towards D-2-HGA and displayed maximal activity at 45 °C. Their activity was completely inhibited by 0.5 mM Mn²⁺, Ni²⁺ or Co²⁺. The discovery of a novel family of D2HGDHs may provide fundamental information for the metabolic engineering of microbial chassis with desired properties.

Diaphorin, a Polyketide Produced by a Bacterial Symbiont of the Asian Citrus Psyllid, Inhibits the Growth and Cell Division of Bacillus subtilis but Promotes the Growth and Metabolic Activity of Escherichia coli

Diaphorin is a polyketide produced by “Candidatus Profftella armatura” (Gammaproteobacteria: Burkholderiales), an obligate symbiont of a notorious agricultural pest, the Asian citrus psyllid Diaphorina citri (Hemiptera: Psyllidae). Diaphorin belongs to the pederin family of bioactive agents found in various host-symbiont systems, including beetles, lichens, and sponges, harboring phylogenetically diverse bacterial producers. Previous studies showed that diaphorin, which is present in D. citri at concentrations of 2 to 20 mM, has inhibitory effects on various eukaryotes, including the natural enemies of D. citri. However, little is known about its effects on prokaryotic organisms. To address this issue, the present study assessed the biological activities of diaphorin on two model prokaryotes, Escherichia coli (Gammaproteobacteria: Enterobacterales) and Bacillus subtilis (Firmicutes: Bacilli). Their growth and morphological features were analyzed using spectrophotometry, optical microscopy followed by image analysis, and transmission electron microscopy. The metabolic activity of E. coli was further assessed using the β-galactosidase assay. The results revealed that physiological concentrations of diaphorin inhibit the growth and cell division of B. subtilis but promote the growth and metabolic activity of E. coli. This finding implies that diaphorin functions as a defensive agent of the holobiont (host plus symbionts) against some bacterial lineages but is metabolically beneficial for others, which potentially include obligate symbionts of D. citri.

IMPORTANCE Certain secondary metabolites, including antibiotics, evolve to mediate interactions among organisms. These molecules have distinct spectra for microorganisms and are often more effective against Gram-positive bacteria than Gram-negative ones. However, it is rare that a single molecule has completely opposite activities on distinct bacterial lineages. The present study revealed that a secondary metabolite synthesized by an organelle-like bacterial symbiont of psyllids inhibits the growth of Gram-positive Bacillus subtilis but promotes the growth of Gram-negative Escherichia coli. This finding not only provides insights into the evolution of microbiomes in animal hosts but also may potentially be exploited to promote the effectiveness of industrial material production by microorganisms.

Gene sdaB Is Involved in the Nematocidal Activity of Enterobacter ludwigii AA4 Against the Pine Wood Nematode Bursaphelenchus xylophilus

Bursaphelenchus xylophilus, a plant parasitic nematode, is the causal agent of pine wilt, a devastating forest tree disease. Essentially, no efficient methods for controlling B. xylophilus and pine wilt disease have yet been developed. Enterobacter ludwigii AA4, isolated from the root of maize, has powerful nematocidal activity against B. xylophilus in a new in vitro dye exclusion test. The corrected mortality of the B. xylophilus treated by E. ludwigii AA4 or its cell extract reached 98.3 and 98.6%, respectively. Morphological changes in B. xylophilus treated with a cell extract from strain AA4 suggested that the death of B. xylophilus might be caused by an increased number of vacuoles in non-apoptotic cell death and the damage to tissues of the nematodes. In a greenhouse test, the disease index of the seedlings of Scots pine (Pinus sylvestris) treated with the cells of strain AA4 plus B. xylophilus or those treated by AA4 cell extract plus B. xylophilus was 38.2 and 30.3, respectively, was significantly lower than 92.5 in the control plants treated with distilled water and B. xylophilus. We created a sdaB gene knockout in strain AA4 by deleting the gene that was putatively encoding the beta-subunit of L-serine dehydratase through Red homologous recombination. The nematocidal and disease-suppressing activities of the knockout strain were remarkably impaired. Finally, we revealed a robust colonization of P. sylvestris seedling needles by E. ludwigii AA4, which is supposed to contribute to the disease-controlling efficacy of strain AA4. Therefore, E. ludwigii AA4 has significant potential to serve as an agent for the biological control of pine wilt disease caused by B. xylophilus.

Enhanced L-ornithine production from glucose and sucrose via manipulation of the fructose metabolic pathway in Corynebacterium glutamicum

L-Ornithine, an important non-essential amino acid, has considerable medicinal value in the treatment of complex liver diseases. Microbial fermentation strategies using robust engineered strains have remarkable potential for producing L-ornithine. We showed that glucose and sucrose co-utilization accumulate more L-ornithine in Corynebacterium glutamicum than glucose alone. Further manipulating the expression of intracellular fructose-1-phosphate kinase through the deletion of pfkB1resulted in the engineered strain C. glutamicum SO30 that produced 47.6 g/L of L-ornithine, which represents a 32.8% increase than the original strain C. glutamicum SO26 using glucose as substrate (35.88 g/L). Moreover, fed-batch cultivation of C. glutamicum SO30 in 5-L fermenters produced 78.0 g/L of L-ornithine, which was a 78.9% increase in yield compared with that produced by C. glutamicum SO26. These results showed that manipulating the fructose metabolic pathway increases L-ornithine accumulation and provides a reference for developing C. glutamicum to produce valuable metabolites.

Feedback regulation and coordination of the main metabolism for bacterial growth and metabolic engineering for amino acid fermentation

Living organisms such as bacteria are often exposed to continuous changes in the nutrient availability in nature. Therefore, bacteria must constantly monitor the environmental condition, and adjust the metabolism quickly adapting to the change in the growth condition. For this, bacteria must orchestrate (coordinate and integrate) the complex and dynamically changing information on the environmental condition. In particular, the central carbon metabolism (CCM), monomer synthesis, and macromolecular synthesis must be coordinately regulated for the efficient growth. It is a grand challenge in bioscience, biotechnology, and synthetic biology to understand how living organisms coordinate the metabolic regulation systems. Here, we consider the integrated sensing of carbon sources by the phosphotransferase system (PTS), and the feed-forward/feedback regulation systems incorporated in the CCM in relation to the pool sizes of flux-sensing metabolites and αketoacids. We also consider the metabolic regulation of amino acid biosynthesis (as well as purine and pyrimidine biosyntheses) paying attention to the feedback control systems consisting of (fast) enzyme level regulation with (slow) transcriptional regulation. The metabolic engineering for the efficient amino acid production by bacteria such as Escherichia coli and Corynebacterium glutamicum is also discussed (in relation to the regulation mechanisms). The amino acid synthesis is important for determining the rate of ribosome biosynthesis. Thus, the growth rate control (growth law) is further discussed on the relationship between (p)ppGpp level and the ribosomal protein synthesis.

Fine-Tuning Multi-Gene Clusters via Well-Characterized Gene Expression Regulatory Elements: Case Study of the Arginine Synthesis Pathway in C. glutamicum

Promoters and ribosome binding sites (RBSs) are routinely applied in gene expression regulation, but their orthogonality and combinatorial effects have not yet been systematically studied in Corynebacterium glutamicum. Here, 17 core promoters and 29 RBSs in C. glutamicum were characterized, which exhibited 470-fold and 430-fold in transcriptional and translational activity, respectively. By comparing the expression of two reporter genes regulated by multiple RBSs, the RBS efficacy showed significant dependence on the gene context, besides the RBSs' strength, reflecting the poor orthogonality of RBSs. Bicistron-modified RBS (referred as bc-RBS) was adapted to C. glutamicum, which improved RBS reliability. By coupling a series of promoters with RBSs/bc-RBSs, a much broader regulation range that spanned 4 orders of magnitude was observed compared with that of a sole element, and the contribution to gene expression of RBS was more than that of promoter. Finally, promoters and RBSs were applied as built-in elements to fine-tune the gene cluster in the arginine synthesis pathway in C. glutamicum. Compared with the original strain, more arginine (1.61-fold) or citrulline (2.35-fold) was accumulated in a 7 L bioreactor by strains with the gene expression regulation system rationally engineered. We demonstrated that, via combination of well-characterized gene elements, and overall consideration for both transcription and translation, the biosynthesis pathway can be effectively balanced, and the yield of a target metabolite can be further improved.

Development of a Cofactor Balanced, Multi Enzymatic Cascade Reaction for the Simultaneous Production of L-Alanine and L-Serine from 2-Keto-3-deoxy-gluconate

Enzymatic reaction cascades represent a powerful tool to convert biogenic resources into valuable chemicals for fuel and commodity markets. Sugars and their breakdown products constitute a significant group of possible substrates for such biocatalytic conversion strategies to value-added products. However, one major drawback of sugar cascades is the need for cofactor recycling without using additional enzymes and/or creating unwanted by-products. Here, we describe a novel, multi-enzymatic reaction cascade for the one-pot simultaneous synthesis of L-alanine and L-serine, using the sugar degradation product 2-keto-3-deoxygluconate and ammonium as precursors. To pursue this aim, we used four different, thermostable enzymes, while the necessary cofactor NADH is recycled entirely self-sufficiently. Buffer and pH optimisation in combination with an enzyme titration study yielded an optimised production of 21.3 +/− 1.0 mM L-alanine and 8.9 +/− 0.4 mM L-serine in one pot after 21 h.

Rational modification of the carbon metabolism of Corynebacterium glutamicum to enhance l-leucine production

l-Leucine is an essential amino acid that has wide and expanding applications in the industry. It is currently fast-growing market demand that provides a powerful impetus to further increase its bioconversion productivity and production stability. In this study, we rationally engineered the metabolic flux from pyruvate to l-leucine synthesis in Corynebacterium glutamicum to enhance both pyruvate availability and l-leucine synthesis. First, the pyc (encoding pyruvate carboxylase) and avtA (encoding alanine-valine aminotransferase) genes were deleted to weaken the metabolic flux of the tricarboxylic acid cycle and reduce the competitive consumption of pyruvate. Next, the transcriptional level of the alaT gene (encoding alanine aminotransferase) was down regulated by inserting a terminator to balance l-leucine production and cell growth. Subsequently, the genes involved in l-leucine biosynthesis were overexpressed by replacing the native promoters PleuA and PilvBNC of the leuA gene and ilvBNC operon, respectively, with the promoter Ptuf of eftu (encoding elongation factor Tu) and using a shuttle expression vector. The resulting strain WL-14 produced 28.47 ± 0.36 g/L l-leucine in shake flask fermentation.

High-yield production of L-serine through a novel identified exporter combined with synthetic pathway in Corynebacterium glutamicum

Background

l-Serine has wide and increasing applications in industries with fast-growing market demand. Although strategies for achieving and improving l-serine production in Corynebacterium glutamicum (C. glutamicum) have focused on inhibiting its degradation and enhancing its biosynthetic pathway, l-serine yield has remained relatively low. Exporters play an essential role in the fermentative production of amino acids. To achieve higher l-serine yield, l-serine export from the cell should be improved. In C. glutamicum, ThrE, which can export l-threonine and l-serine, is the only identified l-serine exporter so far.

Results

In this study, a novel l-serine exporter NCgl0580 was identified and characterized in C. glutamicum ΔSSAAI (SSAAI), and named as SerE (encoded by serE). Deletion of serE in SSAAI led to a 56.5% decrease in l-serine titer, whereas overexpression of serE compensated for the lack of serE with respect to l-serine titer. A fusion protein with SerE and enhanced green fluorescent protein (EGFP) was constructed to confirm that SerE localized at the plasma membrane. The function of SerE was studied by peptide feeding approaches, and the results showed that SerE is a novel exporter for l-serine and l-threonine in C. glutamicum. Subsequently, the interaction of a known l-serine exporter ThrE and SerE was studied, and the results suggested that SerE is more important than ThrE in l-serine export in SSAAI. In addition, probe plasmid and electrophoretic mobility shift assays (EMSA) revealed NCgl0581 as the transcriptional regulator of SerE. Comparative transcriptomics between SSAAI and the NCgl0581 deletion strain showed that NCgl0581 is a positive regulator of NCgl0580. Finally, by overexpressing the novel exporter SerE, combined with l-serine synthetic pathway key enzyme serAΔ197, serC, and serB, the resulting strain presented an l-serine titer of 43.9 g/L with a yield of 0.44 g/g sucrose, which is the highest l-serine titer and yield reported so far in C. glutamicum.

Conclusions

This study provides a novel target for l-serine and l-threonine export engineering as well as a new global transcriptional regulator NCgl0581 in C. glutamicum.

Improving L-serine formation by Escherichia coli by reduced uptake of produced L-serine

Background

Microbial de novo production of l-serine, which is widely used in a range of cosmetic and pharmaceutical products, has attracted increasing attention due to its environmentally friendly characteristics. Previous pioneering work mainly focused on l-serine anabolism; however, in this study, it was found that l-serine could be reimported through the l-serine uptake system, thus hampering l-serine production.

Result

To address this challenge, engineering via deletion of four genes, namely, sdaC, cycA, sstT and tdcC, which have been reported to be involved in l-serine uptake in Escherichia coli, was first carried out in the l-serine producer E. coli ES. Additionally, the effects of these genes on l-serine uptake activity and l-serine production were investigated. The data revealed an abnormal phenomenon regarding serine uptake activity. The serine uptake activity of the ΔsdaC mutant was 0.798 nmol min⁻¹ (mg dry weight) ⁻¹ after 30 min, decreasing by 23.34% compared to that of the control strain. However, the serine uptake activity of the single sstT, cycA and tdcC mutants increased by 34.29%, 78.29% and 48.03%, respectively, compared to that of the control strain. This finding may be the result of the increased level of sdaC expression in these mutants. In addition, multigene-deletion strains were constructed based on an sdaC knockout mutant. The ΔsdaCΔsstTΔtdcC mutant strain exhibited 0.253 nmol min⁻¹ (mg dry weight) ⁻¹l-serine uptake activity and the highest production titer of 445 mg/L in shake flask fermentation, which was more than three-fold the 129 mg/L production observed for the parent. Furthermore, the ΔsdaCΔsstTΔtdcC mutant accumulated 34.8 g/L l-serine with a yield of 32% from glucose in a 5-L fermenter after 36 h.

Conclusion

The results indicated that reuptake of l-serine impairs its production and that an engineered cell with reduced uptake can address this problem and improve the production of l-serine in E. coli.

Metabolic engineering of Escherichia coli for shikimate pathway derivative production from glucose-xylose co-substrate

Glucose and xylose are the major components of lignocellulose. Effective utilization of both sugars can improve the efficiency of bioproduction. Here, we report a method termed parallel metabolic pathway engineering (PMPE) for producing shikimate pathway derivatives from glucose–xylose co-substrate. In this method, we seek to use glucose mainly for target chemical production, and xylose for supplying essential metabolites for cell growth. Glycolysis and the pentose phosphate pathway are completely separated from the tricarboxylic acid (TCA) cycle. To recover cell growth, we introduce a xylose catabolic pathway that directly flows into the TCA cycle. As a result, we can produce 4.09 g L⁻¹cis,cis-muconic acid using the PMPE Escherichia coli strain with high yield (0.31 g g⁻¹ of glucose) and produce l-tyrosine with 64% of the theoretical yield. The PMPE strategy can contribute to the development of clean processes for producing various valuable chemicals from lignocellulosic resources.

In lignocellulose biomass, microbes prefer consuming glucose over xylose, which affects target compound production. Here, the authors achieve simultaneous utilization of glucose and xylose for target chemical production and cell growth, respectively, and realize high-level production of shikimate pathway derivatives.

Industrializing a Bacterial Strain for l-Serine Production through Translation Initiation Optimization

Turning a proof-of-concept synthetic biology design into a robust, high performing cell factory is a major time and money consuming task, which severely limits the growth of the white biotechnology sector. Here, we extend the use of tunable antibiotic resistance markers for synthetic evolution (TARSyn), a workflow for screening translation initiation region (TIR) libraries with antibiotic selection, to generic pathway engineering, and transform a proof-of-concept synbio design into a process that performs at industrially relevant levels. Using a combination of rational design and adaptive evolution, we recently engineered a high-performing bacterial strain for production of the important building block biochemical l-serine, based on two high-copy pET vectors facilitating expression of the serine biosynthetic genes serA, serC, and serB from three independent transcriptional units. Here, we prepare the bacterial strain for industrial scale up by transferring and reconfiguring the three genes into an operon encoded on a single low-copy plasmid. Not surprisingly, this initially reduces production titers considerably. We use TARSyn to screen both experimental and computational optimization designs resulting in high-performing synthetic serine operons and reach industrially relevant production levels of 50 g/L in fed-batch fermentations, the highest reported so far for serine production.

d-2-Hydroxyglutarate dehydrogenase plays a dual role in l-serine biosynthesis and d-malate utilization in the bacterium Pseudomonas stutzeri

Pseudomonas is a very large bacterial genus in which several species can use d-malate for growth. However, the enzymes that can metabolize d-malate, such as d-malate dehydrogenase, appear to be absent in most Pseudomonas species. d-3-Phosphoglycerate dehydrogenase (SerA) can catalyze the production of d-2-hydroxyglutarate (d-2-HG) from 2-ketoglutarate to support d-3-phosphoglycerate dehydrogenation, which is the initial reaction in bacterial l-serine biosynthesis. In this study, we show that SerA of the Pseudomonas stutzeri strain A1501 reduces oxaloacetate to d-malate and that d-2-HG dehydrogenase (D2HGDH) from P. stutzeri displays d-malate-oxidizing activity. Of note, D2HGDH participates in converting a trace amount of d-malate to oxaloacetate during bacterial l-serine biosynthesis. Moreover, D2HGDH is crucial for the utilization of d-malate as the sole carbon source for growth of P. stutzeri A1501. We also found that the D2HGDH expression is induced by the exogenously added d-2-HG or d-malate and that a flavoprotein functions as a soluble electron carrier between D2HGDH and electron transport chains to support d-malate utilization by P. stutzeri These results support the idea that D2HGDH evolves as an enzyme for both d-malate and d-2-HG dehydrogenation in P. stutzeri In summary, D2HGDH from P. stutzeri A1501 participates in both a core metabolic pathway for l-serine biosynthesis and utilization of extracellular d-malate.