Expanding metabolic pathway for de novo biosynthesis of the chiral pharmaceutical intermediate L-pipecolic acid in Escherichia coli

Increasing lysine level improved methanol assimilation toward butyric acid production in Butyribacterium methylotrophicum

BACKGROUND

Methanol, a promising non-food fermentation substrate, has gained increasing interest as an alternative feedstock to sugars for the bio-based production of value-added chemicals. Butyribacterium methylotrophicum, one of methylotrophic-acetogenic bacterium, is a promising host to assimilate methanol coupled with CO₂ fixation for the production of organic acids, such as butyric acid. Although the methanol utilization pathway has been identified in B. methylotrophicum, little knowledge was currently known about its regulatory targets, limiting the rational engineering to improve methanol utilization.

RESULTS

In this study, we found that methanol assimilation of B. methylotrophicum could be significantly improved when using corn steep liquor (CSL) as the co-substrate. The further investigation revealed that high level of lysine was responsible for enhanced methanol utilization. Through the transcriptome analysis, we proposed a potential mechanism by which lysine confers improved methylotrophy via modulating NikABCDE and FhuBCD transporters, both of which are involved in the uptake of cofactors essential for enzymes of methanol assimilation. The improved methylotrophy was also confirmed by overexpressing NikABCDE or FhuBCD operon. Finally, the de novo synthetic pathway of lysine was further engineered and the methanol utilization and butyric acid production of B. methylotrophicum were improved by 63.2% and 79.7%, respectively. After an optimization of cultivation medium, 3.69 g/L of butyric acid was finally achieved from methanol with a yield of 76.3%, the highest level reported to date.

CONCLUSION

This study revealed a novel mechanism to regulate methanol assimilation by lysine in B. methylotrophicum and engineered it to improve methanol bioconversion to butyric acid, culminating in the synthesis of the highest butyric acid titer reported so far in B. methylotrophicum. What's more, our work represents a further advancement in the engineering of methylotrophic-acetogenic bacterium to improve C1-compound utilization.

Interconnected Set of Enzymes Provide Lysine Biosynthetic Intermediates and Ornithine Derivatives as Key Precursors for the Biosynthesis of Bioactive Secondary Metabolites

Bacteria, filamentous fungi, and plants synthesize thousands of secondary metabolites with important biological and pharmacological activities. The biosynthesis of these metabolites is performed by networks of complex enzymes such as non-ribosomal peptide synthetases, polyketide synthases, and terpenoid biosynthetic enzymes. The efficient production of these metabolites is dependent upon the supply of precursors that arise from primary metabolism. In the last decades, an impressive array of biosynthetic enzymes that provide specific precursors and intermediates leading to secondary metabolites biosynthesis has been reported. Suitable knowledge of the elaborated pathways that synthesize these precursors or intermediates is essential for advancing chemical biology and the production of natural or semisynthetic biological products. Two of the more prolific routes that provide key precursors in the biosynthesis of antitumor, immunosuppressant, antifungal, or antibacterial compounds are the lysine and ornithine pathways, which are involved in the biosynthesis of β-lactams and other non-ribosomal peptides, and bacterial and fungal siderophores. Detailed analysis of the molecular genetics and biochemistry of the enzyme system shows that they are formed by closely related components. Particularly the focus of this study is on molecular genetics and the enzymatic steps that lead to the formation of intermediates of the lysine pathway, such as α-aminoadipic acid, saccharopine, pipecolic acid, and related compounds, and of ornithine-derived molecules, such as N⁵-Acetyl-N⁵-Hydroxyornithine and N⁵-anhydromevalonyl-N⁵-hydroxyornithine, which are precursors of siderophores. We provide evidence that shows interesting functional relationships between the genes encoding the enzymes that synthesize these products. This information will contribute to a better understanding of the possibilities of advancing the industrial applications of synthetic biology.

Optimization of the precursor supply for an enhanced FK506 production in Streptomyces tsukubaensis

Tacrolimus (FK506) is a macrolide widely used as immunosuppressant to prevent transplant rejection. Synthetic production of FK506 is not efficient and costly, whereas the biosynthesis of FK506 is complex and the level produced by the wild type strain, Streptomyces tsukubaensis, is very low. We therefore engineered FK506 biosynthesis and the supply of the precursor L-lysine to generate strains with improved FK506 yield. To increase FK506 production, first the intracellular supply of the essential precursor lysine was improved in the native host S. tsukubaensis NRRL 18488 by engineering the lysine biosynthetic pathway. Therefore, a feedback deregulated aspartate kinase AskSt* of S. tsukubaensis was generated by site directed mutagenesis. Whereas overexpression of AskSt* resulted only in a 17% increase in FK506 yield, heterologous overexpression of a feedback deregulated AskCg* from Corynebacterium glutamicum was proven to be more efficient. Combined overexpression of AskCg* and DapASt, showed a strong enhancement of the intracellular lysine pool following increase in the yield by approximately 73% compared to the wild type. Lysine is coverted into the FK506 building block pipecolate by the lysine cyclodeaminase FkbL. Construction of a ∆fkbL mutant led to a complete abolishment of the FK506 production, confirming the indispensability of this enzyme for FK506 production. Chemical complementation of the ∆fkbL mutant by feeding pipecolic acid and genetic complementation with fkbL as well as with other lysine cyclodeaminase genes (pipAf, pipASt, originating from Actinoplanes friuliensis and Streptomyces pristinaespiralis, respectively) completely restored FK506 production. Subsequently, FK506 production was enchanced by heterologous overexpression of PipAf and PipASp in S. tsukubaensis. This resulted in a yield increase by 65% compared to the WT in the presence of PipAf from A. friuliensis. For further rational yield improvement, the crystal structure of PipAf from A. friuliensis was determined at 1.3 Å resolution with the cofactor NADH bound and at 1.4 Å with its substrate lysine. Based on the structure the Ile91 residue was replaced by Val91 in PipAf, which resulted in an overall increase of FK506 production by approx. 100% compared to the WT.

Engineered Halomonas spp. for production of l-Lysine and cadaverine

Cadaverine, a derivative of l-lysine, has been used as a monomer for the synthesis of bio-based nylon-5,6. This study engineered Halomonas bluephagenesis TD1.0 by blocking the feedback inhibition, overexpressing the key l-lysine synthesis genes, strengthening the l-lysine export system and increasing the supply of oxaloacetate for production of l-lysine in the supernatant and PHB in the cells. Subsequently, cadaverine biosynthetic pathway was constructed in H. campaniensis LC-9 to improve the efficiency of de novo cadaverine biosynthesis which combines l-lysine producing H. bluephagenesis TDL8-68-259 and cadaverine producing H. campaniensis LC-9-ldcC-lysP. When H. campaniensis LC-9-ldcC-lysP was used as a whole cell catalysis for cadaverine production, the conversion efficiency of l-lysine to cadaverine reached 100% in the presence of 0.05% Triton X-100 for cell membrane permeability enhancement, resulting in 118 g L^-1 cadaverine formed in the fermentor. Thus, Halomonas spp. have been successfully constructed for l-lysine and cadaverine production.

Biosynthesis of cis-3-hydroxypipecolic acid from L-lysine using an in vivo dual-enzyme cascade

Cis-3-Hydroxypipecolic acid (cis-3-HyPip) is an important intermediate for the synthesis of GE81112 tetrapeptides, a small family of unusual nonribosomal peptide congeners with potent inhibitory activity against prokaryotic translation initiation. In this study, we constructed a microbial cell factory that can convert L-lysine into cis-3-hydroxypipecolic acid (cis-3-HyPip). Lysine cyclodeaminase SpLCD and Fe(II)/α-ketoglutarate (2-OG)-based oxygenase GetF were co-expressed in Escherichia coli. Plasmids with different copy numbers were used to balance the expression of these two enzymes, and the cell with the most appropriate balance of this kind for carrying plasmid pET-duet-getf-splcd was obtained. After determining the temperature (30 °C), pH (7.0), cell biomass, substrate concentration, Fe²⁺ concentration (10 mM), L-ascorbate concentration (10 mM), and TritonX-100 concentration (0.1% w/v) that were optimal for whole-cell catalysis, the yield of cis-3-HyPip reached as high as 25 mM (3.63 g/L).

Strategies to Increase the Production of Biosynthetic Riboflavin

Riboflavin is widely regarded as an essential nutrient that is involved in biological oxidation in vivo. In addition to preventing and treating acyl-CoA dehydrogenase deficiency in patients with keratitis, stomatitis, and glossitis, riboflavin is also closely related to the treatment of radiation mucositis and cardiovascular disease. Chemical synthesis has been the dominant method for producing riboflavin for approximately 50 years. Nevertheless, due to the intricate synthesis process, relatively high cost, and high risk of pollution, alternative methods of chemical syntheses, such as the fermentation method, began to develop and eventually became the main methods for producing riboflavin. At present, there are three types of strains used in industrial riboflavin production: Ashbya gossypii, Candida famata, and Bacillus subtilis. Additionally, many recent studies have been conducted on Escherichia coli and Lactobacillus. Fermentation increases the yield of riboflavin using genetic engineering technology to modify and induce riboflavin production in the strain, as well as to regulate the metabolic flux of the purine pathway and pentose phosphate pathway (PP pathway), thereby optimizing the culture process. This article briefly introduces recent progress in the fermentation of riboflavin.

High-efficiency production of 5-aminovalerate in engineered Escherichia coli controlled by an anaerobically-induced nirB promoter

Biobased production of 5-aminovalerate (5AVA) from biomass can support a sustainable and economic biorefinery process to produce bio-based nylon 5 for food packaging materials. Cost-competitive production of 5AVA from biomass is a key factor in the successful commercialization of nylon 5. Bioproduction of 5AVA is a promising candidate for the industrial process to the current petrochemical route. In this study, we developed an artificial 2-keto-6-aminocaproate-mediated pathway for cost-competitive and high efficiency production of 5AVA in engineered Escherichia coli. Firstly, the combination of native l-lysine α-oxidase (RaiP) from Scomber japonicas, α-ketoacid decarboxylase (KivD) from Lactococcus lactis and aldehyde dehydrogenase (PadA) from Escherichia coli could efficiently convert l-lysine into 5AVA. Moreover, the engineered strains ML03-P_nirB-RKP, ML03-P_PL-PR-RKP, ML03-P_M1-93-RKP induced by anaerobic condition, temperature-induced, constitutive expression instead of expensive isopropyl β-D-thiogalactoside were constructed, respectively. The use of nirB promoter induced by anaerobic condition not only could attain a higher titer of 5AVA than PL-PR and M1-93 promoters, but omit cost of expensive exogenous inducers. After the replacement of industrial materials, 5AVA titer successfully reached 33.68 g/L in engineered strain ML03-P_nirB-RKP via biotransformation. This biotransformation process conduces to the cosmically industrial 5AVA bioproduction.

Expanding the lysine industry: biotechnological production of l-lysine and its derivatives

l-lysine is an essential amino acid that contains various functional groups including α-amino, ω-amino, and α-carboxyl groups, exhibiting high reaction potential. The derivatization of these functional groups produces a series of value-added chemicals, such as cadaverine, glutarate, and d-lysine, that are widely applied in the chemical synthesis, cosmetics, food, and pharmaceutical industries. Here, we review recent advances in the biotechnological production of l-lysine and its derivatives and expatiate key technological strategies. Furthermore, we also discuss the existing challenges and potential strategies for more efficient production of these chemicals.

A High-Efficiency Artificial Synthetic Pathway for 5-Aminovalerate Production From Biobased L-Lysine in Escherichia coli

Bioproduction of 5-aminovalerate (5AVA) from renewable feedstock can support a sustainable biorefinery process to produce bioplastics, such as nylon 5 and nylon 56. In order to achieve the biobased production of 5AVA, a 2-keto-6-aminocaproate-mediated synthetic pathway was established. Combination of L-Lysine α-oxidase from Scomber japonicus, α-ketoacid decarboxylase from Lactococcus lactis and aldehyde dehydrogenase from Escherichia coli could achieve the biosynthesis of 5AVA from biobased L-Lysine in E. coli. The H₂O₂ produced by L-Lysine α-oxidase was decomposed by the expression of catalase KatE. Finally, 52.24 g/L of 5AVA were obtained through fed-batch biotransformation. Moreover, homology modeling, molecular docking and molecular dynamic simulation analyses were used to identify mutation sites and propose a possible trait-improvement strategy: the expanded catalytic channel of mutant and more hydrogen bonds formed might be beneficial for the substrates stretch. In summary, we have developed a promising artificial pathway for efficient 5AVA synthesis.

A pipecolic acid-rich branched cyclic depsipeptide ulleungamide C from a Streptomyces species induces G0/G1 cell cycle arrest in promyelocytic leukemia cells

In this study, screening by LC-MS and cytotoxicity-guided isolation led to the identification of ulleungamide C (1), a previously unknown pipecolic acid-rich branched cyclic depsipeptide, from a soil actinobacterium Streptomyces sp. KCB13F003. The structure of 1 was determined by interpretation of spectroscopic and spectrometric data from 1D and 2D NMR and HRESIMS experiments. Antiproliferative assays using mammalian cancerous cells revealed that 1 inhibits the proliferation of HL-60 human promyelocytic leukemia cells. Cell cycle analysis showed an increased accumulation of cells in the G0/G1 phase after treatment with 1. Results of immunoblotting assays revealed that 1 reduced the expression levels of cyclin-dependent kinase 4 (CDK4), CDK6, retinoblastoma protein (Rb), and phosphorylated Rb, whereas it induced cyclin-dependent kinase inhibitor 1B (p27/Kip1) expression.

Efficient whole-cell catalysis for 5-aminovalerate production from L-lysine by using engineered Escherichia coli with ethanol pretreatment

Microorganisms can utilize biomass to produce valuable chemicals, showing sustainable, renewable and economic advantages compared with traditional chemical synthesis. As a potential five-carbon platform polymer monomer, 5-aminovalerate has been widely used in industrial fields such as clothes and disposable goods. Here we establish an efficient whole-cell catalysis for 5-aminovalerate production with ethanol pretreatment. In this study, the metabolic pathway from L-lysine to 5-aminovalerate was constructed at the cellular level by introducing L-lysine α-oxidase. The newly produced H₂O₂ and added ethanol both are toxic to the cells, obviously inhibiting their growth. Here, a promising strategy of whole-cell catalysis with ethanol pretreatment is proposed, which greatly improves the yield of 5-aminovalerate. Subsequently, the effects of ethanol pretreatment, substrate concentration, reaction temperature, pH value, metal ion additions and hydrogen peroxide addition on the whole-cell biocatalytic efficiency were investigated. Using 100 g/L of L-lysine hydrochloride as raw material, 50.62 g/L of 5-aminovalerate could be excellently produced via fed-batch bioconversion with the yield of 0.84 mol/mol. The results show that a fast, environmentally friendly and efficient production of 5-aminovalerate was established after introducing the engineered whole-cell biocatalysts. This strategy, combined with ethanol pretreatment, can not only greatly enhance the yield of 5-aminovalerate but also be applied to the biosynthesis of other valuable chemicals.

Metabolic engineering advances and prospects for amino acid production

Amino acid fermentation is one of the major pillars of industrial biotechnology. The multi-billion USD amino acid market is rising steadily and is diversifying. Metabolic engineering is no longer focused solely on strain development for the bulk amino acids L-glutamate and L-lysine that are produced at the million-ton scale, but targets specialty amino acids. These demands are met by the development and application of new metabolic engineering tools including CRISPR and biosensor technologies as well as production processes by enabling a flexible feedstock concept, co-production and co-cultivation schemes. Metabolic engineering advances are exemplified for specialty proteinogenic amino acids, cyclic amino acids, omega-amino acids, and amino acids functionalized by hydroxylation, halogenation and N-methylation.

Function of L-Pipecolic Acid as Compatible Solute in Corynebacterium glutamicum as Basis for Its Production Under Hyperosmolar Conditions

Pipecolic acid or L-PA is a cyclic amino acid derived from L-lysine which has gained interest in the recent years within the pharmaceutical and chemical industries. L-PA can be produced efficiently using recombinant Corynebacterium glutamicum strains by expanding the natural L-lysine biosynthetic pathway. L-PA is a six-membered ring homolog of the five-membered ring amino acid L-proline, which serves as compatible solute in C. glutamicum.

Here, we show that de novo synthesized or externally added L-PA partially is beneficial for growth under hyper-osmotic stress conditions. C. glutamicum cells accumulated L-PA under elevated osmotic pressure and released it after an osmotic down shock. In the absence of the mechanosensitive channel YggB intracellular L-PA concentrations increased and its release after osmotic down shock was slower. The proline permease ProP was identified as a candidate L-PA uptake system since RNAseq analysis revealed increased proP RNA levels upon L-PA production. Under hyper-osmotic conditions, a ΔproP strain showed similar growth behavior than the parent strain when L-proline was added externally. By contrast, the growth impairment of the ΔproP strain under hyper-osmotic conditions could not be alleviated by addition of L-PA unless proP was expressed from a plasmid. This is commensurate with the view that L-proline can be imported into the C. glutamicum cell by ProP and other transporters such as EctP and PutP, while ProP appears of major importance for L-PA uptake under hyper-osmotic stress conditions.

Methanol fermentation increases the production of NAD(P)H-dependent chemicals in synthetic methylotrophic Escherichia coli

BACKGROUND

Methanol has attracted increased attention as a non-food alternative carbon source to sugar for biological production of chemicals and fuels. Moreover, the high degree of reduction of methanol offers some advantages in increasing the production yields of NAD(P)H-dependent metabolites. Here, we demonstrate an example of methanol bioconversion with the aim of improving production of NAD(P)H-dependent chemicals in synthetic methylotrophic Escherichia coli.

RESULTS

A synthetic methylotrophic E. coli was engineered with a nicotinamide adenine dinucleotide (NAD⁺)-dependent methanol dehydrogenase (MDH) and ribulose monophosphate (RuMP) pathway. Regarding the limited MDH activity, the role of activator proteins in vivo was investigated, and the NudF protein was identified capable of improving MDH activity and triggering increased methanol metabolism. Using ¹³C-methanol-labeling experiments, we confirmed methanol assimilation in the methylotrophic E. coli. A cycling RuMP pathway for methanol assimilation was also demonstrated by detecting multiple labeled carbons for several compounds. Finally, using the NAD(P)H-dependent metabolite lysine as a test, the potential of methanol bioconversion to generate value-added metabolites was determined. To further characterize the benefit of methanol as the carbon source, extra NADH from methanol oxidation was engineered to generate NADPH to improve lysine biosynthesis by expression of the POS5 gene from Saccharomyces cerevisiae, which resulted in a twofold improvement of lysine production. Moreover, this new sink further pulled upstream methanol utilization.

CONCLUSION

Through engineering methanol metabolism, lysine biosynthesis, and NADPH regeneration pathway from NADH, the bioconversion of methanol to improve chemical synthesis was successfully achieved in methylotrophic E. coli.

Engineering of lysine cyclodeaminase conformational dynamics for relieving substrate and product inhibitions in the biosynthesis of l-pipecolic acid

Efficient biocatalytic process construction by relieving substrate and product inhibitions via identification and engineering of enzyme conformational dynamics.

An economically and environmentally acceptable synthesis of chiral drug intermediate l-pipecolic acid from biomass-derived lysine via artificially engineered microbes

Deficiency in petroleum resources and increasing environmental concerns have pushed a bio-based economy to be built, employing a highly reproducible, metal contaminant free, sustainable and green biomanufacturing method. Here, a chiral drug intermediate l-pipecolic acid has been synthesized from biomass-derived lysine. This artificial bioconversion system involves the coexpression of four functional genes, which encode l-lysine α-oxidase from Scomber japonicus, glucose dehydrogenase from Bacillus subtilis, Δ1-piperideine-2-carboxylase reductase from Pseudomonas putida, and lysine permease from Escherichia coli. Besides, a lysine degradation enzyme has been knocked out to strengthen the process in this microbe. The overexpression of LysP improved the l-pipecolic acid titer about 1.6-folds compared to the control. This engineered microbial factory showed the highest l-pipecolic acid production of 46.7 g/L reported to date and a higher productivity of 2.41 g/L h and a yield of 0.89 g/g. This biotechnological l-pipecolic acid production is a simple, economic, and green technology to replace the presently used chemical synthesis.

Structural Basis for Recognition of L-lysine, L-ornithine, and L-2,4-diamino Butyric Acid by Lysine Cyclodeaminase

L-pipecolic acid is a non-protein amino acid commonly found in plants, animals, and microorganisms. It is a well-known precursor to numerous microbial secondary metabolites and pharmaceuticals, including anticancer agents, immunosuppressants, and several antibiotics. Lysine cyclodeaminase (LCD) catalyzes β-deamination of L-lysine into L-pipecolic acid using β-nicotinamide adenine dinucleotide as a cofactor. Expression of a human homolog of LCD, μ-crystallin, is elevated in prostate cancer patients. To understand the structural features and catalytic mechanisms of LCD, we determined the crystal structures of Streptomyces pristinaespiralis LCD (SpLCD) in (i) a binary complex with NAD+, (ii) a ternary complex with NAD+ and L-pipecolic acid, (iii) a ternary complex with NAD+ and L-proline, and (iv) a ternary complex with NAD+ and L-2,4-diamino butyric acid. The overall structure of SpLCD was similar to that of ornithine cyclodeaminase from Pseudomonas putida. In addition, SpLCD recognized L-lysine, L-ornithine, and L-2,4-diamino butyric acid despite differences in the active site, including differences in hydrogen bonding by Asp236, which corresponds with Asp228 from Pseudomonas putida ornithine cyclodeaminase. The substrate binding pocket of SpLCD allowed substrates smaller than lysine to bind, thus enabling binding to ornithine and L-2,4-diamino butyric acid. Our structural and biochemical data facilitate a detailed understanding of substrate and product recognition, thus providing evidence for a reaction mechanism for SpLCD. The proposed mechanism is unusual in that NAD+ is initially converted into NADH and then reverted back into NAD+ at a late stage of the reaction.

Metabonomics Approach To Comparing the Antistress Effects of Four Panax ginseng Components in Rats

Different components of Panax ginseng have different properties and medicinal effects. Metabonomics was a prospective approach to analyze the global response of endogenous metabolites to physiological and pathological processes. In this study, an untargeted metabonomics method using GC/TOFMS combined with multivariate statistical techniques was applied to compare entire metabolite differences and the antistress variations among four components of P. ginseng, namely, total ginsenosides (TG), panaxadiol (PD), panaxatriol (PT), and ginseng polysaccharide (PS), in Wistar rats. The results of metabolite analysis showed that numerous urine metabolites involving neurotransmitters, amino acids, organic acids, and gut microbiota metabolites were changed after administration of the four components of P. ginseng, with TG having the least impact on urinary metabolites. The urinary metabolite profiling of these rats exposed to acute combined stress (forced swimming and behavior restriction) demonstrated that the four ginseng components attenuated urine metabolite changes involving gut microbiota metabolites, tricarboxylic acid (TCA) cycle and energy metabolites, and organic acids to different degrees, with TG improving most of the metabolites altered by stress.