Molecular engineering of L-aspartate-α-decarboxylase for improved activity and catalytic stability

Promoter engineering for enhanced 3-hydroxypropionic acid production in Pichia pastoris

Enabling tools are essential for facilitating the methanol bioconversion in Pichia pastoris. However, there is still a relative lack of promoters that can stably express high levels without being affected by the carbon source, which hinders the construction and modification of cell factories containing long metabolic pathways. This study mapped a gene expression intensity library of central metabolic pathways in P. pastoris under methanol and glucose conditions. Through modification of the upstream sequences of promoters, an artificial promoter P S2 was developed with a strong intensity up to 90 % of P GAP . By using this promoter, we successfully constructed a hybrid pathway that integrates the β-alanine and malonyl-CoA pathways for the production of 3-hydroxypropionic acid. Further combining rational metabolic engineering strategies, such as optimizing gene copy numbers and blocking byproduct synthesis pathways, the engineered strains CHP9 and CHP20 achieved 3-HP titers of 23 g/L and 22 g/L by using methanol as the sole carbon source. These results indicate that adaptive strength of promoters can facilitate efficient chemical biosynthesis in methanol bioconversion by mitigating glucose repression effects. This work preliminarily explored the expression patterns of genes in the central metabolic pathways of P. pastoris, identified and characterized the intensities of various endogenous promoters, and extended the enabling toolbox for P. pastoris. This result also lays a foundation for the construction of microbial cell factories and the industrial production of 3-HP via methanol bioconversion.

Molecular Engineering L-Aspartate-Alpha-Decarboxylase to Enhance Catalytic Stability and Performance

L-aspartate-alpha-decarboxylase (ADC) catalyzes the decarboxylation of L-aspartate to produce β-alanine, which is the decisive step in the biosynthesis of β-alanine. However, the low catalytic stability and efficiency of ADC limit its industrial applications. In this study, a variant of ADC from Bacillus subtilis were used as a starting point for engineering. After constructing a random mutagenesis library by error-prone PCR, followed by high-throughput screening,four substitutions (S7 N, K63 N, A99T, and K113R) were identified. By screening saturation mutagenesis libraries on these positions and computational analysis, two recombined variants N3(S7 N/K63 N/I88 M/A99E/K113R/I126*) and Y1(S7Y/K63 N/I88 M/A99E/K113R/I126*) with improved performance were obtained. Compared to the wild type, the catalytic efficiency and catalytic stability of the best two variants were enhanced up to 95 %(variant N3) and up to 89 %(variant Y1), respectively. In addition, Y1 exhibited 3.37 times improved half-life and 2-fold improved total turnover number. Hydrophilicity analysis and molecular dynamics (MD) simulation revealed that the increased hydrophilicity and steric hindrance of key amino acid residues would affect the catalytic activity and stability. The improved catalytic performance of the variants could be attributed to their enhanced binding capacity to the substrate within the active pocket and the alleviation of mechanism-based inactivation.

Rational design of lanosterol 14α-demethylase for ergosterol biosynthesis in Saccharomyces cerevisiae

Ergosterol is widely used in skin care products and drug preparation. Lanosterol 14α-demethylase (Erg11p, 14DM, CYP51) is the rate-limiting enzyme for the biosynthesis of various steroid compounds in Saccharomyces cerevisiae. Herein, Erg11p was engineered to extend the in vivo catalytic half-life and increase the turnover rate. Single mutations resulting in lower folding energy were selected, and mutant P201H had an ergosterol yield of 576.9 mg·L-1. Through consensus design, single mutations resulting in higher sequence identity to homologs were tested and mutant K352L had an ergosterol yield of 677.9 mg·L-1. The key residues for substrate binding were confirmed via alanine scanning mutagenesis and mutant F384A had an ergosterol yield of 657.8 mg·L-1. Molecular dynamics (MD) simulation was conducted to investigate the contributions of pocket residues and eight residues were found to engage in weak interactions with lanosterol. Saturation mutagenesis was applied to these residues to enhance binding to lanosterol, and mutant F384E had an ergosterol yield of 733.8 mg·L-1. Meanwhile, MD simulations were conducted to assess the impact of mutant F384E on enzyme activity. The results consistently showed that single point mutation F384E had the greatest effect, outperforming the combination mutations. Batch fermentation increased the ergosterol yield of mutant F384E to 3067.5 mg·L-1, the highest reported to date. The successful engineering of Erg11p may pave the way for industrial-scale production of ergosterol and other steroids.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04136-x.

Fine and combinatorial regulation of key metabolic pathway for enhanced β-alanine biosynthesis with non-inducible Escherichia coli

β-Alanine is the only β-amino acid in nature and one of the most important three-carbon chemicals. This work was aimed to construct a non-inducible β-alanine producer with enhanced metabolic flux towards β-alanine biosynthesis in Escherichia coli. First of all, the assembled E. coli endogenous promoters and 5'-untranslated regions (PUTR) were screened to finely regulate the combinatorial expression of genes panDBS and aspBCG for an optimal flux match between two key pathways. Subsequently, additional copies of key genes (panDBS K104S and ppc) were chromosomally introduced into the host A1. On these bases, dynamical regulation of the gene thrA was performed to reduce the carbon flux directed in the competitive pathway. Finally, the β-alanine titer reached 10.25 g/L by strain A14-R15, 361.7% higher than that of the original strain. Under fed-batch fermentation in a 5-L fermentor, a titer of 57.13 g/L β-alanine was achieved at 80 h. This is the highest titer of β-alanine production ever reported using non-inducible engineered E. coli. This metabolic modification strategy for optimal carbon flux distribution developed in this work could also be used for the production of various metabolic products.

Discovery and Engineering of a Novel Bacterial L-Aspartate α-Decarboxylase for Efficient Bioconversion

L-aspartate α-decarboxylase (ADC) is a pyruvoyl-dependent decarboxylase that catalyzes the conversion of L-aspartate to β-alanine in the pantothenate pathway. The enzyme has been extensively used in the biosynthesis of β-alanine and D-pantothenic acid. However, the broad application of ADCs is hindered by low specific activity. To address this issue, we explored 412 sequences and discovered a novel ADC from Corynebacterium jeikeium (CjADC). CjADC exhibited specific activity of 10.7 U/mg and Km of 3.6 mM, which were better than the commonly used ADC from Bacillus subtilis. CjADC was then engineered leveraging structure-guided evolution and generated a mutant, C26V/I88M/Y90F/R3V. The specific activity of the mutant is 28.8 U/mg, which is the highest among the unknown ADCs. Furthermore, the mutant displayed lower Km than the wild-type enzyme. Moreover, we revealed that the introduced mutations increased the structural stability of the mutant by promoting the frequency of hydrogen-bond formation and creating a more hydrophobic region around the active center, thereby facilitating the binding of L-aspartate to the active center and stabilizing the substrate orientation. Finally, the whole-cell bioconversion showed that C26V/I88M/Y90F/R3V completely transformed 1-molar L-aspartate in 12 h and produced 88.6 g/L β-alanine. Our study not only identified a high-performance ADC but also established a research framework for rapidly screening novel enzymes using a protein database.

Advances in the synthesis of β-alanine

β-Alanine is the only naturally occurring β-type amino acid in nature, and it is also one of the very promising three-carbon platform compounds that can be applied in cosmetics and food additives and as a precursor in the chemical, pharmaceutical and material fields, with very broad market prospects. β-Alanine can be synthesized through chemical and biological methods. The chemical synthesis method is relatively well developed, but the reaction conditions are extreme, requiring high temperature and pressure and strongly acidic and alkaline conditions; moreover, there are many byproducts that require high energy consumption. Biological methods have the advantages of product specificity, mild conditions, and simple processes, making them more promising production methods for β-alanine. This paper provides a systematic review of the chemical and biological synthesis pathways, synthesis mechanisms, key synthetic enzymes and factors influencing β-alanine, with a view to providing a reference for the development of a highly efficient and green production process for β-alanine and its industrialization, as well as providing a basis for further innovations in the synthesis of β-alanine.

MpADC, an L-aspartate-α-decarboxylase, from Myzus persicae, that enables production of β-alanine with high yield by whole-cell enzymatic catalysis

BACKGROUND

β-Alanine is a precursor of many important pharmaceutical products and food additives, its market demand is continuously increasing nowadays. Whole-cell catalysis relying on the recombinant expression of key β-alanine synthesizing enzymes is an important method to produce β-alanine. Nevertheless, β-alanine synthesizing enzymes found so far have problems including easy inactivation, low expression or poor catalytic activity, and it remains necessary to develop new enzymes.

RESULTS

Herein, we characterized an L-aspartate-α-decarboxylase, MpADC, from an aphid, Myzus persicae. It showed excellent catalytic activity at pH 6.0-7.5 and 37 °C. With the help of chaperone co-expression and N-terminal engineering guided by AlphaFold2 structure prediction, the expression and catalytic ability of MpADC in Escherichia coli were significantly improved. Using 50 g/L of E. coli cells expressing the MpADC-∆39 variant cultured in a 15-L fermenter, 232.36 g/L of β-alanine was synthesized in 13.5 h, with the average β-alanine yield of 17.22 g/L/h, which is best known so far.

CONCLUSIONS

Our research should facilitate the production of β-alanine in an environment-friendly manner.

A High-Specific-Activity L-aspartate-α-Decarboxylase from Bacillus aryabhattai Gel-09 and Site-Directed Mutation to Improve Its Substrate Tolerance

L-aspartate-α-decarboxylase (ADC) can recognize L-aspartic acid specifically and catalyze the decarboxylation of L-aspartic acid to β-alanine. In this study, a novel L-aspartate-α-decarboxylase (BaADC) with high specific activity from Bacillus aryabhattai Gel-09 was heterologously expressed and characterized. It exhibited optimal enzyme activity at pH 5.5 and 75 °C, and its specific activity was 33.9 U/mg. To improve the substrate tolerance of BaADC, site-directed mutation was used to construct variants. The optimal variant BaADC_I88M exhibited higher pH stability and thermostability, with 1.2-fold increase in catalytic efficiency. Moreover, through the fed-batch method, the conversion of L-aspartic acid to β-alanine catalyzed by BaADC_I88M reached 98.6% (128.67 g/L) at 12 h, which was 1.42-fold that of the wild-type enzyme. The mechanism of improved substrate tolerance was interpreted by molecular dynamics simulation and structural analysis, which revealed that the local conformational change in the active pocket could promote correct protonation. These results suggested that BaADC and its variant are potential candidates for use in the industrial production of β-alanine.

Effect of amino acid fortified mulberry leaves on economic and biological traits of Bombyx mori L

The demand for silk has been increasing day by day but the average silk production is not enough to meet its demand. In this study, we investigated the effect of amino acid supplemented mulberry feed on the biological and commercial traits of Bombyx mori L. (Lepidoptera; Bombycidae). The silkworm larvae at 5th instar stage were taken and fed with fresh and healthy mulberry leaves coated with Alanine, Glycine and Serine in fourteen different combinations. Results of the current study revealed that the average weight of silkworm larvae and the % ratio of silk gland to body weight on day 7 was significantly (P˂0.05) higher in the group fed with amino acid fortified leaves as compared to the control. The commercial traits of larvae fed with amino acid fortified leaves also improved significantly. The larvae fed with Alanine (1 %) treated mulberry leaves showed the maximum cocoon weight, cocoon length, cocoon width, cocoon shell ratio and fibroin content as compared to the control group. It is evident from the results that the amino acid (particularly alanine) coated mulberry leaves have a positive effect on the commercial and biological traits of Bombyx mori (L.).

Screening and identification of genes involved in β-alanine biosynthesis in Bacillus subtilis

β-alanine is the only naturally occurring β-amino acid, which is widely used in medicine, food, and feed fields, and generally produced through synthetic biological methods based on engineered strains of Escherichia coli or Corynebacterium glutamicum. However, the β-alanine biosynthesis in Bacillus subtilis, a traditional industrial model microorganism of food safety grade, has not been thoroughly explored. In this study, the native l-aspartate-α-decarboxylase was overexpressed in B. subtilis 168 to obtain an increase of 842% in β-alanine production. A total of 16 single-gene knockout strains were constructed to block the competitive consumption pathways to identify a total of 6 genes (i.e., ptsG, fbp, ydaP, yhfS, mmgA, and pckA) involved in β-alanine synthesis, while the multigene knockout of these 6 genes obtained an increased β-alanine production by 40.1%. Ten single-gene suppression strains with the competitive metabolic pathways inhibited revealed that the inhibited expressions of genes glmS, accB, and accA enhanced the β-alanine production. The introduction of heterologous phosphoenolpyruvate carboxylase increased the β-alanine production by 81.7%, which was 17-fold higher than that of the original strain. This was the first study using multiple molecular strategies to investigate the biosynthetic pathway of β-alanine in B. subtilis and to identify the genetic factors limiting the excessive synthesis of β-alanine by microorganisms.

How an overlooked gene in coenzyme a synthesis solved an enzyme mechanism predicament

Coenzyme A (CoA) is an essential cofactor throughout biology. The first committed step in the CoA synthetic pathway is synthesis of β-alanine from aspartate. In Escherichia coli and Salmonella enterica panD encodes the responsible enzyme, aspartate-1-decarboxylase, as a proenzyme. To become active, the E. coli and S. enterica PanD proenzymes must undergo an autocatalytic cleavage to form the pyruvyl cofactor that catalyzes decarboxylation. A problem was that the autocatalytic cleavage was too slow to support growth. A long-neglected gene (now called panZ) was belatedly found to encode the protein that increases autocatalytic cleavage of the PanD proenzyme to a physiologically relevant rate. PanZ must bind CoA or acetyl-CoA to interact with the PanD proenzyme and accelerate cleavage. The CoA/acetyl-CoA dependence has led to proposals that the PanD-PanZ CoA/acetyl-CoA interaction regulates CoA synthesis. Unfortunately, regulation of β-alanine synthesis is very weak or absent. However, the PanD-PanZ interaction provides an explanation for the toxicity of the CoA anti-metabolite, N5-pentyl pantothenamide.

Development of probiotic E. coli Nissle 1917 for β-alanine production by using protein and metabolic engineering

β-alanine has been used in food and pharmaceutical industries. Although Escherichia coli Nissle 1917 (EcN) is generally considered safe and engineered as living therapeutics, engineering EcN for producing industrial metabolites has rarely been explored. Here, by protein and metabolic engineering, EcN was engineered for producing β-alanine from glucose. First, an aspartate-α-decarboxylase variant ADC_K43Y with improved activity was identified and over-expressed in EcN, promoting the titer of β-alanine from an undetectable level to 0.46 g/L. Second, directing the metabolic flux towards L-aspartate increased the titer of β-alanine to 0.92 g/L. Third, the yield of β-alanine was elevated to 1.19 g/L by blocking conversion of phosphoenolpyruvate to pyruvate, and further increased to 2.14 g/L through optimizing culture medium. Finally, the engineered EcN produced 11.9 g/L β-alanine in fed-batch fermentation. Our work not only shows the potential of EcN as a valuable industrial platform, but also facilitates production of β-alanine via fermentation. KEY POINTS: • Escherichia coli Nissle 1917 (EcN) was engineered as a β-alanine producing cell factory • Identification of a decarboxylase variant ADC_K43Y with improved activity • Directing the metabolic flux to L-ASP and expressing ADC_K43Y elevated the titer of β-alanine to 11.9 g/L.

Research progress of L-aspartate-α-decarboxylase and its isoenzyme in the β-alanine synthesis

Driven by the massive demand in recent years, the production of β-alanine has significantly progressed in chemical and biological ways. Although the chemical method is relatively mature compared to biological synthesis, its high cost of waste disposal and environmental pollution does not meet the environmental protection standard. Hence, the biological method has become more prevalent as a potential alternative to the chemical synthesis of β-alanine in recent years. As a result, the aspartate pathway from L-aspartate to β-alanine (the most significant rate-limiting step in the β-alanine synthesis) catalyzed by L-aspartate-α-decarboxylase (ADC) has become a research hotspot in recent years. Therefore, it is vital to comprehensively understand the different enzymes that possess a similar catalytic ability to ADC. This review will investigate the exploratory process of unique synthesis features and catalytic properties of ADC/ADC-like enzymes in particular creatures with similar catalytic capacity or high sequence homology. At the same time, we will discuss the different β-alanine production methods which can apply to future industrialization.

Aspartate α-decarboxylase a new therapeutic target in the fight against Helicobacter pylori infection

Effective eradication therapy for Helicobacter pylori is a worldwide demand. Aspartate α-decarboxylase (ADC) was reported as a drug target in H. pylori, in an in silico study, with malonic acid (MA) as its inhibitor. We evaluated eradicating H. pylori infection through ADC inhibition and the possibility of resistance development. MA binding to ADC was modeled via molecular docking. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of MA were determined against H. pylori ATCC 43504, and a clinical H. pylori isolate. To confirm selective ADC inhibition, we redetermined the MIC in the presence of products of the inhibited enzymatic pathway: β-alanine and pantothenate. HPLC was used to assay the enzymatic activity of H. pylori 6x-his tagged ADC in the presence of different MA concentrations. H. pylori strains were serially exposed to MA for 14 passages, and the MICs were determined. Cytotoxicity in different cell lines was tested. The efficiency of ADC inhibition in treating H. pylori infections was evaluated using a Sprague–Dawley (SD) rat infection model. MA spectrum of activity was determined in different pathogens. MA binds to H. pylori ADC active site with a good docking score. The MIC of MA against H. pylori ranged from 0.5 to 0.75 mg/mL with MBC of 1.5 mg/mL. Increasing β-alanine and pantothenate concentrations proportionally increased MA MIC. The 6x-his tagged ADC activity decreased by increasing MA concentration. No resistance to ADC inhibition was recorded after 14 passages; MA lacked cytotoxicity in all tested cell lines. ADC inhibition effectively eradicated H. pylori infection in SD rats. MA had MIC between 0.625 to 1.25 mg/mL against the tested bacterial pathogens. In conclusion, ADC is a promising target for effectively eradicating H. pylori infection that is not affected by resistance development, besides being of broad-spectrum presence in different pathogens. MA provides a lead molecule for the development of an anti-helicobacter ADC inhibitor. This provides hope for saving the lives of those at high risk of infection with the carcinogenic H. pylori.

Metabolic engineering of E. coli for β-alanine production using a multi-biosensor enabled approach

β-alanine is an important biomolecule used in nutraceuticals, pharmaceuticals, and chemical synthesis. The relatively eco-friendly bioproduction of β-alanine has recently attracted more interest than petroleum-based chemical synthesis. In this work, we developed two types of in vivo high-throughput screening platforms, wherein one was utilized to identify a novel target ribonuclease E (encoded by rne) as well as a redox-cofactor balancing module that can enhance de novo β-alanine biosynthesis from glucose, and the other was employed for screening fermentation conditions. When combining these approaches with rational upstream and downstream module engineering, an engineered E. coli producer was developed that exhibited 3.4- and 6.6-fold improvement in β-alanine yield (0.85 mol β-alanine/mole glucose) and specific β-alanine production (0.74 g/L/OD₆₀₀), respectively, compared to the parental strain in a minimal medium. Across all of the strains constructed, the best yielding strain exhibited 1.08 mol β-alanine/mole glucose (equivalent to 81.2% of theoretic yield). The final engineered strain produced 6.98 g/L β-alanine in a batch-mode bioreactor and 34.8 g/L through a whole-cell catalysis. This approach demonstrates the utility of biosensor-enabled high-throughput screening for the production of β-alanine.

Rerouting Fluxes of the Central Carbon Metabolism and Relieving Mechanism-Based Inactivation of l-Aspartate-α-decarboxylase for Fermentative Production of β-Alanine in Escherichia coli

β-Alanine, with the amino group at the β-position, is an important platform chemical that has been widely applied in pharmaceuticals and feed and food additives. However, the current modest titer and productivity, increased fermentation cost, and complicated operation are the challenges for producing β-alanine by microbial fermentation. In this study, a high-yield β-alanine-producing strain was constructed by combining metabolic engineering, protein engineering, and fed-batch bioprocess optimization strategies. First, an aspartate-α-decarboxylase from Bacillus subtilis was introduced in Escherichia coli W3110 to construct an initial β-alanine-producing strain. Production of β-alanine was obviously increased to 4.36 g/L via improving the metabolic flux and reducing carbon loss by rerouting fluxes of the central carbon metabolism. To further increase β-alanine production, mechanism-based inactivation of aspartate-α-decarboxylase was relieved by rational design to maintain the productivity at a high level in β-alanine fed-batch fermentation. Finally, fed-batch bioprocess optimization strategies were used to improve β-alanine production to 85.18 g/L with 0.24 g/g glucose yield and 1.05 g/L/h productivity in fed-batch fermentation. These strategies can be effectively used in the construction of engineered strains for β-alanine and production of its derivatives, and the final engineered strain was a valuable microbial cell factory that can be used for the industrial production of β-alanine.

High-level expression and optimization of pantoate-β-alanine ligase in Bacillus megaterium for the enhanced biocatalytic production of D-pantothenic acid

D-Pantothenic acid (DPA), also known as vitamin B₅ is associated with several biological functions and its deficiency causes metabolic and energetic disorders in humans. Fortification of foods with DPA is the viable option to address this risk. DPA biological production route employs pantoate-β-alanine ligase (PBL) as the key enzyme, which avoids the tedious and time-consuming optical resolution process. The selection of an efficient PBL enzyme is vital for the biological production of DPA. In this study, the panC gene encoding PBL from Escherichia coli, Bacillus megaterium, Corynebacterium glutamicum and Bacillus subtilis was expressed in B. megaterium. B. subtilis derived panC exhibited high PBL activity 61.62 ± 2.15 U/mL. Co-expression of phosphoenolpyruvate carboxykinase (pckA) did not improve the DPA production in B. megaterium. Biocatalytic fed-batch fermentation with externally supplemented precursor substrates (D-pantoic acid and β-alanine) improved DPA titer to 45.56 ± 0.53 g/L. Daily dietary requirements of DPA for different age groups (including babies, small children, athletes and elderly people) is steadily increasing and the improved DPA production addressed in this study offers advantage for its application in fortification of food products meeting the emerging nutritional demand.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13197-021-05093-6.

A High-Content Microscopy Screening Identifies New Genes Involved in Cell Width Control in Bacillus subtilis

How cells control their shape and size is a fundamental question of biology. In most bacteria, cell shape is imposed by the peptidoglycan (PG) polymeric meshwork that surrounds the cell. Thus, bacterial cell morphogenesis results from the coordinated action of the proteins assembling and degrading the PG shell. Remarkably, during steady-state growth, most bacteria maintain a defined shape along generations, suggesting that error-proof mechanisms tightly control the process. In the rod-shaped model for the Gram-positive bacterium Bacillus subtilis, the average cell length varies as a function of the growth rate, but the cell diameter remains constant throughout the cell cycle and across growth conditions. Here, in an attempt to shed light on the cellular circuits controlling bacterial cell width, we developed a screen to identify genetic determinants of cell width in B. subtilis. Using high-content screening (HCS) fluorescence microscopy and semiautomated measurement of single-cell dimensions, we screened a library of ∼4,000 single knockout mutants. We identified 13 mutations significantly altering cell diameter, in genes that belong to several functional groups. In particular, our results indicate that metabolism plays a major role in cell width control in B. subtilis.

IMPORTANCE Bacterial shape is primarily dictated by the external cell wall, a vital structure that, as such, is the target of countless antibiotics. Our understanding of how bacteria synthesize and maintain this structure is therefore a cardinal question for both basic and applied research. Bacteria usually multiply from generation to generation while maintaining their progenies with rigorously identical shapes. This implies that the bacterial cells constantly monitor and maintain a set of parameters to ensure this perpetuation. Here, our study uses a large-scale microscopy approach to identify at the whole-genome level, in a model bacterium, the genes involved in the control of one of the most tightly controlled cellular parameters, the cell width.

Multiplex modification of Escherichia coli for enhanced β-alanine biosynthesis through metabolic engineering

β-Alanine is the only naturally occurring β-amino acid, widely used in the fine chemical and pharmaceutical fields. In this study, metabolic design strategies were attempted in Escherichia coli W3110 for enhancing β-alanine biosynthesis. Specifically, heterologous L-aspartate-α-decarboxylase was used, the aspartate kinase I and III involved in competitive pathways were down-regulated, the β-alanine uptake system was disrupted, the phosphoenolpyruvate carboxylase was overexpressed, and the isocitrate lyase repressor repressing glyoxylate cycle shunt was delete, the glucose uptake system was modified, and the regeneration of amino donor was up-regulated. On this basis, a plasmid harboring the heterologous panD and aspB was constructed. The resultant strain ALA17/pTrc99a-panD_BS-aspB_CG could yield 4.20 g/L β-alanine in shake flask and 43.94 g/L β-alanine (a yield of 0.20 g/g glucose) in 5-L bioreactor via fed-batch cultivation. These modification strategies were proved effective and the constructed β-alanine producer was a promising microbial cell factory for industrial production of β-alanine.

The Moderately (D)efficient Enzyme: Catalysis-Related Damage In Vivo and Its Repair

Enzymes have in vivo life spans. Analysis of life spans, i.e., lifetime totals of catalytic turnovers, suggests that nonsurvivable collateral chemical damage from the very reactions that enzymes catalyze is a common but underdiagnosed cause of enzyme death. Analysis also implies that many enzymes are moderately deficient in that their active-site regions are not naturally as hardened against such collateral damage as they could be, leaving room for improvement by rational design or directed evolution. Enzyme life span might also be improved by engineering systems that repair otherwise fatal active-site damage, of which a handful are known and more are inferred to exist. Unfortunately, the data needed to design and execute such improvements are lacking: there are too few measurements of in vivo life span, and existing information about the extent, nature, and mechanisms of active-site damage and repair during normal enzyme operation is too scarce, anecdotal, and speculative to act on. Fortunately, advances in proteomics, metabolomics, cheminformatics, comparative genomics, and structural biochemistry now empower a systematic, data-driven approach for identifying, predicting, and validating instances of active-site damage and its repair. These capabilities would be practically useful in enzyme redesign and improvement of in-use stability and could change our thinking about which enzymes die young in vivo, and why.

Enhancing β-alanine production from glucose in genetically modified Corynebacterium glutamicum by metabolic pathway engineering

To directly produce β-alanine from glucose by microbial fermentation, a recombinant Corynebacterium glutamicum strain with high efficiency of β-alanine production was constructed in this study. To do this, the biosynthetic pathway of β-alanine in an L-lysine-producing strain XQ-5 was modified by enhancing carbon flux in biosynthetic pathway and limiting carbon flux in competitive pathway. This study showed that replacement of L-aspartate kinase (AK) with wild-type AK and disruption of lactate dehydrogenase and alanine/valine aminotransferases increase β-alanine production because of decreasing the by-products accumulation. Moreover, L-aspartate-α-decarboxylase (ADC) from Bacillus subtilis was designed as the best enzyme for increasing β-alanine production, and its variant (BsADC^E56S/I88M) showed the highest activity for catalyzing L-aspartate to generate β-alanine. To further increase β-alanine production, expression level of BsADC^E56S/I88M was controlled by optimizing promoter and RBS, indicating that P_gro plus ThirRBS is the best combination for BsADC^E56S/I88M expression and β-alanine production. The resultant strain XQ-5.5 produced 30.7 ± 2.3 g/L of β-alanine with a low accumulation of lactate (from 5.2 ± 0.14 to 0.2 ± 0.09 g/L) and L-alanine (from 7.6 ± 0.22 to 3.8 ± 0. 32 g/L) in shake-flask fermentation and produced 56.5 ± 3.2 g/L of β-alanine with a productivity of 0.79 g/(L·h) and the glucose conversion efficiency (α) of 39.5% in feed-batch fermentation. This is the first report of genetically modifying the biosynthetic pathway of β-alanine that improves the efficiency of β-alanine production in an L-lysine-producing strain, and these results give us a new insight for constructing the other valuable biochemical. KEY POINTS: • Optimization and overexpression of the key enzyme BsADC increased the accumulation of β-alanine. • The AK was replaced with wild-type AK to increase the conversion of aspartic acid to β-alanine. • A 56.5-g/L β-alanine production in fed-batch fermentation was achieved.

Metabolic engineering of methylotrophic Pichia pastoris for the production of β-alanine

β-Alanine (3-aminopropionic acid) is the only naturally occurring β-amino acid and an important precursor for the synthesis of a variety of nitrogen-containing chemicals. Fermentative production of β-alanine from renewable feedstocks such as glucose has attracted significant interest in recent years. Methanol has become an emerging and promising renewable feedstock for biomanufacturing as an alternative to glucose. In this work, we demonstrated the feasibility of β-alanine production from methanol using Pichia pastoris (Komagataella phaffii) as a methylotrophic cell factory. L-Aspartate-α-decarboxylases (ADCs) from different sources were screened and expressed in P. pastoris, followed by the optimization of aspartate decarboxylation by increasing the ADC copy number and C4 precursor supply via the overexpression of aspartate dehydrogenase. The production potential of the best strain was further evaluated in a 1-L fermenter, and a β-alanine titer of 5.6 g/L was obtained. To our best knowledge, this is the highest metabolite production titer ever reached in P. pastoris using methanol as the substrate.

Combinatorial approach for improved production of whole-cell 3-aminopropionic acid in recombinant Bacillus megaterium: codon optimization, gene duplication and process optimization

In this study, we aimed to develop a Bacillus megaterium based whole-cell biocatalyst for the bio-production of 3-aminopropionic acid (3-APA). l-aspartate-α-decarboxylases (ADC) (EC: 4.1.1.11) from Escherichia coli, B. megaterium, Corynebacterium glutamicum, and Bacillus subtilis were expressed in B. megaterium. B. subtilis derived ADC (panD _Bs ) exhibited the highest ADC activity of 0.9 ± 0.02 U/mL in recombinant B. megaterium. Combination of codon optimization and gene duplication strategies resulted in 415.56% enhancement of ADC activity compared to panD _Bs . The culture growth conditions of B. megaterium (BMD-7) for 3-APA production were optimized as follows: inducer concentration, 0.5% (w/v); time of induction, 3 h; induction temperature, 37 °C and post-induction incubation time, 8 h. Improvement of the whole-cell biocatalytic process efficiency, was dealt by optimization of reaction temperature, reaction pH, metal ion additives and l-aspartic acid concentration. Shake flask level experiments yielded an enhanced 3-APA titer (16.18 ± 0.26 g/L) and a yield of 0.89 g/g under optimized conditions viz., 45 °C, pH 6.0 and 20 g/L of l-aspartic acid. This study demonstrates the potential of B. megaterium for 3-APA production and paves the scope for the development of 3-APA producing strains in near future.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02885-7.

Advances in biotechnological production of β-alanine

β-Alanine (3-aminopropionic acid) is the only naturally occurring β-type amino acid. Although it is not incorporated into proteins, it has important physiological functions in the metabolism of animals, plants and microorganisms. Furthermore, it has attracted great interest due to its wide usage as a precursor of many significant industrial chemicals for medicine, feed, food, environmental applications and other fields. With the depletion of fossil fuels and concerns regarding environmental issues, biological production of β-alanine has attracted more attention relative to chemical methods. In this review, we first summarize the pathways through which natural microorganisms synthesize β-alanine. Then, the current research progress in the biological synthesis of β-alanine is also elaborated. Finally, we discuss the main problems and challenges in optimizing the biological pathways, offering perspectives on promising new biological approaches.

Development of a dual-fluorescence reporter system for high-throughput screening of L-aspartate-α-decarboxylase

β-Alanine (3-aminopropionic acid) holds great potential in industrial application. It can be obtained through a chemical synthesis route, which is hazardous to the environment. It is well known that l-aspartate-α-decarboxylase (ADC) can convert l-aspartate to β-alanine in bacteria. However, due to the low activity of ADC, industrial production of β-alanine through the green biological route remains unclear. Thus, improving the activity of ADC is critical to reduce the cost of β-alanine production. In this study, we established a dual-fluorescence high-throughput system for efficient ADC screening. By measuring the amount of β-alanine and the expression level of ADC using two different fluorescence markers, we can rapidly quantify the relative activity of ADC variants. From a mutagenesis library containing 2000 ADC variants, we obtained a mutant with 33% increased activity. Further analysis revealed that mutations of K43R and P103Q in ADC significantly improved the yield of β-alanine produced by the whole-cell biocatalysis. Compared with the previous single-fluorescence method, our system can not only quantify the amount of β-alanine but also measure the expression level of ADC with different fluorescence, making it able to effectively screen out ADC variants with improved relative activity. The dual-fluorescence high-throughput system for rapid screening of ADC provides a good strategy for industrial production of β-alanine via the biological conversion route in the future.

Enhanced production of β-alanine through co-expressing two different subtypes of L-aspartate-α-decarboxylase

β-Alanine (β-Ala) is an important intermediate with numerous applications in food and feed additives, pharmaceuticals, polymeric materials, and electroplating industries. Its biological production routes that employ L-aspartate-α-decarboxylase (ADC) as the key enzyme are attractive. In this study, we developed an efficient and environmentally safe method for β-Ala production by co-expressing two different subtypes of ADC. A bacterial ADC from Bacillus subtilis (BSADC) and an insect ADC from Tribolium castaneum (TCADC) use pyruvoyl and pyridoxal-5'-phosphate (PLP) as cofactor, respectively. 3050 mM (271.5 g/L) β-Ala was achieved from L-aspartic acid by using the whole-cell biocatalyst co-expressing BSADC and TCADC, corresponding to a conversion rate of 92.4%. Meanwhile, one-pot synthesis of β-Ala from fumaric acid through using a tri-enzyme cascade route with two different subtypes of ADC and L-aspartase (AspA) from Escherichia coli was established. 2250 mM (200.3 g/L) β-Ala was obtained from fumaric acid with a conversion rate of 90.0%. This work proposes a novel strategy that improves β-Ala production in the decarboxylation pathway of L-aspartic acid.

Protein Engineering of a Pyridoxal-5'-Phosphate-Dependent l-Aspartate-α-Decarboxylase from Tribolium castaneum for β-Alanine Production

In the present study, a pyridoxal-5′-phosphate (PLP)-dependent L-aspartate-α-decarboxylase from Tribolium castaneum (TcPanD) was selected for protein engineering to efficiently produce β-alanine. A mutant TcPanD-R98H/K305S with a 2.45-fold higher activity than the wide type was selected through error-prone PCR, site-saturation mutagenesis, and 96-well plate screening technologies. The characterization of purified enzyme TcPanD-R98H/K305S showed that the optimal cofactor PLP concentration, temperature, and pH were 0.04% (m/v), 50 °C, and 7.0, respectively. The 1mM of Na⁺, Ni²⁺, Co²⁺, K⁺, and Ca²⁺ stimulated the activity of TcPanD-R98H/K305S, while only 5 mM of Ni²⁺ and Na⁺ could increase its activity. The kinetic analysis indicated that TcPanD-R98H/K305S had a higher substrate affinity and enzymatic reaction rate than the wild enzyme. A total of 267 g/L substrate l-aspartic acid was consumed and 170.5 g/L of β-alanine with a molar conversion of 95.5% was obtained under the optimal condition and 5-L reactor fermentation.

Pathway construction and metabolic engineering for fermentative production of β-alanine in Escherichia coli

β-Alanine is a naturally occurring β-amino acid that has been widely applied in the life and health field. Although microbial fermentation is a promising method for industrial production of β-alanine, an efficient microbial cell factory is still lacking. In this study, a new metabolically engineered Escherichia coli strain for β-alanine production was developed through a series of introduction, deletion, and overexpression of genes involved in its biosynthesis pathway. First, the L-aspartate a-decarboxylase gene, BtADC, from Bacillus tequilensis, with higher catalytic activity to produce β-alanine from aspartate, was constitutively expressed in E. coli, leading to an increased production of β-alanine up to 2.76 g/L. Second, three native aspartate kinase genes, akI, akII, and akIII, were knocked out to promote the production of β-alanine to a higher concentration of 4.43 g/L by preventing from bypass loss of aspartate. To increase the amount of aspartate, the native AspC gene was replaced with PaeAspDH, a L-aspartate dehydrogenase gene from Pseudomonas aeruginosa, accompanied with the overexpression of the native AspA gene, to further improve the production level of β-alanine to 9.27 g/L. Last, increased biosynthesis of oxaloacetic acid (OAA) was achieved by a combination of overexpression of the native PPC, introduction of CgPC, a pyruvate decarboxylase from Corynebacterium glutamicum, and deletion of ldhA, pflB, pta, and adhE in E. coli, to further enhance the production of β-alanine. Finally, the engineered E. coli strain produced 43.12 g/L β-alanine in fed-batch fermentation. Our study will lay a solid foundation for the promising application of β-alanine in the life and health field. KEY POINTS: • Overexpression of BtADC resulted in substantial accumulation of β-alanine. • The native AspC was replaced with PaeAspDH to catalyze the transamination of OAA. • Deletion of gluDH prevented from losing carbon flux in TCA recycle. • A 43.12-g/L β-alanine production in fed-batch fermentation was achieved. Graphical abstract.

Characterization of cysteine sulfinic acid decarboxylase from Tribolium castaneum and its application in the production of β-alanine

β-alanine is a precursor for the production of pharmaceuticals and food additives that is produced by chemical methods in industry. As concerns about the environment and energy are increasing, biocatalysis using L-aspartate-α-decarboxylase (ADC) to convert L-aspartate to β-alanine has great potential. Many studies have focused on the catalytic activity of ADC, but these researches were limited to the prokaryotic enzymes. In this study, the gene encoding cysteine sulfinic acid decarboxylase from Tribolium castaneum (TcCSADC) was synthesized and overexpressed in Escherichia coli, and the enzyme was purified and characterized for the first time. It could use L-aspartate as its substrate, and the specific activity was 4.83 μmol/min/mg, which was much higher than that of ADCs from prokaryotes. A homology modeling assay indicated that TcCSADC had a dimer structure. Based on the evolutionary information from thermophilic bacteria, twenty-three variants were constructed to attempt to improve its abilities that transform L-aspartate to β-alanine. One mutant, G369A, was screened that had improved thermal stability. An analysis of the suitability of the catalytic process showed that the up to 162 g/L β-alanine could be produced using cells expressing the recombinant G369A variant, which is the highest yield to date. The CSADC from T. castaneum has important value for studies of the mechanism of ADCs and CSADCs from eukaryotes, and the engineered strain containing the G369A variant has great potential for the industrial production of β-alanine.

Substrate inactivation of bacterial L-aspartate α-decarboxylase from Corynebacterium jeikeium K411 and improvement of molecular stability by saturation mutagenesis

Bacterial L-aspartate α-decarboxylase (PanD) is a potential biocatalyst for the green production of β-alanine, an important block chemical for manufacturing nitrogen-containing chemicals in bio-refinery field. It was reported that the poor catalytic stability caused by substrate inactivation limited the large-scale application. Here, we investigated the characters of inactivation by L-aspartate of PanD from Corynebacterium jeikeium (PD_Cjei), and found that L-aspartate induced a time-, and concentration-dependent inactivation of PD_Cjei with the values of K_I and k_inact being 288.4 mM and 0.235/min, respectively. To improve the catalytic stability of PD_Cjei, conserved amino acid residues essential to catalytic stability were analyzed by comparing the discrepancy in the observed inactivation rate of various sources. By an efficient colorimetric high-throughput screening method, four mutants with 3.18-24.69% higher activity were obtained from mutant libraries. Among them, the best mutation (R3K) also performed 66.38% higher catalytic stability than the wild type, showing great potential for industrial bio-production of β-alanine.

Identification of mutations restricting autocatalytic activation of bacterial L-aspartate α-decarboxylase

Bacterial L-aspartate α-decarboxylase (PanD) specifically catalyzes the decarboxylation of L-aspartic acid to β-alanine. It is translated as an inactive pro-protein, then processed by self-cleavage to form two small subunits with catalytic activity. There is a significant difference in the efficiency of this process among the reported PanDs, while the structural basis remains unclear. More PanDs with known sequences and characterized properties are needed to shed light on the molecular basis of the self-cleavage process. In this study, PanD genes from 33 selected origins were synthesized and expressed; using purified recombinant enzymes, their self-processing properties were characterized and classified. Three classes of PanDs were acquired based on their self-cleavage efficiency. Combined with the phylogenetic analysis and structure comparison, sited-directed mutagenesis was performed to investigate the effects of four mutants on self-processing. In comparison with the wild-type (96.4%), the self-cleavage efficiencies of mutants V23E, I26C, T27A, and E56S were decreased to 90.5, 83.6, 74.4 and 81.2%, respectively. The results indicated that residues of V23, I26, T27 and E56 were critical to the self-cleavage processing of PanDs. This work provided further understanding to the self-cleavage processing of PanDs, which may contribute to protein engineering of the enzyme.