Improvement of the production of L-tryptophan in Escherichia coli by application of a dissolved oxygen stage control strategy

Engineering of Shikimate Pathway and Terminal Branch for Efficient Production of L-Tryptophan in Escherichia coli

L-tryptophan (L-trp), produced through bio-manufacturing, is widely used in the pharmaceutical and food industries. Based on the previously developed L-trp-producing strain, this study significantly improved the titer and yield of L-trp, through metabolic engineering of the shikimate pathway and the L-tryptophan branch. First, the rate-limiting steps in the shikimate pathway were investigated and deciphered, revealing that the combined overexpression of the genes aroE and aroD increased L-trp production. Then, L-trp synthesis was further enhanced at the shaking flask level by improving the intracellular availability of L-glutamine (L-gln) and L-serine (L-ser). In addition, the transport system and the competing pathway of L-trp were also modified, indicating that elimination of the gene TnaB contributed to the extracellular accumulation of L-trp. Through optimizing formulas, the robustness and production efficiency of engineered strains were enhanced at the level of the 30 L fermenter. After 42 h of fed-batch fermentation, the resultant strain produced 53.65 g/L of L-trp, with a yield of 0.238 g/g glucose. In this study, the high-efficiency L-trp-producing strains were created in order to establish a basis for further development of more strains for the production of other highly valuable aromatic compounds or their derivatives.

Enhanced production of γ-amino acid 3-amino-4-hydroxybenzoic acid by recombinant Corynebacterium glutamicum under oxygen limitation

Background

Bio-based aromatic compounds are of great interest to the industry, as commercial production of aromatic compounds depends exclusively on the unsustainable use of fossil resources or extraction from plant resources. γ-amino acid 3-amino-4-hydroxybenzoic acid (3,4-AHBA) serves as a precursor for thermostable bioplastics.

Results

Under aerobic conditions, a recombinant Corynebacterium glutamicum strain KT01 expressing griH and griI genes derived from Streptomyces griseus produced 3,4-AHBA with large amounts of amino acids as by-products. The specific productivity of 3,4-AHBA increased with decreasing levels of dissolved oxygen (DO) and was eightfold higher under oxygen limitation (DO = 0 ppm) than under aerobic conditions (DO ≥ 2.6 ppm). Metabolic profiles during 3,4-AHBA production were compared at three different DO levels (0, 2.6, and 5.3 ppm) using the DO-stat method. Results of the metabolome analysis revealed metabolic shifts in both the central metabolic pathway and amino acid metabolism at a DO of < 33% saturated oxygen. Based on this metabolome analysis, metabolic pathways were rationally designed for oxygen limitation. An ldh deletion mutant, with the loss of lactate dehydrogenase, exhibited 3.7-fold higher specific productivity of 3,4-AHBA at DO = 0 ppm as compared to the parent strain KT01 and produced 5.6 g/L 3,4-AHBA in a glucose fed-batch culture.

Conclusions

Our results revealed changes in the metabolic state in response to DO concentration and provided insights into oxygen supply during fermentation and the rational design of metabolic pathways for improved production of related amino acids and their derivatives.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01714-z.

Control algorithms and strategies of feeding for fed-batch fermentation of Escherichia coli: a review of 40 years of experience

Fed-batch cultivation is a well-known type of submerged fermentation that is frequently used in manufacture of recombinant proteins and various kinds of enzymes, owing to its ability to produce products with high concentrations and high efficiency. In fed-batch culture, several issues must be considered; most of them are also presented in batch culture. However, feed flow rate calculation only corresponds to fed-batch fermentation and its value has a significant impact on productivity, efficiency, final concentration of product, formation of by-products, and viscosity of the culture. From this background, the present review article is an effort to gather the information on feeding strategies for fed-batch cultivation of Escherichia coli, which is a well-known microorganism in the production of recombinant proteins and industrial enzymes, especially for therapeutic applications. Moreover, this review is an aid to comprehend and compare the fundamental concept of different feeding strategies and their advantages and drawbacks.

Enhancing L-malate production of Aspergillus oryzae by nitrogen regulation strategy

Regulating morphology engineering and fermentation of Aspergillus oryzae makes it possible to increase the titer of L-malate. However, the existing L-malate-producing strain has limited L-malate production capacity and the fermentation process is insufficiently mature, which cannot meet the needs of industrial L-malate production. To further increase the L-malate production capacity of A. oryzae, we screened out a mutant strain (FMME-S-38) that produced 79.8 g/L L-malate in 250-mL shake flasks, using a newly developed screening system based on colony morphology on the plate. We further compared the extracellular nitrogen (N1) and intracellular nitrogen (N2) contents of the control and mutant strain (FMME-S-38) to determine the relationship between the curve of nitrogen content (N1 and N2) and the L-malate titer. This correlation was then used to optimize the conditions for developing a novel nitrogen supply strategy (initial tryptone concentration of 6.5 g/L and feeding with 3 g/L tryptone at 24 h). Fermentation in a 7.5-L fermentor under the optimized conditions further increased the titer and productivity of L-malate to 143.3 g/L and 1.19 g/L/h, respectively, corresponding to 164.9 g/L and 1.14 g/L/h in a 30-L fermentor. This nitrogen regulation-based strategy cannot only enhance industrial-scale L-malate production but also has generalizability and the potential to increase the production of similar metabolites.Key Points• Construction of a new screening system based on colony morphology on the plate.• A novel nitrogen regulation strategy used to regulate the production of L-malate.• A nitrogen supply strategy used to maximize the production of L-malate.

Application of a dissolved oxygen control strategy to increase the expression of Streptococcus suis glutamate dehydrogenase in Escherichia coli

The accumulation of acetate in Escherichia coli inhibits cell growth and desired protein synthesis, and cell density and protein expression are increased by reduction of acetate excretion. Dissolved oxygen (DO) is an important parameter for acetate synthesis, and the accumulation of acetate is inversely correlated to DO level. In this study, the effect of DO levels on glutamate dehydrogenase (GDH) expression was investigated, and then different DO control strategies were tested for effects on GDH expression. DO control strategy IV (50% 0-9 h, 30% 9-18 h) provided the highest cell density (15.43 g/L) and GDH concentration (3.42 g/L), values 1.59- and 1.99-times higher than those achieved at 10% DO. The accumulation of acetate was 2.24 g/L with DO control strategy IV, a decrease of 40.74% relative to that achieved for growth at 10% DO. Additionally, under DO control strategy IV, there was lower expression of PoxB, a key enzyme for acetate synthesis, at both the transcriptional and translational level. At the same time, higher transcription and protein expression levels were observed for a glyoxylate shunt gene (aceA), an acetate uptake gene (acs), gluconeogensis and anaplerotic pathways genes (pckA, ppsA, ppc, and sfcA), and a TCA cycle gene (gltA). The flux of acetate with DO strategy IV was 8.4%, a decrease of 62.33% compared with the flux at 10% DO. This decrease represents both lower flux for acetate synthesis and increased flux of reused acetate.

Application of fermentation process control to increase l-tryptophan production in Escherichia coli

In this study, process engineering and process control were applied to increase the production of l-tryptophan using Escherichia coli Dmtr/pta-Y. Different dissolved oxygen (DO) and pH control strategies were applied in l-tryptophan production. DO and pH were maintained at [20% (0-20 hr); 30% (20-40 hr)] and [7.0 (0-20 hr), 6.5 (20-40 hr)], respectively, which increased l-tryptophan production, glucose conversion percentage [g (l-tryptophan)/g (glucose)], and transcription levels of key genes for tryptophan biosynthesis and tryptophan biosynthesis flux, and decreased the accumulation of acetate and transcription levels of genes related to acetate synthesis and acetate synthesis flux. Using E. coli Dmtr/pta-Y with optimized DO [20% (0-20 hr); 30% (20-40 hr)] and pH [7.0 (0-20 hr), 6.5 (20-40 hr)] values, the highest l-tryptophan production (52.57 g/L) and glucose conversion percentage (20.15%) were obtained. The l-tryptophan production was increased by 26.58%, the glucose conversion percentage was increased by 22.64%, and the flux of tryptophan biosynthesis was increased to 21.5% compared with different conditions for DO [50% (0-20 hr), 20% (20-40 hr)] and pH [7.0].

Using enzymatic hydrolyzate as new nitrogen source for L-tryptophan fermentation by E.coli

This study presents new methods for hydrolyzing bacterial cell in cyclic utilization of waste bacterial cell for L-tryptophan production by fermentation. Using enzymatic hydrolysis of the pre-treated bacterial cells which were collected from an L-tryptophan fermentation broth, trypsin was selected as the optimal protease for hydrolyzing the bacterial cell. The optimum conditions for hydrolysis were determined by the orthogonal test. Hydrolyzate was then dealt with a compound protease to further increase its content of free amino acids. With the optimum conditions of pH = 8, temperature of 37°C, treatment time of 6 h, and E/S of 4%, the final content of free amino acids in the hydrolyzate was 500.61 mg/g. The hydrolyzate and the yeast extract were added to the medium at the proportion of 1:1, which served as an organic nitrogen source for L-tryptophan production by fermentation. The production of L-tryptophan was 53.87 g/L, and the highest biomass was 53.45 g/L. As an organic nitrogen source, this hydrolyzate satisfies the requirements for L-tryptophan production by fermentation.

Improvement of Streptococcus suis glutamate dehydrogenase expression in Escherichia coli through genetic modification of acetate synthesis pathway

Escherichia coli generates acetate as an undesirable by-product that has several negative effects on protein expression, and the reduction of acetate accumulation by modifying genes of acetate synthesis pathway can improve the expression of recombinant proteins. In the present study, the effect of phosphotransacetylase (pta) or/and acetate kinase (ackA) deletion on glutamate dehydrogenase (GDH) expression was investigated. The results indicated that the disruptions of pta or/and ackA decreased the acetate accumulation and synthesis of per gram cell, and increased cell density, and GDH expression and synthesis of per gram cell. The pta gene was more important for acetate formation than the ackA gene. Using the strain with deletions of pta-ackA (SSGPA) for GDH expression, acetate accumulation (2·61 g l^-1 ) and acetate synthesis of per gram cell (0·229 g g^-1 ) were lowest, decreasing by 28·29 and 41·43% compared with those of the parental strain (SSG) respectively. The flux of acetate synthesis (6·6%) was decreased by 72·15% compared with that of SSG, and the highest cell density (11·38 g l^-1 ), GDH expression (2·78 mg ml^-1 ), and GDH formation of per gram cell (0·2442 mg mg^-1 ) were obtained, which were 1·22-, 1·43- and 1·17-times higher than the parental strain respectively. SIGNIFICANCE AND IMPACT OF THE STUDY: Significance and Impact of the Study: Acetate is the key undesirable by-product in Escherichia coli cultivation, and both biomass and production of desired products are increased by the reduction of acetate accumulation. In the present study, the strains with deletions of pta or/and ackA were constructed to reduce the acetate accumulation and improve the GDH expression, and the highest expression level of GDH was obtained using the strain with lesion in pta-ackA that was 1·17-times higher than that of the parental strain. The construction strategy of recombinant E. coli for decreasing the acetate excretion can be used for high expression level of other desired products.

Metabolic control analysis of L-tryptophan production with Escherichia coli based on data from short-term perturbation experiments

E. coli strain NT1259 /pF112aroFBL_kan was able to produce 14.3 g L^-1 L-tryptophan within 68 h in a fed-batch process from glycerol on a 15 L scale. To gain detailed insight into metabolism of this E. coli strain in the fed-batch process, a sample of L-tryptophan producing cells was withdrawn after 47 h, was separated rapidly and then resuspended in four parallel stirred-tank bioreactors with fresh media. Four different carbon sources (glucose, glycerol, succinate, pyruvate) were supplied individually with varying feeding rates within 19 min and the metabolic reactions of the cells in the four parallel reactors were analyzed by quantification of extracellular and intracellular substrate, product and metabolite concentrations. Data analysis allowed the estimation of intracellular carbon fluxes and of thermodynamic limitations concerning intracellular concentrations and reaction energies. Carbon fluxes and intracellular metabolite concentrations enabled the estimation of elasticities and flux control coefficients by applying metabolic control analysis making use of a metabolic model considering 48 enzymatic reactions and 56 metabolites. As the flux control coefficients describe connections between enzyme activities and metabolic fluxes, they reveal genetic targets for strain improvement. Metabolic control analysis of the recombinant E. coli cells withdrawn from the fed-batch production process clearly indicated that (i) the supply of two precursors for L-tryptophan biosynthesis, L-serine and phosphoribosyl-pyrophosphate, as well as (ii) the formation of aromatic byproducts and (iii) the enzymatic steps of igps and trps2 within the L-tryptophan biosynthesis pathway have major impact on fed-batch production of L-tryptophan from glycerol and should be the targets for further strain improvements.

Utilization of acid hydrolysate of recovered bacterial cell as a novel organic nitrogen source for L-tryptophan fermentation

In this study, waste bacterial cell (WBC) was recovered and used as an alternative to yeast extract in L-tryptophan fermentation. The effects of sulfuric acid concentration and temperature on the hydrolysis of WBC were optimized and the amino acid content in the waste bacterial cell hydrolysate (WBCH) was increased. Plackett-Burman and Box-Behnken design analysis revealed the optimum composition of the WBCH-based fermentation medium to be 22.47 g/L WBCH, 2.26 g/L KH₂PO₄, and 1.25 mg/L vitamin H. L-tryptophan yield and productivity with WBCH as the nitrogen source were 52.3 g/L and 2.16 g/L/h, respectively, which were 13% and 18% higher than those obtained with the yeast extract as the nitrogen source. In addition, WBCH did not affect the growth of Escherichia coli during L-tryptophan fermentation. Cost accounting showed that WBCH could be used as a novel and cheap organic nitrogen source for industrial L-tryptophan production.

Hydrolysing the soluble protein secreted by Escherichia coli in trans-4-hydroxy-L-proline fermentation increased dissolve oxygen to promote high-level trans-4-hydroxy-L-proline production

Trans-4-hydroxy-L-proline (Hyp) production by Escherichia coli (E. coli) in fermentation is a high-oxygen-demand process. E. coli secretes large amounts of soluble protein, especially in the anaphase of fermentation, which is an important factor leading to inadequate oxygen supply. And acetic acid that is the major by-product of Hyp production accumulates under low dissolved oxygen (DO). To increase DO and achieve high-level Hyp production, soluble protein was hydrolysed by adding protease in Hyp fermentation. The optimal protease, concentration, and addition time were trypsin, 0.2 g/L, and 18 h, respectively. With the addition of trypsin, the soluble protein in Hyp fermentation decreased by 43.5%. The DO could be maintained at 20–30% throughout fermentation. Hyp production and glucose conversion rate were 45.3 g/L and 18.1%, which were increases of 24.1% and 8.4%, respectively. The accumulation of acetic acid was decreased by 52.1%. The metabolic flux of Hyp was increased by 44.2% and the flux of acetate was decreased by 51.0%.

Gene modification of the acetate biosynthesis pathway in Escherichia coli and implementation of the cell recycling technology to increase L-tryptophan production

The implementation of a novel cell recycling technology based on a special disk centrifuge during microbial fermentation process can continuously separate the product and harmful intermediates, while maintaining the cell viability owing to the installed cooling system. Acetate accumulation is an often encountered problem in L-tryptophan fermentation by Escherichia coli. To extend our previous studies, the current study deleted the key genes underlying acetate biosynthesis to improve l-tryptophan production. The deletion of the phosphotransacetylase (pta)-acetate kinase (ackA) pathway in a gltB (encoding glutamate synthase) mutant of E. coli TRTHB, led to the highest production of l-tryptophan (47.18 g/L) and glucose conversion rate (17.83%), with a marked reduction in acetate accumulation (1.22 g/L). This strain, TRTHBPA, was then used to investigate the effects of the cell recycling process on L-tryptophan fermentation. Four different strategies were developed concerning two issues, the volume ratio of the concentrated cell solution and clear solution and the cell recycling period. With strategy I (concentrated cell solution: clear solution, 1: 1; cell recycling within 24-30 h), L-tryptophan production and the glucose conversion rate increased to 55.12 g/L and 19.75%, respectively, 17.55% and 10.77% higher than those without the cell recycling. In addition, the biomass increased by 13.52% and the fermentation period was shortened from 40 h to 32 h. These results indicated that the cell recycling technology significantly improved L-tryptophan production by E. coli.