Enhancing the efficiency of L-tyrosine by repeated batch fermentation

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

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

Rational strain design with minimal phenotype perturbation

Devising genetic interventions for desired cellular phenotypes remains challenging regarding time and resources. Kinetic models can accelerate this task by simulating metabolic responses to genetic perturbations. However, exhaustive design evaluations with kinetic models are computationally impractical, especially when targeting multiple enzymes. Here, we introduce a framework for efficiently scouting the design space while respecting cellular physiological requirements. The framework employs mixed-integer linear programming and nonlinear simulations with large-scale nonlinear kinetic models to devise genetic interventions while accounting for the network effects of these perturbations. Importantly, it ensures the engineered strain's robustness by maintaining its phenotype close to that of the reference strain. The framework, applied to improve the anthranilate production in E. coli, devises designs for experimental implementation, including eight previously experimentally validated targets. We expect this framework to play a crucial role in future design-build-test-learn cycles, significantly expediting the strain design compared to exhaustive design enumeration.

Ascertaining the Influence of Lacto-Fermentation on Changes in Bovine Colostrum Amino and Fatty Acid Profiles

The aim of this study was to collect samples of bovine colostrum (BCOL) from different sources (agricultural companies A, B, C, D and E) in Lithuania and to ascertain the influence of lacto-fermentation with Lactiplantibacillus plantarum strain 135 and Lacticaseibacillus paracasei strain 244 on the changes in bovine colostrum amino (AA), biogenic amine (BA), and fatty acid (FA) profiles. It was established that the source of the bovine colostrum, the used LAB, and their interaction had significant effects (p < 0.05) on AA contents; lactic acid bacteria (LAB) used for fermentation was a significant factor for aspartic acid, threonine, glycine, alanine, methionine, phenylalanine, lysine, histidine, and tyrosine; and these factor's interaction is significant on most of the detected AA concentrations. Total BA content showed significant correlations with glutamic acid, serine, aspartic acid, valine, methionine, phenylalanine, histidine, and gamma amino-butyric acid content in bovine colostrum. Despite the differences in individual FA contents in bovine colostrum, significant differences were not found in total saturated (SFA), monounsaturated (MUFA), and polyunsaturated (PUFA) fatty acids. Finally, the utilization of bovine colostrum proved to be challenging because of the variability on its composition. These results suggest that processing bovine colostrum into value-added formulations for human consumption requires the adjustment of its composition since the primary production stage. Consequently, animal rearing should be considered in the employed bovine colostrum processing technologies.

Combining genetic engineering and bioprocess concepts for improved phenylpropanoid production

The group of natural aromatic compounds known as phenylpropanoids has diverse applications, but current methods of production which are largely based on synthesis from petrochemicals or extraction from agricultural biomass are unsustainable. Bioprocessing is a promising alternative, but improvements in production titers and rates are required to make this method profitable. Here the recent advances in genetic engineering and bioprocess concepts for the production of phenylpropanoids are presented for the purpose of identifying successful strategies, including adaptive laboratory evolution, enzyme engineering, in-situ product removal, and biocatalysis. The pros and cons of bacterial and yeast hosts for phenylpropanoid production are discussed, also in the context of different phenylpropanoid targets and bioprocess concepts. Finally, some broad recommendations are made regarding targets for continued improvement and areas requiring specific attention from researchers to further improve production titers and rates.

Exploring the potential of Rhizopus oryzae AUMC14899 as a novel endophytic fungus for the production of L-tyrosine and its biomedical applications

BACKGROUND

A significant threat to the public's health is the rise in antimicrobial resistance among numerous nosocomial bacterial infections. This may be a detriment to present initiatives to enhance the health of immune-compromised patients. Consequently, attention has been devoted to exploring new bioactive compounds in the field of drug discovery from endophytes. Therefore, this study is the first on the production of L-tyrosine (LT) as a promising bio-therapeutic agent from endophytic fungi.

RESULTS

A new endophytic fungal isolate has been identified for the first time as Rhizopus oryzae AUMC14899 from Opuntia ficus-indica (L.) and submitted to GenBank under the accession number MZ025968. Separation of amino acids in the crude extract of this fungal isolate was carried out, giving a higher content of LT, which is then characterized and purified. LT exhibited strong antibacterial and anti-biofilm activities against multidrug-resistant Gram-negative and Gram-positive bacteria. The recorded minimum inhibitory concentration (MIC) values ranged from 6 to 20 µg/ml. In addition, LT caused a strong reduction in biofilm formation and disrupted the preformed biofilm. Moreover, results indicated that LT supported cell viability, evidencing hemocompatibility and no cytotoxicity.

CONCLUSION

Our findings suggest that LT has potential as a therapeutic agent due to its potential antibacterial, anti-biofilm, hemocompatibility, and lack of cytotoxic activities, which may also increase the range of therapy options for skin burn infections, leading to the development of a novel fungal-based drug.

Effect of process mode, nitrogen source and temperature on L-malic acid production with Aspergillus oryzae DSM 1863 using acetate as carbon source

Malic acid, mainly used as acidulant and taste enhancer in the food industry, is currently produced from fossil resources. In this study, microbial L-malate production with the filamentous fungus A. oryzae using the carbon source acetate was evaluated. Acetate is for example contained in biomass-derived substrates such as lignocellulosic hydrolysates and condensates of fast pyrolysis, thus avoiding competition with food production. Since research on malic acid synthesis from acetate is limited and reported productivities and yields are low, this work aimed to improve the process. First, different cultivation temperatures were tested. This parameter was found to affect the ratio between malic and succinic acid, which is the major by-product of organic acid production with A. oryzae. At 32°C, the malate share was highest (53.7 ± 1.6%), while it was lowest at 38°C (43.3 ± 1.1%) whereas succinate represented the main product (51.5 ± 1.0%). Besides the temperature, the type of nitrogen source was also found to affect malate synthesis as well as biomass production. In the pre-culture, the biomass concentration was increased by a factor of 3.4–3.9, and germination started earlier with the complex nitrogen sources yeast extract, casein hydrolysate and peptone compared to the defined nitrogen source (NH₄)₂SO₄. Especially with yeast extract, malate synthesis in the main culture was accelerated and the titer obtained after 48 h was about 2.6 times higher than that quantified with (NH₄)₂SO₄. To reduce substrate inhibition in acetate medium, fed-batch and repeated-batch processes were evaluated using (NH₄)₂SO₄ or yeast extract as nitrogen source. In the fed-batch process, the period of malate production was extended, and the maximum product concentration was increased to 11.49 ± 1.84 g/L with (NH₄)₂SO₄ and 12.08 ± 1.25 g/L with yeast extract. In the repeated-batch process, the total acid production was highest within the first 240 h of fermentation, but optimization is required to maintain high production rates in later cycles. The lessons learned in this study will help in the development of further process strategies to maximize malate production using acetate as alternative substrate to the commonly used glucose.

Novel bioreactor internals for the cultivation of spore‐forming fungi in pellet form

This study introduced an automated long‐term fermentation process for fungals grown in pellet form. The goal was to reduce the overgrowth of bioreactor internals and sensors while better rheological properties in the fermentation broth, such as oxygen transfer and mixing time, can be achieved. Because this could not be accomplished with continuous culture and fed‐batch fermentation, repeated‐batch fermentation was implemented with the help of additional bioreactor internals (“sporulation supports”). This should capture some biomass during fermentation. After harvesting the suspended biomass, intermediate cleaning was performed using a cleaning device. The biomass retained on the sporulation support went through the sporulation phase. The spores were subsequently used as inocula for the next batch. The reason for this approach was that the retained pellets could otherwise cause problems (e.g., overgrowth on sensors) in subsequent batches because the fungus would then show undesirable hyphal growth. Various sporulation supports were tested for sufficient biomass fixation to start the next batch. A reproducible spore concentration within the range of the requirements could be achieved by adjusting the sporulation support (design and construction material), and an intermediate cleaning adapted to this.

Poly(ε-L-lysine) and poly(L-diaminopropionic acid) co-produced from spent mushroom substrate fermentation: potential use as food preservatives

Poly(ε-L-lysine) and poly(L-diaminopropionic acid) are valuable homopoly (amino acids) with antimicrobial properties and mainly produced in submerged fermentation. In this study, we investigated their co-production using waste biomass and spent mushroom substrate in solid-state fermentation. Simultaneous production of poly(L-diaminopropionic acid) and poly(ε-L-lysine) was achieved in a single fermentation process using pearl oyster mushroom residues as substrate, with the supplement of glycerol and corn steep liquor. After optimization of the fermentation parameters, the maximum yield of poly(ε-L-lysine) and poly(L-diaminopropionic acid) reached 51.4 mg/g substrate and 25.4 mg/g substrate, respectively. The optimal fermentation conditions were 70% initial moisture content, pH of 6.5, 30°C and an inoculum size of 14%. Furthermore, the fermentation time was reduced from 8 days to 6 days using repeated-batch solid-state fermentation. Finally, the antimicrobial effects of poly(L-diaminopropionic acid) and poly(ε-L-lysine) were evaluated in freshly pressed grape juice, which indicated tremendous potential of this mixture in its use as biological preservative.

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

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

Effects of Methyl Donors on L-Tryptophan Fermentation

Methyl donors, a class of compounds that supply methyl groups to methyl acceptors, play important roles in the function, growth, and proliferation of cells; however, the methyl donor content in cells is not sufficient to meet their normal needs. In L-tryptophan production with E. coli, the growth and acid-producing ability of E. coli cells are weak due to the presence of exogenous plasmids that inhibit the growth of E. coli, and reduce the efficiency of exogenous gene expression. Therefore, the effect of methyl donors on L-tryptophan production was investigated. Among the methyl donors tested, choline chloride showed the most significant effect in promoting fermentation, followed by methionine. The optimum addition method involved the addition of 1.5 g/L methionine to the culture medium, combined with continuous feeding with a glucose solution containing 1 g/L choline chloride. The final tryptophan titer reached 53.5 g/L; the highest biomass of bacteria reached 51.8 g/L; and the main by-product, acetic acid, was reduced to 2.23 g/L, which had a significant impact on the fermentation results.

A new method to recover L-tyrosine from E. coli fermentation broth

Although the production of L-tyrosine by recombinant Escherichia coli has been widely reported, L-tyrosine recovery from the fermentation broth has been rarely reported. Methods to recover L-tyrosine from the broth after alkaline lysis of the bacterial cells have been described. However, the broth becomes viscous and dark following cell lysis, making further extraction and purification difficult. Here, a new method for L-tyrosine extraction and purification from the fermentation broth without the lysis of bacteria is reported. First, acids, rather than bases, were used to dissolve L-tyrosine in the broth without causing lysis of the bacterial cells. E. coli cells in the broth were then removed through centrifugation. Activated carbon was then used to decolorize the supernatant containing L-tyrosine. Finally, sodium hydroxide was added to the clarified L-tyrosine solution for isoelectrocrystallization. L-tyrosine was obtained after filtration and drying. The recovery yield of L-tyrosine was 92%, and the purity was >98.5%, indicating high efficiency of the new method of L-tyrosine recovery from fermented broth. Furthermore, the method provides a reference for the extraction of guanosine, inosine, hypoxanthine, and other biological fermentation products.