Optimization of culture conditions for Mpt64 synthetic gene expression in Escherichia coli BL21 (DE3) using surface response methodology

Optimizing recombinant production of L-asparaginase 1 from Saccharomyces cerevisiae using response surface methodology

L-asparaginase is an essential enzyme used in cancer treatment, but its production faces challenges like low yield, high cost, and immunogenicity. Recombinant production is a promising method to overcome these limitations. In this study, response surface methodology (RSM) was used to optimize the production of L-asparaginase 1 from Saccharomyces cerevisiae in Escherichia coli K-12 BW25113. The Box-Behnken design (BBD) was utilized for the RSM modeling, and a total of 29 experiments were conducted. These experiments aimed to examine the impact of different factors, including the concentration of isopropyl-b-LD-thiogalactopyranoside (IPTG), the cell density prior to induction, the duration of induction, and the temperature, on the expression level of L-asparaginase 1. The results revealed that while the post-induction temperature, cell density at induction time, and post-induction time all had a significant influence on the response, the post-induction time exhibited the greatest effect. The optimized conditions (induction at cell density 0.8 with 0.7 mM IPTG for 4 h at 30 °C) resulted in a significant amount of L-asparaginase with a titer of 93.52 μg/mL, which was consistent with the model-based prediction. The study concluded that RSM optimization effectively increased the production of L-asparaginase 1 in E. coli, which could have the potential for large-scale fermentation. Further research can explore using other host cells, optimizing the fermentation process, and examining the effect of other variables to increase production.

l-Threonine production from whey and fish hydrolysate by E. coli ATCC® 21277TM

In this work production of l-threonine by Escherichia coli ATCC® 21277™ has been studied using a mixture of alternative low-cost substrates, which are recognized to be a major pollution problem. Whey was used as the primary carbon source, whereas Red Tilapia (Oreochromis sp.) viscera hydrolysates constituted the nitrogen source. A Box-Behnken Design was used for optimizing l-threonine and biomass production, using temperature and glucose, whey, and Red Tilapia (Oreochromis sp.) viscera hydrolysate contents as factors. Results indicate that biomass production is affected by the concentration of hydrolysate and temperature. On the other hand, l-threonine production is affected by concentration of whey, hydrolysate, and temperature. In this context, it was possible to maximize l-threonine production, but with a detriment on biomass production. The optimal conditions for biomass and l-threonine maximization (after 24 h) were identified and validated experimentally, resulting in biomass and l-threonine production of 0.767 g/L and 0.406 g/L, respectively. This work has shown the technical feasibility of using whey and Red Tilapia (Oreochromis sp.) viscera hydrolysates for the production of l-threonine by E. coli ATCC® 21277TM. Finally, the complications associated to the use of these low-cost complex substrates for the production of l-threonine by E. coli, suggest that more in detail studies (i.e. at the metabolic level) are required in order to propose strategies to increase the process productivity, before its scale up. This is a first step in our long-term goal of developing a production process for i) dealing with the pollution problems caused by those wastes, and ii) strengthen the milk and fish industries which are important poles of the Colombian economy.

Gel Protein Extraction's Impact on Conformational Epitopes of Linear Non-Tagged MPT64 Protein

The production and purification of recombinant proteins are crucial to acquiring pure MPT64 protein. Due to the fact that protein epitopes may undergo conformational changes during purification, this study, therefore, investigated an effective rapid purification method to produce highly intracellular pure MPT64 protein without causing conformational changes in the epitope under denaturing conditions. MPT64 was isolated from E. coli and electrophoresed using gel SDS-PAGE. Then, the desired protein bands were excised and purified with two methods: electroelution and passive elution. The isolated protein was identified via peptide mass fingerprinting using MALDI-TOF MS and reacted with IgG anti-MPT64, and the cross-reactivity of the isolated protein with IgY anti-MPT64 was confirmed using Western blot. The results show that both of these methods produced pure MPT64 protein, and the MPT64 protein was confirmed based on the MALDI-TOF MS results. Neither of these two methods resulted in epitope changes in the MPT64 protein so it could react specifically with both antibodies. The yield of MPT64 protein was higher with electroelution (2030 ± 41 µg/mL) than with passive elution (179.5 ± 7.5 µg/mL). Thus, it can be inferred that the electroelution method is a more effective method of purifying MPT64 protein and maintaining its epitope than the passive elution method.

Steroid hormone-inducible biosensor based on EGFP-tagged and environmental application

Steroid hormones as a class of emerging organic pollutant and high concern, due to their potential risks for human and environmental. Accurate analytical methods of steroid hormones are necessary in quantifying and monitoring. Biosensor is a promising technique. In this study, though part of 3α-HSD DNA to construct a regulatory plasmid and with the EGFP reporter gene to generate a reporter plasmid. Separately transformed into Escherichia coli strain BL21 and extracted the cell lysates as novel biosensor reagents. Analyzed the total amounts of steroid hormones in water, sediment, and soil samples using biosensor reagents, and compared these results with those obtained by HPLC. In summary, detection method using an EGFP reporter that can detect trace amounts of steroid hormones to reached fg/L. The optimal reaction time range and temperature were 30 min and 30 °C, respectively, while the most suitable organic solvent for the steroid hormone was 100% ethanol, up to 96-well plate format. This method is very suitable for high-throughput detection of environmental steroid hormone pollutants.

Optimized expression of large fragment DNA polymerase I from Geobacillus stearothermophilus in Escherichia coli expression system

Bst DNA polymerase is a DNA polymerase derived from Geobacillus stearothermophilus, has a strand-displacement activity, and is used in loop-mediated isothermal amplification (LAMP) for rapid detection of COVID-19. Despite its potential to be employed in the detection of COVID-19, using commercially available enzymes is not economically feasible. The use of noncommercial enzyme for routine use is desirable. However, research on Bst DNA polymerase is still limited in Indonesia. For those reasons, a preliminary study of scale-up production of recombinant Bst polymerase was conducted. Therefore, the optimization of expression conditions was performed. The optimum conditions for Bst polymerase expression were as follows: 1 mM of IPTG, post-induction incubation time of 6 h, and induction at OD₆₀₀ 1.1. Employing optimum conditions could result in 2.8 times increase in protein yield compared to the initial conditions. Subsequently, an operation in 1 L working volume by a lab-scale bioreactor had been performed, followed by purification and dialysis. The optimum result for a 1 L lab-scale bioreactor was achieved by applying 100 rpm and 3 vvm, giving 11.7 mg/L of protein yield. Bst polymerase was successfully purified showing 813.56 U/mg of polymerase activity.

Purity of maltose-binding protein - Recombinant streptavidin expressed in Escherichia coli BL21 (pD861-MBP: 327892)

Nearly 95% of streptavidin which is expressed in Escherichia coli found as an inclusion body. Protein expressed in an inclusion body form requires further steps for the folding process related to its purification. Whereas the purity level of the recombinant streptavidin is very crucial mainly for the specification test in diagnostic system. In this study, we designed synthetic gene of streptavidin to be fused with maltose-binding protein (MBP) gene to enhance its solubility when expressed in E. coli BL21 (pD861-MBP: 327892) and purified using amylose resin with gradient column buffer. Based on the SDS-PAGE characterization, the majority of recombinant streptavidin was found in soluble than that of insoluble form. Recombinant streptavidin was found at its suitable size at 56.6 kDa in the soluble protein fraction with a concentration of 537.42 mg/L. The purest fraction of streptavidin recombinant was obtained at the 58^th fraction in a concentration of 0.86 mg/L with purity level of 98.77%. Compared to the initial crude protein extract, the level of purity is lower, 6.03%. In summary, the MBP purification method improves the purity level and enhances the solubility of the recombinant streptavidin.

Media optimization for SHuffle T7 Escherichia coli expressing SUMO-Lispro proinsulin by response surface methodology

BACKGROUND

SHuffle is a suitable Escherichia coli (E. coli) strain for high yield cytoplasmic soluble expression of disulfide-bonded proteins such as Insulin due to its oxidative cytoplasmic condition and the ability to correct the arrangement of disulfide bonds. Lispro is an Insulin analog that is conventionally produced in E. coli as inclusion bodies (IBs) with prolonged production time and low recovery. Here in this study, we aimed to optimize cultivation media composition for high cell density fermentation of SHuffle T7 E. coli expressing soluble Lispro proinsulin fused to SUMO tag (SU-INS construct) to obtain high cell density fermentation.

RESULTS

Factors including carbon and nitrogen sources, salts, metal ions, and pH were screened via Plackett-Burman design for their effectiveness on cell dry weight (CDW) as a measure of cell growth. The most significant variables of the screening experiment were Yeast extract and MgCl₂ concentration, as well as pH. Succeedingly, The Central Composite Design was utilized to further evaluate and optimize the level of significant variables. The Optimized media (OM-I) enhanced biomass by 2.3 fold in the shake flask (2.5 g/L CDW) that reached 6.45 g/L (2.6 fold increase) when applied in batch culture fermentation. The efficacy of OM-I media for soluble expression was confirmed in both shake flask and fermentor.

CONCLUSION

The proposed media was suitable for high cell density fermentation of E. coli SHuffle T7 and was applicable for high yield soluble expression of Lispro proinsulin.

Improving of pelB-Secreted MPT64 protein released by Escherichia coli BL21 (DE3) using Triton X-100 and Tween-80

pelB has been known as a successful signal peptide to translocate the protein target extracellularly in the Escherichia coli system. However, in our previous study, the yield of MPT64 protein extracellular recovery was still low and plenty of this protein was remain trapped in cytoplasm and periplasm. Recently, nonionic surfactants were efficiently reported to secrete recombinant protein extracellularly. Nonetheless, it must be clarified whether the surfactant supplementation can improve the yield of MPT64 extracellular protein significantly without giving impact on the structure of isolated MPT64 protein and can minimized the cell lysis effect. MPT64 protein secretion was carried out by comparing the effects of surfactants Tween 80 and Triton × 100 at various concentrations. Triton × 100 was able to increase the extracellular MPT64 protein gain up to 3 times higher than Tween 80 and it was in line with the greater level ratio of cell leakage of Triton × 100 compared to that of Tween 80. Similarly, the viable cell of the cultures decreased dramatically. However, both surfactants did not interfere the structure of MPT64 protein. In conclusion, Triton × 100 can be chosen as the supporting surfactant to assist the act of peptide signal in improving the resulting of MPT64 extracellular protein.

RSM-based Model to Predict Optimum Fermentation Conditions for Soluble Expression of the Antibody Fragment Derived from 4D5MOC-B Humanized Mab in SHuffle™ T7 E. coli

Overexpression of the EpCAM in epithelial-derived neoplasms makes this receptor a promising target in antibody-based therapy. Due to the lack of N-glycosylation, Escherichia coli (E. coli) seems to be the most appropriate choice for the expression of antibody fragments. However, developing a robust and cost-effective process that produces consistent therapeutic proteins from inclusion bodies is a major challenge. Undoubtedly, it can be circumvented by the soluble expression of these proteins. Utilization of numerous genetically modified hosts and optimization of cultivation conditions are two effective approaches widely used to overcome the insolubility problem. Due to the cytoplasmic expression of DsbC and the ability to the correct formation of disulfide bonds, the Shuffle™ T7 strain can be a suitable host for the soluble production of recombinant proteins. Here, Box-Behnken design (BBD)- Response surface methodology (RSM) modeling was employed to develop optimized culture conditions for 4D5MOC-B scFv fragment production in SHuffle™ T7 strain while solubility and production level were considered as responses. Although both responses were significantly influenced by post-induction temperature, cell density at induction time, and IPTG concentration, the temperature had the largest effect. The maximum experimental soluble protein obtained by adding 1 mM of IPTG into the M9 medium when the cell density reached 0.7 at 23 ᵒC was 693.56 µg/mL which was in good correlation with the predicted value of 720.742 µg/mL. Predictable total expression value was also experimentally verified. This strategy can be scaled-up for the production of large amounts of scFvs from SHuffle™ T7 E. coli to facilitate their potential applications as therapeutic and diagnostic agents.

Scale-up fermentation of Escherichia coli for the production of recombinant endoglucanase from Clostridium thermocellum

Endoglucanase (EC 3.2.1.4) catalysing the hydrolysis of β-1.4-glycosidic linkage of cellulose molecules is an enzyme of tremendous industrial importance. The present study describes a response surface methodology based predicted model to deduce a set of fermentation conditions for optimum growth and activity of recombinant endoglucanase in E. coli BL21 (DE3). Numerous significant parameters including fermentation media composition, temperature (Celsius), pH and agitation rate (rpm) were analysed systemically by employing central composite design. This effort reports highly efficient recombinant endoglucanase overproduction (6.9 gl^-1 of biomass) with 30% expression by E. coli in modified M9NG media incubated at 37 °C and pH 7 agitated at 200 rpm. Addition of 3 mM glucose and 24 mM glycerol in the M9NG media has shown positive effect on the enzyme yield and activity. The CMCase activity experimentally estimated was found to be 1185 U/mg with the optimized parameters. The outcomes of both the responses by the predicted quadratic model were found in consensus with the obtained values. Our results well depicted the favourable conditions to further scale-up the volumetric yield of other relevant recombinant enzymes and proteins.

Statistical Design of Experiments for Synthetic Biology

The design and optimization of biological systems is an inherently complex undertaking that requires careful balancing of myriad synergistic and antagonistic variables. However, despite this complexity, much synthetic biology research is predicated on One Factor at A Time (OFAT) experimentation; the genetic and environmental variables affecting the activity of a system of interest are sequentially altered while all other variables are held constant. Beyond being time and resource intensive, OFAT experimentation crucially ignores the effect of interactions between factors. Given the ubiquity of interacting genetic and environmental factors in biology this failure to account for interaction effects in OFAT experimentation can result in the development of suboptimal systems. To address these limitations, an increasing number of studies have turned to Design of Experiments (DoE), a suite of methods that enable efficient, systematic exploration and exploitation of complex design spaces. This review provides an overview of DoE for synthetic biologists. Key concepts and commonly used experimental designs are introduced, and we discuss the advantages of DoE as compared to OFAT experimentation. We dissect the applicability of DoE in the context of synthetic biology and review studies which have successfully employed these methods, illustrating the potential of statistical experimental design to guide the design, characterization, and optimization of biological protocols, pathways, and processes.