Loading...

Abstract

This section presents the successful construction and functional validation of the three core modules designed for our "ProBabyotics" platform, aimed at systemically enhancing the nutritional value of infant formula. Each module was systematically engineered and rigorously tested, providing a robust proof-of-concept for our overall project.

For the Immune Enhancement Module (2'-FL): We successfully established a de novo biosynthetic pathway for 2'-fucosyllactose (2'-FL). Through a multi-stage DBTL (Design-Build-Test-Learn) engineering cycle, we progressively optimized the system. Key improvements included selecting a lacZ-deficient DH5α chassis to eliminate substrate competition (achieving a ~19-fold yield increase) and employing a TrxA fusion tag to enhance the solubility of the rate-limiting futC enzyme (a further 56% boost). This iterative process increased the 2'-FL titer from an initial 8.10 mg/L to a final yield of 279.47 ± 22.09 mg/L. The identity of the product was unequivocally confirmed by HPLC.

For the Protein Hydrolysis Module (Trypsin): We developed a complete "gene-to-function" pipeline for producing active recombinant trypsin. The codon-optimized TRYP gene was successfully cloned and its expression was confirmed via Western Blot. We established an effective protocol to refold the protein from inclusion bodies and activate it via autocatalysis. The resulting enzyme demonstrated high functionality, with a specific activity of 1748 U/mg in a BAEE hydrolysis assay.

For the Lactose Tolerance Module (β-Galactosidase): We successfully expressed and characterized β-galactosidase (lacZ) from the existing BioBrick part BBa_I732005. After confirming the expression of the full-length, ~116 kDa protein via Western Blot, we performed an in vitro functional assay. The purified enzyme proved to be highly effective, degrading 80% of the lactose substrate within 8 hours.

Collectively, these results validate the feasibility of our modular approach. We have successfully produced and characterized all three key functional components, laying a solid scientific foundation for the development of our next-generation infant formula, "2'F-Luxe".


Abstract  Diagram

Figure 1: ProBabyotics: Engineering a Better Formula

System 1: 2'-FL production

This section details the systematic engineering of an E. coli strain for the de novo biosynthesis of 2'-fucosyllactose (2'-FL), a key human milk oligosaccharide(Yang et al., 2025). Our project followed a multi-round 'Design-Build-Test-Learn' (DBTL) cycle to progressively identify and overcome metabolic bottlenecks(Zhao et al., 2025)a. Key strategies included constructing a complete five-gene metabolic pathway, optimizing the host chassis to eliminate substrate competition, and employing protein engineering to enhance the activity of a rate-limiting enzyme. Through these iterative improvements, we successfully increased the 2'-FL titer from an initial proof-of-concept yield of 8.10 mg/L to a final yield of 279.47 ± 22.09 mg/L, demonstrating a clear and successful engineering workflow.


Comparison of 2'-fucosyllactose(2'-FL) yield in BL21-manB+manC after 72-hour fermentation

Objective

The objective of this experiment was to provide a proof-of-concept for our 2'-FL biosynthetic pathway. Specifically, we aimed to determine if the co-expression of the first two key enzymes, manB and manC, is sufficient to initiate the de novo synthesis of 2'-FL in our E. coli BL21 chassis.

Methods

-Genetic Engineering

Synthesize manB and manC and clone the pET28a vector through NdeI and XhoI restriction sites. E. coli BL21 (DE3) (D1009S) and DH5α (DE3) (D0351) supercompetent cells were purchased from Beyotime. Subsequently, the recombinant plasmid is transformed into E. coli DH5α and BL21. Positive clones are screened on LB (Luria Bertani) plates containing 100 μg/mL kanamycin (Kana), followed by sequencing verification (Beijing, Jingke) to obtain the recombinant engineering strain. The strain is stored at -80°C with 25% (v/v) glycerol as a cryoprotectant.

Methods  Diagram

Figure 2: Construction of BL21-manB+manC. (A) The plasmid map of pET28a-manB+manC; (B) The gene circuit of BL21-manB+manC; (C) Flow chart of Genetic engineering

-Bacterial Culture

Transfer the recombinant strains in 50mL Erlenmeyer flasks containing 10 mL LB medium with Kana, under conditions of 25°C, 250 rpm. Measure cell concentration by optical density at 600 nm using a microplate reader (FlexStation 3,Molecular Devices,USA). When OD₆₀₀ reaches 0.6, bacteria are collected by centrifugation at 4000 g for 5 min and resuspended into 100 mL M9 Broth (1 mM MgSO₄ and 50 μM CaCl₂)(A510881, Sangon Biotech, China) with 20 g/L glycerol and 5 g/L yeast extract. As cell OD₆₀₀ reached 0.6 again , 0.5 mM IPTG and 8 g/L lactose are added to produce 2'-fucosyllactose (2'-FL).


Methods  Diagram

Figure 3: Flow chart of bacterial culture.

-2'-FL content assay

To quantify the 2'-FL concentration, 1 mL of fermented broth was collected at designated intervals. The samples were centrifuged at 10,000 g for 1 minute, and the resulting supernatant was collected and stored at -20°C for subsequent analysis.

The 2'-FL content was determined using a commercial detection kit (Synome, 680112), which relies on a two-step enzymatic cascade. A highly specific α-L-fucosidase first hydrolyzes 2'-FL to release L-fucose. Subsequently, L-fucose dehydrogenase (FDH) oxidizes the L-fucose to L-fucono-1,5-lactone. This reaction is coupled with the stoichiometric reduction of NADP⁺ to NADPH. Since NADPH has a strong characteristic absorbance at 340 nm, the increase in absorbance is directly proportional to the amount of NADPH produced, which is equimolar to the initial amount of 2'-FL in the sample. The final concentration was calculated based on the change in absorbance at 340 nm (A₃₄₀).


Methods  Diagram

Figure 4: Flow chart of 2'-FL content assay

Results

The results of the agarose gel electrophoresis are shown in Figure 5. A distinct band of the expected size (1947 bp) was observed, confirming the successful express of manB+manC.


Results Diagram

Figure 5: the agarose gel electrophoresis analysis of the manB+manC gene fragment


The 2'-fucosyllactose content in both BL21 and BL21-p28a is close to 0 mg/L, while the average 2'-fucosyllactose content of BL21- manB+manC is 8.10±1.03 mg/L. 2'-fucosyllactose content is higher in BL21-manB+manC than in BL21 and BL21-p28a.

Results Diagram

Figure 6: Comparison of 2'-FL yield in BL21-manB+manC after 72-hour fermentation


Conclusion

The results demonstrate that the co-expression of manB and manC is both necessary and sufficient to initiate 2'-FL synthesis in E. coli BL21. The engineered strain produced a measurable yield (8.10±1.03 mg/L), whereas the control strains showed negligible production. While modest, this yield serves as a crucial validation that the foundational step of our pathway is functional. This outcome strongly suggests that the downstream enzymes are the next rate-limiting step, guiding our subsequent work to incorporate the complete gene cassette (gmd, fcl, and futC) to improve the final yield(Moriyama et al., 2025).



Yield comparison of 2 '-fucosyllactose after 72 hours of fermentation of BL21 recombinant strain

Objective

This experiment aims to evaluate the effect of expression of different genes in BL21 recombinant strains on the yield of 2'-FL after 72 hours of fermentation.


Methods

-Genetic Engineering

Synthesize manB, manC, gmdfcl and futC, and Clone the pET28a vector through NdeI and XhoI restriction sites. E. coli BL21 (DE3) (D1009S) and DH5α (DE3) (D0351) supercompetent cells were purchased from Beyotime. Subsequently, the recombinant plasmid is transformed into E. coli DH5α and BL21. Positive clones are screened on LB (Luria Bertani) plates containing 100 μg/mL kanamycin (Kana), followed by sequencing verification (Beijing, Jingke) to obtain the recombinant engineering strain. The strain is stored at -80°C with 25% (v/v) glycerol as a cryoprotectant.


Methods Diagram

Figure 7: Construction of BL21-manB+manC+gmd+fcl+futC. (A) The plasmid map of pET28a-manB+manC+gmd+fcl+futC (B) The gene circuit of BL21-manB+manC+gmd+fcl+futC.


-Bacterial Culture

Transfer the recombinant strains in 50mL Erlenmeyer flasks containing 10 mL LB medium with Kana, under conditions of 25°C, 250 rpm. Measure cell concentration by optical density at 600 nm using a microplate reader (FlexStation 3,Molecular Devices,USA). When OD₆₀₀ reaches 0.6, bacteria are collected by centrifugation at 4000 g for 5 min and resuspended into 100 mL M9 Broth (1 mM MgSO₄ and 50 μM CaCl₂)(A510881, Sangon Biotech, China) with 20 g/L glycerol and 5 g/L yeast extract. As cell OD₆₀₀ reached 0.6 again , 0.5 mM IPTG and 8 g/L lactose are added to produce 2'-fucosyllactose (2'-FL).


Methods Diagram

Figure 8: Flow chart of bacterial culture.


-2'-FL content assay

Collect 1mL fermented broth from cultured bacteria at intervals. After centrifugation at 10,000g for 1 min, the supernatant is stored at -20°C. Calculate the 2'-FL content according to the instruction(680112, Synome).


Methods Diagram

Figure 9: Flow chart of 2'-FL content assay


Results

The agarose gel electrophoresis results for the manA, gmd, fcl and futC gene are shown in Figure 10. As indicated by the marker, bands of the correct corresponding lengths were observed for all genes, confirming their successful expression.


Results Diagram

Figure 10: Agarose gel electrophoresis analysis of the manA, gmd, fcl, futC gene fragment


We synthesise manA, manB, manC, gmdfcl and futC at first, but due to the significantly slow growth rate of the recombinant strain after expressing manA, a literature review was conducted. It was determined that the manA gene is not essential for the 2'-FL production pathway. Therefore, the recombinant strain used for subsequent 2'-FL yield measurements contained the gene sequence manB, manC , gmd, fcl, and futC.


As shown in Figure 11, the results indicate that the 2'-FL content in both BL21 and BL21-p28a is close to 0 mg/L. And the average 2'-FL content of BL21-manB+manC and BL21-manB+manC+gmd+fcl+futC are 8.11±1.04 mg/L and 19.66±2.62 mg/L respectively. Overall, BL21-manB+manC+gmd+fcl+futC yields the most 2'-fucosyllactose.


Results Diagram

Figure 11: Yield comparison of 2 '-fucosyllactose after 72 hours of fermentation of BL21 recombinant strain


Conclusion

The maximum yield of the recombinant strain BL21-manB+manC+gmd+fcl+futC reaches 19.66±2.62 mg/L of 2-FL. This indicates that overexpression of manB, manC, gmd, fcl and futC can significantly increase the yield of 2 '-FL, which is consistent with other findings(Liang et al., 2025).


Changes in 2'-FL yield, Lactose Content, and Cell Dry Weight Over Time in BL21-manB+manC+gmd+fcl+futC

Objective

Building upon our initial proof-of-concept, this experiment aimed to quantify the impact of expressing the complete de novo synthesis pathway on 2'-FL production. We hypothesized that by co-expressing the downstream enzymes (gmd, fcl and futC ) alongside manB and manC, we could overcome the metabolic bottleneck identified previously and significantly increase the final 2'-FL yield.

Methods

-Engineered strain used

The BL21-manB+manC+gmd+fcl+futC engineered strain we used is manufactured in the previous steps.

-Bacteria dry cell weight determination

Measure cell optical density at 600nm using a microplate reader (FlexStation 3,Molecular Devices,USA). During fermentation, 1 mL broth samples are collected at designated time intervals to monitor cell growth. The bacterial cells are immediately pelleted by centrifugation at 10,000 × g for 10 minutes. After carefully removing the supernatant, the cell pellets undergo a drying process in a 50°C oven for 8 hours to completely evaporate residual moisture. The resulting dried biomass is then precisely weighed to determine the dry cell weight (DCW), as

DCW(g/L)=(Wtube+cellWtube) /Vsample×dilution factor .

​-2'-FL content assay

Collect 1mL fermented broth from cultured bacteria at intervals. After centrifugation at 10,000g for 1 min, the supernatant is stored at -20°C. Then calculate the 2'-FL content according to the instruction(680112, Synome).

-Lactose content assay

Repeat the first and second steps in the process '2'-FL content assay', follow by the calculation of lactose content according to the instruction(Jonln, JL-T1072).

Methods Diagram

Figure 12: Flow charts of bacteria dry cell weight determination, 2'-FL content assay and lactose content assay.

Results

It is clear from the graph that during the period of 72 hours, the amount of lactose fall consistently while dry cell mass and the figure for 2’-FL and the dry cell mass rised from 0.00 mg/L to about 22.71 mg/L and from 0.00 mg/L to 18.00 mg/L respectively.


Results Diagram

Figure 13: Changes in 2'-FL yield, Lactose Content, and Cell Dry Weight Over Time in BL21-manBC+gmd+fcl+futC


Conclusion

The results strongly support our hypothesis. The introduction of the complete five-gene cassette (manB+manC+gmd+fcl+futC) led to a final 2'-FL yield of 19.66±2.62 mg/L, a statistically significant (p < 0.0001) and 2.4-fold increase over the strain expressing only manB+manC. This demonstrates that the downstream enzymes, particularly the final fucosyltransferase (futC), are crucial for converting the metabolic intermediates into the final product.

Additionally, we learned that including manA in the construct severely impaired cell growth, and a literature review confirmed it was non-essential (Li et al., 2025). This finding refined our final construct design. Overall, we successfully established a functional, multi-gene pathway for 2'-FL synthesis in E. coli, laying the groundwork for further optimization.



HPLC analysis of fermentation products

Objective

While the enzymatic assay provided a convenient method for high-throughput quantification, its detection principle is based on the measurement of L-fucose released after hydrolysis. Consequently, the assay cannot distinguish authentic 2'-FL from other potential fucose-containing byproducts (such as other fucosylated oligosaccharides) or any pre-existing free L-fucose in the fermentation broth. This inherent lack of specificity creates potential for interference and necessitates a more rigorous confirmation of product identity.

Therefore, to provide definitive and orthogonal validation, we employed High-Performance Liquid Chromatography (HPLC). The objective of this experiment was to separate the components of our fermentation supernatant and compare the retention time of the major product peak against that of a pure 2'-FL analytical standard. This method provides unambiguous chemical identification, confirming that the compound we quantified was indeed our target molecule, 2'-FL. Given the complexity of the instrumentation and method development, these experiments were conducted with the invaluable guidance of our instructors.


Objective Diagram

Figure 14: Students performed the complex HPLC analysis under the guidance of our instructors.


Methods

The recombinant strains mentioned above are supplemented into the LB medium containing Kana, under the conditions of 25°C and 250 rpm. Detect the value of OD₆₀₀ and as it reaches a0.6, transfer the strains to M9 medium (20 g/L glycerol, 5 g/L yeast extract, 1 mM MgSO4, 50 μM CaCl2). As OD₆₀₀=0.6 again, the production of 2’-FL will be induced by adding 0.5 mM IPTG and 8 g/L lactose.The production of 2'-FL by engineered bacteria will be analyzed by a high performance liquid chromatography (HPLC) system (WATERS), equipped with a WATERS ACQUITY UPLC BEH Amide (2.1×100 mm, 1.7 μm). The mobile phases are A: 80% acetonitrile and 20% ammonia (0.1%), B: 30% acetonitrile and 70% ammonia (0.1%), with flow rate of 0.3 mL/min and temperature of 45°C. According to the programmed gradient, mobile phase A decreases from 90% to 60% at 0-7 min and recoveres to 90% at 7-10 min. Mobile phase B increases from 10% to 40% at 0-7 min and decreases to 10% at 7-10 min.


Methods Diagram

Figure 15: Mechanism of HPLC

Results & Conclusion

The HPLC chromatogram of the fermentation supernatant from our engineered BL21 strain is presented in Figure 16. A prominent peak was detected at a retention time of 4.25 minutes. This retention time perfectly matched that of the 2'-FL analytical standard run under identical conditions.

This result provides definitive evidence that our engineered metabolic pathway is functional and that the compound being produced is, in fact, 2'-FL. The successful verification of the product's identity is a critical milestone, validating our quantitative yield measurements and confirming the success of our genetic design.

Results & Conclusion Diagram

Figure 16: HPLC analysis of fermentation products of BL21


The effect of two different strains(BL21/DH5α) on 2'FL yield

Objective

Based on the knowledge that the lacZ gene in E. coli BL21 creates a competitive pathway for our lactose substrate, we hypothesized that switching to a lacZ -deficient chassis would significantly increase 2'-FL yield. This experiment was designed to directly test this hypothesis by comparing the productivity of our engineered pathway in E. coli BL21 versus E. coli DH5α under identical fermentation conditions(Chen et al., 2024).

Methods

Our group used the same method to engineer 2 kinds of bacteria: BL21-manB+manC+gmd+fcl+futC and DH5α-manB+manC+gmd+fcl+futC by transferring designed recombinant plasmid to competent E.coli BL21 and DH5α. The concentration of 2'-FL in the sample is detected through absorbance , using a reagent kit and a microplate reader.


Methods Diagram

Figure 17: Methods for Exploring the effect of two different strains(BL21/DH5α) on 2'FL yield. (A)Experimental Methods; (B)Experimental Flowchart


Results

We conducted a head-to-head comparison by fermenting our engineered BL21 and DH5α strains under identical conditions. The results were definitive: the DH5α strain produced 158.26 ± 21.67 mg/L of 2'-FL, a nearly 19-fold improvement over the 8.23 ± 1.86 mg/L from the BL21 strain (Figure 18).


Results Diagram

Figure 18: The effect of two different strains(BL21/DH) on 2'FL production


Conclusion

The results provide a definitive validation of our hypothesis. The lacZ-deficient DH5α strain produced 158.26 ± 21.67 mg/L of 2'-FL, a remarkable ~19-fold increase compared to the BL21 strain. This demonstrates that chassis selection is a critical design parameter in metabolic engineering. By simply eliminating a single competing enzyme (lacZ), we successfully redirected the metabolic flux towards our desired product, achieving a substantial improvement in overall pathway efficiency. This learning was immediately incorporated into our subsequent engineering cycles.



The effect of TrxA tag fusion futC on 2 '-fucosyllactose yield

Objective

The futC gene, which encodes the final and rate-limiting enzyme in our pathway, is of human origin. Heterologous expression of such proteins in E. coli often leads to misfolding and poor solubility. To address this anticipated bottleneck, we employed a protein engineering strategy (Li et al., 2024). This experiment aimed to test the hypothesis that fusing a Thioredoxin A (TrxA) solubility-enhancing tag to the N-terminus of futC would improve its functional expression and thereby boost the final 2'-FL yield in our optimized DH5α chassis.

Methods

First, we used the same method described above to construct the engineered strain DH5α and overexpress the manB+manC+gmd+fcl+futC gene. Then, we introduced TrxA tag fusion into DH5α. We detect the production of 2'-FL by using the 2'-FL Detection Kit according to the manufacturer’s instructions.


Methods  Diagram

Figure 19: Methods for the effect of TrxA tag fusion futC on 2 '-fucosyllactose yield. (A)Experimental Methods; (B)Experimental Flowchart; (C) The gene circuit of DH5α-manB+manC+gmd+fcl+TrxA-futC.


Results

The results showed that fusing futC with a TrxA tag significantly boosted 2'-FL production. The engineered strain with the TrxA-futC fusion yielded 279.47 ± 22.09 mg/L, a 56% improvement over the control strain expressing untagged futC (179.27 ± 11.58 mg/L), as detailed in Figure 20.


Results Diagram

Figure 20: The effect of TrxA tag fusion futC on 2 '-fucosyllactose yield


Conclusion

The data conclusively demonstrates the success of our protein engineering approach. The strain expressing the TrxA-futC fusion protein yielded 279.47 ± 22.09 mg/L of 2'-FL, achieving a significant 56% increase over the control with untagged futC.

This result confirms that the poor solubility of the heterologously expressed futC was indeed a major limiting factor. By leveraging the TrxA fusion tag, we successfully increased the amount of soluble, active futC enzyme in the cell. This serves as a powerful demonstration of how targeted protein engineering can be used to overcome expression challenges and unlock the full potential of a metabolic pathway (Young & Robinson, 2014).


Summary

In summary, our team successfully executed a four-stage engineering cycle that progressively improved 2'-FL production by over 34-fold. Each stage provided critical insights that guided the next round of design:

Pathway Completion: We first established that the full five-gene cassette was essential, increasing the yield by 2.4-fold compared to the initial two-gene construct. This confirmed that downstream enzymes were a primary bottleneck.

Chassis Optimization: We demonstrated the critical impact of host chassis selection. Switching to the lacZ-deficient DH5α strain eliminated substrate competition for lactose, resulting in a remarkable ~19-fold yield increase and identifying a major point of metabolic inefficiency (Chen et al., 2024).

Protein Engineering: We confirmed that the heterologous expression of the human futC enzyme was another limiting factor. By fusing it with a TrxA solubility tag, we successfully improved its functional expression, boosting production by a further 56%(Li et al., 2024).

Collectively, these results provide a robust, step-by-step validation of our metabolic engineering strategy. We have not only created a high-performing production strain but also documented a clear and logical workflow that can serve as a valuable reference for future iGEM teams tackling complex pathway optimization challenges (Gao et al., 2025).


System 2: Trypsin

This section details the complete workflow for the production of a functional recombinant protease, trypsin, designed to improve protein digestion in infant formula (Jakobsson et al., 2000). Our engineering process encompasses the entire journey from gene to function: (1) plasmid construction of a codon-optimized porcine trypsinogen (TRYP) gene; (2) protein expression verification in E. coli BL21(DE3) via Western Blot; and (3) a multi-step process of protein purification, refolding, and activation from inclusion bodies. The success of this workflow was ultimately validated by a quantitative enzymatic assay, which confirmed the high catalytic activity of our final product (Rawlings et al., 1994).


Construction of trypsin Expression Vector

Objective

This experiment aimed to construct a recombinant plasmid for the expression of porcine trypsinogen (TRYP) and verify the successful cloning of the TRYP gene. The goal was to create a foundational tool, the pET-28a-TRYP vector, which would serve as the basis for producing recombinant trypsin in our E. coli BL21(DE3) chassis.

Methods

-The construction of trysin-engineered bacteria

The TRYP gene (Uniprot: P00761) is codon-optimized according to RFC10 standards, synthesized, and cloned into the NdeI/XhoI-digested pET-28a plasmid to construct the pET-28a-TRYP recombinant vector (Buck et al., 1962). This vector is then transformed into E. coli BL21(DE3) competent cells (Beyotime, D1009S). Positive transformants are selected on LB agar plates supplemented with 100 μg/mL Kana and subsequently verified by sequencing (Qingke, Beijing).

The confirmed recombinant strain is preserved at -80°C in 25% (v/v) glycerol for long-term storage. For routine cultivation, the engineered strain is grown in LB liquid medium containing 100 μg/mL Kana at 37°C with shaking at 150 rpm.


Methods Diagram

Figure 21: Construction of BL21-TRYP. (A) The plasmid map of pET28a-TRYP; (B) The gene circuit of BL21-TRYP; (C) The flow chart of Construction of BL21-TRYP.


Results

The agarose gel electrophoresis results for the TRYP gene are shown in Figure 22. As indicated by the marker, bands of the correct corresponding lengths were observed for TRYP genes, confirming it's successful expression.

Results Diagram

Figure 22: the agarose gel electrophoresis analysis of the TRYP gene fragment

Conclusion

The agarose gel electrophoresis result confirms the successful construction of the pET-28a-TRYP expression vector. A single, bright band was observed at the expected size of 693 bp, which corresponds to the length of the codon-optimized TRYP gene. This result validates that the TRYP gene was successfully amplified and cloned into the pET-28a plasmid using standard methods (Sambrook & Russell, 2001), enabling us to proceed with transforming the vector into our expression host for protein production and functional analysis.


Verification of Recombinant TRYP Protein Expression

Objective

Following the successful construction of the pET-28a-TRYP vector, this experiment aimed to verify the expression of the recombinant, His-tagged TRYP protein at the protein level. Western Blot analysis was employed to specifically detect the target protein in the cell lysate of our engineered E. coli strain, confirming that the genetic construct is functional and produces the intended protein(Nyaruhucha et al., 1997)..


Methods

The TRYP-overexpressing engineered strain was inoculated into 50 mL of LB medium supplemented with kanamycin and cultured overnight. The following day, the bacterial culture was harvested by centrifugation at 10,000 × g for 1 minute. The resulting cell pellet was resuspended in PBS and lysed via sonication (150 W, with a cycle of 1 second on and 3 seconds off, for a total of 20 minutes). The cell lysate was then transferred to a new centrifuge tube to serve as the intracellular content sample.

The protein solution was mixed with 5× reducing protein sample buffer at a 4:1 ratio and denatured by boiling for 15 minutes. The proteins were separated on a 12% SDS-PAGE gel at 120 V. Subsequently, the proteins were transferred from the gel to a PVDF membrane under cold conditions.


The membrane was blocked with 5% non-fat milk in TBST for 1 hour at room temperature. To detect the His-tagged protein expressed from the pET vector, the membrane was incubated overnight at 4°C with a mouse anti-His tag primary antibody (1:1000 dilution, Cat AH367, Beyotime). The membrane was then washed three times with TBST for 10 minutes each. Following the washes, it was incubated for 1 hour at room temperature with an HRP-conjugated goat anti-mouse IgG (H+L) secondary antibody (1:1000 dilution, Cat A0216, Beyotime).


After another three 10-minute washes with TBST, ECL chemiluminescent substrates A and B were mixed at a 1:1 ratio. The washed PVDF membrane was briefly placed on absorbent paper to remove excess buffer, then transferred to an imaging tray. The prepared ECL solution was applied to completely cover the membrane. After a 1-minute incubation, excess liquid was carefully wicked away, and the membrane was placed into a chemiluminescence imaging system to capture the signal according to the preset program.


Methods Diagram

Figure 23: This is a flow chart of Western Blot.

Results

Figure 24 validates the successful expression of our recombinant TRYP protein via Western Blot. A specific band is clearly visible at ~26 kDa in the lane corresponding to the TRYP-expressing strain (Lane TRYP). This band, which matches the predicted size of the His-tagged TRYP, is absent in the control lane (Lane lacZ). This confirms that the target protein was successfully expressed.

Results Diagram

Figure 24: SDS-PAGE analysis of recombinant TRYP overexpression in E. coli

Conclusion

The Western Blot result provides unequivocal evidence for the successful expression of the recombinant TRYP protein(Chen et al., 2000). A distinct band appeared at the expected molecular weight of ~26 kDa exclusively in the lane corresponding to the TRYP-expressing strain. The absence of this band in the control lane (lacZ-expressing strain) confirms the high specificity of the detection. This result validates that our engineered system is capable of producing the target protein, which is the essential prerequisite for all subsequent functional assays and applications.


The trypsin expression and refolding

Objective

The ultimate goal of our project is to produce functional trypsin. Having successfully expressed the recombinant trypsinogen, the next critical step was to verify its catalytic activity after refolding and activation. This experiment aimed to quantify the enzymatic activity of our purified trypsin using a BAEE substrate assay and to confirm that the activity was a direct result of our engineered TRYP gene, by comparing it against a control strain.


Methods

Inclusion Body Preparation

BL21-pET-28a-TRYP is inoculated into 50 mL LB (100 μg/mL Kana) in 250-mL flasks and cultured at 37°C, 150 rpm.When the OD₆₀₀ of the bacteria reaches 0.6, 0.5 mM IPTG is added and the temperature is shifted to 16°C for 20-hour induction. Cells are harvested by centrifugation (10,000 × g, 5 min), resuspended in ice-cold PBS (pH 7.5), and sonicated (70W, 3-s pulse/1-s interval, 20 min; Jingxin, Shanghai). Inclusion bodies are collected by centrifugation (10,000 × g, 30 min, 4°C).

--Inclusion Body Refolding

The pellets are washed with PBS containing 2M urea (A68476, Innochem) and incubated at 25°C, 150 rpm for 1 h. Following centrifugation (10,000 × g, 30 min, 4°C), the pellets are solubilized in denaturation buffer (20 mM Tris, 8 M urea, 20 mM DTT, pH 8.5; 10 mL/g pellet) and incubated at 25°C for 4 h with shaking. Subsequently, the supernatant is collected (12,000 × g, 20 min) and diluted 1:40 in refolding buffer (20 mM Tris, 1 mM cystine, 3 mM cysteine, 1 M urea, pH 9), after which the solution is stirred at 4°C overnight.

--Zymogen Activation

Refolded TRYP is concentrated using a 10-kDa ultrafiltration tube (Millipore), resuspended in Tris buffer (40 mM Tris, 0.1 M NaCl, 10 mM CaCl₂, pH 8.0), and activated at 25°C for 1 h. Protein concentration is determined by Bradford assay (P0006, Beyotime). Samples are aliquoted and stored at -80°C.


Methods Diagram

Figure 25: This is a flow chart of "Trypsin Expression and Refolding".


Trypsin Activity Assay

The experiment is carried out in accordance with the instructions of the Trypsin (TRY) Activity Detection Kit (AKPR005M, boxbio). Trypsin can catalyze the hydrolysis of the ester bond in N-Benzoyl-L-Arginine-Ethylester (BAEE), generating N-Benzoyl-L-Arginine (BA), which has a characteristic absorption peak at 253 nm.


The operation process is as follows:

Intracellular proteins of BL21 (DE3) and BL21-TRYP strains are extracted and added to the reaction system (Oppenheimer et al., 1966). First, preheat a UV spectrophotometer or microplate reader for over 30 minutes, set the wavelength to 253 nm, and calibrate to zero using distilled water. Next, prewarm the detection working solution at 25°C for at least 10 minutes before testing. Then, add reagents sequentially to a 96-well UV plate or micro quartz cuvette: dispense 10 μL of crude enzyme solution into the assay group and 10 μL of distilled water into the blank group, with 200 μL of detection working solution added to both groups. For absorbance measurement: mix thoroughly, start timing immediately, and record the absorbance at 253 nm at 10 seconds (total elapsed time) as A1 (for both assay and blank groups). Incubate at 25°C for exactly 60 seconds, then measure the absorbance at 70 seconds (total elapsed time) as A2 (for both groups). Calculate ΔA for the assay group (ΔAassay = A2assay − A1assay) and the blank group (ΔAblank = A2blank − A1blank), then determine the net ΔA as ΔAassay − ΔAblank. The definition of the enzyme activity unit is: At 25 °C, per mg of protein in a 1 mL reaction system, an increase in the absorbance at 253 nm by 0.0005 per minute is defined as 1 enzyme activity unit (U/mg).

Methods Diagram

Figure 26: This is a flow chart of "Trypsin Activity Assay".


Results

The absorbance at 253 nm of the intracellular protein of the BL21 (DE3) strain is near zero, and the corresponding enzyme activity is extremely low. the absorbance at 253 nm of the intracellular protein of the BL21-TRYP strain increased significantly, and the enzyme activity reached 1748 U/mg(Figure 27). Compared with the BL21 (DE3) control group, the trypsin activity of the BL21- TRYP strain is greatly improved, and there is an order-of-magnitude difference in absorbance and enzyme activity.

Results Diagram

Figure 27 : Comparison of BAEE cleavage activity of intracellular proteins between BL21 (DE3) and TRYP-overexpressing strains


Conclusion

The results provide a powerful demonstration of the functionality of our engineered trypsin. The purified protein from the BL21-TRYP strain exhibited high catalytic activity, reaching a specific activity of 1748 U/mg. In stark contrast, the control strain showed negligible activity, confirming that the proteolytic function is derived specifically from our expressed TRYP part (Rinderknecht et al., 1984).

This successful production of a highly active protease from a recombinant source validates our entire workflow, from gene design and expression to protein refolding and activation(Szilagyi et al., 2001). It establishes a solid foundation for the practical application of our enzyme in improving protein digestibility in infant formula.


Summary

In summary, we have successfully developed and validated a robust system for producing highly active recombinant trypsin. Our key achievements are:

Successful Gene Cloning & Protein Expression: We successfully cloned the TRYP gene into an expression vector and confirmed its expression in E. coli at the protein level using Western Blot analysis. This validated our genetic design and established a reliable production strain.

Optimized Protein Processing: We established an effective protocol to overcome the challenge of inclusion body formation, which is common for heterologously expressed proteins. Our workflow for denaturation, refolding, and autocatalytic activation proved successful in converting the non-functional protein aggregates into active enzymes.

High Catalytic Activity: The final, purified trypsin demonstrated high functionality, with a specific activity of 1748 U/mg in a BAEE hydrolysis assay. This is a powerful confirmation that our entire process, from the initial DNA sequence to the final folded protein, was successful(Guy et al., 1978).

This complete, validated workflow provides a solid foundation for our project's goal: using this engineered enzyme to pre-hydrolyze casein and improve the digestibility of infant formula(Sampson et al., 1991). It also serves as a valuable case study for future iGEM teams on the production of active proteases in E. coli.


System 3: lacZ

To address the widespread issue of lactose intolerance, this section details our successful engineering of a system for producing functional β-galactosidase (LacZ). Our work followed a systematic, three-step validation process: (1) Vector Construction, where we successfully cloned the codon-optimized lacZ gene into a pET-28a expression vector; (2) Protein Expression Verification, where we confirmed the production of the full-length, ~116 kDa lacZ protein in E. coli using Western Blot analysis; and (3) Functional Validation, where we quantified the catalytic activity of the purified enzyme in vitro. This comprehensive workflow demonstrates a complete "gene-to-function" pipeline for producing active lactase for potential applications in the food industry (Saqib et al., 2017).


Construction of lacZ Expression Vector

Objective

To address lactose intolerance, our goal is to produce recombinant β-galactosidase (lacZ). The first step is to construct the expression vector that will serve as the tool for this production. This experiment aimed to clone the codon-optimized lacZ gene into the pET-28a plasmid and to verify the successful construction of the resulting pET-28a-lacZ vector. (Bhatia et al., 2002).

Methods

The construction of lacZ-engineered bacteria

We codon optimized the open reading frame (ORF) of lacZ to meet RFC10 standards, synthesized it and inserted it into the pET-28a plasmid digested by NdeI and XhoI to generate the PET-28A-lacZ recombinant vector. The vector was transformed into E.coli BL21 (DE3) (D1009S, Beyotime, China) strain. Positive clones were screened in LB (Luria Bertani) plates containing 100 μg/mL kanamycin (Kana), and sequencing verification was performed (Beijing, Qingke) to obtain recombinant engineered strains. The strain was stored at -80°C with 25% (v/v) glycerol as the antifreeze. In this experiment, the culture conditions of our engineered strain were 37°C, 150 rpm, and LB liquid medium containing 100 μg/mL kana was used for inoculation and expanded culture.


Methods Diagram

Figure 28: Construction of BL21-LacZ. (A) The plasmid map of pET28a-LacZ; (B) The gene circuit of BL21-LacZ; (C)The flow chart of Construction of BL21-LacZ.

Result

As shown in Figure 29, there is a distinct band in the lacZ lane at approximately 3072 bp, which corresponds to the expected size of the lacZ gene fragment. This results demonstrate that the lacZ gene was successfully amplified, yielding a specific product of the expected size.

Result Diagram

Figure 29: the agarose gel electrophoresis analysis of the lacZ gene fragment

Conclusion

The agarose gel electrophoresis result confirms the successful construction of the pET-28a-lacZ expression vector. A single, clear band was observed at the expected size of 3072 bp, which perfectly matches the length of the synthesized lacZ gene. This result validates that the lacZ gene was correctly cloned into the expression plasmid, using standard molecular biology techniques (Sambrook & Russell, 2001), providing us with the essential tool needed to proceed with bacterial transformation and subsequent protein expression studies.


Verification of Recombinant lacZ Protein Expression

Objective

Having successfully constructed the pET-28a-lacZ vector, the next crucial step was to confirm the actual expression of the recombinant lacZ protein within the host cells. This experiment utilized Western Blot analysis, a highly specific immunodetection technique, to verify the presence and correct molecular weight of the His-tagged lacZ protein produced by our engineered E. coli BL21 strain.

Methods

Western Blot

We analyzed the lacZ expression by using Western blot. We inoculated engineered bacteria overexpressing lacZ into 50 mL LB medium thtat contain kanamycin. After overnight culture, cells were harvested by centrifugation at 10,000×g for 1 min, resuspended in PBS, and lysed by ultrasonication (150 W, 1 s on/3 s off, 20 min total). The lysate was collected as intracellular protein. Protein samples were mixed with 5× loading buffer (4:1, v/v), denatured at 100 °C for 15 min, and separated on 12% SDS-PAGE at 120 V. Proteins were transferred onto a PVDF membrane under cold conditions and blocked with 5% skim milk (TBST) for 1 h at room temperature. The membrane was incubated overnight at 4 °C with mouse anti-His antibody (1:1000, AH367, Biyuntian), followed by HRP-conjugated goat anti-mouse IgG (1:1000, A0216, Biyuntian) for 1 h at room temperature. After each incubation, the membrane was washed three times with TBST (10 min each). Chemiluminescence was detected using ECL reagent (1:1, solutions A and B) and imaged with a chemiluminescence detection system.


Western Blot Diagram

Figure 30: This is a flow chart of Western Blot.

Result


Based on the SDS-PAGE analysis, a distinct protein band was detected in the experimental lane, migrating at the expected molecular weight (116 kDa) corresponding to β-galactosidase(Figure 31). The results verify successful expression of the lacZ-encoded protein, consistent with the expected molecular weight of β-galactosidase. These findings confirm that the recombinant construct enabled efficient production of the target protein.


Result Diagram

Figure 31: SDS-PAGE analysis of recombinant lacZ overexpression in E. coli

Conclusion

The Western Blot analysis provides unequivocal proof of successful recombinant lacZ expression. As shown in the results, a single, prominent band was detected at the expected molecular weight of ~116 kDa exclusively in the lane containing lysate from the lacZ-engineered strain (Lane 1). The absence of this band in the control lane (Lane 2, containing TRYP lysate) confirms the high specificity of our detection method. This result validates that our genetic construct is functional and capable of producing the full-length target protein, setting the stage for subsequent enzymatic activity assays(Zhan et al., 2014).


Functional Assay of Purified Recombinant lacZ

Objective

Having confirmed the successful expression of the lacZ protein, the final and most critical step was to quantify its enzymatic activity. This experiment aimed to measure the rate of lactose hydrolysis by our purified recombinant β-galactosidase in vitro. By monitoring the decrease in lactose concentration over an 8-hour period, we sought to provide direct, quantitative evidence of the enzyme's functionality(Zhang et al., 2020)..


Methods

Measurement of the lactose content lacZ breaks down

The purified lacZ enzyme with a final concentration of 0.1 U/mL was added to 1 mL of the lactose reaction system with an initial concentration of 10 mM, incubated at an appropriate temperature, and samples were taken at 0, 2, 4, 6, and 8 hours respectively. The Glucose production was determined by the Abcam Glucose Assay Kit (ab272532) to indirectly reflect lactose consumption. The specific operation is as follows: Add 5 μL of glucose standard or sample to be tested respectively to 1.5 mL centrifuge tubes, then add 500 μL of detection reagent and vortex to mix well. After tightly closing the tube cap, precisely heat in a boiling water bath for 8 minutes, and then cool in an ice water bath for 4 minutes. Take 200 μL of the reaction solution and transfer it to a 96-well plate. Use an enzyme-linked immunosorbent assay (ELISA) reader to detect the absorbance at a wavelength of 630 nm. Calculate the glucose concentration based on the standard curve and then infer the degradation amount of lactose.


Measurement of the lactose content <em>lacZ</em> breaks down Diagram

Figure 32: This is a flow chart of measurement of the lactose content lacZ breaks down


Result

The temporal profile of lactose concentration was monitored over an 8-hour period (Figure 33). The initial lactose concentration at 0 h was 10 mM. A gradual decline was observed with time, decreasing to 9.0 ± 0.6 mM at 2 h, followed by a more pronounced reduction to 6.5 ± 0.8 mM at 4 h. By 6 h, the lactose concentration further decreased to 4.0 ± 0.6 mM, and reached its lowest value of 2.0 ± 0.4 mM at 8 h.

Result Diagram

Figure 33: Efficacy of recombinant β-galactosidase in lactose degradation.


Conclusion

The results clearly demonstrate that our engineered and purified lacZ protein is highly active and functional. The enzyme effectively catalyzed the hydrolysis of lactose, reducing its concentration from 10 mM to approximately 2 mM over 8 hours, which corresponds to an 80% degradation of the initial substrate. This successful in vitro functional validation confirms that our recombinant lacZ is a viable candidate for its intended application: breaking down lactose in dairy products to address lactose intolerance(Urrutia et al., 2013).


Summary

In summary, we have successfully constructed and validated an effective system for producing active β-galactosidase. The key milestones achieved are:

Successful Gene Cloning and Protein Expression: We first verified the correct construction of our pET-28a-lacZ plasmid via gel electrophoresis. Subsequently, Western Blot analysis confirmed the high-level expression of the full-length lacZ protein (~116 kDa) in our engineered E. coli strain.

Demonstrated High Catalytic Activity: The most critical finding was the functional validation of our purified enzyme. The in vitro assay showed that our recombinant lacZ is highly active, capable of degrading 80% of the lactose in the reaction system within 8 hours.

This complete and successful characterization of the existing part BBa_I732005 not only provides new and valuable data for the iGEM community but also establishes a robust foundation for our project's application. We have produced a viable enzymatic solution with the potential to be used in creating lactose-free dairy products, directly addressing the nutritional challenges faced by individuals with lactose intolerance(Füreder et al., 2020).



Reference

  1. Bhatia, Y., Mishra, S., & Bisaria, V. S. (2002). Microbial β-Glucosidases: Cloning, Properties, and Applications. Crit. Rev. Biotechnol., 22, 375–407.
  2. Buck FF, Vithayathil AJ, Bier M and Nord FF (1962). On the mechanism of enzyme action. LXXIII. Studies on trypsins from beef, sheep and pig pancreas. Archives of Biochemistry and Biophysics, 97, 417–424.
  3. Chen, J.M. et al. (2000). Genes, cloned cDNAs, and proteins of human trypsinogens and pancreatitis-associated cationic trypsinogen mutations. Pancreas.
  4. Chen, Y., Zhu, Y., Wang, H., Chen, R., Du, Z., & Mu, W. (2024). Developing a Metabolic Flux Optimized Escherichia coli for Efficient Production of Difucosyllactose. ACS Sustainable Chemistry & Engineering, 12(38), 14249-14257.
  5. Füreder, V., Rodriguez-Colinas, B., Cervantes, F.V., Fernandez-Arrojo, L., & Plou, F.J. (2020). Selective Synthesis of Galactooligosaccharides Containing β(1→3) Linkages with β-Galactosidase from Bifidobacterium bifidum (Saphera). J. Agric. Food Chem., 68, 4930–4938.
  6. Gao, F., Shi, S., Zhao, Y., Yang, D., & Liao, X. (2025). Intersecting precision fermentation for global cell-based food production innovation: Challenges and opportunities. Biotechnology Advances, 391, 108712.
  7. Guy, O. et al. (1978). Two human trypsinogens. Purification, molecular properties, and N-terminal sequences. Biochemistry.
  8. Jakobsson I, Lothe L, Ley D and Borschel MW (2000). Effectiveness of casein hydrolysate feedings in infants with colic. Acta Paediatrica, 89, 18–21.
  9. Li, M., Zhang, T., Li, C., Jia, R., & Miao, M. (2024). Iterative multimodule reprogramming and protein engineering for efficient lactodifucotetraose bioproduction. Food Bioscience, 62, 105364.
  10. Li, Y., Wang, X., Chen, K., Zhuang, Z., Tang, H., Yu, T., & Cao, W. (2025). Efficient production of 2′-fucosyllactose in Pichia pastoris through metabolic engineering and constructing an orthogonal energy supply system. Synthetic and Systems Biotechnology, 10(3), 807-815.
  11. Liang, S., Quan, Q., Liu, D., Yang, S., Yan, Q., & Jiang, Z. (2025). Regulation of Metabolic Pathways to Enhance Difucosyllactose Biosynthesis in Escherichia coli. Journal of Agricultural and Food Chemistry, 73(1), 727-734.
  12. Moriyama, S., Sugita, T., & Yamashita, M. (2025). Efficient fermentative production of lactodifucotetraose by controlling sequential glycosyltransferase reactions in Escherichia coli. Biotechnology Progress, 41(3).
  13. Nyaruhucha, C.N. et al. (1997). Identification and expression of the cDNA-encoding human mesotrypsin(ogen), an isoform of trypsin with inhibitor resistance. J. Biol. Chem.
  14. Oppenheimer, H.L. et al. (1966). Implication of an ionizing group in the control of conformation and activity of chymotrypsin. J. Biol. Chem.
  15. Rawlings, N.D. et al. (1994). Families of serine peptidases. Methods Enzymol.
  16. Rinderknecht, H. et al. (1984). Mesotrypsin: a new inhibitor-resistant protease from a zymogen in human pancreatic tissue and fluid. Gastroenterology.
  17. Sambrook J., Russell D. W. (2001). Molecular Cloning: A Laboratory Manual. 3rd edn. New York: Cold Spring Harbor Laboratory, Cold Spring Harbor.
  18. Sampson HA, Bernhisel‐Braodbent J, Yang E and Scanlon SM (1991). Safety of casein hydrolysate formula in children with cow milk allergy. Journal of Pediatrics, 118, 520–525.
  19. Saqib, S., Akram, A., Halim, S.A., & Tassaduq, R. (2017). Sources of β-galactosidase and its applications in food industry. Biotech., 7, 79.
  20. Szilagyi, L. et al. (2001). Comparative in vitro studies on native and recombinant human cationic trypsins. Cathepsin B is a possible pathological activator of trypsinogen in pancreatitis. J. Biol. Chem.
  21. Urrutia, P., Mateo, C., Guisan, J.M., Wilson, L., & Illanes, A. (2013). Immobilization of Bacillus circulans β-galactosidase and its application in the synthesis of galacto-oligosaccharides under repeated-batch operation. Biochem. Eng. J., 77, 41–48.
  22. Yang, Y., Jing, S., Zhang, L., Shao, J., Chen, J., Xia, G., Yang, H., & Zhou, C. (2025). Structure, function, synthesis and improved strategies of fucosylated human milk oligosaccharides and their future perspectives: A review. Food Bioscience, 68, 106584.
  23. Young, C. L., & Robinson, A. S. (2014). Protein Folding and Secretion: Mechanistic Insights Advancing Recombinant Protein Production in S. C. Curr. Opin. Biotechnol., 30, 168–177.
  24. Zhan, Y., Xu, Z., Li, S., Liu, X., Xu, L., Feng, X., & Xu, H. (2014). Coexpression of β-d-Galactosidase and l-Arabinose Isomerase in the Production of d-Tagatose: A Functional Sweetener. J. Agric. Food Chem., 62, 2412–2417.
  25. Zhang, G., Zabed, H.M., Yun, J., Yuan, J., & Qi, X. (2020). Two-stage biosynthesis of d-tagatose from milk whey powder by an engineered Escherichia coli strain expressing l-arabinose isomerase from Lactobacillus plantarum. Bioresour. Technol., 305, 123010.
  26. Zhao, S., Xie, X., Yang, Y., Yu, H., Wang, J., Luo, L., & Zhou, X. (2025). Intelligent Design of Microbial Carbohydrate Factories: Integrated Chassis-Tools-Strategies Frameworks. Journal of Agricultural and Food Chemistry, 73(33), 20580-20599.