Revision as of 08:55, 2 September 2024

P_GTH1-Xylanase-GCW61

VECTOR DESIGN

The sequences of DNA elements for the GTH1 promoter and GCW61 anchor protein were from Pichia pastoris. To ensure flexibility in connecting to target fusion proteins, a GS linker ((GGSG)3) was added at the N-terminus of GCW61. We selected a thermostable xylanase from Streptomyces thermovulgaris6 as our protein of interest. All DNA fragments were synthesized by Integrated DNA Technologies (IDT) following the standard iGEM Part Registry Rule (RFC10)14, which includes prefix cutting sites EcoRI and XbaI, and suffix cutting sites SpeI and PstI. In the issue of the assembly of the fusion protein, we followed the rules created by the Albert-Ludwigs Universität Freiburg iGEM team in 2007 (Freiburg assembly method, officially named by iGEM HQs as RFC25)15. AgeI cutting site was introduced at C-terminus of the Xylanase gene without the stop codon, and NgoMIV and AgeI sites were introduced at the either end of the GS linker-GCW61 segment.

To create the vector for gene expression in P. pastoris, we utilized the yeast vector pZAHR, developed by Professor Hung-Jen Liu's lab at National Chung Hsing University. This vector is a Zeocin-selectable, AOX1-based Homologous Recombination vector designed specifically for gene knock-in applications in Pichia pastoris. It incorporates the AOX1 gene promoter and terminator to facilitate the integration of desired genes into the Pichia pastoris chromosome through homologous recombination. This process is typically executed following electroporation-directed yeast transformation, a method routinely employed in the Liu’s laboratory.

CONSTRUCTION

The basic parts were built from DNA elements on the pUCIDT-KAN vector of IDT to the iGEM part registry standard pSB1C3 vector, and, in basic parts, designated GTH1 as a registry number of BBa_K5049000, GS-GCW61 as BBa_K5049001 and Xylanase as BBa_K5049003.

The Xylanase-GCW61 fusion protein was connected using the Freiburg assembly method (RFC25)15 to bypass the stop codon of TAG generated by SpeI-XbaI BioBrick scar, developed by the Albert-Ludwigs Universität Freiburg iGEM team in 2007. The composite part was assembled firstly as a registry name of Xylanase-GCW61 and the number of BBa_K5049004. Then, the final composite part was constructed with GTH1 promoter within the context of the following sequence: EcoRI-XbaI-GTH1 promoter-(SpeI/XbaI scar)-Xylanase-(AgeI/NgoMIV scar)-GS linker-GCW61-AgeI-SpeI-PstI. This functional composite part was given an iGEM part registry name of PGTH1-Xylanase-GCW61 and the number of BBa_K5049006.

To express the gene in Pichia pastoris, the composite part was cloned into the pZAHR vector to create the PGTH1-Xylanase-GCW61/pZAHR construct. This construct was verified through colony PCR, using a primer pair targeting the 5’ end of GTH1 and the 3’ end of GCW61, which resulted in an approximately 2100-bp DNA fragment (Figure 1A). Additionally, the integrity of the extracted DNA plasmids was confirmed by digestion with restriction enzymes EcoRI and PstI, yielding DNA fragments of 2070 bp for the insert and 3210 bp for the vector (Figure 1B). Furthermore, the gene sequence of the insert was verified through DNA sequencing performed by Genomics BioSci & Tech. Co. Ltd. in Taiwan.

Figure 1 | Verification of P_GTH1-Xylanase-GCW61/pZAHR construct. (A) Colony PCR using a GTH1-specific forward primer (5’- CCCCAAACATTTGCTCCCCCTAG-3’) and a GCW61-specific reverse primer (5’-AATCAATAGAGCAACACCGGCTA-3’) yielded an expected 2070-bp DNA fragment. The numbers indicate selected colonies, with lane 2 showing a control derived from a mock pick on a clear zone of the agar plate. (B) Plasmids extracted from three successful colony PCR clones underwent a restriction enzyme analysis with EcoRI and PstI. The expected fragment sizes are 2070 bp for the PGTH1-Xylanase-GCW61 insert and 3210 bp for the pZAHR vector. The first lane on the agarose gels features a 1kb DNA marker (FluoroBand™ 1 KB (0.25-10 kb) Fluorescent DNA Ladder, SMOBIO Technology, Inc.).

MEASUREMENT

The transformed Pichia pastoris carrying either the P_GTH1-Xylanase-GCW61/pZAHR construct or the pZAHR vector alone as a control were cultured in BMY media (Buffered Minimal YNB (Yeast Nitrogen Base)). To induce the GTH1 promoter, we added 0.005% (i.e., 0.05 g/L) glucose and incubated the cultures at 28°C for 48 hours to promote xylanase expression. Simultaneously, control groups containing yeast with and without the Xylanase gene were cultured in BMY media without glucose. After incubation, the yeasts were harvested by centrifugation and incubated in the 5% xylan solution at 37°C for 15 minutes to produce xylose. The xylanase activities were measured by the 3,5-dinitrosalicylic acid (DNS) assay. The amount of xylose produced was detected by the color change in the DNS reagent from yellow to reddish-brown at 100°C for 15 minutes, which indicates the presence of reducing sugars. The xylanase activity (Unit/mL/min), is calculated based on the quantity of xylose produced from xylan by the enzyme's catalytic action. For a detailed protocol, including information on prepared buffers and solutions, please refer to our MEASUREMENTpage.

In Figure 2, the data clearly demonstrate significant xylanase activity in Pichia pastoris carrying the Xylanase-GCW61 gene when induced with glucose. However, a low background level of enzyme activity was also detected in the absence of glucose, which is attributed to the constitutive nature of the GTH1 promoter. In summary, the detected xylanase activity in whole intact yeast cells implies that GCW61 is an effective anchor protein for displaying enzymes on the surface of Pichia pastoris.

Figure 2 | Xylanase-GCW61 Activity in Glucose-Induced and Non-Induced Pichia pastoris. The yeasts were cultured in BMY media and maintained without glucose as controls for non-induced groups (Yellow bars). For gene expression driven by the GTH1 promoter, transformed yeasts carrying PGTH1-Xylanase-GCW61/pZAHR were induced with 0.005% glucose (right blue bar). After 48 hours at 28°C, the whole yeast cells were harvested and subjected to reducing DNS assays using 5% xylan as the substrate. The intensity of the color change from yellow to brown, measured at OD540, indicates the amount of xylose generated, reflecting xylanase activity. Additional details on enzyme activity calculations can be found on our MEASUREMENT page. Controls carrying only the pZAHR vector were included for both induced (left blue bar) and non-induced conditions (left yellow bar). Error bars represent the standard error from three independent experiments, demonstrating the reproducibility of the findings.

We engineered Pichia pastoris to express thermostable Xylanase by integrating a genetic construct that included the GTH1 promoter and GCW61 anchor protein. The construct, assembled into the pZAHR vector, was designed to enable surface display of Xylanase for potential application in animal feed. Experimental results confirmed that the induced expression under the presence of glucose significantly enhanced enzyme activity, while a baseline activity was observed in non-induced conditions, due to the constitutive nature of the GTH1 promoter. This demonstrates the efficacy of the GCW61 anchor protein in displaying functional enzymes on yeast cell surfaces, supporting its use in industrial biotechnological applications.

PROOF OF CONCEPT

In order to create an effective animal feed additive, especially for pigs, we have demonstrated the activities of the Xylanase-GCW61 fusion protein within the Pichia pastoris surface display system. Based on these promising results, the following sections will further explore the feasibility of this application across a range of practical parameters. We aim to evaluate the optimal temperature and pH levels for enzyme activity, ensuring functionality in the specific environments of a pig's stomach and small intestine26. Additionally, we tested the enzyme's resistance to gastric proteases, including pepsin and trypsin, to assess its durability and functionality within the animal's digestive system. For processing as animal feeds27, we explored the temperature tolerances necessary for maintaining enzymatic activity. Following this, we evaluated the shelf-life in a freeze-dried form28, which is crucial for ensuring the long-term viability and efficacy of the enzyme when used in commercial feed additives. These comprehensive analyses are designed to provide a convincing proof-of-concept for the application of Xylanase-GCW61, highlighting its practical viability and operational benefits.

Xylanase Protein Expression

Electroporation Transformation

We transformed Pichia pastoris GS115 with the linearized plasmid PGTH1-Xylanase-GCW61/pZAHR using electroporation. The plasmid DNA was prepared by digesting 10 μg of the vector with SacI and dissolving it in sterile water. This linear plasmid DNA was then added to competent cells and kept on ice before electroporation at 25 μF, 1.5 kV, and 0.5 msec using the ECM 830 Square Wave Mode in the BTX Gemini System. Following electroporation, cells were recovered in 1 M sorbitol and incubated at 28°C for 2-4 hours. The cells were then plated on YPDS (Yeast Peptone Dextrose Sorbitol) agar plates containing 2000 μg/ml Zeocin and incubated at 28°C for 3-5 days until colonies were visible (Figure 6). This high concentration of Zeocin ensured the selection of successfully transformed colonies.

Figure 2 | Xylanase-GCW61 Activity in Glucose-Induced and Non-Induced Pichia pastoris. The yeasts were cultured in BMY media and maintained without glucose as controls for non-induced groups (Yellow bars). For gene expression driven by the GTH1 promoter, transformed yeasts carrying PGTH1-Xylanase-GCW61/pZAHR were induced with 0.005% glucose (right blue bar). After 48 hours at 28°C, the whole yeast cells were harvested and subjected to reducing DNS assays using 5% xylan as the substrate. The intensity of the color change from yellow to brown, measured at OD540, indicates the amount of xylose generated, reflecting xylanase activity. Additional details on enzyme activity calculations can be found on our MEASUREMENT page. Controls carrying only the pZAHR vector were included for both induced (left blue bar) and non-induced conditions (left yellow bar). Error bars represent the standard error from three independent experiments, demonstrating the reproducibility of the findings.

We engineered Pichia pastoris to express thermostable Xylanase by integrating a genetic construct that included the GTH1 promoter and GCW61 anchor protein. The construct, assembled into the pZAHR vector, was designed to enable surface display of Xylanase for potential application in animal feed. Experimental results confirmed that the induced expression under the presence of glucose significantly enhanced enzyme activity, while a baseline activity was observed in non-induced conditions, due to the constitutive nature of the GTH1 promoter. This demonstrates the efficacy of the GCW61 anchor protein in displaying functional enzymes on yeast cell surfaces, supporting its use in industrial biotechnological applications.

Sequence and Features