Difference between revisions of "Part:BBa K5049006"

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    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.  
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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.  
 
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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.
 
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.
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= <span style="color:#87CEEB; font-weight:bold;">CONSTRUCTION</span> =
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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.
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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.
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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.
 
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Revision as of 08:27, 2 September 2024


PGTH1-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.



Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 493
    Illegal BamHI site found at 1504
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 1831
    Illegal AgeI site found at 1819
    Illegal AgeI site found at 2014
  • 1000
    COMPATIBLE WITH RFC[1000]