Team:Groningen/Parts
Parts
Parts overview
Achieving the highest alpha amylase activity is the main engineering goal of the team this year. We explored the possibilities of Saccharomyces spp. as a cell factory by testing enzymes from different organisms; Bacillus subtilis, Bacillus amyloliquefaciens, Bacillus licheniformis and Aspergillus oryzae.
It is sometimes hard to predict which combination of promoter, secretion signal and gene will lead to better yield. Therefore, we aimed to test as many promoters, secretion signal peptides and genes as possible. For this purpose, we used Golden Gate Assembly and took advantage of its modularity to clone our genes into a vector, creating 60 different combinations of promoters, secretion peptides and genes.
The native sequence of alpha amylase codes for a secretion signal that is used in the native host to secrete the enzyme (as these enzymes act extracellularly). To increase the possibilities of achieving higher yields of extracellular protein, besides testing for the native secretion peptide, we isolate the CDS (coding sequence) of alpha amylase and add a different secretion peptide that has been proven to work on yeast[1]. To know more about the genetic design approach go to the engineering page.
Basic parts
The sequences of alpha amylase from 4 different organisms were codon optimized for the chassis. The basic parts were designed from the native sequence and synthesized de novo. The basic parts can be found in Table 1.
| Name | Type | Description | Designer | Length |
|---|---|---|---|---|
| Coding | Alpha amylase from Bacillus amyloliquefaciens. | iGEM Groningen | 1545 | |
| Coding | Alpha amylase from Bacillus licheniformis. | iGEM Groningen | 1539 | |
| Coding | Alpha amylase from Bacillus subtilis. | iGEM Groningen | 1980 | |
| Coding | Alpha amylase from Aspergillus Oryzae. | iGEM Groningen | 1500 | |
|
|
Coding | Secreted Alpha amylase from Bacillus amyloliquefaciens. | iGEM Groningen | 1545 |
| Coding | Secreted Alpha amylase from Bacillus licheniformis. | iGEM Groningen | 1539 | |
| Coding | Secreted Alpha amylase from Bacillus subtilis. | iGEM Groningen | 1980 | |
| Coding | Secreted Alpha amylase from Aspergillus Oryzae. | iGEM Groningen | 1500 |
Composite parts - Groningen Collection
A library of constructs was created (Table 2) in which we included different elements (go to Engineering page) The strategy followed to fuse the different parts can be seen in Figure 1.
Promoters, secretion signals and terminators are taken from previous characterized genetic parts[1],[2]. 10 promoters were chosen among the 20 promoters described in Lee ME et al. 2015 based on their strength, selecting promoters representing all strengths, from strong to weak. We also decided to include the most characterized secretion signal, as well as a regular terminator, tTDH1. The process to create the set of samples from all the possible combinations achieving an even distribution of all the elements from the different categories can be found in the model page.
| Name | Type | Description | Designer | Length |
|---|---|---|---|---|
| Composite | SP001 - pPGK1, αMF, BS, tTDH1 | iGEM Groningen | 3082 bp | |
| Composite | SP002 - pRNR1, αMFΔ, AO, tTDH1 | iGEM Groningen | 2565 bp | |
| Composite | SP005 - pHHF1, αMF, BS, tTDH1 | iGEM Groningen | 3083 bp | |
| Composite | SP008 - pHHF1, Part3 BS, tTDH1 | iGEM Groningen | 2933 bp | |
| Composite | SP009 - pRNR1, Part3 BS, tTDH1 | iGEM Groningen | 2933 bp | |
| Composite | SP010 - pHHF1, αMF, BS, tTDH1 | iGEM Groningen | 3083 bp | |
| Composite | SP012 - pRNR1, Part3 AO, tTDH1 | iGEM Groningen | 2451 bp | |
| Composite | SP013 - pRAD27, αMF, BS, tTDH1 | iGEM Groningen | 2678 bp | |
| Composite | SP014 - pREV1, αMF, BA, tTDH1 | iGEM Groningen | 2678 bp | |
| Composite | SP015 - pPGK1, αMFΔ, AO, tTDH1 | iGEM Groningen | 2565 bp | |
| Composite | SP016 - pRAD27, Part3 BL, tTDH1 | iGEM Groningen | 2486 bp | |
| Composite | SP018 - pRAD27, αMFΔ, BA, tTDH1 | iGEM Groningen | 2576 bp | |
| Composite | SP019 - pTEF1, Part3 BL, tTDH1 | iGEM Groningen | 2492 bp | |
| Composite | SP022 - pREV1, αMF, BA, tTDH1 | iGEM Groningen | 2678 bp | |
| Composite | SP023 - pRNR2, αMF_no_EAEA, BL, tTDH1 | iGEM Groningen | 2666 bp | |
| Composite | SP024 - pTEF1, αMFΔ, BL, tTDH1 | iGEM Groningen | 2582 bp | |
| Composite | SP025 - pPAB1, Part3 BA, tTDH1 | iGEM Groningen | 2498 bp | |
| Composite | SP026 - pHHF1, αMF, BL, tTDH1 | iGEM Groningen | 2678 bp | |
| Composite | SP027 - pRNR1, Part3 BS, tTDH1 | iGEM Groningen | 2933 bp | |
| Composite | SP028 - pTEF1, αMF, BA, tTDH1 | iGEM Groningen | 2678 bp | |
| Composite | SP029 - pRPL18B, αMF, BL, tTDH1 | iGEM Groningen | 2678 bp | |
| Composite | SP030 - pTDH3, αMFΔ, BA, tTDH1 | iGEM Groningen | 2562 bp | |
| Composite | SP031 - pPGK1, αMFΔ, BA, tTDH1 | iGEM Groningen | 2582 bp | |
| Composite | SP033 - pREV1, αMF, BS, tTDH1 | iGEM Groningen | 3083 bp | |
| Composite | SP034 - pTEF1, αMF, BL, tTDH1 | iGEM Groningen | 2678 bp | |
| Composite | SP035 - pPAB1, αMF_no_EAEA, BL, tTDH1 | iGEM Groningen | 2666 bp | |
| Composite | SP037 - pRPL18B, αMF, BS, tTDH1 | iGEM Groningen | 3083 bp | |
| Composite | SP038 - pRNR2, αMF, BS, tTDH1 | iGEM Groningen | 3083 bp | |
| Composite | SP039 - pTEF1, αMF, BL, tTDH1 | iGEM Groningen | 2678 bp | |
| Composite | SP041 - pHHF1, Part3 BA, tTDH1 | iGEM Groningen | 2498 bp | |
| Composite | SP044 - pRNR2, αMFΔ, BL, tTDH1 | iGEM Groningen | 2582 bp | |
| Composite | SP045 - pPAB1, αMF, BL, tTDH1 | iGEM Groningen | 2678 bp | |
| Composite | SP046 - pTDH3, αMFΔ, BL, tTDH1 | iGEM Groningen | 2562 bp | |
| Composite | SP047 - pPGK1, AO, tTDH1 | iGEM Groningen | 2451 bp | |
| Composite | SP049 - pRAD27, Part3 AO, tTDH1 | iGEM Groningen | 2445 bp | |
| Composite | SP050 - pPGK1, αMF_no_EAEA, BA, tTDH1 | iGEM Groningen | 2666 bp | |
| Composite | SP051 - pRNR1, αMF_no_EAEA, BL, tTDH1 | iGEM Groningen | 2666 bp | |
| Composite | SP052 - pPAB1, αMF, BA, tTDH1 | iGEM Groningen | 2678 bp | |
| Composite | SP053 - pHHF1, Part3 AO, tTDH1 | iGEM Groningen | 2451 bp | |
| Composite | SP054 - pRPL18B, αMFΔ, BS, tTDH1 | iGEM Groningen | 2987 bp | |
| Composite | SP055 - pRPL18B, αMF, BL, tTDH1 | iGEM Groningen | 2678 bp | |
| Composite | SP056 - pPAB1, Part3 BL, tTDH1 | iGEM Groningen | 2492 bp | |
| Composite | SP058 - pRNR2, Part3 AO, tTDH1 | iGEM Groningen | 2451 bp | |
| Composite | SP060 - pREV1, Part3 BS, tTDH1 | iGEM Groningen | 2933 bp | |
| Composite | SP061 - pREV1, αMF_no_EAEA, BA, tTDH1 | iGEM Groningen | 2666 bp | |
| Composite | SP062 - pRAD27, αMF, BA, tTDH1 | iGEM Groningen | 2672 bp | |
| Composite | SP063 - pRNR2, αMF, BL, tTDH1 | iGEM Groningen | 2678 bp |
References
- Obst, U., Lu, T. K., & Sieber, V. (2017). A Modular Toolkit for Generating Pichia pastoris Secretion Libraries. ACS Synthetic Biology, 6(6), 1016–1025. https://doi.org/10.1021/acssynbio.6b00337
- Lee, M. E., Deloache, W. C., Cervantes, B., & Dueber, J. E. (2015). A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly. ACS Synth. Biol., 4, 975–986. https://doi.org/10.1021/sb500366v