Overview
Inspired by the spirit of iGEM towards furthering open collaboration and teamwork, we focused on developing tools that can facilitate further research and innovation for our fellow iGEMers. This philosophy has permeated many aspects of our project, ensuring we contribute meaningful resources across various domains. We prioritised the creation of versatile tools that future teams could leverage in their endeavours, and each component we designed was planned to advance our project and serve as a valuable asset to support other teams.
Our contributions page reflects our dedication towards serving the scientific community, highlighting that knowledge and resources can and should be accessible to all. By equipping future teams with the necessary tools, we can collectively push the boundaries of science and inspire the upcoming generations to develop innovative solutions for global challenges. Here is a summary of our key contributions to the iGEM community, science and society:
Biobricks: Basic and Composite Parts
Our team has designed 17 basic parts and 4 composite parts which are responsible for the santalene and santalol synthesis from PET monomers. They are our contribution for future iGEM teams and synthetic biology community. Part (BBa_K5181014) is designed and experimentally shown successfully working in our chassis. Hence we present this part as our contribution and best new composite part.
| Sr.No. | Name of part in registry | Part name | Part Type | Part description | No.of bp | RFC type |
|---|---|---|---|---|---|---|
| 1 | BBa_K5181000 | P450_native | Coding | This part is a transmembrane cytochrome p450 mono-oxygenase (SaCYP736A167 )gene sequence from Santalum album. It catalyzes the conversion of Santalene to Santalol. | 1519 bp | 1000 |
| 2 | BBa_K5181001 | P450_truncated | Coding | This part is a modified BBa_K518100 with N terminal truncation of the transmembrane domain of the SaCYP736A167 gene. | 1455 bp | 1000 |
| 3 | BBa_K5181002 | CPR_native | Coding | This part contains a Cytochrome P450 reductase (CPR) gene from the Santalum album genome. This enzyme is a reductase partner for(BBa_K5181000). It replenishes and shuttles the FADH2 required for its function. | 2097 bp | 1000 |
| 4 | BBa_K5181003 | CPR_truncated | Coding | This is a modified version of CPR (BBa_K5181002) with a truncation of the N terminal of transmembrane domain to achieve a functional reductase partner of BBa_K5181001 in the cytosol of Pseudomonas putida. | 1950 bp | 10 |
| 5 | BBa_K5181004 | SaSSy_Santalum album | Coding | SaSSy gene codes for the enzyme Santalene Synthase were obtained from the genome of the Santalum album. It converts Farnasyl pyrophosphate (FPP) into isomers of Santalene. | 1726 bp | 10 |
| 6 | BBa_K5181005 | FPPS_Santalum album | Coding | The enzyme (FPPS) Farnesyl pyrophosphate synthase from Santalum album is involved in the MEP pathway and converts IPP/DMAPP to FPP, the precursor of santalene. | 1050 bp | 10 |
| 7 | BBa_K5181006 | Self-sufficient araBAD_RBS | Intermediate | This part is a self-sufficient arabinose promoter with its supporting gene AraC and RBS (Ribosome Binding site). | 1272 bp | 10 |
| 8 | BBa_K5181007 | araBAD_RBS_2 | Intermediate | This part is a variant of the self-sufficient arabinose promoter part BBa_K5181006 (with NsiI cut site) | 1250 bp | 10 |
| 9 | BBa_K5181009 | Self-sufficient tet_RBS | Intermediate | This part is a self-sufficient tetracyclin promoter with its supporting gene tetR and Ribosome Binding Site. | 755 bp | 1000 |
| 10 | BBa_K5181010 | rhaBAD_RBS | Intermediate | This part is a self-sufficient rhamnose promoter with its supporting gene Rha and RBS (Ribosome Binding site). | 2029 bp | 1000 |
| 11 | BBa_K5181011 | GST_linker | Protein Domain | This part codes for a linker sequence used to make CPR-P450 fusion protein, encoding a glycine-serine-threonine (GST) sequence, which was chosen for engineering a GSTSSGSG junction. | 36 bp | 10/1000 |
| 12 | BBa_K5181012 | BM_linker | Protein Domain | This part codes for a linker sequence used to make CPR-P450 fusion protein. The sequence is obtained from a soluble P450 enzyme from Bacillus megaterium (P450BM-3) | 90 bp | 10/1000 |
| 13 | BBa_K5181008 | P450-CPR_fusion protein (BC_linker) | Coding, composite | This codes for a fusion protein composed of truncated P450 and CPR domain(BBa_K5181001, BBa_K5181003) connected by BC linker from the naturally existing bifunctional P450 of Bacillus cereus. | 3384 bp | 1000 |
| 14 | BBa_K5181013 | IRES_PETAL_1 | Intermediate | Inter-ribosomal entry site. It is a binding site for another ribosome to translate the later gene. | 36 bp | 10/1000 |
| 15 | BBa_K5181016 | P450-CPR_fusion protein (BM_linker) | Coding, composite | This codes for a fusion protein of the truncated cytochrome P450 monooxygenase domain from CYP736A167 and truncated reductase domain of CPR1 from Santalum album connected by BM linker from the naturally existing bifunctional P450 of Bacillus megaterium. | 3369 bp | 1000 |
| 16 | BBa_K5181017 | pRGPDuo3_P450_CPR | Plasmid | It is a dual expression vector with truncated P450 and CPR genes under tac promoters. | 8421 bp | 1000 |
| 17 | BBa_K5181018 | pRGPDuo4_SaSSy_FPPS | Plasmid | It is a dual expression vector with SaSSy and FPPS genes under araBAD and tac promoter, respectively. | 9390 bp |
| Sr.No. | Name of part in registry | Part name | Part Type | Part description | No.of bp | RFC type |
|---|---|---|---|---|---|---|
| 1 | BBa_K5181014 | araBAD_RBS_SaSSy_FPPS | composite | This is a bicistronic part consisting of araBAD promoter with RBS(BBa_K5181006), SaSSy(BBa_K5181004), IRES (BBa_K5181013), FPPS(BBa_K5181005) genes. | 4079 bp | 10 |
| 2 | BBa_K5181015 | tet_RBS_P450-CPR_fusion protein (BC_linker) | composite | This part is a bicistronic composite part (BBa_K5181001, BBa_K5181003, BBa_K5181009), consisting of truncated CPR-P450 fusion protein genes with BC linker under the control of tet promoter. | 4139 bp | 1000 |
| 3 | BBa_K5181019 | rhaBAD_RBS_P450-CPR-fusion protein(BM linker) | composite | This part is a bicistronic composite part (BBa_K5181001, BBa_K5181003, BBa_K5181010), consisting of truncated CPR-P450 fusion protein genes with BM linker under the control of araBAD promoter. | 5481 bp | 1000 |
| 4 | BBa_K5181020 | araBAD_RBS_P450-CPR-fusion protein(BM linker) | composite | This part is a bicistronic composite part (BBa_K5181001, BBa_K5181003, BBa_K5181007), consisting of truncated CPR-P450 fusion protein genes with BM linker under the control of araBAD promoter | 1950 bp | 10 |
Synthetic Biology Book
The contents of the Synbio book include a story, a glossary section for essential terms, a section containing fun games like crosswords, puzzles, quizzes, word searches, synthetic biology sudoku, matching games, informative facts, and a timeline of the development of the field of synthetic biology. Through stories, we have attempted to break down complex scientific concepts into more manageable, digestible pieces of information that students could easily understand.
Synbio Loteria
We created the game "Synbio Loteria” to introduce school students to new synthetic biology terms. It is inspired by the Mexican board game ‘Loteria’ which is known to support language use and vocabulary development in the Spanish language. The game is designed in such a way that it aids in memory retention by creating a stronger association between the picture in the board and the concept in the card.
iHP Handbook
Team iGEM Stanford reached out to us for a handbook, focusing on developing a human-centric approach for human practices in iGEM projects, along with iGEM CityU. The handbook titled "Digging into the Challenge: A Guide to Integrated Human Practices in Synthetic Biology Research" serves as a comprehensive resource for applying human-centredhuman-centered design (HCD) principles in synthetic biology projects. The guide is structured to support both novice and experienced practitioners in navigating the complexities of project development while fostering critical thinking and responsible scientific practices.
m-RNA_Predictor_+
Your personal gene transcript predictor, and amino acid sequence predictor are available with common functionalities like finding complement and reverse complement of your input.
This was used for all the transcripts of our project and will be valuable for other fellow iGEMers.
Available at: https://github.com/Mayukh-0-0/igem-codes/blob/main/mRNA_predictor_plus.py