A chart containing all parts classified with basic or composite part and a statement about our part collection is listed in the later section. Firstly, we have classified our parts according to the function they serves.
Mucosal healing
In the mucosal healing project, all parts are built on the frame of this ternary system (Fig.1), including three major groups, therapeutic proteins, secretion peptides, and sensor elements. The three elements are spatially and functionally constructed together for mucosal healing purpose, and each element group contains several candidate genes as listed below. All three groups of genes are collected together as our team's first part collection: Mucosal healing collection.
Fig.1 General design of the treatment ternary system
Therapeutic proteins
Among the following therapeutic protein parts, Trefoil factor (TFF) 1, 2 and 3 were truly constructed in our wet lab. Others were potentially effective proteins discovered by literature research. Note: the following parts are all basic parts.
| Therapeutic protein | Function | Part name |
|---|---|---|
| TFF1 | Maintain and protect mucosal surface | BBa_K3924000 |
| TFF2 | Maintain and protect mucosal surface | BBa_K3924001 |
| TFF3 | Maintain and protect mucosal surface | BBa_K3924002 |
| Chromofungin | Suppress pro-inflammatory macrophage function through TLR4 | BBa_K3924003 |
| IL10 | Downregulates the production of Th1-derived cytokines | BBa_K3924004 |
| Defensin5 | Present antimicrobial activity against Gram-negative and Gram-positive bacteria | BBa_K3924005 |
| GLP2 | Reduce epithelial barrier damage and lower bacterial infection | BBa_K3924006 |
| Fgl2 | Suppress intestinal inflammation and CAC development | BBa_K3924007 |
| SOCS1-KIR | Inhibit STAT1α phosphorylation | BBa_K3924008 |
| tkip | Reduce the phosphorylation of JAKs and STATs | BBa_K3924009 |
| G-CSF | Augment the intestinal innate immune defense and improve T regulatory cell activity | BBa_K3924037 |
| GM-CSF | Similar to G-CSF | BBa_K3924038 |
| Beta-defensin 4A(hBD2) | Decrease NF-κB and increase CREB phosphorylation, curb inflammation | BBa_K3924039 |
Secretion peptides
All secretion peptides are constructed with a GFP added and tested in our wet lab. Note: secretion peptides along are basic parts, peptides with GFP-added are composite parts.
| Secretion peptide | Part name | Peptide with GFP added | Part name |
|---|---|---|---|
| DsbA | BBa_K3924010 | DsbA-GFP | BBa_K3924055 |
| CsgA | BBa_K3924011 | CsgA-GFP | BBa_K3924056 |
| OmpA | BBa_K3924012 | OmpA-GFP | BBa_K3924057 |
| PelB | BBa_K3924013 | PelB-GFP | BBa_K3924058 |
| phoA | BBa_K3924014 | phoA-GFP | BBa_K3924059 |
| STⅡ | BBa_K3924015 | STⅡ-GFP | BBa_K3924060 |
| TorA | BBa_K3924016 | TorA-GFP | BBa_K3924061 |
Sensor elements
We have tested and improved the previous IBD sensor from iGEM Part Registry by designing 3 more effective IBD sensor elements.
The previous IBD sensor parts are:
| Element Name | Part name |
|---|---|
| thsS/R | BBa_K2507000 BBa_K2507001 |
| ttrS/R | BBa_K2507006 BBa_K2507007 |
| PnorV | BBa_K1153000 |
Our newly constructed IBD sensor parts (all composite parts) are:
| Element Name | Part name |
|---|---|
| Pttr-RiboJ | BBa_K3924040 |
| Pths-RiboJ | BBa_K3924041 |
| PnorV-RiboJ | BBa_K3924042 |
Microbiota regulation
Microbiota regulation project aims to construct functional microcin MccH47, which requires co-expression of several genes. During the construction process, we have produced basic parts with only one gene each, composite parts containing several genes in a single polycistron and composite parts containing several polycistrons. These basic parts and composite parts together make up our second part collection: Microcin-related collection.
Single genes
These parts are all basic parts.
| Gene description | Part name |
|---|---|
| mchI, microcin inhibitory gene | BBa_K3924017 |
| mchB, microcin precursor | BBa_K3924018 |
| mchX, microcin expression regulator | BBa_K3924019 |
| mcmK, post-transcriptional modificaiton of microcin precursor | BBa_K3924020 |
| mcmL, post-transcriptional modificaiton of microcin precursor | BBa_K3924021 |
| mchD, post-transcriptional modificaiton of microcin precursor | BBa_K3924022 |
| mchC, function unknown | BBa_K3924025 |
| mchE, microcin transporter | BBa_K3924023 |
| mchF, microcin transporter | BBa_K3924024 |
Single polycistrons with multiple genes
These parts are all composite parts.
| Polycistrons description | Part name |
|---|---|
| mchI-mchB polycistrons with Ptac lacO promoter | BBa_K3924043 |
| mchI-mchB-mchX polycistrons with Ptac lacO promoter | BBa_K3924044 |
| mcmK-mcmL polycistrons with Ptac lacO promoter | BBa_K3924045 |
| mchC-mchD polycistrons with Ptac lacO promoter | BBa_K3924046 |
| mchE-mchF polycistrons with Ptac lacO promoter | BBa_K3924047 |
| mchI-mchB-mcmK-mcmL polycistrons with Ptac lacO promoter | BBa_K3924048 |
Multiple polycistrons
This part is a composite part.
| Polycistrons description | Part name |
|---|---|
| A huge plasmids containing mchB, mchC, mchD, mchE,mchF, mchI, mchX, mcmK, mcmL to produce and transport mature microcin | BBa_K3924034 |
Metabolic balancing
In metabolic balancing project, three basic parts including two enzymes and one adhesion protein has been designed and constructed.
| Protein | Part name |
|---|---|
| BSH1 | BBa_K3924035 |
| BSH2 | BBa_K3924036 |
| LAP | BBa_K3924033 |
PRO-LAC
In PRO-LAC diagnostic project, two parts are constructed.
One basic part is:
| Protein | Part name |
|---|---|
| mini-SOG | BBa_K3924031 |
One composite part is:
| Protein | Part name |
|---|---|
| PRO-LAC, specifically labeling RNA by sgRNA guiding after blue light exposed | BBa_K3924032 |
Safety
In Biosafety project, three composite parts related to CRISPR-AID system are constructed.
| Protein | Part name |
|---|---|
| dCas9-CDA | BBa_K3924052 |
| ParaBAD-dCas9-linker-PmCDA1-terminator | BBa_K3924053 |
| J23119-guideRNA-sgRNAscarffold terminator | BBa_K3924054 |
That's all for our part. For judging convenience, we have listed all our parts and classified as basic parts or composite parts below. And we will make some conclusions about our two part collections.
Basic parts and Composite parts
| Basic parts | Composite parts |
|---|---|
| BBa_K3924000 | BBa_K3924027 |
| BBa_K3924001 | BBa_K3924028 |
| BBa_K3924002 | BBa_K3924029 |
| BBa_K3924003 | BBa_K3924032 |
| BBa_K3924004 | BBa_K3924034 |
| BBa_K3924005 | BBa_K3924040 |
| BBa_K3924006 | BBa_K3924041 |
| BBa_K3924007 | BBa_K3924042 |
| BBa_K3924008 | BBa_K3924043 |
| BBa_K3924009 | BBa_K3924044 |
| BBa_K3924010 | BBa_K3924045 |
| BBa_K3924011 | BBa_K3924046 |
| BBa_K3924012 | BBa_K3924047 |
| BBa_K3924013 | BBa_K3924048 |
| BBa_K3924014 | BBa_K3924052 |
| BBa_K3924015 | BBa_K3924053 |
| BBa_K3924016 | BBa_K3924054 |
| BBa_K3924017 | BBa_K3924055 |
| BBa_K3924018 | BBa_K3924056 |
| BBa_K3924019 | BBa_K3924057 |
| BBa_K3924020 | BBa_K3924058 |
| BBa_K3924021 | BBa_K3924059 |
| BBa_K3924022 | BBa_K3924060 |
| BBa_K3924023 | BBa_K3924061 |
| BBa_K3924024 | |
| BBa_K3924025 | |
| BBa_K3924031 | |
| BBa_K3924033 | |
| BBa_K3924035 | |
| BBa_K3924036 | |
| BBa_K3924037 | |
| BBa_K3924038 | |
| BBa_K3924039 |
Part collections
Our project established two part collections, one is Mucosal healing collection, described in section Mucosal healing; the other is Microcin-related collection, described in section Microbiota regulation.