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Team:ETHZ Basel/Achievements/BioBrick Toolbox
From 2010.igem.org
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= BioBrick Toolbox = | = BioBrick Toolbox = | ||
| - | [[Image: | + | [[Image:Part_fusion.png|thumb|500px|'''BioBrick assembly''' A-parts are used for N-Terminal and C-parts for C-terminal fusion. B-part is the linker that connects the two entities.]] |
| - | To construct the aimed fusion proteins, we first blunt-end cloned our BioBricks into the storage vector | + | To construct the aimed fusion proteins, we first blunt-end cloned our BioBricks into the storage vector pSEVA231 <partinfo>BBa_K422002</partinfo> (Victor de Lorenzo's lab, KanR, pBBR1 ori). This allowed easy sequencing ans storage. |
| - | All parts are | + | |
| + | All parts are compatible with BBF RFC28 (http://dspace.mit.edu/handle/1721.1/46721). The cloning strategy BBF RFC28 is a method for combinatorial multi-part assembly based on the Type IIs restriction enzyme AarI. The big advantage of this strategy is that we can simultaneously clone up to 3 different inserts into one single expression vector. Part A can be fused to the Linker Part B which is connected to Part C, the C-terminal part of the fusion protein. | ||
| - | |||
{| class="wikitable sortable" border="0" style="text-align: left" | {| class="wikitable sortable" border="0" style="text-align: left" | ||
|-bgcolor=#cccccc | |-bgcolor=#cccccc | ||
| - | |+ align="top, left"|'''table 1''': Our | + | |+ align="top, left"|'''table 1''': Our BioBricks parts for the Chemotaxis, the Anchor, the Light Sensing and the Reporter BrickBox. |
|+ align="bottom"|<nowiki>* compatible for insertion of microRNA binding sites</nowiki> | |+ align="bottom"|<nowiki>* compatible for insertion of microRNA binding sites</nowiki> | ||
| - | |width=100px|ID||width= | + | |width=100px|ID||width=80px|Insert||width=120px|Orientation||width=100px|ID||width=85px|Insert||width=120px|Orientation||width=500px|Description |
|- | |- | ||
|<partinfo>BBa_K422003</partinfo>||CheB||A-part||<partinfo>BBa_K422003</partinfo>||CheB||C-part||Demthylase: Demethylates methyl accepting chemotaxis proteins MCPs | |<partinfo>BBa_K422003</partinfo>||CheB||A-part||<partinfo>BBa_K422003</partinfo>||CheB||C-part||Demthylase: Demethylates methyl accepting chemotaxis proteins MCPs | ||
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| || || ||<partinfo>BBa_K422013</partinfo>||PhyB||C-part||Phytochromes type II: Biologically inactive form Pr absorbs red light and active configuration Pfr far-red light | | || || ||<partinfo>BBa_K422013</partinfo>||PhyB||C-part||Phytochromes type II: Biologically inactive form Pr absorbs red light and active configuration Pfr far-red light | ||
|- | |- | ||
| - | |<partinfo>BBa_K422014</partinfo>||mcyPet||A-part|| || || ||CFP | + | |<partinfo>BBa_K422014</partinfo>||mcyPet||A-part|| || || ||Optimized cyan fluorescent protein CFP, mutation in A206K preventing it from forming dimers |
|- | |- | ||
|} | |} | ||
| - | |||
| + | |||
| + | = Fusion protein assembly = | ||
| + | To influence fusion protein ratio in a bacterial cell, two expression vectors (called working vectors) with different origins of replications were generated. Both the repressor protein AraC and the corresponding promoter ParaBAD were inserted into these vectors followed by an insert flanked by AarI-recognition sites. Digest with AarI releases this insert and generates a vector with assembly-compatible overhangs. | ||
We also gave a lot of thoughts how to make BBF RFC28 (method for combinatorial multi-part assembly based on the Type II restriction enzyme AarI) compatible with Tom Knight's OAS standard. Check out our general scheme for the easy construction of Tom Knight's OAS and BBF RFC28 compatible working vectors [https://2010.igem.org/Team:ETHZ_Basel/Biology/Cloning]! | We also gave a lot of thoughts how to make BBF RFC28 (method for combinatorial multi-part assembly based on the Type II restriction enzyme AarI) compatible with Tom Knight's OAS standard. Check out our general scheme for the easy construction of Tom Knight's OAS and BBF RFC28 compatible working vectors [https://2010.igem.org/Team:ETHZ_Basel/Biology/Cloning]! | ||
| + | |||
| + | {| class="wikitable sortable" border="0" style="text-align: left" | ||
| + | |-bgcolor=#cccccc | ||
| + | |+ align="top, left"|'''table 2''': Our working vectors for fusion protein expression. | ||
| + | |+ align="bottom"|<nowiki>* compatible for insertion of microRNA binding sites</nowiki> | ||
| + | |width=100px|ID||width=40px|Name||width=40px|Ori||width=100px|Resistance||width=100px|Source | ||
| + | |- | ||
| + | |<partinfo>BBa_K422015</partinfo>||pSEVA132||pBBR1||Amp||Victor de Lorenzo's lab | ||
| + | |- | ||
| + | | ||pSEVA421||RK2 ||Spec||Victor de Lorenzo's lab | ||
| + | |- | ||
| + | |} | ||
Revision as of 12:01, 26 October 2010
BioBrick Toolbox
To construct the aimed fusion proteins, we first blunt-end cloned our BioBricks into the storage vector pSEVA231 <partinfo>BBa_K422002</partinfo> (Victor de Lorenzo's lab, KanR, pBBR1 ori). This allowed easy sequencing ans storage.
All parts are compatible with BBF RFC28 (http://dspace.mit.edu/handle/1721.1/46721). The cloning strategy BBF RFC28 is a method for combinatorial multi-part assembly based on the Type IIs restriction enzyme AarI. The big advantage of this strategy is that we can simultaneously clone up to 3 different inserts into one single expression vector. Part A can be fused to the Linker Part B which is connected to Part C, the C-terminal part of the fusion protein.
| ID | Insert | Orientation | ID | Insert | Orientation | Description |
| <partinfo>BBa_K422003</partinfo> | CheB | A-part | <partinfo>BBa_K422003</partinfo> | CheB | C-part | Demthylase: Demethylates methyl accepting chemotaxis proteins MCPs |
| <partinfo>BBa_K422005</partinfo> | CheR | A-part | <partinfo>BBa_K422003</partinfo> | CheR | C-part | Methyltransferase: Methylates methyl accepting chemotaxis proteins MCPs |
| <partinfo>BBa_K422007</partinfo> | CheY | A-part | <partinfo>BBa_K422003</partinfo> | CheY | C-part | Induces tumbling by interacting with the flagellar switch protein FliM |
| <partinfo>BBa_K422009</partinfo> | tetR | A-part | Tetracyclin repressor: Binds to its operator tetO for spatial localization of a fusion protein to the DNA | |||
| <partinfo>BBa_K422010</partinfo> | trig | A-part | Ribosome binding domain of the trigger factor: Binds to the large subunit of the ribosome | |||
| <partinfo>BBa_K422011</partinfo> | MreB | C-part | Prokaryotic actin homologue: Assembles into helical filaments underneath the cytoplasmic membrane | |||
| <partinfo>BBa_K422012</partinfo> | Pif3 | C-part | Phytochrome interacting factor: Binds Prf form of PhyB and rapidly dissociates in response to reconversion to the Pr state | |||
| <partinfo>BBa_K422013</partinfo> | PhyB | C-part | Phytochromes type II: Biologically inactive form Pr absorbs red light and active configuration Pfr far-red light | |||
| <partinfo>BBa_K422014</partinfo> | mcyPet | A-part | Optimized cyan fluorescent protein CFP, mutation in A206K preventing it from forming dimers |
Fusion protein assembly
To influence fusion protein ratio in a bacterial cell, two expression vectors (called working vectors) with different origins of replications were generated. Both the repressor protein AraC and the corresponding promoter ParaBAD were inserted into these vectors followed by an insert flanked by AarI-recognition sites. Digest with AarI releases this insert and generates a vector with assembly-compatible overhangs. We also gave a lot of thoughts how to make BBF RFC28 (method for combinatorial multi-part assembly based on the Type II restriction enzyme AarI) compatible with Tom Knight's OAS standard. Check out our general scheme for the easy construction of Tom Knight's OAS and BBF RFC28 compatible working vectors [1]!
| ID | Name | Ori | Resistance | Source |
| <partinfo>BBa_K422015</partinfo> | pSEVA132 | pBBR1 | Amp | Victor de Lorenzo's lab |
| pSEVA421 | RK2 | Spec | Victor de Lorenzo's lab |
