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Team:Macquarie Australia/Project/Parts
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<h4> Parts Submitted by Team Macquarie Australia 2014 </h4> | <h4> Parts Submitted by Team Macquarie Australia 2014 </h4> | ||
Revision as of 14:51, 17 October 2014
Parts & Characterization
The Macquarie 2014 team designed and constructed the following three operons required for the chlorophyll biosynthesis pathway. These three operons have been sent to the registry.
Functional Operons
Operon 1:BBa_K1326008
In anaerobic bacteria, the bch1 and bchD genes are part of an operon. Macquarie 2014 have constructed an equivalent synthetic operon in E. coli, using separate ChlI1 and ChlD taken from oxygenic photosynthetic eukaryotes. We have shown that our artificial operon works, and that proteins self-assemble to form a functional ChlI1:ChlD complex in E. coli. This part works together with ChlH to insert magnesium into protoporphyrin IX. Although our operon does not contain ChlH as originally planned (due to issues in fully assembling the part), in vitro assays indicated full functionality of self-assembly and catalytic functionality.
Figure 1. Operon 1, made up of the lac promoter, ChlI1, ChlD, and GUN4. The BioBrick plasmid backbone encodes chloramphenicol resistance.
Operon 2:BBa_K1326002
This gene has been used in an operon with other genes responsible for catalysing the biosynthesis pathway from Mg-protoporphyrin IX to Protochlorophyllide. CTH1, Plastocyanin, and YCF54 are involved in the oxidative cyclase pathway. ChlM methylates Mg-protoporphyrin IX, facilitating the highly-regulated catalysis of Mg-chelatase. CTH1 catalyses the conversion of Mg-protoporphyrin IX monomethyl into divinyl protochlorophyllide, interacting with YCF54 and Plastocyanin.
Figure 3. Operon 2, made up of the lac promoter, CTH1, YCF54, Plasto, and ChlM. The BioBrick plasmid backbone encodes chloramphenicol resistance.
Operon 3:BBa_K1326003
This gene has been used in an operon with other genes responsible for the terminal steps of the chlorophyll biosynthesis pathway, in the conversion of divinyl protochlorophyllide to chlorophyll a. DVR1 reduces divinyl protochlorophyllide, POR converts protochlorophyllide to chlorophyllide, ChlG adds the geranylgeranyl pyrophosphate chain to the chlorophyllide molecule, and ChlP reduces the double bonds on GGPP. The final product is chlorophyll a.
Figure 4. Operon 3, made up of the lac promoter, POR, DVR1, ChlP, and ChlG. The BioBrick plasmid backbone encodes chloramphenicol resistance.
The ChlD Story: the repair of the registry ChlD
Team:iGEM2013_Macquarie_Australia designed all 13 parts required for the biosynthesis pathway and successfully synthesized most of these, including ChlD [BBa_K1080002.]. However, this part was not received by the registry in 2013.
We screened and verified the identity of all their parts, as we required them to assemble composite parts with the aim of forming functional operons. When ChlD was sequenced, we determined that there was a 50 base-pair deletion in the middle of the gene. Team:iGEM2014_Macquarie_Australia has repaired this part, ensuring the full correct sequence is present. We incorporated this part it into operon 1, and have verified that the part is functional, guaranteeing it has been properly repaired.
This part has now been successfully sent to the registry in a functional state.
Parts Annotated and Improved
The following parts were again designed and synthesized by Team:iGEM2013_Macquarie_Australia. Many of these were not received by the registry in 2013. Following our efforts to confirm the DNA sequences, we improved their documentation to further elucidate the interactions between each part of the system. Information regarding each part's function, role in the biosynthesis pathway, protein structure, and enzymatic reactions, all of which can be found in the iGEM parts registry.
Parts from previous teams used
| Parts | Type | Description | Designer | Length |
|---|---|---|---|---|
| BBa_K1080002 | Coding | ChlD | iGEM13_Macquarie_Australia | 2154 |
| BBa_K1080003 | Coding | GUN4 | iGEM13_Macquarie_Australia | 728 |
| BBa_K1080006 | Coding | Plastocyanin | iGEM13_Macquarie_Australia | 324 |
| BBa_K1080000 | Coding | ChlI1 | iGEM13_Macquarie_Australia | 1116 |
| BBa_K1080001 | Coding | ChlH | iGEM13_Macquarie_Australia | 4125 |
| BBa_K1080005 | Coding | CTH1 | iGEM13_Macquarie_Australia | 1152 |
| BBa_K1080007 | Coding | POR | iGEM13_Macquarie_Australia | 1067 |
| BBa_K1080008 | Coding | ChlP | iGEM13_Macquarie_Australia | 1299 |
| BBa_K1080009 | Coding | ChlG | iGEM13_Macquarie_Australia | 1050 |
| BBa_K1080010 | Coding | YCF54 | iGEM13_Macquarie_Australia | 471 |
| BBa_K1080011 | Coding | ChlI2 | iGEM13_Macquarie_Australia | 1212 |
| BBa_K1080012 | Coding | DVR1 | iGEM13_Macquarie_Australia | 1106 |
| BBa_K1080013 | Composite | GUN4 (+ Ptac Promoter) | iGEM13_Macquarie_Australia | 797 |
| BBa_K1080014 | Composite | Plasto (+ Ptac promoter) | iGEM13_Macquarie_Australia | 393 |
| BBa_K1080015 | Composite | POR (+ Ptac promoter) | iGEM13_Macquarie_Australia | 1136 |
| BBa_K1080016 | Composite | ChlI1 (+Ptac promoter) | iGEM13_Macquarie_Australia | 1185 |
| BBa_K1080017 | Composite | ChlH (+ Ptac promoter) | iGEM13_Macquarie_Australia | 4194 |
| BBa_K1080018 | Composite | ChlD (+ Ptac promoter) | iGEM13_Macquarie_Australia | 2223 |
| BBa_K1080019 | Composite | ChlM (+ Ptac promoter) | iGEM13_Macquarie_Australia | 942 |
| BBa_K1080020 | Composite | CTH1 (+ Ptac promoter) | iGEM13_Macquarie_Australia | 1221 |
| BBa_K1080021 | Composite | ChlP (+ Ptac promoter) | iGEM13_Macquarie_Australia | 1368 |
| BBa_K1080022 | Composite | ChlG (+ Ptac promoter) | iGEM13_Macquarie_Australia | 1119 |
| BBa_K1080023 | Composite | YCF54 (+ Ptac promoter) | iGEM13_Macquarie_Australia | 540 |
| BBa_K1080024 | Composite | ChlI2 (+ ptac promoter) | iGEM13_Macquarie_Australia | 1281 |
| BBa_K1080025 | Composite | DVR1 (+ Ptac promoter) | iGEM13_Macquarie_Australia | 1175 |
| BBa_K864400 | Regulatory | Ptac, trp & lac regulated promoter | iGEM12_Uppsala | 61 |
Parts improved
| Part Name | Type | Descriptor | Length |
|---|---|---|---|
| BBa_K1080002 | Singular/Coding | ChlD | 2154 |
