Gene: Xylose-inducible promoter (Pxyl) BBa_K4358000

Short description: Pxyl can be regulated by xylose.

Long description: xylose-inducible promoter
Gene expression with xylose promoter can be induced by the addition of xylose. When xylose is presented, the inducer, xylose, would bind to the xylose regulator protein and change its structure. Hence, XylR wouldn’t bind to the operator(XylR-binding site) to inhibit the downstream gene of the XylR-binding site.

So we design the plasmid with Pxyl, Xylr and XylR-binding site. Then we transformed pqqC, pqqD and pqqE in the downstream of the XylR-binding site in addition to controlling the expression of pqqC, pqqD and pqqE to let more resources be used for the biosynthesis of PqqA and PqqB.

Figure1. It illustrated the mechanism of how xylose regulator protein interacts with xylose promoter and inhibits the performance of the downstream genes. The XylR would bind to the XylR binding site until the structure being changed because of xylose.

Gene: XylR(Xylose repressor) BBa_K4358001

Short description: Xylose repressor

Long description: xylose repressor
Gene expression with xylose promoter can be induced by the addition of xylose. When xylose is presented, the inducer, xylose, would bind to the xylose regulator protein and change its structure. Hence, XylR wouldn’t bind to the operator(XylR-binding site) to inhibit the performance of the downstream genes of the XylR-binding site.

So we design the plasmid with Pxyl, XylR and XylR-binding sites. Then we transformed pqqC, pqqD and pqqE in the downstream of the XylR-binding site in addition to control the expression of pqqC, pqqD and pqqE to let more resources be used for the biosynthesis of PqqA and PqqB.

Figure1. It illustrated the mechanism of how xylose regulator protein interacts with xylose promoter and inhibits the performance of the downstream genes. The XylR would bind to the XylR binding site until the structure changed because of xylose.

Figure 2. The 3D structure of xylose repressor

Gene: ColiE1 ori BBa_K4358002

Short description: origin of replication

Long description: ColiE1ori is a E.coli-derived ori and needs a short doubling time, so that the plasmid stored in E.coli can be more stable.

Gene: pBC16 ori BBa_K4358003

Short description: origin of replication

Long description: pBC16 ori is allowed to be used by Bacillus subtilis natto. We make the plasmid to perform in Bacillus subtilis natto.

Gene: XylR-binding site BBa_K4358006

Short description: XylR-binding site

Long description: XylR-binding site
Gene expression with xylose promoter can be induced by the addition of xylose. When xylose is presented, the inducer, xylose, would bind to the xylose regulator protein and change its structure. Hence, XylR wouldn’t bind to the operator(XylR-binding site) to inhibit the downstream gene of the XylR-binding site.

So we design the plasmid with Pxyl, XylR and XylR-binding site. Then we transformed pqqC, pqqD and pqqE in the downstream of the XylR-binding site in addition to controlling the expression of pqqC, pqqD and pqqE to let more resources be used for the biosynthesis of PqqA and PqqB.

Figure1. It illustrated that how xylose regulator protein interacts with xylose promoter and inhibits the performance of the downstream genes.

Protein: Coenzyme PQQ synthesis protein A

Part: pqqA BBa_K3830004

Organism: Gluconobacter oxydans

Short description: Pyrroloquinoline quinone (PQQ) is a peptide-derived redox cofactor produced by prokaryotes and it also plays beneficial roles in other organisms. We focus on the mechanisms of PqqE,PqqA,PqqC,PqqD and PqqB.

Long description: The pqqA is translated into a short peptide that contains the fully conserved residues, glutamate, and tyrosine.

This picture shows how it works and the 3D protein structure.

Protein: Coenzyme PQQ synthesis protein B

Part: pqqB BBa_K3830003

Organism: Gluconobacter oxydans

Short description: Pyrroloquinoline quinone (PQQ) is a peptide-derived redox cofactor produced by prokaryotes and it also plays beneficial roles in other organisms. we focusing on the mechanisms of PqqE,PqqA,PqqC,PqqD and PqqB.

Long description: PqqB(Figure A) belongs to the metallo-b-lactamase superfamily . Enzymes in this superfamily generally catalyze the hydrolysis of small molecules using metal centers(Figure B) that range from zinc to manganese, nickel, magnesium, and iron . PqqB serve as an oxygenase to modify the tyrosine side-chain within PqqA, and it can cross-over between the metallo-b-lactamase superfamily and the nonheme iron hydroxylases.

This picture shows how it works and the 3D protein structure.

Protein: Coenzyme PQQ synthesis protein C

Part: pqqC BBa_K3830005

Organism: Gluconobacter oxydans

Short description: Pyrroloquinoline quinone (PQQ) is a peptide-derived redox cofactor produced by prokaryotes and it also plays beneficial roles in other organisms. We focused on the mechanisms of PqqE,PqqA,PqqC,PqqD and PqqB.

Long description: PqqC catalyzes an eight-electron and eight-proton oxidation on AHQQ in the absence of organic metal cofactor, consuming three equivalents of O₂. The utilization of O₂ is accompanied by a progressive conformational change of PqqC, resulting in the reduction of product H₂O₂, rather than exogenous O₂..

This picture shows how it works and the 3D protein structure.

Protein: Coenzyme PQQ synthesis protein D

Part: pqqD BBa_K3830006

Organism: Gluconobacter oxydans

Short description: Pyrroloquinoline quinone (PQQ) is a peptide-derived redox cofactor produced by prokaryotes and it also plays beneficial roles in other organisms. We focus on the mechanisms of PqqE,PqqA,PqqC,PqqD and PqqB.

Long description:PqqD, a peptide chaperone, forms a ternary complex with the radical SAM protein calls PqqE. And it can assist PqqE to do the modification on PqqA.

This picture shows how it works and the 3D protein structure.

Protein: Coenzyme PQQ synthesis protein E

Part: pqqE BBa_K3830007

Organism: Gluconobacter oxydans

Short description: Pyrroloquinoline quinone (PQQ) is a peptide-derived redox cofactor produced by prokaryotes and it also plays beneficial roles in other organisms. We focus on the mechanisms of PqqE,PqqA,PqqC,PqqD and PqqB.

Long description: In the structure of PqqE, a [2Fe-2S] cluster appeared in the AuxI site of the SPASM domain A [4Fe-4S] cluster within the AuxI site, and the Cys-to-His variant catalyzes reductive site.

This picture shows how it works and the 3D protein structure.