Coding

Part:BBa_K4960035

Designed by: Ziying Wang   Group: iGEM23_NUDT-CHINA   (2023-10-11)
Revision as of 05:30, 12 October 2023 by Aaachengcheng (Talk | contribs) (→‎Usage and Biology)


pPVC promoter->pvc1-pvc12->pvc13_ NTD-CKGGRAKDC -pVc13_CTD->pvc14-pvc16

Structural and accessory genes

Profile

Name:pvc1-pvc12,pvc13_ NTD-CKGGRAKDC-pVc13_CTD,pvc14-pvc16
Origin: Photorhabdus
Properties: Structural and accessory genes


Usage and Biology

This part is necessary for the assembly of a functional injection system. PVCs probably recognize target cells via tail fibres (Pvc13), leading to a contraction of the sheath mechanism that drives a spike through the cellular membrane.[1]
Pvc2, Pvc3 and Pvc4 compose the sheath of PVC. Pvc16 is sheath terminator of PVC. Pvc13 is tail fibres of PVC. Pvc9, Pvc11 and Pvc12 compose the baseplate of PVC. Pvc8 and Pvc10 compose the spike of PVC. Pvc1, Pvc5 and Pvc7 compose the tube of PVC.[2]
This part also has a special sequence CKGGRAKDC(Fig.1), which can recognize our target cells, making PVC tropism toward specific cells.

Figure 1.AlphaFold2 based prediction of engineered PVC tail fiber trimer structure.
Structure of adipose-targeting CKGGRAKDC peptide-presenting PVC tail fiber with indicated linkers were shown.

Special Design

This part has a special sequence CKGGRAKDC, which can recognize our target cells.

Sequence and Features

Tube:pvc1, pvc5, pvc7
Sheath:pvc2, pvc3, pvc4
Sheath terminator:pvc15
Tail fbres:pvc13_ NTD-CKGGRAKDC-pVc13_CTD
Baseplate:pvc9, pvc11, pvc12
Spike:pvc8, pvc10
Assembly method:3A Assembly

Figure 2.PVC composition diagram


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 7406
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 2407
    Illegal BglII site found at 11264
    Illegal BglII site found at 14099
    Illegal BglII site found at 16930
    Illegal XhoI site found at 2691
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 11792
    Illegal NgoMIV site found at 17461
    Illegal NgoMIV site found at 17600
    Illegal AgeI site found at 6704
    Illegal AgeI site found at 9641
    Illegal AgeI site found at 10327
    Illegal AgeI site found at 10468
    Illegal AgeI site found at 11576
    Illegal AgeI site found at 17899
    Illegal AgeI site found at 19587
  • 1000
    COMPATIBLE WITH RFC[1000]


References

[1]Kreitz J, Friedrich MJ, Guru A, Lash B, Saito M, Macrae RK, Zhang F. Programmable protein delivery with a bacterial contractile injection system. Nature. 2023 Apr;616(7956):357-364.
[2]Kolonin MG, Saha PK, Chan L, Pasqualini R, Arap W. Reversal of obesity by targeted ablation of adipose tissue. Nat Med. 2004 Jun;10(6):625-32.

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Parameters
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