Coding

Part:BBa_K3782008

Designed by: Cyntia Lukala   Group: iGEM21_UNILausanne   (2021-10-17)
Revision as of 12:28, 20 October 2021 by Audi (Talk | contribs) (→‎Tailocin Gene Cluster)

Pseudomonas syringae DSM50252 derived tailocin gene cluster

Tailocin Gene Cluster

This part is the tailocin gene cluster of Pseudomonas syringae pv. aptata DSM50252. Tailocins are phage-derived bacteriocins produced by several species of bacteria in order to compete against closely related bacterial strains (often even of the same species) without harming the producer cells[1]. They are structurally similar to phage tails and are encoded by phage genes repurposed by bacteria[2]. When tailocins encounter their target bacteria, they bind to their cell wall and contract, thus perforating the wall. This creates a pore, which dissipates the proton gradient and kill the target cell. This mechanism allows a potent killing efficiency, as only one or few particles are sufficient to kill the cell[3].



Profile

Name Tailocin Gene Cluster
Base pairs
Number of amino acids
Molecular weight 25.35 kDa
Origin Pseudomonas syringae pv. aptata DSM50252, extracted

Usage and Biology

This gene cluster is found naturally in Pseudomonas syringae pv. aptata DSM50252. It contains both structural genes, necessary to building the tailocin, and lysis genes, which lyse the producer cell in order to release the tailocins. The genes were identified using PHASTER, the detailed annotation results are available here.

Figure 1: Tailocin gene cluster of Pseudomonas syringae DSM50252. Gene annotation as identified by PHASTER[4].

This tailocin targets several strains of Pseudomonas syringae, a detailed list of which can be found in Baltrus et al. 2019[5].
In our project, we aimed at using this protein complex to kill the plant pathogen Pseudomonas syringae pv. syringae B301D.

We aimed at cloning it in E. coli BL21 pLys, in a vector carrying a lac inducible T7 promoter but were not able to achieve this due to lack of time.

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal EcoRI site found at 2030
    Illegal EcoRI site found at 5264
    Illegal EcoRI site found at 11011
    Illegal PstI site found at 182
    Illegal PstI site found at 606
    Illegal PstI site found at 2085
    Illegal PstI site found at 2348
    Illegal PstI site found at 2387
    Illegal PstI site found at 3804
    Illegal PstI site found at 5597
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 2030
    Illegal EcoRI site found at 5264
    Illegal EcoRI site found at 11011
    Illegal PstI site found at 182
    Illegal PstI site found at 606
    Illegal PstI site found at 2085
    Illegal PstI site found at 2348
    Illegal PstI site found at 2387
    Illegal PstI site found at 3804
    Illegal PstI site found at 5597
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 2030
    Illegal EcoRI site found at 5264
    Illegal EcoRI site found at 11011
    Illegal BglII site found at 11166
    Illegal BamHI site found at 1330
    Illegal BamHI site found at 10503
    Illegal XhoI site found at 9613
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal EcoRI site found at 2030
    Illegal EcoRI site found at 5264
    Illegal EcoRI site found at 11011
    Illegal PstI site found at 182
    Illegal PstI site found at 606
    Illegal PstI site found at 2085
    Illegal PstI site found at 2348
    Illegal PstI site found at 2387
    Illegal PstI site found at 3804
    Illegal PstI site found at 5597
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal EcoRI site found at 2030
    Illegal EcoRI site found at 5264
    Illegal EcoRI site found at 11011
    Illegal PstI site found at 182
    Illegal PstI site found at 606
    Illegal PstI site found at 2085
    Illegal PstI site found at 2348
    Illegal PstI site found at 2387
    Illegal PstI site found at 3804
    Illegal PstI site found at 5597
    Illegal NgoMIV site found at 1365
    Illegal NgoMIV site found at 1790
    Illegal NgoMIV site found at 2072
    Illegal NgoMIV site found at 2485
    Illegal NgoMIV site found at 2747
    Illegal NgoMIV site found at 3574
    Illegal NgoMIV site found at 4028
    Illegal AgeI site found at 1032
    Illegal AgeI site found at 2377
    Illegal AgeI site found at 3245
    Illegal AgeI site found at 5176
    Illegal AgeI site found at 6840
    Illegal AgeI site found at 8051
    Illegal AgeI site found at 9867
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 7258
    Illegal BsaI site found at 8089
    Illegal BsaI site found at 11930
    Illegal BsaI site found at 12494
    Illegal BsaI.rc site found at 1134
    Illegal BsaI.rc site found at 3436
    Illegal BsaI.rc site found at 3905
    Illegal BsaI.rc site found at 4016
    Illegal BsaI.rc site found at 7805
    Illegal SapI.rc site found at 6651

References

Template:Reflist
  1. ↑ Patz, S. et al. Phage tail-like particles are versatile bacterial nanomachines – A mini-review. Journal of Advanced Research vol. 19 75–84 (2019).
  2. ↑ Ghequire, M. G. K. & Mot, R. de. The Tailocin Tale: Peeling off Phage Tails. Trends in Microbiology 23, 587–590 (2015).
  3. ↑ Carim, S. et al. Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins. ISME Journal (2021) doi:10.1038/s41396-021-00921-1.
  4. ↑ PHASTER. https://phaster.ca/submissions/AEAN00000000.1
  5. ↑ Baltrus, D. A., Clark, M., Smith, C. & Hockett, K. L. Localized recombination drives diversification of killing spectra for phage-derived syringacins. ISME Journal 13, 237–249 (2019).
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