Difference between revisions of "Part:BBa K4593020:Design"

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===Design Notes===
 
===Design Notes===
−
The promoter, RBS, and codon frequency of the circuit are optimized for protein expression in E. coli. However, the P2 promoter shows a high background expression in E. coli, making the device unable to conduct its designated function in E. coli. For a modified version for the expression in B. subtilis, see BBa K4593021
+
The promoter, RBS, and codon frequency of the circuit are optimized for protein expression in E. coli. However, the P2 promoter shows a high background expression in E. coli, making the device unable to conduct its designated function in E. coli. For a modified version for the expression in B. subtilis, see BBa_K4593021.
  
 
===Source===
 
===Source===
 +
LysDZ25 is from bacteriophage DZ25[1], LysGH15 is from Bacteriophage GH15[2], and ClyC is a hybrid endolysin with CBD of LysPALS1 and EAD of LysSA12[3]; Spn1s_LysRZ is from bacteriophage SPN1S[4].
  
−
various
+
The QS system is from the S. aureus genome, contributed by iGEM07_Cambridge.
  
 
===References===
 
===References===
 +
[1] Chang, Y., Li, Q., Zhang, S., Zhang, Q., Liu, Y., Qi, Q., & Lu, X. (2023). Identification and Molecular Modification of Staphylococcus aureus Bacteriophage Lysin LysDZ25. ACS Infectious Diseases, 9(3), 497–506. https://doi.org/10.1021/acsinfecdis.2c00493
 +
 +
[2] Gu, J., Feng, Y., Feng, X., Sun, C., Lei, L., Ding, W., Niu, F., Jiao, L., Yang, M., Li, Y., Liu, X., Song, J., Cui, Z., Dong Soo Han, Du, C., Yang, Y., Liu, Z.-J., Liu, Z.-J., & Han, W. (2014). Structural and Biochemical Characterization Reveals LysGH15 as an Unprecedented “EF-Hand-Like” Calcium-Binding Phage Lysin. 10(5), e1004109–e1004109. https://doi.org/10.1371/journal.ppat.1004109
 +
 +
[3] Lee, Chanyoung, et al. “Development of Advanced Chimeric Endolysin to Control Multidrug-Resistant Staphylococcus Aureus through Domain Shuffling.” ACS Infectious Diseases, vol. 7, no. 8, 28 May 2021, pp. 2081–2092. https://doi.org/10.1021/acsinfecdis.0c00812
 +
 +
[4] Lim, J.-S., Shin, H., Kang, D.-H., & Ryu, S. (2012). Characterization of endolysin from a Salmonella Typhimurium-infecting bacteriophage SPN1S. Research in Microbiology, 163(3), 233–241. https://doi.org/10.1016/j.resmic.2012.01.002

Latest revision as of 23:52, 8 October 2023


S. aureus in vivo elimination apparatus for E. coli


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 7
    Illegal NheI site found at 30
    Illegal NheI site found at 3468
    Illegal NheI site found at 3491
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 418
    Illegal BglII site found at 6040
    Illegal BamHI site found at 1302
    Illegal XhoI site found at 2591
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 5684
    Illegal NgoMIV site found at 6524
    Illegal NgoMIV site found at 7198
    Illegal AgeI site found at 3090
    Illegal AgeI site found at 3228
    Illegal AgeI site found at 5553
    Illegal AgeI site found at 6668
    Illegal AgeI site found at 6896
    Illegal AgeI site found at 7067
    Illegal AgeI site found at 7180
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

The promoter, RBS, and codon frequency of the circuit are optimized for protein expression in E. coli. However, the P2 promoter shows a high background expression in E. coli, making the device unable to conduct its designated function in E. coli. For a modified version for the expression in B. subtilis, see BBa_K4593021.

Source

LysDZ25 is from bacteriophage DZ25[1], LysGH15 is from Bacteriophage GH15[2], and ClyC is a hybrid endolysin with CBD of LysPALS1 and EAD of LysSA12[3]; Spn1s_LysRZ is from bacteriophage SPN1S[4].

The QS system is from the S. aureus genome, contributed by iGEM07_Cambridge.

References

[1] Chang, Y., Li, Q., Zhang, S., Zhang, Q., Liu, Y., Qi, Q., & Lu, X. (2023). Identification and Molecular Modification of Staphylococcus aureus Bacteriophage Lysin LysDZ25. ACS Infectious Diseases, 9(3), 497–506. https://doi.org/10.1021/acsinfecdis.2c00493

[2] Gu, J., Feng, Y., Feng, X., Sun, C., Lei, L., Ding, W., Niu, F., Jiao, L., Yang, M., Li, Y., Liu, X., Song, J., Cui, Z., Dong Soo Han, Du, C., Yang, Y., Liu, Z.-J., Liu, Z.-J., & Han, W. (2014). Structural and Biochemical Characterization Reveals LysGH15 as an Unprecedented “EF-Hand-Like” Calcium-Binding Phage Lysin. 10(5), e1004109–e1004109. https://doi.org/10.1371/journal.ppat.1004109

[3] Lee, Chanyoung, et al. “Development of Advanced Chimeric Endolysin to Control Multidrug-Resistant Staphylococcus Aureus through Domain Shuffling.” ACS Infectious Diseases, vol. 7, no. 8, 28 May 2021, pp. 2081–2092. https://doi.org/10.1021/acsinfecdis.0c00812

[4] Lim, J.-S., Shin, H., Kang, D.-H., & Ryu, S. (2012). Characterization of endolysin from a Salmonella Typhimurium-infecting bacteriophage SPN1S. Research in Microbiology, 163(3), 233–241. https://doi.org/10.1016/j.resmic.2012.01.002