Composite

Part:BBa_K4757999:Design

Designed by: Marik Müller   Group: iGEM23_Heidelberg   (2023-10-07)
Revision as of 13:46, 11 October 2023 by Marik (Talk | contribs) (→‎References)


Synthetic expression cassette regulated by terepthalic acid and alkanes for PET and PE sensing


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal EcoRI site found at 4202
    Illegal EcoRI site found at 4298
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 4202
    Illegal EcoRI site found at 4298
    Illegal NotI site found at 1625
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 4202
    Illegal EcoRI site found at 4298
    Illegal BglII site found at 212
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal EcoRI site found at 4202
    Illegal EcoRI site found at 4298
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal EcoRI site found at 4202
    Illegal EcoRI site found at 4298
    Illegal NgoMIV site found at 934
    Illegal NgoMIV site found at 2716
    Illegal NgoMIV site found at 3187
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

Source

XylS/Pm, AlkS/pAlkB is natively found in Pseudomonas putida, sRNA scaffold (SgrS) is natively found in Escherichia coli, mKate2 originiated from Entacmaea quadricolor. All sequences, except XylS/Pm were obtained by gene synthesis

References

Bao, T., Qian, Y., Xin, Y., Collins, J. J., & Lu, T. (2023). Engineering microbial division of labor for plastic upcycling. Nature communications, 14(1), 5712. <a href="https://doi.org/10.1038/s41467-023-40777-x">https://doi.org/10.1038/s41467-023-40777-x</a>

Chen, D., Xu, S., Li, S., Tao, S., Li, L., Chen, S., & Wu, L. (2023). Directly Evolved AlkS-Based Biosensor Platform for Monitoring and High-Throughput Screening of Alkane Production. ACS synthetic biology, 12(3), 832-841. <a href="https://doi.org/10.1021/acssynbio.2c00620">https://doi.org/10.1021/acssynbio.2c00620</a>

Gallegos, M. T., Marqués, S., & Ramos, J. L. (1996). Expression of the tol plasmid xylS gene in pseudomonas putida occurs from a alpha 70-dependent promoter or from alpha 70- and Alpha 54-dependent tandem promoters according to the compound used for Growth. Journal of Bacteriology, 178(8), 2356-2361. https://doi.org/10.1128/jb.178.8.2356-2361.1996

Gawin, A., Valla, S., & Brautaset, T. (2017). The XylS/Pm regulator/promoter system and its use in fundamental studies of bacterial gene expression, recombinant protein production and metabolic engineering. Microbial biotechnology, 10(4), 702-718. <a href="https://doi.org/10.1111/1751-7915.12701">https://doi.org/10.1111/1751-7915.12701</a>

<a>Geyer, R., Jambeck, J. R., & Law, K. L. (2017). Production, use, and fate of all plastics ever made.</a> Science advances, 3(7), e1700782. <a href="https://doi.org/10.1126/sciadv.1700782">https://doi.org/10.1126/sciadv.1700782</a>

Gottesman S. (2004). The small RNA regulators of Escherichia coli: roles and mechanisms*. Annual review of microbiology, 58, 303-328.</a> <a href="https://doi.org/10.1146/annurev.micro.58.030603.123841">https://doi.org/10.1146/annurev.micro.58.030603.123841</a>

Kelly, C. L., Harris, A. W. K., Steel, H., Hancock, E. J., Heap, J. T., & Papachristodoulou, A. (2018). Synthetic negative feedback circuits using engineered small RNAs. Nucleic acids research, 46(18), 9875-9889. <a href="https://doi.org/10.1093/nar/gky828">https://doi.org/10.1093/nar/gky828</a>

Li, J., Nina, M. R. H., Zhang, X., & Bai, Y. (2022). Engineering Transcription Factor XylS for Sensing Phthalic Acid and Terephthalic Acid: An Application for Enzyme Evolution. ACS synthetic biology, 11(3), 1106-1113. <a href="https://doi.org/10.1021/acssynbio.1c00275">https://doi.org/10.1021/acssynbio.1c00275</a>

Lu, H., Diaz, D. J., Czarnecki, N. J., Zhu, C., Kim, W., Shroff, R., Acosta, D. J., Alexander, B. R., Cole, H. O., Zhang, Y., Lynd, N. A., Ellington, A. D., & Alper, H. S. (2022). Machine learning-aided engineering of hydrolases for PET depolymerization. Nature, 604(7907), 662-667. <a href="https://doi.org/10.1038/s41586-022-04599-z">https://doi.org/10.1038/s41586-022-04599-z</a>

Modi, S. R., Camacho, D. M., Kohanski, M. A., Walker, G. C., & Collins, J. J. (2011). Functional characterization of bacterial sRNAs using a network biology approach. Proceedings of the National Academy of Sciences of the United States of America, 108(37), 15522-15527. <a href="https://doi.org/10.1073/pnas.1104318108">https://doi.org/10.1073/pnas.1104318108</a>

MĂžller, T., Franch, T., HĂžjrup, P., Keene, D. R., BĂ€chinger, H. P., Brennan, R. G., & Valentin-Hansen, P. (2002). Hfq: a bacterial Sm-like protein that mediates RNA-RNA interaction. Molecular cell, 9(1), 23-30. <a href="https://doi.org/10.1016/s1097-2765(01)00436-1">https://doi.org/10.1016/s1097-2765(01)00436-1</a>

Na, D., Yoo, S. M., Chung, H., Park, H., Park, J. H., & Lee, S. Y. (2013). Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nature biotechnology, 31(2), 170-174. <a href="https://doi.org/10.1038/nbt.2461">https://doi.org/10.1038/nbt.2461</a>

Sharma, S.R. (2018). Bioremediation of Polythenes and Plastics: A Microbial Approach. In: Prasad, R., Aranda, E. (eds) Approaches in Bioremediation. Nanotechnology in the Life Sciences. Springer, Cham. <a href="https://doi.org/10.1007/978-3-030-02369-0_6">https://doi.org/10.1007/978-3-030-02369-0_6</a>

Storz, G., Vogel, J., & Wassarman, K. M. (2011). Regulation by small RNAs in bacteria: expanding frontiers. Molecular cell, 43(6), 880-891. <a href="https://doi.org/10.1016/j.molcel.2011.08.022">https://doi.org/10.1016/j.molcel.2011.08.022</a>

Tournier, V., Topham, C. M., Gilles, A., David, B., Folgoas, C., Moya-Leclair, E., Kamionka, E., Desrousseaux, M. L., Texier, H., Gavalda, S., Cot, M., Guémard, E., Dalibey, M., Nomme, J., Cioci, G., Barbe, S., Chateau, M., André, I., Duquesne, S., & Marty, A. (2020). An engineered PET depolymerase to break down and recycle plastic bottles. Nature, 580(7802), 216-219. <a href="https://doi.org/10.1038/s41586-020-2149-4">https://doi.org/10.1038/s41586-020-2149-4</a>

Wu, P., Wang, Z., Zhu, Q., Xie, Z., Mei, Y., Liang, Y., & Chen, Z. (2021). Stress preadaptation and overexpression of rpoS and hfq genes increase stress resistance of Pseudomonas fluorescens ATCC13525. Microbiological research, 250, 126804. <a href="https://doi.org/10.1016/j.micres.2021.126804">https://doi.org/10.1016/j.micres.2021.126804</a>

Wu, W., Zhang, L., Yao, L., Tan, X., Liu, X., & Lu, X. (2015). Genetically assembled fluorescent biosensor for in situ detection of bio-synthesized alkanes. Scientific reports, 5, 10907. <a href="https://doi.org/10.1038/srep10907">https://doi.org/10.1038/srep10907</a>