Difference between revisions of "Part:BBa K5236002"

 
 
(11 intermediate revisions by 3 users not shown)
Line 1: Line 1:
  
 +
<partinfo>BBa-K5236002 short</partinfo>
 +
 +
IsPETase is  friendly to enviorment and energy-saving to chemical recycling of PET. However, the temperature for it to react is even lower than glass transition temperature of PET. As one of the most-confident mutants created in our lab, this basic part encodes mutated IsPETase M10L.
 +
 +
===Usage and Biology===
 +
To generate mutated variants, we have trained a Transformer AI model. This model predicts the top 10 potential mutation sites, which are likely to have significant impacts on the enzyme's structure and function. Next, we analyzed the top 10 potential sites via Meta's ESM-1b model to eliminate the silent mutations, which involve changes in nucleotides that do not altering the corresponding amino acids. This ensures that the mutations result in changes in the enzyme's structure and thereby its function. For further information, please check the model page on our wiki. https://2024.igem.wiki/basis-china/model
 +
 +
The IsPETase M10L sequence is expressed in E.coli BL21(DE3) using the pET28a vector. The pET-28a is a classical plasmid vector used for protein expression in E.coli. This vector contains the T7 promoter, the lac operator, a ribosome binding site, the 6xHis sequence, and the T7 terminator. The T7 promoter is a strong promoter recognizable by T7 RNA polymerase, used to regulate gene expression of recombinant proteins. The lac operator can be activated by IPTG and used to control gene expression. The 6xHis sequence encodes for a tag that facilitates protein purification. Asides from the features included in the plasmid backbone, we added a signal peptide sequence — pELB — before the IsPETase M10L sequence, which is inserted between the promoter and terminator.
 +
 +
<center><html><img src ="https://static.igem.wiki/teams/5236/part-images/m10l-plasmid.png " width = "50%"><br></html></center>
 +
<center>Fig.1 M10L complete pathway in plasmid </center>
 +
 +
We tested for successful plasmid construction and transformation into E.coli through colony PCR and gel electrophoresis. The following gel result demonstrates that the plasmid transformed into E.coli are correct. The plasmid should have a total of 891 base pairs and the results match.
 +
 +
<center><html><img src ="https://static.igem.wiki/teams/5236/part-images/colony-pcr.png " width = "50%"><br></html></center>
 +
<center>Fig.2 The DNA gel electrophiresis result </center>
 +
 +
Sequencing also demonstrated successful plasmid construction.
 +
 +
<center><html><img src ="https://static.igem.wiki/teams/5236/part-images/m10l-sequence-cycle-3.png" width = "50%"><br></html></center>
 +
<center>Fig.3 The result of IsPETase M10L DNA sequencing  </center>
 +
 +
 +
To test the potential PET degradation efficiency of the IsPETase M10L synthesized in E.coli we applied the p-nitrophenyl butryte degradation assay from the iGEM19_Toronto team (for more details, please see protocols). The following graph shows the enzyme activities of IsPETase WT compared to the mutations. The mutation IsPETase M10L has a higher enzyme activity than BhrPETase WT at 30 min, and has certain potential to surpass the efficiency of IsPETase if given more time.
 +
 +
<center><html><img src ="https://static.igem.wiki/teams/5236/yh/ispet-relative-activity.jpg" width = "50%"><br></html></center>
 +
<center>Fig.4 Mutated IsPETase Dynamic Curve </center>
 +
 +
 +
 +
<!-- -->
 +
<span class='h3bb'>Sequence and Features</span>
 +
<partinfo>BBa_K5236002 SequenceAndFeatures</partinfo>
 +
 +
 +
<!-- Uncomment this to enable Functional Parameter display
 +
===Functional Parameters===
 +
<partinfo>BBa_K5236002 parameters</partinfo>
 +
<!-- -->
 +
 +
 +
===Reference===
 +
Lu, Hongyuan, et al. “Machine Learning-Aided Engineering of Hydrolases for Pet Depolymerization.” Nature News, Nature Publishing Group, 27 Apr. 2022, www.nature.com/articles/s41586-022-04599-z. Kato, Shingo, et al. “Long-Term Cultivation and Metagenomics Reveal Ecophysiology of Previously Uncultivated Thermophiles Involved in Biogeochemical Nitrogen Cycle.” Microbes and Environments, vol. 33, no. 1, Jan. 2018, pp. 107–10. https://doi.org/10.1264/jsme2.me17165.
 +
Brott, S., Pfaff, L., Schuricht, J., Schwarz, J.-N., Böttcher, D., Badenhorst, C. P. S., Wei, R., & Bornscheuer, U. T. (2021, November 29). Engineering and evaluation of thermostable isPETASE variants for PET degradation. Engineering in life sciences. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8961046/

Latest revision as of 12:52, 2 October 2024

IsPETase M10L

IsPETase is friendly to enviorment and energy-saving to chemical recycling of PET. However, the temperature for it to react is even lower than glass transition temperature of PET. As one of the most-confident mutants created in our lab, this basic part encodes mutated IsPETase M10L.

Usage and Biology

To generate mutated variants, we have trained a Transformer AI model. This model predicts the top 10 potential mutation sites, which are likely to have significant impacts on the enzyme's structure and function. Next, we analyzed the top 10 potential sites via Meta's ESM-1b model to eliminate the silent mutations, which involve changes in nucleotides that do not altering the corresponding amino acids. This ensures that the mutations result in changes in the enzyme's structure and thereby its function. For further information, please check the model page on our wiki. https://2024.igem.wiki/basis-china/model

The IsPETase M10L sequence is expressed in E.coli BL21(DE3) using the pET28a vector. The pET-28a is a classical plasmid vector used for protein expression in E.coli. This vector contains the T7 promoter, the lac operator, a ribosome binding site, the 6xHis sequence, and the T7 terminator. The T7 promoter is a strong promoter recognizable by T7 RNA polymerase, used to regulate gene expression of recombinant proteins. The lac operator can be activated by IPTG and used to control gene expression. The 6xHis sequence encodes for a tag that facilitates protein purification. Asides from the features included in the plasmid backbone, we added a signal peptide sequence — pELB — before the IsPETase M10L sequence, which is inserted between the promoter and terminator.


Fig.1 M10L complete pathway in plasmid

We tested for successful plasmid construction and transformation into E.coli through colony PCR and gel electrophoresis. The following gel result demonstrates that the plasmid transformed into E.coli are correct. The plasmid should have a total of 891 base pairs and the results match.


Fig.2 The DNA gel electrophiresis result

Sequencing also demonstrated successful plasmid construction.


Fig.3 The result of IsPETase M10L DNA sequencing


To test the potential PET degradation efficiency of the IsPETase M10L synthesized in E.coli we applied the p-nitrophenyl butryte degradation assay from the iGEM19_Toronto team (for more details, please see protocols). The following graph shows the enzyme activities of IsPETase WT compared to the mutations. The mutation IsPETase M10L has a higher enzyme activity than BhrPETase WT at 30 min, and has certain potential to surpass the efficiency of IsPETase if given more time.


Fig.4 Mutated IsPETase Dynamic Curve


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]



Reference

Lu, Hongyuan, et al. “Machine Learning-Aided Engineering of Hydrolases for Pet Depolymerization.” Nature News, Nature Publishing Group, 27 Apr. 2022, www.nature.com/articles/s41586-022-04599-z. Kato, Shingo, et al. “Long-Term Cultivation and Metagenomics Reveal Ecophysiology of Previously Uncultivated Thermophiles Involved in Biogeochemical Nitrogen Cycle.” Microbes and Environments, vol. 33, no. 1, Jan. 2018, pp. 107–10. https://doi.org/10.1264/jsme2.me17165. Brott, S., Pfaff, L., Schuricht, J., Schwarz, J.-N., Böttcher, D., Badenhorst, C. P. S., Wei, R., & Bornscheuer, U. T. (2021, November 29). Engineering and evaluation of thermostable isPETASE variants for PET degradation. Engineering in life sciences. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8961046/