Difference between revisions of "Part:BBa K5117010"
 
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<partinfo>BBa_K5117010 short</partinfo>
 
<partinfo>BBa_K5117010 short</partinfo>
  
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gene of the uncultured thermophilic bacterium HR29 encoding a polyethylene terephthalate hydrolase (PETase), a homologue of the leaf-branch compost cutinase (LCC), already codon optimized for Bacillus subtilis (Xi et al. 2021), but additionally including the signal peptide of the aprE gene for secretion in Bacillus subtilis
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This part contains the gene of the uncultured bacterium HR29 encoding a polyethylene terephthalate hydrolase (PETase, EC 3.1.1.101). It is a homologue of the leaf-branch compost cutinase (LCC) and codon optimized for <i>Bacillus subtilis</i> (Xi <i>et al.</i> 2021). In addition to the coding sequence, the signal peptide of the <i>aprE</i> gene for secretion in <i>Bacillus subtilis</i> is included.
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BhrPET only served for design purposes of the TU Dresden iGEM 2024 Team and was required for the construction of composite parts (see <html><a href="https://2024.igem.wiki/tu-dresden/contribution">Contribution</a></html> page).
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<b>Biosafety level:</b> S1
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<b>Target organism:</b> <i>Bacillus subtilis</i>
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<b>Main purpose of use:</b> Expression in the host <i>B. subtilis</i>
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<b> Potential application:</b> Degradation of PET
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===Design===
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For compatibility with the BioBrick RFC[10] standard, the restriction sites <i>Eco</i>RI, <i>Xba</i>I, <i>Spe</i>I, <i>Pst</i>I and <i>Not</i>I were removed from the coding sequence. To make the part compatible with the Type IIS standard, <i>Bsa</i>I and <i>Sap</i>I sites were removed as well. This was achieved by codon exchange using the codon usage table of <i>Bacillus subtilis</i> <html><a href="https://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=1423&aa=1&style=N">(Codon Usage Database Kazusa)</a></html>.
  
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<!-- Add more about the biology of this part here
 
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===Usage and Biology===
 
  
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<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>
 
<partinfo>BBa_K5117010 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K5117010 SequenceAndFeatures</partinfo>
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===Enzyme characterization according to literature===
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In the study by Xi <i>et al.</i> (2021) titled "Secretory expression in <i>Bacillus subtilis</i> and biochemical characterization of a highly thermostable polyethylene terephthalate hydrolase from bacterium HR29", a polyethylene terephthalate (PET) hydrolase BhrPETase was heterologously overexpressed in <i>B. subtilis</i> and biochemically characterized (Xi <i>et al.</i> 2021).
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The gene encoding BhrPETase was first discovered in a metagenomic study by Kato <i>et al.</i> (2018). Its sequence is homologous to that of the leaf-branch compost cutinase (LCC) variant (94 % sequence identity) (Xi <i>et al.</i> 2021).
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In the work of Xi <i>et al.</i>, a secretory expression of BhrPETase was performed in <i>B. subtilis</i>, which was improved by the development of the chaperone-overexpression mutant strain. After protein overexpression, supernatants were collected and subsequently purified with hydrophobic interaction chromatography (HIC) followed by ion exchange chromatography (IEC). The collected fractions from each purification step were analyzed with SDS-PAGE and a purified protein band corresponding to the expected molecular weight of 27.5 kDa was detected (Xi <i>et al.</i> 2021).
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The optimal pH and temperature of BhrPETase were determined using 4-nitrophenyl octanoate (pNO) as substrate. The pH optimum of BhrPETase was found to be in the range between 6 and 8. A drastic loss of activity was observed at pH < 6 and pH > 9. Temperature profiling of BhrPETase showed an almost linear increase from 30 °C to 90 °C (Xi <i>et al.</i> 2021).
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The thermostability study of BhrPETase was also conducted with pNO as substrate. It was shown that BhrPETase can retain 80 % of its activity when incubated at 80 °C for 2 h. A complete loss of activity was observed when BhrPETase was incubated at 90 °C. Notably, the thermostability of BhrPETase could be improved by the addition of CaCl<sub>2</sub>, which resulted in 80% residual activity after incubation at 90 °C (Xi <i>et al.</i> 2021).
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<b>More information related to this part can be found in the following publications and databases:</b>
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<ul>
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<li>Wang J. & Wang Y.H., HR-PETase from Bacterium HR29 (2021) https://doi.org/10.2210/pdb7EOA/pdb</li>
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<li>Wang N., Li Y., Zheng M., Dong W., Zhang Q., Wang, W. (2024): BhrPETase catalyzed polyethylene terephthalate depolymerization: A quantum mechanics/molecular mechanics approach. Journal of Hazardous Materials 477, 135414. https://doi.org/10.1016/j.jhazmat.2024.135414 </li>
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<li>Gene sequence: Codon optimized sequence for <i>Bacillus subtilis</i> can be found in the supplementary data of Xi <i>et al.</i> (2021) </li>
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<li>Protein sequence: https://www.ncbi.nlm.nih.gov/protein/GBD22443</li>
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<li>UniProtKB: https://www.uniprot.org/uniprotkb/A0A2H5Z9R5/entry</li>
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</ul>
  
  
 
===References===
 
===References===
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Xi X., Ni K., Hao H., Shang Y., Zhao B., Qian Z. (2021): Secretory expression in Bacillus subtilis and biochemical characterization of a highly thermostable polyethylene terephthalate hydrolase from bacterium HR29. Enzyme and microbial technology 143, 109715.
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Xi X., Ni K., Hao H., Shang Y., Zhao B., Qian Z. (2021): Secretory expression in <i>Bacillus subtilis</i> and biochemical characterization of a highly thermostable polyethylene terephthalate hydrolase from bacterium HR29. Enzyme and microbial technology 143, 109715. https://doi.org/10.1016/j.enzmictec.2020.109715
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Kato S., Sakai S., Hirai M., Tasumi E., Nishizawa M., Suzuki K., Takai K. (2018): Long-term cultivation and metagenomics reveal ecophysiology of previously uncultivated thermophiles involved in biogeochemical nitrogen cycle. Microbes and environments 33(1), 107-110. https://doi.org/10.1264/jsme2.ME17165
  
  

Latest revision as of 23:50, 1 October 2024


BhrPET

This part contains the gene of the uncultured bacterium HR29 encoding a polyethylene terephthalate hydrolase (PETase, EC 3.1.1.101). It is a homologue of the leaf-branch compost cutinase (LCC) and codon optimized for Bacillus subtilis (Xi et al. 2021). In addition to the coding sequence, the signal peptide of the aprE gene for secretion in Bacillus subtilis is included.

BhrPET only served for design purposes of the TU Dresden iGEM 2024 Team and was required for the construction of composite parts (see Contribution page).


Biosafety level: S1

Target organism: Bacillus subtilis

Main purpose of use: Expression in the host B. subtilis

Potential application: Degradation of PET


Design

For compatibility with the BioBrick RFC[10] standard, the restriction sites EcoRI, XbaI, SpeI, PstI and NotI were removed from the coding sequence. To make the part compatible with the Type IIS standard, BsaI and SapI sites were removed as well. This was achieved by codon exchange using the codon usage table of Bacillus subtilis (Codon Usage Database Kazusa).


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
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 579
    Illegal AgeI site found at 624
  • 1000
    COMPATIBLE WITH RFC[1000]


Enzyme characterization according to literature

In the study by Xi et al. (2021) titled "Secretory expression in Bacillus subtilis and biochemical characterization of a highly thermostable polyethylene terephthalate hydrolase from bacterium HR29", a polyethylene terephthalate (PET) hydrolase BhrPETase was heterologously overexpressed in B. subtilis and biochemically characterized (Xi et al. 2021).

The gene encoding BhrPETase was first discovered in a metagenomic study by Kato et al. (2018). Its sequence is homologous to that of the leaf-branch compost cutinase (LCC) variant (94 % sequence identity) (Xi et al. 2021).

In the work of Xi et al., a secretory expression of BhrPETase was performed in B. subtilis, which was improved by the development of the chaperone-overexpression mutant strain. After protein overexpression, supernatants were collected and subsequently purified with hydrophobic interaction chromatography (HIC) followed by ion exchange chromatography (IEC). The collected fractions from each purification step were analyzed with SDS-PAGE and a purified protein band corresponding to the expected molecular weight of 27.5 kDa was detected (Xi et al. 2021).

The optimal pH and temperature of BhrPETase were determined using 4-nitrophenyl octanoate (pNO) as substrate. The pH optimum of BhrPETase was found to be in the range between 6 and 8. A drastic loss of activity was observed at pH < 6 and pH > 9. Temperature profiling of BhrPETase showed an almost linear increase from 30 °C to 90 °C (Xi et al. 2021).

The thermostability study of BhrPETase was also conducted with pNO as substrate. It was shown that BhrPETase can retain 80 % of its activity when incubated at 80 °C for 2 h. A complete loss of activity was observed when BhrPETase was incubated at 90 °C. Notably, the thermostability of BhrPETase could be improved by the addition of CaCl2, which resulted in 80% residual activity after incubation at 90 °C (Xi et al. 2021).


More information related to this part can be found in the following publications and databases:


References

Xi X., Ni K., Hao H., Shang Y., Zhao B., Qian Z. (2021): Secretory expression in Bacillus subtilis and biochemical characterization of a highly thermostable polyethylene terephthalate hydrolase from bacterium HR29. Enzyme and microbial technology 143, 109715. https://doi.org/10.1016/j.enzmictec.2020.109715

Kato S., Sakai S., Hirai M., Tasumi E., Nishizawa M., Suzuki K., Takai K. (2018): Long-term cultivation and metagenomics reveal ecophysiology of previously uncultivated thermophiles involved in biogeochemical nitrogen cycle. Microbes and environments 33(1), 107-110. https://doi.org/10.1264/jsme2.ME17165