Difference between revisions of "Part:BBa K5117008"
 
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PpBglB 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).  
 
PpBglB 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).  
  
 +
 +
<b>Biosafety level:</b> S1
  
 
<b>Target organism:</b> <i>Bacillus subtilis</i>
 
<b>Target organism:</b> <i>Bacillus subtilis</i>
  
−
<b>Main purpose of use:</b> Gene expression and protein production using the host <i>Bacillus subtilis</i>
+
<b>Main purpose of use:</b> Expression in the host <i>B. subtilis</i>
 +
 
 +
<b> Potential application:</b> Degradation of cellobiose
  
  
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In the study titled "Sequences and homology analysis of two genes encoding β-glucosidases from <i>Bacillus polymyxa</i>" (González-Candelas <i>et al.</i> 1990), the nucleotide sequences of the <i>bglA</i> and <i>bglB</i> genes were determined. These genes encode two β-glucosidase enzymes, each with coding regions of 1344 bp, corresponding to polypeptides with molecular weights of 51.6 kDa and 51.5 kDa, respectively (González-Candelas <i>et al.</i> 1990).
 
In the study titled "Sequences and homology analysis of two genes encoding β-glucosidases from <i>Bacillus polymyxa</i>" (González-Candelas <i>et al.</i> 1990), the nucleotide sequences of the <i>bglA</i> and <i>bglB</i> genes were determined. These genes encode two β-glucosidase enzymes, each with coding regions of 1344 bp, corresponding to polypeptides with molecular weights of 51.6 kDa and 51.5 kDa, respectively (González-Candelas <i>et al.</i> 1990).
  
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In a more recent study titled "One-step purification and characterization of β-glucosidase enzyme from Paenibacillus polymyxa" (Tsabitah <i>et al.</i> 2024), the researchers focused on the purification and characterization of recombinant β-glucosidase from <i>Paenibacillus polymyxa</i>. The enzyme was expressed heterologously in <i>E. coli</i> BL21 (DE3) and purified using a one-step 6x-His tag purification method (Tsabitah <i>et al.</i> 2024).
+
In a more recent study titled "One-step purification and characterization of β-glucosidase enzyme from <i>Paenibacillus polymyxa</i>" (Tsabitah <i>et al.</i> 2024), the researchers focused on the purification and characterization of recombinant β-glucosidase from <i>Paenibacillus polymyxa</i>. The enzyme was expressed heterologously in <i>E. coli</i> BL21 (DE3) and purified using a one-step 6x-His tag purification method (Tsabitah <i>et al.</i> 2024).
  
 
The enzyme was successfully purified in a single step. SDS-PAGE analysis revealed a single band corresponding to a molecular weight of 52 kDa, confirming the enzyme’s purity. The specific activity of the purified enzyme was measured using the p-nitrophenol β-D-glucopyranoside (pNPG) assay, yielding a specific activity of 4.1 U/mg. The enzyme displayed optimal activity at pH 6.0. The enzyme was most active at 55°C. The enzyme activity was affected by metal ions, with Zn²⁺ showing the most significant effect on its activity (Tsabitah <i>et al.</i> 2024).
 
The enzyme was successfully purified in a single step. SDS-PAGE analysis revealed a single band corresponding to a molecular weight of 52 kDa, confirming the enzyme’s purity. The specific activity of the purified enzyme was measured using the p-nitrophenol β-D-glucopyranoside (pNPG) assay, yielding a specific activity of 4.1 U/mg. The enzyme displayed optimal activity at pH 6.0. The enzyme was most active at 55°C. The enzyme activity was affected by metal ions, with Zn²⁺ showing the most significant effect on its activity (Tsabitah <i>et al.</i> 2024).
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<b>More information related to this part can be found in the following publications and databases:</b>
 
<b>More information related to this part can be found in the following publications and databases:</b>
 
<ul>
 
<ul>
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<li>Isorna, Pablo <i>et al.</i>, beta-glucosidase B from Paenibacillus polymyxa (2006) https://doi.org/10.2210/pdb2O9P/pdb<li>
+
<li>Isorna, Pablo <i>et al.</i>, beta-glucosidase B from <i>Paenibacillus polymyxa</i> (2006) https://doi.org/10.2210/pdb2O9P/pdb</li>
 
<li>Isorna P., Polaina J., Latorre-García L., Cañada F. J., González B., Sanz-Aparicio, J. (2007): Crystal structures of <i>Paenibacillus polymyxa</i> β-glucosidase B complexes reveal the molecular basis of substrate specificity and give new insights into the catalytic machinery of family I glycosidases. Journal of molecular biology 371(5), 1204-1218. https://doi.org/10.1016/j.jmb.2007.05.082</li>
 
<li>Isorna P., Polaina J., Latorre-García L., Cañada F. J., González B., Sanz-Aparicio, J. (2007): Crystal structures of <i>Paenibacillus polymyxa</i> β-glucosidase B complexes reveal the molecular basis of substrate specificity and give new insights into the catalytic machinery of family I glycosidases. Journal of molecular biology 371(5), 1204-1218. https://doi.org/10.1016/j.jmb.2007.05.082</li>
 
<li>Gene sequence: https://www.ncbi.nlm.nih.gov/nuccore/M60211</li>
 
<li>Gene sequence: https://www.ncbi.nlm.nih.gov/nuccore/M60211</li>

Latest revision as of 23:49, 1 October 2024


PpBglB

This part contains the bglB gene of Paenibacillus polymyxa (synonym Bacillus polymyxa), encoding a β-glucosidase (EC 3.2.1.21).

PpBglB 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 cellobiose


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
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Enzyme characterization according to literature

In the study titled "Sequences and homology analysis of two genes encoding β-glucosidases from Bacillus polymyxa" (González-Candelas et al. 1990), the nucleotide sequences of the bglA and bglB genes were determined. These genes encode two β-glucosidase enzymes, each with coding regions of 1344 bp, corresponding to polypeptides with molecular weights of 51.6 kDa and 51.5 kDa, respectively (González-Candelas et al. 1990).

In a more recent study titled "One-step purification and characterization of β-glucosidase enzyme from Paenibacillus polymyxa" (Tsabitah et al. 2024), the researchers focused on the purification and characterization of recombinant β-glucosidase from Paenibacillus polymyxa. The enzyme was expressed heterologously in E. coli BL21 (DE3) and purified using a one-step 6x-His tag purification method (Tsabitah et al. 2024).

The enzyme was successfully purified in a single step. SDS-PAGE analysis revealed a single band corresponding to a molecular weight of 52 kDa, confirming the enzyme’s purity. The specific activity of the purified enzyme was measured using the p-nitrophenol β-D-glucopyranoside (pNPG) assay, yielding a specific activity of 4.1 U/mg. The enzyme displayed optimal activity at pH 6.0. The enzyme was most active at 55°C. The enzyme activity was affected by metal ions, with Zn²⁺ showing the most significant effect on its activity (Tsabitah et al. 2024).


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


References

González-Candelas L., Ramón D., Polaina J. (1990): Sequences and homology analysis of two genes encoding β-glucosidases from Bacillus polymyxa. Gene 95(1), 31-38. https://doi.org/10.1016/0378-1119(90)90410-s

Tsabitah K., Saksono B., Khayyira A. S., Zulfa A., Ubaidillah M., Ermawar R. A. (2024): One-step purification and characterization of β-glucosidase enzyme from Paenibacillus polymyxa. AIP Conference Proceedings 2973 (1). https://doi.org/10.1063/5.0184761