Difference between revisions of "Part:BBa K5205012"

 
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This is the complete urease gene cluster of S. pasteurii DSM33 consisting of ureA-ureB-ureC-ureE-ureF-ureG-ureD (Pei et al., 2023). ureA [https://parts.igem.org/Part:BBa_K5205005 BBa_K5205005], ureB [https://parts.igem.org/Part:BBa_K5205006 BBa_K5205006], and ureC [https://parts.igem.org/Part:BBa_K5205007 BBa_K5205007] encode for structure subunits of the ureases, and ureE [https://parts.igem.org/Part:BBa_K5205008 BBa_K5205008], ureF [https://parts.igem.org/Part:BBa_K5205009 BBa_K5205009], ureG [https://parts.igem.org/Part:BBa_K5205010 BBa_K5205010], and ureD [https://parts.igem.org/Part:BBa_K5205011 BBa_K5205011] encode for assisting proteins (Ciurli et al., 2002; Moersdorf et al., 1994; Remaut et al., 2001; Zambelli et al., 2005). The urease enzyme complex is crucial for catalyzing the hydrolysis of urea into ammonia and carbon dioxide, a key step in the process of microbially induced calcite precipitation (MICP).  
 
This is the complete urease gene cluster of S. pasteurii DSM33 consisting of ureA-ureB-ureC-ureE-ureF-ureG-ureD (Pei et al., 2023). ureA [https://parts.igem.org/Part:BBa_K5205005 BBa_K5205005], ureB [https://parts.igem.org/Part:BBa_K5205006 BBa_K5205006], and ureC [https://parts.igem.org/Part:BBa_K5205007 BBa_K5205007] encode for structure subunits of the ureases, and ureE [https://parts.igem.org/Part:BBa_K5205008 BBa_K5205008], ureF [https://parts.igem.org/Part:BBa_K5205009 BBa_K5205009], ureG [https://parts.igem.org/Part:BBa_K5205010 BBa_K5205010], and ureD [https://parts.igem.org/Part:BBa_K5205011 BBa_K5205011] encode for assisting proteins (Ciurli et al., 2002; Moersdorf et al., 1994; Remaut et al., 2001; Zambelli et al., 2005). The urease enzyme complex is crucial for catalyzing the hydrolysis of urea into ammonia and carbon dioxide, a key step in the process of microbially induced calcite precipitation (MICP).  
  
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===Usage and Biology===
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<center><img src = "https://static.igem.wiki/teams/5205/parts/05-1.png" style = "width:600px"></center>
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<figcaption><center>Figure 1. A. Schematic of urease and microbially induced calcite precipitation (MICP) in S. pasteurii (Wu et al., 2021); B. Map of the urease gene cluster of S. pasteurii DSM33 (Pei et al., 2023). </center></figcaption>
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<span class='h3bb'>Sequence and Features</span>
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===Sequence and Features===
 
<partinfo>BBa_K5205012 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K5205012 SequenceAndFeatures</partinfo>
  
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<partinfo>BBa_K5205012 parameters</partinfo>
 
<partinfo>BBa_K5205012 parameters</partinfo>
 
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===Usage and Biology===
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Microbiologically Induced Calcite Precipitation (MICP) involves hydrolyzing urea into ammonia and carbonate ions, raising pH to form calcium carbonate precipitates (Sarayu et al., 2014). This process can also precipitate heavy metals like cadmium and remove them from the water (Qasem et al., 2021). By introducing the urease gene cluster from S. pasteurii into E. coli, E. coli can be engineered to be a heavy metal remover.
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<center><img src = "https://static.igem.wiki/teams/5205/parts/12-1.png" style = "width:300px"></center>
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<figcaption><center>Figure 2. Gel electrophoresis of PCR product of the urease gene cluster of S. pasteurii DSM33.  </center></figcaption>
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===References===
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Ciurli, S., Safarov, N., Miletti, S., Dikiy, A., Christensen, S. K., Kornetzky, K., Bryant, D. A., Vandenberghe, I., Devreese, B., Samyn, B., Remaut, H., & van Beeumen, J. (2002). Molecular characterization of Bacillus pasteurii UreE, a metal-binding chaperone for the assembly of the urease active site. J Biol Inorg Chem, 7(6), 623-631. https://doi.org/10.1007/s00775-002-0341-7
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Moersdorf, G., Weinmann, P., & Kaltwasser, H. (1994). Nucleotide sequence of three genes on a urease encoding DNA-fragment from Bacillus pasteurii.
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Pei, D., Liu, Z., & Hu, B. (2023). A novel urease gene structure of Sporosarcina pasteurii with double operons.
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Qasem, N. A. A., Mohammed, R. H., & Lawal, D. U. (2021). Removal of heavy metal ions from wastewater: a comprehensive and critical review. npj Clean Water, 4(1), 36. https://doi.org/10.1038/s41545-021-00127-0
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Remaut, H., Safarov, N., Ciurli, S., & Van Beeumen, J. (2001). Structural basis for Ni(2+) transport and assembly of the urease active site by the metallochaperone UreE from Bacillus pasteurii. J Biol Chem, 276(52), 49365-49370. https://doi.org/10.1074/jbc.M108304200
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Sarayu, K., Iyer, N. R., & Murthy, A. R. (2014). Exploration on the biotechnological aspect of the ureolytic bacteria for the production of the cementitious materials--a review. Appl Biochem Biotechnol, 172(5), 2308-2323. https://doi.org/10.1007/s12010-013-0686-0
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Wu, Y., Li, H., & Li, Y. (2021). Biomineralization Induced by Cells of Sporosarcina pasteurii: Mechanisms, Applications and Challenges. Microorganisms, 9(11). https://doi.org/10.3390/microorganisms9112396
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Zambelli, B., Stola, M., Musiani, F., De Vriendt, K., Samyn, B., Devreese, B., Van Beeumen, J., Turano, P., Dikiy, A., Bryant, D. A., & Ciurli, S. (2005). UreG, a chaperone in the urease assembly process, is an intrinsically unstructured GTPase that specifically binds Zn2+. J Biol Chem, 280(6), 4684-4695. https://doi.org/10.1074/jbc.M408483200

Revision as of 04:01, 24 September 2024


The urease gene cluster from Sporosarcina pasteurii DSM33

This is the complete urease gene cluster of S. pasteurii DSM33 consisting of ureA-ureB-ureC-ureE-ureF-ureG-ureD (Pei et al., 2023). ureA BBa_K5205005, ureB BBa_K5205006, and ureC BBa_K5205007 encode for structure subunits of the ureases, and ureE BBa_K5205008, ureF BBa_K5205009, ureG BBa_K5205010, and ureD BBa_K5205011 encode for assisting proteins (Ciurli et al., 2002; Moersdorf et al., 1994; Remaut et al., 2001; Zambelli et al., 2005). The urease enzyme complex is crucial for catalyzing the hydrolysis of urea into ammonia and carbon dioxide, a key step in the process of microbially induced calcite precipitation (MICP).

Figure 1. A. Schematic of urease and microbially induced calcite precipitation (MICP) in S. pasteurii (Wu et al., 2021); B. Map of the urease gene cluster of S. pasteurii DSM33 (Pei et al., 2023).

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 4619
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 3403
    Illegal BamHI site found at 5120
    Illegal XhoI site found at 4157
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 4415
    Illegal BsaI.rc site found at 461
    Illegal BsaI.rc site found at 2189
    Illegal BsaI.rc site found at 4704


Usage and Biology

Microbiologically Induced Calcite Precipitation (MICP) involves hydrolyzing urea into ammonia and carbonate ions, raising pH to form calcium carbonate precipitates (Sarayu et al., 2014). This process can also precipitate heavy metals like cadmium and remove them from the water (Qasem et al., 2021). By introducing the urease gene cluster from S. pasteurii into E. coli, E. coli can be engineered to be a heavy metal remover.

Figure 2. Gel electrophoresis of PCR product of the urease gene cluster of S. pasteurii DSM33.

References

Ciurli, S., Safarov, N., Miletti, S., Dikiy, A., Christensen, S. K., Kornetzky, K., Bryant, D. A., Vandenberghe, I., Devreese, B., Samyn, B., Remaut, H., & van Beeumen, J. (2002). Molecular characterization of Bacillus pasteurii UreE, a metal-binding chaperone for the assembly of the urease active site. J Biol Inorg Chem, 7(6), 623-631. https://doi.org/10.1007/s00775-002-0341-7

Moersdorf, G., Weinmann, P., & Kaltwasser, H. (1994). Nucleotide sequence of three genes on a urease encoding DNA-fragment from Bacillus pasteurii.

Pei, D., Liu, Z., & Hu, B. (2023). A novel urease gene structure of Sporosarcina pasteurii with double operons.

Qasem, N. A. A., Mohammed, R. H., & Lawal, D. U. (2021). Removal of heavy metal ions from wastewater: a comprehensive and critical review. npj Clean Water, 4(1), 36. https://doi.org/10.1038/s41545-021-00127-0

Remaut, H., Safarov, N., Ciurli, S., & Van Beeumen, J. (2001). Structural basis for Ni(2+) transport and assembly of the urease active site by the metallochaperone UreE from Bacillus pasteurii. J Biol Chem, 276(52), 49365-49370. https://doi.org/10.1074/jbc.M108304200

Sarayu, K., Iyer, N. R., & Murthy, A. R. (2014). Exploration on the biotechnological aspect of the ureolytic bacteria for the production of the cementitious materials--a review. Appl Biochem Biotechnol, 172(5), 2308-2323. https://doi.org/10.1007/s12010-013-0686-0

Wu, Y., Li, H., & Li, Y. (2021). Biomineralization Induced by Cells of Sporosarcina pasteurii: Mechanisms, Applications and Challenges. Microorganisms, 9(11). https://doi.org/10.3390/microorganisms9112396

Zambelli, B., Stola, M., Musiani, F., De Vriendt, K., Samyn, B., Devreese, B., Van Beeumen, J., Turano, P., Dikiy, A., Bryant, D. A., & Ciurli, S. (2005). UreG, a chaperone in the urease assembly process, is an intrinsically unstructured GTPase that specifically binds Zn2+. J Biol Chem, 280(6), 4684-4695. https://doi.org/10.1074/jbc.M408483200