Difference between revisions of "Part:BBa K5115067"
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The Ni-Fe hydrogenase include the part [https://parts.igem.org/Part:BBa_K5115020 BBa_K5115020（hox and hyp operon）]. Multiple subunits work together to complete the hydrogenase function. Two main subunits are hoxF and hoxH, one working as NADH dehydrogenase, another working as catalytic centre of hydrogen reaction.<ref>Löscher, S., Burgdorf, T., Zebger, I., Hildebrandt, P., Dau, H., Friedrich, B., & Haumann, M. (2006). Bias from H2 Cleavage to Production and Coordination Changes at the Ni−Fe Active Site in the NAD+-Reducing Hydrogenase from Ralstonia eutropha. Biochemistry, 45(38), 11658–11665.</ref> The hyp operon plays a critical role in the maturation of hydrogenase. The hypA and hypB are involved in nickel binding and transport, ensuring that the hydrogenase subunits receive the required metal ions for optimal activity.<ref>Anne K. Jones, Oliver Lenz, Angelika Strack, Thorsten Buhrke, and, & Friedrich*, B. (2004, October 2). NiFe Hydrogenase Active Site Biosynthesis: Identification of Hyp Protein Complexes in Ralstonia eutropha† (world) [Research-article]. ACS Publications; American Chemical Society.</ref> Through the synergistic integration of the hox and hyp operon, our system effectively enhances hydrogen production and enables the reduction of nickel ions into nanoparticles, thereby maximizing the efficiency of nickel recovery from industrial wastewater. | The Ni-Fe hydrogenase include the part [https://parts.igem.org/Part:BBa_K5115020 BBa_K5115020（hox and hyp operon）]. Multiple subunits work together to complete the hydrogenase function. Two main subunits are hoxF and hoxH, one working as NADH dehydrogenase, another working as catalytic centre of hydrogen reaction.<ref>Löscher, S., Burgdorf, T., Zebger, I., Hildebrandt, P., Dau, H., Friedrich, B., & Haumann, M. (2006). Bias from H2 Cleavage to Production and Coordination Changes at the Ni−Fe Active Site in the NAD+-Reducing Hydrogenase from Ralstonia eutropha. Biochemistry, 45(38), 11658–11665.</ref> The hyp operon plays a critical role in the maturation of hydrogenase. The hypA and hypB are involved in nickel binding and transport, ensuring that the hydrogenase subunits receive the required metal ions for optimal activity.<ref>Anne K. Jones, Oliver Lenz, Angelika Strack, Thorsten Buhrke, and, & Friedrich*, B. (2004, October 2). NiFe Hydrogenase Active Site Biosynthesis: Identification of Hyp Protein Complexes in Ralstonia eutropha† (world) [Research-article]. ACS Publications; American Chemical Society.</ref> Through the synergistic integration of the hox and hyp operon, our system effectively enhances hydrogen production and enables the reduction of nickel ions into nanoparticles, thereby maximizing the efficiency of nickel recovery from industrial wastewater. | ||
| − | The carboxysome include the part [https://parts.igem.org/Part:BBa_K5115065 BBa_K5115065（cso, without csoS3）]. It encodes a series of proteins essential for the assembly of α-carboxysomes, a type of microcompartment that facilitates the sequestration and concentration of enzymes involved in carbon fixation, particularly ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco)<ref>Oltrogge, L. M., Chaijarasphong, T., Chen, A. W., Bolin, E. R., Marqusee, S., & Savage, D. F. (2020). Multivalent interactions between CsoS2 and Rubisco mediate α-carboxysome formation. Nature structural & molecular biology, 27(3), 281–287. </ref>These microcompartments are advantageous for engineering metabolic pathways, especially in enhancing the efficiency of carbon fixation and enzyme activity. | + | The carboxysome include the part [https://parts.igem.org/Part:BBa_K5115065 BBa_K5115065（cso, without csoS3）]. It encodes a series of proteins essential for the assembly of α-carboxysomes, a type of microcompartment that facilitates the sequestration and concentration of enzymes involved in carbon fixation, particularly ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco)<ref>Oltrogge, L. M., Chaijarasphong, T., Chen, A. W., Bolin, E. R., Marqusee, S., & Savage, D. F. (2020). Multivalent interactions between CsoS2 and Rubisco mediate α-carboxysome formation. Nature structural & molecular biology, 27(3), 281–287. </ref>These microcompartments are advantageous for engineering metabolic pathways, especially in enhancing the efficiency of carbon fixation and enzyme activity. The overall design not only supports nickel ion reduction but also promotes enhanced carbon capture, thereby contributing to a more sustainable bioprocess. |
| − | + | ||
| + | The EP is the part [https://parts.igem.org/Part:BBa_K5115002 BBa_K5115002]. It is designed to facilitate the effective encapsulation of enzymes within the carboxysome structure, enhancing the efficiency of biochemical reactions. It serves as a linker that connects the target enzymes to the carboxysome, ensuring proper localization and functionality.<ref>Li, T., Jiang, Q., Huang, J., Aitchison, C. M., Huang, F., Yang, M., Dykes, G. F., He, H. L., Wang, Q., Sprick, R. S., Cooper, A. I., & Liu, L. N. (2020). Reprogramming bacterial protein organelles as a nanoreactor for hydrogen production. Nature communications, 11(1), 5448.</ref> In this F module, EP is combined with hoxF. And in U module [https://parts.igem.org/Part:BBa_K5115066 BBa_K5115066], EP is combined with hoxU. Different sites of combination can influence the effect of the carboxysome encapsulation, so we decided to choose the better one through experient. | ||
Based on the ribozyme-assisted polycistronic co-expression system, all of the proteins above can express at a equalized level. To learn more about our pRAP system, please check [https://2022.igem.wiki/fudan/parts part wiki of 2022 Fudan iGEM]. | Based on the ribozyme-assisted polycistronic co-expression system, all of the proteins above can express at a equalized level. To learn more about our pRAP system, please check [https://2022.igem.wiki/fudan/parts part wiki of 2022 Fudan iGEM]. | ||
===Usage and Biology=== | ===Usage and Biology=== | ||
| + | The F module harnesses the collaborative power of hydrogenase enzymes, carboxysome compartments, and encapsulation peptides to drive an innovative approach for nickel reduction in E. coli. This integrated module not only advances the biotechnological potential of engineered microorganisms but also addresses environmental concerns related to nickel contamination by converting harmful ions into less toxic nanoparticles. | ||
===Characterization=== | ===Characterization=== | ||
Latest revision as of 09:24, 30 September 2024
mineral, F module
Introduction
This part is made up of Ni-Fe hydrogenase and carboxysome, the former is encapsulated into the latter by EP. All the subunits of the proteins constructed into our ribozyme-assisted polycistronic co-expression system.
The Ni-Fe hydrogenase include the part BBa_K5115020（hox and hyp operon）. Multiple subunits work together to complete the hydrogenase function. Two main subunits are hoxF and hoxH, one working as NADH dehydrogenase, another working as catalytic centre of hydrogen reaction.[1] The hyp operon plays a critical role in the maturation of hydrogenase. The hypA and hypB are involved in nickel binding and transport, ensuring that the hydrogenase subunits receive the required metal ions for optimal activity.[2] Through the synergistic integration of the hox and hyp operon, our system effectively enhances hydrogen production and enables the reduction of nickel ions into nanoparticles, thereby maximizing the efficiency of nickel recovery from industrial wastewater.
The carboxysome include the part BBa_K5115065（cso, without csoS3）. It encodes a series of proteins essential for the assembly of α-carboxysomes, a type of microcompartment that facilitates the sequestration and concentration of enzymes involved in carbon fixation, particularly ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco)[3]These microcompartments are advantageous for engineering metabolic pathways, especially in enhancing the efficiency of carbon fixation and enzyme activity. The overall design not only supports nickel ion reduction but also promotes enhanced carbon capture, thereby contributing to a more sustainable bioprocess.
The EP is the part BBa_K5115002. It is designed to facilitate the effective encapsulation of enzymes within the carboxysome structure, enhancing the efficiency of biochemical reactions. It serves as a linker that connects the target enzymes to the carboxysome, ensuring proper localization and functionality.[4] In this F module, EP is combined with hoxF. And in U module BBa_K5115066, EP is combined with hoxU. Different sites of combination can influence the effect of the carboxysome encapsulation, so we decided to choose the better one through experient.
Based on the ribozyme-assisted polycistronic co-expression system, all of the proteins above can express at a equalized level. To learn more about our pRAP system, please check part wiki of 2022 Fudan iGEM.
Usage and Biology
The F module harnesses the collaborative power of hydrogenase enzymes, carboxysome compartments, and encapsulation peptides to drive an innovative approach for nickel reduction in E. coli. This integrated module not only advances the biotechnological potential of engineered microorganisms but also addresses environmental concerns related to nickel contamination by converting harmful ions into less toxic nanoparticles.
Characterization
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12INCOMPATIBLE WITH RFC[12]Illegal NheI site found at 208
Illegal NotI site found at 5126 - 21INCOMPATIBLE WITH RFC[21]Illegal BglII site found at 366
Illegal BglII site found at 5743
Illegal BglII site found at 5821
Illegal BglII site found at 14467
Illegal BglII site found at 15285
Illegal BglII site found at 15578
Illegal BamHI site found at 6214
Illegal XhoI site found at 5751
Illegal XhoI site found at 5943
Illegal XhoI site found at 6421
Illegal XhoI site found at 8660
Illegal XhoI site found at 10489
Illegal XhoI site found at 11651
Illegal XhoI site found at 13490 - 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal NgoMIV site found at 6514
Illegal NgoMIV site found at 7194
Illegal NgoMIV site found at 9801
Illegal NgoMIV site found at 9908
Illegal NgoMIV site found at 10178
Illegal NgoMIV site found at 11024
Illegal NgoMIV site found at 11256
Illegal AgeI site found at 874
Illegal AgeI site found at 1825
Illegal AgeI site found at 2506
Illegal AgeI site found at 3460
Illegal AgeI site found at 5704
Illegal AgeI site found at 10976
Illegal AgeI site found at 16361 - 1000INCOMPATIBLE WITH RFC[1000]Illegal BsaI site found at 5525
Illegal BsaI site found at 5687
Illegal BsaI site found at 8314
Illegal BsaI.rc site found at 14515
Illegal BsaI.rc site found at 15019
Illegal SapI site found at 266
Illegal SapI.rc site found at 5636
References
- ↑ Löscher, S., Burgdorf, T., Zebger, I., Hildebrandt, P., Dau, H., Friedrich, B., & Haumann, M. (2006). Bias from H2 Cleavage to Production and Coordination Changes at the Ni−Fe Active Site in the NAD+-Reducing Hydrogenase from Ralstonia eutropha. Biochemistry, 45(38), 11658–11665.
- ↑ Anne K. Jones, Oliver Lenz, Angelika Strack, Thorsten Buhrke, and, & Friedrich*, B. (2004, October 2). NiFe Hydrogenase Active Site Biosynthesis: Identification of Hyp Protein Complexes in Ralstonia eutropha† (world) [Research-article]. ACS Publications; American Chemical Society.
- ↑ Oltrogge, L. M., Chaijarasphong, T., Chen, A. W., Bolin, E. R., Marqusee, S., & Savage, D. F. (2020). Multivalent interactions between CsoS2 and Rubisco mediate α-carboxysome formation. Nature structural & molecular biology, 27(3), 281–287.
- ↑ Li, T., Jiang, Q., Huang, J., Aitchison, C. M., Huang, F., Yang, M., Dykes, G. F., He, H. L., Wang, Q., Sprick, R. S., Cooper, A. I., & Liu, L. N. (2020). Reprogramming bacterial protein organelles as a nanoreactor for hydrogen production. Nature communications, 11(1), 5448.