Contribution

Wet Lab

1. Development of Standardized BioBrick Parts for PAH Degradation

  The core contribution of this project to the iGEM Registry lies in the construction of four functional BioBrick parts, each corresponding to key genes in the PAH degradation system: rhlAB, nahABFEDG-phnC, phnS-P-R, and composite elements nah-phnC, nah-nahC, phnS-P-R-EGFP. These parts have been optimized for prokaryotic expression (in Escherichia coli, the chassis organism most commonly used by iGEM teams), enabling future teams to directly reuse them without the need for additional cloning:

  rhlAB gene: Cloned from Pseudomonas aeruginosa, this part enables chassis microbes to produce rhamnolipids, a type of biosurfactant. For future teams focused on pollutant capture applications—such as detaching weakly polar pollutants from soil—this part can directly replace the labor-intensive process of gene cloning, providing a ready-to-use tool for biosurfactant production and enhancing the efficiency of pollutant extraction.

  nahABFEDG-phnC: A chimeric or fusion-designed genetic element that combines portions of the nah gene cluster responsible for naphthalene degradation from Pseudomonas putida G7 with the phnC gene from Burkholderia. The phnC gene enables the processing of intermediate metabolites that nahC cannot efficiently recognize, thus bridging a critical gap in the phenanthrene degradation pathway. This element exemplifies a strategy for pathway integration and optimization, offering a model for addressing "bottleneck" issues in natural degradation pathways. iGEM teams can draw from this design approach to combine genes from different sources, creating more efficient and complete metabolic pathways, particularly in the context of the degradation of polycyclic aromatic hydrocarbons or other complex organic compounds.

  nahABFEDG-nahC: A key gene cluster in naphthalene degradation, encodes a series of dioxygenases and isomerases responsible for converting naphthalene into intermediate products in the salicylic acid pathway. It serves as the first catalytic step in initiating the naphthalene degradation pathway. As a well-characterized and functionally defined degradation gene, nahABFEDG-nahC can serve as a foundational module for iGEM teams to construct naphthalene degradation pathways. Its standardization and reusability facilitate the rapid assembly of degradation systems, providing a solid platform for subsequent optimization or extension.

  phnS-P-R-EGFP: A reporting system, regulated by the phnS promoter (P) to control the expression of EGFP, can be used to sense phenanthrene (or its metabolites). When phenanthrene is present in the environment, the promoter is activated, leading to the expression of enhanced green fluorescent protein (EGFP), thereby enabling real-time visualization of the phenanthrene degradation process. This element provides iGEM teams with an environmental sensing and reporting tool for dynamically monitoring the degradation activity of engineered bacteria in contaminated environments. Such biosensor modules are valuable for assessing degradation efficiency, optimizing culture conditions, and enabling process monitoring in real-world applications, offering significant experimental and practical value.

  

2. Providing a Replicable "Cross-Species Gene Complementation + Shared Metabolic Cycle" Model

  Our project’s core design logic—using cross-species gene integration to complement functional defects and building a shared metabolic cycle for multiple pollutants—is a replicable model for future iGEM teams working on multi-pollutant biodegradation:

  Key principle: For pollutants with overlapping metabolic intermediates, such as various polycyclic aromatic hydrocarbons (PAHs) or other aromatic compounds, teams can follow a three-step approach: First, identify functional gene defects within individual degradation pathways, as demonstrated by our nahC defect in the naphthalene degradation pathway. Second, screen for complementary genes from other species that can fill in these gaps, as seen with our use of the phnC gene from Burkholderia. Third, integrate these complementary genes into a single chassis organism, creating a shared metabolic cycle capable of degrading multiple pollutants.

  Application example: A future team focusing on the co-degradation of anthracene (another PAH) and naphthalene could adopt our model by replacing the phnC gene with an anthracene-specific degradation gene, such as antC, which would complement defects in the anthracene degradation pathway. The team could then reuse our rhl and nahD-G parts to construct their integrated degradation system.

  This model reduces the need for teams to redesign entire systems from scratch, accelerating the development of environmental remediation projects.

  In summary, our wet lab contributions extend beyond individual parts. We deliver an integrated system and strategic insights for "debugging" and enhancing natural metabolic pathways, empowering the iGEM community to tackle environmental remediation challenges with greater precision and efficiency.

Human Practice

Building a Bridge Between Synthetic Biology and Public Perception Through Targeted Communication

  Our human practice efforts have always been guided by a core belief: scientific research should not exist in isolation but should interact with and serve society. Through targeted education (rural volunteer teaching, public science popularization events) and innovative promotional materials (brochures, posters, seed paper), we have achieved three core outcomes:

  1. Enhancing Public Scientific Literacy: We demystified synthetic biology and phenanthrene pollution, transforming obscure concepts into understandable knowledge—with a particular focus on groups with limited access to scientific resources, such as rural children and elementary school students.

  2. Promoting Public Action and Participation: By linking phenanthrene to daily life and providing practical solutions, we guided the public to shift from passive awareness to active concern. Meanwhile, interactive activities fostered a "sense of ownership" among the public in environmental protection.

  3. Verifying the Social Value of the Project: Based on feedback from events and materials, we optimized our communication strategies (e.g., further simplifying concepts for younger audiences) to ensure the project aligns with public needs and cognitive levels.

  Our work has proven that scientific innovation can only realize its maximum value when combined with effective communication and community engagement. We have not only increased public awareness of our project but also helped foster a "science-based environmental protection culture"—laying the groundwork for deeper collaboration between scientific research and society in the future.

Safety

  The research team will conduct rigorous screening and precise functional regulation of core genetic elements. Notably, all genetic fragments integrated into engineered E. coli are derived from microbial strains with well-characterized features and clear backgrounds, and their functions are strictly limited to promoting the degradation of polycyclic aromatic hydrocarbons (PAHs) without any redundant or unknown activities. This design not only fundamentally prevents the enhancement of microbial pathogenicity but also effectively eliminates the possibility of accidentally generating harmful traits, providing a solid guarantee for the safety of environmental applications.

  To ensure the safety of personnel operations, we strictly adhere to the standardized "training-before-experiment" procedure: All staff members must complete systematic theoretical knowledge training and safety specification assessments before entering the laboratory. After passing the assessments, they will receive one-on-one guidance from senior personnel with rich experimental experience to gradually familiarize themselves with the laboratory environment and operating procedures. This ensures that every step of the experimental operation complies with safety standards and minimizes operational risks to the greatest extent.