Biodegradation of PET Plastic: RNA-seq Analysis and Enzyme Discovery

Undergraduate thesis project combining bioinformatics and biology to identify enzymes involved in PET plastic biodegradation. RNA-seq pipeline, metabolic pathway analysis, and publication in IJMS.

Keywords

bioinformatics, RNA-seq, PET degradation, enzymes, biodegradation, plastic waste, Reed College, Willamette University, data wrangling

This project was the focus of my undergraduate thesis at Willamette University, conducted with Dr. Rosa León-Zayas and Grace Sheehan. The goal was to identify enzymes involved in the biodegradation of polyethylene terephthalate (PET) plastic using bioinformatics and RNA-seq analysis.

Workflow

1. Experimental design
   • Bacteria were exposed to PET plastic, and RNA was sequenced to capture gene expression changes.
2. Pipeline development
   • Built a custom RNA-seq pipeline for cleaning, alignment, and expression analysis (Fig. 1).
     
   • Ensured reproducibility and accuracy despite data loss in one control group.
3. Gene and enzyme analysis
   • Identified abnormal expression patterns linked to PET exposure.
     
   • Mapped expression results to protein and enzymatic functions.
4. Metabolic pathway reconstruction
   • Proposed a hypothetical pathway for PET degradation (Fig. 2).
     
   • Validated results against enzyme databases and literature.

Results

Through database searches, we found evidence of previously uncharacterized enzymes that may contribute to PET degradation. The metabolic pathways constructed from RNA-seq data showed promising targets for future biodegradation research.

Fig. 1 - RNA-seq pipeline and pathway reconstruction. Created with Biorender.

Fig. 2 - Proposed enzymatic pathway for PET degradation. A more complete pathway is described in the publication. Created with Biorender.

Discussion

This work resulted in a publication and a conference presentation:
- Presented at the Murdock College Science Research Conference
- Published in the International Journal of Molecular Sciences:
👉 Microbial Consortia and Mixed Plastic Waste: Pangenomic Analysis Reveals Potential for Degradation of Multiple Plastic Types via Previously Identified PET Degrading Bacteria

The findings suggest opportunities for developing natural waste treatment systems using bacteria, as well as the possibility of engineering organisms to synthesize new plastic polymers from waste.

Acknowledgments

This project was supported by the National Science Foundation (NSF), the Murdock Trust, and our collaborators at Reed College.

Oliver F. Anderson, MS – Computational Biologist, Data Scientist, and Research Consultant based in Portland, Oregon. I design data-driven solutions in bioinformatics, machine learning, and AI automation for research and biotech.