Functional genomics in a microbe that degrades and metabolizes PET plastic

Crits-Christoph, A.; Leung, J.; Piedra, F.-A.; Brumwell, S. L.; Sajtovich, V. A.; Abrams, M. B.; Esmurria, A.; Kang, S. C.; Mendler, K.; Gilbert, C.; Lee, H. H.; Ostrov, N.

doi:10.1101/2025.11.11.687616

bioRxiv · 10.1101/2025.11.11.687616

Functional genomics in a microbe that degrades and metabolizes PET plastic

Crits-Christoph, A.·Leung, J.·Piedra, F.-A.·Brumwell, S. L.·Sajtovich, V. A.·Abrams, M. B.·Esmurria, A.·Kang, S. C.·Mendler, K.·Gilbert, C.·Lee, H. H.·Ostrov, N.

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Abstract

Piscinibacter sakaiensis (formerly Ideonella sakaiensis) was the first bacterial species known to both completely degrade and assimilate polyethylene terephthalate (PET). However, the absence of efficient genetic tools has limited direct engineering of this organism, forcing most efforts to rely on heterologous expression of PET-degrading enzymes in model hosts. Here, we establish foundational genetic tools to engineer P. sakaiensis. We identify a functional plasmid origin of replication, multiple new selectable markers, and a transposon system for the strain. We use these tools to construct a genome-wide, barcoded transposon mutant library for pooled high-throughput functional screens. We apply this mutant library to growth on PET and identify metabolic and physiological genes that impact PET biodegradation. We also use this library to reveal mutants with improved DNA uptake for genome engineering. Together, these advances provide a platform for functional genomics in P. sakaiensis and positions this naturally evolved plastic-degrading bacterium as an engineerable chassis for synthetic biology and sustainable materials research.

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Crits-Christoph, A., Leung, J., Piedra, F.-A., Brumwell, S. L., Sajtovich, V. A., Abrams, M. B., Esmurria, A., Kang, S. C., Mendler, K., Gilbert, C., Lee, H. H., Ostrov, N.. 2025-11-11. Functional genomics in a microbe that degrades and metabolizes PET plastic. https://doi.org/10.1101/2025.11.11.687616

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