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bioRxiv · 10.1101/2025.03.18.643695

Biosensor-Driven Strain Engineering Reveals Key Cellular Processes for Maximizing Isoprenol Production in Pseudomonas putida

Menasalvas, J.·Kulakowski, S.·Chen, Y.·Gin, J. W.·Turumtay, E. A.·Apolonio, M. A.·Baral, N. R.·Rivier, A.·Yunus, I. S.·Garber, M. E.·Scown, C. D.·Adams, P. D.·Lee, T. S.·Blaby, I. K.·Baidoo, E. E. K.·Petzold, C. J.·Eng, T.·Mukhopadhyay, A.
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Abstract

Synthetic biology tools have accelerated the generation of simple mutants, but combinatorial testing remains challenging. High-throughput methods struggle translating from proof-of-principle molecules to advanced bioproducts. We address this challenge with a biosensor-driven strategy for enhanced isoprenol production in Pseudomonas putida, a key precursor for sustainable aviation fuel and platform chemicals. This biosensor leverages P. putidas native response to short-chain alcohols via a previously uncharacterized hybrid histidine kinase signaling cascade. Refactoring the biosensor for a conditional growth-based selection enabled identification of competing cellular processes with a [~]16,500-member CRISPRi-library. An iterative combinatorial strain engineering approach yielded an integrated P. putida strain producing [~]900 mg/L isoprenol in glucose minimal medium, a 36-fold increase. Ensemble -omics analysis revealed metabolic rewiring, including amino acid accumulation as key drivers of enhanced production. Techno-economic analysis elucidated the path to economic viability and confirmed the benefits of adding amino acids outweigh the additional costs. This study establishes a robust biosensor driven approach for optimizing other heterologous pathways, accelerating microbial cell factory development. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/643695v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@533605org.highwire.dtl.DTLVardef@ff98fforg.highwire.dtl.DTLVardef@9592fdorg.highwire.dtl.DTLVardef@1e52993_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Menasalvas, J., Kulakowski, S., Chen, Y., Gin, J. W., Turumtay, E. A., Apolonio, M. A., Baral, N. R., Rivier, A., Yunus, I. S., Garber, M. E., Scown, C. D., Adams, P. D., Lee, T. S., Blaby, I. K., Baidoo, E. E. K., Petzold, C. J., Eng, T., Mukhopadhyay, A.. 2025-03-18. Biosensor-Driven Strain Engineering Reveals Key Cellular Processes for Maximizing Isoprenol Production in Pseudomonas putida. https://doi.org/10.1101/2025.03.18.643695

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