Ensemble and Iterative Engineering for Maximized Bioconversion to the Blue Pigment, Indigoidine from Non-Canonical Sustainable Carbon Sources

Eng, T. T.; Banerjee, D.; Menasalvas, J.; Chen, Y.; Gin, J.; Choudhary, H.; Baidoo, E.; Chen, J. H.; Ekman, A.; Kakumanu, R.; Diercks, Y. L.; Codik, A.; Larabell, C.; Gladden, J.; Simmons, B. A.; Keasling, J. D.; Petzold, C. J.; Mukhopadhyay, A.

doi:10.1101/2023.03.16.532821

bioRxiv · 10.1101/2023.03.16.532821

Ensemble and Iterative Engineering for Maximized Bioconversion to the Blue Pigment, Indigoidine from Non-Canonical Sustainable Carbon Sources

Eng, T. T.·Banerjee, D.·Menasalvas, J.·Chen, Y.·Gin, J.·Choudhary, H.·Baidoo, E.·Chen, J. H.·Ekman, A.·Kakumanu, R.·Diercks, Y. L.·Codik, A.·Larabell, C.·Gladden, J.·Simmons, B. A.·Keasling, J. D.·Petzold, C. J.·Mukhopadhyay, A.

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Abstract

While many heterologous molecules can be produced via microbial bioconversion processes, maximizing their titers, rates, and yields from lignin-derived carbon streams remains challenging. Growth coupling can not only increase titers and yields but also shift the production period from stationary phase to growth phase. These methods for designing growth-coupling strains however require multi-gene edits for implementation which may be perceived as impractical. Here, we computationally evaluated 4,114 potential solutions for growth coupling para-coumarate to indigoidine production and prototype two cut sets in Pseudomonas putida KT2440. We used adaptive laboratory evolution (ALE) on the initial triple deletion strain to restore growth on p-CA. Using X-ray tomography on this post-ALE strain we revealed increased cell density and decreased cell volume. Proteomics identified upregulated peroxidases that mitigate reactive oxygen species formation. Nine iterative stepwise modifications further informed by model-guided and rational approaches realized a growth coupled strain that produced 7.3 g/L indigoidine at 77% MTY in para-coumarate minimal medium. These ensemble strategies provide a blueprint for producing target molecules at high product titers, rates, and yields. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/532821v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@f0754aorg.highwire.dtl.DTLVardef@a45d24org.highwire.dtl.DTLVardef@df0596org.highwire.dtl.DTLVardef@1e7e140_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Eng, T. T., Banerjee, D., Menasalvas, J., Chen, Y., Gin, J., Choudhary, H., Baidoo, E., Chen, J. H., Ekman, A., Kakumanu, R., Diercks, Y. L., Codik, A., Larabell, C., Gladden, J., Simmons, B. A., Keasling, J. D., Petzold, C. J., Mukhopadhyay, A.. 2023-03-20. Ensemble and Iterative Engineering for Maximized Bioconversion to the Blue Pigment, Indigoidine from Non-Canonical Sustainable Carbon Sources. https://doi.org/10.1101/2023.03.16.532821

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