Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale

Deepanwita Banerjee, Thomas Eng, Andrew K. Lau, Yusuke Sasaki, Brenda Wang, Yan Chen, Jan Philip Prahl, Vasanth R. Singan, Robin A. Herbert, Yuzhong Liu, Deepti Tanjore, Christopher J. Petzold, Jay D. Keasling, Aindrila Mukhopadhyay*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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Abstract

High titer, rate, yield (TRY), and scalability are challenging metrics to achieve due to trade-offs between carbon use for growth and production. To achieve these metrics, we take the minimal cut set (MCS) approach that predicts metabolic reactions for elimination to couple metabolite production strongly with growth. We compute MCS solution-sets for a non-native product indigoidine, a sustainable pigment, in Pseudomonas putida KT2440, an emerging industrial microbe. From the 63 solution-sets, our omics guided process identifies one experimentally feasible solution requiring 14 simultaneous reaction interventions. We implement a total of 14 genes knockdowns using multiplex-CRISPRi. MCS-based solution shifts production from stationary to exponential phase. We achieve 25.6 g/L, 0.22 g/l/h, and ~50% maximum theoretical yield (0.33 g indigoidine/g glucose). These phenotypes are maintained from batch to fed-batch mode, and across scales (100-ml shake flasks, 250-ml ambr®, and 2-L bioreactors).
Original languageEnglish
Article number5385
JournalNature Communications
Volume11
Issue number1
Number of pages11
ISSN2041-1723
DOIs
Publication statusPublished - 2020

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