Genome-scale metabolic rewiring to improve titers, rates and yields of the non-native non-ribosomal peptide product indigoidine at scale

High titer, rates, yields (TRY) and scalability are challenging metrics to achieve due to trade-offs between carbon use for growth and production. To achieve these metrics, we took the minimal cut set (MCS) approach that predicts metabolic reactions for elimination to couple metabolite production strongly with growth. We computed MCS solution-sets for a non-native product indigoidine, a sustainable pigment, in Pseudomonas putida KT2440, an emerging industrial microbe. From 63 computed solution-sets, our -omics guided process identified one experimentally feasible solution requiring 14 simultaneous reaction interventions. Using multiplex-CRISPRi, this is the first experimental implementation of a 14-gene MCS-based solution that shifted production from stationary to exponential phase. We achieved 25.6 g/L, 0.22 g/l/h, and ~50% maximum theoretical yield (0.33 g indigoidine/g glucose) TRY respectively. These phenotypes were maintained from batch to fed-batch mode, and across scales (100-ml shake flasks, 250-ml ambr® and 2-L bioreactors).