ArticleNature communications2020
Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
- Growth-coupled microbial biosynthesis of the animal pigment xanthommatin.Nature biotechnology · 2026Article
- Simultaneous optimization of lignocellulosic sugar catabolism via systematic laboratory evolution under complex selection pressure.Nature communications · 2026Article
- A Novel Indigoidine-like NRPS Gene fromAntioxidants (Basel, Switzerland) · 2026Article
- Cross-Strain Transferability of CRISPRi Systems and Design Rules from Laboratory to ClinicalACS synthetic biology · 2026Article
- Cross-strain transferability of CRISPRi systems and design rules from laboratory to clinicalbioRxiv : the preprint server for biology · 2026Article
- Advances in natural product discovery: strategies, technologies, and insights.Natural products and bioprospecting · 2026Review
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- Biosensor-driven strain engineering reveals key cellular processes for maximizing isoprenol production inScience advances · 2025Article
- RB-TnSeq elucidates dicarboxylic-acid-specific catabolism in β-proteobacteria for improved plastic monomer upcycling.Applied and environmental microbiology · 2025Article
- Balancing Cell Growth and Product Synthesis for Efficient Microbial Cell Factories.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- FluxRETAP: a REaction TArget Prioritization genome-scale modeling technique for selecting genetic targets.Bioinformatics (Oxford, England) · 2025Article
- Alternate routes to acetate tolerance lead to varied isoprenol production from mixed carbon sources inApplied and environmental microbiology · 2025Article
- A rapid and efficient strategy for combinatorial repression of multiple genes in Escherichia coli.Microbial cell factories · 2025Article
- Minimal cut sets in metabolic networks: from conceptual foundations to applications in metabolic engineering and biomedicine.Briefings in bioinformatics · 2025Review
- Microbial Pathways for Cost-Effective Low-Carbon Renewable Indigoidine.ACS sustainable chemistry & engineering · 2025Article
- Mitigating genetic instability caused by the excision activity of theApplied and environmental microbiology · 2025Article
- Addressing genome scale design tradeoffs in Pseudomonas putida for bioconversion of an aromatic carbon source.NPJ systems biology and applications · 2025Article
- Unraveling the metabolic landscape of Exophiala spinifera strain FM: Model reconstruction, insights into biodesulfurization and beyond.PloS one · 2025Article
- A versatile microbial platform as a tunable whole-cell chemical sensor.Nature communications · 2024Article
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
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).
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.