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 and Aindrila Mukhopadhyay ()
Additional contact information
Deepanwita Banerjee: Lawrence Berkeley National Laboratory
Thomas Eng: Lawrence Berkeley National Laboratory
Andrew K. Lau: Lawrence Berkeley National Laboratory
Yusuke Sasaki: Lawrence Berkeley National Laboratory
Brenda Wang: Lawrence Berkeley National Laboratory
Yan Chen: Lawrence Berkeley National Laboratory
Jan-Philip Prahl: Lawrence Berkeley National Laboratory
Vasanth R. Singan: Lawrence Berkeley National Laboratory
Robin A. Herbert: Lawrence Berkeley National Laboratory
Yuzhong Liu: Lawrence Berkeley National Laboratory
Deepti Tanjore: Lawrence Berkeley National Laboratory
Christopher J. Petzold: Lawrence Berkeley National Laboratory
Jay D. Keasling: Lawrence Berkeley National Laboratory
Aindrila Mukhopadhyay: Lawrence Berkeley National Laboratory

Nature Communications, 2020, vol. 11, issue 1, 1-11

Abstract: 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).

Date: 2020
References: Add references at CitEc
Citations: View citations in EconPapers (2)

Downloads: (external link)
https://www.nature.com/articles/s41467-020-19171-4 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-19171-4

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-020-19171-4

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().