TY  - JOUR
A1  - Pereira, Filipa
A1  - Lopes, Helder
A1  - Maia, Paulo
A1  - Meyer, Britta
A1  - Nocon, Justyna
A1  - Jouhten, Paula
A1  - Konstantinidis, Dimitrios
A1  - Kafkia, Eleni
A1  - Rocha, Miguel
A1  - Kötter, Peter
A1  - Rocha, Isabel
A1  - Patil, Kiran Raosaheb
T1  - Model-guided development of an evolutionarily stable yeast chassis
T2  - Molecular systems biology
N2  - First-principle metabolic modelling holds potential for designing microbial chassis that are resilient against phenotype reversal due to adaptive mutations. Yet, the theory of model-based chassis design has rarely been put to rigorous experimental test. Here, we report the development of Saccharomyces cerevisiae chassis strains for dicarboxylic acid production using genome-scale metabolic modelling. The chassis strains, albeit geared for higher flux towards succinate, fumarate and malate, do not appreciably secrete these metabolites. As predicted by the model, introducing product-specific TCA cycle disruptions resulted in the secretion of the corresponding acid. Adaptive laboratory evolution further improved production of succinate and fumarate, demonstrating the evolutionary robustness of the engineered cells. In the case of malate, multi-omics analysis revealed a flux bypass at peroxisomal malate dehydrogenase that was missing in the yeast metabolic model. In all three cases, flux balance analysis integrating transcriptomics, proteomics and metabolomics data confirmed the flux re-routing predicted by the model. Taken together, our modelling and experimental results have implications for the computer-aided design of microbial cell factories.
KW  - adaptive laboratory evolution
KW  - chassis cell
KW  - metabolic engineering
KW  - multi-objective optimization
KW  - systems biology
Y1  - 2021
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/62821
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-628217
SN  - 1744-4292
N1  - Corresponding author: Rocha, Isabel; Tel: +351 214469608; E-mail: irocha@itqb.unl.pt
Corresponding author: Patil, Kiran Raosaheb; Tel: +44 1223 3 35640; E-mail: kp533@cam.ac.uk
N1  - This study was supported by national funds through FCT/MCTES (Portugal, Ref. ERA-IB-2/0003/2013) and BMBF (Germany, Grant number: 031A343A, Ref. ERA-IB-2/0003/2013). The Portuguese Foundation for Science and Technology (FCT) supported HL through grant ref. PD/BD/52336/2013. FCT also supported this study under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684) and through the Project RECI/BBB-EBI/0179/2012 (FCOMP-01-0124-FEDER-027462). Open Access funding enabled and organized by Projekt DEAL.
VL  - 17
IS  - 7, art. e10253
SP  - 1
EP  - 18
PB  - EMBO Press
CY  - Heidelberg
ER  -