Dynamics of benzoate metabolism in Pseudomonas putida KT2440

Metabolic Engineering Communications
Suresh SudarsanMatthias Reuss

Abstract

Soil microorganisms mineralize lignin-derived aromatic carbon sources using oxidative catabolic pathways, such as the β-ketoadipate pathway. Although this aromatic pathway is one of the best-studied pathways in biochemistry, the complete pathway, including its regulation by aromatic carbon sources, has not been integrated into the metabolic network. In particular, information about the in vivo operation (e.g., kinetics and flux capacity) of the pathway is lacking. In this contribution, we use kinetic modeling and thermodynamic analysis to evaluate the in vivo operation of this key aromatic multi-step pathway. The resulting ab initio deterministic model of benzoate degradation via the β-ketoadipate (ortho-cleavage) pathway in Pseudomonas putida KT2440 is presented. The kinetic model includes mechanistic rate expressions for the enzymes and transport processes. The design and experimental validation of the model are driven by data generated from short-term perturbation experiments in a benzoate-limited continuous culture. The results of rigorous modeling of the in vivo dynamics provide strong support for flux regulation by the benzoate transporter and the enzymes forming and cleaving catechol. Revisiting the β-ketoadipate pathway...Continue Reading

Citations

Mar 17, 2017·Applied Microbiology and Biotechnology·Krithika RaviGunnar Lidén
Dec 29, 2020·Current Opinion in Biotechnology·Charles J FosterCostas D Maranas
Jan 12, 2021·Frontiers in Bioengineering and Biotechnology·Yuqian GaoKristin E Burnum-Johnson
Apr 1, 2021·Biotechnology Advances·Maria Martin-PascualVitor A P Martins Dos Santos
Jun 15, 2021·Frontiers in Bioengineering and Biotechnology·Lakshika Dissanayake, Lahiru N Jayakody
Jul 6, 2021·Essays in Biochemistry·Nora Lisa BitzenhoferAnita Loeschcke

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Methods Mentioned

BETA
PCA

Software Mentioned

LINDO API
FiatFlux
NETTO
SBPD
anNET
MATLAB function fmincon
NET
SBtoolbox2
Matlab

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