In silico genome‐scale metabolic analysis of Pseudomonas putida KT2440 for polyhydroxyalkanoate synthesis, degradation of aromatics and anaerobic survival

Abstract

Genome-scale metabolic models have been appearing with increasing frequency and have been employed in a wide range of biotechnological applications as well as in biological studies. With the metabolic model as a platform, engineering strategies have become more systematic and focused, unlike the random shotgun approach used in the past. Here we present the genome-scale metabolic model of the versatile Gram-negative bacterium Pseudomonas putida, which has gained widespread interest for various biotechnological applications. With the construction of the genome-scale metabolic model of P. putida KT2440, PpuMBEL1071, we investigated various characteristics of P. putida, such as its capacity for synthesizing polyhydroxyalkanoates (PHA) and degrading aromatics. Although P. putida has been characterized as a strict aerobic bacterium, the physiological characteristics required to achieve anaerobic survival were investigated. Through analysis of PpuMBEL1071, extended survival of P. putida under anaerobic stress was achieved by introducing the ackA gene from Pseudomonas aeruginosa and Escherichia coli.

iSCHRUNK – In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks

“…Genome--scale stoichiometric models (GEMs) of metabolism are now widely available for many organisms (Henry et al, 2010;Herrgard et al, 2008;Orth et al, 2011;Osterlund et al, 2013;Sohn et al, 2010;Thiele et al, 2013) and they have been used in studies of cellular physiology and metabolic engineering (Asadollahi et al, 2009;Borodina et al, 2015;Bro et al, 2006;Dash et al, 2014;King and Feist, 2014;Snitkin et al, 2008). However, these models are not suitable for predicting the responses of metabolism to changes in enzyme expression because they are lacking information about enzyme kinetics (Miskovic and Hatzimanikatis, 2010).…”

Pseudomonas putida KT2440 Strain Metabolizes Glucose through a Cycle Formed by Enzymes of the Entner-Doudoroff, Embden-Meyerhof-Parnas, and Pentose Phosphate Pathways

“…Currently available metabolic models of P. putida KT2440, based on genome annotations, entertain a simple top-down operation of a linear ED pathway (17)(18)(19). Yet, the co-existence of a complete ED route along with a partial EMP route and three alternative possibilities for glucose uptake (Fig.…”

Mathematical Modelling as a Tool for Optimized PHA Production

“…For further information, the reader should consult the cited reference 101 . The same strain was also investigated by Sohn et al 102 . Various characteristics of P. putida KT2440, such as capacity for PHA synthesis and degradation of aromatics were investigated using the constructed genome scale metabolic model (PpuMBEL1071).…”