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The metabolic response of P. putida KT2442 producing high levels of polyhydroxyalkanoate under single- and multiple-nutrient-limited growth: Highlights from a multi-level omics approach

Ignacio Poblete-Castro15*, Isabel F Escapa2, Christian Jäger3, Jacek Puchalka1, Carolyn Ming Chi Lam1, Dietmar Schomburg3, María Auxiliadora Prieto2 and Vítor AP Martins dos Santos14

Author Affiliations

1 Systems and Synthetic Biology Group, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany

2 Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, c/Ramiro de Maeztu 9, 28040 Madrid, Spain

3 Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Langer Kamp 19B, 38106 Braunschweig, Germany

4 Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, Building number 316, 6703 HB, Wageningen, The Netherlands

5 Department of Loss Risk and Environmental Science, Universidad Tecnológica Metropolitana, Dieciocho 390, Santiago, Chile

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Microbial Cell Factories 2012, 11:34  doi:10.1186/1475-2859-11-34

Published: 20 March 2012

Abstract

Background

Pseudomonas putida KT2442 is a natural producer of polyhydroxyalkanoates (PHAs), which can substitute petroleum-based non-renewable plastics and form the basis for the production of tailor-made biopolymers. However, despite the substantial body of work on PHA production by P. putida strains, it is not yet clear how the bacterium re-arranges its whole metabolism when it senses the limitation of nitrogen and the excess of fatty acids as carbon source, to result in a large accumulation of PHAs within the cell. In the present study we investigated the metabolic response of KT2442 using a systems biology approach to highlight the differences between single- and multiple-nutrient-limited growth in chemostat cultures.

Results

We found that 26, 62, and 81% of the cell dry weight consist of PHA under conditions of carbon, dual, and nitrogen limitation, respectively. Under nitrogen limitation a specific PHA production rate of 0.43 (g·(g·h)-1) was obtained. The residual biomass was not constant for dual- and strict nitrogen-limiting growth, showing a different feature in comparison to other P. putida strains. Dual limitation resulted in patterns of gene expression, protein level, and metabolite concentrations that substantially differ from those observed under exclusive carbon or nitrogen limitation. The most pronounced differences were found in the energy metabolism, fatty acid metabolism, as well as stress proteins and enzymes belonging to the transport system.

Conclusion

This is the first study where the interrelationship between nutrient limitations and PHA synthesis has been investigated under well-controlled conditions using a system level approach. The knowledge generated will be of great assistance for the development of bioprocesses and further metabolic engineering work in this versatile organism to both enhance and diversify the industrial production of PHAs.

Keywords:
P. putida KT2442; Nutrient limitation; Systems biology; Polyhydroxyalkanoates