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

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.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.Microorganisms constantly face fluctuations of nutrient concentrations in their natural environments. One of the common evoked responses by bacteria is the storage of carbon and energy sources, as shown by the considerable increase in the accumulation of various compounds, such as glycogen, polyesters, and polyphosphates etc. [1]. The primary feature of these compounds is that they can be readily degraded by the cell to satisfy metabolic demands, thus ensuring its survival during famine. Pseudomonas putida KT2440 is a metabolically versatile bacterium [2] normally found in aerobic and semi-aerobic soil and water habitats [3], which has become an efficient cell factory for the biotechnological production of value-added compounds [4]. It synthesizes medium-chain-length polyhydroxyalkanoate (PHA) that exhibit different physical properties th