Multi-omics analysis unravels a segregated metabolic flux network that tunes co-utilization of sugar and aromatic carbons in Pseudomonas putida

Authors: KYKURUGYA, MENDONCA - Cornell University; MENDONCA, C - Cornell University; SOLHTALAB, M - Cornell University; WILKINES, R - Cornell University; Thannhauser, Theodore - Ted; ARISTILDE, L - Cornell University

Submitted to: Journal of Biological Chemistry
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/26/2019
Publication Date: 4/1/2019
Citation: Kykurugya, M.M., Mendonca, C.M., Solhtalab, M., Wilkines, R.A., Thannhauser, T.W., Aristilde, L. 2019. Multi-omics analysis unravels a segregated metabolic flux network that tunes co-utilization of sugar and aromatic carbons in Pseudomonas putida. International Journal of Polymer Science. 1-16. https://doi.org/10.1074/jbc.RA119.007885.
DOI: https://doi.org/10.1074/jbc.RA119.007885

Interpretive Summary: Different Pseudomonas species grow well in different nutritional environments and can break down and utilize different carbon containing compounds to thrive. This ability has important consequences for their role natural processes but also in their potential use in bio-engineered industrial processing of carbon. Unfortunately, the metabolic processes that enable Pseudomonads to utilize mixed substrates remain poorly understood. Therefore, in this study we used a multi-discipline approach to investigate the metabolic networks involved in the simultaneous use of two distinct carbon sources. The insights gained add to our understanding of the diverse metabolic capabilities of this class of bacteria and suggest that they may be useful as attractive bacterial “cell factories” in various industrial applications.

Technical Abstract: Pseudomonas species thrive in different nutritional environments and can catabolize divergent carbon substrates. These capabilities have important implications for the role of these species in natural and engineered carbon processing. However, the metabolic phenotypes enabling Pseudomonas to utilize mixed substrates remain poorly understood. Here, we employed a multi-omics approach involving stable isotope tracers, metabolomics, fluxomics, and proteomics in Pseudomonas putida KT2440 to investigate the constitutive metabolic network that achieves co-utilization of glucose and benzoate, respectively a monomer of carbohydrate polymers and a derivative of lignin monomers. Despite nearly equal consumption of both substrates, metabolite isotopologues revealed nonuniform assimilation throughout the metabolic network. Gluconeogenic flux of benzoate-derived carbons from the tricarboxylic acid cycle did not reach the upper Embden–Meyerhof–Parnas pathway nor the pentose–phosphate pathway. These latter two pathways were populated exclusively by glucose-derived carbons through a cyclic connection with the Entner–Doudoroff pathway. We integrated the 13C-metabolomics data with physiological parameters for quantitative flux analysis, demonstrating that the metabolic segregation of the substrate carbons optimally sustained biosynthetic flux demands and redox balance. Changes in protein abundance partially predicted the metabolic flux changes in cells grown on the glucose: benzoate mixture versus on glucose alone. Notably, flux magnitude and directionality were also maintained by metabolite levels and regulation of phosphorylation of key metabolic enzymes. These findings provide new insights into the metabolic architecture that affords adaptability of P. putida to divergent carbon substrates and highlight regulatory points at different metabolic nodes that may underlie the high nutritional flexibility of Pseudomonas species