High-quality genome-scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities

Juan Nogales, Joshua Mueller, Steinn Gudmundsson, Francisco J. Canalejo, Estrella Duque, Jonathan Monk, Adam M. Feist, Juan Luis Ramos, Wei Niu, Bernhard O. Palsson

Research output: Contribution to journalArticle

22 Scopus citations

Abstract

Genome-scale reconstructions of metabolism are computational species-specific knowledge bases able to compute systemic metabolic properties. We present a comprehensive and validated reconstruction of the biotechnologically relevant bacterium Pseudomonas putida KT2440 that greatly expands computable predictions of its metabolic states. The reconstruction represents a significant reactome expansion over available reconstructed bacterial metabolic networks. Specifically, iJN1462 (i) incorporates several hundred additional genes and associated reactions resulting in new predictive capabilities, including new nutrients supporting growth; (ii) was validated by in vivo growth screens that included previously untested carbon (48) and nitrogen (41) sources; (iii) yielded gene essentiality predictions showing large accuracy when compared with a knock-out library and Bar-seq data; and (iv) allowed mapping of its network to 82 P. putida sequenced strains revealing functional core that reflect the large metabolic versatility of this species, including aromatic compounds derived from lignin. Thus, this study provides a thoroughly updated metabolic reconstruction and new computable phenotypes for P. putida, which can be leveraged as a first step toward understanding the pan metabolic capabilities of Pseudomonas.

Original languageEnglish (US)
Pages (from-to)255-269
Number of pages15
JournalEnvironmental microbiology
Volume22
Issue number1
DOIs
StatePublished - Jan 1 2020

ASJC Scopus subject areas

  • Microbiology
  • Ecology, Evolution, Behavior and Systematics

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    Nogales, J., Mueller, J., Gudmundsson, S., Canalejo, F. J., Duque, E., Monk, J., Feist, A. M., Ramos, J. L., Niu, W., & Palsson, B. O. (2020). High-quality genome-scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities. Environmental microbiology, 22(1), 255-269. https://doi.org/10.1111/1462-2920.14843