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High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities
Author(s) -
Nogales Juan,
Mueller Joshua,
Gudmundsson Steinn,
Canalejo Francisco J.,
Duque Estrella,
Monk Jonathan,
Feist Adam M.,
Ramos Juan Luis,
Niu Wei,
Palsson Bernhard O.
Publication year - 2020
Publication title -
environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.954
H-Index - 188
eISSN - 1462-2920
pISSN - 1462-2912
DOI - 10.1111/1462-2920.14843
Subject(s) - pseudomonas putida , biology , computational biology , metabolic network , genome , metabolic pathway , metabolomics , metabolic engineering , gene , genetics , bioinformatics
Summary 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, i JN1462 (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 .