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

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

doi:10.1111/1462-2920.14843

Title: High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities

Journal Article · Mon Nov 11 00:00:00 EST 2019 · Environmental Microbiology

DOI:https://doi.org/10.1111/1462-2920.14843· OSTI ID:1574030

^[1]; Mueller, Joshua ^[2]; Gudmundsson, Steinn ^[3]; Canalejo, Francisco J. ^[4]; Duque, Estrella ^[5]; Monk, Jonathan ^[6]; Feist, Adam M. ^[6];

^[5]; Niu, Wei ^[7]; Palsson, Bernhard O. ^[6]

Department of Systems Biology Centro Nacional de Biotecnología (CNB‐CSIC) Madrid Spain, Department of Bioengineering University of California, San Diego La Jolla CA USA
Department of Bioengineering University of California, San Diego La Jolla CA USA, Department of Chemical and Biomolecular Engineering University of Nebraska‐Lincoln Lincoln NE USA
Center for Systems Biology, University of Iceland Reykjavík Iceland
Department of Systems Biology Centro Nacional de Biotecnología (CNB‐CSIC) Madrid Spain
Department of Environmental Protection Estación Experimental del Zaidín (CSIC) Granada Spain
Department of Bioengineering University of California, San Diego La Jolla CA USA
Department of Chemical and Biomolecular Engineering University of Nebraska‐Lincoln Lincoln NE USA

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 .

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: DE‐AC02‐05CH11231; AC02-05CH11231

OSTI ID:: 1574030

Alternate ID(s):: OSTI ID: 1574031; OSTI ID: 1625852

Journal Information:: Environmental Microbiology, Journal Name: Environmental Microbiology Vol. 22 Journal Issue: 1; ISSN 1462-2912

Publisher:: Wiley-BlackwellCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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Cited by: 71 works

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