title: The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis.
abstract: By the time the complete genome sequence of the soil bacterium Pseudomonas putida KT2440 was published in 2002 (Nelson et al., ) this bacterium was considered a potential agent for environmental bioremediation of industrial waste and a good colonizer of the rhizosphere. However, neither the annotation tools available at that time nor the scarcely available omics data-let alone metabolic modeling and other nowadays common systems biology approaches-allowed them to anticipate the astonishing capacities that are encoded in the genetic complement of this unique microorganism. In this work we have adopted a suite of state-of-the-art genomic analysis tools to revisit the functional and metabolic information encoded in the chromosomal sequence of strain KT2440. We identified 242 new protein-coding genes and re-annotated the functions of 1548 genes, which are linked to almost 4900 PubMed references. Catabolic pathways for 92 compounds (carbon, nitrogen and phosphorus sources) that could not be accommodated by the previously constructed metabolic models were also predicted. The resulting examination not only accounts for some of the known stress tolerance traits known in P. putida but also recognizes the capacity of this bacterium to perform difficult redox reactions, thereby multiplying its value as a platform microorganism for industrial biotechnology.
authors.affiliation: Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism, 2 rue Gaston Crémieux, 91057, Evry, France. eugeni.belda-cuesta@pasteur.fr.|Institut Pasteur, Unit of Insect Vector Genetics and Genomics, Department of Parasitology and Mycology, 28, rue du Dr. Roux, Paris, Cedex 15, 75724, France. eugeni.belda-cuesta@pasteur.fr.
authors.forename: Eugeni
authors.initials: E
authors.lastname: Belda
authors.affiliation: Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, Building number 316, 6703, HB, Wageningen, The Netherlands.
authors.forename: Ruben G A
authors.initials: RG
authors.lastname: van Heck
authors.affiliation: Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism, 2 rue Gaston Crémieux, 91057, Evry, France.|AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France.
authors.forename: Maria
authors.initials: M
authors.lastname: José Lopez-Sanchez
authors.affiliation: Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism, 2 rue Gaston Crémieux, 91057, Evry, France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Cruveiller
authors.affiliation: Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute, National Sequencing Center, 2 rue Gaston Crémieux, 91057, Evry, France.
authors.forename: Valérie
authors.initials: V
authors.lastname: Barbe
authors.affiliation: Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
authors.forename: Claire
authors.initials: C
authors.lastname: Fraser
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.|School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Klenk
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
authors.forename: Jörn
authors.initials: J
authors.lastname: Petersen
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, CH-1206, Switzerland.
authors.forename: Anne
authors.initials: A
authors.lastname: Morgat
authors.affiliation: Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), C/Darwin 3, 28049, Madrid, Spain.
authors.forename: Pablo I
authors.initials: PI
authors.lastname: Nikel
authors.affiliation: Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism, 2 rue Gaston Crémieux, 91057, Evry, France.
authors.forename: David
authors.initials: D
authors.lastname: Vallenet
authors.affiliation: Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism, 2 rue Gaston Crémieux, 91057, Evry, France.
authors.forename: Zoé
authors.initials: Z
authors.lastname: Rouy
authors.affiliation: AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France.
authors.forename: Agnieszka
authors.initials: A
authors.lastname: Sekowska
authors.affiliation: Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, Building number 316, 6703, HB, Wageningen, The Netherlands.
authors.forename: Vitor A P
authors.initials: VA
authors.lastname: Martins Dos Santos
authors.affiliation: Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), C/Darwin 3, 28049, Madrid, Spain.
authors.forename: Víctor
authors.initials: V
authors.lastname: de Lorenzo
authors.affiliation: AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France.
authors.forename: Antoine
authors.initials: A
authors.lastname: Danchin
authors.affiliation: Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism, 2 rue Gaston Crémieux, 91057, Evry, France.
authors.forename: Claudine
authors.initials: C
authors.lastname: Médigue
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D002244:Carbon / Q000378:metabolism; D016680:Genome, Bacterial; D023281:Genomics; D009584:Nitrogen / Q000378:metabolism; D016958:Pseudomonas putida / Q000235:genetics* / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D002244:Carbon; D009584:Nitrogen