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

Authors:
ORCiD logo [1];  [2];  [3];  [4];  [5];  [6];  [6]; ORCiD logo [5];  [7];  [6]
  1. Department of Systems BiologyCentro Nacional de Biotecnología (CNB‐CSIC) Madrid Spain, Department of BioengineeringUniversity of California, San Diego La Jolla CA USA
  2. Department of BioengineeringUniversity of California, San Diego La Jolla CA USA, Department of Chemical and Biomolecular EngineeringUniversity of Nebraska‐Lincoln Lincoln NE USA
  3. Center for Systems Biology, University of Iceland Reykjavík Iceland
  4. Department of Systems BiologyCentro Nacional de Biotecnología (CNB‐CSIC) Madrid Spain
  5. Department of Environmental ProtectionEstación Experimental del Zaidín (CSIC) Granada Spain
  6. Department of BioengineeringUniversity of California, San Diego La Jolla CA USA
  7. Department of Chemical and Biomolecular EngineeringUniversity of Nebraska‐Lincoln Lincoln NE USA
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1574030
Alternate Identifier(s):
OSTI ID: 1574031
Grant/Contract Number:  
DE‐AC02‐05CH11231
Resource Type:
Published Article
Journal Name:
Environmental Microbiology
Additional Journal Information:
Journal Name: Environmental Microbiology; Journal ID: ISSN 1462-2912
Publisher:
Wiley-Blackwell
Country of Publication:
United Kingdom
Language:
English

Citation Formats

Nogales, Juan, Mueller, Joshua, Gudmundsson, Steinn, Canalejo, Francisco J., Duque, Estrella, Monk, Jonathan, Feist, Adam M., Ramos, Juan Luis, Niu, Wei, and Palsson, Bernhard O. High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities. United Kingdom: N. p., 2019. Web. doi:10.1111/1462-2920.14843.
Nogales, Juan, Mueller, Joshua, Gudmundsson, Steinn, Canalejo, Francisco J., Duque, Estrella, Monk, Jonathan, Feist, Adam M., Ramos, Juan Luis, Niu, Wei, & Palsson, Bernhard O. High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities. United Kingdom. doi:10.1111/1462-2920.14843.
Nogales, Juan, Mueller, Joshua, Gudmundsson, Steinn, Canalejo, Francisco J., Duque, Estrella, Monk, Jonathan, Feist, Adam M., Ramos, Juan Luis, Niu, Wei, and Palsson, Bernhard O. Mon . "High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities". United Kingdom. doi:10.1111/1462-2920.14843.
@article{osti_1574030,
title = {High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities},
author = {Nogales, Juan and Mueller, Joshua and Gudmundsson, Steinn and Canalejo, Francisco J. and Duque, Estrella and Monk, Jonathan and Feist, Adam M. and Ramos, Juan Luis and Niu, Wei and Palsson, Bernhard O.},
abstractNote = {},
doi = {10.1111/1462-2920.14843},
journal = {Environmental Microbiology},
number = ,
volume = ,
place = {United Kingdom},
year = {2019},
month = {11}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1111/1462-2920.14843

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Works referenced in this record:

Convergent Peripheral Pathways Catalyze Initial Glucose Catabolism in Pseudomonas putida: Genomic and Flux Analysis
journal, May 2007

  • del Castillo, T.; Ramos, J. L.; Rodriguez-Herva, J. J.
  • Journal of Bacteriology, Vol. 189, Issue 14
  • DOI: 10.1128/JB.00203-07

Large-Scale Evaluation of In Silico Gene Deletions in Saccharomyces cerevisiae
journal, July 2003

  • Förster, Jochen; Famili, Iman; Palsson, Bernhard Ø.
  • OMICS: A Journal of Integrative Biology, Vol. 7, Issue 2
  • DOI: 10.1089/153623103322246584

Pseudomonas putida—a versatile host for the production of natural products
journal, June 2015


Identification of conditionally essential genes for growth of Pseudomonas putida KT2440 on minimal medium through the screening of a genome-wide mutant library
journal, March 2010


High-throughput generation, optimization and analysis of genome-scale metabolic models
journal, August 2010

  • Henry, Christopher S.; DeJongh, Matthew; Best, Aaron A.
  • Nature Biotechnology, Vol. 28, Issue 9
  • DOI: 10.1038/nbt.1672

A metabolic pathway for catabolizing levulinic acid in bacteria
journal, September 2017

  • Rand, Jacqueline M.; Pisithkul, Tippapha; Clark, Ryan L.
  • Nature Microbiology, Vol. 2, Issue 12
  • DOI: 10.1038/s41564-017-0028-z

Isolation and characterization of lignin-degrading bacteria from rainforest soils
journal, February 2013

  • Huang, Xing-Feng; Santhanam, Navaneetha; Badri, Dayakar V.
  • Biotechnology and Bioengineering, Vol. 110, Issue 6
  • DOI: 10.1002/bit.24833

Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism
journal, February 2019


The Life History of Pseudomonas syringae : Linking Agriculture to Earth System Processes
journal, August 2013


Analysis of the plant growth-promoting properties encoded by the genome of the rhizobacterium Pseudomonas putida  BIRD-1 : PGPR properties
journal, December 2012

  • Roca, Amalia; Pizarro-Tobías, Paloma; Udaondo, Zulema
  • Environmental Microbiology, Vol. 15, Issue 3
  • DOI: 10.1111/1462-2920.12037

Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis
journal, December 2016

  • Broddrick, Jared T.; Rubin, Benjamin E.; Welkie, David G.
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 51
  • DOI: 10.1073/pnas.1613446113

Review: Lipopolysaccharide biosynthesis in Pseudomonas aeruginosa
journal, August 2009


Iron uptake and metabolism in pseudomonads
journal, March 2010


Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
journal, August 2011

  • Schellenberger, Jan; Que, Richard; Fleming, Ronan M. T.
  • Nature Protocols, Vol. 6, Issue 9
  • DOI: 10.1038/nprot.2011.308

Biotechnological domestication of pseudomonads using synthetic biology
journal, April 2014

  • Nikel, Pablo I.; Martínez-García, Esteban; de Lorenzo, Víctor
  • Nature Reviews Microbiology, Vol. 12, Issue 5
  • DOI: 10.1038/nrmicro3253

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments
journal, November 2013

  • Monk, J. M.; Charusanti, P.; Aziz, R. K.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 50
  • DOI: 10.1073/pnas.1307797110

Iron-Regulated Expression of Alginate Production, Mucoid Phenotype, and Biofilm Formation by Pseudomonas aeruginosa
journal, February 2014

  • Wiens, Jacinta R.; Vasil, Adriana I.; Schurr, Michael J.
  • mBio, Vol. 5, Issue 1
  • DOI: 10.1128/mBio.01010-13

Network Context and Selection in the Evolution to Enzyme Specificity
journal, August 2012


Cell envelope mutants of Pseudomonas putida: physiological characterization and analysis of their ability to survive in soil
journal, December 1999


Response of Pseudomonas putida KT2440 to Increased NADH and ATP Demand
journal, July 2011

  • Ebert, Birgitta E.; Kurth, Felix; Grund, Marcel
  • Applied and Environmental Microbiology, Vol. 77, Issue 18
  • DOI: 10.1128/AEM.05588-11

Lignin valorization through integrated biological funneling and chemical catalysis
journal, August 2014

  • Linger, J. G.; Vardon, D. R.; Guarnieri, M. T.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 33, p. 12013-12018
  • DOI: 10.1073/pnas.1410657111

Analysis of the core genome and pangenome of P seudomonas putida : The
journal, September 2015

  • Udaondo, Zulema; Molina, Lázaro; Segura, Ana
  • Environmental Microbiology, Vol. 18, Issue 10
  • DOI: 10.1111/1462-2920.13015

Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis
journal, March 2011

  • Oberhardt, Matthew A.; Puchałka, Jacek; Martins dos Santos, Vítor A. P.
  • PLoS Computational Biology, Vol. 7, Issue 3
  • DOI: 10.1371/journal.pcbi.1001116

Eliminating a global regulator of carbon catabolite repression enhances the conversion of aromatic lignin monomers to muconate in Pseudomonas putida KT2440
journal, December 2017

  • Johnson, Christopher W.; Abraham, Paul E.; Linger, Jeffrey G.
  • Metabolic Engineering Communications, Vol. 5
  • DOI: 10.1016/j.meteno.2017.05.002

The polyhydroxyalkanoate metabolism controls carbon and energy spillage in Pseudomonas putida: PHA metabolism in Pseudomonas putida
journal, January 2012


Integrating high-throughput and computational data elucidates bacterial networks
journal, May 2004

  • Covert, Markus W.; Knight, Eric M.; Reed, Jennifer L.
  • Nature, Vol. 429, Issue 6987
  • DOI: 10.1038/nature02456

A comprehensive genome‐scale reconstruction of Escherichia coli metabolism—2011
journal, January 2011

  • Orth, Jeffrey D.; Conrad, Tom M.; Na, Jessica
  • Molecular Systems Biology, Vol. 7, Issue 1
  • DOI: 10.1038/msb.2011.65

Genome-Scale Reconstruction and Analysis of the Pseudomonas putida KT2440 Metabolic Network Facilitates Applications in Biotechnology
journal, October 2008


Robustness and Plasticity of Metabolic Pathway Flux among Uropathogenic Isolates of Pseudomonas aeruginosa
journal, April 2014


Pathways for degradation of lignin in bacteria and fungi
journal, January 2011

  • Bugg, Timothy D. H.; Ahmad, Mark; Hardiman, Elizabeth M.
  • Natural Product Reports, Vol. 28, Issue 12, p. 1883-1896
  • DOI: 10.1039/c1np00042j

Regulatory Tasks of the Phosphoenolpyruvate-Phosphotransferase System of Pseudomonas putida in Central Carbon Metabolism
journal, March 2012


Engineering Pseudomonas putida KT2440 for efficient ethylene glycol utilization
journal, July 2018


Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model
journal, October 2012

  • Tanaka, Kosei; Henry, Christopher S.; Zinner, Jenifer F.
  • Nucleic Acids Research, Vol. 41, Issue 1
  • DOI: 10.1093/nar/gks963

Analysis of optimality in natural and perturbed metabolic networks
journal, November 2002

  • Segre, D.; Vitkup, D.; Church, G. M.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 23
  • DOI: 10.1073/pnas.232349399

Pseudomonas aeruginosa : new insights into pathogenesis and host defenses
journal, March 2013


A genome‐scale metabolic reconstruction for Escherichia coli K‐12 MG1655 that accounts for 1260 ORFs and thermodynamic information
journal, January 2007

  • Feist, Adam M.; Henry, Christopher S.; Reed, Jennifer L.
  • Molecular Systems Biology, Vol. 3, Issue 1
  • DOI: 10.1038/msb4100155

Variation in Lignin Content and Composition (Mechanisms of Control and Implications for the Genetic Improvement of Plants)
journal, January 1996

  • Campbell, M. M.; Sederoff, R. R.
  • Plant Physiology, Vol. 110, Issue 1
  • DOI: 10.1104/pp.110.1.3

Reconciling in vivo and in silico key biological parameters of Pseudomonas putidaKT2440 during growth on glucose under carbon-limited condition
journal, October 2013

  • van Duuren, Jozef BJH; Puchałka, Jacek; Mars, Astrid E.
  • BMC Biotechnology, Vol. 13, Issue 1
  • DOI: 10.1186/1472-6750-13-93

Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans-metabolism
journal, November 2018


The Pseudomonas Story: Editorial
journal, June 2010


Comparative genomics and functional analysis of niche-specific adaptation in Pseudomonas putida
journal, March 2011


Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity
journal, June 2016

  • Bosi, Emanuele; Monk, Jonathan M.; Aziz, Ramy K.
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 26
  • DOI: 10.1073/pnas.1523199113

Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440
journal, December 2002


Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism
journal, May 2019

  • Thompson, Mitchell G.; Blake-Hedges, Jacquelyn M.; Cruz-Morales, Pablo
  • mBio, Vol. 10, Issue 3
  • DOI: 10.1128/mBio.02577-18

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory
journal, January 2008

  • Nogales, Juan; Palsson, Bernhard Ø; Thiele, Ines
  • BMC Systems Biology, Vol. 2, Issue 1
  • DOI: 10.1186/1752-0509-2-79

Variability of peptidoglycan structural parameters in Gram-negative bacteria
journal, January 1995


Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits
journal, September 2018


Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides
journal, June 2017


Pseudomonas genomes: diverse and adaptable
journal, July 2011


Optimizing genome-scale network reconstructions
journal, May 2014

  • Monk, Jonathan; Nogales, Juan; Palsson, Bernhard O.
  • Nature Biotechnology, Vol. 32, Issue 5
  • DOI: 10.1038/nbt.2870

Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli
journal, June 2013


Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis
journal, January 2012

  • Nogales, J.; Gudmundsson, S.; Knight, E. M.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 7
  • DOI: 10.1073/pnas.1117907109

iML1515, a knowledgebase that computes Escherichia coli traits
journal, October 2017

  • Monk, Jonathan M.; Lloyd, Colton J.; Brunk, Elizabeth
  • Nature Biotechnology, Vol. 35, Issue 10
  • DOI: 10.1038/nbt.3956

What is flux balance analysis?
journal, March 2010

  • Orth, Jeffrey D.; Thiele, Ines; Palsson, Bernhard Ø
  • Nature Biotechnology, Vol. 28, Issue 3
  • DOI: 10.1038/nbt.1614

The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis : Re-annotation of the Pseudomonas putida KT2440 genome
journal, April 2016

  • Belda, Eugeni; van Heck, Ruben G. A.; José Lopez-Sanchez, Maria
  • Environmental Microbiology, Vol. 18, Issue 10
  • DOI: 10.1111/1462-2920.13230

Optimization for biodegradation of 2,4,6-trinitrotoluene (TNT) by Pseudomonas putida
journal, January 2003


Genome-scale Reconstruction of Metabolic Network in Bacillus subtilis Based on High-throughput Phenotyping and Gene Essentiality Data
journal, June 2007

  • Oh, You-Kwan; Palsson, Bernhard O.; Park, Sung M.
  • Journal of Biological Chemistry, Vol. 282, Issue 39
  • DOI: 10.1074/jbc.M703759200

From lignin to nylon: Cascaded chemical and biochemical conversion using metabolically engineered Pseudomonas putida
journal, May 2018