The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis

The Crc/CrcZ-CrcY global regulatory system helps the integration of gluconeogenic and glycolytic metabolism inPseudomonas putida

(2015) Ruggero La Rosa et al.   ENVIRONMENTAL MICROBIOLOGY

Analysis of the core genome and pangenome of P seudomonas putida

(2015) Zulema Udaondo et al.   ENVIRONMENTAL MICROBIOLOGY

Pseudomonas putidaKT2440 Strain Metabolizes Glucose through a Cycle Formed by Enzymes of the Entner-Doudoroff, Embden-Meyerhof-Parnas, and Pentose Phosphate Pathways

(2015) Pablo I. Nikel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria

(2015) S. Hui et al.   Molecular Systems Biology

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data

(2015) Laurence Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

It's the metabolism, stupid!

(2015) Víctor de Lorenzo   Environmental Microbiology Reports

Biotechnological domestication of pseudomonads using synthetic biology

(2014) Pablo I. Nikel et al.   NATURE REVIEWS MICROBIOLOGY

Expanded microbial genome coverage and improved protein family annotation in the COG database

(2014) Michael Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

HAMAP in 2015: updates to the protein family classification and annotation system

(2014) Ivo Pedruzzi et al.   NUCLEIC ACIDS RESEARCH

Updates in Rhea—a manually curated resource of biochemical reactions

(2014) Anne Morgat et al.   NUCLEIC ACIDS RESEARCH

BRENDA in 2015: exciting developments in its 25th year of existence

(2014) Antje Chang et al.   NUCLEIC ACIDS RESEARCH

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

The Gluconeogenesis Pathway Is Involved in Maintenance of Enterohaemorrhagic Escherichia coli O157:H7 in Bovine Intestinal Content

(2014) Yolande Bertin et al.   PLoS One

Draft Genome Sequence Analysis of a Pseudomonas putida W15Oct28 Strain with Antagonistic Activity to Gram-Positive and Pseudomonas sp. Pathogens

(2014) Lumeng Ye et al.   PLoS One

How drugs get into cells: tested and testable predictions to help discriminate between transporter-mediated uptake and lipoidal bilayer diffusion

(2014) Douglas B. Kell et al.   Frontiers in Pharmacology

Homeostasis and Catabolism of Choline and Glycine Betaine: Lessons from Pseudomonas aeruginosa

(2013) Matthew J. Wargo   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks

(2013) M. Ganter et al.   BIOINFORMATICS

Reconciling in vivo and in silico key biological parameters of Pseudomonas putida KT2440 during growth on glucose under carbon-limited condition

(2013) Jozef BJH van Duuren et al.   BMC BIOTECHNOLOGY

The logic of metabolism and its fuzzy consequences

(2013) Antoine Danchin et al.   ENVIRONMENTAL MICROBIOLOGY

Revealing the hidden functional diversity of an enzyme family

(2013) Karine Bastard et al.   Nature Chemical Biology

Comprehensive analysis of DNA polymerase III α subunits and their homologs in bacterial genomes

(2013) Kęstutis Timinskas et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Transcriptomic fingerprinting ofPseudomonas putidaunder alternative physiological regimes

(2013) Juhyun Kim et al.   Environmental Microbiology Reports

Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance

(2013) Benjamin D. Heavner et al.   Database-The Journal of Biological Databases and Curation

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Trends in bacterial trehalose metabolism and significant nodes of metabolic pathway in the direction of trehalose accumulation

(2013) Rohit Ruhal et al.   Microbial Biotechnology

Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC

(2012) Stefan Engelen et al.   BMC GENOMICS

Reconciliation of metabolites and biochemical reactions for metabolic networks

(2012) T. Bernard et al.   BRIEFINGS IN BIOINFORMATICS

Small Multidrug Resistance Protein EmrE Reduces Host pH and Osmotic Tolerance to Metabolic Quaternary Cation Osmoprotectants

(2012) D. C. Bay et al.   JOURNAL OF BACTERIOLOGY

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

(2012) David Vallenet et al.   NUCLEIC ACIDS RESEARCH

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013

(2012) Janna Hastings et al.   NUCLEIC ACIDS RESEARCH

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

From essential to persistent genes: a functional approach to constructing synthetic life

(2012) Carlos G. Acevedo-Rocha et al.   TRENDS IN GENETICS

The Pathway Tools Pathway Prediction Algorithm

(2012) Peter D. Karp et al.   Standards in Genomic Sciences

The CanOE Strategy: Integrating Genomic and Metabolic Contexts across Multiple Prokaryote Genomes to Find Candidate Genes for Orphan Enzymes

(2012) Adam Alexander Thil Smith et al.   PLoS Computational Biology

Pseudomonas putida KT2440 genome update by cDNA sequencing and microarray transcriptomics

(2011) Sarah Frank et al.   ENVIRONMENTAL MICROBIOLOGY

Unexpected and widespread connections between bacterial glycogen and trehalose metabolism

(2011) G. Chandra et al.   MICROBIOLOGY-SGM

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

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

(2011) Jan Schellenberger et al.   Nature Protocols

Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis

(2011) Matthew A. Oberhardt et al.   PLoS Computational Biology

In silicogenome-scale metabolic analysis ofPseudomonas putidaKT2440 for polyhydroxyalkanoate synthesis, degradation of aromatics and anaerobic survival

(2010) Seung Bum Sohn et al.   Biotechnology Journal

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Regulatory exaptation of the catabolite repression protein (Crp)-cAMP system in Pseudomonas putida

(2010) Paola Milanesio et al.   ENVIRONMENTAL MICROBIOLOGY

Escherichia coli Dihydropyrimidine Dehydrogenase Is a Novel NAD-Dependent Heterotetramer Essential for the Production of 5,6-Dihydrouracil

(2010) R. Hidese et al.   JOURNAL OF BACTERIOLOGY

Last Step in the Conversion of Trehalose to Glycogen

(2010) Alan D. Elbein et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida

(2010) Juan Nogales et al.   MOLECULAR MICROBIOLOGY

PSORTdb--an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and Archaea

(2010) N. Y. Yu et al.   NUCLEIC ACIDS RESEARCH

Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes

(2010) G. L. Winsor et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Identification of genes required for Pseudomonas aeruginosa carnitine catabolism

(2009) M. J. Wargo et al.   MICROBIOLOGY-SGM

The ATP-binding cassette transporter Cbc (choline/betaine/carnitine) recruits multiple substrate-binding proteins with strong specificity for distinct quaternary ammonium compounds

(2009) Chiliang Chen et al.   MOLECULAR MICROBIOLOGY

Genome evolution and adaptation in a long-term experiment with Escherichia coli

(2009) Jeffrey E. Barrick et al.   NATURE

FIGfams: yet another set of protein families

(2009) Folker Meyer et al.   NUCLEIC ACIDS RESEARCH

GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions

(2009) Vinay Satish Kumar et al.   PLoS Computational Biology

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

(2009) Marie Touchon et al.   PLoS Genetics

Amidohydrolases of the reductive pyrimidine catabolic pathway

(2008) Klaus D. Schnackerz et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

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

(2008) Juan Nogales et al.   BMC Systems Biology

Genetic analyses and molecular characterization of the pathways involved in the conversion of 2-phenylethylamine and 2-phenylethanol into phenylacetic acid in Pseudomonas putida U

(2008) Sagrario Arias et al.   ENVIRONMENTAL MICROBIOLOGY

Logical Identification of an Allantoinase Analog (puuE) Recruited from Polysaccharide Deacetylases

(2008) Ileana Ramazzina et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Deciphering the genetic determinants for aerobic nicotinic acid degradation: The nic cluster from Pseudomonas putida KT2440

(2008) J. I. Jimenez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) Jacek Puchałka et al.   PLoS Computational Biology