The relevance of enzyme specificity for coenzymes and the presence of 6-phosphogluconate dehydrogenase for polyhydroxyalkanoates production in the metabolism of Pseudomonas sp. LFM046.

[1]  Adam M. Feist,et al.  High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities , 2019, Environmental microbiology.

[2]  S. Molin,et al.  Adapting to the Airways: Metabolic Requirements of Pseudomonas aeruginosa during the Infection of Cystic Fibrosis Patients , 2019, Metabolites.

[3]  C. Pezzella,et al.  Conversion of no/low value waste frying oils into biodiesel and polyhydroxyalkanoates , 2019, Scientific Reports.

[4]  T. Krell,et al.  The involvement of McpB chemoreceptor from Pseudomonas aeruginosa PAO1 in virulence , 2019, Scientific Reports.

[5]  V. de Lorenzo,et al.  Functional implementation of a linear glycolysis for sugar catabolism in Pseudomonas putida. , 2019, Metabolic engineering.

[6]  Lucia Marucci,et al.  Genome-driven cell engineering review: in vivo and in silico metabolic and genome engineering , 2019, Essays in biochemistry.

[7]  Mary J. Biddy,et al.  Innovative Chemicals and Materials from Bacterial Aromatic Catabolic Pathways , 2019, Joule.

[8]  A. Bezbaruah,et al.  Adaption of microarray primers for iron transport and homeostasis gene expression in Pseudomonas fluorescens exposed to nano iron , 2019, MethodsX.

[9]  Marcin J. Skwark,et al.  Mycobacterial genomics and structural bioinformatics: opportunities and challenges in drug discovery , 2019, Emerging microbes & infections.

[10]  Bernhard O. Palsson,et al.  The Use of In Silico Genome-Scale Models for the Rational Design of Minimal Cells , 2019 .

[11]  K. Sohn,et al.  Using Bioinformatics and Molecular Biology to Streamline Construction of Effector Libraries for Phytopathogenic Pseudomonas syringae Strains. , 2019, Methods in molecular biology.

[12]  C. Angione,et al.  In silico engineering of Pseudomonas metabolism reveals new biomarkers for increased biosurfactant production , 2018, PeerJ.

[13]  L. Aristilde,et al.  A Cyclic Metabolic Network in Pseudomonas protegens Pf-5 Prioritizes the Entner-Doudoroff Pathway and Exhibits Substrate Hierarchy during Carbohydrate Co-Utilization , 2018, Applied and Environmental Microbiology.

[14]  Anna S. Blazier,et al.  Reconciling high-throughput gene essentiality data with metabolic network reconstructions , 2018, bioRxiv.

[15]  Q. Ji,et al.  CRISPR/Cas9-based Genome Editing in Pseudomonas aeruginosa and Cytidine Deaminase-Mediated Base Editing in Pseudomonas Species , 2018, iScience.

[16]  Rick L. Stevens,et al.  KBase: The United States Department of Energy Systems Biology Knowledgebase , 2018, Nature Biotechnology.

[17]  V. de Lorenzo,et al.  Refactoring the upper sugar metabolism of Pseudomonas putida for co-utilization of cellobiose, xylose, and glucose. , 2018, Metabolic engineering.

[18]  A. Kremling,et al.  Engineering sucrose metabolism in Pseudomonas putida highlights the importance of porins , 2018, Microbial biotechnology.

[19]  Gabriela Soto,et al.  Plant growth-promoting bacterium Pseudomonas fluorescens FR1 secrets a novel type of extracellular polyhydroxybutyrate polymerase involved in abiotic stress response in plants , 2018, Biotechnology Letters.

[20]  T. Pokój,et al.  Transcriptome remodeling of Pseudomonas putida KT2440 during mcl-PHAs synthesis: effect of different carbon sources and response to nitrogen stress , 2018, Journal of Industrial Microbiology & Biotechnology.

[21]  M. K. Taciro,et al.  A non-naturally-occurring P(3HB-co-3HAMCL) is produced by recombinant Pseudomonas sp. from an unrelated carbon source. , 2018, International journal of biological macromolecules.

[22]  J. Frestedt.  Foods, Food Additives, and Generally Regarded as Safe (GRAS) Food Assessments , 2018 .

[23]  R. Benz,et al.  Conversion of OprO into an OprP-like Channel by Exchanging Key Residues in the Channel Constriction. , 2017, Biophysical journal.

[24]  J. Malone,et al.  Quick change: post-transcriptional regulation in Pseudomonas , 2017, FEMS microbiology letters.

[25]  F. Klawonn,et al.  Transcriptome Profiling of Antimicrobial Resistance in Pseudomonas aeruginosa , 2016, Antimicrobial Agents and Chemotherapy.

[26]  Woojun Park,et al.  Role of Glyoxylate Shunt in Oxidative Stress Response* , 2016, The Journal of Biological Chemistry.

[27]  M. Reis,et al.  Valorization of fatty acids-containing wastes and byproducts into short- and medium-chain length polyhydroxyalkanoates. , 2016, New biotechnology.

[28]  Raymond Lo,et al.  Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database , 2015, Nucleic Acids Res..

[29]  Philip Miller,et al.  BiGG Models: A platform for integrating, standardizing and sharing genome-scale models , 2015, Nucleic Acids Res..

[30]  A. Amézquita,et al.  A Systems Level Approach for Identification of Molecular Targets for Antimicrobial Intervention against Pseudomonas Aeruginosa, while Predicting Biofilm Formation☆ , 2016 .

[31]  Q. Shen,et al.  Bacillus amyloliquefaciens T-5 may prevent Ralstonia solanacearum infection through competitive exclusion , 2015, Biology and Fertility of Soils.

[32]  Marina Pupke Marone,et al.  Quantifying NAD(P)H production in the upper Entner–Doudoroff pathway from Pseudomonas putida KT2440 , 2015, FEBS open bio.

[33]  Jaques Reifman,et al.  Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism , 2015, PLoS Comput. Biol..

[34]  U. Sauer,et al.  Pseudomonas putida KT2440 Strain Metabolizes Glucose through a Cycle Formed by Enzymes of the Entner-Doudoroff, Embden-Meyerhof-Parnas, and Pentose Phosphate Pathways* , 2015, The Journal of Biological Chemistry.

[35]  Paulo Moises Raduan Alexandrino,et al.  Draft Genome Sequence of Pseudomonas sp. Strain LFM046, a Producer of Medium-Chain-Length Polyhydroxyalkanoate , 2015, Genome Announcements.

[36]  Pietro Liò,et al.  MeDuSa: a multi-draft based scaffolder , 2015, Bioinform..

[37]  Chia-Lung Chen,et al.  Bioconversion of Styrene to Poly(hydroxyalkanoate) (PHA) by the New Bacterial Strain Pseudomonas putida NBUS12 , 2015, Microbes and environments.

[38]  Fangfang Xia,et al.  RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes , 2015, Scientific Reports.

[39]  Adam M. Feist,et al.  Metabolic impact of an NADH-producing glucose-6-phosphate dehydrogenase in Escherichia coli. , 2014, Microbiology.

[40]  Adam M. Feist,et al.  Optimal cofactor swapping can increase the theoretical yield for chemical production in Escherichia coli and Saccharomyces cerevisiae. , 2014, Metabolic engineering.

[41]  C. Wittmann,et al.  Production of medium chain length polyhydroxyalkanoate in metabolic flux optimized Pseudomonas putida , 2014, Microbial Cell Factories.

[42]  Fangfang Xia,et al.  The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) , 2013, Nucleic Acids Res..

[43]  W. Kessler,et al.  Improved production of medium-chain-length polyhydroxyalkanoates in glucose-based fed-batch cultivations of metabolically engineered Pseudomonas putida strains. , 2014, Journal of microbiology and biotechnology.

[44]  P. Engel.  Glutamate Dehydrogenases: The Why and How of Coenzyme Specificity , 2013, Neurochemical Research.

[45]  V. de Lorenzo,et al.  The Entner-Doudoroff pathway empowers Pseudomonas putida KT2440 with a high tolerance to oxidative stress. , 2013, Environmental microbiology.

[46]  Christoph Wittmann,et al.  In-silico-driven metabolic engineering of Pseudomonas putida for enhanced production of poly-hydroxyalkanoates. , 2013, Metabolic engineering.

[47]  Gunasekaran Paramasamy,et al.  Pseudomonas sp. as a Source of Medium Chain Length Polyhydroxyalkanoates for Controlled Drug Delivery: Perspective , 2012, International journal of microbiology.

[48]  S. Panke,et al.  A reduction in growth rate of Pseudomonas putida KT2442 counteracts productivity advances in medium-chain-length polyhydroxyalkanoate production from gluconate , 2011, Microbial cell factories.

[49]  Jason A. Papin,et al.  Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis , 2011, PLoS Comput. Biol..

[50]  H. Azaizeh,et al.  Biodegradation of Organic Xenobiotic Pollutants in the Rhizosphere , 2011 .

[51]  C. Nomura,et al.  Monitoring differences in gene expression levels and polyhydroxyalkanoate (PHA) production in Pseudomonas putida KT2440 grown on different carbon sources. , 2010, Journal of bioscience and bioengineering.

[52]  S Venkata Mohan,et al.  Phosphatase and dehydrogenase activities in anodic chamber of single chamber microbial fuel cell (MFC) at variable substrate loading conditions. , 2010, Bioelectrochemistry.

[53]  J. Pradella,et al.  PHA(MCL) biosynthesis systems in Pseudomonas aeruginosa and Pseudomonas putida strains show differences on monomer specificities. , 2009, Journal of biotechnology.

[54]  Edmar Chartone-Souza,et al.  Molecular identification and dynamics of microbial communities in reactor treating organic household waste , 2009, Applied Microbiology and Biotechnology.

[55]  J. Ramos,et al.  Regulation of Glucose Metabolism in Pseudomonas , 2009, The Journal of Biological Chemistry.

[56]  Uwe Sauer,et al.  Different Biochemical Mechanisms Ensure Network-Wide Balancing of Reducing Equivalents in Microbial Metabolism , 2009, Journal of bacteriology.

[57]  A. Steinbüchel,et al.  Ralstonia eutropha Strain H16 as Model Organism for PHA Metabolism and for Biotechnological Production of Technically Interesting Biopolymers , 2008, Journal of Molecular Microbiology and Biotechnology.

[58]  M. K. Taciro.  PROCESSO CONTÍNUO DE PRODUÇÃO DE POLIHIDROXIALCANOATOS DE CADEIA MÉDIA (PHAMCL) SOB LIMITAÇÃO MÚLTIPLA DE NUTRIENTES , 2008 .

[59]  Jason A. Papin,et al.  * Corresponding authors , 2006 .

[60]  U. Sauer,et al.  Convergent Peripheral Pathways Catalyze Initial Glucose Catabolism in Pseudomonas putida: Genomic and Flux Analysis , 2007, Journal of bacteriology.

[61]  Anne Pohlmann,et al.  Genome sequence of the bioplastic-producing “Knallgas” bacterium Ralstonia eutropha H16 , 2006, Nature Biotechnology.

[62]  D. Stroman,et al.  Pseudomonas otitidis sp. nov., isolated from patients with otic infections. , 2006, International journal of systematic and evolutionary microbiology.

[63]  A. Dean,et al.  The Selective Cause of an Ancient Adaptation , 2005, Science.

[64]  James R. Cole,et al.  The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis , 2004, Nucleic Acids Res..

[65]  G. W. Haywood,et al.  A survey of the accumulation of novel polyhydroxyalkanoates by bacteria , 1989, Biotechnology Letters.

[66]  B. Rehm,et al.  Nitrogen-dependent regulation of medium-chain length polyhydroxyalkanoate biosynthesis genes in pseudomonads , 2005, Biotechnology Letters.

[67]  J. Pradella,et al.  High-Cell-Density cultivation of pseudomonas putida IPT 046 and medium-chain-length polyhydroxyalkanoate production from sugarcane carbohydrates , 2004, Applied biochemistry and biotechnology.

[68]  Sudhir Kumar,et al.  MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment , 2004, Briefings Bioinform..

[69]  A. Steinbüchel,et al.  Formation of blends of various poly(3-hydroxyalkanoic acids) by a recombinant strain of Pseudomonas oleovorans , 1990, Applied Microbiology and Biotechnology.

[70]  B. Kim.  Production of medium chain length polyhydroxyalkanoates by fed-batch culture of Pseudomonas oleovorans , 2004, Biotechnology Letters.

[71]  J. Pradella,et al.  Medium-chain-length polyhydroxyalkanoic acids (PHAmcl) produced by Pseudomonas putida IPT 046 from renewable sources , 2003 .

[72]  D. Solaiman.  Biosynthesis of medium-chain-length poly(hydroxyalkanoates) with altered composition by mutant hybrid PHA synthases , 2003, Journal of Industrial Microbiology and Biotechnology.

[73]  O. White,et al.  Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. , 2002, Environmental microbiology.

[74]  S. Lory,et al.  Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen , 2000, Nature.

[75]  M. Dauner,et al.  Inactivation of Isocitrate Lyase Leads to Increased Production of Medium-Chain-Length Poly(3-Hydroxyalkanoates) inPseudomonas putida , 2000, Applied and Environmental Microbiology.

[76]  José Gregário Cabrera Gomez,et al.  Produção por "Pseudomonas" sp. de polihidroxialcanoatos contendo monômeros de cadeia média a partir de carboidratos: avaliação da eficiência, modificação da composição e obtenção de mutantes , 2000 .

[77]  Christina M. Preston,et al.  Visualization and Enumeration of Marine Planktonic Archaea and Bacteria by Using Polyribonucleotide Probes and Fluorescent In Situ Hybridization , 1999, Applied and Environmental Microbiology.

[78]  B. Witholt,et al.  High cell density fermentations of Pseudomonas oleovorans for the production of mcl-PHAs in two-liquid phase media , 1999 .

[79]  A. Steinbüchel,et al.  A sensitive, viable-colony staining method using Nile red for direct screening of bacteria that accumulate polyhydroxyalkanoic acids and other lipid storage compounds , 1999, Archives of Microbiology.

[80]  A Grigoriev,et al.  Analyzing genomes with cumulative skew diagrams. , 1998, Nucleic acids research.

[81]  T. Foglia,et al.  Poly(hydroxyalkanoate) biosynthesis from triglyceride substrates , 1998, Applied Microbiology and Biotechnology.

[82]  B. Witholt,et al.  Efficient production of medium-chain-length poly(3-hydroxyalkanoates) from octane by Pseudomonas oleovorans: economic considerations , 1997, Applied Microbiology and Biotechnology.

[83]  G. Eggink,et al.  Production of poly(3-hydroxyalkanoates) by Pseudomonas putida KT2442 in continuous cultures , 1996, Applied Microbiology and Biotechnology.

[84]  R. C. P. Alli,et al.  Evaluation of soil gram-negative bacteria yielding polyhydroxyalkanoic acids from carbohydrates and propionic acid , 1996, Applied Microbiology and Biotechnology.

[85]  D. Roop,et al.  Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. , 1995, Gene.

[86]  Ho Nam Chang,et al.  Regulation of poly-β-hydroxybutyrate biosynthesis by nicotinamide nucleotide in Alcaligenes eutrophus , 1995 .

[87]  C. Choi,et al.  Gas chromatography-mass spectrometric analysis and its application to a screening procedure for novel bacterial polyhydroxyalkanoic acids containing long chain saturated and unsaturated monomers , 1995 .

[88]  T. Conway,et al.  The Entner-Doudoroff pathway: history, physiology and molecular biology. , 1992, FEMS microbiology reviews.

[89]  C. Chavarie,et al.  Production of poly-(beta-hydroxybutyric-co-beta-hydroxyvaleric) acids , 1990, Applied and environmental microbiology.

[90]  R. Gross,et al.  Pseudomonas oleovorans as a Source of Poly(β-Hydroxyalkanoates) for Potential Applications as Biodegradable Polyesters , 1988, Applied and environmental microbiology.

[91]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[92]  P. Phibbs,et al.  Alternative pathways of carbohydrate utilization in pseudomonads. , 1984, Annual review of microbiology.

[93]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[94]  M. M. Bradford.  A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. , 1976, Analytical biochemistry.

[95]  J L Cánovas,et al.  Glucolysis in Pseudomonas putida: Physiological Role of Alternative Routes from the Analysis of Defective Mutants , 1973, Journal of bacteriology.