Reconstruction and metabolic profiling of the genome-scale metabolic network model of Pseudomonas stutzeri A1501

Yan, 2010, Global transcriptional analysis of nitrogen fixation and ammonium repression in root-associated Pseudomonas stutzeri A1501, BMC Genom, 11, 1, 10.1186/1471-2164-11-11 Vermeiren, 1999, The rice inoculant strain Alcaligenes faecalis A15 is a nitrogen-fixing Pseudomonas stutzeri, Syst Appl Microbiol, 22, 215, 10.1016/S0723-2020(99)80068-X Lalucat, 2006, Biology of Pseudomonas stutzeri, Microbiol Mol Biol Rev, 70, 510, 10.1128/MMBR.00047-05 Yan, 2008, Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501, Proc Natl Acad Sci USA, 105, 7564, 10.1073/pnas.0801093105 Venieraki, 2011, Characterization of nitrogen-fixing bacteria isolated from field-grown barley, oat, and wheat, J Microbiol, 49, 525, 10.1007/s12275-011-0457-y Gilvanova, 2022, Potential of the bacterium Pseudomonas Stutzeri as a plant growth stimulator and a destructor of technogenic pollutants, 10.1063/5.0092850 Sanow, 2023, Molecular mechanisms of Pseudomonas assisted plant nitrogen uptake-opportunities for modern agriculture, Mol Plant Microbe Interact Mehmood, 2023 Mao, 2023, CAVE: a cloud-based platform for analysis and visualization of metabolic pathways, Nucleic Acids Res, 10.1093/nar/gkad360 Babaei, 2015, Genome-scale reconstruction of the metabolic network in Pseudomonas stutzeri A1501, Mol Biosyst, 11, 3022, 10.1039/C5MB00086F Aziz, 2008, The RAST Server: rapid annotations using subsystems technology, BMC Genom, 9, 1, 10.1186/1471-2164-9-75 Devoid, 2013, Automated genome annotation and metabolic model reconstruction in the SEED and Model SEED, Syst Metabol Eng: Method Protocol, 17, 10.1007/978-1-62703-299-5_2 Caspi, 2010, The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases, Nucleic Acids Res, 38, D473, 10.1093/nar/gkp875 Kanehisa, 2014, Data, information, knowledge and principle: back to metabolism in KEGG, Nucleic Acids Res, 42, D199, 10.1093/nar/gkt1076 KaAWAI, 1988, Ornithine‐containing lipids of some Pseudomonas species, Eur J Biochem, 175, 633, 10.1111/j.1432-1033.1988.tb14239.x Luo, 2022, Reconstruction of a genome-scale metabolic network for shewanella oneidensis MR-1 and analysis of its metabolic potential for bioelectrochemical systems, Front Bioeng Biotechnol, 10, 913077, 10.3389/fbioe.2022.913077 Orth, 2010, What is flux balance analysis?, Nat Biotechnol, 28, 245, 10.1038/nbt.1614 Schellenberger, 2011, Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2. 0, Nat Protoc, 6, 1290, 10.1038/nprot.2011.308 Seaver, 2021, The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes, Nucleic Acids Res, 49, D575, 10.1093/nar/gkaa746 Yuan, 2017, Pathway-consensus approach to metabolic network reconstruction for Pseudomonas putida KT2440 by systematic comparison of published models, PLoS One, 12, 10.1371/journal.pone.0169437 Gilis, 2001, Optimality of the genetic code with respect to protein stability and amino-acid frequencies, Genome Biol, 2, 1, 10.1186/gb-2001-2-11-research0049 Hormoz, 2013, Amino acid composition of proteins reduces deleterious impact of mutations, Sci Rep, 3, 2919, 10.1038/srep02919 Balakrishnan, 2022, Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria, Science, 378, eabk2066, 10.1126/science.abk2066 Puchałka, 2008, Genome-scale reconstruction and analysis of the Pseudomonas putid a KT2440 metabolic network facilitates applications in biotechnology, PLoS Comput Biol, 4, 10.1371/journal.pcbi.1000210 Pramanik, 1998, Effect of Escherichia coli biomass composition on central metabolic fluxes predicted by a stoichiometric model, Biotechnol Bioeng, 60, 230, 10.1002/(SICI)1097-0290(19981020)60:2<230::AID-BIT10>3.0.CO;2-Q Zumft, 1997, Cell biology and molecular basis of denitrification, Microbiol Mol Biol Rev, 61, 533 Oberhardt, 2008 Monk, 2017, i ML1515, a knowledgebase that computes Escherichia coli traits, Nat Biotechnol, 35, 904, 10.1038/nbt.3956 Jüngst, 1991, Close linkage in Pseudomonas stutzeri of the structural genes for respiratory nitrite reductase and nitrous oxide reductase, and other essential genes for denitrification, Mol Gen Genet MGG, 225, 241, 10.1007/BF00269855 Dückers, 2010, Threonine aldolases—screening, properties and applications in the synthesis of non-proteinogenic β-hydroxy-α-amino acids, Appl Microbiol Biotechnol, 88, 409, 10.1007/s00253-010-2751-8 Kertesz, 2000, Riding the sulfur cycle – metabolism of sulfonates and sulfate esters in Gram-negative bacteria, FEMS (Fed Eur Microbiol Soc) Microbiol Rev, 24, 135 Guzmán, 2015, Model-driven discovery of underground metabolic functions in Escherichia coli, Proc Natl Acad Sci USA, 112, 929, 10.1073/pnas.1414218112 Shi, 2023, Enzyme commission number prediction and benchmarking with hierarchical dual-core multitask learning framework, Research, 6, 10.34133/research.0153 Bogorad, 2014, Building carbon-carbon bonds using a biocatalytic methanol condensation cycle, Proc Natl Acad Sci U S A, 111, 15928, 10.1073/pnas.1413470111 Yang, 2019, Systematic design and in vitro validation of novel one-carbon assimilation pathways, Metab Eng, 56, 142, 10.1016/j.ymben.2019.09.001 Chambers, 1971, Cysteine and S-sulphocysteine biosynthesis in bacteria, Archiv fuer Mikrobiol, 77, 165, 10.1007/BF00408609