A kinetic platform for in silico modeling of the metabolic dynamics in Escherichia coli

References

• ChanPFHolmesDJPayneDJFinding the gems using genomic discovery: antibacterial drug discovery strategies – the successes and the challengesDrug Discov Today Ther Strateg200414519527
   Google Scholar
• PayneDJGwynnMNHolmesDJPomplianoDLDrugs for bad bugs: confronting the challenges of antibacterial discoveryNat Rev Drug Discov200761294017159923
   PubMed Web of Science ®Google Scholar
• BlackMTBrutonGInhibitors of bacterial signal peptidasesCurr Pharm Des19984213315410197037
   PubMed Web of Science ®Google Scholar
• EisenthalRCornish-BowdenAProspects for antiparasitic drugs. The case of Trypanosoma brucei, the causative agent of African sleeping sicknessJ Biol Chem199827310550055059488673
   PubMed Web of Science ®Google Scholar
• KohanskiMADwyerDJHayeteBLawrenceCACollinsJJA common mechanism of cellular death induced by bactericidal antibioticsCell2007130579781017803904
   PubMed Web of Science ®Google Scholar
• KaurPAgarwalSDattaSDelineating bacteriostatic and bactericidal targets in mycobacteria using IPTG inducible antisense expressionPLoS One200946e592319526063
   PubMed Web of Science ®Google Scholar
• DattaSUnderstanding the characteristics of a good anti-infective drug targetJ Parasitic Dis199923139140
   Google Scholar
• FongSSNanchenAPalssonBOSauerULatent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymesJ Biol Chem2006281128024803316319065
   PubMed Web of Science ®Google Scholar
• WalshKKoshlandDEJrBranch point control by the phosphorylation state of isocitrate dehydrogenase. A quantitative examination of fluxes during a regulatory transitionJ Biol Chem198526014843084372861202
   PubMed Web of Science ®Google Scholar
• WalshKKoshlandDEJrDetermination of flux through the branch point of two metabolic cycles. The tricarboxylic acid cycle and the glyoxylate shuntJ Biol Chem198425915964696546378912
   PubMed Web of Science ®Google Scholar
• HolmsHFlux analysis and control of the central metabolic pathways in Escherichia coliFEMS Microbiol Rev1996192851168988566
   PubMed Web of Science ®Google Scholar
• WendischVFde GraafAASahmHEikmannsBJQuantitative determination of metabolic fluxes during coutilization of two carbon sources: comparative analyses with Corynebacterium glutamicum during growth on acetate and/or glucoseJ Bacteriol2000182113088309610809686
   PubMed Web of Science ®Google Scholar
• TweeddaleHNotley-McRobbLFerenciTEffect of slow growth on metabolism of Escherichia coli, as revealed by global metabolite pool (“metabolome”) analysisJ Bacteriol199818019510951169748443
   PubMed Web of Science ®Google Scholar
• PurvisJEYomanoLPIngramLOEnhanced trehalose production improves growth of Escherichia coli under osmotic stressAppl Environ Microbiol20057173761376916000787
   PubMed Web of Science ®Google Scholar
• BabaTAraTHasegawaMConstruction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collectionMol Syst Biol2006220062008
   PubMed Web of Science ®Google Scholar
• ChohnanSIzawaHNishiharaHTakamuraYChanges in size of intracellular pools of coenzyme A and its thioesters in Escherichia coli K-12 cells to various carbon sources and stressesBiosci Biotechnol Biochem1998626112211289692193
   PubMed Web of Science ®Google Scholar
• SongWJJackowskiSCloning, sequencing, and expression of the pantothenate kinase (coaA) gene of Escherichia coliJ Bacteriol199217420641164171328157
   PubMed Web of Science ®Google Scholar
• ZhangYMFrankMWVirgaKGAcyl carrier protein is a cellular target for the antibacterial action of the pantothenamide class of pantothenate antimetabolitesJ Biol Chem200427949509695097515459190
   PubMed Web of Science ®Google Scholar
• TulliusMVHarthGMaslesa-GalicSDillonBJHorwitzMAA Replication-Limited Recombinant Mycobacterium bovis BCG vaccine against tuberculosis designed for human immunodeficiency virus-positive persons is safer and more efficacious than BCGInfect Immun200876115200521418725418
   PubMed Web of Science ®Google Scholar
• DaileyFECronanJEJrAcetohydroxy acid synthase I, a required enzyme for isoleucine and valine biosynthesis in Escherichia coli K-12 during growth on acetate as the sole carbon sourceJ Bacteriol198616524534603511034
   PubMed Web of Science ®Google Scholar
• FeistAMHenryCSReedJLA genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic informationMol Syst Biol 2007312117593909
   PubMed Web of Science ®Google Scholar
• FeistAMPalssonBOThe growing scope of applications of genome-scale metabolic reconstructions using Escherichia coliNat Biotechnol200826665966718536691
   PubMed Web of Science ®Google Scholar
• SinghVKGhoshIKinetic modeling of tricarboxylic acid cycle and glyoxylate bypass in Mycobacterium tuberculosis, and its application to assessment of drug targetsTheor Biol Med Model 200632716887020
   PubMed Web of Science ®Google Scholar
• DwyerDJKohanskiMAHayeteBCollinsJJGyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coliMol Syst Biol 200739117353933
   PubMed Web of Science ®Google Scholar
• JorgensenCMHammerKJensenPRMartinussenJExpression of the pyrG gene determines the pool sizes of CTP and dCTP in Lactococcus lactisEur J Biochem2004271122438244515182359
   PubMedGoogle Scholar
• ChristophersonRIDugglebyRGMetabolic resistance: the protection of enzymes against drugs which are tight-binding inhibitors by the accumulation of substrateEur J Biochem198313423313356873066
   PubMedGoogle Scholar
• IngrahamJLNFEscherichia coli and Salmonella typhimurium: Cellular and Molecular Biology1st editionAmerican Society for Microbiology Press1987
   Google Scholar
• KarpPDKeselerIMShearerAMultidimensional annotation of the Escherichia coli K-12 genomeNucleic Acids Res200735227577759017940092
   PubMed Web of Science ®Google Scholar
• DavisMSCronanJEJrInhibition of Escherichia coli acetyl coenzyme A carboxylase by acyl-acyl carrier proteinJ Bacteriol200118341499150311157970
   PubMed Web of Science ®Google Scholar
• HeathRJRockCOInhibition of beta-ketoacyl-acyl carrier protein synthase III (FabH) by acyl-acyl carrier protein in Escherichia coliJ Biol Chem19962711810996110008631920
   PubMed Web of Science ®Google Scholar
• UmbargerHEAmino acid biosynthesis and its regulationAnnu Rev Biochem197847532606354503
   PubMed Web of Science ®Google Scholar
• FavreRWiaterAPuppoSIaccarinoMExpression of a valineresistant acetolactate synthase activity mediated by the ilv O and ilv G genes of Escherichia coli K-12Mol Gen Genet19761433243252765758
   PubMedGoogle Scholar
• BeyerAHollunderJNasheuerHPWilhelmTPost-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scaleMol Cell Proteomics20043111083109215326222
   PubMed Web of Science ®Google Scholar
• IshihamaYSchmidtTRappsilberJProtein abundance profiling of the Escherichia coli cytosolBMC Genomics 2008910218304323
   PubMed Web of Science ®Google Scholar
• IshiiNNakahigashiKBabaTMultiple high-throughput analyses monitor the response of E. coli to perturbationsScience2007316582459359717379776
   PubMed Web of Science ®Google Scholar
• DWThe Physiology and Biochemistry of Prokaryotes2nd editionOxford University PressUSA1999
   Google Scholar
• ValiSChintaSJPengJInsights into the effects of alpha-synuclein expression and proteasome inhibition on glutathione metabolism through a dynamic in silico model of Parkinson’s disease: validation by cell culture dataFree Radic Biol Med20084591290130118761401
   PubMed Web of Science ®Google Scholar
• FunahashiAMorohashiMKitanoHTanimuraNCellDesigner: a process diagram editor for gene-regulatory and biochemical networksBIOSILICO200315159162
   Google Scholar
• FunahashiAMatsuokaYJourakuACellDesigner 35: a versatile modeling tool for biochemical networksProceedings of the IEEE200896812541265
   Web of Science ®Google Scholar
• KholodenkoBNNegative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascadesEur J Biochem200026761583158810712587
   PubMedGoogle Scholar
• PengLShimizuKGlobal metabolic regulation analysis for Escherichia coli K-12 based on protein expression by 2-dimensional electrophoresis and enzyme activity measurementAppl Microbiol Biotechnol200361216317812655459
   PubMed Web of Science ®Google Scholar
• LiuMDurfeeTCabreraJEGlobal transcriptional programs reveal a carbon source foraging strategy by Escherichia coliJ Biol Chem200528016159211592715705577
   PubMed Web of Science ®Google Scholar
• PetranovicDMijakovicIPhotometric assay for measuring the intracellular concentration of branched-chain amino acids in bacteriaJ Microbiol Methods200456113313614706758
   PubMed Web of Science ®Google Scholar
• LaRossaRASchlossJVThe sulfonylurea herbicide sulfometuron methyl is an extremely potent and selective inhibitor of acetolactate synthase in Salmonella typhimuriumJ Biol Chem198425914875387576378902
   PubMed Web of Science ®Google Scholar
• HeinriksonRLMeredithSCAmino acid analysis by reverse-phase high-performance liquid chromatography: precolumn derivatization with phenylisothiocyanateAnal Biochem1984136165746711815
   PubMed Web of Science ®Google Scholar