2023
Separating Inner and Outer Membranes of Escherichia coli by EDTA-free Sucrose Gradient Centrifugation
Shu S, Mi W. Separating Inner and Outer Membranes of Escherichia coli by EDTA-free Sucrose Gradient Centrifugation. Bio-protocol 2023, 13: e4638. PMID: 36968434, PMCID: PMC10031520, DOI: 10.21769/bioprotoc.4638.Peer-Reviewed Original ResearchInner membraneOuter membraneGram-negative bacteriaPeptidoglycan cell wallEscherichia coliMembrane protein purificationTotal cell membranesSucrose gradient centrifugationMembrane proteinsCell wallProtein structureFunctional studiesProtein purificationTotal membranesCell membraneSucrose gradientsBiochemical proceduresGradient centrifugationProteinMembraneColiBacteriaGradient ultracentrifugationLipidsUltracentrifugation method
2022
Regulatory mechanisms of lipopolysaccharide synthesis in Escherichia coli
Shu S, Mi W. Regulatory mechanisms of lipopolysaccharide synthesis in Escherichia coli. Nature Communications 2022, 13: 4576. PMID: 35931690, PMCID: PMC9356133, DOI: 10.1038/s41467-022-32277-1.Peer-Reviewed Original ResearchConceptsRegulatory mechanismsAnti-adaptor proteinsFirst committed stepMost Gram-negative bacteriaEssential glycolipidEssential membraneGram-negative bacteriaTransmembrane helicesAdaptor proteinCommitted stepCytoplasmic domainFtsHLPS synthesisAnalysis unravelsLipopolysaccharide synthesisLapBEscherichia coliE. coliPermeability barrierProtein levelsLpxCProtease activityProteinColiYejM
2021
Escherichia coli chemotaxis is information limited
Mattingly H, Kamino K, Machta B, Emonet T. Escherichia coli chemotaxis is information limited. Nature Physics 2021, 17: 1426-1431. PMID: 35035514, PMCID: PMC8758097, DOI: 10.1038/s41567-021-01380-3.Peer-Reviewed Original ResearchEscherichia coli small molecule metabolism at the host–microorganism interface
Gatsios A, Kim CS, Crawford JM. Escherichia coli small molecule metabolism at the host–microorganism interface. Nature Chemical Biology 2021, 17: 1016-1026. PMID: 34552219, PMCID: PMC8675634, DOI: 10.1038/s41589-021-00807-5.Peer-Reviewed Original ResearchConceptsSmall molecule metabolismE. coliHost-bacteria interfaceModel organismsHost-bacterial interactionsChemical arsenalMolecule metabolismEscherichia coliHuman microbiotaColiSmall molecule chemistryMetabolismCommon componentSignalingOrganismsBiologyDisease modulationCommensalEscherichiaHostPathogenic roleRoleMicrobiotaMembersHistorical, current, and emerging tools for identification and serotyping of Shigella
Halimeh F, Rafei R, Osman M, Kassem I, Diene S, Dabboussi F, Rolain J, Hamze M. Historical, current, and emerging tools for identification and serotyping of Shigella. Brazilian Journal Of Microbiology 2021, 52: 2043-2055. PMID: 34524650, PMCID: PMC8441030, DOI: 10.1007/s42770-021-00573-5.Peer-Reviewed Original ResearchInterconnecting solvent quality, transcription, and chromosome folding in Escherichia coli
Xiang Y, Surovtsev IV, Chang Y, Govers SK, Parry BR, Liu J, Jacobs-Wagner C. Interconnecting solvent quality, transcription, and chromosome folding in Escherichia coli. Cell 2021, 184: 3626-3642.e14. PMID: 34186018, DOI: 10.1016/j.cell.2021.05.037.Peer-Reviewed Original Research
2020
Cellular Stress Upregulates Indole Signaling Metabolites in Escherichia coli
Kim CS, Li JH, Barco B, Park HB, Gatsios A, Damania A, Wang R, Wyche TP, Piizzi G, Clay NK, Crawford JM. Cellular Stress Upregulates Indole Signaling Metabolites in Escherichia coli. Cell Chemical Biology 2020, 27: 698-707.e7. PMID: 32243812, PMCID: PMC7306003, DOI: 10.1016/j.chembiol.2020.03.003.Peer-Reviewed Original ResearchConceptsPlant-pathogen defense responsesPlant innate immune responsesPathogen defense responsesSmall molecule signalsEscherichia coliPersister cell formationStress-induced metabolitesPrimary human tissuesDefense responsesRedox stressorsInnate immune responseDistinct immunological responsesMolecule signalsMolecular studiesCell formationColiBacterial metabolitesDefensive responsesSmall moleculesPlantsHuman tissuesImmune responseImmunological responseInfection modelMetabolites
2018
Characterization of Natural Colibactin–Nucleobase Adducts by Tandem Mass Spectrometry and Isotopic Labeling. Support for DNA Alkylation by Cyclopropane Ring Opening
Xue M, Shine E, Wang W, Crawford JM, Herzon SB. Characterization of Natural Colibactin–Nucleobase Adducts by Tandem Mass Spectrometry and Isotopic Labeling. Support for DNA Alkylation by Cyclopropane Ring Opening. Biochemistry 2018, 57: 6391-6394. PMID: 30365310, PMCID: PMC6997931, DOI: 10.1021/acs.biochem.8b01023.Peer-Reviewed Original ResearchConceptsGenotoxic secondary metabolitesMethionine auxotrophic strainsE. coliGut commensal Escherichia coliClb gene clusterColibactin biosynthesisElectrophilic CyclopropanesGene clusterDNA alkylationPrevious biosynthetic studiesSecondary metabolitesAuxotrophic strainsEscherichia coliCommensal Escherichia coliBiosynthetic studiesFirst identificationBiosynthesisColiColibactinPUC19 DNAIsotopic labelingNucleotidesDNATandem mass spectrometryCertain strains
2017
Comparative Proteomics Enables Identification of Nonannotated Cold Shock Proteins in E. coli
D’Lima N, Khitun A, Rosenbloom AD, Yuan P, Gassaway BM, Barber KW, Rinehart J, Slavoff SA. Comparative Proteomics Enables Identification of Nonannotated Cold Shock Proteins in E. coli. Journal Of Proteome Research 2017, 16: 3722-3731. PMID: 28861998, PMCID: PMC5647875, DOI: 10.1021/acs.jproteome.7b00419.Peer-Reviewed Original ResearchConceptsCold shock proteinsComparative proteomicsShock proteinsRelated Gram-negative bacteriaMass spectrometry-based proteomicsSmall open reading framesMolecular genetic approachesWhole genome databaseSpectrometry-based proteomicsOpen reading frameE. coliEukaryotic genomesGram-negative bacteriaCellular functionsDifferent organismsGenetic approachesReading frameBiological roleProteomicsMicroproteinsEnable identificationProteinColiGenomeRecent advancesAn insider's perspective: Bacteroides as a window into the microbiome
Wexler AG, Goodman AL. An insider's perspective: Bacteroides as a window into the microbiome. Nature Microbiology 2017, 2: 17026. PMID: 28440278, PMCID: PMC5679392, DOI: 10.1038/nmicrobiol.2017.26.Peer-Reviewed Original ResearchConceptsGut bacteriumHuman gut BacteroidesModel organismsMicrobial communitiesMetagenome sequencesGut BacteroidesClose relativesGut microorganismsEscherichia coliCommensal microorganismsCentury of studyBacteriumMicroorganismsGut microbiotaImportant insightsBacteroidesSheer diversityHuman healthGenomicsEcologyOrganismsEcosystemsDiversityMicrobiomeColi
2016
A Mechanistic Model for Colibactin-Induced Genotoxicity
Healy AR, Nikolayevskiy H, Patel JR, Crawford JM, Herzon SB. A Mechanistic Model for Colibactin-Induced Genotoxicity. Journal Of The American Chemical Society 2016, 138: 15563-15570. PMID: 27934011, PMCID: PMC5359767, DOI: 10.1021/jacs.6b10354.Peer-Reviewed Original ResearchConceptsGene clusterE. coliDNA double-strand breaksDouble-strand breaksProbiotic Nissle 1917Clb gene clusterEukaryotic cellsCertain commensalDNA bindingProbiotic E. coliDisparate phenotypesPrecolibactinsAlkylate DNAColibactinIsolation effortsFermentation productsColiDNA alkylationDNANissle 1917Mechanistic modelSide chainsNatural productsMetabolite structuresEfficient DNA alkylationStructure of the BAM complex and its implications for biogenesis of outer-membrane proteins
Han L, Zheng J, Wang Y, Yang X, Liu Y, Sun C, Cao B, Zhou H, Ni D, Lou J, Zhao Y, Huang Y. Structure of the BAM complex and its implications for biogenesis of outer-membrane proteins. Nature Structural & Molecular Biology 2016, 23: 192-196. PMID: 26900875, DOI: 10.1038/nsmb.3181.Peer-Reviewed Original ResearchAn Engineered Rare Codon Device for Optimization of Metabolic Pathways
Wang Y, Li C, Khan M, Wang Y, Ruan Y, Zhao B, Zhang B, Ma X, Zhang K, Zhao X, Ye G, Guo X, Feng G, He L, Ma G. An Engineered Rare Codon Device for Optimization of Metabolic Pathways. Scientific Reports 2016, 6: 20608. PMID: 26852704, PMCID: PMC4745014, DOI: 10.1038/srep20608.Peer-Reviewed Original ResearchConceptsRare codonsCognate tRNAMetabolic pathwaysExpression levelsProtein expressionTarget protein expressionAspartyl-tRNA synthetaseCodons AGGReporter geneRelevant enzymesCopy numberEscherichia coliCodonFatty acid yieldGenesSteady-state kineticsE. coliTRNAPathwayExpressionColiIntermediate levelsTwo-fold increaseSynthetaseAcid yield
2015
A flexible codon in genomically recoded Escherichia coli permits programmable protein phosphorylation
Pirman NL, Barber KW, Aerni HR, Ma NJ, Haimovich AD, Rogulina S, Isaacs FJ, Rinehart J. A flexible codon in genomically recoded Escherichia coli permits programmable protein phosphorylation. Nature Communications 2015, 6: 8130. PMID: 26350500, PMCID: PMC4566969, DOI: 10.1038/ncomms9130.Peer-Reviewed Original ResearchConceptsProtein phosphorylationProtein phosphorylation eventsFull-length proteinNon-phosphorylated formPhosphoserine-containing proteinsPhosphorylation eventsMEK1 kinaseUAG codonKinase activityRecombinant DNADNA templateEscherichia coliE. coliCodonPhosphorylationFunctional informationSerineProteinColiBiochemical investigationsPhosphoproteomeInefficient productionKinasePhosphoserineDNA
2014
A Constant Size Extension Drives Bacterial Cell Size Homeostasis
Campos M, Surovtsev IV, Kato S, Paintdakhi A, Beltran B, Ebmeier SE, Jacobs-Wagner C. A Constant Size Extension Drives Bacterial Cell Size Homeostasis. Cell 2014, 159: 1433-1446. PMID: 25480302, PMCID: PMC4258233, DOI: 10.1016/j.cell.2014.11.022.Peer-Reviewed Original ResearchConceptsCell size homeostasisCell size controlSize homeostasisSingle-cell microscopyCell cycle controlCaulobacter crescentusAsymmetric divisionHomeostasis mechanismsBacteria Escherichia coliCell cycleEscherichia coliDifferent growth ratesCell growthCell lengthSize controlCell sizeHomeostasisBacteriaSize thresholdGrowth rateDivisionDirect experimental evidenceCrescentusSize paradigmColiExpanded Cellular Amino Acid Pools Containing Phosphoserine, Phosphothreonine, and Phosphotyrosine
Steinfeld JB, Aerni HR, Rogulina S, Liu Y, Rinehart J. Expanded Cellular Amino Acid Pools Containing Phosphoserine, Phosphothreonine, and Phosphotyrosine. ACS Chemical Biology 2014, 9: 1104-1112. PMID: 24646179, PMCID: PMC4027946, DOI: 10.1021/cb5000532.Peer-Reviewed Original ResearchConceptsNonstandard amino acidsAmino acidsGenetic codeOrthogonal aminoacyl-tRNA synthetaseCellular amino acid poolsIntracellular levelsPhosphorylated amino acidsAminoacyl-tRNA synthetaseE. coliLow-phosphate mediumAmino acid poolCotranslational insertionTRNA pairsMetabolic engineeringRecombinant proteinsDeficient cellsStandard amino acidsProtein synthesisWT cellsPhosphoserinePhosphotyrosinePhosphothreonineProteinAcid poolColiAdaptability of non-genetic diversity in bacterial chemotaxis
Frankel NW, Pontius W, Dufour YS, Long J, Hernandez-Nunez L, Emonet T. Adaptability of non-genetic diversity in bacterial chemotaxis. ELife 2014, 3: e03526. PMID: 25279698, PMCID: PMC4210811, DOI: 10.7554/elife.03526.Peer-Reviewed Original ResearchConceptsGene regulationNon-genetic diversityBacterial chemotaxis systemHeritable controlChemotaxis systemSelectable traitAdvantageous diversityEnvironmental variationBacterial chemotaxisEnvironmental variabilityClonal populationsDiverse environmentsDiversityE. coliProtein levelsMutationsDifferent environmentsRegulationForagingTraitsColiDiversificationBacteriaColonizationPopulation
2011
Expanding the Genetic Code of Escherichia coli with Phosphoserine
Park HS, Hohn MJ, Umehara T, Guo LT, Osborne EM, Benner J, Noren CJ, Rinehart J, Söll D. Expanding the Genetic Code of Escherichia coli with Phosphoserine. Science 2011, 333: 1151-1154. PMID: 21868676, PMCID: PMC5547737, DOI: 10.1126/science.1207203.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acyl-tRNA SynthetasesAnticodonChloramphenicolChloramphenicol O-AcetyltransferaseCodon, TerminatorDrug Resistance, BacterialEscherichia coliGenetic CodeGenetic EngineeringHumansMAP Kinase Kinase 1Peptide Elongation Factor TuPhosphoserineProtein EngineeringProtein Modification, TranslationalRecombinant Fusion ProteinsRNA, BacterialRNA, Transfer, Amino Acid-SpecificRNA, Transfer, Amino AcylRNA, Transfer, CysTransfer RNA AminoacylationConceptsGenetic codeEF-TuMitogen-activated ERKQuality control functionTransfer RNAProtein engineeringEscherichia coli strainsKinase 1Phosphoamino acidsMolecular biologyEscherichia coliO-phosphoserineColi strainsGeneral utilityDisease researchCanonical positionPhosphoproteomePhosphoserineRNABiologyERKProteinSynthetaseColiResiduesPrecise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement
Isaacs FJ, Carr PA, Wang HH, Lajoie MJ, Sterling B, Kraal L, Tolonen AC, Gianoulis TA, Goodman DB, Reppas NB, Emig CJ, Bang D, Hwang SJ, Jewett MC, Jacobson JM, Church GM. Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement. Science 2011, 333: 348-353. PMID: 21764749, PMCID: PMC5472332, DOI: 10.1126/science.1205822.Peer-Reviewed Original ResearchConceptsGenome engineeringSynonymous codon substitutionsGenome engineering technologiesSynthetic lethal effectMegabase scaleCodon replacementsTAA codonCodon substitutionsRecombination frequencyCodon modificationGenetic landscapeEscherichia coliGenomeChromosomesCodonPrecise changesLethal effectsPrecise manipulationEngineering technologyNucleotidesColiPhenotypeTagsModificationObscured phylogeny and possible recombinational dormancy in Escherichia coli
Leopold S, Sawyer S, Whittam T, Tarr P. Obscured phylogeny and possible recombinational dormancy in Escherichia coli. BMC Ecology And Evolution 2011, 11: 183. PMID: 21708031, PMCID: PMC3152902, DOI: 10.1186/1471-2148-11-183.Peer-Reviewed Original ResearchConceptsComplex recombination historyDefinition of speciesE. coliSegments of chromosomesPhylogenetic structureSingle nucleotide polymorphismsNew speciesGenetic materialE. coli groupEscherichia coliNucleotide polymorphismsRepresentative strainsPhylogenySpeciesColiChromosomesRecombination historyDormancyOrganismsColi groupBiologyDNARecombinationPolymorphismStrains
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