2022
Cross-kingdom expression of synthetic genetic elements promotes discovery of metabolites in the human microbiome
Patel JR, Oh J, Wang S, Crawford JM, Isaacs FJ. Cross-kingdom expression of synthetic genetic elements promotes discovery of metabolites in the human microbiome. Cell 2022, 185: 1487-1505.e14. PMID: 35366417, PMCID: PMC10619838, DOI: 10.1016/j.cell.2022.03.008.Peer-Reviewed Original ResearchConceptsSynthetic genetic elementsGenetic elementsBiosynthetic gene clusterCross-species expressionCross-species interactionsDiverse organismsGene clusterBiosynthetic machineryHeterologous expressionRegulatory regionsTRNA synthetasesBiosynthetic pathwayNative contextTranslational activityBiosynthetic capacityHuman microbiomeMetabolic capacityPositive bacteriaSmall moleculesExpressionPathwayValuable compoundsLactobacillus inersEukaryotesSynthetases
2021
A Conserved Nonribosomal Peptide Synthetase in Xenorhabdus bovienii Produces Citrulline-Functionalized Lipopeptides
Li JH, Cho W, Hamchand R, Oh J, Crawford JM. A Conserved Nonribosomal Peptide Synthetase in Xenorhabdus bovienii Produces Citrulline-Functionalized Lipopeptides. Journal Of Natural Products 2021, 84: 2692-2699. PMID: 34581573, PMCID: PMC9970011, DOI: 10.1021/acs.jnatprod.1c00573.Peer-Reviewed Original ResearchConceptsNonribosomal peptide synthetasePeptide synthetaseBiosynthetic gene clusterComparative genomic analysisFree-living infective juvenilesNRPS genesEffector proteinsInsect larvaeSpecialized metabolitesGene clusterMutualistic relationshipXenorhabdus bovieniiHeterologous expressionGenomic analysisRichest producersEntomopathogenic bacteriumSecondary metabolitesHost larvaeInfective juvenilesTermination domainInhibitor pathwayExogenous alcoholsLarvaeSpeciesComplex array
2019
Structure elucidation of colibactin and its DNA cross-links
Xue M, Kim CS, Healy AR, Wernke KM, Wang Z, Frischling MC, Shine EE, Wang W, Herzon SB, Crawford JM. Structure elucidation of colibactin and its DNA cross-links. Science 2019, 365 PMID: 31395743, PMCID: PMC6820679, DOI: 10.1126/science.aax2685.Peer-Reviewed Original ResearchConceptsColibactin-producing bacteriaCell biology dataColibactin gene clusterCombination of geneticsComplex secondary metabolitesGene clusterIsotope labelingSecondary metabolitesBiology dataColibactinHuman gutTandem mass spectrometryBacteriaPhysiological effectsMass spectrometryStructure elucidationGutGeneticsDNAEnzymeChemical synthesisEscherichiaElucidationMetabolitesLabelingBacterial Analogs of Plant Tetrahydropyridine Alkaloids Mediate Microbial Interactions in a Rhizosphere Model System
Lozano GL, Park HB, Bravo JI, Armstrong EA, Denu JM, Stabb EV, Broderick NA, Crawford JM, Handelsman J. Bacterial Analogs of Plant Tetrahydropyridine Alkaloids Mediate Microbial Interactions in a Rhizosphere Model System. Applied And Environmental Microbiology 2019, 85: e03058-18. PMID: 30877115, PMCID: PMC6498172, DOI: 10.1128/aem.03058-18.Peer-Reviewed Original ResearchConceptsRhizosphere communitiesGene clusterUncharacterized biosynthetic gene clustersMicrobiome of plantsRhizosphere microbial communitiesBiosynthetic gene clusterIndividual species' behaviorSecretion of antibioticsRhizosphere model systemPlant photosynthatesGenetic screenInterbacterial competitionConvergent evolutionRhizosphere bacteriaMicrobial interactionsRhizosphere inhabitantsCommunity compositionMicrobial communitiesRepertoire of antibioticsDiverse consortiumSoybean rhizosphereSelective environmentGenetic basisMultidimensional nuclear magnetic resonanceSoybean rootsCharacterization of a Hybrid Nonribosomal Peptide–Carbohydrate Biosynthetic Pathway in Photorhabdus luminescens
Perez CE, Crawford JM. Characterization of a Hybrid Nonribosomal Peptide–Carbohydrate Biosynthetic Pathway in Photorhabdus luminescens. Biochemistry 2019, 58: 1131-1140. PMID: 30694662, DOI: 10.1021/acs.biochem.8b01120.Peer-Reviewed Original ResearchConceptsHypothetical proteinsBiosynthetic pathwayNRPS machineryHybrid nonribosomal peptide synthetaseBacterial biosynthetic pathwaysStable isotope labelingNonribosomal peptide synthetaseProtein mass spectrometryEntomopathogen PhotorhabdusFascinating chemistryOrphan pathwaysCharacterization of oligosaccharidesAcetyl-glucosamine moietyProduction of metabolitesGenomic islandsGlycoamino acidsNovel chemistryGene clusterHeterologous expressionProtein biochemistryPeptide synthetaseBiological functionsGenome sequencingMass spectrometryIsotope labeling
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 strainsDiscovering antibiotics from the global microbiome
Lam YC, Crawford JM. Discovering antibiotics from the global microbiome. Nature Microbiology 2018, 3: 392-393. PMID: 29588534, DOI: 10.1038/s41564-018-0135-5.Peer-Reviewed Original ResearchFunctional Characterization of a Condensation Domain That Links Nonribosomal Peptide and Pteridine Biosynthetic Machineries in Photorhabdus luminescens
Perez CE, Park HB, Crawford JM. Functional Characterization of a Condensation Domain That Links Nonribosomal Peptide and Pteridine Biosynthetic Machineries in Photorhabdus luminescens. Biochemistry 2018, 57: 354-361. PMID: 29111689, DOI: 10.1021/acs.biochem.7b00863.Peer-Reviewed Original ResearchConceptsNonribosomal peptide synthetasesCondensation domainMetabolic pathwaysSecondary metabolite biosynthesisSpecialized metabolic pathwaysBiosynthetic gene clusterNRPS condensation domainDistinct enzymatic systemsImportant small moleculesSecondary metabolite analysisCitric acid cycleMetabolite biosynthesisFunctional diversityGene clusterBiosynthetic machineryCellular redoxPeptide synthetasesNonribosomal peptidesBiosynthetic systemsQuorum sensingFunctional characterizationSolution studiesGenetic lociNatural productsBiochemical level
2017
ClbS Is a Cyclopropane Hydrolase That Confers Colibactin Resistance
Tripathi P, Shine EE, Healy AR, Kim CS, Herzon SB, Bruner SD, Crawford JM. ClbS Is a Cyclopropane Hydrolase That Confers Colibactin Resistance. Journal Of The American Chemical Society 2017, 139: 17719-17722. PMID: 29112397, PMCID: PMC6202678, DOI: 10.1021/jacs.7b09971.Peer-Reviewed Original ResearchConceptsGene productsBiosynthetic gene clusterSpecific mechanistic roleMolecular functionsGene clusterResidue mutantsHost bacteriaCancer formationColorectal cancer formationEscherichia coliCommensal Escherichia coliColibactinMechanistic roleHydrolase activityPrecolibactinsX-ray structureMolecular-level viewShare similaritiesElectrophilic CyclopropanesBacterial viabilityBacteriaHydrolaseGenotoxic effectsMutantsBiosynthesisStructure and Functional Analysis of ClbQ, an Unusual Intermediate-Releasing Thioesterase from the Colibactin Biosynthetic Pathway
Guntaka NS, Healy AR, Crawford JM, Herzon SB, Bruner SD. Structure and Functional Analysis of ClbQ, an Unusual Intermediate-Releasing Thioesterase from the Colibactin Biosynthetic Pathway. ACS Chemical Biology 2017, 12: 2598-2608. PMID: 28846367, PMCID: PMC5830302, DOI: 10.1021/acschembio.7b00479.Peer-Reviewed Original ResearchConceptsColibactin gene clusterÅ crystal structurePolyketide secondary metabolitesAcyl-thioester substratesColibactin biosynthesisGene clusterBiosynthetic pathwayAtypical roleGene productsBiochemical characterizationFunctional analysisSecondary metabolitesGreater catalytic efficiencyCancer formationColorectal cancer formationHuman gutSpecific functionsNovel insightsCarrier proteinThioesteraseGenetic deletionClbQColibactinCatalytic efficiencyPathwayGenome mining unearths a hybrid nonribosomal peptide synthetase-like-pteridine synthase biosynthetic gene cluster
Park HB, Perez CE, Barber KW, Rinehart J, Crawford JM. Genome mining unearths a hybrid nonribosomal peptide synthetase-like-pteridine synthase biosynthetic gene cluster. ELife 2017, 6: e25229. PMID: 28431213, PMCID: PMC5384830, DOI: 10.7554/elife.25229.Peer-Reviewed Original ResearchConceptsBiosynthetic gene clusterNonribosomal peptide synthetaseGene clusterPeptide synthetaseGenome synteny analysisHybrid nonribosomal peptide synthetaseSecondary metabolic enzymesQuantitative proteomic analysisExtensive gene deletionsRedox-active cofactorsSynteny analysisMutualistic roleGenome miningBiosynthetic machineryPhenotypic variationBiosynthetic potentialNonribosomal peptidesProteomic analysisQuorum sensingGenetic lociMetabolic enzymesAcyl side chainPhenotypic variantsGene deletionDistinct classesAcyl Histidines: New N‐Acyl Amides from Legionella pneumophila
Tørring T, Shames SR, Cho W, Roy CR, Crawford JM. Acyl Histidines: New N‐Acyl Amides from Legionella pneumophila. ChemBioChem 2017, 18: 638-646. PMID: 28116768, PMCID: PMC5546091, DOI: 10.1002/cbic.201600618.Peer-Reviewed Original ResearchConceptsBiosynthetic gene clusterOrphan biosynthetic gene clustersPathogen-insect interactionsAmino acid-derived metabolitesLegionella pneumophilaOrphan pathwaysBiosynthetic genesVariety of protozoanGene clusterN-acyl amidesMolecular networkingHuman macrophagesDistinct groupsPneumophilaCausative agentPathwayMetabolitesHistidine metabolitesNew N-acylGenesLegionnaires' diseaseAmoebaeProtozoaMacrophagesPathogens
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 alkylationLinking Biosynthetic Gene Clusters to their Metabolites via Pathway-Targeted Molecular Networking
Trautman EP, Crawford JM. Linking Biosynthetic Gene Clusters to their Metabolites via Pathway-Targeted Molecular Networking. Current Topics In Medicinal Chemistry 2016, 16: 1705-1716. PMID: 26456470, PMCID: PMC5055756, DOI: 10.2174/1568026616666151012111046.Peer-Reviewed Original ResearchConceptsBiosynthetic gene clusterGene clusterMicrobial biosynthetic gene clustersMetabolic pathwaysGenome sequence informationSecondary metabolic pathwaysMolecular networkingHuman-microbe interactionsNew metabolic pathwaysComplex metabolomeSmall moleculesBiosynthetic logicActive small moleculesFunctional characterizationBioinformatics predictionSequence informationSmall molecule metabolitesHuman microbiomeExperimental structural characterizationGut bacteriaPathwayNatural productsMetabolitesPharmacological potentialAvailable databases
2015
Gut Symbionts from Distinct Hosts Exhibit Genotoxic Activity via Divergent Colibactin Biosynthesis Pathways
Engel P, Vizcaino MI, Crawford JM. Gut Symbionts from Distinct Hosts Exhibit Genotoxic Activity via Divergent Colibactin Biosynthesis Pathways. Applied And Environmental Microbiology 2015, 81: 1502-1512. PMID: 25527542, PMCID: PMC4309719, DOI: 10.1128/aem.03283-14.Peer-Reviewed Original ResearchConceptsNonribosomal peptide synthetaseBiosynthetic pathwayBacterial symbiontsGut symbiontsSecondary metabolitesEukaryotic cellsGenomic islandsBacterial gut symbiontDiverse symbiotic associationsDivergent variantsDNA damagePolyketide synthase pathwayE. coliComparative metabolomic analysisRelated secondary metabolitesPathway-dependent mannerSymbiotic associationGene clusterMicrobial interactionsBiosynthesis pathwayDistinct hostsPeptide synthetaseMammalian gutHoney beesSymbionts
2014
An Atypical Orphan Carbohydrate-NRPS Genomic Island Encodes a Novel Lytic Transglycosylase
Guo X, Crawford JM. An Atypical Orphan Carbohydrate-NRPS Genomic Island Encodes a Novel Lytic Transglycosylase. Cell Chemical Biology 2014, 21: 1271-1277. PMID: 25219963, PMCID: PMC4224617, DOI: 10.1016/j.chembiol.2014.07.025.Peer-Reviewed Original ResearchConceptsGenome synteny analysisSynteny analysisGenomic islandsLytic transglycosylaseNatural product gene clustersOrphan biosynthetic pathwaysGene deletion analysisGenome sequencing platformsRare structural featureBiochemical reconstructionHypothetical proteinsGene clusterAcetyl-glucosamine moietyHeterologous expressionDeletion analysisProtein homologyBiosynthetic pathwayIsland contentNew small moleculesSequencing platformsMetabolic chemistryTransglycosylasePathwaySmall moleculesNatural productsMerging chemical ecology with bacterial genome mining for secondary metabolite discovery
Vizcaino MI, Guo X, Crawford JM. Merging chemical ecology with bacterial genome mining for secondary metabolite discovery. Journal Of Industrial Microbiology & Biotechnology 2014, 41: 285-299. PMID: 24127069, PMCID: PMC3946945, DOI: 10.1007/s10295-013-1356-5.Peer-Reviewed Original ResearchConceptsBacterial genome miningOrphan biosynthetic pathwaysGenome miningChemical ecologyBiosynthetic pathwayBacterial secondary metabolismBiosynthetic gene clusterSecondary metabolic pathwaysSecondary metabolite discoveryLaboratory cultivation conditionsBioactive secondary metabolitesHost-bacteria interactionsMicrobial chemicalSymbiotic lifestylePhotorhabdus bacteriaSecondary metabolismGene clusterMutualistic relationshipSmall moleculesPhenotypic variationEcological nichesDiverse natural productsNatural productsPhysiological attributesSymbiotic system
2010
Absence of the aflatoxin biosynthesis gene, norA, allows accumulation of deoxyaflatoxin B1 in Aspergillus flavus cultures
Ehrlich KC, Chang P, Scharfenstein LL, Cary JW, Crawford JM, Townsend CA. Absence of the aflatoxin biosynthesis gene, norA, allows accumulation of deoxyaflatoxin B1 in Aspergillus flavus cultures. FEMS Microbiology Letters 2010, 305: 65-70. PMID: 20158523, PMCID: PMC2891446, DOI: 10.1111/j.1574-6968.2010.01914.x.Peer-Reviewed Original ResearchConceptsBiosynthetic gene clusterAflatoxin biosynthesis genesCytochrome P450 monooxygenaseAflatoxin biosynthetic gene clusterWild-type A. flavusBiosynthesis genesGene clusterP450 monooxygenaseAflatoxin biosynthesisCarcinogenic aflatoxinsAccumulation of aflatoxinBiosynthesisA. flavusMinor toxinsO-methylsterigmatocystinAspergillus speciesFinal stepAspergillus flavusNew metabolitesQuantities of aflatoxinElevated quantitiesMutantsAccumulationFlavusGenes