2022
Transcriptional Divergence Underpinning Sexual Development in the Fungal Class Sordariomycetes
Kim W, Wang Z, Kim H, Pham K, Tu Y, Townsend JP, Trail F. Transcriptional Divergence Underpinning Sexual Development in the Fungal Class Sordariomycetes. MBio 2022, 13: e01100-22. PMID: 35638737, PMCID: PMC9239162, DOI: 10.1128/mbio.01100-22.Peer-Reviewed Original ResearchConceptsSingle-copy orthologous genesFungal class SordariomycetesTranscriptional divergenceOrthologous genesHypothetical proteinsNovel genesPerithecial developmentTranscriptional activationClass SordariomycetesGene expressionRich genomic resourceGene expression divergenceMulticellular fruiting bodiesBody developmentSuccessful sexual reproductionKey developmental genesSpecies-specific functionsFunctional protein domainsKnockout of genesRecent common ancestorGene expression levelsOrthologous counterpartsSordariomycetes speciesDevelopmental transcriptomeExpression divergence
2020
Making and Breaking Leupeptin Protease Inhibitors in Pathogenic Gammaproteobacteria
Li J, Oh J, Kienesberger S, Kim NY, Clarke DJ, Zechner EL, Crawford J. Making and Breaking Leupeptin Protease Inhibitors in Pathogenic Gammaproteobacteria. Angewandte Chemie International Edition 2020, 59: 17872-17880. PMID: 32609431, DOI: 10.1002/anie.202005506.Peer-Reviewed Original ResearchConceptsBacterial small moleculesTripeptide aldehyde protease inhibitorsHeterologous expression analysisProtease inhibitorsColonization phenotypesPhotorhabdus speciesHypothetical proteinsNematode hostsPathogenic GammaproteobacteriaExpression analysisBacterial productionAccessory enzymesGenetic distributionProteolytic degradationSmall moleculesEnzymeLeupeptinKlebsiella oxytocaInhibitorsGammaproteobacteriaLigasesXenorhabdusPhotorhabdusBiosynthesisSpeciesMaking and Breaking Leupeptin Protease Inhibitors in Pathogenic Gammaproteobacteria
Li J, Oh J, Kienesberger S, Kim N, Clarke D, Zechner E, Crawford J. Making and Breaking Leupeptin Protease Inhibitors in Pathogenic Gammaproteobacteria. Angewandte Chemie 2020, 132: 18028-18036. DOI: 10.1002/ange.202005506.Peer-Reviewed Original ResearchBacterial small moleculesTripeptide aldehyde protease inhibitorsHeterologous expression analysisProtease inhibitorsPhotorhabdus speciesColonization phenotypesHypothetical proteinsNematode hostsPathogenic GammaproteobacteriaExpression analysisBacterial productionAccessory enzymesGenetic distributionProteolytic degradationSmall moleculesEnzymeLeupeptinKlebsiella oxytocaInhibitorsLigasesXenorhabdusGammaproteobacteriaPhotorhabdusBiosynthesisSpecies
2019
Characterization 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
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 products
2012
Thousands of missed genes found in bacterial genomes and their analysis with COMBREX
Wood DE, Lin H, Levy-Moonshine A, Swaminathan R, Chang YC, Anton BP, Osmani L, Steffen M, Kasif S, Salzberg SL. Thousands of missed genes found in bacterial genomes and their analysis with COMBREX. Biology Direct 2012, 7: 37. PMID: 23111013, PMCID: PMC3534567, DOI: 10.1186/1745-6150-7-37.Peer-Reviewed Original ResearchConceptsProtein-coding genesProkaryotic genome annotationCost of sequencingGenome annotationHypothetical proteinsBacterial genomesProkaryotic genomesShort genesArcady MushegianLikely geneGenesPhenotype informationGenomeHomologPotential targetPathogenic organismsAnnotationSequencingProteinFunction databaseAnnotation methodDramatic reductionGenBankOrganismsPharmaceutical research
2002
mda-5: An interferon-inducible putative RNA helicase with double-stranded RNA-dependent ATPase activity and melanoma growth-suppressive properties
Kang DC, Gopalkrishnan RV, Wu Q, Jankowsky E, Pyle AM, Fisher PB. mda-5: An interferon-inducible putative RNA helicase with double-stranded RNA-dependent ATPase activity and melanoma growth-suppressive properties. Proceedings Of The National Academy Of Sciences Of The United States Of America 2002, 99: 637-642. PMID: 11805321, PMCID: PMC117358, DOI: 10.1073/pnas.022637199.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphatasesAmino Acid SequenceAnimalsApoptosisCell DifferentiationCell DivisionCloning, MolecularDEAD-box RNA HelicasesDNA, ComplementaryGrowth InhibitorsHumansInterferon Type IInterferon-Induced Helicase, IFIH1MelanomaMolecular Sequence DataRecombinant ProteinsRNA HelicasesRNA, Double-StrandedSequence Homology, Amino AcidTumor Cells, CulturedTumor Stem Cell AssayConceptsRNA-dependent ATPase activityCaspase recruitment domainHelicase motifsHuman melanoma cellsRecruitment domainRNA helicase motifsRNA-dependent ATPaseMDA-5RNA helicase domainPutative RNA helicaseMelanoma cellsEarly response genesATPase activityProtein kinase C activationGrowth-suppressive propertiesMelanoma differentiation-associated gene 5Appropriate pharmacological manipulationKinase C activationHypothetical proteinsRNA helicaseHelicase domainDifferentiation-associated gene 5Mediator of IFNSubtraction hybridizationMda-5 expression
1998
An Evolutionarily Conserved Gene on Human Chromosome 5q33–q34,UBH1,Encodes a Novel Deubiquitinating Enzyme
Hansen-Hagge T, Janssen J, Hameister H, Papa F, Zechner U, Seriu T, Jauch A, Becke D, Hochstrasser M, Bartram C. An Evolutionarily Conserved Gene on Human Chromosome 5q33–q34,UBH1,Encodes a Novel Deubiquitinating Enzyme. Genomics 1998, 49: 411-418. PMID: 9615226, DOI: 10.1006/geno.1998.5275.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBase SequenceCaenorhabditis elegansChromosome MappingChromosomes, Human, Pair 14Chromosomes, Human, Pair 5Conserved SequenceDNA PrimersEndopeptidasesEvolution, MolecularHumansIn Situ HybridizationLeukemiaMiceMolecular Sequence DataMultigene FamilyNervous SystemNeuronsPolymerase Chain ReactionPseudogenesSaccharomyces cerevisiaeSequence AlignmentSequence Homology, Amino AcidTranscription, GeneticTranslocation, GeneticUbiquitin ThiolesteraseConceptsGene familyDeubiquitinating enzymeNovel multigene familyGalactosidase fusion proteinSitu hybridizationNovel deubiquitinating enzymeNorthern blot analysisConserved geneCaenorhabditis elegansHypothetical proteinsMultigene familyHuman genesLow-level expressionFunctional membersHuman chromosomesProtein displayFusion proteinMouse tissuesEscherichia coliChromosome 5q33Blot analysisBreakpoint sequencesEnzyme 1GenesEnzyme
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