2024
Gene-edited Mtsoc1 triple mutant Medicago plants do not flower
Poulet A, Zhao M, Peng Y, Tham F, Jaudal M, Zhang L, van Wolfswinkel J, Putterill J. Gene-edited Mtsoc1 triple mutant Medicago plants do not flower. Frontiers In Plant Science 2024, 15: 1357924. PMID: 38469328, PMCID: PMC10926907, DOI: 10.3389/fpls.2024.1357924.Peer-Reviewed Original ResearchTriple mutant linesSingle mutantsFlowering timeMutant linesMultiple gene duplication eventsGene duplication eventsSOC1-like genesModel Arabidopsis thalianaMADS transcription factorsWild-type backgroundRegulation of floweringOptimal flowering timeNon-flowering plantsShort-day photoperiodCRISPR-Cas9 gene editingGene expression analysisDuplication eventsArabidopsis thalianaSOC1 genesDelayed floweringFloral promotersCrop productionFlower developmentFlowering pathwayMedicago truncatulaTemporal control of the Aux/IAA genes BnIAA32 and BnIAA34 mediates Brassica napus dual shade responses
Li Y, Guo Y, Cao Y, Xia P, Xu D, Sun N, Jiang L, Dong J. Temporal control of the Aux/IAA genes BnIAA32 and BnIAA34 mediates Brassica napus dual shade responses. Journal Of Integrative Plant Biology 2024, 66: 928-942. PMID: 37929685, DOI: 10.1111/jipb.13582.Peer-Reviewed Original ResearchConceptsB. napus seedlingsShade responseAuxin biosynthesisHypocotyl elongationGenome-wide selective sweep analysisAuxin/indole-3-acetic acidSelective sweep analysisShade-avoiding plantsIncreased auxin biosynthesisShade avoidance responseSensitivity to auxinInhibit hypocotyl elongationAuxin signalingArabidopsis thalianaShort hypocotylsPhytochrome AShade toleranceGenetic studiesB. napusPlant growthMolecular mechanismsBrassica napusLight qualitySeedlingsArabidopsis
2022
Increasing the resilience of plant immunity to a warming climate
Kim JH, Castroverde CDM, Huang S, Li C, Hilleary R, Seroka A, Sohrabi R, Medina-Yerena D, Huot B, Wang J, Nomura K, Marr SK, Wildermuth MC, Chen T, MacMicking JD, He SY. Increasing the resilience of plant immunity to a warming climate. Nature 2022, 607: 339-344. PMID: 35768511, PMCID: PMC9279160, DOI: 10.1038/s41586-022-04902-y.Peer-Reviewed Original ResearchConceptsSalicylic acidTranscription factorsSA productionPlant immune systemEffector-triggered immunityPlant growth temperatureFamily transcription factorsAspects of plantImmune transcription factorsElevated growth temperaturesPlant immunityArabidopsis thalianaBiosynthetic genesBasal immunityPlant growthSA receptorsCBP60Disease triangleWarming climateImpaired recruitmentGrowth temperatureAnimal lifeExtreme weather conditionsSARD1Climate changePlant mitochondrial FMT and its mammalian homolog CLUH controls development and behavior in Arabidopsis and locomotion in mice
Ralevski A, Apelt F, Olas JJ, Mueller-Roeber B, Rugarli EI, Kragler F, Horvath TL. Plant mitochondrial FMT and its mammalian homolog CLUH controls development and behavior in Arabidopsis and locomotion in mice. Cellular And Molecular Life Sciences 2022, 79: 334. PMID: 35652974, PMCID: PMC11071973, DOI: 10.1007/s00018-022-04382-3.Peer-Reviewed Original ResearchConceptsMitochondrial genesWhole plant morphologySalt stress responseNormal growth conditionsLeaf expansion growthArabidopsis thalianaHigher eukaryotesGene familyMitochondrial proteinsPlant morphologyHomologous functionsMitochondrial morphologyExpansion growthStress responseMitochondrial functionAnimal speciesPlantsSimilar roleGrowth conditionsHeterozygous knockout miceGenesDevelopmental alterationsKnockout miceCLUHArabidopsisKARRIKIN UP-REGULATED F-BOX 1 (KUF1) imposes negative feedback regulation of karrikin and KAI2 ligand metabolism in Arabidopsis thaliana
Sepulveda C, Guzmán MA, Li Q, Villaécija-Aguilar JA, Martinez SE, Kamran M, Khosla A, Liu W, Gendron JM, Gutjahr C, Waters MT, Nelson DC. KARRIKIN UP-REGULATED F-BOX 1 (KUF1) imposes negative feedback regulation of karrikin and KAI2 ligand metabolism in Arabidopsis thaliana. Proceedings Of The National Academy Of Sciences Of The United States Of America 2022, 119: e2112820119. PMID: 35254909, PMCID: PMC8931227, DOI: 10.1073/pnas.2112820119.Peer-Reviewed Original ResearchConceptsKAI2-ligandsF-BOX 1Fire-prone environmentsArabidopsis thalianaNegative feedback loopKarrikinsNegative feedback regulationFeedback regulationExpression increasesPlantsGerminationLigand metabolismFeedback loopFurther activationMetabolismThalianaBiosynthesisGenesSpeciesRegulationPathwayActivationDiscoveryResponseGrowth
2021
A phase-separated nuclear GBPL circuit controls immunity in plants
Huang S, Zhu S, Kumar P, MacMicking JD. A phase-separated nuclear GBPL circuit controls immunity in plants. Nature 2021, 594: 424-429. PMID: 34040255, PMCID: PMC8478157, DOI: 10.1038/s41586-021-03572-6.Peer-Reviewed Original ResearchMeSH KeywordsArabidopsisCell NucleusChromatinCryoelectron MicroscopyGene Expression Regulation, PlantGTP-Binding ProteinsIntrinsically Disordered ProteinsMediator ComplexMultigene FamilyOrganellesPhase TransitionPlant CellsPlant DiseasesPlant ImmunityPromoter Regions, GeneticRNA Polymerase IITranscription, GeneticConceptsLiquid-liquid phase separationRNA polymerase II machineryMembraneless organellesSitu cryo-electron tomographyDefense gene promotersDiverse cellular activitiesSpecific transcriptional coactivatorsHost gene expressionPhase-separated condensatesCryo-electron tomographyGuanylate-binding proteinsPlant defenseArabidopsis thalianaBiotic stressesAllosteric switchMediator complexTranscriptional responseTranscriptional coactivatorDisease resistanceGene expressionCellular activitiesIndispensable playerBiological importanceOrganellesImmune cuesH3.1K27me1 maintains transcriptional silencing and genome stability by preventing GCN5-mediated histone acetylation
Dong J, LeBlanc C, Poulet A, Mermaz B, Villarino G, Webb KM, Joly V, Mendez J, Voigt P, Jacob Y. H3.1K27me1 maintains transcriptional silencing and genome stability by preventing GCN5-mediated histone acetylation. The Plant Cell 2021, 33: 961-979. PMID: 33793815, PMCID: PMC8226292, DOI: 10.1093/plcell/koaa027.Peer-Reviewed Original ResearchConceptsGenome stabilityGenomic instabilityHistone acetylationSAGA-like complexesMultiple lysine residuesArabidopsis GCN5ARABIDOPSIS TRITHORAXArabidopsis thalianaTranscriptional silencingHeterochromatin defectsDouble mutantDNA replicationEpigenetic mechanismsGCN5Molecular roleEssential functionsDiverse rolesMolecular mechanismsLysine residuesProtein 5AcetylationMutantsPlantsADA2bATXR6
2018
Flavonol rhamnosylation indirectly modifies the cell wall defects of RHAMNOSE BIOSYNTHESIS1 mutants by altering rhamnose flux
Saffer AM, Irish VF. Flavonol rhamnosylation indirectly modifies the cell wall defects of RHAMNOSE BIOSYNTHESIS1 mutants by altering rhamnose flux. The Plant Journal 2018, 94: 649-660. PMID: 29505161, DOI: 10.1111/tpj.13885.Peer-Reviewed Original ResearchConceptsCell wallHyponastic cotyledonsRoot hair defectsEpidermal cellsCell wall defectCotyledon epidermal cellsShort root hairsCell wall polymersCotyledon phenotypeArabidopsis thalianaPetal phenotypeRhamnose synthaseRoot hairsFlavonol synthesisFlavonol glycosylationWall polymersDevelopmental defectsHair defectsMutantsBroader rolePectic polysaccharidesCotyledonsRhamnosylationPhenotypeDecreased levels
2017
Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana
Reimegård J, Kundu S, Pendle A, Irish VF, Shaw P, Nakayama N, Sundström JF, Emanuelsson O. Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana. Nucleic Acids Research 2017, 45: 3253-3265. PMID: 28175342, PMCID: PMC5389543, DOI: 10.1093/nar/gkx087.Peer-Reviewed Original ResearchConceptsMale reproductive developmentArabidopsis thalianaStamen developmentChromatin conformationTranscriptional activationReproductive developmentGenome-wide identificationRepressive histone marksCoordinated gene regulationChromatin re-organizationOpen chromatin conformationCo-regulated genesSitu hybridizationGene expression dataChromosomal organizationHistone marksChromatin levelChromosomal clusteringPHD domainGene regulationGene homologyExpression activationSelective advantageDNA fluorescenceExpression data
2013
Arabidopsis thaliana Nfu2 Accommodates [2Fe-2S] or [4Fe-4S] Clusters and Is Competent for in Vitro Maturation of Chloroplast [2Fe-2S] and [4Fe-4S] Cluster-Containing Proteins
Gao H, Subramanian S, Couturier J, Naik S, Kim S, Leustek T, Knaff D, Wu H, Vignols F, Huynh B, Rouhier N, Johnson M. Arabidopsis thaliana Nfu2 Accommodates [2Fe-2S] or [4Fe-4S] Clusters and Is Competent for in Vitro Maturation of Chloroplast [2Fe-2S] and [4Fe-4S] Cluster-Containing Proteins. Biochemistry 2013, 52: 6633-6645. PMID: 24032747, PMCID: PMC3819817, DOI: 10.1021/bi4007622.Peer-Reviewed Original ResearchConceptsYeast two-hybrid studiesIron-sulfur (Fe-SAdenosine 5'-phosphosulfate reductaseChloroplastic Fe-S proteinsReductive sulfur assimilationTwo-hybrid studiesBiosynthesis of cysteineFe-S cluster incorporationCombination of UV-visible absorptionNfu proteinsArabidopsis thalianaNFU2CXXC motifSulfur assimilationPlant metabolismFe proteinCluster transferGel filtration studiesArabidopsisFe-S clustersProteinGlutaredoxinUV-visible absorptionCysteineCluster incorporationNatural Variation Identifies Multiple Loci Controlling Petal Shape and Size in Arabidopsis thaliana
Abraham MC, Metheetrairut C, Irish VF. Natural Variation Identifies Multiple Loci Controlling Petal Shape and Size in Arabidopsis thaliana. PLOS ONE 2013, 8: e56743. PMID: 23418598, PMCID: PMC3572026, DOI: 10.1371/journal.pone.0056743.Peer-Reviewed Original ResearchConceptsPetal lengthPetal shapeAllelic variationAllelic differencesNatural variationOrgan morphologyNatural phenotypic variationReceptor-like kinasesSerine-threonine kinaseArabidopsis thalianaMorphological diversificationPhenotypic variationCell divisionAdaptive significanceOrgan sizeGenetic basisDistinct lociQuantitative variationER locusErectaLociCell proliferationKinaseProliferation patternSuch variation
2010
Crystallization and preliminary X-ray analysis of tubulin-folding cofactor A from Arabidopsis thaliana
Lu L, Nan J, Mi W, Wei C, Li L, Li Y. Crystallization and preliminary X-ray analysis of tubulin-folding cofactor A from Arabidopsis thaliana. Acta Crystallographica Section F: Structural Biology Communications 2010, 66: 954-6. PMID: 20693679, PMCID: PMC2917302, DOI: 10.1107/s1744309110023900.Peer-Reviewed Original Research
2009
Fleshy Fruit Expansion and Ripening Are Regulated by the Tomato SHATTERPROOF Gene TAGL1
Vrebalov J, Pan IL, Arroyo AJ, McQuinn R, Chung M, Poole M, Rose J, Seymour G, Grandillo S, Giovannoni J, Irish VF. Fleshy Fruit Expansion and Ripening Are Regulated by the Tomato SHATTERPROOF Gene TAGL1. The Plant Cell 2009, 21: 3041-3062. PMID: 19880793, PMCID: PMC2782289, DOI: 10.1105/tpc.109.066936.Peer-Reviewed Original ResearchConceptsTomato AGAMOUS-LIKE1MADS-box genesSeed dispersalBox genesFleshy fruitsMolecular functionsFruit expansionDistinct molecular functionsTomato orthologArabidopsis counterpartsArabidopsis thalianaMutant phenotypeAccumulation of lycopeneSeed maturationTomato plantsDevelopmental programPod shatterFruit ripeningEctopic expressionReduced carotenoidsArabidopsisSynthase 2 expressionFruit tissuesDispersalGenes
2008
STN1 protects chromosome ends in Arabidopsis thaliana
Song X, Leehy K, Warrington R, Lamb J, Surovtseva Y, Shippen D. STN1 protects chromosome ends in Arabidopsis thaliana. Proceedings Of The National Academy Of Sciences Of The United States Of America 2008, 105: 19815-19820. PMID: 19064932, PMCID: PMC2604966, DOI: 10.1073/pnas.0807867105.Peer-Reviewed Original ResearchConceptsChromosome end protectionEnd chromosome fusionsOligonucleotide/oligosaccharideSignificant sequence similarityDNA repair machineryDouble-strand breaksDistinct subcomplexesMulticellular eukaryotesTelomere capChromosome fusionsArabidopsis thalianaTelomere proteinsChromosome endsSubtelomeric DNASchizosaccharomyces pombeShelterin componentsTelomere integrityVertebrate telomeresRepair machinerySequence similarityNucleolytic attackTelomere recombinationEnd protectionDevelopmental defectsStn1
2005
The Pattern of Polymorphism in Arabidopsis thaliana
Nordborg M, Hu T, Ishino Y, Jhaveri J, Toomajian C, Zheng H, Bakker E, Calabrese P, Gladstone J, Goyal R, Jakobsson M, Kim S, Morozov Y, Padhukasahasram B, Plagnol V, Rosenberg N, Shah C, Wall J, Wang J, Zhao K, Kalbfleisch T, Schulz V, Kreitman M, Bergelson J. The Pattern of Polymorphism in Arabidopsis thaliana. PLOS Biology 2005, 3: e196. PMID: 15907155, PMCID: PMC1135296, DOI: 10.1371/journal.pbio.0030196.Peer-Reviewed Original ResearchConceptsPatterns of polymorphismA. thalianaArabidopsis thalianaEvolutionary functional genomicsLinkage disequilibrium decayGenome-wide excessLevel of polymorphismStandard neutral modelDisequilibrium decayFunctional genomicsGene densityNatural populationsSegmental duplicationsGenomic regionsNatural selectionPopulation structureThalianaPolymorphism dataNeutral modelTheoretical null distributionRare allelesShort fragmentsPolymorphismWide surveyGenomics
2002
Divergent regulation of the HEMA gene family encoding glutamyl-tRNA reductase in Arabidopsis thaliana: expression of HEMA2 is regulated by sugars, but is independent of light and plastid signalling
Ujwal ML, McCormac AC, Goulding A, Madan Kumar A, Söll D, Terry MJ. Divergent regulation of the HEMA gene family encoding glutamyl-tRNA reductase in Arabidopsis thaliana: expression of HEMA2 is regulated by sugars, but is independent of light and plastid signalling. Plant Molecular Biology 2002, 50: 81-89. PMID: 12139011, DOI: 10.1023/a:1016081114758.Peer-Reviewed Original ResearchMeSH KeywordsAldehyde OxidoreductasesArabidopsisBase SequenceCarbohydratesDNA, PlantFructoseGene Expression Regulation, EnzymologicGene Expression Regulation, PlantGlucoseGlucuronidaseLightMolecular Sequence DataPlants, Genetically ModifiedPlastidsPromoter Regions, GeneticRecombinant Fusion ProteinsSequence DeletionSignal TransductionSucroseConceptsGlutamyl-tRNA reductaseSynthesis pathwayLight-dependent mannerProduction of hemeKey regulatory stepL. ColPlastid signalingPlastid signalsTransgenic ArabidopsisArabidopsis thalianaHemA geneGene familyPhotosynthetic tissuesGusA expressionDeletion analysisFirst enzymeRegulatory stepALA synthesisHEMA2HEMA1Fusion constructsBp fragmentDivergent regulationArabidopsisPromoter
2001
Regulation of HEMA1 expression by phytochrome and a plastid signal during de‐etiolation in Arabidopsis thaliana
McCormac A, Fischer A, Kumar A, Söll D, Terry M. Regulation of HEMA1 expression by phytochrome and a plastid signal during de‐etiolation in Arabidopsis thaliana. The Plant Journal 2001, 25: 549-561. PMID: 11309145, DOI: 10.1046/j.1365-313x.2001.00986.x.Peer-Reviewed Original ResearchConceptsPhotosynthesis-related nuclear genesRNA gel blot analysisTetrapyrrole biosynthetic genesTransgenic Arabidopsis linesGlutamyl-tRNA reductaseGel blot analysisLow-fluence response modeRoots of seedlingsPlastid signalsArabidopsis linesNuclear genesArabidopsis thalianaPlant tetrapyrrolesBiosynthetic genesHemA genePhytochrome familyPhotosynthetic tissuesGusA expressionChlorophyll accumulationFactor signalsPromoter fragmentCis elementsALA synthesisTranscriptional levelPromoter constructs
1999
Selective inhibition of HEMA gene expression by photooxidation in Arabidopsis thaliana
Kumar M, Chaturvedi S, Söll D. Selective inhibition of HEMA gene expression by photooxidation in Arabidopsis thaliana. Phytochemistry 1999, 51: 847-851. PMID: 10423858, DOI: 10.1016/s0031-9422(99)00114-4.Peer-Reviewed Original ResearchConceptsArabidopsis thalianaChloroplasts of plantsGlutamyl-tRNA reductaseCarotenoid biosynthesisFirst enzymeALA formationPhotobleaching herbicidesPhotooxidative damageGene expressionSelective inhibitionCarotenoid pigmentsNorflurazonThalianaPlantsChloroplastsFirst precursorPathwayExpressionEnzymeInitial metaboliteAlaBiosynthesisInhibitionTetrapyrrolesGlutamateEvolution of genetic mechanisms controlling petal development
Kramer E, Irish V. Evolution of genetic mechanisms controlling petal development. Nature 1999, 399: 144-148. PMID: 10335842, DOI: 10.1038/20172.Peer-Reviewed Original ResearchConceptsGenetic mechanismsB-class genes APETALA3Expression patternsOrgan identity genesClasses of genesPI homologuesStamen identityMolecular genetic studiesOrgan identityArabidopsis thalianaPetal developmentFloral organsHigher eudicotsFlowering plantsAPETALA3Angiosperm petalsGenetic studiesGenesOrthologuesAngiospermsPetalsExpressionEudicotsThalianaHomologuesStructure and functional analyses of the 26S proteasome subunits from plants – Plant 26S proteasome
Fu H, Girod P, Doelling J, van Nocker S, Hochstrasser M, Finley D, Vierstra R. Structure and functional analyses of the 26S proteasome subunits from plants – Plant 26S proteasome. Molecular Biology Reports 1999, 26: 137-146. PMID: 10363660, DOI: 10.1023/a:1006926322501.Peer-Reviewed Original ResearchConceptsProteasome degrades ubiquitinated proteinsUbiquitin fusion degradation (UFD) pathwayStructure/function analysisAAA-ATPase subunitsC-terminal motifDegradation of proteinsRegulatory particle subunitsCore particlesPlant 26SRpn10 geneArabidopsis genesYeast counterpartMoss PhyscomitrellaArabidopsis thalianaPlant hormonesUbiquitin systemProteasome genesDevelopmental programHomologous recombinationProteolytic complexPlant subunitsReverse geneticsUbiquitinated proteinsUbiquitin conjugatesVivo function
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