2024
Distinct functional constraints driving conservation of the cofilin N-terminal regulatory tail
Sexton J, Potchernikov T, Bibeau J, Casanova-Sepúlveda G, Cao W, Lou H, Boggon T, De La Cruz E, Turk B. Distinct functional constraints driving conservation of the cofilin N-terminal regulatory tail. Nature Communications 2024, 15: 1426. PMID: 38365893, PMCID: PMC10873347, DOI: 10.1038/s41467-024-45878-9.Peer-Reviewed Original ResearchConceptsN-terminal regionActin bindingSequence requirementsLIM kinaseAnalysis of individual variantsInactivates cofilinS. cerevisiaeRegulatory tailFamily proteinsActin depolymerizationPhosphorylation sitesKinase recognitionSequence variantsInhibitory phosphorylationCofilinN-terminusIndividual variantsFunctional constraintsActinDisordered sequencesPhosphorylationSequenceBiochemical analysisSequence constraintsKinase
2022
Rational engineering of industrial S. cerevisiae: towards xylitol production from sugarcane straw
de Mello FDSB, Maneira C, Suarez FUL, Nagamatsu S, Vargas B, Vieira C, Secches T, Coradini ALV, de Carvalho Silvello M, Goldbeck R, Pereira GAG, Teixeira GS. Rational engineering of industrial S. cerevisiae: towards xylitol production from sugarcane straw. Journal Of Genetic Engineering And Biotechnology 2022, 20: 80. PMID: 35612634, PMCID: PMC9133290, DOI: 10.1186/s43141-022-00359-8.Peer-Reviewed Original ResearchXylose reductaseS. cerevisiaeBrazilian bioethanol industryIndustrial S. cerevisiaeMajor yeastGenomic integrationNucleotide sequenceCRISPR editingGenetic engineeringInhibitor toleranceXylitol productionIndustrial strainsRobust chassisHigh economic valueNADPH availabilityNADPH cofactorAvailable cofactorsRational engineeringRedox environmentGenetic backgroundXylitol titerHemicellulosic materialLaboratory strainsFermentation performanceCerevisiaeA mechanism of origin licensing control through autoinhibition of S. cerevisiae ORC·DNA·Cdc6
Schmidt JM, Yang R, Kumar A, Hunker O, Seebacher J, Bleichert F. A mechanism of origin licensing control through autoinhibition of S. cerevisiae ORC·DNA·Cdc6. Nature Communications 2022, 13: 1059. PMID: 35217664, PMCID: PMC8881611, DOI: 10.1038/s41467-022-28695-w.Peer-Reviewed Original ResearchConceptsOrigin recognition complexS. cerevisiaeCyclin-dependent kinase phosphorylationMcm2-7 loadingN-terminal domainCryo-electron microscopyCDK phosphorylationRecognition complexDNA replicationReplication originsÅ resolutionKinase phosphorylationMechanism of originCdc6Coordinated actionCerevisiaePhosphorylationDNAInhibitory signalsStructural detailsSite regulationRecruitmentOrc6AssemblyCdt1
2017
Structural Characterization of the Recognition of U6 snRNA by the Yeast U6 Biogenesis Protein Usb1
DeLaitsch A, Didychuk A, Montemayor E, Larson M, Lucarelli S, Butcher S. Structural Characterization of the Recognition of U6 snRNA by the Yeast U6 Biogenesis Protein Usb1. The FASEB Journal 2017, 31 DOI: 10.1096/fasebj.31.1_supplement.910.8.Peer-Reviewed Original ResearchU6 snRNAU6 RNAMutation of active site residuesTerminal phosphateDenaturing polyacrylamide gel electrophoresisBinding of RNACatalytically active spliceosomePrecursor messenger RNANon-coding intronsActive site residuesPolyacrylamide gel electrophoresisSnRNA biogenesisExoribonuclease activityS. cerevisiaeSequence identityActive spliceosomeEukaryotic cellsConserved UFluorescent RNADiffracted X-raysU6 snRNPActive siteProtein complexesSite residuesUSB1
2014
Site-specific cation release drives actin filament severing by vertebrate cofilin
Kang H, Bradley MJ, Cao W, Zhou K, Grintsevich EE, Michelot A, Sindelar CV, Hochstrasser M, De La Cruz EM. Site-specific cation release drives actin filament severing by vertebrate cofilin. Proceedings Of The National Academy Of Sciences Of The United States Of America 2014, 111: 17821-17826. PMID: 25468977, PMCID: PMC4273407, DOI: 10.1073/pnas.1413397111.Peer-Reviewed Original ResearchConceptsFilament severingActin filamentsActin filament severingKey regulatory functionsConcentration of endsActin filament fragmentationEukaryotic cellsCation-binding sitesProtein cofilinDeletion mutantsS. cerevisiaeSubunit exchangeFilament turnoverActin polymerizationEssential functionsSite-specific interactionsCofilinMolecular mechanismsAssembly dynamicsRegulatory functionsActin moleculesFilament fragmentationFilament structureSustained motilitySevering
2013
Extra‐transcriptional effects of RNA polymerase III transcription complex on neighboring RNA polymerase II transcribing genes in Saccharomyces cerevisiae
Korde A, Rosselot J, Donze D. Extra‐transcriptional effects of RNA polymerase III transcription complex on neighboring RNA polymerase II transcribing genes in Saccharomyces cerevisiae. The FASEB Journal 2013, 27: 980.8-980.8. DOI: 10.1096/fasebj.27.1_supplement.980.8.Peer-Reviewed Original ResearchChromatin proteinsTranscription complexRNA polymerase III transcription complexesPol III transcription complexesTransfer RNA genesPol III machineryPol III complexesPol II progressionRNA polymerase IIRNA polymerase IIINon-coding RNAsChromosome functionIntergenic transcriptionIntergenic transcriptsChromatin boundariesRNA genesInsulator functionPolymerase IIReadthrough transcriptsPolymerase IIIReduced translationRegulatory elementsS. cerevisiaeAtg31RNA analysis
2012
Proteome-wide Analysis of Lysine Acetylation Suggests its Broad Regulatory Scope in Saccharomyces cerevisiae *
Henriksen P, Wagner SA, Weinert BT, Sharma S, Bačinskaja G, Rehman M, Juffer AH, Walther TC, Lisby M, Choudhary C. Proteome-wide Analysis of Lysine Acetylation Suggests its Broad Regulatory Scope in Saccharomyces cerevisiae *. Molecular & Cellular Proteomics 2012, 11: 1510-1522. PMID: 22865919, PMCID: PMC3494197, DOI: 10.1074/mcp.m112.017251.Peer-Reviewed Original ResearchConceptsAcetylation sitesLysine acetylationS. cerevisiaeUnicellular eukaryotic model organismBudding yeast Saccharomyces cerevisiaeRegulatory roleBroader regulatory scopeProtein synthesisEukaryotic model organismYeast Saccharomyces cerevisiaePost-translational modificationsLysine acetylation sitesImportant regulatory roleChromatin organizationLysine acetyltransferasesModel organismsWide analysisPutative substratesRegulatory domainCritical regulatory domainsHistone H2BAcetylated proteinsProtein foldingSaccharomyces cerevisiaeBioinformatics analysis
2011
An integrative approach to ortholog prediction for disease-focused and other functional studies
Hu Y, Flockhart I, Vinayagam A, Bergwitz C, Berger B, Perrimon N, Mohr SE. An integrative approach to ortholog prediction for disease-focused and other functional studies. BMC Bioinformatics 2011, 12: 357. PMID: 21880147, PMCID: PMC3179972, DOI: 10.1186/1471-2105-12-357.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesIdentification of orthologsModel organismsDisease genesFunctions of human disease genesHuman disease-associated genesGenome-wide association study data setsOrthologous gene relationshipsFunction of orthologsHuman disease genesPercent amino acid identityAmino acid identityDisease-associated genesOnline Mendelian InheritancePossible orthologsOrthologous genesOrtholog predictionOrtholog pairsFunctional genomicsGene functionC. elegansOrthology predictionOrthologous pairsGene relationshipsS. cerevisiaeThe initial U3 snoRNA:pre‐rRNA base‐pairing interaction required for pre‐18S rRNA folding revealed by in vivo chemical probing
Baserga S, Dutca L, Gallagher J. The initial U3 snoRNA:pre‐rRNA base‐pairing interaction required for pre‐18S rRNA folding revealed by in vivo chemical probing. The FASEB Journal 2011, 25: 704.1-704.1. DOI: 10.1096/fasebj.25.1_supplement.704.1.Peer-Reviewed Original ResearchU3 snoRNABase-pairing interactionsSmall subunitRibosomal subunitU3 small nucleolar RNAPre-rRNA foldingVivo chemical probingSmall nucleolar RNAsSmall ribosomal subunitRRNA foldingEukaryotic nucleolusRibosomal proteinsU3 snoRNPCytoplasmic ribosomesNucleolar RNAsGenetic manipulationS. cerevisiaeChemical probingSnoRNAsVivo chemicalRRNAEssential processSubunitsFoldingNucleotide reactivitySIR2 and other genes are abundantly expressed in long-lived natural segregants for replicative aging of the budding yeast Saccharomyces cerevisiae
Guo Z, Adomas AB, Jackson ED, Qin H, Townsend JP. SIR2 and other genes are abundantly expressed in long-lived natural segregants for replicative aging of the budding yeast Saccharomyces cerevisiae. FEMS Yeast Research 2011, 11: 345-355. PMID: 21306556, DOI: 10.1111/j.1567-1364.2011.00723.x.Peer-Reviewed Original ResearchMeSH KeywordsCell CycleCell ProliferationGene Expression ProfilingGene Expression Regulation, FungalGenes, FungalHSP30 Heat-Shock ProteinsHydrogen PeroxideMicrobial ViabilityMitochondrial Membrane Transport ProteinsMitochondrial Precursor Protein Import Complex ProteinsOligonucleotide Array Sequence AnalysisPhenotypePolymerase Chain ReactionSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSilent Information Regulator Proteins, Saccharomyces cerevisiaeSirtuin 2Up-RegulationConceptsReplicative agingWhole genome gene expressionNatural S. cerevisiaeExpression levelsLife span variationDifferential expression levelsDifferent expression levelsEffects of genesNatural populationsYeast SaccharomycesOrganelle organizationS. cerevisiaeGene expressionNatural variationCell cycleStress responseSir2Mitochondrial functionGenesSaccharomycesAllelic associationSpan variationProgenyMetabolic responseTim17Role of the ubiquitin-like protein Urm1 as a noncanonical lysine-directed protein modifier
Van der Veen AG, Schorpp K, Schlieker C, Buti L, Damon JR, Spooner E, Ploegh HL, Jentsch S. Role of the ubiquitin-like protein Urm1 as a noncanonical lysine-directed protein modifier. Proceedings Of The National Academy Of Sciences Of The United States Of America 2011, 108: 1763-1770. PMID: 21209336, PMCID: PMC3033243, DOI: 10.1073/pnas.1014402108.Peer-Reviewed Original ResearchConceptsProtein modifiersLysine residuesMammalian cellsUbiquitin-like protein Urm1Cellular apoptosis susceptibility proteinC-terminal glycine residueSpecific lysine residuesUb-like modifiersCovalent peptide bondPeroxiredoxin Ahp1Protein urmylationSusceptibility proteinUrm1S. cerevisiaeTarget proteinsGlycine residueThioester intermediateUnique substrateAdditional roleUrmylationAhp1Sulfur carrierOxidant treatmentResiduesDual role
2009
Role of Inn1 and its interactions with Hof1 and Cyk3 in promoting cleavage furrow and septum formation in S. cerevisiae
Nishihama R, Schreiter JH, Onishi M, Vallen EA, Hanna J, Moravcevic K, Lippincott MF, Han H, Lemmon MA, Pringle JR, Bi E. Role of Inn1 and its interactions with Hof1 and Cyk3 in promoting cleavage furrow and septum formation in S. cerevisiae. Journal Of Cell Biology 2009, 185: 995-1012. PMID: 19528296, PMCID: PMC2711614, DOI: 10.1083/jcb.200903125.Peer-Reviewed Original ResearchConceptsCleavage furrowChitin synthase Chs2C-terminal regionActomyosin ring contractionCytokinesis proteinsDivision siteMitotic exitPXXP motifSH3 domainSeptum formationC2 domainS. cerevisiaePlasma membraneBind phospholipidsAMR contractionN-terminusCyk3Inn1Extracellular matrixChs2ProteinImportant interactionsHof1MembraneCytokinesisCharacterization of Novel PtdIns(4,5)P2 Effector Domains
Moravcevic K, Lemmon M. Characterization of Novel PtdIns(4,5)P2 Effector Domains. The FASEB Journal 2009, 23: 873.6-873.6. DOI: 10.1096/fasebj.23.1_supplement.873.6.Peer-Reviewed Original ResearchEffector domainPrevious genome-wide studiesPhosphoinositide-binding proteinsKey cellular processesGenome-wide studiesDifferent protein domainsEffector proteinsCellular functionsCellular processesProtein domainsBiochemical approachesS. cerevisiaeBiochemical basisCellular activitiesCandidate novelDirect interactionProteinNew insightsDomainCerevisiaeMajor rolePhosphoinositideBiologyEffectorsDiversityConservation and dispersion of sequence and function in fungal TRK potassium transporters: focus on Candida albicans
Miranda M, Bashi E, Vylkova S, Edgerton M, Slayman C, Rivetta A. Conservation and dispersion of sequence and function in fungal TRK potassium transporters: focus on Candida albicans. FEMS Yeast Research 2009, 9: 278-292. PMID: 19175416, DOI: 10.1111/j.1567-1364.2008.00471.x.Peer-Reviewed Original ResearchMeSH KeywordsCandida albicansCation Transport ProteinsChloridesConserved SequenceFungal ProteinsModels, BiologicalModels, MolecularPhylogenyPolymorphism, Single NucleotidePotassiumProtein ConformationProtein Structure, TertiarySaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSequence Homology, Amino AcidConceptsPotassium transportersHuman pathogen Candida albicansTrk potassium transportersPathogen Candida albicansDetailed molecular investigationAnimal cellsSingle nucleotide polymorphismsDNA sequencesS. cerevisiaeComplete sequenceC. albicansTrk proteinSequence analysisCandida albicansInhibitor sensitivityFunctional comparisonNucleotide polymorphismsSelective drug actionMolecular investigationsAntimicrobial peptidesHomologuesPotential targetSecondary functionSalivary antimicrobial peptidesProtein
2007
Investigation of Novel Molecular Targets for Pleckstrin Homology (PH) Domains Found in Oncogenes Implicated in Breast Cancer
Keleti D, Lemmon M. Investigation of Novel Molecular Targets for Pleckstrin Homology (PH) Domains Found in Oncogenes Implicated in Breast Cancer. 2007 DOI: 10.21236/ada469536.Peer-Reviewed Original ResearchHomology domainPH domainHuman PH domainsOSBP PH domainHost adaptor proteinsMembrane-targeting modulesPleckstrin homology domainGTPase Arf1Adaptor proteinNovel molecular targetsS. cerevisiaePlasma membraneMembrane lipidsSpecific membraneHigh affinityPPInsDirect interactionComparable affinityDomain classesMolecular targetsGolgiBinding propertiesMembraneRecent studiesAffinity
2006
Population structure and gene evolution in Saccharomyces cerevisiae
Aa E, Townsend JP, Adams RI, Nielsen KM, Taylor JW. Population structure and gene evolution in Saccharomyces cerevisiae. FEMS Yeast Research 2006, 6: 702-715. PMID: 16879422, DOI: 10.1111/j.1567-1364.2006.00059.x.Peer-Reviewed Original ResearchConceptsPopulation genetic variationPopulation structureS. cerevisiaeDistinct population structureSaccharomyces sensu strictoSulfur-based fungicidesSulfite exporterGene evolutionGene treesGene SSU1Historical selectionTranscription factorsHigh polymorphismNatural isolatesProtein productsCerevisiaeSequence analysisSSU1Oak forestsGreater polymorphismSensu strictoWine yeastSequence studiesFZF1Expression levelsSingle-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
Newman JR, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 2006, 441: 840-846. PMID: 16699522, DOI: 10.1038/nature04785.Peer-Reviewed Original ResearchConceptsSingle-cell proteomic analysisBiological noiseSingle-cell resolutionProtein abundance measurementsDNA microarray analysisProtein noise levelsSingle-cell dataHigh-throughput flow cytometryProtein-specific differencesProteomic analysisS. cerevisiaeMinimal mediumProtein abundanceMicroarray analysisCellular behaviorCellular responsesProtein synthesisMessenger RNAEnvironmental changesProtein modesProtein levelsProtein expressionFlow cytometryDetailed viewRemarkable structureEcological and evolutionary genomics of Saccharomyces cerevisiae
LANDRY CR, TOWNSEND JP, HARTL DL, CAVALIERI D. Ecological and evolutionary genomics of Saccharomyces cerevisiae. Molecular Ecology 2006, 15: 575-591. PMID: 16499686, DOI: 10.1111/j.1365-294x.2006.02778.x.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsEvolutionary genomic studiesPrime model systemImportant genetic variationPowerful model speciesEvolutionary genomicsEvolutionary geneticsEvolutionary forcesFunctional genomicsYeast genomeNumerous habitatsModel speciesGenomic studiesUnicellular fungiGenetic variationBiology questionsS. cerevisiaeNatural isolatesGenetic levelGenomicsSaccharomycesModel systemYeastEukaryotesGenomeHabitats
2005
Rsp5 ubiquitin ligase affects isoprenoid pathway and cell wall organization in S. cerevisiae.
Kamińska J, Kwapisz M, Grabińska K, Orłowski J, Boguta M, Palamarczyk G, Zoładek T. Rsp5 ubiquitin ligase affects isoprenoid pathway and cell wall organization in S. cerevisiae. Acta Biochimica Polonica 2005, 52: 207-20. PMID: 15827618, DOI: 10.18388/abp.2005_3510.Peer-Reviewed Original ResearchConceptsCell wall integrityIsoprenoid pathwayWall integrityPlasma membraneRsp5 ubiquitin-protein ligaseCell wallCell wall organizationRsp5 ubiquitin ligaseUbiquitin-protein ligaseCell wall structureWild-type strainNorthern blot analysisWall organizationProtein glycosylationDimethylallyl diphosphateType strainUbiquitin ligaseIsopentenyl diphosphateS. cerevisiaeCytosolic distributionErgosterol biosynthesisKey enzymeRegulatory roleChitin levelsMolecular level
2004
The Glc7p Nuclear Phosphatase Promotes mRNA Export by Facilitating Association of Mex67p with mRNA
Gilbert W, Guthrie C. The Glc7p Nuclear Phosphatase Promotes mRNA Export by Facilitating Association of Mex67p with mRNA. Molecular Cell 2004, 13: 201-212. PMID: 14759366, DOI: 10.1016/s1097-2765(04)00030-9.Peer-Reviewed Original ResearchMeSH KeywordsBiological TransportCell NucleusGenetic VectorsIn Situ HybridizationModels, BiologicalmRNA Cleavage and Polyadenylation FactorsNuclear ProteinsNucleocytoplasmic Transport ProteinsPhosphoprotein PhosphatasesPhosphorylationPoly AProtein BindingProtein Phosphatase 1Protein Structure, TertiaryRNA-Binding ProteinsRNA, MessengerSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsTemperatureUltraviolet RaysConceptsMRNA exportMammalian SR proteinsPromote mRNA exportSR-like proteinsEfficient mRNA exportS. cerevisiaeExport receptorAdaptor proteinCytoplasmic kinasesDephosphorylation eventsAlternative adaptorsFacilitative associationsBind mRNANpl3pSR proteinsGlc7pMex67pSerine-phosphorylationCytoplasmic phosphorylationProteinMRNAPhosphorylationAdaptorDephosphorylationRNA
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