2023
7SK methylation by METTL3 promotes transcriptional activity
Perez-Pepe M, Desotell A, Li H, Li W, Han B, Lin Q, Klein D, Liu Y, Goodarzi H, Alarcón C. 7SK methylation by METTL3 promotes transcriptional activity. Science Advances 2023, 9: eade7500. PMID: 37163588, PMCID: PMC10171809, DOI: 10.1126/sciadv.ade7500.Peer-Reviewed Original ResearchConceptsTranscriptional elongationTranscriptional responseAdaptive transcriptional responseHeterogeneous nuclear ribonucleoproteinsElongation factor complexPositive transcription elongation factor complexGrowth factorExtracellular signalsRNA modificationsRNA 7SKEpidermal growth factorCell signalingInduces phosphorylationMethyltransferase 3Nuclear ribonucleoproteinFactor complexTranscriptional activityUnknown functionMethylationMETTL3RibonucleoproteinPhosphorylationTEFbElongationSignaling
2022
An essential periplasmic protein coordinates lipid trafficking and is required for asymmetric polar growth in mycobacteria
Gupta K, Gwin C, Rahlwes K, Biegas K, Wang C, Park J, Liu J, Swarts B, Morita Y, Rego E. An essential periplasmic protein coordinates lipid trafficking and is required for asymmetric polar growth in mycobacteria. ELife 2022, 11: e80395. PMID: 36346214, PMCID: PMC9678360, DOI: 10.7554/elife.80395.Peer-Reviewed Original ResearchConceptsPeriplasmic proteinsPolar growthNew cell wall materialOld poleQuantitative time-lapse imagingAsymmetric polar growthCell wall synthesisCell envelope compositionCell wall materialTime-lapse imagingCellular asymmetryEssential proteinsBacterial geneticsEssential transporterSingle geneWall synthesisLipid traffickingPopulation of cellsPlasma membraneTMM transportUnknown functionBroad functionsMycolic acidsTrehalose monomycolateEnvelope compositionGut Commensal Bacteroidetes Encode a Novel Class of Vitamin B12-Binding Proteins
Putnam EE, Abellon-Ruiz J, Killinger BJ, Rosnow JJ, Wexler AG, Folta-Stogniew E, Wright AT, van den Berg B, Goodman AL. Gut Commensal Bacteroidetes Encode a Novel Class of Vitamin B12-Binding Proteins. MBio 2022, 13: e02845-21. PMID: 35227073, PMCID: PMC8941943, DOI: 10.1128/mbio.02845-21.Peer-Reviewed Original ResearchConceptsComplex microbial communitiesHuman gut commensalTerminal globular domainModel organismsGut microbiomeMicrobial communitiesCompetitive fitnessTransport systemStructural homologsAccessory proteinsNew proteinsAdditional proteinsTransport proteinsGlobular domainUnknown functionMultiple transport systemsSystem lociKey roleGut commensalsProteinDiverse repertoireRelated moleculesMajor groupsFitnessOrganisms
2021
Nodal modulator (NOMO) is required to sustain endoplasmic reticulum morphology
Amaya C, Cameron C, Devarkar SC, Seager S, Gerstein MB, Xiong Y, Schlieker C. Nodal modulator (NOMO) is required to sustain endoplasmic reticulum morphology. Journal Of Biological Chemistry 2021, 297: 100937. PMID: 34224731, PMCID: PMC8327139, DOI: 10.1016/j.jbc.2021.100937.Peer-Reviewed Original ResearchConceptsEndoplasmic reticulumER structural integrityGenetic epistasis analysisMembrane-bound organellesP62/sequestosome 1Endoplasmic reticulum morphologyImmunoglobulin-like domainsProtein light chain 3Light chain 3Epistasis analysisIdentical orthologsProteomic screenER morphologyHuman genomeMolecular playersNOMO1Protein foldingSequestosome 1Unknown functionER networkChain 3Lipid synthesisProper functionProtein 1OrthologsSystematic functional analysis of Rab GTPases reveals limits of neuronal robustness to environmental challenges in flies
Kohrs F, Daumann I, Pavlovic B, Jin E, Kiral F, Lin S, Port F, Wolfenberg H, Mathejczyk T, Linneweber G, Chan C, Boutros M, Hiesinger P. Systematic functional analysis of Rab GTPases reveals limits of neuronal robustness to environmental challenges in flies. ELife 2021, 10: e59594. PMID: 33666175, PMCID: PMC8016483, DOI: 10.7554/elife.59594.Peer-Reviewed Original ResearchConceptsRab GTPasesMembrane traffickingSystematic functional analysisObvious morphological defectsAutophagy-independent roleMutant collectionNull mutantsFertile fliesMaintenance defectsGTPasesNeuronal robustnessFunctional analysisMolecular switchMorphological defectsUnknown functionHalf exhibitMutantsFliesNeuronal functionGenesTraffickingEnvironmental challengesRabRab26Nervous system
2020
CPAMD8 loss-of-function underlies non-dominant congenital glaucoma with variable anterior segment dysgenesis and abnormal extracellular matrix
Bonet-Fernández J, Aroca-Aguilar J, Corton M, Ramírez A, Alexandre-Moreno S, García-Antón M, Salazar J, Ferre-Fernández J, Atienzar-Aroca R, Villaverde C, Iancu I, Tamayo A, Méndez-Hernández C, Morales-Fernández L, Rojas B, Ayuso C, Coca-Prados M, Martinez-de-la-Casa J, García-Feijoo J, Escribano J. CPAMD8 loss-of-function underlies non-dominant congenital glaucoma with variable anterior segment dysgenesis and abnormal extracellular matrix. Human Genetics 2020, 139: 1209-1231. PMID: 32274568, DOI: 10.1007/s00439-020-02164-0.Peer-Reviewed Original ResearchMeSH KeywordsAdultalpha-MacroglobulinsAnimalsAnterior ChamberCase-Control StudiesComplement C3CRISPR-Cas SystemsEmbryo, NonmammalianExtracellular MatrixEye AbnormalitiesFemaleGene EditingGene ExpressionGenes, RecessiveGlaucomaHigh-Throughput Nucleotide SequencingHumansLoss of Function MutationMaleMiddle AgedPedigreeTrabecular MeshworkTrabeculectomyTrypsin Inhibitor, Kazal PancreaticZebrafishConceptsZebrafish embryosAnterior segment dysgenesisExtracellular matrixPrimary congenital glaucomaNext-generation DNA sequencingGross developmental abnormalitiesFunction pathogenic mechanismQuantitative reverse transcription PCRAbnormal extracellular matrixCongenital glaucomaCRISPR/Mesenchyme-like cellsTrabecular meshwork cellsReverse transcription-PCRUnknown functionExtracellular matrix disorganizationDNA sequencingGenesGenetic alterationsEmbryosMeshwork cellsDevelopmental abnormalitiesTranscription-PCRAnterior chamber angleDisease Role
2018
FcpB Is a Surface Filament Protein of the Endoflagellum Required for the Motility of the Spirochete Leptospira
Wunder EA, Slamti L, Suwondo DN, Gibson KH, Shang Z, Sindelar CV, Trajtenberg F, Buschiazzo A, Ko AI, Picardeau M. FcpB Is a Surface Filament Protein of the Endoflagellum Required for the Motility of the Spirochete Leptospira. Frontiers In Cellular And Infection Microbiology 2018, 8: 130. PMID: 29868490, PMCID: PMC5953323, DOI: 10.3389/fcimb.2018.00130.Peer-Reviewed Original ResearchConceptsUnique motility apparatusRandom transposon mutantsWild-type morphologyCryo-electron microscopyHypothetical genesMotility-deficient mutantsMotility apparatusFlagellar proteinsTransposon mutantsMotility phenotypeNovel componentUnknown functionProtein B.Spiral-shaped endsFilament proteinsMutantsGenesSpirochete LeptospiraFCPbEndoflagellaBacteriaProteinFilamentsPhenotypeSurface components
2017
Sensing Self and Foreign Circular RNAs by Intron Identity
Chen YG, Kim MV, Chen X, Batista PJ, Aoyama S, Wilusz JE, Iwasaki A, Chang HY. Sensing Self and Foreign Circular RNAs by Intron Identity. Molecular Cell 2017, 67: 228-238.e5. PMID: 28625551, PMCID: PMC5610545, DOI: 10.1016/j.molcel.2017.05.022.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceDEAD Box Protein 58Encephalitis Virus, Venezuelan EquineEncephalomyelitis, Venezuelan EquineHEK293 CellsHeLa CellsHost-Pathogen InteractionsHumansImmune ToleranceImmunity, InnateIntronsMiceNucleic Acid ConformationProtein BindingRAW 264.7 CellsReceptors, ImmunologicRNARNA Processing, Post-TranscriptionalRNA-Binding ProteinsRNA, CircularRNA, MessengerSpliceosomesTransfectionConceptsCircular RNAsInnate immunity genesMammalian transcriptionDiverse RNACytoplasmic fociHuman circRNAsMammalian cellsImmunity genesEndogenous splicingHuman intronsInnate immune sensingPrimary sequenceCircRNA sequenceRNA structureCircRNAsUnknown functionIntronsRNASensor RIGImmune sensingInnate immunitySelf-nonself discriminationPotent inductionSequenceBiogenesisStructural and Biochemical Characterization of a Periplasmic Lipoprotein with a Role in Adaptation of Salmonella to Magnesium Limitation
May J, Rasmussen D, Davie T, Vaneerd C, Groisman E, Bhattacharyya B. Structural and Biochemical Characterization of a Periplasmic Lipoprotein with a Role in Adaptation of Salmonella to Magnesium Limitation. The FASEB Journal 2017, 31 DOI: 10.1096/fasebj.31.1_supplement.761.11.Peer-Reviewed Original ResearchPeriplasmic lipoproteinMagnesium limitationAtomic-resolution structural dataFamily of proteinsFundamental biochemical processesBeta-sheet secondary structureAdaptation of SalmonellaGenetic screenCircular dichroism spectroscopyBacterial adaptationLocalization sequenceSalmonella proteinsBiochemical approachesIon homeostasisBacterial virulenceProtein monomersBiochemical characterizationCertain pathogenic bacteriaMolecular mechanismsMonomeric molecular weightUnknown functionPhysiological functionsLiving cellsSecondary structureDichroism spectroscopyARPP-16 Is a Striatal-Enriched Inhibitor of Protein Phosphatase 2A Regulated by Microtubule-Associated Serine/Threonine Kinase 3 (Mast 3 Kinase)
Andrade EC, Musante V, Horiuchi A, Matsuzaki H, Brody AH, Wu T, Greengard P, Taylor JR, Nairn AC. ARPP-16 Is a Striatal-Enriched Inhibitor of Protein Phosphatase 2A Regulated by Microtubule-Associated Serine/Threonine Kinase 3 (Mast 3 Kinase). Journal Of Neuroscience 2017, 37: 2709-2722. PMID: 28167675, PMCID: PMC5354324, DOI: 10.1523/jneurosci.4559-15.2017.Peer-Reviewed Original ResearchConceptsSerine/threonine protein phosphataseSerine/threonine kinase 3Threonine protein phosphataseARPP-16Protein phosphataseKinase 3Protein phosphatase 2AProtein kinase A (PKA) signalingSmall acid-soluble proteinsKinase A SignalingAcid-soluble proteinsActivation of PKAPP2A substratesPhosphatase 2AARPP-16/19Heterotrimeric formMarked dephosphorylationSignal transductionSelective inhibitorPP2AA SignalingUnknown functionStriatal medium spiny neuronsMedium spiny neuronsSer46
2016
Upstream ORFs are prevalent translational repressors in vertebrates
Johnstone TG, Bazzini AA, Giraldez AJ. Upstream ORFs are prevalent translational repressors in vertebrates. The EMBO Journal 2016, 35: 706-723. PMID: 26896445, PMCID: PMC4818764, DOI: 10.15252/embj.201592759.Peer-Reviewed Original ResearchConceptsUpstream open reading framesUntranslated mRNA regionsPost-transcriptional regulationOpen reading frameMRNA leader sequenceClear repressionVertebrate transcriptomesRibosome footprintingCellular diversityTranslational repressorIndividual genesNatural selectionUpstream ORFsReading frameLeader sequenceRegulatory potentialActive translationRegulatory codeInitiation contextGene expressionMRNA regionsUnknown functionReporter experimentsVertebratesIntercistronic distance
2015
Deletion of MLIP (Muscle-enriched A-type Lamin-interacting Protein) Leads to Cardiac Hyperactivation of Akt/Mammalian Target of Rapamycin (mTOR) and Impaired Cardiac Adaptation*
Cattin ME, Wang J, Weldrick JJ, Roeske CL, Mak E, Thorn SL, DaSilva JN, Wang Y, Lusis AJ, Burgon PG. Deletion of MLIP (Muscle-enriched A-type Lamin-interacting Protein) Leads to Cardiac Hyperactivation of Akt/Mammalian Target of Rapamycin (mTOR) and Impaired Cardiac Adaptation*. Journal Of Biological Chemistry 2015, 290: 26699-26714. PMID: 26359501, PMCID: PMC4646324, DOI: 10.1074/jbc.m115.678433.Peer-Reviewed Original ResearchMeSH KeywordsAdaptation, PhysiologicalAnimalsCardiomegalyCarrier ProteinsCo-Repressor ProteinsFemaleGene Expression RegulationGenome-Wide Association StudyHeart Function TestsHemodynamicsIsoproterenolMaleMiceMice, Inbred C57BLMice, KnockoutMyocardiumMyocytes, CardiacNuclear ProteinsPhosphorylationProto-Oncogene Proteins c-aktSignal TransductionStress, PhysiologicalTOR Serine-Threonine KinasesUltrasonographyConceptsAKT/mTOR pathwayGenome-wide association studiesAkt/mammalian targetMTOR pathwayAkt/mTOR activityAkt/mTORUnique proteinsUnknown functionAssociation studiesMTOR activityMammalian targetCardiac adaptationRegenerative abilityGenetic associationAdult heartPathwayHomeostasisMyocardial metabolic abnormalitiesNormal cardiac functionAdaptationEarly responseMetabolic abnormalitiesCardiac functionMLIPCardiac stressFlagella-independent surface motility in Salmonella enterica serovar Typhimurium
Park SY, Pontes MH, Groisman EA. Flagella-independent surface motility in Salmonella enterica serovar Typhimurium. Proceedings Of The National Academy Of Sciences Of The United States Of America 2015, 112: 1850-1855. PMID: 25624475, PMCID: PMC4330729, DOI: 10.1073/pnas.1422938112.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphatasesAmino Acid SequenceBacterial ProteinsBase SequenceCation Transport ProteinsComputational BiologyFlagellaGene Expression Regulation, BacterialMagnesiumMembrane Transport ProteinsMitochondrial Proton-Translocating ATPasesMolecular Sequence DataMovementMutagenesisSalmonella typhimuriumSequence AlignmentSequence Analysis, DNAConceptsSalmonella enterica serovar TyphimuriumEnterica serovar TyphimuriumPhoP/PhoQ regulatory systemMgtC mutantFlagellum-independent mannerFlagella-mediated motilitySerovar TyphimuriumForm of motilityWild-type SalmonellaNull mutantsMultiprotein complexesMgtC proteinF1Fo-ATPaseHeterologous promoterSmall proteinsUnknown functionProteinase K treatmentSurface motilityMgtAMutantsGroup motilityAllelic formsRegulatory systemBacterial replicationGenes
2014
A Role for Noncoding Variation in Schizophrenia
Roussos P, Mitchell A, Voloudakis G, Fullard J, Pothula V, Tsang J, Stahl E, Georgakopoulos A, Ruderfer D, Charney A, Okada Y, Siminovitch K, Worthington J, Padyukov L, Klareskog L, Gregersen P, Plenge R, Raychaudhuri S, Fromer M, Purcell S, Brennand K, Robakis N, Schadt E, Akbarian S, Sklar P. A Role for Noncoding Variation in Schizophrenia. Cell Reports 2014, 9: 1417-1429. PMID: 25453756, PMCID: PMC4255904, DOI: 10.1016/j.celrep.2014.10.015.Peer-Reviewed Original ResearchMeSH KeywordsArthritis, RheumatoidCalcium Channels, L-TypeDatabases, GeneticDNA, IntergenicEnhancer Elements, GeneticGene Expression RegulationGenetic LociGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansMolecular Sequence AnnotationOrgan SpecificityPolymorphism, Single NucleotidePromoter Regions, GeneticProtein BindingRisk FactorsSchizophreniaConceptsExpression quantitative trait lociGenome-wide significant lociCommon variant lociQuantitative trait lociPluripotent stem cell-derived neuronsDistal regulatory elementsStem cell-derived neuronsPotential physical interactionsCell-derived neuronsRegulatory element sequencesPotential functional roleGenome architectureChromosomal loopingTranscriptional regulationFunctional annotationTrait lociSignificant lociNoncoding SNPsRegulatory elementsNoncoding variationsRisk lociVariant lociUnknown functionFunctional linkElement sequences
2011
A Viral Nuclear Noncoding RNA Binds Re-localized Poly(A) Binding Protein and Is Required for Late KSHV Gene Expression
Borah S, Darricarrère N, Darnell A, Myoung J, Steitz JA. A Viral Nuclear Noncoding RNA Binds Re-localized Poly(A) Binding Protein and Is Required for Late KSHV Gene Expression. PLOS Pathogens 2011, 7: e1002300. PMID: 22022268, PMCID: PMC3192849, DOI: 10.1371/journal.ppat.1002300.Peer-Reviewed Original ResearchConceptsPAN RNAKaposi's Sarcoma-Associated HerpesvirusNuclear noncoding RNANuclear noncoding RNAsShutoff effectLytic phaseKSHV gene expressionRepertoire of functionsTail of mRNATransient transfection experimentsConsequence of expressionLate viral proteinsNoncoding RNAsExonuclease proteinNuclear RNAProtein C1Translation efficiencyHost mRNAsMRNA stabilityGene expressionUnknown functionTransfection experimentsViral mRNAsPABPC1Binding proteinInteraction of Recombinant Myocilin with the Matricellular Protein SPARC: Functional Implications
Aroca-Aguilar JD, Sánchez-Sánchez F, Ghosh S, Fernández-Navarro A, Coca-Prados M, Escribano J. Interaction of Recombinant Myocilin with the Matricellular Protein SPARC: Functional Implications. Investigative Ophthalmology & Visual Science 2011, 52: 179-189. PMID: 20926826, PMCID: PMC3053273, DOI: 10.1167/iovs.09-4866.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBlotting, WesternCalcium-Binding ProteinsCell LineChromatography, High Pressure LiquidCytoskeletal ProteinsExtracellular Matrix ProteinsEye ProteinsGene Expression ProfilingGlycoproteinsHumansKidneyMicroscopy, FluorescenceMolecular Sequence DataOsteonectinPolymerase Chain ReactionProtein BindingRecombinant Fusion ProteinsRecombinant ProteinsTwo-Hybrid System TechniquesConceptsHEK 293T cellsSolid-phase binding assaysInteraction of myocilinRecombinant proteinsRecombinant myocilinMatricellular proteinEC domainTerminal olfactomedin domainTwo-hybrid analysisTwo-hybrid systemProtein-protein interactionsFull-length myocilinC-terminal domainN-terminal domainC-terminal regionCalcium binding domainsBinding assaysOlfactomedin domainC-terminal fragmentBinding domainsLinker regionUnknown functionExtracellular glycoproteinIntracellular interactionsSPARC family
2010
New insights into the formation of fungal aromatic polyketides
Crawford JM, Townsend CA. New insights into the formation of fungal aromatic polyketides. Nature Reviews Microbiology 2010, 8: 879-889. PMID: 21079635, PMCID: PMC3181163, DOI: 10.1038/nrmicro2465.Peer-Reviewed Original ResearchConceptsAromatic polyketide biosynthesisPolyketide synthasesStarter unitAromatic polyketidesNR-PKSsAcyl carrier protein domainIterative polyketide synthasesProduct template (PT) domainsAcyl-CoA poolSingle genomeProduct releaseKetosynthase domainCorrect substrateProtein domainsSubsequent product releaseBiosynthesis systemTemplate domainFilamentous fungiUnknown functionEnzyme structureDiverse familySynthesis pathwayKey cyclizationCyclization patternsPolyketidesDown-Regulation of a Host MicroRNA by a Herpesvirus saimiri Noncoding RNA
Cazalla D, Yario T, Steitz JA. Down-Regulation of a Host MicroRNA by a Herpesvirus saimiri Noncoding RNA. Science 2010, 328: 1563-1566. PMID: 20558719, PMCID: PMC3075239, DOI: 10.1126/science.1187197.Peer-Reviewed Original ResearchConceptsHSURs 1Noncoding RNAsHost cell gene expressionMiR-27Binding-dependent mannerPotential binding sitesMiRNA pathwayHost cell microRNAsCoimmunoprecipitation experimentsEctopic expressionTarget genesTransient knockdownGene expressionUnknown functionHost microRNAsViral strategiesDown regulationBinding sitesMiRNAsMicroRNAsRNAExpressionCellsT cellsNcRNAStabilization of VEGFR2 Signaling by Cerebral Cavernous Malformation 3 Is Critical for Vascular Development
He Y, Zhang H, Yu L, Gunel M, Boggon TJ, Chen H, Min W. Stabilization of VEGFR2 Signaling by Cerebral Cavernous Malformation 3 Is Critical for Vascular Development. Science Signaling 2010, 3: ra26. PMID: 20371769, PMCID: PMC3052863, DOI: 10.1126/scisignal.2000722.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCardiovascular SystemEndothelial CellsFluorescent Antibody Technique, IndirectGene DeletionGene Expression ProfilingGene Knockdown TechniquesHematopoiesisHumansImmunoblottingImmunohistochemistryImmunoprecipitationMiceReverse Transcriptase Polymerase Chain ReactionSignal TransductionVascular Endothelial Growth Factor Receptor-2ConceptsCarboxyl-terminal domainVascular endothelial growth factor receptor 2Vascular developmentHuman vascular malformationsCerebral cavernous malformation 3Early embryonic stagesCerebral cavernous malformationsEndothelial cell-specific deletionApoptotic stimuliCell-specific deletionVivo functionEmbryonic angiogenesisEndothelial growth factor receptor 2Unknown functionVEGF stimulationVEGFR2 signalingEmbryonic stagesMessenger RNASmooth muscle cellsGrowth factor receptor 2DeletionCCM3 genesFactor receptor 2Muscle cellsGenesThe large, noncoding OLE RNA is associated with membrane biochemistry
Block K, Wallace J, Puerta‐Fernandez E, Breaker R. The large, noncoding OLE RNA is associated with membrane biochemistry. The FASEB Journal 2010, 24: 493.2-493.2. DOI: 10.1096/fasebj.24.1_supplement.493.2.Peer-Reviewed Original ResearchOLE RNAB. haloduransMembrane biochemistryMembrane-spanning proteinsHigh-throughput sequencingEnergy-generating pathwaysEscherichia coli cellsGel shift assaysNorthern blot analysisRNA fluorescenceSpecific ribonucleoproteinGram-positive bacteriaShift assaysColi cellsUnknown functionProbable binding siteSitu hybridizationBlot analysisBinding sitesHaloduransHoward Hughes Medical InstituteRNAProteinBiochemistryCells
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