2025
Polyamine metabolism is dysregulated in COXFA4-related mitochondrial disease
Marquez J, Viviano S, Beckman E, Thies J, Friedland-Little J, Lam C, Deniz E, Shelkowitz E. Polyamine metabolism is dysregulated in COXFA4-related mitochondrial disease. Human Genetics And Genomics Advances 2025, 6: 100418. PMID: 39967265, PMCID: PMC11946867, DOI: 10.1016/j.xhgg.2025.100418.Peer-Reviewed Original ResearchOrnithine decarboxylase pathwayCytochrome c oxidaseMitochondrial diseaseCause of mitochondrial diseaseAnalysis of cellular gene expressionSubunits of cytochrome c oxidaseC oxidaseTissue-specific diseasesCellular gene expressionDeficiency of cytochrome c oxidaseLeigh-like diseaseElectron donor NADHDownstream deficienciesMitochondrial membraneProtein complexesCellular functionsOxidative phosphorylationProtein subunitsGene expressionMetabolic pathwaysPolyamine metabolismPathwayProteinPoor growthAdenosine triphosphateCapturing eukaryotic ribosome dynamics in situ at high resolution
Cheng J, Wu C, Li J, Yang Q, Zhao M, Zhang X. Capturing eukaryotic ribosome dynamics in situ at high resolution. Nature Structural & Molecular Biology 2025, 1-11. PMID: 39789210, DOI: 10.1038/s41594-024-01454-9.Peer-Reviewed Original Research
2024
The T4bSS of Legionella features a two-step secretion pathway with an inner membrane intermediate for secretion of transmembrane effectors
Malmsheimer S, Grin I, Bohn E, Franz-Wachtel M, Macek B, Sahr T, Smollich F, Chetrit D, Meir A, Roy C, Buchrieser C, Wagner S. The T4bSS of Legionella features a two-step secretion pathway with an inner membrane intermediate for secretion of transmembrane effectors. PLOS Pathogens 2024, 20: e1012118. PMID: 39546547, PMCID: PMC11602083, DOI: 10.1371/journal.ppat.1012118.Peer-Reviewed Original ResearchConceptsEukaryotic host cellsEffector proteinsMembrane intermediatesC-terminal secretion signalHost cellsSoluble effector proteinsCytoplasmic sideBacterial inner membraneMechanism of secretionSecretion systemSecretion signalPeriplasmic loopTransmembrane effectorSecretion pathwayT4BSSInner membraneSubcellular locationIntracellular survivalMembrane targetingProtein complexesEfficient translocationBacterial cellsProteomic analysisL. pneumophilaSecretion processNext steps for targeted protein degradation
Krone M, Crews C. Next steps for targeted protein degradation. Cell Chemical Biology 2024, 32: 219-226. PMID: 39500325, DOI: 10.1016/j.chembiol.2024.10.004.Peer-Reviewed Original ResearchRab6a enables BICD2/dynein-mediated trafficking of human papillomavirus from the trans-Golgi network during virus entry
Choi J, Speckhart K, Tsai B, DiMaio D. Rab6a enables BICD2/dynein-mediated trafficking of human papillomavirus from the trans-Golgi network during virus entry. MBio 2024, 15: e02811-24. PMID: 39431827, PMCID: PMC11559006, DOI: 10.1128/mbio.02811-24.Peer-Reviewed Original ResearchRab proteinsDNA virusesVirus entryHPV traffickingIntra-Golgi transportTrans-Golgi networkIntracellular vesicular transportMotor protein complexInfected cellsIntra-GolgiL2 capsid proteinRab GTPasesDynein adaptorsNon-enveloped DNA virusesRetrograde traffickingGolgi apparatusPotential targetProtein complexesVesicular transportRab6ADyneinTGNCapsid proteinRabCellular enzymesAn RNA-centric view of transcription and genome organization
Henninger J, Young R. An RNA-centric view of transcription and genome organization. Molecular Cell 2024, 84: 3627-3643. PMID: 39366351, PMCID: PMC11495847, DOI: 10.1016/j.molcel.2024.08.021.Peer-Reviewed Original ResearchConceptsGene regulationGenome architectureTranscriptional regulationModel of transcriptional regulationAssembly of protein complexesAssembly of transcription complexesLocal genome architectureSilencing of genesGenomic compartmentsGenome organizationGenomic structureRNA polymeraseChromatin regulationTranscription complexActive genesProtein complexesRNA moleculesTranscription factorsGenomeProtein kinaseSpecific genesGenesFeedback regulationRNASpatial compartmentsProximity analysis of native proteomes reveals phenotypic modifiers in a mouse model of autism and related neurodevelopmental conditions
Gao Y, Shonai D, Trn M, Zhao J, Soderblom E, Garcia-Moreno S, Gersbach C, Wetsel W, Dawson G, Velmeshev D, Jiang Y, Sloofman L, Buxbaum J, Soderling S. Proximity analysis of native proteomes reveals phenotypic modifiers in a mouse model of autism and related neurodevelopmental conditions. Nature Communications 2024, 15: 6801. PMID: 39122707, PMCID: PMC11316102, DOI: 10.1038/s41467-024-51037-x.Peer-Reviewed Original ResearchConceptsSpatial proteomicsRisk genesHigh-confidence risk genesRegulation of expressionAutism risk genesGenetic interactionsProximity proteomicsHuman genesEndogenous proteomesProtein complexesCellular functionsNative proteomeProteomicsPhenotypic modifiersRisk allelesRelevant to autismGenesFunctional interactionsGenetic riskProteinMouse brainMouse model of autismCellular driversProximity interactionsMouse modelHyd/UBR5 defines a tumor suppressor pathway that links Polycomb repressive complex to regulated protein degradation in tissue growth control and tumorigenesis
Wen P, Lei H, Deng H, Deng S, Tirado C, Wang M, Mu P, Zheng Y, Pan D. Hyd/UBR5 defines a tumor suppressor pathway that links Polycomb repressive complex to regulated protein degradation in tissue growth control and tumorigenesis. Genes & Development 2024, 38: 675-691. PMID: 39137945, PMCID: PMC11368183, DOI: 10.1101/gad.351856.124.Peer-Reviewed Original ResearchConceptsPolycomb Repressive Complex1Tumor suppressor pathwayTissue growth controlSuppressor pathwayProtein degradationZinc finger genesGrowth controlUbiquitin-mediated degradationE3 ubiquitin ligasePolycomb repressive complexesProtein degradation pathwaysTumor suppressor geneHyperplastic discsFinger genesMammalian homologSubstrate adaptorRepressive complexesUbiquitin ligaseEmbryonic segmentationProtein complexesModel organismsHuman geneticsUpstream regulatorSuppressor geneProstate cancer tumorigenesisKinetic study of membrane protein interactions: from three to two dimensions
Adrien V, Reffay M, Taulier N, Verchère A, Monlezun L, Picard M, Ducruix A, Broutin I, Pincet F, Urbach W. Kinetic study of membrane protein interactions: from three to two dimensions. Scientific Reports 2024, 14: 882. PMID: 38195620, PMCID: PMC10776792, DOI: 10.1038/s41598-023-50827-5.Peer-Reviewed Original ResearchConceptsMembrane proteinsMembrane protein interactionsProtein-protein interactionsProtein complexesProtein interactionsMembrane environmentOpposite membranesBacterial efflux pumpsProtein behaviorProtein systemsMolecular interactionsEfflux pumpsProteinExploration distanceMembraneFluorescence recovery experimentsInteractionBinding rateBinding constantsComplexes
2023
A quantitative assessment of (bacterio)chlorophyll assignments in the cryo-EM structure of the Chloracidobacterium thermophilum reaction center
Gisriel C, Flesher D, Long Z, Liu J, Wang J, Bryant D, Batista V, Brudvig G. A quantitative assessment of (bacterio)chlorophyll assignments in the cryo-EM structure of the Chloracidobacterium thermophilum reaction center. Photosynthesis Research 2023, 162: 187-196. PMID: 37749456, DOI: 10.1007/s11120-023-01047-5.Peer-Reviewed Original ResearchCryo-EM mapsCryogenic electron microscopy structureReaction centersHydrogen bond donorCryo-EM structureElectron microscopy structureReaction center complexBond donorPhotosynthetic organismsMicroscopy structureProtein complexesElectron transferMolecular structureFunctional insightsStructural biologyLight harvestingProtein environmentChemical environmentExperimental cryo-EM mapsDownstream investigationsCenter complexPrimary pigmentEnergy transferStructural dataAcetyl moietyCoordinating nucleoporin condensation and nuclear pore complex assembly
Kuiper E, Prophet S, Schlieker C. Coordinating nucleoporin condensation and nuclear pore complex assembly. FEBS Letters 2023, 597: 2534-2545. PMID: 37620293, DOI: 10.1002/1873-3468.14725.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsNPC assemblyNuclear pore complexNuclear pore complex assemblyPore complex assemblyAberrant condensationNPC biogenesisAssembly machineryPore complexProtein complexesComplex assemblyRepeat nucleoporinsHuman disordersAmyotrophic lateral sclerosisAssemblyEukaryotesNucleoporinsBiogenesisRibosomesRecent progressProteasomeComplexesLateral sclerosisMachineryHomeostasisTherapeutic interventionsThe active zone protein CLA-1 (Clarinet) bridges two subsynaptic domains to regulate presynaptic sorting of ATG-9
Xuan Z, Colón-Ramos D. The active zone protein CLA-1 (Clarinet) bridges two subsynaptic domains to regulate presynaptic sorting of ATG-9. Autophagy 2023, 19: 2807-2808. PMID: 37389488, PMCID: PMC10472863, DOI: 10.1080/15548627.2023.2229227.Peer-Reviewed Original ResearchConceptsATG-9Forward genetic screenAdaptor protein complexesIntegral synaptic vesicle proteinsActive zone proteinsSynaptic vesicle cycleCLA-1Synaptic vesicle proteinsGenetic screenPeriactive zoneAutophagosome biogenesisProtein complexesVesicle cycleVesicle proteinsLong isoformNovel roleSubsynaptic domainsZone proteinNeuronal synapsesSynaptic vesiclesProteinDistinct mechanismsVesiclesMutantsPresynaptic localizationAlternative glucose uptake mediated by β-catenin/RSK1 axis under stress stimuli in mammalian cells
Wang C, Lin R, Qi X, Xu Q, Sun X, Zhao Y, Jiang T, Jiang J, Sun Y, Deng Y, Wen J. Alternative glucose uptake mediated by β-catenin/RSK1 axis under stress stimuli in mammalian cells. Biochemical Pharmacology 2023, 214: 115645. PMID: 37321415, DOI: 10.1016/j.bcp.2023.115645.Peer-Reviewed Original ResearchConceptsPhosphorylation of TBC1D4Glucose uptakeGlucose transportActivation of RSK1Stress conditionsMechanism of glucose uptakeTranslocation of GLUT4Translocation of glucose transportersGlucose transporter translocationStress stimuliIncreased glucose uptakeB-cateninGlucose starvationEfficiency of glucose uptakeProtein complexesMammalian cellsScaffold proteinStress signalsCellular energy utilizationFamily 4TBC1D4Kinase activityRSK1Cellular adaptationCellular membranesThe active zone protein Clarinet regulates synaptic sorting of ATG-9 and presynaptic autophagy
Xuan Z, Yang S, Clark B, Hill S, Manning L, Colón-Ramos D. The active zone protein Clarinet regulates synaptic sorting of ATG-9 and presynaptic autophagy. PLOS Biology 2023, 21: e3002030. PMID: 37053235, PMCID: PMC10101500, DOI: 10.1371/journal.pbio.3002030.Peer-Reviewed Original ResearchConceptsATG-9Presynaptic autophagyAdaptor protein complexesZone proteinActive zone proteinsC. elegans neuronsSynaptic vesicle proteinsGenetic screenPeriactive zoneAutophagosome biogenesisCellular homeostasisProtein complexesVesicle proteinsGenetic analysisLong isoformNovel roleSynaptic vesiclesAutophagyDistinct mechanismsProteinVesiclesSortingCLA-1Abnormal accumulationActive zoneDetermining protein structures in cellular lamella at pseudo-atomic resolution by GisSPA
Cheng J, Liu T, You X, Zhang F, Sui S, Wan X, Zhang X. Determining protein structures in cellular lamella at pseudo-atomic resolution by GisSPA. Nature Communications 2023, 14: 1282. PMID: 36922493, PMCID: PMC10017804, DOI: 10.1038/s41467-023-36175-y.Peer-Reviewed Original ResearchConceptsProtein complexesCellular lamellaTarget protein complexesCryo-electron tomographyProtein structure determinationCryo-electron microscopy imagesHigh-throughput data collectionProtein structureAtomic resolutionStructure determinationComplexesPhycobilisomesComplex structureMajor toolLamellaeHigh-resolution reconstructionRibbon Synapses and Retinal Disease: Review
Frederick C, Zenisek D. Ribbon Synapses and Retinal Disease: Review. International Journal Of Molecular Sciences 2023, 24: 5090. PMID: 36982165, PMCID: PMC10049380, DOI: 10.3390/ijms24065090.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsPresynaptic protein complexesRibbon synapsesDefective synaptic transmissionMolecular machineryProtein complexesRetinal malfunctionSynaptic transmissionRetinal diseasesSynaptic ribbonsNeurotransmitter releaseMuscular dystrophyVisual diseaseSynapsesDiseaseSensory informationMutagenesisMachineryPresent understandingSynaptopathyVisual systemReviewPathogenesisRetinaPathologyHPV is a cargo for the COPI sorting complex during virus entry
Harwood M, Woo T, Takeo Y, DiMaio D, Tsai B. HPV is a cargo for the COPI sorting complex during virus entry. Science Advances 2023, 9: eadc9830. PMID: 36662862, PMCID: PMC9858521, DOI: 10.1126/sciadv.adc9830.Peer-Reviewed Original ResearchConceptsCoat protein complex ITrans-Golgi networkProtein complex IGene knockdown strategyVirus entryCOPI complexProtein complexesCellular fractionationUnbiased proteomicsRetrograde traffickingCytoplasmic segmentGolgi stacksCellular cargoL2 mutantKnockdown strategyGolgi apparatusComplex IIncoming virusCell surfaceGolgiHost factorsCargoComplexesMutantsEndosomesHigh-Resolution Structural Analysis of Dyneins by Cryo-electron Microscopy
Chai P, Rao Q, Wang Y, Zhang K. High-Resolution Structural Analysis of Dyneins by Cryo-electron Microscopy. Methods In Molecular Biology 2023, 2623: 257-279. PMID: 36602691, PMCID: PMC10371436, DOI: 10.1007/978-1-0716-2958-1_16.ChaptersConceptsCryo-electron microscopyHigh-resolution structural informationLarge molecular machineHigh-resolution structuresCryo-EM approachResolution structural analysisProtein complexesStructural biologistsCellular cargoMolecular machinesDyneinDepth mechanistic understandingMolecular motorsMechanistic understandingCiliary motilityFlexible conformationIntricate architectureStructural informationMacromolecular structureForce generatorStructural analysisBiologistsSimilar structureCargoMicroscopy
2022
Orientia tsutsugamushi OtDUB Is Expressed and Interacts with Adaptor Protein Complexes during Infection
Adcox H, Berk J, Hochstrasser M, Carlyon J. Orientia tsutsugamushi OtDUB Is Expressed and Interacts with Adaptor Protein Complexes during Infection. Infection And Immunity 2022, 90: e00469-22. PMID: 36374099, PMCID: PMC9753657, DOI: 10.1128/iai.00469-22.Peer-Reviewed Original ResearchConceptsObligate intracellular lifestyleClathrin adaptor protein complex 1Adaptor protein complex 1Non-integral membrane proteinsAdaptor protein complexesHost endocytic pathwayMembrane traffic regulatorsCell wall proteinsWall proteinsProtein complexesIntracellular lifestyleRho GTPasesAdapter proteinEndocytic pathwayMembrane proteinsUbiquitin bindingCellular pathwaysCell wallStructured illumination microscopyPhospholipid phosphatidylserineIntact bacteriaO. tsutsugamushi infectionProteinRecombinant versionInteractomeNative Planar Asymmetric Suspended Membrane for Single‐Molecule Investigations: Plasma Membrane on a Chip
Sundaram R, Bera M, Coleman J, Weerakkody J, Krishnakumar S, Ramakrishnan S. Native Planar Asymmetric Suspended Membrane for Single‐Molecule Investigations: Plasma Membrane on a Chip. Small 2022, 18: e2205567. PMID: 36328714, DOI: 10.1002/smll.202205567.Peer-Reviewed Original ResearchConceptsPlasma membraneProtein assembliesNative plasma membrane vesiclesTotal internal reflection fluorescence microscopySingle-molecule levelSingle-molecule investigationsCellular plasma membranePlasma membrane vesiclesSingle-molecule precisionReflection fluorescence microscopyKnowledge of lipidProtein complexesProtein architectureCell signalingMovement of moleculesProtein orientationLipid membranesBiological processesCellular membranesMembrane vesiclesMicroarray platformFluorescence investigationsLipid domainsFluorescence microscopyMembrane
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