Featured Publications
Phosphorylated WNK kinase networks in recoded bacteria recapitulate physiological function
Schiapparelli P, Pirman NL, Mohler K, Miranda-Herrera PA, Zarco N, Kilic O, Miller C, Shah SR, Rogulina S, Hungerford W, Abriola L, Hoyer D, Turk BE, Guerrero-Cázares H, Isaacs FJ, Quiñones-Hinojosa A, Levchenko A, Rinehart J. Phosphorylated WNK kinase networks in recoded bacteria recapitulate physiological function. Cell Reports 2021, 36: 109416. PMID: 34289367, PMCID: PMC8379681, DOI: 10.1016/j.celrep.2021.109416.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsCell Line, TumorCell MovementCell ProliferationEscherichia coliFemaleGlioblastomaHEK293 CellsHumansMaleMice, NudeMiddle AgedPhosphorylationPhosphoserineProtein Serine-Threonine KinasesRecombinant ProteinsSignal TransductionSmall Molecule LibrariesSubstrate SpecificityWNK Lysine-Deficient Protein Kinase 1ConceptsKinase networkAuthentic post-translational modificationsGenetic code expansionPost-translational modificationsProduction of proteinsSmall molecule kinase inhibitorsKinase inhibitorsGenetic codePhosphorylated proteinsCode expansionKinase proteinWNK kinasesPhysiological functionsWNK4 kinaseBiochemical propertiesGlioblastoma cellsKinaseBacterial strainsProteinDistinct sitesPhosphoserineSPAKBacteriaCellular systemsCellsTargeting Pyruvate Kinase M2 Phosphorylation Reverses Aggressive Cancer Phenotypes
Apostolidi M, Vathiotis IA, Muthusamy V, Gaule P, Gassaway BM, Rimm DL, Rinehart J. Targeting Pyruvate Kinase M2 Phosphorylation Reverses Aggressive Cancer Phenotypes. Cancer Research 2021, 81: 4346-4359. PMID: 34185676, PMCID: PMC8373815, DOI: 10.1158/0008-5472.can-20-4190.Peer-Reviewed Original ResearchMeSH KeywordsActive Transport, Cell NucleusAnimalsBiomarkers, TumorCarrier ProteinsCell Line, TumorCollagenCyclic N-OxidesDrug CombinationsGenome, HumanHumansIndolizinesLamininMCF-7 CellsMembrane ProteinsMiceNeoplasm InvasivenessNeoplasm TransplantationNeoplasmsOxidation-ReductionPhenotypePhosphorylationProtein IsoformsProteoglycansProteomicsPyridazinesPyridinium CompoundsPyrrolesPyruvate KinaseThyroid HormonesTriple Negative Breast NeoplasmsConceptsTriple-negative breast cancerPyruvate kinase M2TEPP-46Breast cancerAggressive breast cancer cell phenotypesCharacteristic nuclear staining patternAggressive breast cancer subtypeAggressive breast cancer phenotypeBreast cancer cell phenotypeCDK inhibitor dinaciclibCombination of dinaciclibLack of biomarkersEffective therapeutic approachBreast cancer phenotypeBreast cancer subtypesCancer phenotypePhosphorylation of PKM2Cyclin-dependent kinase (CDK) pathwayMouse xenograft modelAggressive cancer phenotypeNuclear staining patternLower survival rateImpaired redox balancePrognostic valueCancer cell phenotypeA flexible codon in genomically recoded Escherichia coli permits programmable protein phosphorylation
Pirman NL, Barber KW, Aerni HR, Ma NJ, Haimovich AD, Rogulina S, Isaacs FJ, Rinehart J. A flexible codon in genomically recoded Escherichia coli permits programmable protein phosphorylation. Nature Communications 2015, 6: 8130. PMID: 26350500, PMCID: PMC4566969, DOI: 10.1038/ncomms9130.Peer-Reviewed Original ResearchConceptsProtein phosphorylationProtein phosphorylation eventsFull-length proteinNon-phosphorylated formPhosphoserine-containing proteinsPhosphorylation eventsMEK1 kinaseUAG codonKinase activityRecombinant DNADNA templateEscherichia coliE. coliCodonPhosphorylationFunctional informationSerineProteinColiBiochemical investigationsPhosphoproteomeInefficient productionKinasePhosphoserineDNAGenomically Recoded Organisms Expand Biological Functions
Lajoie MJ, Rovner AJ, Goodman DB, Aerni HR, Haimovich AD, Kuznetsov G, Mercer JA, Wang HH, Carr PA, Mosberg JA, Rohland N, Schultz PG, Jacobson JM, Rinehart J, Church GM, Isaacs FJ. Genomically Recoded Organisms Expand Biological Functions. Science 2013, 342: 357-360. PMID: 24136966, PMCID: PMC4924538, DOI: 10.1126/science.1241459.Peer-Reviewed Original ResearchConceptsNew genetic codesRelease factor 1UAG stop codonNonstandard amino acidsEscherichia coli MG1655UAA codonGenetic codeColi MG1655Biological functionsStop codonChemical diversityT7 bacteriophageAmino acidsFactor 1CodonMG1655OrganismsProteinDiversityDeletionBacteriophagesViral resistanceTranslation functionGROVivoEncoding human serine phosphopeptides in bacteria for proteome-wide identification of phosphorylation-dependent interactions
Barber KW, Muir P, Szeligowski RV, Rogulina S, Gerstein M, Sampson JR, Isaacs FJ, Rinehart J. Encoding human serine phosphopeptides in bacteria for proteome-wide identification of phosphorylation-dependent interactions. Nature Biotechnology 2018, 36: 638-644. PMID: 29889213, PMCID: PMC6590076, DOI: 10.1038/nbt.4150.Peer-Reviewed Original Research
2024
Nuclear PKM2 binds pre-mRNA at folded G-quadruplexes and reveals their gene regulatory role
Anastasakis D, Apostolidi M, Garman K, Polash A, Umar M, Meng Q, Scutenaire J, Jarvis J, Wang X, Haase A, Brownell I, Rinehart J, Hafner M. Nuclear PKM2 binds pre-mRNA at folded G-quadruplexes and reveals their gene regulatory role. Molecular Cell 2024, 84: 3775-3789.e6. PMID: 39153475, PMCID: PMC11455610, DOI: 10.1016/j.molcel.2024.07.025.Peer-Reviewed Original ResearchRNA-binding proteinsPre-mRNANon-canonical RNA-binding proteinsGene regulatory roleCancer cellsRNA G-quadruplexesG-quadruplexInvasion of cancer cellsTriple-negative breast cancer cellsBreast cancer cellsEpithelial-to-mesenchymal transitionCancer typesNuclear localizationPrecursor mRNANuclear accumulationGene expressionXenograft mouse modelNuclear PKM2Regulatory roleRG4sPKM2Reduced migrationMouse modelTumor progressionPatient survivalStructural bases for Na+-Cl− cotransporter inhibition by thiazide diuretic drugs and activation by kinases
Zhao Y, Schubert H, Blakely A, Forbush B, Smith M, Rinehart J, Cao E. Structural bases for Na+-Cl− cotransporter inhibition by thiazide diuretic drugs and activation by kinases. Nature Communications 2024, 15: 7006. PMID: 39143061, PMCID: PMC11324901, DOI: 10.1038/s41467-024-51381-y.Peer-Reviewed Original ResearchConceptsNa+-Cl- cotransporterFamilial hyperkalemic hypertensionRenal salt retentionThiazide diuretic drugsNa+-Cl-Cotransporter inhibitionNCC activitySalt reabsorptionDiuretic drugsBlood pressureBalanced electrolyteTreat hypertensionIon translocation pathwayIon translocationThiazideHypertensionSalt retentionOrthosteric siteCo-structureCarboxyl-terminal domainKinase cascadeEdemaChlorthalidoneCotransporterTranslocationElastocapillary effects determine early matrix deformation by glioblastoma cell spheroids
Ang I, Yousafzai M, Yadav V, Mohler K, Rinehart J, Bouklas N, Murrell M. Elastocapillary effects determine early matrix deformation by glioblastoma cell spheroids. APL Bioengineering 2024, 8: 026109. PMID: 38706957, PMCID: PMC11069407, DOI: 10.1063/5.0191765.Peer-Reviewed Original Research
2023
SPAK-dependent cotransporter activity mediates capillary adhesion and pressure during glioblastoma migration in confined spaces.
Lee S, Yousafzai M, Mohler K, Yadav V, Amiri S, Szuszkiewicz J, Levchenko A, Rinehart J, Murrell M. SPAK-dependent cotransporter activity mediates capillary adhesion and pressure during glioblastoma migration in confined spaces. Molecular Biology Of The Cell 2023, 34: ar122. PMID: 37672340, PMCID: PMC10846615, DOI: 10.1091/mbc.e23-03-0103.Peer-Reviewed Original ResearchSystem‐wide optimization of an orthogonal translation system with enhanced biological tolerance
Mohler K, Moen J, Rogulina S, Rinehart J. System‐wide optimization of an orthogonal translation system with enhanced biological tolerance. Molecular Systems Biology 2023, 19: msb202110591. PMID: 37477096, PMCID: PMC10407733, DOI: 10.15252/msb.202110591.Peer-Reviewed Original ResearchConceptsOrthogonal translation systemHost interactionsNon-standard amino acidsPost-translational modificationsSystems-level biologyStress response activationTranslation systemSynthetic biological systemsCellular physiologyProtein phosphorylationOTS performanceHost physiologyCellular environmentAmino acidsCellular mechanismsDeleterious interactionsResponse activationBiological systemsPhysiologyOTS developmentUnparalleled accessPhosphorylationHost toxicityBiologyInteractionMapping the in vivo fitness landscape of a tethered ribosome
Radford F, Rinehart J, Isaacs F. Mapping the in vivo fitness landscape of a tethered ribosome. Science Advances 2023, 9: eade8934. PMID: 37115918, PMCID: PMC10146877, DOI: 10.1126/sciadv.ade8934.Peer-Reviewed Original ResearchConceptsPeptidyl transfer centerEpistatic interactionsFitness landscapeMacromolecular machinesLaboratory evolutionRibosome functionDeleterious mutationsVivo fitness landscapeComplete mutagenesisLethal mutationsGenetic elementsRibosomesProtein synthesisDominant lethal mutationsMost nucleotidesMutationsSequence spaceNucleotidesNext-generation biomaterialsLandscapeMutagenesisOrganismsSequenceInteractionDeeper understanding
2022
Enhanced access to the human phosphoproteome with genetically encoded phosphothreonine
Moen J, Mohler K, Rogulina S, Shi X, Shen H, Rinehart J. Enhanced access to the human phosphoproteome with genetically encoded phosphothreonine. Nature Communications 2022, 13: 7226. PMID: 36433969, PMCID: PMC9700786, DOI: 10.1038/s41467-022-34980-5.Peer-Reviewed Original ResearchConceptsUbiquitous post-translational modificationCo-translational insertionKinase activation mechanismProtein interaction platformOrthogonal translation systemProtein-protein interactionsPost-translational modificationsPhospho-amino acidsAminoacyl-tRNA synthetaseHuman phosphoproteomePhosphorylation eventsTRNA pairsFunctional assignmentCellular processesProtein phosphorylationUpstream kinasePhysiological functionsActivation mechanismTranslation systemKinasePhosphorylationInteraction platformPhosphoproteomePhosphothreoninePhosphoCorrection: The mechanism of β-N-methylamino-L-alanine inhibition of tRNA aminoacylation and its impact on misincorporation
Han N, Bullwinkle T, Loeb K, Faull K, Mohler K, Rinehart J, Ibba M. Correction: The mechanism of β-N-methylamino-L-alanine inhibition of tRNA aminoacylation and its impact on misincorporation. Journal Of Biological Chemistry 2022, 298: 102544. PMCID: PMC9547288, DOI: 10.1016/j.jbc.2022.102544.Peer-Reviewed Original Research
2020
CSIG-08. TARGETING ION TRANSPORT-REGULATORY KINASES AS A NOVEL TREATMENT FOR GLIOBLASTOMA
Schiapparelli P, Meade P, Miranda-Herrera P, Bechtle A, Issacs F, Levchenko A, Rinehart J, Quinones-Hinojosa A. CSIG-08. TARGETING ION TRANSPORT-REGULATORY KINASES AS A NOVEL TREATMENT FOR GLIOBLASTOMA. Neuro-Oncology 2020, 22: ii29-ii29. PMCID: PMC7650317, DOI: 10.1093/neuonc/noaa215.120.Peer-Reviewed Original ResearchOxidative stress-responsive kinase 1Small molecule inhibitorsGBM cellsMolecule inhibitorsAggressive primary brain tumorCell migrationComplete surgical resectionMaximal safe resectionPrimary brain tumorsAdjacent brain parenchymaCell proliferationOrthotopic murine modelPatient-derived GBM cell linesDose-dependent reductionImportant therapeutic componentGBM cell linesCell cycle analysisGBM cell migrationSurgical resectionSafe resectionBrain parenchymaCell infiltrationCell cycle arrestMurine modelRadiation therapy205-OR: Hepatic Protein Kinase C-e Is Necessary and Sufficient in Mediating Lipid-Induced Hepatic Insulin Resistance
LYU K, ZHANG D, KAHN M, RODRIGUES M, HIRABARA S, LUUKKONEN P, LEE S, BHANOT S, RINEHART J, BLUME N, RASCH M, SERLIE M, BOGAN J, CLINE G, SAMUEL V, SHULMAN G. 205-OR: Hepatic Protein Kinase C-e Is Necessary and Sufficient in Mediating Lipid-Induced Hepatic Insulin Resistance. Diabetes 2020, 69 DOI: 10.2337/db20-205-or.Peer-Reviewed Original ResearchThe mechanism of β-N-methylamino-l-alanine inhibition of tRNA aminoacylation and its impact on misincorporation
Han N, Bullwinkle T, Loeb K, Faull K, Mohler K, Rinehart J, Ibba M. The mechanism of β-N-methylamino-l-alanine inhibition of tRNA aminoacylation and its impact on misincorporation. Journal Of Biological Chemistry 2020, 295: 1402-1410. DOI: 10.1016/s0021-9258(17)49898-x.Peer-Reviewed Original ResearchAmino acid activationSerine codonsProtein synthesisHuman protein extractsHuman seryl-tRNA synthetaseAminoacyl-tRNA synthetaseSeryl-tRNA synthetaseAmyotrophic lateral sclerosisAlanyl-tRNA synthetaseN-methylaminoNonproteinogenic amino acidsCotranslational incorporationTRNA aminoacylationAlzheimer's diseaseProtein extractsBiochemical assaysAmino acidsExchange assayBMAAAcid activationSynthetaseCodonAminoacylationNeurodegenerative diseasesMultiple different mechanisms
2019
Distinct Hepatic PKA and CDK Signaling Pathways Control Activity-Independent Pyruvate Kinase Phosphorylation and Hepatic Glucose Production
Gassaway BM, Cardone RL, Padyana AK, Petersen MC, Judd ET, Hayes S, Tong S, Barber KW, Apostolidi M, Abulizi A, Sheetz JB, Kshitiz, Aerni HR, Gross S, Kung C, Samuel VT, Shulman GI, Kibbey RG, Rinehart J. Distinct Hepatic PKA and CDK Signaling Pathways Control Activity-Independent Pyruvate Kinase Phosphorylation and Hepatic Glucose Production. Cell Reports 2019, 29: 3394-3404.e9. PMID: 31825824, PMCID: PMC6951436, DOI: 10.1016/j.celrep.2019.11.009.Peer-Reviewed Original ResearchConceptsCyclin-dependent kinasesMetabolic control pointPhosphorylation sitesNuclear retentionCDK activityPKL activityDays high-fat dietKinase phosphorylationImportant enzymePyruvate kinaseHigh-fat dietS113KinaseEnzyme kineticsPhosphorylationAdditional control pointsRegulationGlucose productionHepatic glucose productionInsulin resistanceGlycolysisEnzymePKAPathwayActivity
2017
Characterization of an Unprecedented Hybrid Pteridine‐Nonribosomal Peptide Synthetase‐Like Biosynthetic Gene Cluster
Perez C, Park H, Barber K, Rinehart J, Crawford J. Characterization of an Unprecedented Hybrid Pteridine‐Nonribosomal Peptide Synthetase‐Like Biosynthetic Gene Cluster. The FASEB Journal 2017, 31 DOI: 10.1096/fasebj.31.1_supplement.766.19.Peer-Reviewed Original ResearchEncoding the Human Phosphoproteome in an Engineered Bacterial System
Barber K, Rinehart J. Encoding the Human Phosphoproteome in an Engineered Bacterial System. The FASEB Journal 2017, 31 DOI: 10.1096/fasebj.31.1_supplement.614.33.Peer-Reviewed Original Research
2015
Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids
Amiram M, Haimovich AD, Fan C, Wang YS, Aerni HR, Ntai I, Moonan DW, Ma NJ, Rovner AJ, Hong SH, Kelleher NL, Goodman AL, Jewett MC, Söll D, Rinehart J, Isaacs FJ. Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids. Nature Biotechnology 2015, 33: 1272-1279. PMID: 26571098, PMCID: PMC4784704, DOI: 10.1038/nbt.3372.Peer-Reviewed Original Research