Publications

2020

• Systems biochemistry approaches to defining mitochondrial protein function
  Sung AY, Floyd BJ, and Pagliarini DJ
  Cell Metabolism, 2020, 31 (4): 669-678
• Pathogenic biallelic mutations in NDUFAF8 cause Leigh syndrome with an isolated complex I deficiency
  Alston CL*, Veling MT*, Heidler J, Taylor LC, Alaimo JT, Sung AY, He L, Hopton S, Broomfield A, Pavaine J, Pavaine J, Diaz J, Wolf P, McFarland R, Prokisch H, Wortmann SB, Bonnen PE, Wittig I, Pagliarini DJ†, and Taylor RW†
  American Journal of Human Genetics, 2020 Jan 2;106(1):92-101. doi: 10.1016/j.ajhg.2019.12.001
• Mass spectrometry proteomics reveals a function for mammalian Calcoco1 in mTOR regulated selective autophagy
  Stefely JA, Zhang Y, Freiberger EC, Kwiecien NW, Thomas HE, Davis AM, Lowry ND, Clark NA, Medvedovic M, Coon JJ,Pagliarini DJ, and Mercer CA
  Autophagy, 2020 doi: 10.1080/15548627.2020.1719746

2019

• ADCK3/COQ8A: The choice target of the UbiB protein kinase-like family
  Asquith CRM†, Murray NH, and Pagliarini DJ†
  Nature Reviews Drug Discovery, 2019 doi: 10.1038/d41573-019-00158-w
• Pptc7 is an essential phosphatase that promotes mitochondrial metabolism by enabling protein import and processing
  Niemi NM, Wilson GM, Overmyer KA, Vögtle FN, Lohman DC, Schueler KL, Attie AD, Meisinger C, Coon JJ, and Pagliarini DJ
  Nature Communications, 2019 10: 3197
• Two-stage metabolic remodeling in macrophages in response to LPS and IFN-γ stimulation
  Seim GL, Britt EC, John SV, Yeo F, Johnson A, Eisenstein R, Pagliarini DJ, and Fan J
  Nature Metabolism, 2019 1:731–742
• Obesity-dependent Cdk1 Signaling Stimulates Mitochondrial Respiration at Complex I in Pancreatic β-cells
  Gregg T, Sdao SM, Dhillon RS, Rensvold JW, Pagliarini DJ, Denu JM, and Merrins MJ
  Journal of Biological Chemistry 2019 294(12):4656-4666
• Mitochondrial Coenzyme Q biosynthetic proteins cooperatively assemble in a substrate-dependent manner into domains spatially linked to ER-mitochondria contact site
  Subramanian K, Jochem A, Lewis, S, Le Vasseur M, Paulson BR, Reddy TR, Russell JD, Coon JJ, Pagliarini DJ, and Nunnari J
  Journal of Cell Biology, 2019 218(4):1353-1369
• An isoprene lipid binding protein promotes eukaryotic coenzyme Q biosynthesis
  Lohman DC*, Aydin D*, Von Bank H, Smith R, Linke V, Weisenhorn EM, McDevitt MT, Hutchins PD, Wilkerson EM, Wancewicz B, Russell JD, Stefely MS, Beebe ET, Jochem A, Coon JJ, Bingman CA, Dal Peraro M†, and Pagliarini DJ†
  Molecular Cell, 2019 73(4): 763-774

2018

• Systems analyses reveal physiological roles and genetic regulators of liver lipid species
  Jha P*, McDevitt MT*, Gupta R*, Quiros PM, Williams EG, Gariani K, Sleiman MB, Diserens L, Jochem A, Ulbrich A, Coon JJ, Auwerx J†, and Pagliarini DJ†
  Cell Systems, 2018 6(6):722-733
• Genetic regulation of plasma lipid species and their association with metabolic phenotypes
  Jha P*, McDevitt MT*, Halilbasic E, Williams EG, Quiros PM, Gariani K, Sleiman MB, Ulbrich A, Coon JJ, Trauner M, Pagliarini DJ†, and Auwerx J†
  Cell Systems, 2018 6(6):709-721
• Multi-Omics Reveal Specific Targets of the RNA-Binding Protein Puf3p and Its Orchestration of Mitochondrial Biogenesis
  Lapointe CP*, Stefely JA*, Jochem A, Hutchins PD, Wilson GM, Kwiecien NW, Coon JJ, Wickens MP†, and Pagliarini DJ†
  Cell Systems, 2018 6(1):125-135
• Conserved lipid and small molecule modulation of COQ8 reveals regulation of the ancient kinase-like UbiB family
  Reidenbach AG, Kemmerer ZA, Aydin D, Jochem A, McDevitt MT, Hutchins PD, Stark JL, Stefely JA, Reddy T, Hebert AS, Wilkerson EM, JA, Johnson IE, Bingman CA, Markley JL, Coon JJ, Dal Peraro M, and Pagliarini DJ
  Cell Chemical Biology, 2018 25(2):154-165

2017

• Multi-omic mitoprotease profiling defines a role for Oct1p in coenzyme Q production
  Veling MT, Reidenbach AG, Freiberger EC, Kwiecien NW, Hutchins PD, Drahnak MJ, Jochem A, Ulbrich A, Rush JPR, Russell JD, Coon JJ, and Pagliarini DJ
  Molecular Cell, 2017 doi: 10.1016/j.molcel.2017.11.023
• Biochemistry of Mitochondrial Coenzyme Q Biosynthesis
  Stefely JA and Pagliarini DJ
  Trends in Biochemical Sciences, 2017 doi.org/10.1016/j.tibs.2017.06.008
• Erythropoietin signaling regulates heme biosynthesis
  Chung J, Wittig JG, Ghamari A, Maeda M, Dailey TA, Begonia H, Coughlin EE, Minogue CE, Hebert AS, Li L, Kaplan J, Lodish HF, Bauer DE, Orkin SH, Cantor AB, Maeda T, Phillips JD, Coon JJ, Pagliarini DJ, Dailey HA, and Paw BH
  eLife, 2017 May 29;6. pii: e24767
• Integrative proteomics and biochemical analyses define Ptc6p as the Saccharomyces cerevisiae pyruvate dehydrogenase phosphatase
  Guo X, Niemi NM, Coon JJ, Pagliarini DJ
  Journal of Biological Chemistry, 2017 Jul 14;292(28):11751-11759. PMCID: PMC5512070
• Ptc7p Dephosphorylates Select Mitochondrial Proteins to Enhance Metabolic Function
  Guo X*, Niemi NM*, Hutchins PD, Condon SG, Jochem A, Ulbrich A, Higbee AJ, Russell JD, Senes A, Coon JJ, Pagliarini DJ
  Cell Reports, 2017 Jan 10 PMID: 28076776

2016

• Mitochondrial Protein Functions Elucidated by Multi-Omic Mass Spectrometry Profiling
  Stefely JA*, Kwiecien NW*, Freiberger EC, Richards AL, Jochem A, Rush MJ, Ulbrich A, Robinson KP, Hutchins PD, Veiling MT, Guo X, Kemmerer ZA, Connors KJ, Trujillo EA, Sokol J, Marx H, Westphall MS, Hebert AS, Pagliarini DJ†, Coon JJ†
  Nature Biotechnology, 2016 Sep 26 PMID: 27669165
  PREVIEW
• Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function
  Floyd BJ*, Wilkerson EM*, Veling MT*, Minogue CE*, Xia C, Beebe ET, Wrobel RL, Cho H, Kremer LS, Alston CL, Gromek KA, Dolan BK, Ulbrich A, Stefely JA, Bohl SL, Werner KM, Jochem A, Westphall MS, Rensvold JW, Taylor RW, Prokisch H, Kim JJ, Coon JJ, Pagliarini DJ
  Molecular Cell, 2016 Aug 18;63(4):621-32
• Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity
  Stefely JA*, Licitra F*, Laredj L, Reidenbach AG, Kemmerer ZA, Grangeray A, Jaeg-Ehret T, Minogue CE, Ulbrich A, Hutchins PD, Wilkerson EM, Ruan Z, Aydin D, Hebert AS, Guo X, Freiberger EC, Reutenauer L, Jochem A, Chergova M, Johnson IE, Lohman DC, Rush MJ, Kwiecien NW, Singh PK, Schlagowski AI, Floyd BJ, Forsman U, Sindelar PJ, Westphall MS, Pierrel F, Zoll J, Dal Peraro M, Kannan N, Bingman CA, Coon JJ, Isope P, Puccio H†, Pagliarini DJ†
  Molecular Cell, 2016 Aug 18;63(4):608-2.
• Iron Deprivation Induces Transcriptional Regulation of Mitochondrial Biogenesis
  Rensvold JW, Krautkramer KA, Dowell JA, Denu JM, Pagliarini DJ
  Journal of Biological Chemistry, 2016 Aug 5 PMID: 27497435
• Transomics: Mitochondrial Systems Analyses Get Supercomplex
  Pagliarini DJ
  Cell Metabolism, 2016 Jul 12;24(1):13-4
• Mitochondrial protein hyperacetylation in the failing heart
  Overmyer KA, Evans CR, Qi NR, Minogue CE, Carson JJ, Chermside-Scabbo CJ, Koch LG, Britton SL, Pagliarini DJ, Coon JJ, Burant CF
  JCI Insight, 2016 Feb;2(1)

2015

• A Single Kinase Generates the Majority of the Secreted Phosphoproteome
  Tagliabracci VS, Wiley SE, Guo X, Kinch LN, Durrant E, Wen J, Xiao J, Cui J, Nguyen KB, Engel JL, Coon JJ, Grishin N, Pinna LA, Pagliarini DJ, Dixon JE
  Cell, 2015 Jun 18;161(7):1619-32
• Maximal Oxidative Capacity during Exercise Is Associated with Skeletal Muscle Fuel Selection and Dynamic Changes in Mitochondrial Protein Acetylation
  Overmyer KA, Evans CR, Qi NR, Minogue CV, Chermside-Scaboo CJ, Kock LG, Britton SL, Pagliarini DJ, Coon JJ and Burant CF
  Cell Metabolism, 2015, 3;21(3):468-78
• Multiplexed Quantification for Data-independent Acquisition
  Minogue CE, Hebert AS, Rensvold JW, Westphall MS, Pagliarini DJ and Coon JJ
  Analytical Chemistry, 2015, 3;87(5):2570-5
• Mitochondrial ADCK3 Employs an Atypical Protein Kinase-like Fold to Enable Coenzyme Q Biosynthesis
  Stefely JA*, Reidenbach AG*, Ulbrich A, Oruganty K, Floyd BJ, Jochem A, Saunders JM, Johnson IE, Minogue CE, Wrobel RL, Barber GE, Lee D, Li S, Kannan N, Coon JJ, Bingman CA and Pagliarini DJ
  Molecular Cell, 2015, 57(1):83-94

2014

• Mitochondrial COQ9 is a lipid binding protein that associates with COQ7 to enable coenzyme Q biosynthesis
  Lohman DC*, Forouhar F*, Beebe ET, Stefeley MS, Minogue CE, Ulbrich A, Stefely JA, Sukumar S, Luna-Sánchez M, Lew S, Seetharaman J, Xiao R, Wang H, Wrobel RL, Everett JK, Mitchell JC, López LC, Coon JJ, Tong L† and Pagliarini DJ†
  Proceedings of the National Academy of Sciences, 2014 111(44):E4697-705
• A Gly-zipper motif mediates homo-dimerization of the transmembrane domain of the mitochondrial kinase ADCK3
  Khadria AS, Mueller BK, Stefely JA, Tan CH, Pagliarini DJ† and Senes A†
  Journal of the American Chemical Society, 2014 136, 14068-77
• Intelligent data acquisition blends targeted and discovery methods
  Bailey DJ, McDevitt MT, Westphall MS, Pagliarini DJ, Coon JJ
  Journal of Proteome Research, 2014 Apr 4;13(4):2152-61
• Mitochondrial DNA variant in COX1 subunit significantly alters energy metabolism of geographically divergent wild isolates in Caenorhabditis elegans
  Dingley SD, Polyak E, Ostrovsky J, Srinivasan S, Lee I, Rosenfeld A, Tsukikawa M, Xiao R, Selak M, Coon JJ, Hebert AS, Grimsrud PA, Pagliarini DJ, Gai X, Schurr TG, Huttemann M, Nakamaru-Ogiso E and Falk MJ
  Journal of Molecular Biology, 2014 Feb 14, Epub ahead of print
• Neutron-encoded mass signatures for quantitative top-down proteomics
  Rhoads TW, Rose CM, Bailey DJ, Molden RC, Still AJ, Riley NM, Merrill AE, Hebert AS, Westphall MS, Pagliarini DJ, Garcia BA and Coon JJ
  Analytical Chemistry, 2014 Mar 4;86(5):2314-9

2013

• Hallmarks of a new era in mitochondrial biochemistry
  Pagliarini DJ† and Rutter J†
  Genes and Development 2013, 27(24): 2615-27 PMCID: PMC3877752
• Amine-reactive neutron-encoded labels for highly-plexed proteomic quantitation
  Hebert AS, Merrill AE, Stefely JA, Westphall MS, Pagliarini DJ and Coon JJ
  Molecular and Cellular Proteomics 2013, 12(11): 3360-9 PMCID: PMC3820946
• Quantification of mitochondrial acetylation dynamics highlights prominent sites of metabolic regulation
  Still AJ*, Floyd BJ*, Hebert AS*, Bingman CA, Carson JJ, Gunderson DR, Dolan BK, Grimsrud PA, Dittenhafer-Reed KE, Stapleton DS, Keller MP, Westphall MS, Denu JM, Attie AD, Coon JJ, and Pagliarini DJ
  Journal of Biological Chemistry 2013, 288(36): 26209-19 PMCID: PMC3764825
• Neutron-encoded mass signatures for multiplexed proteome quantification
  Hebert AS, Merrill AE, Bailey DJ, Still AJ, Westphall MS, Strieter ER, Pagliarini DJ and Coon JJ
  Nature Methods 2013, 10(4): 332-4 PMCID: PMC3612390
• Complementary RNA and protein profiling identifies iron as a key regulator of mitochondrial biogenesis
  Rensvold JW, Ong SE, Jeevananthan A, Carr SA, Mootha VK and Pagliarini DJ
  Cell Reports 2013, 3(1): 237-245 PMCID: PMC3812070
• Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome
  Hebert AS*, Dittenhafer-Reed KE*, Yu W, Bailey DJ, Selen ES, Boersma MD, Carson JJ, Tonelli M, Balloon AJ, Higbee AJ, Westphall MS, Pagliarini DJ, Prolla TA, Assadi-Porter F, Roy S, Denu JM and Coon JJ
  Molecular Cell 2013, 49: 186-199 PMCID: PMC3704155
• Inhibitors of bacterial tubulin target bacterial membranes in vivo
  Foss MH, Eun YJ, Grove CI, Pauw DA, Sorto NA, Rensvold JW, Pagliarini DJ, Shaw JT and Weibel DB
  MedChemCommun 2013: 4, 112-119 PMCID: PMC3607388

2012

• Solution NMR structure of yeast succinate dehydrogenase flavinylation factor Sdh5 reveals a putative Sdh1
  binding site
  Eletsky A, Jeong M, Kim H, Lee H, Xiao R, Pagliarini DJ, Prestegard JH, Winge DR, Montelione GT and Szyperski T
  Biochemistry 2012, 51: 8475-7 PMCID: PMC3667956
• Automated gas-phase purification for accurate, multiplexed quantification on a stand-alone ion trap mass spectrometer
  Vincent CE, Rensvold JW, Wenger CD, Peterson AC, Westphall MS, Pagliarini DJ and Coon JJ
  Analytical Chemistry 2012, 85(4): 2079-86 PMCID: PMC3568235
• A quantitative map of the liver mitochondrial phosphoproteome reveals posttranslational control of ketogenesis
  Grimsrud PA*, Carson JJ*, Hebert AS, Hubler SL, Niemi NM, Bailey DJ, Jochem A, Stapleton DS, Keller MP, Westphall MS, Yandell BS, Attie AD, Coon JJ and Pagliarini DJ
  Cell Metabolism 2012, 16: 672-83 PMCID: PMC3506251
• Analysis of the acidic proteome with negative electron-transfer dissociation mass spectrometry
  McAlister GC, Russell JD, Rumachik NG, Hebert AS, Syka JE, Geer LY, Westphall MS, Pagliarini DJ and Coon JJ
  Analytical Chemistry 2012, 84(6): 2875-82 PMCID: PMC3310326

Pre-Madison

• Pharmacological targeting of the mitochondrial phosphatase PTPMT1
  Doughty-Shenton DD, Joseph JD, Zhang J, Pagliarini DJ, Kim Y, Lu D, Dixon JE and Casey PJ
  The Journal of Pharmacology and Experimental Therapeutics 2010, 332(2): 584-92 PMCID: PMC2872949
• Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans
  Calvo SE*, Pagliarini DJ* and Mootha VK
  Proceedings of the National Academy of Sciences USA 2009, 106: 7507-12 PMCID: PMC2669787
• Mutation of C20orf7 disrupts complex I assembly and causes lethal infantile mitochondrial disease
  Sugiana C*, Pagliarini DJ*, McKenzie M, Kirby DM, Salemi R, Dahl HHM, Hutchison WM, Vascotto KA, Smith SM, Christodoulou J, Calvo SE, Mootha VK, Ryan MT and Thorburn DR
  American Journal of Human Genetics 2008, 83(4): 468-78. PMCID: PMC2561934
• A mitochondrial protein compendium elucidates complex I disease biology
  Pagliarini DJ*, Calvo SE*, Chang B, Sheth SA, Vafai SB, Ong SE, Walford GA, Sugiana C, Boneh A, Chen WK, Hill DE, Vidal M, Evans JG, Thorburn DR, Carr SA, and Mootha VK
  Cell 2008, 134(1): 112-23. PMCID: PMC2778844
  PREVIEW
• Dual specific phosphatases 18 and 21 target to opposing sides of the mitochondrial inner membrane
  Rardin MJ, Wiley SE, Murphy AN, Pagliarini DJ, and Dixon JE
  Journal of Biological Chemistry 2008, 283(22): 15440-50. PMCID: PMC2397459
• Mitochondrial modulation: reversible phosphorylation takes center stage?
  Pagliarini DJ and Dixon JE
  Trends in Biochemical Sciences 2006, 31(1): 26-34
• Involvement of a mitochondrial phosphatase in the regulation of ATP production and insulin secretion in pancreatic Beta cells
  Pagliarini DJ, Wiley SE, Kimple ME, Dixon JR, Kelly P, Casey PJ, and Dixon JE
  Molecular Cell 2005, 19(2): 197-207
  PREVIEW
• Protein tyrosine phosphatases
  Pagliarini, DJ *, Robinson, FL*, and Dixon, JE
  Encyclopedia of Biochemistry 2004, 3: 536-42
• A PTEN-like phosphatase with a novel substrate specificity
  Pagliarini DJ, Worby CA, and Dixon JE
  Journal of Biological Chemistry 2004, 279(37): 38590-6
• A PTEN-related 5-phosphatidylinositol phosphatase localized in the Golgi
  Merlot S, Meili R, Pagliarini D, Maehama T, Dixon E, and Firtel RA
  Journal of Biological Chemistry 2003, 278(41): 39866-73