Pagliarini Lab
Pagliarini Lab
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    • Home
    • Research
      • Overview
      • Systems Biochemistry
      • CoQ Biosynthesis
      • Mitochondrial Regulation
    • Publications
      • Featured
      • All by year
    • News
    • Meet Our Team
      • Current Lab
      • Lab Alumni
    • Contact
  • Home
  • Research
    • Overview
    • Systems Biochemistry
    • CoQ Biosynthesis
    • Mitochondrial Regulation
  • Publications
    • Featured
    • All by year
  • News
  • Meet Our Team
    • Current Lab
    • Lab Alumni
  • Contact

PUBLICATIONS

2025

  

  • Identification of a new COQ4 spliceogenic variant causing severe primary coenzyme Q deficiency
    Alcázar-Fabra M, Østergaard E, Fernández-Ayala DJM, Desbats MA, Morbidoni V, Tomás-Gallado L, García-Corzo L, Blanquer-Roselló MM, Bartlett AK, Sánchez-Cuesta A, Sena L, Cortés-Rodríguez A, Cascajo-Almenara MV, Pagliarini DJ, Trevisson E, Gronborg SW, and Brea-Calvo G  
    Molecular Genetics and Metabolism Reports (2025)  
  • Triacylglycerol mobilization underpins mitochondrial stress recovery   
    Baker ZN, Zhu Y, Guerra RM, Smith AJ, Arra A, Serrano LR, Overmyer KA, Mukherji S, Craig EA, Coon JJ, Pagliarini DJ.  
    Nature Cell Biology (2025) 
  • Multiomics reveals that triacylglycerol mobilization helps drive recovery from mitochondrial stress
    Baker ZN and Pagliarini DJ
    Nature Cell Biology (2025)
  • DFCP1 is a regulator of starvation-driven ATGL-mediated lipid droplet lipolysis  
    Ismail VA, Schuetz M, Baker ZN, Castillo-Badillo JA, Naismith TV, Pagliarini DJ, Kast DJ
    Journal of Lipid Research (2025) 

Cover submission (not selected) for Baker, Z.N., Zhu, Y., Guerra, R.M. et al.

2024

  • Fast and Deep Phosphoproteome Analysis with the Orbitrap Astral Mass Spectrometer
    Lancaster NM, Sinitcyn P, Forny P, Peters-Clarke TM, Fecher C, Smith AJ, Shishkova E, Arrey TN, Pashkova A, Roninson ML, Arp N, Fan J, Hansen J, Galmozzi A, Serrano LR, Rojas J, Gasch AP, Westphall MS, Stewart H, Hock C, Damoc E, Pagliarini DJ, Zabrouskov V, and Coon JJ  
    Nature Communications 2024 
  • Systematic analysis of NDUFAF6 in complex I assembly and mitochondrial disease
    Sung AY, Guerra RM, Steenberge LH, Alston CL, Murayama K, Okazaki Y, Shimura M, Prokisch H, Ghezzi D, Torraco A, Carrozzo R, Rötig A, Taylor RW, Keck JL, and Pagliarini DJ  
    Nature Metabolism 2024
  • A systematic mutational framework for studying oxidative phosphorylation-related proteins
    Sung AY and Pagliarini DJ
    Nature Metabolism 2024
  • Coenzyme Q4 is a functional substitute for coenzyme Q10 and can be targeted to the mitochondria
    Steenberge LH, Rogers S, Sung AY, Fan J, and Pagliarini DJ
    Journal of Biological Chemistry 2024
  • ACAD10 and ACAD11 enable mammalian 4-hydroxy acid lipid catabolism  
    Rashan EH, Bartlett AK, Khana DB, Zhang J, Jain R, Smith AJ, Baker ZN, Cook T, Caldwell A, Chevalier AR, Pfleger BF, Yuan P, Amador-Noguez D, Simcox JA, and Pagliarini DJ
    bioRxiv 2024

Figure model for Sung, A.Y., Guerra, R.M., Steenberge, L.H. et al.

Nature Metabolism 2024

2023

  • TOMM40 and TOMM22 of the Translocase Outer Mitochondrial Membrane Complex rescue statin-impaired mitochondrial dynamics, morphology, and mitophagy in skeletal myotubes
    Yang NV, Rogers S, Guerra R, Pagliarini DJ, Theusch, E, and Krauss RM
    bioRxiv 2023
  • COQ4 is required for the oxidative decarboxylation of the C1 carbon of Coenzyme Q in eukaryotic cells
    Pelosi P, Morbiato L, Burgardt A, Tonello F, Bartlett AK, Guerra RM, Ferizhendi KK, Desbats MA, Rascalou B, Marchi M, Vazquez-Fonseca L, Agosto C, Zanotti G, Roger-Margueritat M, Alcázar-Fabra M, García-Corzo L, Sánchez-Cuesta A, Navas P, Brea-Calvo G, Trevisson E,  Wendisch VF,  Pagliarini DJ, Salviati L, and Pierrel F
    Molecular Cell, 2024 
  • Reducing mitochondrial mysteries
    Guerra RM and Pagliarini DJ
    Nature Chemical Biology 2023
  • Pptc7 maintains mitochondrial protein content by suppressing receptor-mediated mitophagy
    Niemi NM†, Serrano L, Muehlbauer LK, Balnis C, Kozul K, Rashan EH, Shishkova E, Schueler K, Keller MP, Attie AD, Pagan J, Coon JJ, and Pagliarini DJ†
    Nature Communications, 2023
  • Hem25p is required for mitochondrial IPP transport in fungi
    Tai JT, Guerra RM, Rogers SW, Fang Z, Muehlbauer KL, Shishkova E, Overmyer KA, Coon JJ, and Pagliarini DJ
    Nature Cell Biology, 2023
  • Mitochondrial proteome research: the road ahead
    Baker ZN, Forny P, and Pagliarini DJ
    Nature Reviews Molecular Cell Biology, 2023
  • Aim18p and Aim46p are chalcone isomerase (CHI)-domain-containing mitochondrial hemoproteins in Saccharomyces cerevisiae
    Schmitz JM, Wolters JF, Murray NH, Guerra RM, Saunders JM, Jochem J, Smith RW, Bingman CA, Hittinger CT and Pagliarini DJ
    Journal of Biological Chemistry, 2023
  • Coenzyme Q biochemistry and biosynthesis
    Guerra RM and Pagliarini DJ
    Trends in Biochemical Sciences, 2023

Model figure: Baker, Z.N., Forny, P. & Pagliarini, D.J.

Nature Reviews Molecular Cell Biology, 2023

2022

  • Small Molecule Inhibition of the Archetypal UbiB protein COQ8
    Murray NH, Asquith CR, Fang Z, Smith RW, Vasta JD, Zimprich CA, Corona CR, Robers MB, Bingman CA, and Pagliarini DJ
    Nature Chemical Biology, 2022
  • Structure and functionality of a multimeric human COQ7:COQ9 complex
    Manicki M*, Aydin H*, Abriata LA, Overmyer KA, Guerra RM, Coon JJ, Dal Peraro M, Frost A† and Pagliarini DJ†
    Molecular Cell, 2022
  • Nitric oxide-driven modifications of lipoic arm inhibit α-ketoacid dehydrogenases
    Seim G, John SV, Arp NL, Fang Z, Pagliarini DJ, and Fan J
    Nature Chemical Biology, 2022
  • 2-propylphenol Allosterically Modulates COQ8A to Enhance ATPase Activity
    Murray NH*, Lewis A*, Rincon Pabon JP, Gross ML, Henzler-Wildman K and Pagliarini DJ
    ACS Chemical Biology, 2022 
  • Defining mitochondrial protein functions through deep multiomic profiling
    Rensvold JW*, Shishkova E*, Miller IJ, Sverchkov Y, Cetinkaya A, Pyle A, Manicki M, Brademan DR, Alanay Y, Raiman J, Jochem J, Peters SR, Linke V, Hutchins PD, Overmyer KA, Salome AZ, Hebert AS, Balnis CV, Kwiecien NW, Rush MJ, Westphall MS, Craven M, Akarsu NA, Taylor RW, Coon JJ†, and Pagliarini DJ†
    Nature, 2022  

Cover submission  for Murray et al., Nature Chem Bio 2022 (not selected)

Created by Galen Hicks

2021

  • Prolyl endopeptidase-like is a (thio)esterase involved in mitochondrial respiratory chain function
    Rosier K, McDevitt MT, Smet J, Floyd BJ, Verschoore M, Marcaida MJ, Bingman CA, Lemmens I, Dal Peraro M, Tavernier J, Cravatt BF, Gounko NV, Vints K, Monnens Y, Bhalla K, Aerts L, Rashan EH, Vanlander A, Van Coster R, Régal L, Pagliarini DJ†, and Creemers JWM†
    iScience, 2021 
  • UbiB proteins regulate cellular CoQ distribution in Saccharomyces cerevisiae
    Kemmerer ZA, Robinson KP, Schmitz JM, Manicki M, Paulson BR, Jochem A, Hutchins PD, Coon JJ, and Pagliarini DJ
    Nature Communications, 2021 Aug 6;12(1):4769
  • The extensive and functionally uncharacterized mitochondrial phosphoproteome
    Niemi NM and Pagliarini DJ
    Journal of Biological Chemistry, 2021 Jun 15:100880
  • Loss of C2orf69 defines a fatal auto-inflammatory syndrome in Humans and Zebrafish that evokes a Glycogen storage-associated mitochondriopathy
    Wong HH, Seet SH, Maier M, Gurel A, Traspas RM, Lee C , Shan Z, Talim B, Loh AYT, Chia CY, Teoh TS, Sng D, Rensvold R, Unal S, Shishkova E, Cepn E, Nathan FM, Sirota FL, Chao L, Yarali N, Simsek-Kiper PS, Tadahiro M, Ceylaner S, Arman-Bilir O, Mbarek H, Gumruk F, Efthymiou S, Çi̇men DU, i Georgiadou D, Sotiropoulou K, Houlden H, Paul F, Pehlivan D, Lainé C, Chai G, Ali NA, Choo SC, Keng SS, Boisson B, Yılmaz E, Xue S, Coon JJ, Ly TTN, Gilani N, Hasbini D, Kayserili H, Zaki M, Isfort RJ, Ordonez N, Tripolszki K, Bauer P, Rezaei N, Seyedpour S, Khotaei GT, Bascom CC, Maroofian R, Chaabouni M, AlSubhi A, Eyaid W, Işıkay S, Gleeson JS, Lupski JR, Casanova J-L, Pagliarini DJ, Akarsu NA, Maurer-Stroh S, Cetinkaya A, Bertoli-Avella A, Mathuru AS, Ho L, Bard F, Reversade B
    American Journal of Human Genetics, 2021 May 21:S0002-9297(21)00187-7
  • Defining intermediates and redundancies in coenzyme Q precursor biosynthesis
    Robinson KP, Jochem A, Johnson  SE, Reddy TR, Russell JD, Coon JJ, and Pagliarini DJ
    Journal of Biological Chemistry, 2021 Apr 14;296:100643
  • Multi-Omic Single-Shot Technology for Integrated Proteome and Lipidome Analysis
    He Y, Rashan EH, Linke V, Shishkova E, Hebert AS, Jochem A, Westphall MS, Pagliarini DJ, Overmyer KA, and Coon JJ
    Anal. Chem., 2021 Mar 9;93(9):4217-4222

Model figure for Kemmerer, Robinson et al., Nature Communications 2021

2020

  • Quantitative shotgun proteome analysis by direct infusion
    Meyer JG, Niemi NM, Pagliarini DJ, and Coon JJ
    Nature Methods, 2020 Dec;17(12):1222-1228
  • Argonaut: a Web Platform for Collaborative Multi-Omic Data Visualization and Exploration
    Brademan DR, Miller IJ, Kwiecien KW, Pagliarini DJ, Westphall MS, Coon JJ, and Shishkova E
    Patterns, 2020 Oct 9;1(7)
  • Label-free Method for Classification of T cell Activation
    Walsh AJ, Mueller K, Jones I, Walsh CM, Piscopo N, Niemi NM, Pagliarini DJ, Saha K and Skala MC
    Nature Biomedical Engineering, 2021 Jan;5(1):77-88
  • Clinical, imaging, biomarker, and molecular delineation of COQ8A-ataxia: a multicenter study of 59 patients
    Traschütz A, Schirinzi T, Laugwitz L, Murray NH, Reich S, Heinzmann A, Vasco G, Bertini E, Zanni G, Durr A, Magri S, Malandrini A, Taroni F, Baets J, de Jonghe P, de Ridder W, Bereau M, Demuth S, Ganos C, Basak N, Hanagasi H, Kurul SH, Bender B, Schöls L, Grashoff U, Klopstock T, Horvath R, van de Warrenburg B, Burglen L, Rougeot C, Ewenczyk C, Koenig M, Santorelli FM, Anheim M, Munhoz RP, Haack T, Distelmaier F, Pagliarini DJ, Puccio H, Synofzik M
    Annals of Neurology, 2020 Aug;88(2):251-263
  • 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 Dec;16(12):2219-2237

Cover submission (not selected) for Sung, Floyd, & Pagliarini 2020

Created by Matt Stefely

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 Oct;18(11):815
  • 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

Cover submission (not selected) for Lohman et al. 2019

Created by Huston Design

2018

  • Identification and Quantification of Murine Mitochondrial Proteoforms Using an Integrated Top-Down and Intact-Mass Strategy
    Schaffer LV, Rensvold JW, Shortreed MR, Cesnik AJ, Jochem A, Scalf M, Frey BL, Pagliarini DJ, and Smith LM
    Journal of Proteome Research 2018 17(10):3526-3536
  • 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
  • A path to the powerhouse: systems-to-structure approaches for studying mitochondrial proteins
    Pagliarini DJ
    Protein Science, 2018 27(8):1518-1525
  • DNA Polymerase θ Increases DNA Polymerase θ Increases Mutational Rates in Mitochondrial DNA
    Wisnovsky S, Sack T, Pagliarini DJ, Laposa RR, and Kelley SO
    ACS Chemical Biology, 2018 13(4):900-908
  • 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
    PREVIEW

Accepted cover for Reidenbach et al. 2018

Created by Amy Lin

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 68(5):970-977
  • Biochemistry of Mitochondrial Coenzyme Q Biosynthesis
    Stefely JA and Pagliarini DJ
    Trends in Biochemical Sciences, 2017 42(10):824-843
  • 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
  • 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 18(2):307-313

Cover submission (not selected) for Veling et al. 2017

Created by Mike Veling

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 291(40):20827-20837
  • 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)

Accepted cover for Floyd et al. 2016

Created by Red Spark Creative

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

Cover submission (not selected) for Stefely et al. 2015

Created by Jon Stefely

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 426(11):2199-216
  • 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

Cover submission (not selected) for Lohman et al. 2014

Created by Danielle Lohman

2013

  • Hallmarks of a new era in mitochondrial biochemistry
    Pagliarini DJ† and Rutter J†
    Genes and Development 2013, 27(24): 2615-27 
  • 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 
  • 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 
  • 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 
  • 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 
  • 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 
  • 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 

Accepted cover for Rensvold et al. 2013

Created by Jarred Rensvold

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 
  • 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 
  • 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 
  • 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 

Cover submission (not selected) for Grimsrud et al. 2012

Created by AJ Bureta

Pre-2012

  • 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 
  • 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 
  • 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. 
  • 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.
    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. 
  • 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

Accepted cover for Pagliarini, Robinson, Dixon 2005

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