University of Dundee

MRC Protein Phosphorylation and Ubiquitylation Unit 2017

Bakshi, S., Taylor, J., Strickson, S., McCartney, T. and Cohen, P. (2017) Identification of TBK1 complexes required for the phosphorylation of IRF3 and the production of interferon beta. Biochem. J. 474, 1163-1174 
doi. 10.1042/BCJ20160992, 2017 
PMID 28159912 
PMC 5350611

Cohen, P. and Strickson, S. (2017) The role of hybrid ubiquitin chains in the MyD88 and other innate immune signalling pathways. Cell Death Differ. 24, 1153-1159 
doi. 10.1038/cdd.2017.17, 2017 
PMID 28475177 
PMC 5520163

Cummins, T. D. and Sapkota, G. P. (2017) Characterization of Protein Complexes Using Chemical Cross-Linking Coupled Electrospray Mass Spectrometry. Methods Mol. Biol., 
doi. 10.1007/7651_2017_85, 2017 
PMID 29064006 

Cummins, T. D., Wu, K. Z. L., Bozatzi, P., Dingwell, K. S., Macartney, T. J., Wood, N. T., Varghese, J., Gourlay, R., Campbell, D. G., Prescott, A., Griffis, E., Smith, J. C. and Sapkota, G. P. (2018) PAWS1 controls cytoskeletal dynamics and cell migration through association with the SH3 adaptor CD2AP. J. Cell Sci. 131, 
doi. 10.1242/jcs.202390, 2018 
PMID 29175910 

Darling, N. J., Toth, R., Arthur, J. S. and Clark, K. (2017) Inhibition of SIK2 and SIK3 during differentiation enhances the anti-inflammatory phenotype of macrophages. Biochem. J. 474, 521-537 
doi. 10.1042/BCJ20160646, 2017 
PMID 27920213 
PMC 5290485

Feeney, L., Munoz, I. M., Lachaud, C., Toth, R., Appleton, P. L., Schindler, D. and Rouse, J. (2017) RPA-Mediated Recruitment of the E3 Ligase RFWD3 Is Vital for Interstrand Crosslink Repair and Human Health. Mol. Cell. 66, 610-621 e614 
doi. 10.1016/j.molcel.2017.04.021, 2017 
PMID 28575657 
PMC 5459755

Fernandez-Alonso, R., Bustos, F., Williams, C. A. C. and Findlay, G. M. (2017) Protein Kinases in Pluripotency-Beyond the Usual Suspects. J. Mol. Biol. 429, 1504-1520 
doi. 10.1016/j.jmb.2017.04.013, 2017 
PMID 28456524 

Fernandez-Alonso, R., Davidson, L., Hukelmann, J., Zengerle, M., Prescott, A. R., Lamond, A., Ciulli, A., Sapkota, G. P. and Findlay, G. M. (2017) Brd4-Brd2 isoform switching coordinates pluripotent exit and Smad2-dependent lineage specification. EMBO reports. 18, 1108-1122 
doi. 10.15252/embr.201643534, 2017 
PMID 28588073 PMC 5494510

Findlay, G. M., David, L. and Beyer, T. A. (2017) Molecular Mechanisms of Stem Cell Pluripotency and Cell Fate Specification. J. Mol. Biol. 429, 1439-1440 
doi. 10.1016/j.jmb.2017.03.011, 2017
PMID 28302388 

Fulcher, L. J., Hutchinson, L. D., Macartney, T. J., Turnbull, C. and Sapkota, G. P. (2017) Targeting endogenous proteins for degradation through the affinity-directed protein missile system. Open Biol. 7, 
doi. 10.1098/rsob.170066, 2017 
PMID 28490657 
PMC 5451546

Hall, E. A., Nahorski, M. S., Murray, L. M., Shaheen, R., Perkins, E., Dissanayake, K. N., Kristaryanto, Y., Jones, R. A., Vogt, J., Rivagorda, M., Handley, M. T., Mali, G. R., Quidwai, T., Soares, D. C., Keighren, M. A., McKie, L., Mort, R. L., Gammoh, N., Garcia-Munoz, A., Davey, T., Vermeren, M., Walsh, D., Budd, P., Aligianis, I. A., Faqeih, E., Quigley, A. J., Jackson, I. J., Kulathu, Y., Jackson, M., Ribchester, R. R., von Kriegsheim, A., Alkuraya, F. S., Woods, C. G., Maher, E. R. and Mill, P. (2017) PLAA Mutations Cause a Lethal Infantile Epileptic Encephalopathy by Disrupting Ubiquitin-Mediated Endolysosomal Degradation of Synaptic Proteins. Am. J. Hum. Genet. 100, 706-724 
doi. 10.1016/j.ajhg.2017.03.008, 2017 
PMID 28413018 
PMC 5420347

Hardie, D. G. (2017) An Oncogenic Role for the Ubiquitin Ligase UBE2O by Targeting AMPK-α2 for Degradation. Cancer Cell. 31, 163-165 
doi. 10.1016/j.ccell.2017.01.010, 2017 
PMID 28196589 

Hartlova, A., Peltier, J., Bilkei-Gorzo, O. and Trost, M. (2017) Isolation and Western Blotting of Latex-Bead Phagosomes to Track Phagosome Maturation. Methods Mol. Biol. 1519, 241-248 
doi. 10.1007/978-1-4939-6581-6_16, 2017 
PMID 27815884 

Hatcher, J. M., Choi, H. G., Alessi, D. R. and Gray, N. S. (2017) Small-Molecule Inhibitors of LRRK2. Adv Neurobiol. 14, 241-264 
doi. 10.1007/978-3-319-49969-7_13, 2017 
PMID 28353288 

Jayachandran, N., Landego, I., Hou, S., Alessi, D. R. and Marshall, A. J. (2017) B-cell-intrinsic function of TAPP adaptors in controlling germinal center responses and autoantibody production in mice. Eur. J. Immunol. 47, 280-290 
doi. 10.1002/eji.201646596, 2017 
PMID 27859053 

Kategaya, L., Di Lello, P., Rouge, L., Pastor, R., Clark, K. R., Drummond, J., Kleinheinz, T., Lin, E., Upton, J. P., Prakash, S., Heideker, J., McCleland, M., Ritorto, M. S., Alessi, D. R., Trost, M., Bainbridge, T. W., Kwok, M. C. M., Ma, T. P., Stiffler, Z., Brasher, B., Tang, Y., Jaishankar, P., Hearn, B. R., Renslo, A. R., Arkin, M. R., Cohen, F., Yu, K., Peale, F., Gnad, F., Chang, M. T., Klijn, C., Blackwood, E., Martin, S. E., Forrest, W. F., Ernst, J. A., Ndubaku, C., Wang, X., Beresini, M. H., Tsui, V., Schwerdtfeger, C., Blake, R. A., Murray, J., Maurer, T. and Wertz, I. E. (2017) USP7 small-molecule inhibitors interfere with ubiquitin binding. Nature. 550, 534-538 
doi. 10.1038/nature24006, 2017 
PMID 29045385 

Kristariyanto, Y. A., Abdul Rehman, S. A., Weidlich, S., Knebel, A. and Kulathu, Y. (2017) A single MIU motif of MINDY-1 recognizes K48-linked polyubiquitin chains. EMBO reports. 18, 392-402 
doi. 10.15252/embr.201643205, 2017 
PMID 28082312 
PMC 5331195

Kumar, A., Chaugule, V. K., Condos, T. E. C., Barber, K. R., Johnson, C., Toth, R., Sundaramoorthy, R., Knebel, A., Shaw, G. S. and Walden, H. (2017) Parkin-phosphoubiquitin complex reveals cryptic ubiquitin-binding site required for RBR ligase activity. Nat. Struct. Mol. Biol. 24, 475-483 
doi. 10.1038/nsmb.3400, 2017 
PMID 28414322 
PMC 5420311

Kumar, A., Tamjar, J., Waddell, A. D., Woodroof, H. I., Raimi, O. G., Shaw, A. M., Peggie, M., Muqit, M. M. and van Aalten, D. M. (2017) Structure of PINK1 and mechanisms of Parkinson's disease-associated mutations. Elife. 6, 
doi. 10.7554/eLife.29985, 2017 
PMID 28980524 
PMC 5679756

Leznicki, P. and Kulathu, Y. (2017) Mechanisms of regulation and diversification of deubiquitylating enzyme function. J. Cell Sci. 130, 1997-2006 
doi. 10.1242/jcs.201855, 2017 
PMID 28476940 

Lopez-Guerrero, A. M., Tomas-Martin, P., Pascual-Caro, C., Macartney, T., Rojas-Fernandez, A., Ball, G., Alessi, D. R., Pozo-Guisado, E. and Martin-Romero, F. J. (2017) Regulation of membrane ruffling by polarized STIM1 and ORAI1 in cortactin-rich domains. Sci. Rep. 7, 383 
doi. 10.1038/s41598-017-00331-4, 2017 
PMID 28341841 
PMC 5428229

Magiera, K., Tomala, M., Kubica, K., De Cesare, V., Trost, M., Zieba, B. J., Kachamakova-Trojanowska, N., Les, M., Dubin, G., Holak, T. A. and Skalniak, L. (2017) Lithocholic Acid Hydroxyamide Destabilizes Cyclin D1 and Induces G0/G1 Arrest by Inhibiting Deubiquitinase USP2a. Cell chemical biology. 24, 458-470 e418 
doi. 10.1016/j.chembiol.2017.03.002, 2017 
PMID 28343940 
PMC 5404848

Maniaci, C., Hughes, S. J., Testa, A., Chen, W., Lamont, D. J., Rocha, S., Alessi, D. R., Romeo, R. and Ciulli, A. (2017) Homo-PROTACs: bivalent small-molecule dimerizers of the VHL E3 ubiquitin ligase to induce self-degradation. Nat Commun. 8, 830 
doi. 10.1038/s41467-017-00954-1, 2017 
PMID 29018234 
PMC 5635026

Maric, M., Mukherjee, P., Tatham, M. H., Hay, R. and Labib, K. (2017) Ufd1-Npl4 Recruit Cdc48 for Disassembly of Ubiquitylated CMG Helicase at the End of Chromosome Replication. Cell Rep. 18, 3033-3042 
doi. 10.1016/j.celrep.2017.03.020, 2017 
PMID 28355556 
PMC 5382235

Morreale, F. E., Bortoluzzi, A., Chaugule, V. K., Arkinson, C., Walden, H. and Ciulli, A. (2017) Allosteric Targeting of the Fanconi Anemia Ubiquitin-Conjugating Enzyme Ube2T by Fragment Screening. J. Med. Chem. 60, 4093-4098 
doi. 10.1021/acs.jmedchem.7b00147, 2017 
PMID 28437106 
PMC 5441753

Osgerby, L., Lai, Y. C., Thornton, P. J., Amalfitano, J., Le Duff, C. S., Jabeen, I., Kadri, H., Miccoli, A., Tucker, J. H. R., Muqit, M. M. K. and Mehellou, Y. (2017) Kinetin Riboside and Its ProTides Activate the Parkinson's Disease Associated PTEN-Induced Putative Kinase 1 (PINK1) Independent of Mitochondrial Depolarization. J. Med. Chem. 60, 3518-3524 
doi. 10.1021/acs.jmedchem.6b01897, 2017 
PMID 28323427 
PMC 5410652

Pauwels, A. M., Trost, M., Beyaert, R. and Hoffmann, E. (2017) Patterns, Receptors, and Signals: Regulation of Phagosome Maturation. Trends Immunol. 38, 407-422 
doi. 10.1016/j.it.2017.03.006, 2017 
PMID 28416446 
PMC 5455985

Peltier, J., Hartlova, A. and Trost, M. (2017) Assessing the Phagosome Proteome by Quantitative Mass Spectrometry. Methods Mol. Biol. 1519, 249-263 
doi. 10.1007/978-1-4939-6581-6_17, 2017 
PMID 27815885 

Rena, G., Hardie, D. G. and Pearson, E. R. (2017) The mechanisms of action of metformin. Diabetologia. 60, 1577-1585 
doi. 10.1007/s00125-017-4342-z, 2017 
PMID 28776086 
PMC 5552828

Ross, F. A., Hawley, S. A., Auciello, F. R., Gowans, G. J., Atrih, A., Lamont, D. J. and Hardie, D. G. (2017) Mechanisms of Paradoxical Activation of AMPK by the Kinase Inhibitors SU6656 and Sorafenib. Cell chemical biology. 24, 813-824 e814 
doi. 10.1016/j.chembiol.2017.05.021, 2017 
PMID 28625738 
PMC 5522529

Selvan, N., Williamson, R., Mariappa, D., Campbell, D. G., Gourlay, R., Ferenbach, A. T., Aristotelous, T., Hopkins-Navratilova, I., Trost, M. and van Aalten, D. M. F. (2017) A mutant O-GlcNAcase enriches Drosophila developmental regulators. Nat. Chem. Biol. 13, 882-887 
doi. 10.1038/nchembio.2404, 2017 
PMID 28604694 

Shekarabi, M., Zhang, J., Khanna, A. R., Ellison, D. H., Delpire, E. and Kahle, K. T. (2017) WNK Kinase Signaling in Ion Homeostasis and Human Disease. Cell metabolism. 25, 285-299 
doi. 10.1016/j.cmet.2017.01.007, 2017 
PMID 28178566 

Sonneville, R., Moreno, S. P., Knebel, A., Johnson, C., Hastie, C. J., Gartner, A., Gambus, A. and Labib, K. (2017) CUL-2(LRR-1) and UBXN-3 drive replisome disassembly during DNA replication termination and mitosis. Nat. Cell Biol. 19, 468-479 
doi. 10.1038/ncb3500, 2017 
PMID 28368371 
PMC 5410169

Strickson, S., Emmerich, C. H., Goh, E. T. H., Zhang, J., Kelsall, I. R., Macartney, T., Hastie, C. J., Knebel, A., Peggie, M., Marchesi, F., Arthur, J. S. C. and Cohen, P. (2017) Roles of the TRAF6 and Pellino E3 ligases in MyD88 and RANKL signaling. Proc. Natl. Acad. Sci. U. S. A. 114, E3481-E3489 
doi. 10.1073/pnas.1702367114, 2017 
PMID 28404732 
PMC 5410814

Virdee, S. (2017) 2016 EMBO Chemical Biology Conference. ChemBioChem. 18, 66-71 
doi. 10.1002/cbic.201600597, 2017 
PMID 27862792 

Vollmer, S., Strickson, S., Zhang, T., Gray, N., Lee, K. L., Rao, V. R. and Cohen, P. (2017) The mechanism of activation of IRAK1 and IRAK4 by interleukin-1 and Toll-like receptor agonists. Biochem. J. 474, 2027-2038 
doi. 10.1042/BCJ20170097, 2017 
PMID 28512203 
PMC 5460469

Walden, H. and Muqit, M. M. (2017) Ubiquitin and Parkinson's disease through the looking glass of genetics. Biochem. J. 474, 1439-1451 
doi. 10.1042/BCJ20160498, 2017
PMID 28408429 
PMC 5390927

Williams, C. A. C., Gray, N. S. and Findlay, G. M. (2017) A Simple Method to Identify Kinases That Regulate Embryonic Stem Cell Pluripotency by High-throughput Inhibitor Screening. J Vis Exp. 
doi. 10.3791/55515, 2017 
PMID 28570543 
PMC 5607952

Zhang, C. S., Hawley, S. A., Zong, Y., Li, M., Wang, Z., Gray, A., Ma, T., Cui, J., Feng, J. W., Zhu, M., Wu, Y. Q., Li, T. Y., Ye, Z., Lin, S. Y., Yin, H., Piao, H. L., Hardie, D. G. and Lin, S. C. (2017) Fructose-1,6-bisphosphate and aldolase mediate glucose sensing by AMPK. Nature. 548, 112-116 
doi. 10.1038/nature23275, 2017 
PMID 28723898 
PMC 5544942

Zhang, J., Macartney, T., Peggie, M. and Cohen, P. (2017) Interleukin-1 and TRAF6-dependent activation of TAK1 in the absence of TAB2 and TAB3. Biochem. J. 474, 2235-2248 
doi. 10.1042/BCJ20170288, 2017 
PMID 28507161 
PMC 5632801

Zibrova, D., Vandermoere, F., Goransson, O., Peggie, M., Marino, K. V., Knierim, A., Spengler, K., Weigert, C., Viollet, B., Morrice, N. A., Sakamoto, K. and Heller, R. (2017) GFAT1 phosphorylation by AMPK promotes VEGF-induced angiogenesis. Biochem. J. 474, 983-1001 
doi. 10.1042/BCJ20160980, 2017 
PMID 28008135