University of Dundee

MRC Protein Phosphorylation and Ubiquitylation Unit 2016

Abdul Rehman, S. A., Kristariyanto, Y. A., Choi, S. Y., Nkosi, P. J., Weidlich, S., Labib, K., Hofmann, K. and Kulathu, Y. (2016) MINDY-1 Is a Member of an Evolutionarily Conserved and Structurally Distinct New Family of Deubiquitinating Enzymes. Mol Cell. 63, 146-155 
doi. 10.1016/j.molcel.2016.05.009, 
PMC 4942677
PMID 27292798

Alpi, A. F., Chaugule, V. and Walden, H. (2016) Mechanism and disease association of E2-conjugating enzymes: lessons from UBE2T and UBE2L3. Biochem J. 473, 3401-3419 
doi. 10.1042/BCJ20160028, 
PMID 27729585

Aregger, M., Kaskar, A., Varshney, D., Fernandez-Sanchez, M. E., Inesta-Vaquera, F. A., Weidlich, S. and Cowling, V. H. (2016) CDK1-Cyclin B1 Activates RNMT, Coordinating mRNA Cap Methylation with G1 Phase Transcription. Mol Cell. 61, 734-746 
doi. 10.1016/j.molcel.2016.02.008, 
PMC 4781437
PMID 26942677

Armbruster, N. S., Richardson, J. R., Schreiner, J., Klenk, J., Gunter, M., Kretschmer, D., Poschel, S., Schenke-Layland, K., Kalbacher, H., Clark, K. and Autenrieth, S. E. (2016) PSM Peptides of Staphylococcus aureus Activate the p38-CREB Pathway in Dendritic Cells, Thereby Modulating Cytokine Production and T Cell Priming. J Immunol. 196, 1284-1292 
doi. 10.4049/jimmunol.1502232, 
PMID 26729806

Bago, R., Sommer, E., Castel, P., Crafter, C., Bailey, F. P., Shpiro, N., Baselga, J., Cross, D., Eyers, P. A. and Alessi, D. R. (2016) The hVps34-SGK3 pathway alleviates sustained PI3K/Akt inhibition by stimulating mTORC1 and tumour growth. EMBO J. 35, 1902-1922 
doi. 10.15252/embj.201693929, 
PMC 5007552
PMID 27481935

Bell, S. P. and Labib, K. (2016) Chromosome Duplication in Saccharomyces cerevisiae. Genetics. 203, 1027-1067 
doi. 10.1534/genetics.115.186452, 
PMC4937469 
PMID 27384026

Buser, R., Kellner, V., Melnik, A., Wilson-Zbinden, C., Schellhaas, R., Kastner, L., Piwko, W., Dees, M., Picotti, P., Maric, M., Labib, K., Luke, B. and Peter, M. (2016) The Replisome-Coupled E3 Ubiquitin Ligase Rtt101Mms22 Counteracts Mrc1 Function to Tolerate Genotoxic Stress. PLoS Genet. 12, e1005843 
doi. 10.1371/journal.pgen.1005843, 
PMC 4743919
PMID 26849847

Cammareri, P., Rose, A. M., Vincent, D. F., Wang, J., Nagano, A., Libertini, S., Ridgway, R. A., Athineos, D., Coates, P. J., McHugh, A., Pourreyron, C., Dayal, J. H., Larsson, J., Weidlich, S., Spender, L. C., Sapkota, G. P., Purdie, K. J., Proby, C. M., Harwood, C. A., Leigh, I. M., Clevers, H., Barker, N., Karlsson, S., Pritchard, C., Marais, R., Chelala, C., South, A. P., Sansom, O. J. and Inman, G. J. (2016) Inactivation of TGFbeta receptors in stem cells drives cutaneous squamous cell carcinoma. Nat Commun. 7, 12493 
doi. 10.1038/ncomms12493, 
PMC 5007296
PMID 27558455

Castel, P., Ellis, H., Bago, R., Toska, E., Razavi, P., Carmona, F. J., Kannan, S., Verma, C. S., Dickler, M., Chandarlapaty, S., Brogi, E., Alessi, D. R., Baselga, J. and Scaltriti, M. (2016) PDK1-SGK1 Signaling Sustains AKT-Independent mTORC1 Activation and Confers Resistance to PI3Kalpha Inhibition. Cancer Cell. 30, 229-242 
doi. 10.1016/j.ccell.2016.06.004, 
PMC 4982440
PMID 27451907

Chaugule, V. K. and Walden, H. (2016) Specificity and disease in the ubiquitin system. Biochem Soc Trans. 44, 212-227 
doi. 10.1042/BST20150209, 
PMID 26862208

Cianfanelli, F. R., Alcoforado Diniz, J., Guo, M., De Cesare, V., Trost, M. and Coulthurst, S. J. (2016) VgrG and PAAR Proteins Define Distinct Versions of a Functional Type VI Secretion System. PLoS Pathog. 12, e1005735 
doi. 10.1371/journal.ppat.1005735, 
PMC 4924876
PMID 27352036

Darling, N. J., Toth, R., Arthur, J. S. and Clark, K. (2016) Inhibition of SIK2 and SIK3 during differentiation enhances the anti-inflammatory phenotype of macrophages. Biochem J
doi. 10.1042/BCJ20160646, 
PMID 27920213

Emmerich, C. H., Bakshi, S., Kelsall, I. R., Ortiz-Guerrero, J., Shpiro, N. and Cohen, P. (2016) Lys63/Met1-hybrid ubiquitin chains are commonly formed during the activation of innate immune signalling. Biochem Biophys Res Commun. 474, 452-461 
doi. 10.1016/j.bbrc.2016.04.141, 
PMC 4880150
PMID 27133719

Fulcher, L. J., Macartney, T., Bozatzi, P., Hornberger, A., Rojas-Fernandez, A. and Sapkota, G. P. (2016) An affinity-directed protein missile system for targeted proteolysis. Open Biol. 6
doi. 10.1098/rsob.160255, 
PMC 5090066
PMID 27784791

Gandin, V., Masvidal, L., Cargnello, M., Gyenis, L., McLaughlan, S., Cai, Y., Tenkerian, C., Morita, M., Balanathan, P., Jean-Jean, O., Stambolic, V., Trost, M., Furic, L., Larose, L., Koromilas, A. E., Asano, K., Litchfield, D., Larsson, O. and Topisirovic, I. (2016) mTORC1 and CK2 coordinate ternary and eIF4F complex assembly. Nat Commun. 7, 11127 
doi. 10.1038/ncomms11127, 
PMC 4822005
PMID 27040916

Grasso, L., Suska, O., Davidson, L., Gonatopoulos-Pournatzis, T., Williamson, R., Wasmus, L., Wiedlich, S., Peggie, M., Stavridis, M. P. and Cowling, V. H. (2016) mRNA Cap Methylation in Pluripotency and Differentiation. Cell Rep. 16, 1352-1365 
doi. 10.1016/j.celrep.2016.06.089, 
PMC 4977272
PMID 27452456

Hjerpe, R., Bett, J. S., Keuss, M. J., Solovyova, A., McWilliams, T. G., Johnson, C., Sahu, I., Varghese, J., Wood, N., Wightman, M., Osborne, G., Bates, G. P., Glickman, M. H., Trost, M., Knebel, A., Marchesi, F. and Kurz, T. (2016) UBQLN2 Mediates Autophagy-Independent Protein Aggregate Clearance by the Proteasome. Cell. 166, 935-949 
doi. 10.1016/j.cell.2016.07.001, 
PMC 5003816
PMID 27477512

Hoxhaj, G., Caddye, E., Najafov, A., Houde, V. P., Johnson, C., Dissanayake, K., Toth, R., Campbell, D. G., Prescott, A. R. and MacKintosh, C. (2016) The E3 ubiquitin ligase ZNRF2 is a substrate of mTORC1 and regulates its activation by amino acids. Elife. 5, e12278 
doi. 10.7554/eLife.12278, 
PMC 4889327
PMID 27244671

Huguenin-Dezot, N., De Cesare, V., Peltier, J., Knebel, A., Kristaryianto, Y. A., Rogerson, D. T., Kulathu, Y., Trost, M. and Chin, J. W. (2016) Synthesis of Isomeric Phosphoubiquitin Chains Reveals that Phosphorylation Controls Deubiquitinase Activity and Specificity. Cell Rep. 16, 1180-1193 
doi. 10.1016/j.celrep.2016.06.064, 
PMC 4967478
PMID 27425610

Ito, G., Katsemonova, K., Tonelli, F., Lis, P., Baptista, M. A., Shpiro, N., Duddy, G., Wilson, S., Ho, P. W., Ho, S. L., Reith, A. D. and Alessi, D. R. (2016) Phos-tag analysis of Rab10 phosphorylation by LRRK2: a powerful assay for assessing kinase function and inhibitors. Biochem J. 473, 2671-2685 
doi. 10.1042/BCJ20160557, 
PMC 5003698
PMID 27474410

Jayachandran, N., Landego, I., Hou, S., Alessi, D. R. and Marshall, A. J. (2016) B-cell-intrinsic function of TAPP adaptors in controlling germinal center responses and autoantibody production in mice. Eur J Immunol
doi. 10.1002/eji.201646596, 
PMID 27859053

Kahle, K. T., Flores, B., Bharucha-Goebel, D., Zhang, J., Donkervoort, S., Hegde, M., Hussain, G., Duran, D., Liang, B., Sun, D., Bonnemann, C. G. and Delpire, E. (2016) Peripheral motor neuropathy is associated with defective kinase regulation of the KCC3 cotransporter. Sci Signal. 9, ra77 
doi. 10.1126/scisignal.aae0546, 
PMID 27485015

Kahle, K. T., Schmouth, J. F., Lavastre, V., Latremoliere, A., Zhang, J., Andrews, N., Omura, T., Laganiere, J., Rochefort, D., Hince, P., Castonguay, G., Gaudet, R., Mapplebeck, J. C., Sotocinal, S. G., Duan, J., Ward, C., Khanna, A. R., Mogil, J. S., Dion, P. A., Woolf, C. J., Inquimbert, P. and Rouleau, G. A. (2016) Inhibition of the kinase WNK1/HSN2 ameliorates neuropathic pain by restoring GABA inhibition. Sci Signal. 9, ra32 
doi. 10.1126/scisignal.aad0163, 
PMID 27025876

Kapuria, V., Rohrig, U. F., Bhuiyan, T., Borodkin, V. S., van Aalten, D. M., Zoete, V. and Herr, W. (2016) Proteolysis of HCF-1 by Ser/Thr glycosylation-incompetent O-GlcNAc transferase:UDP-GlcNAc complexes. Genes Dev. 30, 960-972 
doi. 10.1101/gad.275925.115, 
PMID 27056667

Keuss, M. J., Thomas, Y., McArthur, R., Wood, N. T., Knebel, A. and Kurz, T. (2016) Characterization of the mammalian family of DCN-type NEDD8 E3 ligases. J Cell Sci. 129, 1441-1454 
doi. 10.1242/jcs.181784, 
PMC 4886823
PMID 26906416

King, M. A., Ganley, I. G. and Flemington, V. (2016) Inhibition of cholesterol metabolism underlies synergy between mTOR pathway inhibition and chloroquine in bladder cancer cells. Oncogene. 35, 4518-4528 
doi. 10.1038/onc.2015.511, 
PMC 5000518
PMID 26853465

Klionsky, D. J. and et al inc Ganley, I. G. (2016) Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). Autophagy. 12, 1-222 
doi. 10.1080/15548627.2015.1100356, 
PMC4835977
PMID 26799652

Komatsu, T. and Virdee, S. (2016) ICBS and ECBS Chemical Biology Meeting 2015 - Let Them Come to Berlin! ACS Chem Biol. 11, 1159-1166 
doi. 10.1021/acschembio.6b00268, 
PMID 27198933

Kulathu, Y. (2016) Novel Diubiquitin Probes Expand the Chemical Toolkit to Study DUBs. Cell Chem Biol. 23, 432-434 
doi. 10.1016/j.chembiol.2016.04.001, 
PMID 27105279

Lachaud, C., Moreno, A., Marchesi, F., Toth, R., Blow, J. J. and Rouse, J. (2016) Ubiquitinated Fancd2 recruits Fan1 to stalled replication forks to prevent genome instability. Science. 351, 846-849 
doi. 10.1126/science.aad5634, 
PMC 4770513
PMID 26797144

Lachaud, C. and Rouse, J. (2016) A route to new cancer therapies: the FA pathway is essential in BRCA1- or BRCA2-deficient cells. Nat Struct Mol Biol. 23, 701-703 
doi. 10.1038/nsmb.3276, 
PMID 27487393

Lachaud, C., Slean, M., Marchesi, F., Lock, C., Odell, E., Castor, D., Toth, R. and Rouse, J. (2016) Karyomegalic interstitial nephritis and DNA damage-induced polyploidy in Fan1 nuclease-defective knock-in mice. Genes Dev. 30, 639-644 
doi. 10.1101/gad.276287.115, 
PMC 4803050
PMID 26980188

Maure, J. F., Moser, S. C., Jaffray, E. G., A, F. A. and Hay, R. T. (2016) Loss of ubiquitin E2 Ube2w rescues hypersensitivity of Rnf4 mutant cells to DNA damage. Sci Rep. 6, 26178 
doi. 10.1038/srep26178, 
PMC 4868978
PMID 27185577

McGuire, V. A., Ruiz-Zorrilla Diez, T., Emmerich, C. H., Strickson, S., Ritorto, M. S., Sutavani, R. V., Weibeta, A., Houslay, K. F., Knebel, A., Meakin, P. J., Phair, I. R., Ashford, M. L., Trost, M. and Arthur, J. S. (2016) Dimethyl fumarate blocks pro-inflammatory cytokine production via inhibition of TLR induced M1 and K63 ubiquitin chain formation. Sci Rep. 6, 31159 
doi. 10.1038/srep31159, 
PMC 4976367
PMID 27498693

McWilliams, T. G. and Ganley, I. G. (2016) Life in lights: Tracking mitochondrial delivery to lysosomes in vivo. Autophagy, 1-2 
doi. 10.1080/15548627.2016.1234567, 
PMID 27715383

McWilliams, T. G., Prescott, A. R., Allen, G. F., Tamjar, J., Munson, M. J., Thomson, C., Muqit, M. M. and Ganley, I. G. (2016) mito-QC illuminates mitophagy and mitochondrial architecture in vivo. J Cell Biol. 214, 333-345 
doi. 10.1083/jcb.201603039, 
PMC 4970326
PMID 27458135

Morreale, F. E. and Walden, H. (2016) Types of Ubiquitin Ligases. Cell. 165, 248-248 e241 
doi. 10.1016/j.cell.2016.03.003, 
PMID 27015313

Nanda, S. K., Lopez-Pelaez, M., Arthur, J. S., Marchesi, F. and Cohen, P. (2016) Suppression of IRAK1 or IRAK4 Catalytic Activity, but Not Type 1 IFN Signaling, Prevents Lupus Nephritis in Mice Expressing a Ubiquitin Binding-Defective Mutant of ABIN1. J Immunol. 197, 4266-4273 
doi. 10.4049/jimmunol.1600788, 
PMC 5114882
PMID 27807192

Naujoks, J., Tabeling, C., Dill, B. D., Hoffmann, C., Brown, A. S., Kunze, M., Kempa, S., Peter, A., Mollenkopf, H. J., Dorhoi, A., Kershaw, O., Gruber, A. D., Sander, L. E., Witzenrath, M., Herold, S., Nerlich, A., Hocke, A. C., van Driel, I., Suttorp, N., Bedoui, S., Hilbi, H., Trost, M. and Opitz, B. (2016) IFNs Modify the Proteome of Legionella-Containing Vacuoles and Restrict Infection Via IRG1-Derived Itaconic Acid. PLoS Pathog. 12, e1005408 
doi. 10.1371/journal.ppat.1005408, 
PMC 4734697
PMID 26829557

Pao, K. C., Stanley, M., Han, C., Lai, Y. C., Murphy, P., Balk, K., Wood, N. T., Corti, O., Corvol, J. C., Muqit, M. M. and Virdee, S. (2016) Probes of ubiquitin E3 ligases enable systematic dissection of parkin activation. Nat Chem Biol. 12, 324-331 
doi. 10.1038/nchembio.2045, 
PMC 4909137
PMID 26928937

Schumacher, F. R., Schubert, S., Hannus, M., Sonnichsen, B., Ittrich, C., Kreideweiss, S., Kurz, T. and Rippmann, J. F. (2016) RNAi Screen for NRF2 Inducers Identifies Targets That Rescue Primary Lung Epithelial Cells from Cigarette Smoke Induced Radical Stress. PLoS One. 11, e0166352 
doi. 10.1371/journal.pone.0166352, 
PMC 5104413
PMID 27832175

Scott, D. C., Rhee, D. Y., Duda, D. M., Kelsall, I. R., Olszewski, J. L., Paulo, J. A., de Jong, A., Ovaa, H., Alpi, A. F., Harper, J. W. and Schulman, B. A. (2016) Two Distinct Types of E3 Ligases Work in Unison to Regulate Substrate Ubiquitylation. Cell. 166, 1198-1214 e1124 
doi. 10.1016/j.cell.2016.07.027, 
PMID 27565346

Stanley, M. and Virdee, S. (2016) Chemical ubiquitination for decrypting a cellular code. Biochem J. 473, 1297-1314 
doi. 10.1042/BJ20151195, 
PMID 27208213

Stanley, M. and Virdee, S. (2016) Genetically Directed Production of Recombinant, Isosteric and Nonhydrolysable Ubiquitin Conjugates. Chembiochem. 17, 1472-1480 
doi. 10.1002/cbic.201600138, 
PMID 27197715

Steger, M., Tonelli, F., Ito, G., Davies, P., Trost, M., Vetter, M., Wachter, S., Lorentzen, E., Duddy, G., Wilson, S., Baptista, M. A., Fiske, B. K., Fell, M. J., Morrow, J. A., Reith, A. D., Alessi, D. R. and Mann, M. (2016) Phosphoproteomics reveals that Parkinson's disease kinase LRRK2 regulates a subset of Rab GTPases. Elife. 5, e12813 
doi. 10.7554/eLife.12813, 
PMC 4769169
PMID 26824392

Swamy, M., Pathak, S., Grzes, K. M., Damerow, S., Sinclair, L. V., van Aalten, D. M. and Cantrell, D. A. (2016) Glucose and glutamine fuel protein O-GlcNAcylation to control T cell self-renewal and malignancy. Nat Immunol. 17, 712-720 
doi. 10.1038/ni.3439, 
PMID 27111141

Trapannone, R., Mariappa, D., Ferenbach, A. T. and van Aalten, D. M. (2016) Nucleocytoplasmic human O-GlcNAc transferase is sufficient for O-GlcNAcylation of mitochondrial proteins. Biochem J. 473, 1693-1702 
doi. 10.1042/BCJ20160092, 
PMC 4901358
PMID 27048592

Trapannone, R., Rafie, K. and van Aalten, D. M. (2016) O-GlcNAc transferase inhibitors: current tools and future challenges. Biochem Soc Trans. 44, 88-93 
doi. 10.1042/BST20150189, 
PMID 26862193

Varshney, D., Petit, A. P., Bueren-Calabuig, J. A., Jansen, C., Fletcher, D. A., Peggie, M., Weidlich, S., Scullion, P., Pisliakov, A. V. and Cowling, V. H. (2016) Molecular basis of RNA guanine-7 methyltransferase (RNMT) activation by RAM. Nucleic Acids Res. 44, 10423-10436 
doi. 10.1093/nar/gkw637, 
PMC 5137418
PMID 27422871

Villa, F., Simon, A. C., Ortiz Bazan, M. A., Kilkenny, M. L., Wirthensohn, D., Wightman, M., Matak-Vinkovic, D., Pellegrini, L. and Labib, K. (2016) Ctf4 Is a Hub in the Eukaryotic Replisome that Links Multiple CIP-Box Proteins to the CMG Helicase. Mol Cell. 63, 385-396 
doi. 10.1016/j.molcel.2016.06.009, 
PMC 4980431
PMID 27397685

Williams, C. A., Fernandez-Alonso, R., Wang, J., Toth, R., Gray, N. S. and Findlay, G. M. (2016) Erk5 Is a Key Regulator of Naive-Primed Transition and Embryonic Stem Cell Identity. Cell Rep. 16, 1820-1828 
doi. 10.1016/j.celrep.2016.07.033, 
PMC 4987282
PMID 27498864

Yang, G., Buhrlage, S. J., Tan, L., Liu, X., Chen, J., Xu, L., Tsakmaklis, N., Chen, J. G., Patterson, C. J., Brown, J. R., Castillo, J. J., Zhang, W., Zhang, X., Liu, S., Cohen, P., Hunter, Z. R., Gray, N. and Treon, S. P. (2016) HCK is a survival determinant transactivated by mutated MYD88, and a direct target of ibrutinib. Blood. 127, 3237-3252 
doi. 10.1182/blood-2016-01-695098, 
PMID 27143257

Zhang, J., Deng, X. and Kahle, K. T. (2016) Leveraging unique structural characteristics of WNK kinases to achieve therapeutic inhibition. Sci Signal. 9, pe3 
doi. 10.1126/scisignal.aaj2227, 
PMID 27811182

Zhang, J., Gao, G., Begum, G., Wang, J., Khanna, A. R., Shmukler, B. E., Daubner, G. M., de Los Heros, P., Davies, P., Varghese, J., Bhuiyan, M. I., Duan, J., Zhang, J., Duran, D., Alper, S. L., Sun, D., Elledge, S. J., Alessi, D. R. and Kahle, K. T. (2016) Functional kinomics establishes a critical node of volume-sensitive cation-Cl- cotransporter regulation in the mammalian brain. Sci Rep. 6, 35986 
doi. 10.1038/srep35986, 
PMID 27782176