University of Dundee

MRC Protein Phosphorylation and Ubiquitylation Unit 2015

Akbar, N., Nanda, S., Belch, J., Cohen, P. and Khan, F. (2015) An important role for A20-binding inhibitor of nuclear factor-kB-1 (ABIN1) in inflammation-mediated endothelial dysfunction: an in vivo study in ABIN1 (D485N) mice. Arthritis Res. Ther. 17, 22
doi. 10.1186/s13075-015-0543-3,
PMC 4342941
PMID 25648164

Arrowsmith, C. H., Audia, J. E. and et al including Cohen, P. (2015) The promise and peril of chemical probes. Nat. Chem. Biol. 11, 536-541
doi. 10.1038/nchembio.1867,
 PMID 26196764

Bett, J. S., Ritorto, M. S., Ewan, R., Jaffray, E. G., Virdee, S., Chin, J. W., Knebel, A., Kurz, T., Trost, M., Tatham, M. H. and Hay, R. T. (2015) Ubiquitin C-terminal hydrolases cleave isopeptide- and peptide-linked ubiquitin from structured proteins but do not edit ubiquitin homopolymers. Biochem. J. 466, 489-498
doi. 10.1042/BJ20141349,
PMC 4353193
PMID 25489924

Bulatov, E., Martin, E. M., Chatterjee, S., Knebel, A., Shimamura, S., Konijnenberg, A., Johnson, C., Zinn, N., Grandi, P., Sobott, F. and Ciulli, A. (2015) Biophysical studies on interactions and assembly of full-size E3 ubiquitin ligase: suppressor of cytokine signaling 2 (SOCS2)-elongin BC-cullin 5-ring box protein 2 (RBX2). J. Biol. Chem. 290, 4178-4191
doi. 10.1074/jbc.M114.616664,
PMC 4326827
PMID 25505247

Cohen, P. (2015) Bill Whelan's impact on my life and career. Mol. Aspects Med. 46, 11-13
doi. 10.1016/j.mam.2015.08.001,
PMID 26275344

Dill, B. D., Gierlinski, M., Hartlova, A., Arandilla, A. G., Guo, M., Clarke, R. G. and Trost, M. (2015) Quantitative proteome analysis of temporally resolved phagosomes following uptake via key phagocytic receptors. Mol. Cell. Proteomics. 14, 1334-1349
doi. 10.1074/mcp.M114.044594,
PMC 4424403
PMID 25755298

Emmerich, C. H. and Cohen, P. (2015) Optimising methods for the preservation, capture and identification of ubiquitin chains and ubiquitylated proteins by immunoblotting. Biochem. Biophys. Res. Commun. 466, 1-14
doi. 10.1016/j.bbrc.2015.08.109,
 PMID 26325464

Garcia-Rodriguez, L. J., De Piccoli, G., Marchesi, V., Jones, R. C., Edmondson, R. D. and Labib, K. (2015) A conserved Pol binding module in Ctf18-RFC is required for S-phase checkpoint activation downstream of Mec1. Nucleic Acids Res. 43, 8830-8838
doi. 10.1093/nar/gkv799,
PMC 4605302
PMID 26250113

Gilsbach, B. K., Messias, A. C., Ito, G., Sattler, M., Alessi, D. R., Wittinghofer, A. and Kortholt, A. (2015) Structural Characterization of LRRK2 Inhibitors. J. Med. Chem. 58, 3751-3756
doi. 10.1021/jm5018779,
 PMID 25897865

Guo, M., Hartlova, A., Dill, B. D., Prescott, A. R., Gierlinski, M. and Trost, M. (2015) High-resolution quantitative proteome analysis reveals substantial differences between phagosomes of RAW 264.7 and bone marrow derived macrophages. Proteomics. 15, 3169-3174
doi. 10.1002/pmic.201400431,
 PMID 25504905

Han, C., Pao, K. C., Kazlauskaite, A., Muqit, M. M. and Virdee, S. (2015) A Versatile Strategy for the Semisynthetic Production of Ser65 Phosphorylated Ubiquitin and Its Biochemical and Structural Characterisation. ChemBioChem. 16, 1574-1579
doi. 10.1002/cbic.201500185,
PMC 4581463
PMID 26010437

Hatcher, J. M., Zhang, J., Choi, H. G., Ito, G., Alessi, D. R. and Gray, N. S. (2015) Discovery of a Pyrrolopyrimidine (JH-II-127), a Highly Potent, Selective, and Brain Penetrant LRRK2 Inhibitor. ACS Med. Chem. Lett. 6, 584-589
doi. 10.1021/acsmedchemlett.5b00064,
PMID 26005538

Herhaus, L., Perez-Oliva, A. B., Cozza, G., Gourlay, R., Weidlich, S., Campbell, D. G., Pinna, L. A. and Sapkota, G. P. (2015) Casein kinase 2 (CK2) phosphorylates the deubiquitylase OTUB1 at Ser16 to trigger its nuclear localization. Sci Signal. 8, ra35
doi. 10.1126/scisignal.aaa0441,
PMC 4421874
PMID 25872870

Jacob, W., Rosenzweig, D., Vazquez-Martin, C., Duce, S. L. and Cohen, P. T. W. (2015) Decreased adipogenesis and adipose tissue in mice with inactivated protein phosphatase 5. Biochem. J. 466, 163-176
doi. 10.1042/BJ20140428,
PMID 25437352

Karelina, K., Liu, Y., Alzate-Correa, D., Wheaton, K. L., Hoyt, K. R., Arthur, J. S. and Obrietan, K. (2015) Mitogen and stress-activated kinases 1/2 regulate ischemia-induced hippocampal progenitor cell proliferation and neurogenesis. Neuroscience. 285, 292-302
doi. 10.1016/j.neuroscience.2014.10.053,
PMID 25451279

Kazlauskaite, A., Martinez-Torres, R. J., Wilkie, S., Kumar, A., Peltier, J., Gonzalez, A., Johnson, C., Zhang, J., Hope, A. G., Peggie, M., Trost, M., van Aalten, D. M., Alessi, D. R., Prescott, A. R., Knebel, A., Walden, H. and Muqit, M. M. (2015) Binding to serine 65-phosphorylated ubiquitin primes Parkin for optimal PINK1-dependent phosphorylation and activation. EMBO Rep. 16, 939-954
doi. 10.15252/embr.201540352,
PMC 4552487
PMID 26116755

Kazlauskaite, A. and Muqit, M. M. (2015) PINK1 and Parkin - mitochondrial interplay between phosphorylation and ubiquitylation in Parkinson's disease. FEBS J. 282, 215-223
doi. 10.1111/febs.13127,
PMC 4368378
PMID 25345844

Kristariyanto, Y. A., Abdul Rehman, S. A., Campbell, D. G., Morrice, N. A., Johnson, C., Toth, R. and Kulathu, Y. (2015) K29-selective ubiquitin binding domain reveals structural basis of specificity and heterotypic nature of k29 polyubiquitin. Mol. Cell. 58, 83-94
doi. 10.1016/j.molcel.2015.01.041,
PMC 4386640
PMID 25752573

Kristariyanto, Y. A., Choi, S. Y., Rehman, S. A., Ritorto, M. S., Campbell, D. G., Morrice, N. A., Toth, R. and Kulathu, Y. (2015) Assembly and structure of Lys33-linked polyubiquitin reveals distinct conformations. Biochem. J. 467, 345-352
doi. 10.1042/BJ20141502,
PMC 4390085
PMID 25723849

Kumar, A., Aguirre, J. D., Condos, T. E., Martinez-Torres, R. J., Chaugule, V. K., Toth, R., Sundaramoorthy, R., Mercier, P., Knebel, A., Spratt, D. E., Barber, K. R., Shaw, G. S. and Walden, H. (2015) Disruption of the autoinhibited state primes the E3 ligase parkin for activation and catalysis. EMBO J. 34, 2506-2521
doi. 10.15252/embj.201592337,
PMID 26254304

Lai, Y. C., Kondapalli, C., Lehneck, R., Procter, J. B., Dill, B. D., Woodroof, H. I., Gourlay, R., Peggie, M., Macartney, T. J., Corti, O., Corvol, J. C., Campbell, D. G., Itzen, A., Trost, M. and Muqit, M. M. (2015) Phosphoproteomic screening identifies Rab GTPases as novel downstream targets of PINK1. EMBO J. 34, 2840-2861
doi. 10.15252/embj.201591593,
PMC 4654935
PMID 26471730

Li, M., Quan, C., Toth, R., Campbell, D. G., MacKintosh, C., Wang, H. Y. and Chen, S. (2015) Fasting and Systemic Insulin Signaling Regulate Phosphorylation of Brain Proteins That Modulate Cell Morphology and Link to Neurological Disorders. J. Biol. Chem. 290, 30030-30041
doi. 10.1074/jbc.M115.668103,
PMID 26499801

Maculins, T., Nkosi, P. J., Nishikawa, H. and Labib, K. (2015) Tethering of SCF(Dia2) to the Replisome Promotes Efficient Ubiquitylation and Disassembly of the CMG Helicase. Curr. Biol. 25, 2254-2259
doi. 10.1016/j.cub.2015.07.012,
PMC 4562905
PMID 26255844

Madeira, F., Tinti, M., Murugesan, G., Berrett, E., Stafford, M., Toth, R., Cole, C., MacKintosh, C. and Barton, G. J. (2015) 14-3-3-Pred: improved methods to predict 14-3-3-binding phosphopeptides. Bioinformatics. 31, 2276-2283
doi. 10.1093/bioinformatics/btv133,
PMC 4495292
PMID 25735772

Madrzak, J., Fiedler, M., Johnson, C. M., Ewan, R., Knebel, A., Bienz, M. and Chin, J. W. (2015) Ubiquitination of the Dishevelled DIX domain blocks its head-to-tail polymerization. Nat Commun. 6, 6718
doi. 10.1038/ncomms7718,
PMC 4423210
PMID 25907794

Malik, N., Vollmer, S., Nanda, S. K., Lopez-Pelaez, M., Prescott, A., Gray, N. and Cohen, P. (2015) Suppression of Interferon beta gene transcription by inhibitors of Bromodomain and Extra-Terminal (BET) family members. Biochem. J. 468, 363-372
doi. 10.1042/BJ20141523,
PMC 4613535
PMID 25891802

Meir, M., Galanty, Y., Kashani, L., Blank, M., Khosravi, R., Fernandez-Avila, M. J., Cruz-Garcia, A., Star, A., Shochot, L., Thomas, Y., Garrett, L. J., Chamovitz, D. A., Bodine, D. M., Kurz, T., Huertas, P., Ziv, Y. and Shiloh, Y. (2015) The COP9 signalosome is vital for timely repair of DNA double-strand breaks. Nucleic Acids Res. 43, 4517-4530
doi. 10.1093/nar/gkv270,
PMC 4482063
PMID 25855810

Miles, J. A., Frost, M. G., Carroll, E., Rowe, M. L., Howard, M. J., Sidhu, A., Chaugule, V. K., Alpi, A. F. and Walden, H. (2015) The Fanconi Anemia DNA Repair Pathway Is Regulated by an Interaction between Ubiquitin and the E2-like Fold Domain of FANCL. J. Biol. Chem. 290, 20995-21006
doi. 10.1074/jbc.M115.675835,
PMC 4543658
PMID 26149689

Munson, M. J., Allen, G. F., Toth, R., Campbell, D. G., Lucocq, J. M. and Ganley, I. G. (2015) mTOR activates the VPS34-UVRAG complex to regulate autolysosomal tubulation and cell survival. EMBO J. 34, 2272-2290
doi. 10.15252/embj.201590992,
PMC 4585463
PMID 26139536

Ozanne, J., Prescott, A. R. and Clark, K. (2015) The clinically approved drugs dasatinib and bosutinib induce anti-inflammatory macrophages by inhibiting the salt-inducible kinases. Biochem. J. 465, 271-279
doi. 10.1042/BJ20141165,
PMC 4286194
PMID 25351958

Perez-Oliva, A. B., Lachaud, C., Szyniarowski, P., Munoz, I., Macartney, T., Hickson, I., Rouse, J. and Alessi, D. R. (2015) USP45 deubiquitylase controls ERCC1-XPF endonuclease-mediated DNA damage responses. EMBO J. 34, 326-343
doi. 10.15252/embj.201489184,
PMC 4339120
PMID 25538220

Petherick, K. J., Conway, O. J., Mpamhanga, C., Osborne, S. A., Kamal, A., Saxty, B. and Ganley, I. G. (2015) Pharmacological Inhibition of ULK1 Kinase Blocks Mammalian Target of Rapamycin (mTOR)-dependent Autophagy. J. Biol. Chem. 290, 11376-11383
doi. 10.1074/jbc.C114.627778,
PMC 4416842
PMID 25833948

Rogerson, D. T., Sachdeva, A., Wang, K., Haq, T., Kazlauskaite, A., Hancock, S. M., Huguenin-Dezot, N., Muqit, M. M., Fry, A. M., Bayliss, R. and Chin, J. W. (2015) Efficient genetic encoding of phosphoserine and its nonhydrolyzable analog. Nat. Chem. Biol. 11, 496-503
doi. 10.1038/nchembio.1823,
PMID 26030730

Rojas-Fernandez, A., Herhaus, L., Macartney, T., Lachaud, C., Hay, R. T. and Sapkota, G. P. (2015) Rapid generation of endogenously driven transcriptional reporters in cells through CRISPR/Cas9. Sci. Rep. 5, 9811
doi. 10.1038/srep09811,
PMC 4413877
PMID 25922883

Schumacher, F. R., Siew, K., Zhang, J., Johnson, C., Wood, N., Cleary, S. E., Al Maskari, R. S., Ferryman, J. T., Hardege, I., Yasmin, Figg, N. L., Enchev, R., Knebel, A., O'Shaughnessy, K. M. and Kurz, T. (2015) Characterisation of the Cullin-3 mutation that causes a severe form of familial hypertension and hyperkalaemia. EMBO Mol. Med. 7, 1285-1306
doi. 10.15252/emmm.201505444,
PMC 4604684
PMID 26286618

Sonneville, R., Craig, G., Labib, K., Gartner, A. and Blow, J. J. (2015) Both Chromosome Decondensation and Condensation Are Dependent on DNA Replication in C. elegans Embryos. Cell Rep. 12, 405-417
doi. 10.1016/j.celrep.2015.06.046,
PMC 4521082
PMID 26166571

Stanley, M., Han, C., Knebel, A., Murphy, P., Shpiro, N. and Virdee, S. (2015) Orthogonal Thiol Functionalization at a Single Atomic Center for Profiling Transthiolation Activity of E1 Activating Enzymes. ACS Chem. Biol. 10, 1542-1554
doi. 10.1021/acschembio.5b00118,
PMID 25845023

Stretton, C., Hoffmann, T. M., Munson, M. J., Prescott, A., Taylor, P. M., Ganley, I. G. and Hundal, H. S. (2015) GSK3-mediated raptor phosphorylation supports amino-acid-dependent mTORC1-directed signalling. Biochem. J. 470, 207-221
doi. 10.1042/BJ20150404,
PMC 4652938
PMID 26348909

Tan, L., Nomanbhoy, T., Gurbani, D., Patricelli, M., Hunter, J., Geng, J., Herhaus, L., Zhang, J., Pauls, E., Ham, Y., Choi, H. G., Xie, T., Deng, X., Buhrlage, S. J., Sim, T., Cohen, P., Sapkota, G., Westover, K. D. and Gray, N. S. (2015) Discovery of Type II Inhibitors of TGFbeta-Activated Kinase 1 (TAK1) and Mitogen-Activated Protein Kinase Kinase Kinase Kinase 2 (MAP4K2). J. Med. Chem. 58, 183-196
doi. 10.1021/jm500480k,
PMC 4292808
PMID 25075558

Varshney, D., Vavrova-Anderson, J., Oler, A. J., Cowling, V. H., Cairns, B. R. and White, R. J. (2015) SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation. Nat Commun. 6, 6569
doi. 10.1038/ncomms7569,
PMC 4382998
PMID 25798578

Virts, E. L., Jankowska, A. e. a., including, Mackay, C. and Alpi, A. F. (2015) AluY-mediated germline deletion, duplication and somatic stem cell reversion in UBE2T defines a new subtype of Fanconi anemia. Hum. Mol. Genet. 24, 5093-5108
doi. 10.1093/hmg/ddv227,
PMC 4550815
PMID 26085575

Yue, M., et al including Davies, P. and Melrose, H. L. (2015) Progressive dopaminergic alterations and mitochondrial abnormalities in LRRK2 G2019S knock-in mice. Neurobiol. Dis. 78, 172-195
doi. 10.1016/j.nbd.2015.02.031,
PMC 4526103
PMID 25836420

Zhang, J., Siew, K., Macartney, T., O'Shaughnessy, K. M. and Alessi, D. R. (2015) Critical role of the SPAK protein kinase CCT domain in controlling blood pressure. Hum. Mol. Genet. 24, 4545-4558
doi. 10.1093/hmg/ddv185,
PMC 4512625
PMID 25994507