New for 2012/2013 DSTT PhD Studentships
The Medical Research Council and the University of Dundee have obtained renewed funding from July 2012-2016 for the Division of Signal Transduction Therapy (DSTT) a unique collaboration between scientists in the MRC Protein Phosphorylation Unit and the College of Life Sciences at the University of Dundee and six of the world's leading pharmaceutical companies.
A number of studentships are available to work in the research field of the collaboration, which is “kinases and the ubiquitin system”.
Applicants should select up to 4 potential laboratories that they are interested to do their PhD in.
The participating laboratories are:
Dario Alessi Understanding the functions of kinases and ubiquitylation pathway components mutated in inherited disorders
Gabriela Alexandru Exploration of the p97 and UBX-protein interaction networks and identification of novel p97 targets
Arno Alpi Ubiquitin-signaling pathways that regulate cellular responses to DNA damage
Simon Arthur Signalling in the immune system
Doreen Cantrell Signaling pathways that control effector and regulatory gut lymphocytes
Philip Cohen The interplay between protein phosphorylation and protein ubiquitylation in regulating innate immunity
Vicky Cowling Synthesis, function and therapeutic potential of the mRNA methyl cap
Ian Ganley Molecular regulation of autophagy in health and disease
Grahame Hardie Understanding the importance of AMPK signalling pathway in cancer
Ronald Hay Understanding SUMO biology
Thimo Kurz Function and regulation of cullin-based E3 ubiquitin ligases
Carol Mackintosh 14-3-3-binding phosphoproteome in cancer and brain metabolism
Patrick Pedrioli Development and application of methodologies for proteomics analysis of ubiquitin like modifiers
John Rouse Forks and molecular knives at the cutting edge of DNA repair
Gopal Sapkota Understanding TGFβ/BMP signal transduction pathways in cells and human diseases
Matthias Trost Development of new mass spectrometry technology to accelerate analysis of protein phosphorylation
Satpal Virdee Development of tools for advancing our understanding of the ubiquitin system
Studentships may start any time between July 2012 to October 2013
The deadline for all PhD applications is August 1 2012
MRC PhD Studentships
We are not accepting PhD applications for the following group leaders: Dario Alessi, Ian Ganley and Matthias Trost for PhDs starting in 2012.
Dario Alessi - Study of kinases that are mutated in human disease
No spaces available for 2012
Simon Arthur
No PhD projects available for 2012
Philip Cohen - PhD studentships available from Sept 2011
Background
The major goal of my research is to discover how the signaling pathways that control the innate immune system are regulated during infection by bacteria and viruses and to work out how they trigger the production of inflammatory mediators and interferons. These substances are crucial for defence against infection, but their overproduction causes chronic inflammatory and autoimmune diseases, such as rheumatoid arthritis, psoriasis, lupus, sepsis and some leukaemias. Identifying the protein kinases and components of the ubiquitin system involved in regulating this process, finding out how they are controlled and how they exert their effects is therefore critical to evaluate their potential as drug targets for the treatment of inflammatory and autoimmune diseases. The following projects are available:-
Project 1. Identifying the roles of Pellino isoforms in regulating innate immunity.
Pellino was originally identified in the fruit fly Drosophila melanogaster as a protein that interacts with Pelle, the orthologue of interleukin-receptor associated kinase 1 (IRAK1) in the fly. Mammalian cells express three isoforms of Pellino, Pellino 1, 2 and 3. We established that all these isoforms are phosphorylated by IRAK1 and IRAK4 in vitro and that this transforms them from inactive to active E3 ubiquitin ligases [1, 2]. More recently, we made the surprising finding that the IKK-related kinases (TBK1 and IKKε), and not the IRAKs, phosphorylate and activate Pellino 1 in macrophages stimulated by synthetic (Poly(I:C), a mimetic of viral double-stranded RNA which activates Toll-Like Receptor 3 (TLR3), and by the TLR4 ligand bacterial lipopolysaccharide (LPS) [3]. We also found that by activating the transcription factor Interferon Regulatory Factor 3 (IRF3) the IKK-related kinases stimulate transcription of the gene encoding Pellino 1, greatly increasing the level of expression of the Pellino 1 protein [3]. We generated a knock-in mouse in which the normal form of Pellino 1 has been replaced by an E3 ligase-deficient mutant and studies with macrophages from these mice indicate that the poly(I:C)-stimulated production of interferon β or the production of interferon β induced by infection with Sendai virus is greatly impaired (unpublished work).
These findings have demonstrated a role for Pellino 1 in interferon β production that cannot be replaced by the other isoforms Pellino 2 and Pellino 3. The aim of the project is therefore to discover how Pellino 2 and Pellino 3 are regulated, to identify their physiological substrate(s) and to understand their roles in regulating the innate immune system. To this end, we are generating antibodies that recognize these proteins and have recently generated further knock-in mice in which the normal forms of Pellino 2 and Pellino 3 have been replaced by E3 ligase defective mutants. The project will also exploit novel techniques that we have developed for capturing Lys63-linked polyubiquitylated proteins.
References
1. Ordureau, A., Smith, H., Windheim, M., Peggie, M., Carrick, E., Morrice, N. and Cohen, P. (2008). The IRAK-catalysed activation of the E3 ligase function of Pellino isoforms induces the Lys63-linked polyubiquitination of IRAK1. Biochem. J. 409, 43-52.
2. Smith, H., Peggie, M., Campbell, D.G., Vandermoere, F., Carrick, E. and Cohen, P. (2009) Identification of the phosphorylation sites on the E3 ubiquitin ligase Pellino that are critical for activation by IRAK1 and IRAK4. Proc. Natl.Acad. Sci. USA 106, 4584-4590.
3. Smith, H. L., Liu, X. Y., Dai, L., Goh, E. T., Chan, A. T., Xi, J., Seh, C. C., Qureshi, I. A., Lescar, J., Ruedl, C., Gourlay, R., Morton, S., Hough, J., McIver, E. G., Cohen, P. and Cheung, P. C. (2011). The role of TBK1 and IKKe in the expression and activation of Pellino 1. Biochem. J. 434, 537-548
Project 2. The identification of novel substrates and physiological roles of the IKK-related kinases.
The four members of the IKK subfamily of protein kinases play critical roles in regulating innate immunity. IKKα and IKKβ (called “the canonical IKKs”) activate the key transcription factor NFκB and the protein kinase Tpl2 stimulating the production of inflammatory mediators, while TBK1 and IKKε (called the "IKK-related kinases") activate the transcription factor IRF3 and the E3 ligase Pellino 1 to stimulate the production of interferon β. More recently, we developed the first potent and specific inhibitor of the IKK-related kinases in collaboration with MRC Technology and exploited it to identify a novel role for these protein kinases in preventing the hyper-activation of the canonical IKKs by TLR-activating ligands that do not induce the production of interferon β [1]. This may explain, at least in part, why the canonical IKKs are hyper-activated in macrophages that do not express TANK, a protein interacts with TBK1 and TANK, and why TANK-/- mice develop a lupus-like autoimmune disease. However, we have obtained preliminary evidence that that IKK-related kinases may limit the strength of innate immune signaling pathways in other ways by phosphorylating additional proteins. The aims of the project are therefore to exploit the new inhibitor of the "IKK-related kinases" together with fibroblasts that do not express the IKK-related kinases, in order to identify novel substrates of these kinases that mediate protection against autoimmune disease. The project will use a number of state-of-the-art techniques, such as phospho-proteomics and mass spectrometry
References
1. Clark, K., Peggie, M., Plater, L., Sorcek, R.J., Young, E.R., Madwed, J.B., Hough, J., McIver, E.G. and Cohen, P. (2010) Novel cross-talk within the IKK family controls innate immunity.Biochem j. 434, 93-104.
2. Clark, K., Takeuchi, O., Akira, S. and Cohen, P. (2011) TANK facilitates cross-talk within the IKK family during TLR signaling" Proc. Natl. Acad. Sci. In Press
Project 3. A reinvestigation of the physiological role of the protein kinases IRAK1 and IRAK2.
In the innate immune system, the bacterial components activating Toll-Like Receptors (TLRs) 1,2 5, 7, 8 and 9 signal via a common adaptor MyD88. MyD88 then recruits the protein kinase IRAK4, which in turn recruits the kinases IRAK1 and IRAK2. The accepted dogma in the field for many years is that IRAK4 phosphorylates and activates IRAK1 and IRAK2, when can then dissociate from the receptor to interact with and activate the E3 ubiquitin ligase TRAF6. TRAF6 then generates Lys63-linked polyubiquitin chains, which switch on the signaling pathways that lead to the production of pro-inflammatory cytokines. We have recently generated mice in which wild type IRAK1 is replaced by a protein-kinase deficient mutant, further mice that do not express IRAK1 and a mouse line in which the normal form of IRAK2 is replaced by signaling-deficient mutant. A double knock-in expressing both the catalytically inactive IRAK1 and signaling defective IRAK2 has also been generated. Preliminary studies with macrophages derived from these mice and a potent and specific pharmacological inhibitor of IRAK4, suggest that the accepted dogma in the field is wrong. The aims of the project are therefore to establish the real roles of the IRAKs in controlling innate immunity, the proteins that they really phosphorylate and how their protein kinase activities control innate immunity.
Ian Ganley - Characterization of the ULK1 kinase complex and its role in autophagy
No spaces available for 2012
Carol MacKintosh
There are no PhDs available with Carol MacKintosh for 2012
John Rouse - Characterisation of novel regulators of genome stability in human cells
DNA damage occurs very frequently in cells and poses a serious threat to genome integrity. Unrepaired DNA damage causes mutations that underlie aging and many diseases such as cancer. In the past few years, my team has identified a range of exciting new regulators of DNA repair – the SLX4 complex, the MMS22L-TONSL complex, and FAN1. Several of these proteins are nucleases – enzymes that cut specific DNA structures that occur during DNA repair. Mutations in one of these proteins in humans – SLX4, a scaffold for DNA repair nucleases, causes the cancer predisposition syndrome Fanconi anemia. The work going on in my lab aims to understand how these proteins work at the molecular level, and also at the organism level. In addition, we recently identified some more new regulators of DNA repair. The PhD project offered involves the detailed characterization of these new factors to determine which aspects of the cellular DNA damage response they are involved in.
References
1. Muñoz, I. M., Hain, K., Déclais, A.–C., Gardiner, M., Toh, G. W., Sanchez-Pulido, L., Heuckmann, J., Toth, R., Macartney, T., Eppink, B., Kanaar, R., Ponting, C. P., Lilley, D. M. J. and Rouse, J. (2009) Coordination of structure–specific nucleases by human SLX4/BTBD12 is required for DNA repair. Mol. Cell 35, 116–127.
2. MacKay, C., Declais, A.–C., Lundin, C., Agostinho, A., Deans, A.J., MacArtney, T.J., Hofmann, K., Gartner, A., West, S.C., Helleday, T., Lilley, D.M.J, and Rouse, J. (2010) Identification of KIAA1018/FAN1, a DNA repair endonuclease recruited to DNA damage by mono-ubiquitinated FANCD2. Cell 142, 65-76.
3. Duro, E., Lundin, C., Ask, K., Sanchez–Pulido, Macartney, T.J., Toth, R., Ponting, C.P., Groth, A., Helleday and Rouse, J. (2010) Identification of the MMS22L–TONSL complex that promotes homologous recombination. Mol. Cell. 40, 632-644.
4. Stoepker, C., Hain, K., Schuster, B., Hilhorst–Hofstee Y., Rooimans, M.A., Steltenpool, J., Oostra, A.B., Eirich, K., Korthof, E.T., Nieuwint, A.W.M, Jaaspers, Bettecken, T., N.J.G., Joenje, H., Schindler, D.*, Rouse, J. and de Winter, J. P. (2011) SLX4, a coordinator of structure–specific endonucleases, is mutated in a new Fanconi anemia subtype. Nat. Genet. 43, 138-141.
Gopal Sapkota - Understanding how the crosstalk inputs regulate the outcome of TGFβ signalling pathway in cells and human diseases
Aberrant transforming growth factor – beta (TGFß) signaling leads to severe developmental defects as well as many human diseases, including bone defects, autoimmune disorders, heart diseases and cancer. The TGFß family of ligands initiates a cascade of signaling events in cells resulting in the expression of hundreds of downstream genes, which produces a context-specific cellular response. My lab is interested in elucidating the molecular mechanisms by which signaling pathways mediated by TGFβ and BMP family of ligands are controlled. Two potential Ph.D. projects are on offer:
1. Regulation of the TGFß pathway by reversible ubiquitylation:
Reversible ubiquitylation of proteins in the TGFß pathway plays a critical role in controlling the outcome of the TGFß pathway. By employing a comprehensive proteomic approach using cutting-edge mass spectrometric technologies, we have identified novel E3-ubiquitin ligases and deubiquitylating enzymes (DUBs) as interactors of various SMAD proteins, the intracellular mediators of the TGFß pathway. Prospective PhD candidates will work on one or more of these Smad-interacting E3-ligases or DUBs and investigate the molecular mechanisms by which their interaction with specific Smads controls the outcome of TGFβ signaling pathways in cells, during development and in human diseases.
2. Understanding the role of PAWS1 in Cancer Progression:
PAWS1, a protein of unknown function, was identified an in interactor of SMAD1, a mediator of the bone morphogenetic protein (BMP) signals. While its role in regulating the BMP pathway is still under investigation, we observed that PAWS1 expression is lost in majority of cancers. By mass spectrometry, we have demonstrated that PAWS1 interacts with proteins that may regulate cell cycle progression. Prospective PhD candidates will investigate the roles of PAWS1 in cancer progression and determine the molecular mechanisms by which PAWS1 functions in cells.
Recommended Reading
1. Sapkota G, Alarcón C, Spagnoli FM, Brivanlou AH and Massagué J. (2007) Balancing BMP signaling through integrated inputs into the Smad1 linker. Mol Cell 2007, 25, 441-454
2. Shi Y & Massague J. Mechanisms of TGF-beta signaling from cell membrane to the nucleus. (2003) Cell 113, 685-700
3. Inoue Y, Imamura T. (2008) Regulation of TGF-beta family signaling by E3 ubiquitin ligases. Cancer Sci. 99, 2107-12.
4. Komander D, Clague MJ, Urbé S. (2009) Breaking the chains: structure and function of the deubiquitinases. Nat Rev Mol Cell Biol. 10, 550-563
Matthias Trost - Proteomics Characterisation of Signalling on the Phagosome
No PhD projects available for 2012
