Research activities

My laboratory is firmly focused on establishing the role of ubiquitin and ubiquitin-like proteins in important biological processes. We presently have a number of exciting projects linking SUMO modification to ubiquitylation, in stress responses, DNA damage and arsenic therapy and in determining the mechanism of E3 ligase mediated conjugation.

We are engaged in 4 related areas of research

1. SUMO-targeted ubiquitin E3 ligase RNF4 and its role in the response of human cells to DNA damage.

DNA-damage signaling utilizes a variety of posttranslational modifiers as molecular switches to regulate the signaling network. Ubiquitin and, more recently, Small Ubiquitin-Like Modifier (SUMO) have been shown to be important mediators of this response, although molecular targets and mechanism of action remain to be determined. We demonstrated (Bruderer et al., 2011) that RNF4, a highly conserved small ubiquitin-like modifier (SUMO)-targeted ubiquitin E3 ligase could interact with extensive networks of SUMO modified proteins involved in chromatin remodeling and DNA repair. In subsequent work we demonstrated that RNF4 plays a critical role in the response of mammalian cells to DNA damage. Human cells in which RNF4 expression was ablated by siRNA or chicken DT40 cells with a homozygous deletion of the RNF4 gene displayed increased sensitivity to DNA-damaging agents. Thus, RNF4 is a novel DNA damage-responsive protein that plays a role in homologous recombination and integrates SUMO modification and ubiquitin signaling in the cellular response to genotoxic stress (Yin et al., 2012).

2.  Establishing the mechanism of action of arsenic trioxide in the treatment of Acute Promyelocytic Leukaemia (APL).

Arsenic trioxide therapy for Acute Promyelocytic Leukaemia (APL) is mediated by SUMO-dependent degradation of Promyelocytic Leukaemia (PML)-Retinoic Acid Receptor a (RARa) oncogenic fusion protein. We demonstrated (Tatham et al., 2008) that ubiquitin mediated proteolysis of PML requires RNF4 E3 ubiquitin ligase. This allows terminal differentiation of tumour cells and cures disease. Our objective is to establish the molecular basis for the remarkable specificity of arsenic in APL and to determine if it can be employed therapeutically in other situations. We have analyzed the nuclear trafficking dynamics of PML and its SUMO-dependent ubiquitin E3 ligase, RNF4 in response to arsenic. After administration of arsenic, PML immediately transits into nuclear bodies where it undergoes SUMO modification. This initial recruitment of PML into nuclear bodies is not dependent on RNF4, but RNF4 quickly follows PML into the nuclear bodies where it is responsible for ubiquitylation of SUMO-modified PML and its degradation by the proteasome.

While arsenic restricts the mobility of PML, FRAP analysis indicates that RNF4 continues to rapidly shuttle into PML nuclear bodies in a SUMO-dependent manner. Under these conditions FRET studies indicate that RNF4 interacts with SUMO in PML bodies but not directly with PML. These studies (Geoffroy et al., 2010) indicate that arsenic induces the rapid reorganization of the cell nucleus by SUMO modification of nuclear body-associated PML and uptake of the ubiquitin E3 ligase RNF4 leading to the ubiquitin-mediated degradation of PML. The movement of PML into and out of the nuclear bodies is controlled by the SUMO specific protease SENP6 (Hattersley et al., 2011).

3. Determining the mechanism of RING mediated ubiquitin modification.

Ubiquitin modification is achieved by the sequential action of 3 enzymes: an E1 activating enzyme that links ubiquitin to a cysteine residue in an E2 conjugating enzyme and E3 ubiquitin ligases that catalyse the transfer of the ubiquitin from the E2~ubiquitin onto the substrate protein. There are more than 600 human genes that encode ubiquitin E3 ligases and as they influence almost all aspects of biological activity they often play critical roles in the development of disease. By far the most common E3 ligases belong to the RING family but how they stimulate ubiquitin transfer has been a long-standing mystery. This mystery has now been solved by our determination of the crystal structure of the RNF4 RING E3 ligase bound to ubiquitin linked E2. This gives a view of an E3 ligase, E2~ubiquitin complex primed for catalysis and suggests a unified mechanism for ubiquitin transfer that could apply to most other E3 enzymes (Plechanovova et al., 2011, 2012).

4. System wide analysis of SUMO modification in response to stress

The small ubiquitin-like modifiers (SUMOs) alter the functions of diverse cellular proteins involved in gene transcription, cell cycle, and DNA repair. Although conjugation by ubiquitin and SUMO-2/3 are largely functionally and mechanistically independent from one another, both appear to increase under conditions of proteasome inhibition. To establish the relationship between SUMO and protein degradation by the proteasome, we performed a quantitative proteomic analysis of SUMO-2 substrates after short- and long-term inhibition of the proteasome with MG132. Comparisons with changes to the SUMO-2 conjugate subproteome in response to heat stress (Golebiowski et al., 2009) revealed qualitative and quantitative parallels between both conditions. However, in contrast to heat stress, the MG132-triggered increase in SUMO-2 conjugation depended strictly on protein synthesis, implying that the accumulation of newly synthesized, misfolded proteins destined for degradation by the proteasome triggered the SUMO conjugation response. Furthermore, proteasomal inhibition resulted in the accumulation of conjugated forms of all SUMO paralogs in insoluble protein inclusions and in the accumulation on SUMO-2 substrates of lysine-63-linked polyubiquitin chains, which are not thought to serve as signals for proteasome-mediated degradation. Together, these findings suggest multiple, proteasome-independent roles for SUMOs in the cellular response to the accumulation of misfolded proteins (Tatham et al., 2011). We are continuing to develop proteomic methods based on our Q-Exactive mass spectrometer that will allow us to identify and quantify SUMO modification sites in vivo (Matic et al., 2011).

Positions and Employment

1982-1985     Member of scientific staff of Medical Research Council Virology Unit, University of Glasgow UK

1985-2005     Lecturer and Professor of Molecular Biology in the School of Biology, University of St Andrews UK

2005-             Professor of Molecular Biology, Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee UK

2008-             Honorary member Scottish Institute for Cell Signaling (SCILLS), University of Dundee UK

Academic Prizes

2008              Presented the Danny Thomas Lecture, St Judes Childrens Research Hospital, Memphis, USA

2012             Novartis Medal and Prize of the Biochemical Society

Elected membership of societies

1996             Fellow of the Royal Society of Edinburgh

2005             Fellow of the Academy of Medical Sciences

2009             Member of the European Molecular Biology Organisation

2010             Fellow of the Royal Society

2012             Fellow of Academia Europaea

Membership of Grant and Advisory Boards

2001            Member, advisory board of the Biomedical Research Institute, University of Dundee Medical School

2002-           Member of the Biomedical and Therapeutic Research Committee of the Scottish Executive

2007            Clinical Fellowships Committee Cancer Research UK

2008-           Royal Society Research Grants Scheme, Board E

2008            Member of the advisory board for the Deutsche Forschungsgemeinschaft (DFG) Priority Programme: "The regulatory and functional network of ubiquitin family proteins"

2009            Association for International Cancer Research Grants panel

2012-            Wellcome Trust Peer Review College