Dr Miratul Muqit, Wellcome Trust Senior Research Fellow and Programme Leader in the MRC-PPU, has been awarded the prestigious 2013 Linacre Medal and Prize Lecture of the Royal College of Physicians.
The award recognises recent advances which Dr Muqit and his research group have made in understanding the role of enzymes which underlie neurodegeneration in Parkinson’s disease.
“I am delighted to be awarded the Linacre Medal, which is really a reflection of the work done by all in my lab in making the key advances in our research,” said Dr Muqit. “Our research has also benefitted hugely from the outstanding research environment and resources provided by the MRC unit and College of Life Sciences.”
Dr Muqit’s research has shed light on the function of a protein kinase called PINK1 that is mutated in families with Parkinson’s disease. The findings have led to new ideas to potentially monitor and treat the disorder and he will discuss this in his Linacre lecture, which will take place in London next year.
Founded in 1518, the Royal College of Physicians is England’s oldest medical institution and the Linacre Lecture is the College’s most distinguished lecture for Physicians under the age of 40. Dr Muqit, who is also a Consultant Neurologist at Ninewells Hospital in Dundee, is the first Scottish-based recipient of the lecture since 1991.
Dario Alessi, Director of the MRC-PPU, said, “Miratul is undertaking fabulous research into understanding how PINK1 and Parkin enzymes involved in Parkinson's disease are regulated and function. Miratul's research is starting to lead to significant new understanding of how this system operates and how mutations in PINK1 or Parkin results in Parkinson's. This is very important work that could lead to new improved therapies for this condition. This award is richly deserved.”
Patrick Pedrioli has been awarded a £400,703 BBSRC responsive mode research grant to further his research into the function and regulation of tRNA post-transcriptional modifications.
Cells tightly coordinate the composition of their proteomes in order to respond to external and internal stimuli. Degradation via the ubiquitin proteasome system and control of the amount of messenger RNA are two of the main mechanisms a cell can use to affect the abundance of a protein. The Pedrioli lab has recently demonstrated that post-transcriptional modification of transfer RNA molecules plays an important role in ensuring efficient synthesis of a subset of the proteome. The BBSRC grant will allow him to investigate the possibility that dynamic regulation of tRNA modifications provides a further mechanism cells use to alter the activity and composition of their proteomes in response to changes in growth conditions.
Well done to Eeva Sommer a PhD Student Dario Alessi's lab who successfully defended her PhD thesis on better understanding of the roles that SGK isoforms play in breast cancer. Her work has revealed that high levels of SGK isoforms and phosphorylation of NDRG1 that is insensitive to Akt inhibitors are strong predictors for resistance of breast cancer cells to Akt inhibitors. Pictured is Eeva celebrating her success with her examiners Florian Lang (University of Tubingen, one of the world's leading SGK experts) and two Dundee Signalling experts based at Ninewells hospital namely Adrian Saurin and Steve Keyse.
We are delighted to announce that Greg Findlay has opened his first independent laboratory here at the MRC Protein Phosphorylation and Ubiquitylation Unit (MRC-PPU).
Greg comes to us from the Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada where he was a Postdoctoral Research Fellow in the laboratory of Tony Pawson. During his postdoctoral research studies Greg became interested in understanding signalling mechanisms that regulate cell-fate determination by analysing embryonic stem cell differentiation. One of the highlights was the discovery that the Grb2/Sos1 complex integrates a number of complex upstream signals to ensure that primitive endoderm specification occurs in a selective and timely manner, as is required during mammalian development. The manuscript reporting this work was recently published in Cell
In his new lab Greg's game-plan is to uncover novel protein kinase as well as protein ubiquitylation signalling networks controlling embryonic stem cell pluripotency.
Greg was a University of Dundee Biochemistry Undergraduate student (1997-2001) where he developed his interest in signal transduction by undertaking an honours project with MRC-PPU Principal Investigator Tricia Cohen. Greg then undertook his PhD with Richard Lamb at the Institute of Cancer Research on defining how the mTOR pathway was activated by amino acids (2002-2007), before moving to Tony Pawson's lab in 2007.
Congratulations to Kei Sakamoto who is currently Head of Diabetes at the Néstle Institute of Health Sciences in Lausanne, Switzerland. Kei has been promoted to full professor at the nearby École Polytechnique Fédérale de Lausanne (EPFL) where he holds a joint appointment.
Kei was a postdoc in Dario Alessi's lab between 2003 and 2006 where he unravelled the role of LKB1 in activating AMPK in muscle tissues, before opening up his own independent laboratory at the MRC-PPU in 2006, where using elegant knock-in technology Kei was able to define the role that allosteric regulation of glycogen synthase by glucose-6-phosphate played in muscle and liver. In early 2012 Kei moved his lab to Lausanne where his laboratory is playing a leading role in defining roles that allosteric regulation of metabolic and signalling enzymes play.
Jeremy Nichols who is now the Director of Signal Transduction & LRRK2 Biology Program at the Parkinson's Institute and Clinical Center in Sunnyvale California has just received a Citation award for his paper entitled “14-3-3 binding to LRRK2 is disrupted by multiple Parkinson's disease-associated mutations and regulates cytoplasmic localization” published in 2010 in the Biochemical Journal.
This paper was the most cited paper in the knowledge environment of Signalling for that year and currently has 46 citations. Jeremy trained in Dario Alessi's lab, as a postdoc from November 2006 - April 2010.
Jeremy stated “This work was enabled by an environment of discovery at the MRCPPU, in a laboratory focused on disease signaling. All of the authors involved were able to make an impact in the LRRK2 field as is evidenced by this acknowledgement. In fact, detection of phosphorylation at Serines 910 and 935 as a measure of LRRK2 inhibition LRRK2 has enabled many drug discovery programs to continue and are windows into LRRK2 biology.”
To aide worldwide research in protein phosphorylation and ubiquitylation, the MRC-PPU has launched a new website termed "MRC-PPU Reagents" in which researchers working in any academic laboratory can request any of our cDNA clones, antibodies or recombinant proteins that is listed on the website. This currently contains 19422 clones, 274 antibodies and 223 recombinant proteins.
To visit the “MRC-PPU Reagents” website and peruse what reagents we possess that could help your research please visit https://mrcppureagents.dundee.ac.uk/
Once on the website, simply type into the “search box” on the top left hand corner of the page the name of reagent you are looking for and press enter. Hopefully, in under 30 seconds, a list displaying all clones, antibodies or proteins for the reagent you are searching for will be displayed.
Online datasheets for each reagent should also be available for you to peruse. The available cDNA clones will be listed according to the type of expression vector that they are in as well as by their epitope tag.
Please feel free to circulate this information to your colleagues and collaborators.
Please note that we also have a large number of plasmids in commonly used commercial vectors such as GFP and FRT modules that we are currently seeking permission from the vendors of these to list on our website. The intention is to list these soon, but in the meantime please email both Hilary McLauchlan email@example.com and James Hastie firstname.lastname@example.org with your query and they will do everything they can to help you obtain these.
Finally as this is a brand new website and there are likely to be many improvements that we can make. We would therefore very much appreciate to hear your comments and suggestions on how our reagent website could be improved. Please send us all of your suggestions no matter how minor on how to improve the website to Matthew Elliott email@example.com (the designer of this website).
This website was launched on 19th November to mark the centenary celebration in Scotland of the UK Medical Research Council (MRC) who fund the majority of our Units research. To learn more about the MRC and what it has achieved over the last 100 years please visit here
Mitochondria are the powerhouses of the cell as they supply most of the fuel, known as ATP, that drives essential chemical reactions. They also perform many other important functions involved in metabolism, signalling, development and cell death. Given their important role, it comes as no surprise that mitochondrial dysfunction has been linked to many diseases including cancer and neurodegeneration. Faulty mitochondria are thought to be major cellular polluters as they release toxic reactive oxygen species; therefore it is vital to remove such mitochondria before they can cause cellular damage. One mechanism by which mitochondria are degraded and recycled is through the autophagy pathway.
Very little is known about the specifics of mitochondrial turnover by autophagy (mitophagy), so George Allen, a postdoc in Ian Ganley’s lab, developed a novel assay to aid in studying this process. The assay is very simple, yet very powerful as it allows rapid measurement of the level of mitophagy occurring in a cell. Mitochondria are tagged with green and red fluorescent dyes, such that both fluoresce under the microscope under normal conditions. However, when mitochondria undergo mitophagy they are delivered to the lysosome, where the acidity quenches the green signal, but not the red. Therefore the number of mitochondria can be assessed by total fluorescence and the degree of mitophagy calculated by the increase in the red:green fluorescent ratio. Using this assay, George discovered that loss of iron from the cell strongly stimulated mitophagy and he is now trying to identify the precise signals that trigger this event.
Many neurological disorders, such as Parkinson’s, are believed to arise at least in part, from mitochondrial dysfunction. It is also interesting to note that iron often accumulates in the brains of these patients. Given this, the Ganley Lab hopes that this work will be important in developing new therapies for conditions where mitochondrial clearance would be advantageous. This work has just been published in EMBO Reports and is currently top of the most recent downloaded articles from the journal.
Parkinson’s disease is an incurable neurodegenerative disorder and the MRC-PPU is at the frontline of research trying to understand the origins of this disease and developing new ideas on diagnosis and treatment.
On November 6th two PhD students, Agne Kazlauskaite and Chandana Kondapalli from the laboratories of Dario Alessi and Miratul Muqit were invited to a special event at the Scottish Parliament entitled “Scotland’s Brainpower – Parkinson’s UK Research”. The event was organized by Parkinson's UK and hosted by Jim Eadie MSP, convenor of the Cross Party Group on Life Sciences at the Parliament.
Parkinson’s UK is now Europe’s largest charity supporting Parkinson’s related research and their support has been pivotal to the recent advances made by Chandana and Agne in the lab. Chandana is a recipient of a Parkinson’s UK PhD studentship and Agne a recipient of a J Menzies Macdonald Charitable Trust Prize Studentship in Parkinson’s disease. Both presented their recent groundbreaking research in which they have uncovered how the Parkinson’s associated protein kinase PINK1 regulates another Parkinson’s protein Parkin through phosphorylation at Serine 65.
The event was attended by nearly 100 guests including MSPs, policymakers, patients, carers, and clinicians with a special interest in Parkinson’s.
Congratulations to MRC-PPU Principal Investigator (PI) Vicky Cowling, who has received an esteemed European Molecular Biology Organisation (EMBO) Young Investigator Programme (YIP) Prize. Every year EMBO go to great efforts to scour Europe, Israel, Turkey and Singapore to identify the brightest young Life science researchers and award them with an EMBO YIP Prize.
In addition to the prestige the EMBO YIP Prize also provides awardees with significant academic, practical and financial support. Vicky is one of a group of only 23 early stage PIs who have received the award this year, of which only 5 are from the UK (Vicky was the only Scotland-based researcher to receive an EMBO YIP this year).
Vicky’s research aims to find new methods of killing cancer cells by targeting how proteins are made. Vicky has recently made a significant breakthrough on our understanding how the machinery that controls mRNA cap formation is regulated by signalling pathways and oncogenes. Vicky is also investigating whether targeting the apparatus that controls the mRNA Cap formation could be deployed as a novel therapeutic strategy to treat cancer in the future.
Upon receiving news of the prize Vicky said, "I am delighted to join the EMBO Young Investigator Programme. I’m looking forward to working with the fellows from across Europe and beyond. I’d like to thank the members of my lab for their contributions to this fellowship, and the MRC Unit and the College of Life Sciences for their support”.
Dario Alessi, Director of the MRC Unit added “I am delighted that Vicky has been awarded this great accolade that is richly deserved. Vicky is the fifth PI from the MRC-PPU to be awarded an EMBO YIP, with John Rouse, Daan van Aalten, Karim Labib and Helen Walden previously receiving this honour. This is a great reflection of the strength and calibre of our Unit's researchers".
NUAK1 and NUAK2 are members of the AMPK family of protein kinase that are activated by the LKB1 tumour suppressor kinase. Recent work suggests they play important roles in regulating key biological processes including Myc driven tumourigenesis, senescence, cell adhesion and neuronal polarity.
In a major Collaboration with Sara Buhrlage, Nathanael Gray, and several of their colleagues at the Dana Farber Cancer Institute, Sourav Banerjee working in Dario Alessi’s lab has published a paper reporting on two compounds termed WZ4003 and HTH-01-015 that are highly selective NUAK isoform inhibitors.
Sourav found that WZ4003 inhibited both NUAK isoforms (IC50 for NUAK1 20 nM and NUAK2 100 nM), whereas HTH-01-015 inhibits only NUAK1 (IC50 100 nM). These compounds display extreme selectivity and do not significantly inhibit the activity of 139 other kinases tested, including 10 AMPK family members. WZ4003 and HTH-01-015 inhibited the phosphorylation of the only well-characterised substrate namely MYPT1 that is phosphorylated by NUAK1 at Ser445.
Sourav also identified a mutation (A195T) that does not affect basal NUAK1 activity but renders it ~50-fold resistant to both WZ4003 and HTH-01-015. Consistent with NUAK1 mediating phosphorylation of MYPT1 he found that in cells overexpressing drug resistant NUAK1[A195T], but not wild type NUAK1, phosphorylation of MYPT1 at Ser445 is no longer suppressed by WZ4003 or HTH-01-015.
Sourav also demonstrated that administration of WZ4003 and HTH-01-015 significantly inhibited migration and proliferation of cells to a similar extent as knock-out of NUAK1.
Given the very high similarity of the catalytic domains of AMPK family kinases, it is likely that these kinases will phosphorylate non-physiological substrates normally phosphorylated by other family members. The identification of highly specific NUAK inhibitors offers encouragement that it will be feasible to develop specific inhibitors of all AMPK family inhibitors.
Sourav’s data establish that HTH-01-015 and WZ4003 comprise useful tools for probing the physiological functions of the NUAK isoforms. To read a copy of Sourav’s paper please click here.
Sourav also needs to be congratulated for very recently successfully defending his PhD thesis that was examined by two AMPK grand masters namely David Carling and Grahame Hardie. Sourav has one more paper to write up before moving to the USA to undertake postdoctoral research.
A group of postdocs and PhD students from the MRC-PPU, Frances Rose-Schumacher, Michael Munson, Sam Strickson, Catherine Rodger, Yosua Kristariyanto, George Allen, Nicola Phillips, Anna Kelner, Flora Keppie and Owen Conway, aided by MRC Communications Manager, Hazel Lambert, hosted a stand at the Dundee Science Festival that took place on Sunday 3rd November at Dundee Science Centre.
They hosted two activities for children and parents. In the first, children and their parents built a cell from play-dough. In the second they took part in an experiment that allowed visitors to see the dramatic influence of alcohol on the heartbeat of a small water-flea. The fleas were under a microscope hooked up to a TV screen.
The MRC-PPU stand was mobbed all day. More than 400 children visited the stand as judged by the number of petri-dishes used by children to take home the cell they made in them. The feedback received was extremely positive.
Frances Rose-Schumacher who helped coordinate the event said “It was a lot of fun and everyone who participated got a lot out of it too. It is quite nice to talk about what we do, and it totally made me realise that what 'being a scientist' means is such a mystery to many people, so I think maybe we helped communicate that we look at cells and signals and that science is pretty cool! It was also great for children and their parents to interact with 'real life scientists', take home their play-dough cells and look at the waterfleas close up’’.
Congratulations to Manman Guo of the Trost lab who was awarded a prize at the College of Life Sciences 2nd Year PhD student poster competition on Friday 19th October 2013. Manman presented a poster entitled “Characterization of phagosomal proteomes in activated macrophages”.
The University of Dundee’s award-winning Division of Signal Transduction Therapy (DSTT) has this week celebrated the 50th meeting of the collaboration, which brings scientists at the University together with the world’s biggest pharmaceutical companies.
Established in 1998, DSTT is a unique collaboration between researchers in the MRC Protein Phosphorylation and Ubiquitylation Unit (MRC-PPU) at Dundee and six global pharma giants - AstraZeneca, Boehringer Ingelheim, GlaxoSmithKline, Janssen Pharmaceutica, Merck Serono and Pfizer.
Professor Dario Alessi, Director MRC-PPU, said, “This is an incredible milestone for us to reach. Since the collaboration started in 1998 we have held several meetings in Dundee each year. These three-day meetings include a scientific symposia to present our latest research data and a series of one-to-one meetings with research groups as requested by the companies”.
“These meetings prove extremely valuable in disseminating our latest results and assisting companies with their development programmes”.
Established in 1998, DSTT is a unique collaboration between scientists in the MRC-PPU, signalling researchers at the University of Dundee’s College of Life Sciences and six of the world’s leading pharmaceutical companies (AstraZeneca, Boehringer Ingelheim, GlaxoSmithKline, Janssen Pharmaceutica, Merck Serono and Pfizer).
The research focuses on the understanding of the biological roles of phosphorylation and ubiquitylation and how disruption of these processes cause human diseases such as neurodegeneration, cancer, hypertension and immune disorders. The ultimate goal of the MRC-PPU research programmes is to help develop new improved strategies to treat disease.
The DSTT is widely regarded as a model of best practice in the interaction between academia and industry, and it was awarded the Queen’s Anniversary Prize for Higher Education in 2006. A key remit of the research undertaken in Dundee is to help define and validate new drug targets with the aim of obtaining sufficiently convincing results to persuade pharmaceutical companies to develop drugs against these targets.
RING-in-between-RING (RBR) enzymes are a distinct class of E3 ubiquitin ligases possessing a cluster of three zinc-binding domains that cooperate to catalyze ubiquitin transfer. The best known members of this group are PARKIN and HOIP, defects in which are associated with neuronal degenerative disease and innate immune deficiency respectively. Intriguingly, all RBR E3s investigated to date are auto-inhibited for ubiquitylation. Elucidating the mechanisms of their activation and regulation is currently an area of intense investigation.
Now work performed by Ian Kelsall in Arno Alpi’s lab has revealed an unexpected mechanism for activating RBR E3s. Ian found that RBR E3s of the Ariadne subfamily, TRIAD1 and HHARI, interacted with distinct members of the cullin-RING ligase family of E3 ubiquitin ligases. Moreover, these interactions triggered the E3 ligase activity of the Ariadne E3s. Structural studies carried out by David Duda and Jennifer Olszewski from the laboratory of Brenda Schulman in St. Jude Children’s Research Hospital, (Memphis, US) revealed that HHARI possesses an auto-inhibitory “Ariadne domain” – likely a characteristic for the Ariadne subfamily – which masks critical residues in HHARI’s active site. Cullin-RING ligase binding therefore acts to induce conformational changes that relieve auto-inhibition of Ariadne E3s. Ian’s work also suggests that a reciprocal regulatory arrangement may exist, with TRIAD1 and HHARI impacting on both the levels of neddylation (the attachment of the ubiquitin-like modifier NEDD8 to the cullin protein) and the activity of cullin-RING ligase complexes.
It is hoped that this work, recently published in The EMBO Journal, will form the foundation of further structural and functional studies to determine the molecular mechanisms underlying the inter-dependent regulation of Ariadne and cullin-RING ligase E3 ligases.
We are delighted to announce that Helen Walden and her PhD student Mark Frost have joined the MRC Protein Phosphorylation and Ubiquitylation Unit (MRC-PPU). Helen has relocated her laboratory from the CRUK London Research Institute at Lincoln’s Inn fields.
Helen will take up a senior group leader position within the MRC-PPU.
Helen’s research centres on understanding how post-translational modification of proteins by ubiquitylation impacts on cellular process, related to understanding diseases such as cancer and Parkinson’s.
Highlights of Helen’s recent work include analysing the structure of the Parkinson’s disease E3 ligase termed Parkin. This has revealed how Parkin is regulated and maintained in an inactive conformation via an auto-inhibitory interaction of a UBL domain with the catalytic E3 ligase domain. This work has also revealed how disease-causing mutations affect Parkin by interfering with the catalytic mechanism as well as by disrupting the ability of Parkin adopt and auto-inhibited conformation.
Helen has also undertaken ground-breaking structural and functional analysis of the a critical E3 ligase termed FANCL that is mutated in patients with Fanconi Anemia and that plays a critical role in the DNA Repair pathway.
Helen has very exciting plans to continue unravelling the role and molecular mechanism by which ubiquitylation controls fundamental biological processes of high relevance to understanding human diseases. She will employ a blend of the state of the art X-ray crystallographic and biochemical techniques to achieve her aims.
Congratulations to Jamie Wilson (a Wellcome Trust Clinical Fellow in John Rouse's lab) who made a big advance in understanding SLX4 with help from Agueda Tejera in Maria Blasco’s lab at CNIO, Madrid. He showed that around half of the SLX4 complex localizes constitutively at chromosome ends. This is mediated by a new motif we identified in SLX4 that interacts with the telomere binding protein TRF2. Mutations in this motif release SLX4 complex from telomeres. Jamie also found that the proper localization of SLX4 at telomeres is required to prevent telomeres from becoming too long. Mutations that release SLX4 from telomeres cause telomeres lengthening, and they cause telomere fragility and damage. These data indicate that the SLX4 complex acts as a sensor of telomere length and mediates "telomere trimming". Jamie's data were published recently in Cell Reports
Congratulations to Dennis Castor and Nidhi Nair who have published a paper which solves a long-standing problem regarding how cells deal with chromosome “tangles” that link them in a way that is deleterious to cell function. Holliday junctions are 4-way DNA junctions that intertwine – tangle – chromosomes. They arise normally during DNA repair, and if they are not removed then cells die as they try to segregate their chromosomes in mitosis. It was known that Holliday junction removal requires special nucleases (enzymes that cut DNA) – or “resolvases”. The resolvases in bacteria and phages that remove Holliday junctions are known; they act as homodimers, with each subunit of the homodimer introducing one of the two cuts in Holliday junctions necessary for their resolution. For over 30 years scientists have been searching for the resolvases in eukaryotes that remove Holliday junctions from our DNA in vivo. Dennis and Nidhi showed that HJ resolution in eukaryotes requires two separate nucleases - MUS81 and SLX1 - that act together as a HJ resolvase. The two nucleases act cooperatively – the first cut is probably introduced by SLX1 to create the preferred substrate for MUS81, which makes the second cut to finish resolution. Consistent with this idea, both SLX1 and MUS81 nucleases bind close together on the SLX4 scaffold, and this tethering is essential for HJ resolution in cells. So in eukaryotes the two incisions in Holliday junctions necessary to remove them are made by two separate nucleases tethered close together on a scaffold, instead of by the two subunits of a homodimer. We propose this arrangement in eukaryotes increases the ease of regulating resolvase activity. These findings provide the mechanism for HJ removal in eukaryotes, and they provide the first demonstration of the physiological roles of SLX1. Dennis and Nidhi made their findings with help from Simon Arthur, and from Anne Cecile Declais in David Lilley's lab. They are joint first authors on a paper describing these data that was published online recently in Molecular Cell.
Chandana Kondapalli who has been supervised by Miratul Muqit and Dario Alessi over the last 4 years on a project to uncover the function of the PINK1 kinase has been awarded her PhD. Her examiners were Michel Goedert of the MRC Laboratory of Molecular Biology in Cambridge and Anton Gartner of the Wellcome Trust Centre for Gene Regulation and Expression in Dundee.
Pictured with Michel and Chandana is John Rouse, Director of the MRC-PPU PhD Programme. In 1997 Michel was John's PhD external examiner here in Dundee.
Researchers at the University of Dundee have played a key role in the development of a new anti-cancer drug targeting melanoma.
GlaxoSmithKline have announced that their BRAF protein kinase inhibitor Dabrafenib (Tafinlar), has been approved by both the European Commission and the United States Food and Drug Administration for the treatment of unresectable or metastatic melanoma associated with the BRAF V600E mutation.
Unresectable melanoma is that which cannot be removed by surgery, while metastatic melanoma is that which has spread to other parts of the body.
The new drug was developed employing BRAF enzymes generated by researchers in the Division of Signal Transduction Therapy (DSTT) in the College of Life Sciences at Dundee.
The Division has been operating for the past 15 years and is a collaboration with GlaxoSmithKline and other major pharmaceutical companies, aimed at developing
drugs that target protein kinases.
Professor Dario Alessi, Director of the DSTT collaboration, said, “I am absolutely delighted that we have been able to play a significant role in aiding GlaxoSmithKline develop a new anti-cancer drug. An important remit of our research is to come up with innovative ideas, technology and reagents to help with the development of new drugs. I personally spent several years in the mid 1990s, whilst a postdoctoral researcher in Professor Philip Cohen's lab, studying the function and regulation of RAF enzymes.
“The technology and assays that we developed to manufacture and investigate the BRAF enzyme was transferred to our DSTT collaboration and DSTT staff Samantha Raggett, Carla Baillie, Shabana Anwar-Topping, Susan Finn, James Hastie, and Hilary McLauchlan devoted huge effort to produce sufficient quantities of the BRAF enzyme for GlaxoSmithKline. It is extremely gratifying to learn that the fruits of this labour have played a role in the discovery of a new drug that can benefit patients.
“We are helping GlaxoSmithKline as well as the five other companies that support the DSTT collaboration (AstraZeneca, Boehringer Ingelheim, Janssen Pharmaceutica NV, Merck-Serono [the Pharmaceutical division of Merck KGaA] and Pfizer) with many other important projects that I hope in the future will also contribute to the development of further new drugs that target components of the phosphorylation and ubiquitylation system.”
The DSTT was founded in 1998, expanded in 2003 and renewed for a second time in 2008. At its third renewal in 2012, the DSTT had attracted £50 million in funding since it started. It is widely regarded as a model for how academia and industry can interact productively and was awarded a Queen’s Anniversary Prize for Higher Education in 2006.
The DSTT works to accelerate the development of new drug treatments for major global diseases including cancer, arthritis, lupus, hypertension and Parkinson’s disease in a market that is estimated to be worth £15 billion per annum and projected to reach £30 billion per annum by 2025.
Lina Herhaus, PhD student in Gopal Sapkota's lab, has published a paper on the role of OTUB1 in TGFβ signalling in Nature Communications.
The TGFβ signalling pathway controls plethora of cellular functions during embryogenesis and in adult tissues. Consequently abnormal TGFβ signalling is associated with multiple human diseases such as fibrosis, immune disorders and cancer. TGFβ signalling is initiated upon ligand binding to a pair of receptor serine/threonine protein kinases on the cell surface. This triggers the phosphorylation of SMAD2/3 leading to the assembly and nuclear translocation of active SMAD2/3/4 transcriptional complex, which, together with other co-factors, drives the transcription of hundreds of target genes. The activity of SMAD transcription factors is tightly regulated. Reversible ubiquitylation of active SMAD complexes serves to fine-tune the cellular responses to TGFβ signals. While much is known about the E3 ubiquitin ligases that modulate the ubiquitylation of SMADs, the deubiquitylating enzymes that act on active SMAD complexes, which drive the TGFβ signalling, remain undefined.
Lina’s work in the past two years has uncovered a unique role for the deubiquitylating enzyme OTUB1 in regulating the active SMAD complexes and thereby the TGFβ pathway.
The key novel findings that Lina’s research has made are highlighted below:
• OTUB1 is recruited to the active phospho-SMAD2/3-SMAD4 complex only upon TGFβ-induction.
• TGFβ-induced phosphorylation of SMAD2/3 is necessary and sufficient for their interaction with OTUB1.
• OTUB1 enhances TGFβ-induced gene transcription and cellular migration.
• OTUB1 promotes TGFβ signalling by binding to phospho-SMAD2/3 and preventing their ubiquitylation and degradation through the inhibition of E2 ubiquitin conjugating enzymes.
Lina’s findings uncover for the first time a signal-induced phosphorylation-dependent recruitment of OTUB1 to its target in the TGFβ pathway. OTUB1 is the only DUB shown thus far to act on active SMAD2/3, while the deubiquitylase activity of OTUB1 appears not to be necessary. More recent studies have also reported such non-canonical mode of action for OTUB1 in the control of chromatin stability and DNA-damage responses. Lina’s findings are not only significant within the TGFβ pathway, but may advance the field of deubiquitylation, especially when taking into account stimuli-induced phospho-dependent recruitment of a DUB to its target.
Mazin Al-Salihi, Thomas Macartney and Simone Weidlich also contributed to this research.
The paper entitled “OTUB1 enhances TGFβ signalling by inhibiting the ubiquitylation and degradation of active SMAD2/3” can be accessed through Nature Communications, here
We are delighted to announce that Karim Labib and his current lab, consisting of Pedro Nkosi (Senior Scientific Officer), Marija Maric (PhD student) and Cecile Evrin (postdoc), have joined the MRC Protein Phosphorylation and Ubiquitylation Unit (MRC-PPU). Karim will take up a senior group leader position within the MRC-PPU and he will also become Dundee University’s Professor of Genome Integrity.
Karim has relocated his laboratory from the CRUK Paterson Institute in Manchester, where he has undertaken ground-breaking work on the the mechanisms by which DNA is replicated and faithfully maintained during the cell division cycle, using an elegant combination of genetics and biochemistry.
Karim has made some seminal contributions to the genome stability and cell cycle fields, including the identification and characterisation of the Replisome Progression Complex, a large protein machine that drives progression of the replication fork. He discovered that the Mcm2-7 proteins provide helicase activity to the replication fork, and went on to show that the Mcm2-7 proteins, along with their activating proteins Cdc45 and GINS, comprise the core of the Replisome Progression Complex.
Karim has also investigated how the Replisome Progression Complex is assembled and what happens when replication forks are stalled. He has also challenged the dogma that the activity of checkpoint kinases is required to prevent disassembly of the replication fork proteins.
More recently Karim has identified new roles for cell cycle kinases and ubiquitin ligases in stabilising the replisome and in regulating mitosis. One of Karim’s priorities and main reasons for relocating his laboratory to the MRC-PPU will be to focus in much more depth on how ubiquitylation and phosphorylation control the replisome. He will also be exploiting our expertise and technologies to extend some of his research from yeast to the mammalian system. Karim will also pursue his important work in dissecting the fundamental mechanisms that underpin genome integrity.
The MRC-PPU support teams and PIs have generated an impressive array of reagents for the study of the ubiquitylation system. This stimulated the establishment of the start-up company, Ubiquigent which exploits research and expertise based in the PPU. The company currently offers many reagents, kits and drug discovery services. Ubiquigent recently launched a successful deubiquitylase (DUB) profiling service that currently has over 30 enzymes on the panel, an E2 scan kit and a custom assay development service from which PPU receives royalties which are re-invested in our research programmes.
Ubiquigent have just announced £0.5million funding from IP Group plc and the Scottish Investment Bank, the investment arm of Scottish Enterprise. The investment will be used to accelerate the development and commercialisation of these drug discovery platforms. Ubiquigent has also announced the appointment of Mark Treherne to strengthen its board of directors. Mark has been active in the pharmaceutical industry for over 25 years. In this time, he has been involved in starting and raising over £140million for a number of early-stage biotechnology companies. Amongst these, Mark was a co-founder and Chief Executive of Cambridge Drug Discovery, which was acquired by BioFocus plc. Mark has served on the boards of over 14 private and public biopharmaceutical companies in both executive and non-executive roles.
For more information on Ubiquigent please click here.
A series of discoveries made by scientists at the University of Dundee is helping to uncover the secrets of how chronic inflammatory and autoimmune diseases such as Lupus and rheumatoid arthritis are caused and could lead to new treatments being developed.
The body’s immune system is vital to fight infection by bacteria and viruses, but when it gets out of control is the cause of many autoimmune diseases. Understanding this system is therefore vital to identify ways in which the treatment of these diseases can be improved without compromising the body’s ability to fight infection,
Sir Philip Cohen and colleagues in the Medical Research Council Protein Phosphorylation and Ubiquitylation Unit at the University of Dundee have published a series of recent papers uncovering the behaviour of proteins that control the immune system and their role in a range of human auto-immune diseases.
Dundee is among the world’s leading centres for research into phosphorylation and ubiquitylation, areas which are becoming increasingly important in determining how abnormalities in cellular proteins can affect our health.
“In these latest papers we have documented some very intriguing findings about enzymes known as protein kinases and how they control the immune system” said Professor Cohen.
“For example, we have identified unique roles for two members of the IRAK sub-family of kinases, which suggests they may be suitable targets for the development of drugs to treat chronic inflammatory and autoimmune diseases. These are attractive targets because by switching them off we may be able to suppress autoimmune diseases while only having minor effects on other processes which are critical to fighting infection and for stopping inflammation once it has served its purpose.
“In another piece of work with colleagues at the University of Kentucky we have contributed to the discovery that mutations in the ABIN1 protein cause a predisposition to a particular form of Lupus, a serious autoimmune disorder which affects around 3.5 million people worldwide. These findings may lead to the improved diagnosis and treatment of this disease.
“We have also made an unexpected discovery about the innate immune system is controlled by ubiquitylation, which is likely to become an important area of drug discovery in the future. To prepare for this, we have established a significant research grouping in ubiquitylation over the past five years, in addition to our major presence in phosphorylation, as we firmly believe that it is going to be a major frontier in advancing our understanding of human health.
“We are finding that the pharmaceutical industry is paying increasing attention to ubiquitylation research as its potential importance in understanding and treating many diseases becomes increasingly clear.”
The MRC-PPU was established in 1990 by the MRC to investigate the role that protein phosphorylation play in regulating human diseases and originally comprised two research groups and less than 20 staff. It was led by Sir Philip for 21 years until he was succeeded in April 2012 by Professor Dario Alessi. By the end of 2013 the MRC-PPU will comprise nearly 20 major research groups and over 150 staff.
Its researchers have published over 500 research papers that have greatly contributed to our understanding of a variety of human diseases such as cancer, diabetes, immune disorders and neurodegeneration.
In this paper Christoph Emmerich and Sam Strickson in Philip Cohen’s lab have made several surprising findings about the structure and formation of the polyubiquitin chains that control the protein kinases that switch on the transcription factor NF-κB. Their findings, reported in the latest issue of Proceedings of the National Academy of Sciences of the USA, may have important implications for the regulation of other biological processes.
NF-κB plays a central role in the regulation of the immune system and other biological processes, such as the response to DNA damage. It is one of the most studied of all transcription factors, with entire scientific meetings being devoted to discussions about how it is regulated and how it controls cellular processes. The activation of NFκB is catalyzed by the canonical IκB kinase (IKK) complex, which comprises the protein kinases IKKα and IKKβ and a regulatory subunit called NEMO. Protein ubiquitylation and protein phosphorylation events are known to be needed for the IKK complex to be activated: Met1-linked (or linear) polyubiquitin chains have to bind to NEMO, and the activation loops of IKKα and IKKβ have to become phosphorylated by the protein kinase TAK1. Intriguingly, the activation of TAK1 itself requires the binding of Lys63-linked ubiquitin chains to its regulatory subunits TAB2 and TAB3.
There has been an intense debate about the relative roles and importance of Lys63-linked versus Met1-linked ubiquitin chains in the activation of the canonical IKK complex by inflammatory stimuli. Now Christoph Emmerich has introduced a new twist to this story by discovering that the TAK1-dependent activation of the IKK complex requires a new type of ubiquitin chain in which Met1-linked and Lys63-linked ubiquitin oligomers are attached covalently to one another as “hybrid” ubiquitin chains. In the same paper Sam Strickson found that the formation of Lys63-linked ubiquitin chains is a pre-requisite for the formation of Met1-linked ubiquitin chains, since Met1-linked ubiquitin chains were not formed in response to interleukin-1 in cells lacking Ubc13, the E2 conjugating enzyme that specifies the formation of Lys63-linked ubiquitin chains. The authors point out that forming Lys63/Met1-linked hybrids makes more physiological sense than producing two different ubiquitin chains, because it enables the co-localisation of the canonical IKK complex and the TAK1 complex to the same polyubiquitin chain, which may facilitate the activation of the canonical IKK complex by TAK1.
The new paper also establishes that LUBAC (the Linear UBiquitin Assembly Complex) is the only E3 ligase that forms Met1-linked ubiquitin chains in response to IL-1, that HOIP is the catalytic subunit of LUBAC and that Met1-linked ubiquitin chains are required to increase the efficiency with which the canonical IKK complex is activated.
Although the paper will help to resolve the debate about the relative roles of Lys63-linked and Met1-linked ubiquitin chains in the activation of NFκB, it also raises many interesting new questions. For example, are the Lys63/Met1-linked ubiquitin hybrids formed in response to IL-1 also produced during the activation of other cellular processes? What is the precise topology of the ubiquitin oligomers in the hybrid molecules and what length do they need to be to activate NEMO-dependent processes efficiently? Do these ubiquitin chains need to be attached covalently to other proteins to control cellular events or are ubiquitin chains that are not anchored to any other protein sufficient for activation? What other proteins does NEMO interact with in an ubiquitin-dependent manner and what are their functions? What other protein kinases besides TAK1 are needed for the activation of the canonical IKK complex by signals other than IL-1? The answers to these and other questions will undoubtedly emerge from research performed in the years to come.
In this paper Eduardo Pauls and Sambit Nanda in Philip Cohen’s lab have identified unique and distinctive roles for two members of the IRAK sub-family of protein kinases, which suggest that they may be attractive targets for the development of drugs to treat chronic inflammatory and autoimmune diseases.
The lab developed and studied knock-in mice in which wild type IRAK1 was replaced by a mutant devoid of kinase activity. They found that the activation of Toll-Like Receptor 7 (TLR7) and TLR9 by single-stranded RNA or DNA of viral origin, respectively, did not produce interferonβ in plasmacytoid dendritic cells expressing catalytically inactive IRAK1. In contrast, the production of pro-inflammatory cytokines, such as Tumour Necrosis Factor (TNF) and interleukin 6, was similar in macrophages from the IRAK1 knock-in mice and wild type mice after stimulation of TLR7 or other TLRs. The overproduction of type 1 interferons by plasmacytoid dendritic cells resulting from the abnormal activation of TLR9 by “self” DNA is thought to be a cause of some types of lupus. The new findings therefore suggest that inhibitors of IRAK1 should be evaluated for the treatment this autoimmune disease.
In contrast to IRAK1, IRAK2 is an inactive “pseudokinase”. A knock-in mouse was therefore made in which wild type IRAK2 was replaced by a mutant in which serine 525 was replaced by alanine to create a mutant that was unable to interact with TRAF6, an E3 ubiquitin ligase required to activate the TLR signaling network. Studies with macrophages from the IRAK2 knock-in mice revealed that the IRAK2-TRAF6 interaction was needed to maintain a low level of activation of the protein kinase IKKβ after prolonged TLR activation, without which the late surge in TNF and IL-6 mRNA production and the secretion of these cytokines did not occur. They found that the time at which IRAK2 function became rate limiting correlated with the time at which the IRAK1 protein was degraded, suggesting that the early phase of TNF and IL-6 mRNA production may be sustained by IRAK1 in the absence of a functional IRAK2. Importantly, the loss of the IRAK2-TRAF6 interaction had little effect on the production of anti-inflammatory molecules, such as interleukin 10 and the protein phosphatase DUSP1, which are produced during the early phase of TLR signaling. These findings suggest that IRAK2 may be an attractive target for the development of drugs to treat chronic inflammatory diseases, such as rheumatoid arthritis, which are caused by the overproduction of TNF and other inflammatory mediators. An advantage of such drugs is that they may only have a minor effect on the production of interleukin 10, which is critical for the resolution of inflammation.
In this paper a collaboration between Sambit Nanda in Philip Cohen’s lab and David Powell at the University of Kentucky, has led to the discovery that mutations in ABIN1 predispose to a particular form of Systemic Lupus Erythematosus, a serious autoimmune disorder affecting 3.5 million people worldwide. Many different organs of the body can be damaged in different types of lupus, and the new findings have identified mutations in ABIN1 that are associated with kidney damage in lupus patients. These findings may lead to the improved diagnosis and treatment of this disease.
ABIN1 is a polyubiquitin-binding protein that plays an important role in restricting the strength of activation of the MyD88 signaling network in the innate immune system. In an paper published a couple of years ago Sambit Nanda found that knock-in mice in which Asp485 of ABIN1 was mutated to Asn, to generate a a polyubiquitin-binding-defective mutant, developed a lupus-like autoimmune disease. He found that the disease was caused by the hyper-activation of the MyD88-dependent signaling network because it was prevented by crossing the ABIN1[D485N] mice to MyD88 knock-out mice (Nanda et al, 2011, J. Exp. Med. 208, 1215-1228). In the new paper, published on-line on August 22nd in the Journal of the American Society of Nephrology, the ABIN1[D485N] mice were found to develop progressive glomerular nephritis (GN), which closely resembles Class III and IV lupus nephritis in humans. These findings sparked a major collaboration with human geneticists in many Universities in America and Europe, who analysed five single-nucleotide polymorphisms found in TNIP1 (the gene encoding ABIN1) in samples from European-American, African American, Asian, Gullah, and Hispanic participants in a Large Lupus Association Study. This identified one polymorphism present in European Americans and another in African Americans that are strongly associated with the risk of developing kidney disease in Lupus. These findings suggest that drugs that suppress the MyD88-dependent signaling network may have potential for the treatment and/or prevention of lupus nephritis and that the ABIN1[D485N] knock-in mice may be a good model for pre-clinical testing of the efficacy of these compounds.
In this paper Alban Ordureau, Karine Enesa and Sambit Nanda in Philip Cohen’s lab have identified DEAF1 as a new transcription factor required for the production of Type 1 interferons (IFNs). These findings have enhanced our understanding of the signaling networks that regulate the production of the interferons needed to fight infection by viruses.
Double-stranded (ds) RNA, formed as an intermediate in the replication of some RNA viruses, activates the dsRNA receptors TLR3 and MDA5, which are located on the endosomal membranes and in the cytosol of host cells, respectively. The engagement of these receptors induces the activation of the protein kinase TBK1, which then phosphorylates the transcription factor IRF3. This stimulates the translocation of IRF3 to the nucleus, where it dimerises and activates the IFNβ promoter. In earlier papers, the Cohen lab had reported that TBK1 also phosphorylates and activates the E3 ubiquitin ligase Pellino1 (Smith et al, 2011, Biochem. J. 434, 537-548) and that the TLR3- or MDA5-induced production of IFNβ was greatly reduced in cells from mice in which Pellino1 had been replaced by an E3 ligase-inactive mutant (Enesa et al, 2012, J. Biol. Chem. 287,34825-34835). In the new paper the lab identified the transcription factor Deformed Epidermal Associated Factor 1 DEAF1 as a Pellino1-interacting protein and went on to show that IFNβ production induced by synthetic dsRNA or by infection with Sendai virus was greatly reduced in fibroblasts or macrophages from DEAF1 knock-out mice. Interestingly, they also found that the phosphorylation of Pellino1 induced its dissociation from DEAF1, that DEAF1 interacted with IRF3 and the related transcription factor IRF7, and that DEAF1 interacted with the same region of the IFNβ promoter as IRF3.
Although Pellino1 and DEAF1 were both known to be required for the production of the anti-bacterial peptides Drosomycin and Metchnikowin in Drosophila following bacterial infection of the fruit fly, the idea that these proteins might actually interact, or that DEAF1 might have a function in the mammalian innate immune system had not been considered previously. Instead, a number of other roles for DEAF1 have been identified in mammalian cells. For example, it has been linked to depression and suicide through its role in controlling the production of serotonin, and to diseases such as cancer and type1 diabetes.
The phosphorylation of Pellino1 induces its dissociation from DEAF1 in vitro, which may enable DEAF1 to translocate to the nucleus and control IFNβ gene transcription. Similar observations were made with an E3 ligase-inactive mutant of Pellino1, and no ubiquitylation of DEAF1 by Pellino1 could be detected in co-transfection experiments. The reversible interaction of Pellino1 and DEAF1 does not therefore explain why the E3 ligase activity of Pellino1 is needed for IFNβ production and further research is clearly needed to identify how the E3 ligase activity of Pellino1 regulates IFNβ production.
Dr Victoria Cowling, of the University of Dundee, has been awarded a prestigious Medical Research Council Senior Non-Clinical Fellowship to continue her ground breaking research on how mutations in cancer genes can result in tumours forming.
The Fellowship will provide Dr Cowling, who is based in the Medical Research Council Protein Phosphorylation and Ubiquitylation Unit (MRC-PPU) at Dundee, with £2.5million over seven years to build upon the discoveries that her research group has made over the last five years.
Dr Cowling made a major molecular discovery about how genes are regulated and how mutations in cancer genes promote unrestrained cell growth which can result in tumour formation.
Dr Cowling’s research has revealed a completely unexpected and critical role of a chemical structure within cells called the `mRNA methyl cap’. She has shown that the mRNA methyl cap operates as a master integrator of cellular signals which drives protein production in the cell. This research has revealed a new fundamental biological process relevant to understanding how all cells regulate cell growth. Research in this area has taken on added urgency as her results suggest that mutations in several genes that cause cancer may exert their influence through methyl cap formation and function.
Dr Cowling now plans to build upon her initial discoveries to investigate how mutations in genes that drive cancers impact on the machinery that controls the methyl cap.
“A major goal is to exploit this knowledge to develop new approaches and technology to devise future anti-cancer drugs,” said Dr Cowling. “The aim of our research is to counteract cancer-causing genes by targeting the machinery controlling the mRNA methyl cap.”
Upon receiving news of the prize Dr Cowling said, “I am very grateful to receive the MRC Senior Fellowship. This generous long-term funding gives us the freedom to pursue the most important and interesting questions and to take our research in new directions. I’d like to thank the members of my lab and other labs in Dundee for their contributions to this Fellowship.”
Professor Dario Alessi, Director of the MRC-PPU, added, “I am delighted that Vicky has been able to secure this esteemed Fellowship to pursue her important research into better understanding the fundamental mechanisms that control protein production. This is a very important area of research of great relevance to better understanding diseases such as cancer. Vicky was the only scientist in the United Kingdom to be awarded an MRC Senior Non-Clinial Fellowship in this round, an indication of the exceptionally high quality of her research.”
Miratul Muqit, a Clinician and Programme Leader in the MRC-PPU, has been awarded a prestigious Wellcome Trust Senior Research Fellowship in Clinical Science to continue his groundbreaking studies on the regulation and function of the Parkinson’s disease associated enzymes PINK1 and Parkin.
Miratul is a clinically active Neurologist who treats patients with Parkinson’s. During his graduate studies he played a major role in the discovery of PINK1 mutations in patients with familial Parkinson’s. Miratul had previously shown that PINK1 was localized to the mitochondria but little was known on the catalytic activity of PINK1 since the enzyme appeared to be inactive when expressed by various methods. He joined the MRC-PPU in 2008 as a Wellcome Trust Intermediate Clinical Fellow to work with Dario Alessi to investigate the regulation and function of the PINK1 kinase.
Over the last 5 years, Miratul has made several fundamental discoveries relating to the PINK1 kinase. These have culminated in the elucidation of a signaling pathway for PINK1 in which PINK1, upon activation by mitochondrial depolarization, directly phosphorylates the RING-IBR-RING E3 ligase, Parkin, at Serine 65. This then leads to activation of Parkin E3 ligase activity.
Over the next 5 years, Miratul’s lab will focus on determining how disruption of PINK1-Parkin signaling ultimately leads to Parkinson’s. In particular he will address how PINK1 is activated; define new substrates for PINK1; and determine physiological substrates for the Parkin E3 ligase. In parallel he hopes to generate state-of-the-art phospho-specific antibodies to study PINK1-Parkin signaling in Parkinson’s patients with a view to developing the first biomarkers for the disease.
Commenting on the award Miratul said: “This funding boost from the Wellcome Trust is really a reflection of the many talented people who have contributed to the project including a trio of fantastic PhD students, Helen Woodroof, Chandana Kondapalli and Agne Kazlauskaite. Our work would also not have been possible without the outstanding research environment and resources of the MRC Unit as well as generous funding from the Wellcome Trust.”
“We have entered a really exciting phase of our research and over the next few years we hope to have a much better understanding of how PINK1 and Parkin mutations lead to Parkinson’s. This may lead to novel ideas to better diagnose and treat the disorder.”
Dario Alessi, Director of the MRC Unit added: “I am delighted that Miratul has been able to secure this highly sought after fellowship to pursue his valuable research into better understanding the molecular causes of Parkinson’s. Miratul is on the cusp of making some tremendous breakthroughs in the area of PINK1 and Parkin biology that could lead to new ideas about how to better treat and diagnose Parkinson’s in the future. Miratul is the first clinician working in Dundee to ever secure a Wellcome Trust Senior Research Fellowship in Clinical Science and is currently the only Clinician in Scotland to hold one of these positions. The University of Dundee MRC Unit is privileged to be able to host Miratul’s research laboratory”
Applications are invited for a post-doctoral position to work with Dr Matthias Trost on a project aimed at studying cell signalling events affecting phagosome maturation. Phagosomes are organelles formed by the uptake of particulate material by specialised phagocytic cells such as macrophages. After internalisation, newly formed phagosomes engage in a maturation process leading to the formation of phagolysosomes within which the foreign matter is degraded. Microbe degradation in the phagosome produces antigens which are presented at the cell surface to activate specific lymphocytes and to elicit appropriate immune responses, linking innate to adaptive immunity. Our understanding of phagosome biology is of great importance as several pathogens, including Mycobacterium tuberculosis are able to inhibit phagosome maturation.
Click here for details.
Our Unit is an exciting and dynamic place to do a PhD. We have world-class, state-of-the art facilities, we have Principal Investigators who are field-leaders and we have fantastic resources all of our researchers tap into. These include a range of support teams who take care of our cloning, and production of proteins and antibodies. You will have the chance to carry out an exciting research project in a disease-related area.
Protein phosphorylation and ubiquitylation – their interplay in important cell processes and diseases – are very hot topics! You can choose from 18 labs exploring distinct but somewhat related research areas.
There are many excellent reasons to come to our Unit for a PhD but here are just 10:
1. You will get a world-class training in one of the most highly respected cell centres for studying cell signalling in the world. Many of the world leaders in the field of cell signaling have trained here – and some of them are based here!
2. Almost all of our students publish at least one first-author papers during their PhD and often more. Some of these papers have caught the attention of the world media!
3. A high proportion of our students go on to run their own research labs, and many are now leaders in their fields
4. The research in the MRC Unit places a lot of emphasis on understanding what goes wrong in cells to cause human diseases – this means our research is useful
5. A lot of our research aims to find new drug targets for the treatment of diseases such as cancer, inflammation, diabetes and neurodegenerative conditions such as Parkinson’s disease - so our research is even more useful!
6. Through the award-winning Division of Signal Transduction Therapy created by, and annexed to, the MRC Unit we have strong links with six of the biggest pharmaceutical companies in the world. So you will see first-hand how drug companies works
7. Interaction with DSTT companies has made it easier for some of our students to make excellent careers in industry
8. The MRC Unit employs dedicated teams for DNA cloning, protein production and antibody production. This means that although you will learn these techniques at the beginning, you won't have to do these routinely during your PhD. This will allow more time for the exciting parts of research!
9. Our Director, Prof. Dario Alessi and the previous Director Sir Philip Cohen are two of the most highly cited scientists in the world
10. University of Dundee is the number one University in the UK (and number 9 in the world) in Biological Sciences research, according to the QS World University Rankings based on citations per paper. University of Cambridge is number 17 and University of Oxford is number 30.
For full details of our PhD programme please click here.
New exciting computational proteomics Postdoctoral Research Assistant position available within the group of Patrick Pedrioli. We are looking for somebody to develop bioinformatic tools for proteomics data analysis, that will help us in the study of ubiquitin signalling networks.
Closing date 02 August 2013.
We are very excited to announce that two new members of the DNA sequencing team have arrived and are already performing outstanding work. Their names are Bert and Ernie, which in a departure from previous naming conventions, are not members of Donald Duck’s family tree. They are, however, named after cartoon characters and are a well known double act (at least for parents with young children or anyone else who remembers well their childhood!).
Bert and Ernie are, in fact, both Thermo Fisher Kingfisher Flex 96 robots. These compact robotic units will enhance the service we can provide by increasing consistency and reproducibility yet further during the reaction clean-up stage. Customers may recall that last year we changed to a magnetic bead-based purification procedure and that this has had significant benefits already. By now automating the magnetic bead cleanup, we can achieve even greater benefits for customers. Apart from the added consistency across a set of samples, the robots undertake the purification much more quickly than can be done manually. Also, the way in which the robot performs the cleanup (by moving the beads and not the liquids) results in an increased purity of products going onto the sequencers, which means cleaner results for customers.
We undertook an extensive review of available magnetic bead-handling robots before deciding to trial the Kingfisher Flex earlier this year. What really impresses us about the robot is its compact footprint, autonomous operation (no need to have a computer constantly connected to it), speed of operation, ability to use standard 96 well PCR plates, simplicity of setup and use and, crucially, the quality of the purification achieved.
The DNA sequencing facility within the MRC Unit provides a fast and accurate service for hundreds of customers within the University of Dundee and throughout the UK. With over 30 years combined experience of DNA sequencing, the staff within the facility are also able to offer expert advice on all aspects of Sanger DNA sequencing. Turnaround time is within 24 hours from receipt of the samples and prices are very competitive, with individual samples costing as little as £3.5 each. For more information on the range of services provided by the facility, please see here.
As part of the MRC’s week of Centenary Celebrations, the MRC-PPU held an Open Day on Parkinson’s disease to showcase cutting edge research being undertaken at the Unit that one day may lead to new treatments for this devastating condition.
The event, organised in conjunction with the leading charity Parkinson's UK, was hosted by Dario Alessi and Miratul Muqit and saw a record attendance of 60 visitors comprising Parkinson’s patients, carers and members of the public. A special visitor was 11-year old Fife schoolboy, Andrew Hornyak, who was inspired to climb a mountain after his mother was diagnosed with Parkinson’s. Andrew initially set himself a target of raising £300 to help Parkinson’s sufferers as this was 10% of the 3000 feet he climbed, however by the time he climbed Ben Chonzie on April 26th he had exceeded his target and had raised a staggering £2200 for Parkinson’s UK research.
The event began with an introduction by Dario on the history and achievements of the MRC and the future mission of the MRC-PPU in tackling common human diseases including neurodegenerative disorders such as Parkinson’s. Miratul gave a clinical talk on Parkinson’s emphasising the impact of genetics in providing clues to the potential pathways involved. The audience then heard presentations from two PhD students in Miratul’s and Dario’s labs, Chandana Kondapalli and Agne Kazlauskaite, whose research are both funded by Parkinson’s UK. Chandana talked about her latest findings studying the PINK1 kinase whilst Agne explained her studies on the Parkin RING E3 ligase enzyme.
A highlight of the afternoon was a special presentation from Dr Andrew Woodland from the Dundee Drug Discovery Unit who gave an overview on the drug discovery process before exciting the audience with potential strategies to find drugs effective against Parkinson’s.
The day ended with tours of the labs in which the visitors were able to see first hand the state-of-the-art facilities housed within the MRC-PPU including the new mass spectrometry suite expertly led by Facilities Manager, Dr David Campbell. The visitors were also led by Andrew and his colleague, Dr Anthony Hope, through the Drug Discovery Unit labs to catch a glimpse of high-throughput robotic technology normally found in medium to large sized pharmaceutical companies.
Overall all the visitors were impressed with the research progress and enthusiasm of the researchers and a big thank you was given on behalf of all who attended by Katherine Crawford, Head of Parkinson’s UK in Scotland.
To read more about Andrew's achievements, click here.
We are delighted to announce that the outcome of our recent quinquennial review has been very successful and the Medical Research Council (MRC) has awarded our Unit approximately £24million core funding over the next five years to enable its researchers to undertake their investigations into the role that phosphorylation and ubiquitylation plays in regulating biology and how disruptions in these processes are linked to disease. This funding will support the majority of our PIs, Postdocs, PhD students researchers as well as the fantastic support staff who operate all the key scientific services that our scientists depend on.
The funding will also excitingly enable the MRC-PPU to expand and recruit three major new researcher groups to Dundee. These groups have already been recruited and will considerably expand the talent of our Units research. The newly appointed groups will relocate their laboratories from Toronto, London and Manchester to the MRC-PPU in October to December 2013 (these will be announced on our website soon).
This funding will also enable the integration into the MRC-PPU of the Scottish Institute for Cell Signalling (SCILLS), which was established at Dundee in 2008 following support of £10m from the Scottish Government click here for further information on the integration of SCLLS in the MRC-PPU.
The MRC-PPU already supports 16 research groups as well as the main Division of Signal transduction Therapy Laboratories (DSTT) who provide critical scientific services for our Unit researchers as well as the six major pharmaceutical companies that currently participate in this collaboration (AstraZeneca, Boehringer Ingelheim, GlaxoSmithKline, Janssen Pharmaceutica, Merck Serono and Pfizer). Altogether the MRC-PPU supports 162 staff from 25 countries. This new core funding from the MRC will be critical in sustaining all of these staff positions. With the addition of three further groups to the Unit our staff number will probably expand to ~180 over the next few years.
Professor Dario Alessi, Director of the MRC-PPU, said, “At these financially challenging times this is incredibly generous support from the MRC. It is a strong endorsement of our research that aims to improve our understanding of human diseases. Importantly this investment by the MRC will enable us to expand our research activities to new exciting areas such as investigating the role of ubiquitylation in human disease. It will also enable us to recruit new creative and talented researchers from all over the world to our Unit. Our researchers thrive on their collaborations with the pharmaceutical industry. Our ability to expand into the ubiquitylation research areas and to recruit additional researchers will greatly boost our links with the pharmaceutical industry. I hope that this will enable us to make a significant contribution towards aiding these companies develop new therapies for the treatment of diseases in the future. We will also use this new funding to ensure that we provide all of our staff with an extraordinary research and training experience. Funding will also support training of clinician scientists and increase our engagement with the clinical community to enhance translational opportunities for the ultimate benefit of patients. This is particularly welcome in the Centenary year of the MRC.”
The funding is announced in the week that the MRC celebrates 100 years of life saving research funded by the taxpayer. Founded in 1913 to tackle tuberculosis, the MRC now invests taxpayer's money in some of the best medical research in the world including the team at the MRC-PPU. Sir John Savill, Chief Executive of the Medical Research Council, who recently visited the MRC-PPU said, “It’s important for people to know how crucial their own money has been in uncovering health improvements that have saved millions of lives. If I asked the person on the street, ‘did you know you’ve helped invent the MRI scanner and DNA fingerprinting, or helped make skin grafts work or proved the link between smoking and cancer?’ … he’d probably look blankly at me. And these discoveries are just the tip of the iceberg of what the taxpayer has funded - through the MRC - over the course of its history. On the MRC’s 100 year birthday, I’d like everyone to celebrate their own contribution to making the UK a world leader in medical research. Long may MRC-funded research continue to have such an impact on the health and wealth of the UK and beyond.”
As part of MRC's week of Centenary Celebrations, the MRC-PPU is collaborating with the Dundee Contemporary Arts (DCA)on their screening of the “I AM BREATHING” documentary. The film is a personal account of the last months in the life of Neil Platt who was diagnosed with Motor Neuron Disease at the age of 34. Neil faces Motor Neurone Disease with incredible humour and honesty, determined to share this last stage of his life through a blog that touched many people. With his posts forming the film’s narration, I AM BREATHING tries to listen to Neil as he asks in the last months of his life: "What makes us human?"
The documentary screening will be followed by a short scientific presentation and a Q&A session hosted by our colleagues:
Dr. Esther Sammler, Clinical PhD Student in Dario Alessi's lab.
Dr. Thimo Kurz, PI at the MRC-PPU and Dr. Elena Speretta, a Postdoc in John Rouse's lab in the MRC-PPU.
Further information is available at
and on the DCA website http://www.dca.org.uk/whats-on/films/i-am-breathing.html
Please join us at the DCA on June 21st starting at 6pm.
This is a public event and your help in spreading the word about it is greatly appreciated.
To launch the Medical Research Council (MRC) centenary celebrations, its chief executive Sir John Savill, gave an inspirational presentation on the history and past achievements of this fabulous organisation that has thus far supported the work that has lead to 29 Nobel prizes. Highlights of MRC supported work over the last century include:
1916: Rickets caused by lack of vitamin D (Sir Edward Mellanby)
1940s: Development of penicillin as a drug (Sir Alexander Fleming Sir Ernst Chain and Lord Florey)
1940s: Randomised controlled trials for tuberculosis (Austin Bradford-Hill and Philip D'Arcy Hart)
1946: The first cohort study (The MRC National Survey of Health and Development study has followed the lives of a group of people born in one particular week in 1946)
1953: Discovery of the structure of DNA (James Watson, Francis Crick, Maurice Wilkins and Rosalind Franklin)
1956: Smoking causes cancer (Sir Richard Doll and Sir Austin Bradford Hill)
1970s: Clinical trials of chemotherapy for leukaemia (The success of these studies was particularly dramatic in children, increasing the survival rate from around one in five to around four in five)
1973: MRI invented (Sir Peter Mansfield)
1980s onwards: Vaccination in The Gambia Vaccination programmes introduced to The Gambia since the 1980s have reduced childhood mortality six-fold
1991: Folic acid cuts risk of spina bifida (A nine-year-long MRC clinical trial showed that giving pregnant women folic acid reduces the risk of major birth defects of the brain and spine
2010: Bowel screening test developed (The flexi-scope bowel cancer screening test for the over 65s allows doctors to both detect early stages of bowel cancer and remove precancerous polyps to prevent bowel cancer. Developed with MRC and Cancer Research UK funding, the test is expected to save 3,000 lives each year in the UK alone)
Sir John also discussed the importance of the MRC-PPU’s own Division of Signal Transduction Therapy Unit (DSTT) as a model of how academic groups can interact with pharmaceutical companies in order to accelerate drug discovery.
Sir John then looked forward and speculated what the next 100 years might bring. He predicted that “we’re going to have a much more sophisticated understanding of the links between nature and nurture and the interplay between a person’s genetic make-up and their environment and lifestyle. Once we know more about this interaction between genome and exposome, we will have a far better understanding of the risk factors that make us more or less likely to develop a disease, allowing us to make more choices that promote health.” Other well-known researchers predicted breakthroughs in individualisation of therapy, tissue regeneration, advances in synthetic biology as well as revolutionary cures for infectious diseases, Alzheimer and all cancers! If this is all achieved will we still need a Medical Research Council in 100 years time?
In a very lively question and answer session Sir John discussed the future of the MRC with PPU staff.
MRC-PPU Director Dario Alessi reflected that most of the ~160 members of staff of the Unit would not be working in Dundee had it not been for the generous long-term support that the Unit has received from the MRC spanning nearly 24 years. Over this period MRC support has enabled training of over 100 PhD students, 300 postdocs, and provided tremendous employment opportunities for many talented support staff. This has greatly contributed to our understanding of how signal transduction pathways are organised and function and how disruptions in these networks results in diseases such as cancer, immune disorders and neurodegeneration. Most of the researchers who have worked in our Unit have gone on to highly successful careers all over the world that include starting companies, running major research institutes and laboratories, working in pharmaceutical companies as well as undertaking senior administrative roles.
Gopal Sapkota has published a single-author research paper in Open BIology that puts a question mark on the notion that transforming growth factor beta (TGFβ) activates TGFβ Activated Kinase 1 (TAK1).
The activation of p38 MAPK by transforming growth factor β (TGFβ) plays an important role in determining cell fate. It was long thought that a protein kinase termed TAK1 (TGFβ activated kinase 1; also known as MAP3K7) was responsible for the TGFβ-induced activation of p38 MAPK in cells. By employing mouse embryo fibroblasts derived from TAK1-deficient mice, Gopal’s research demonstrates that TAK1 is dispensable for TGFβ-induced activation of p38 MAPK. Instead his research proposes the role for two other protein kinases, namely MAP3K4 andMAP3K10, in mediating the activation of p38 MAPK in response to TGFβ.
To read Gopal’s paper entitled “The TGFβ-induced phosphorylation and activation of p38 mitogen-activated protein kinase is mediated by MAP3K4 and MAP3K10 but not TAK1” please click here
The MRC-PPU hosted a visit by Mr Mike Nithavrianakis, British Deputy High Commissioner in Chennai. After an introduction from Miratul Muqit about the Unit, the Deputy High Commissioner met Sourav Banerjee, a PhD student in Dario Alessi's lab, and Chandana Kondapalli who is jointly supervised by Miratul and Dario.
Sourav and Chandana had an opportunity to explain how their research may lead to new ideas for therapies against cancer and Parkinson’s disease respectively. The MRC-PPU attracts young scientists from all over the world for its PhD program and the Deputy High Commissioner offered Sourav and Chandana an open invitation to meet again in the future should either return to their native India to pursue their research careers.
Several MRC-PPU researchers pictured before the race, took part in the the 10 km Monikie Run in aid of Diabetes research.
Results from right to left were:
-Paola de los Heros (Dario Alessi lab) Time: 59:29 min
-Frances-Rose Schumacher (Thimo Kurz lab) Time: 51:38 min
-Sam Strickson (Philip Cohen lab) Time: 48:17 min
-Eeva Sommer (Dario Alessi lab) Time: 49:40 min
-Dario Alessi Time: 50:39 min
-Ana Perez-Olivia (Dario Alessi lab) Time: 61:00 min
-Alberto Moreno (Julian Blow lab) Time: 51:03 min
-Jose Vicente-Fernandez (Ana's husband) Time:61:00 min
Alex Varshavsky from the California Institute of Technology, USA delivered the 5th SCILLS Lecture today May 1 2013. He presented work on recent discoveries about the ubiquitin system and the N-end rule pathway.
The “SCILLS Lecture” is one of our Named Lecture series and serves to celebrate the establishment in 2008 of a major ubiquitylation research Unit within the College of Life at the University of Dundee.
Alexander Varshavsky has made an important contribution to defining the biological importance of the field of ubiquitylation. His laboratory working in this field since the 1980s has made a major contribution to establishing that ubiquitin-dependent processes plays a strikingly broad and unsuspected role in controlling cellular physiology, primarily by regulating the in vivo levels of specific proteins. Research from the Varshavsky laboratory has shown that ubiquitin conjugation is required for the protein degradation in vivo, for cell viability, and also, for the cell cycle, DNA repair, protein synthesis, transcriptional regulation, and stress responses.
Varshavsky also cloned and analysed many of the first ubiquitin genes, namely the first specific E3 ubiquitin ligase (UBR1), the first deubiquitylating enzymes (UBP1 and UBP2). He also identified the first physiological substrate of the ubiquitin system, the MATalpha2 transcriptional repressor. He showed that ubiquitin-dependent proteolysis involves a polyubiquitin chain of unique Lys-48 linked topology is required for protein degradation.
Varshavsky is also well known for his discovery of the “N-end rule” that shows that the N-terminal amino acid of a protein plays an important role in determining its half-life. He has undertaken critical research delineating the processive proteolytic system that targets proteins bearing "destabilising" N-terminal residues.
Varshavsky’s biological discoveries have made a major contribution to the paradigm of regulated proteolysis for controlling levels of proteins in vivo. His findings suggest that control of protein expression by ubiquitylation rivals regulation through transcription and translation.
This has major ramifications for medicine and the multitude of ways in which ubiquitin-dependent processes can malfunction in disease or in the course of ageing, from cancer and neurodegenerative syndromes to perturbations of immunity and many other illnesses, including birth defects and regulation of blood pressure.
Alexander started off his career in Moscow before moving to MIT in the US. Varshavsky wanted to deliver the SCILLS lecture on the May 1st “because in my old country, which I left 35 years ago, May 1 was a special date. The Day of Proletarian Solidarity it was called. A huge, well-behaving demonstration in the Red Square. The entire Politburo stood on Mausoleum of the man who started that misfortune. And with nothing to eat in grocery shops even on May 1. There will be plenty to eat in Dundee on May 1, 2013”.
The majority of human cancers harbour mutations promoting activation of the Akt protein kinase. Because of this there are over 200 clinical trials listed on the NIH clinical trials website that have been initiated or planned to evaluate therapeutic efficacy of Akt inhibitors for the treatment of diverse human cancers.
Ability to predict which tumours will be most responsive to Akt inhibitors is an important question and of relevance to Akt inhibitor clinical trials. To tackle this, MRC-PPU PhD student Eeva Sommer, working in Dario Alessi's lab teamed up with the group of Barry Davies and his other colleagues (Darren Cross, Hannah Dry and Sylvie Guichard) in AstraZeneca.
The AstraZeneca group are involved in developing and clinical evaluation of one of the Akt inhibitors termed AZD5363 that is currently being evaluated in the clinic. They had identified a number of breast cancer cell lines that were sensitive to AZD5363 Akt inhibitor but others that were resistant. Mutational analysis revealed that both the sensitive and resistant cells possessed mutations that would be expected to result in the activation of the Akt kinase but no other patterns emerged that provide clues as to why cells were sensitive or resistant to the inhibitors. Immunoblot analysis also confirmed that in both resistant and sensitive cells the Akt pathway was highly activated and downstream targets of this pathway phosphorylated, therefore also not divulging why certain cells were sensitive and others resistant to Akt inhibitors.
There is a neglected, much less well studied group of protein kinases termed SGK, of which there are three isoforms termed SGK1, SGK2 and SGK3 that are highly related to Akt. Interestingly SGK isoforms are also activated by the same upstream machinery as Akt namely by PI 3-kinase-PDK1-mTORC2 system. SGK and Akt isoforms have overlapping substrate specificities and therefore have the potential to possess analogous functions. Akt inhibitors such as AZD5363 and MK-2206 that are being evaluated in cancer clinical trials do not inhibit SGK isoforms.
Eeva wondered whether elevated levels of one of the SGK isoforms activity might account for the differing sensitivities of breast cancer cells to Akt inhibitors. Expression of SGK isoforms is much more variable between cells and tissues than Akt, which might also explain why only a subset of tumour cells would possess elevated SGK activity.
Eeva’s experiments revealed strikingly that the majority (but not all) of Akt inhibitor resistant breast cancer cells possess markedly elevated levels of SGK1 mRNA and protein. In contrast, none of the Akt inhibitor sensitive breast cancer cells displayed high levels of SGK1. Eeva also studied SGK2 and SGK3 but found no major differences in the expression of these enzymes between the sensitive and resistant cells.
Eeva next demonstrated that SGK1 knockdown markedly reduced proliferation and migration of Akt inhibitor resistant cells displaying high SGK1 levels but not sensitive cells. Furthermore, Eeva also found that inhibition of SGK1 activity by treating the Akt inhibitor resistant cells with an mTOR inhibitor markedly suppressed proliferation.
Previous work has suggested that SGK1 specifically phosphorylates the substrate N-myc Downstream-Regulated Gene 1 (NDRG1). Eeva therefore expected to only see elevated NDRG1 phosphorylation in the Akt inhibitor resistant cells that express high levels of SGK1. However, Eeva observed significant phosphorylation of NDRG1 in both the Akt inhibitor resistant and sensitive cells. Further experimentation revealed that in the Akt inhibitor sensitive cells, NDRG1 was in fact phosphorylated by Akt-as NDRG1 phosphorylation was potently suppressed by Akt inhibitors. In contrast, in the Akt inhibitor resistant cells displaying high SGK1 activity phosphorylation of NDRG1 was not impacted by treatment with Akt inhibitors.
Our data suggests that the trick to work out whether a tumour will be sensitive to an Akt inhibitor or not will be to monitor the effect that Akt inhibitors have on NDRG1 phosphorylation. This will be helped by the excellent monoclonal antibodies that can be used to recognise phosphorylated NDRG1 in clinical samples. The prediction that will need to be tested in future work is that if Akt inhibitors are found to reduce NDRG1 phosphorylation-then the tumour will likely be sensitive to Akt inhibitors. In contrast, the observation of high NDRG1 phosphorylation that is unaffected by Akt inhibitors-would suggest that SGK activity is elevated and that this cancer will be resistant to Akt inhibitors and may be better treated with mTOR inhibitors.
Our findings also suggest that development of SGK inhibitors or dual Akt/SGK inhibitors might be worthwhile for treatment of cancers displaying elevated SGK activity. To read a copy of our paper paper click here
Cullin-RING ligases (CRLs) are multi-subunit ubiquitin E3 enzymes, which ligate the small modifier ubiquitin to other cellular proteins. CRLs are modular complexes containing a core catalytic unit, which is combined with variable substrate-specific adaptors to target a large array of proteins for ubiquitylation. Because of their modularity, CRLs are very versatile and can form hundreds of different E3s, making them the largest family of ubiquitin ligases in the cell.
As all CRLs are built around a common catalytic scaffold, the substrate specificity subunits need to be carefully assembled when they are needed and again disassembled when the substrate has been ubiquitylated. For many years it has been puzzling how this activation and inactivation is achieved at the molecular level.
PhD work performed by Aleksandra Zemła in the laboratory of Thimo Kurz and published in a recent article in Nature Communications has now shed light on this process. Aleksandra used the well-characterised budding yeast SCF CRL complex to study the dynamics of activation and inactivation of these enzymes. She first identified a trigger that rapidly inactivates SCF by switching yeast cells from growth on fermentable to non-fermentable carbon sources. Aleksandra noticed that during inactivation the substrate-specificity subunits of the SCF are released from the core complex. This observation led her to investigate the requirements for the release, and she discovered that both, a large protein complex called the COP9 Signalosome, and a protein called CAND1 are needed. It has previously been known that the COP9 Signalosome removes a modification from the complex, allowing CAND1 to interact with the CRL. Aleksandra could now show that this sequence of events is required for the removal of substrate specificity modules directly by CAND1. Most importantly, she also demonstrated that the CRL cannot properly be reactivated if the removal is inhibited by mutation of the COP9 Signalosome or CAND1, as “old” substrate-specificity modules occupy the complex and prevent the binding of new substrate-specific adaptors. As a consequence, SCF substrate ubiquitylation is inhibited.
These findings for the first time shed light on how the dynamic assembly and disassembly of this highly conserved and important class of E3 ubiquitin ligases is regulated. The groups of Dieter Wolf from the Burnham Institute in San Diego and Ray Deshaies from Caltech in Los Angeles published similar findings in the same issue of Nature Communications and of the journal Cell, respectively. All three papers are also covered in a Preview article published in the most recent issue of Cell.
Aleksandra’s paper describing her results can be found here, and the Preview in Cell is located here.
The MRC Protein Phosphorylation Unit and the SCottish Institute of ceLL Signalling (SCILLS) have merged into the MRC Protein Phosphorylation and Ubiquitylation Unit.
The new Unit will still retain the MRC-PPU brand name. Its scientists will focus on investigating the regulation and function of protein phosphorylation and ubiquitylation networks that are strongly linked to understanding fundamental biology as well as disease. Dario Alessi is the current Director of the MRC-PPU and SCILLS and will direct the new merged Unit.
The MRC Protein Phosphorylation Unit was established by Philip Cohen in 1990 and has grown in size over the years from 2 research groups (Philip Cohen and Tricia Cohen) to around 11 groups in 2013. Many ground-breaking results have been made in Protein Phosphorylation Unit over the last 23 years. Highlights include:
- Defining the mechanism by which insulin regulates glycogen synthesis (PI 3-kinase-PDK1-Akt-GSK3-glycogen synthase)
- Understanding how growth factors stimulate the MAP kinase cascade (RAF-MEK-ERK-RSK/MSK)
- Cloning and characterising most of the critical serine/threonine protein phosphatases and their regulatory subunits
- Uncovering many important aspects of the stress activated p38 and JNK signalling pathways including how the upstream and downstream components operate and are regulated
- Identification of novel key pathways regulating double stranded break DNA damage repair pathways such as the SLX nuclease complexes, FAM60A and more recently DVC1
- Playing a major role in uncovering the key role that 14-3-3 protein phosphate recognition adaptors play in regulating biological responses and identifying >500 interactors of these proteins
- Discovery of PDK1 and identification of most of the 24 downstream AGC kinases substrates that PDK1 phosphorylates and activates
- Discovery of mechanism by which the LKB1 tumour suppressor kinase is regulated by the STRAD pseudokinase and MO25 and identifying all 14 AMPK family protein kinases that are phosphorylated and activated by LKB1
- Discovery of the mechanism by which the WNK family kinases regulate blood pressure via the SPAK/OSR1 protein kinases
- Dissecting pathways activated by the innate immune signalling Toll-Like Receptors that induce activation of MAP kinase pathways as well as MSK1. Helping to define the critical roles these pathways play in triggering the production of anti-inflammatory and pro-inflammatory cytokines
- Uncovering the first physiological substrate for the Parkinson’s disease PINK1 kinase and showing that it functions to activate the PARKIN E3 ubiquitin ligase whose mutation also results in Parkinson’s disease
- Playing a major role in promoting research into developing specific and potent protein kinase inhibitors by helping characterise two of the prototypic kinase inhibits (PD98059 and SB203580) and establishing kinase profiling as a method to quantify the selectivity of kinase inhibitors. MRC-PPU researchers have played an instrumental role in helping characterise dozens of highly specific kinase inhibitors that have had a major impact on our ability to dissect the physiological functions of signal transduction pathways. This has stimulated Pharmaceutical companies to develop kinase inhibitors and ~20 of these are now approved drugs that have cumulative sales of approaching $20 billion dollars per annum
- Setting up the Division of Signal Transduction Therapy Unit (DSTT), which is widely regarded as a model for how academia should interact with industry
To address these issues, Philip Cohen persuaded the Scottish Funding Council (via an election pledge from the Scottish National Party) to provide £10 million to set up SCILLS in 2008. SCILLS has thus far made an excellent start. It has enabled five up and coming junior PIs to set up their lab in this area (Gabriela Alexandru, Arno Alpi, Thimo Kurz, Patrick Pedrioli and Satpal Virdee) and permitted the establishment of a number of talented support teams to generate a critical set of reagents and technology to better study of protein ubiquitylation.
Many exciting research projects have been launched to uncover the role of ubiquitin pathways play in mediating diverse processes of relevance to understanding cancer, innate immune pathways, hypertension and neurodegenerative disorders. The research undertaken by SCILLS has also played a major role in our recent £14.4 million renewal of the DSTT collaboration in July 2012 and in founding a new ubiquitin reagent company called Ubiquigent, which is based in Dundee and commercialises many of our ubiquitin reagents and technologies.
The hope is that integration of research being undertaken in the new merged MRC Protein Phosphorylation and Ubiquitylation Unit will result in tremendous synergies and open up new opportunities to understand how the effects of phosphorylation and ubiquitylation work together to control biological systems. The aim is for the MRC-PPU is to act as a major hub of research for basic and clinical researchers as well as pharmaceutical companies to come together to study protein phosphorylation and ubiquitylation systems.
The merger of SCILLS and the MRC Protein Phosphorylation Unit was marked by a special inaugural lecture by Tony Pawson, OC OOnt CH FRS FRSC (Samuel Lunenfeld Research Institute of Mount Sinai Hospital, Toronto) on Wednesday 27th March 2013. Tony Pawson is one of the leading researchers in cell-signalling field whose work has inspired us and provided a framework of knowledge that has helped reveal how disruptions in signalling pathways cause many diseases including cancer, diabetes and immune disorders.
Philip Cohen's research into the causes of inflammatory and autoimmune diseases has been boosted by the award of a grant of almost £1.7million from the Wellcome Trust to support his work over the next five years.
The grant is to help him unravel the MyD88 signalling network. This pathway plays a key role in helping to fight infection by pathogens, such as bacteria and viruses, by producing inflammatory mediators. However, the uncontrolled production of these substances is also a cause of many inflammatory and autoimmune diseases such as asthma, lupus, psoriasis and rheumatoid arthritis, which affects millions of people worldwide.
“There is considerable interest in developing drugs to treat inflammatory and autoimmune diseases by targeting the protein components of the MyD88 signalling network,” said Philip. With this grant from the Wellcome Trust, together with the Programme Grant that I was awarded by the Medical Research Council a few months ago, my laboratory now has nearly all the funding in place that it needs to make inroads into understanding the MyD88 signalling system and to validate drug targets for the treatment of inflammatory and autoimmune diseases. The next few years therefore promise to be most exciting.”
Philip has also recently received a further grant of nearly £76,000 from MRC Technology’s Development Gap Fund to help accelerate work over the next year aimed at validating a novel drug target in the MyD88 system that his laboratory has recently identified.
The MRC Protein Phosphorylation and Ubiquitylation Unit's flagship collaboration with pharmaceutical companies, termed Division of Signal Transduction Research (DSTT), is named by Health Science Scotland as their organisation of the month.
Click here for more details.
MRC Protein Phosphorylation Unit PI, Vicky Cowling, will deliver a special Lister Prize Lecture today, Monday 4th March, to all researchers in the College of Life Sciences. In attendance will be the Chairman, Sir Alex Markham and the Director, Dr Trevor Hince of the Lister Institute.
Vicky was awarded one of the three highly coveted Lister Research Prizes for 2011. These prizes give young scientists the opportunity to develop their potential as research scientists by giving them £200,000 in flexible funding over a five-year period. The Lister Institute's approach to scientific support continues to be unique in that it funds tenured and non-tenured researchers, clinicians and non-clinicians and has no priority diseases or restrictions on the research area supported. The Institute also grants its Research Prize holders the freedom to develop their research careers individually while fostering a sense of identity and community.
Vicky’s group investigates the synthesis and regulation of the mRNA methyl cap, an essential structure in gene expression and how this process is regulated by phosphorylation and ubiquitylation. Vicky will present exciting recent data that her group have obtained and explain how this has led to the uncovering of potential novel anti-cancer drug targets.
Before her lecture Vicky said, "I am very grateful to receive this Lister Fellowship. The funds are enabling my group to carry out some vital experiments. Its also an award for the whole lab since it was the lab members' hard work which resulted in us receiving it."
Professor Sir Philip Cohen, of the University of Dundee, will receive the highest award given by the Medical Research Council at a ceremony in the House of Commons today, Wednesday 27th February.
The Millenium Medal is the MRC’s most prestigious award, presented every two years to an outstanding scientist who has made a major contribution towards the MRC’s mission to improve human health through world class medical research.
This year the MRC are presenting two medals, to Sir Philip and to Professor Sir Gregory Winter, of the University of Cambridge.
Professor Sir John Savill, Chief Executive of the MRC, said, “The MRC is proud to award this year’s Millenium Medal to Sir Philip and Sir Greg. Over the past century the MRC has been at the forefront of scientific discovery to improve human health.
“It is with great pleasure that I, along with the MRC’s Council, can recognise those that have contributed so significantly to the transformation of healthcare and the advancement of the way the research community collaborates and innovates.”
Sir Philip said, “I am deeply honoured to accept this award from the Medical Research Council. The MRC has given me tremendous support over the past 35 years for the research that I have carried out in Dundee and I am happy that, with the support of the 45 Ph.D. students and 65 postdoctoral researchers who have worked with me over this period, I have been able to make discoveries that are now having a significant impact on human health and wealth creation.
Sir Philip is Deputy Director of the Division of Signal Transduction Therapy and was Director of the MRC Protein Phosphorylation Unit from the time of its inception in 1990 until April 2012. Both research Divisions are situated within the College of Life Sciences at the University of Dundee.
He has devoted his career to studying a cell regulation process called phosphorylation. This endeavour has contributed to what has become the largest and fastest growing area of drug discovery over the past decade.
Sir Philip had been a researcher for 25 years before he first received a phone call from a pharmaceutical company.
“People used to say ‘Oh, what you're doing is interesting but it will never be of the slightest use for improving health or for wealth creation’,” he recalled.
Phosphorylation is a type of cell regulation that involves the attachment to, or removal of, phosphate groups from proteins, thereby switching their biological functions on or off, or making them more or less stable. Once thought to be a highly specialised process, Sir Philip’s research helped to show that it was, in fact, universal, regulating almost all aspects of cell life. When phosphorylation goes wrong, it can cause diseases such as cancer, diabetes and arthritis.
That first phone call marked the beginning of Philip’s long and fruitful collaborations with pharmaceutical companies. In 1998 he established the Division of Signal Transduction Therapy, a unique collaboration between researchers from the MRC Protein Phosphorylation Unit, the College of Life Sciences of the University of Dundee and five pharmaceutical companies. The collaboration employs 200 research and support staff in Dundee and has brought in more than £50 million in funding in its 14-year history. It has helped to accelerate drug development in this area and become a model for effective collaboration between academia and industry. It also led to the creation of biotechnology company Upstate in Dundee in 1999, which is now part of the Merck-Millipore empire.
Therapies based on phosphorylation are one of the largest and fastest growing areas of drug discovery: there are 24 approved drugs that target this process, sales of which were £18 billion globally in 2011, with over 150 others still undergoing clinical trials.
So what has his experience taught him? “I think it shows how important it is to fund ‘blue skies’ research. It can take an awfully long time for research to reach the stage where it becomes obvious how it can be exploited for the benefit of mankind,” he said.
The Colworth Medal is awarded by the Biochemical Society to ‘an outstanding young British biochemist’ under the age of 36. On Thursday 21 February the Biochemical Society celebrated 50 years of the Colworth Medal at a special event in London which most of the previous recipients (who are remarkably still all alive) attended.
To read wide-ranging interviews with the three MRC-PPU PIs who are past recipients of the Colworth Medal (John Rouse, Philip Cohen and Dario Alessi) click here
Gordon’s hypertension syndrome is caused by mutations that increase expression of WNK1 protein kinase as well as specific missense mutations lying within a non-catalytic region of the WNK4 protein kinase. Patients with this condition suffer from high blood pressure and hyperkalemia (high serum potassium), and can be treated using thiazide diuretic hypertension drugs that inhibit the NCC ion co-transporter in the kidney. Much research from our Unit and elsewhere points towards WNK1/WNK4 kinases controlling blood pressure by activating two related kinases termed-SPAK and OSR1 that once switched on regulate hypertension blood pressure by modulating the activity of ion co-transporters in the kidney termed NCC and NKCC2.
Exciting recent studies by the laboratories of Richard Lifton at Yale and Xavier Jeunemaitre in Paris have identified new players that control Gordon’s syndrome. These researchers identified over 50 patients, in which Gordon’s syndrome was caused by mutations in Ubiquitin E3 ligase components termed Cullin-3 (CUL3) or Kelch-like 3 (KLHL3) rather than WNK isoforms.
Previous work suggested that CUL3 and KLHL3 would form a heterodimeric complex. Data indicated that CUL3 would function as the catalytic entity mediating the ubiquitylation of substrates whereas KLHL3 would operate as the substrate recognition moiety directing the E3 ligase complex to its specific cellular substrates.
To explore how a CUL3:KLHL3 complex might operate to control blood pressure a Postdoc in Dario Alessi's lab, Akihito Ohta, immunoprecipitated KLHL3 and strikingly found that it associated strongly with WNK1, WNK2 and WNK3 isoforms as well as CUL3. However, in parallel studies no interaction of KLHL3 with other components of the WNK signalling pathway such as SPAK/OSR1 or NCC/NKCC1 was observed. Interestingly, many dominant KLHL3 disease mutations analysed inhibited binding to either WNK1 or CUL3, indicating that the association of WNK isoforms with KLHL3 is relevant to Gordon’s syndrome.
A postdoc in Thimo Kurz's lab, Frances-Rose Schumacher, then got together with Axel Knebel and Clare Johnson in the MRC-PPU ubiquitylation component purification and assay team, to generate recombinant wild type and a non-WNK1 binding disease mutant CUL3:KLHL3 complex. Frances-Rose was then able to show that wild type but not the disease mutant complex potently ubiquitylated WNK1 in vitro. Consistent with CUL3 regulating ubiquitylation and stability of WNK1, Akihito was next able to demonstrate that siRNA-mediated knockdown of CUL3 moderately increased WNK1 protein levels and kinase activity in HeLa cells.
Akihito then mapped the KLHL3 interaction site in to a non-catalytic moiety located just C-terminal to the kinase catalytic region of WNK1 (residues 479 to 667). Interestingly, the equivalent region in WNK4 encompasses residues that are mutated in Gordon syndrome patients. Strikingly, Akihitio found that the Gordon’s disease causing WNK4[E562K] and WNK4[Q565E] mutations as well as the equivalent mutation in WNK1[479-667] fragment, abolished ability to interact with KLHL3.
These results suggest that mutations in WNK4 that cause hypertension exert their effects by hindering the interaction with KLHL3:CUL3. More work is required to establish this concept, but our prediction is that these missense mutations in WNK4 exert their physiological effects by ablating KLHL3 binding thereby leading to reduced ubiquitylation and hence enhanced expression of WNK4. If this was the case it could result in inappropriate activation of the SPAK/OSR1 kinases resulting in overstimulation of the NCC/NKCC2 ion co-transporters. This would lead to too much salt retention and hence hypertension. In future work it would be critical to properly compare expression levels of WNK4 in WNK4[D561A] knock-in mice that have been generated by the Uchida laboratory in Japan or even in Gordon’s syndrome patients.
All our results points towards Gordon’s syndrome causing mutations in WNK1, WNK4, KLHL3 and probably CUL3 leading to hypertension by inducing the overexpression of WNK isoforms. Our data suggests that the CUL3-KLHL3 E3 ligase complex regulates blood pressure via its ability to interact with and ubiquitylate WNK isoforms. More generally this research reveals how mutations that disrupt the ability of an E3 ligase to interact and ubiquitylate a critical cellular substrate such as WNK isoforms can trigger a chronic disease such as hypertension.
To read Akihito and Frances-Rose’s paper describing these results click here.
We are delighted that our newest PI recruit, Yogesh Kulathu, will starting his independent laboratory within the MRC-PPU today, February 1st 2013. Until now Yogesh has been undertaking tremendous postdoctoral research in David Komander's lab at the LMB deciphering how new ubiquitin binding domains interact with ubiquitin chains and investigating regulation and structure of various deubiquitinylases.
Yogesh's new laboratory will be focused on uncovering the biology and mechanism of atypical ubiquitin chains. Yogesh is also an experienced structural biologist and we will be creating a new crystallisation suite and associated robotics to automatically set up crystallisation trays within the MRC-PPU space to enable Yogesh and Daan van Aalten, as well as other PIs in our Unit, to readily crystallise the proteins they are working on.
More details on Yogesh's research plans will be uploaded to the research pages of the MRC-PPU shortly. Yogesh will also be advertising for PhD and Postdoc positions soon but any potentially interested candidates are free to informally discuss these positions with Yogesh. Please email Yogesh - firstname.lastname@example.org - if you are interested in applying for a position in his lab.
The Scottish Institute for Cell Signalling (SCILLS) and the MRC Protein Phosphorylation Unit will be merging into a new MRC Protein Phosphorylation and Ubiquitylation Unit at the end of March 2013.
To mark this important event, but also to celebrate previous achievements of SCILLS and the MRC-PPU that have brought us to where we are now, we are delighted to announce that Tony Pawson , OC OOnt CH FRS FRSC working at the Samuel Lunenfeld Research Institute of Mount Sinai Hospital, Toronto will deliver an inaugural lecture of our new Unit at 1 pm on Wednesday 27 March 2013 in the MSI Small Lecture Theatre.
Tony Pawson is one of one of the leading players in cell-signalling field. His lab has contributed to many great advances. Tony Pawson was the first recognise that Src homology 2 (SH2) domains functioned to recognise specific phosphorylated tyrosine residues. This led to the discovery that receptor tyrosine kinases operate to create docking sites for the SH2 domains on diverse effectors. This simple mechanism enables tyrosine kinase receptors to link to specific target effectors in response to signals such as growth factors.
In more recent work Tony Pawson’s lab has gone on to identify many different modular domains on proteins that control protein-protein or protein-lipid interactions modulated by diverse extracellular signals. This has made an incredibly important contribution to establishing the multi-domain nature and modularity of cell regulatory proteins relevant for understanding the dynamic organisation of normal cells, the evolution and function of multi-cellular animals, and the genesis of disease.
The research undertaken in the Pawson lab has provided a framework of knowledge that has enabled many signalling pathways to be dissected and helped reveal how disruptions in these pathways cause many diseases including cancer, diabetes and immune disorders. These findings have been instrumental in the development of new kinase inhibitor therapies targeting signalling pathway components that are benefiting many cancer patients (soon patients with immune disorders) which currently generate approximately $20 billion dollars of sales annually .
Tony Pawson's contributions have been recognised by many significant prizes including the Gairdner Foundation International Award, Wolf Prize in Medicine, The Royal Medal from The Royal Society of London, a Companion of Honour and more recently the Kyoto Prize - "Japan's Nobel".
The Division of Signal Transduction Therapy (DSTT) is 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. The DSTT is dedicated to accelerating the development of specific inhibitors of signal transduction for the treatment of disease, as well as the study of cell signaling. It involves 17 laboratories comprising approximately 200 scientific and support staff and is one of the world’s largest ever collaborations between the pharmaceutical industry and an academic centre.
We currently have several postdoc vacancies to work on important collaborative projects between our PIs and specific DSTT companies. These projects would be for from 3 months up to 1 year in the first instance, at the University of Dundee Grade 7 (£29,249 - £35,938).
These projects might suit any researcher coming to the end of their current PhD or postdoc position and looking to gain some additional research experience. You would forge links with the pharmaceutical companies we interact with and gain the opportunity of learning more about company research and what it might be like to work for a company in the future. There could also be the possibility of extending contracts for longer periods
Anyone interested in learning more about this opportunity please email Dario Alessi (email@example.com) and Rob Ford (firstname.lastname@example.org) with a brief letter outlining your previous research experience and indicate the date you could in principal embark on this project. Also include an up to date CV. Please feel free to contact Dario or Rob to learn more about these positions if you are interested.
These are varied positions involving different technologies and labs within the MRC-PPU. You would also collaborate and interact with one or more of the pharmaceutical companies that support the DSTT. Expertise in biochemistry, signal transduction, cell culture, immunoblot analysis would be advantageous but we would of course provide training in any new techniques or methodologies required for the project.
Exciting research postdoctoral positions available in Dario Alessi's lab - please click here for further information
We are delighted to announce that Dr Nicholas Helps has completed a Postgraduate Certificate in the Management of Occupational Health and Safety that he undertook via distance learning with Portsmouth University. The course duration was 12 months and after a lot of hard work and many late nights, Nick has passed with a distinction award. This qualification will allow Nick to provide in-depth health and safety advice to the Unit. It also allows him to become a "Graduate" member of the Institute of Occupational Safety and Health (the professional body for safety and health practitioners) and work towards full "Chartered" membership. The course was funded by the Unit in recognition of the benefit it would bring to the Unit and to Nick's professional development
Researchers of the laboratories of Matthias Trost in the MRC Protein Phosphorylation Unit and Patrick Pedrioli in SCILLS have developed, in collaboration with Thermo-Fisher Scientific, a novel strong-anion exchange chromatography improving current technology for the identification of complex proteomes. Lead author Stella Ritorto shows in a publication in Journal of Proteome Research that this novel fractionation technique allows a deep analysis of the proteome with almost 10,000 proteins identified in macrophage cell lysate. This deep-proteome analysis will allow researchers in the future to identify and quantify low-abundant proteins which are notoriously difficult to analyse. This exciting new technology is already being applied in several projects in the Unit focussing on phosphorylation and ubiquitylation pathways in Parkinson’s disease and cancer providing new insights into molecular pathways affected by these diseases.