The seven wonders of ubiquitin: a multi-interview
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Published online: January 7, 2014
Science & Society
The seven wonders of ubiquitin:
a multi-interview
Personal insights into the ubiquitin field
different types of ubiquitin linkages recruit
PARTICIPANTS different ubiquitin receptors that lead to
completely different outcomes. There is a lot
Ivan Dikic, Professor and Director of Institute of Biochemistry II at the Goethe University and more diversity in the ubiquitin system than
Director of the Buchmann Institute for Molecular Life Sciences (BMLS), Germany we originally thought, when ubiquitin was
Wade Harper, Professor of Cell Biology, Harvard Medical School, USA
solely thought to be a tag targeting proteins to
Ron Hay, Chair of Molecular Biology, University of Dundee, UK
Thomas Langer, Professor at the Institute for Genetics, University of Cologne, Germany the proteasome. It started with the discovery
Michael Rape, Professor of Cell and Developmental Biology, University of California at Berkeley and that K63 linkages lead to signaling. Then
Investigator, Howard Hughes Medical Institute, USA linear linkages were also shown to play a
Titia Sixma, Division of Biochemistry, Netherlands Cancer Institute, Netherlands role in signaling, even though there were
Henning Walczak, Professor of Cancer Biology, University College London, UK
some controversies about this when this was
first reported. I think it is now obvious that
not only linear and K63, but also other linkage
T
his issue of EMBO reports highlights EMBO reports: What would you say have
types, lead to signaling outputs depending
a new Review series on ‘Ubiquityla- been the most significant contributions to
on the context they are in. There is a lot of
tion: mechanism and functions’ that the ubiquitin field in recent years?
plasticity in all of the signaling complexes
started last issue with a discussion of the
that involve ubiquitin.
mechanisms of cullin-RING E3 ligase assem- Ivan Dikic: The biggest advance came from
bly. This month includes an analysis of the the realization that ubiquitin is involved in
role of ubiquitin in the immune system, and Wade Harper: One of the major advances is
most of biological processes in so many the integration of mechanisms in structural
subsequent issues of the journal will feature unexpected ways. For example, different
the roles of ubiquitylation in mitochondrial biology. For a long time, you would know
biological and physiological processes are
homeostasis and in stem cells, as well as that ubiquitin was connected to a given
regulated by specific ubiquitin signals. There pathway, or you might know what the mole-
how RING-between-RING (RBR) E3 ligases are also numerous examples in which not
function and how recent structural work has cules involved were, but actually knowing
only defects but also rewiring of ubiquitin how they work together was not really pos-
contributed to our understanding of the ub- networks is involved in human diseases. A
iquitylation cascade. sible. It took time to develop methods to
significant progress in targeting the ubiquitin analyze these often complex reactions. Now
Most of the senior authors of the Reviews system for therapy has been accomplished.
included in this series came together at the we have a pretty good understanding of the
One good example is the clinically approved
recent EMBO Conference on ‘Ubiquitin and fundamental biochemical mechanisms for
drug Bortezomib that targets the protea- the key enzymatic processes. However,
Ubiquitin-like proteins: from structure to some, but there are also other drugs, such as
function’, held in Riva del Garda in Novem- much still needs to be done to understand
inhibitors of different conjugation enzymes the entire molecular pathways for the most
ber 2013. It was a good opportunity to and blockers of the ubiquitin decoding
gather their personal insights into the most complex ubiquitin transfer cascades.
machinery. Altogether, the biggest advance
important recent developments, future chal- is the spread of ubiquitin functions across
lenges and their impressions on working in biology and medicine. Michael Rape: I wouldn’t want to point it
the ubiquitin field. We also took the oppor- down to a single finding, rather to general
tunity to include the viewpoint of two of our concepts about specificity in the ubiquitin
Titia Sixma: I think it is the realization that,
Editorial Advisory Board members—Ivan system: that it extends beyond single proteo-
although the interactions are weak, there is
Dikic and Michael Rape. lytic modifications; that there are many
a lot more specificity in the system than we
The following multi-interview is an different chains, different deubiquinating
had initially realized, that these modifica-
excerpt of their comments. Coming from enzymes (DUBs). How the degree of com-
tions are selective.
various fields and at different career stages, plexity is currently recognized, not only in
this collage of their very personal opinions terms of numbers, but also of functional
is a good overview of the current state of all Henning Walczak: In my view, one of the interactions, which have been identified
things ubiquitin. most important realizations has been that through dynamic and quantitative proteomic
ª 2014 The Author EMBO reports Vol 15 | No 1 | 2014 7
Published online: January 7, 2014
EMBO reports Personal insights into the ubiquitin field Interview
inhibitors or binding site modulators. Cancer
Wade Harper is the Bert and Natalie Vallee genomics over the last few years has shown
Professor of Molecular Pathology in the
that there are very good targets to be attacked
Department of Cell Biology at Harvard Medical
School (Boston, MA, USA). He received his PhD in for diseases with no good therapeutics avail-
Chemistry at the Georgia Institute of Technology able, so there is a big need. I think ubiquitin
(Atlanta, GA, USA) prior to post-doctoral studies can fill that. Such drugs could be used to treat
in biological chemistry at Harvard Medical cancer, chronic inflammation and neurode-
School. In 1988, he joined the faculty in the
generative diseases, for example. You can
Department of Biochemistry at Baylor College of
Medicine (Houston TX, USA) before moving to
think about autophagy as a pathway linked
Harvard Medical School in 2003. His work to ubiquitin, and modulating this pathway
focuses on the analysis of ubiquitin-driven would have a lot of therapeutic benefit. An
signaling systems and the integration of increasing number of ligases are also linked
quantitative proteomics to understand to developmental processes, so their misregu-
mechanism. [Photo credit: Nathan Harper].
lation causes developmental diseases.
RH: Up to now, we really only had inhibi-
tors against the proteasome or the NEDD8
E1. I think the big translational challenge is
analysis. The combination between in vivo if you can identify drugs that work in can- to find inhibitors of the specificity step,
cell biology and in vitro biochemical recon- cer, it will have an important impact on which is catalyzed by the E3 ligase. We now
stitution has always been a strength in the other diseases. In addition, a large amount have assays that are suitable for high
field. Over the last years, many interesting of protein aggregation occurs in neurodegen- throughput screening and there are many
developments have occurred at that inter- erative diseases. The challenge is to develop screens underway to try to identify such
face, and new technologies have pushed the methods that would reverse some of the inhibitors. However this may be difficult,
field forward. effects of aggregated proteins, or otherwise because the libraries we have may not con-
find ways to eliminate aggregates. tain chemical matter that can inhibit the
Ron Hay: For me, the biggest advances have components of the ubiquitin system. Over
come from the structural analysis of the MR: Having founded a company myself, I the next couple of years this may be possible
components of the conjugation machinery. strongly believe that there are a lot of as better libraries come on stream.
We now have a pretty good understanding opportunities in this field; the proteasome
of how ubiquitin is activated at the E1 step, inhibitors and the thalidomides and related Er: In which direction do you see your lab
how it is transferred onto the E2 and from compounds are just the tip of an iceberg. We going in the next few years?
E2s onto both HECT E3 ligases and sub- will have to learn to translate the recent find-
strates. There is also structural work on ings regarding the mechanism of ubiquityla- Thomas Langer: My group is interested in
large complexes—like the anaphase promot- tion—how you generate specific chains, how mitochondria, mitochondrial quality control,
ing complex—that is benefiting from the you get activity and timing right—into drugs. mitochondrial proteases and protein turn-
combination of electron microscopy and X- It is not going to be a simple ATP-binding over, which is how we entered the ubiquitin
ray crystallography. In all, I think the whole pocket as for kinases, but rather one will field. It became clear that ubiquitin plays
ubiquitin transfer cascade has been illumi- need to find allosteric activators, allosteric a major role, not only in regulating the
nated over the last couple of years by really
nice structural biology.
Titia Sixma is Head of the Division of
Er: What kind of translational/medical Biochemistry at the Netherlands Cancer
applications or developments could come Institute and Professor by special appointment
from this field in the mid-term? at the Erasmus Medical Center. She was trained
as protein crystallographer, received a PhD from
WH: We have already seen the beginnings Groningen University and performed post-
doctoral research at Yale University. Her
of it, with inhibitors in the cullin system. Big
research uses structural biology and biochemical
pharmaceutical companies have had less approaches to understand ubiquitin signalling
impact in the field than a lot of the smaller pathways with particular emphasis on DNA and
ones, in terms of actually identifying targets chromatin-associated pathways. She is a
and molecules. Within the biotech industry, member of the Royal Netherlands Academy of
Arts and Sciences, of the Academia Europaea
there are several compounds that are
and of EMBO. [Photo credit: Ben Balster].
making significant progress. There is a
major emphasis on trying to target the
ubiquitin pathway to treat neurodegenera-
tive diseases. I think the role of aberrant
protein turnover in cancer is pretty clear and
8 EMBO reports Vol 15 | No 1 | 2014 ª 2014 The Author
Published online: January 7, 2014
Interview Personal insights into the ubiquitin field EMBO reports
ubiquitylation sites, for example, can be
Thomas Langer is Professor at the Institute for used in traditional cell lines but applying
Genetics, University of Cologne (Germany). He these approaches to more relevant cells can
studied biological sciences at the University of
sometimes present a challenge. For example,
Regensburg (Germany) and obtained his PhD at
the Ludwig-Maximilians-University Munich studying certain pathways in cancer cell
(Germany). After working as a visiting scientist lines is not optimal for understanding the
at the Memorial Sloan-Kettering Cancer actual mechanism in vivo, or connecting it
Institute in New York, he became group leader with a disease. One of the things that we are
at the Ludwig-Maximilians-University Munich.
trying to do is develop induced pluripotent
Since 2000 he holds a position as Professor of
Genetics at the University of Cologne, where he stem (iPS) cell systems to study some of the
serves as coordinator of the collaborative ubiquitin-related pathways at a systems
research center 635 of the DFG (German level, using the tools that we developed in
Research Council), as vice-coordinator of the cancer cells. However, there is a technical
Cluster of Excellence Cologne (CECAD) and as hurdle: you don’t get a comparable number
prorector for research and young academics. He
of cells and so the ability to detect things is
is interested in mitochondrial quality control,
membrane and phospholipid dynamics. In 2008 much lower, and moreover, the purity of
he was awarded an ERC advanced career grant. differentiated iPS cells might limit interpreta-
Thomas Langer is an elected member of EMBO, of the Academy of Sciences and Arts North- tions based on tools that ask questions about
Rhine Westphalia and of the Leopoldina (German National Academy of Sciences). the bulk population. Initially, it may be
necessary to scale back and focus on either
particular questions or particular pathways,
mitochondrial proteome at the outer mem- are known for 10% or less of them. There and not just generate one more set of data.
brane, but also regulating the dynamics of other must be a reason for this and I doubt that it We are taking this approach in the context
mitochondrial processes, such as autophagy. is just technical. I think we did not look in of neurodegenerative diseases.
We are really interested in identifying the right model systems; we tend to focus on
how ubiquitylation determines the regula- cancer cells, for example. One big direction RH: In the short term, our big challenge is to
tion of mitochondrial dynamics, for exam- my lab has recently taken is to move away understand how E3 ligases work, particu-
ple. Many components have been identified, from cancer cell lines to untransformed larly the RING type. Within the last year or
but under what physiological conditions is systems: stem cells and differentiation so, we managed to understand how the
this regulated? Regarding protein turnover at models. We can study ubiquitylation, which RING activates the ubiquitin~E2, but we
mitochondria, there is a lot of discussion is a dynamic modification, in these dynami- still don’t have an analysis of how substrate
about ERAD pathways at the mitochondrial cally changing environments. In so doing, is really brought to the ubiquitin~E2. We
outer membrane (MOM), but I think this is we have picked up many interesting ligases are now trying to obtain the structure of
by far not fully understood and we would and substrates. SUMO-targeted ubiquitin ligase RNF4 bound
like to explore this. Parallels between ERAD to a poly-SUMO chain of a defined length, in
and turnover of MOM proteins do exist but WH: In general, the tools that we routinely complex with Ubiquitin~E2. We hope this
there is a tendency to oversimplification. It use to examine interaction networks or map will allow us to see how the lysine residue
is likely to be much more complex, in terms
of regulation and membrane dynamics,
exchange with other lipids and vesicle, etc. I Ron Hay is Professor of Molecular Biology at
think ubiquitylation plays a central role in the Centre for Gene Regulation and Expression
the regulation of these processes. and Honorary Member of the MRC Protein
Phosphorylation and Ubiquitination Unit,
University of Dundee. He attended Heriot-Watt
TS: We are now interested in the specificity University, Edinburgh and obtained his PhD
of ubiquitylation, and we will study this, both from the University of Glasgow. His postdoctoral
on the DUBs and E3 ligases. I am also inter- research was carried out at Harvard Medical
ested in how DUBs and E3 ligases collaborate School, Boston before joining the MRC Virology
and talk to each other, although we have not Unit, Glasgow as an Independent Investigator.
In 1985 he joined the Biochemistry Department
been working directly on this so far.
of the University of St Andrews and in 2005
took up his present position in Dundee. Ron’s
MR: We always tend to let the biology drive work focuses on establishing the roles of
the questions that we study, so it is hard to Ubiquitin and Small Ubiquitin-like Modifier
predict. About seven years ago, when I (SUMO) as signaling components. Ron is a
Wellcome Trust Senior Investigator and a fellow
started my lab, I would not have predicted I
of the Royal Society, the Royal Society of
would work on specific ubiquitin chain Edinburgh, the Academy of Medical Sciences,
types, for example. One big knowledge gap Academia Europaea and is a member of the EMBO. In 2012, Ron was awarded the Novartis
in our field is that there are 600–800 E3 Medal and Prize of the Biochemical Society.
ubiquitin ligases in humans and substrates
ª 2014 The Author EMBO reports Vol 15 | No 1 | 2014 9
Published online: January 7, 2014
EMBO reports Personal insights into the ubiquitin field Interview
biology. What spirit would you say domi-
Henning Walczak is Professor of Cancer nates the field?
Biology at University College London (UCL) and
Chair of the Centre for Cell Death, Cancer and
TL: I think it is both collegial and competi-
Inflammation (CCCI) at UCL’s Cancer Institute.
Following his PhD in 1995 at the German tive. It is collegial because many people
Cancer Research Centre in Heidelberg, Henning from different backgrounds come together,
Walczak worked as a postdoctoral researcher at so there is a lot of potential for collaboration
Immunex Corporation in Seattle (WA, USA), without having the problem of too much
before returning to the German Cancer
overlap. I think it is a very attractive field
Research Centre as group leader in 1998. In
2007 he was appointed Chair of Tumour for young people. Of course, it is a competi-
Immunology at Imperial College London, and tive field, but a field that is not competitive
joined UCL in 2013 to assume his current is maybe also less interesting. We came into
position. He has received the Biofuture Prize of this field unexpectedly and felt very wel-
the German Ministry for Science and Education come. We had no problems in interacting
(2000), an ERC Advanced Grant (2012) and a
with other groups, possibly because we
Wellcome Trust Senior Investigator Award
(2012). Henning’s lab works on cell death and came from a different angle. From that point
inflammation with a special focus on the of view, it is a positive and open field. In
biology of the different death receptor-ligand and the ubiquitin systems. His research aims at general, I have had no bad experiences,
developing new therapies for cancer. [Photo credit: Kerstin Schmid]. quite the opposite.
HW: As I said, there was some controversy
that is going to be modified is poised in the seen for example on the surface of cytosolic when linear ubiquitination was discovered
active site of the enzyme, which will give us Salmonella. We are also focusing on how to be important in TNF-induced signaling.
some insight into how the acceptor lysine is ubiquitin can regulate selectivity in auto- Some people misinterpreted that as a state-
selected. I think it is going to be quite a diffi- phagy, which is one of the processes where ment against a role for K63 in this process
cult challenge. Ub plays an important role. The transfer of but that was never my take on it. And in
ubiquitin knowledge to the autophagy field the end it did turn out that both linear
HW: I am very interested in deciphering the has given us good recognition. I am always and non-linear ubiquitylation were impor-
ubiquitin code at the tumor necrosis factor intrigued by the possibilities of molecular tant in this process. As it now stands the
(TNF) receptor-signaling complex, which is medicine, and ubiquitin might lead us to non-linear component actually doesn’t
a molecular machine that I find fascinating. another medically relevant application. At have to be K63, it can also be K11 or
In fact that is the short title of my ERC the moment, we are focused on infection another linkage type. In general, I find the
Grant! Linear ubiquitination plays a role in and cancer. ubiquitin field very collegial and at the
TNF signaling, but we have also found K63, same time highly competitive. I sense a
K11, K48, and there may be more. We need Er: The ubiquitin field is growing tremen- real spirit of excitement in the field
to find out the exact sequence of events, dously and spans virtually all aspects of cell because of the recent discoveries of
where exactly is which linkage type placed
and how do the different DUBs de-construct
this. The other aspect my lab is interested in
is to understand the outcome of this signal- Ivan Dikic is Professor and Chairman of
ing in terms of autoimmunity and cancer. Institute of Biochemistry 2 at the Goethe
Can we harness what we have learned about University Medical School and Scientific Director
linear and other types of ubiquitination at of the Buchmann Institute for Molecular Life
Sciences in Frankfurt (Germany). Before joining
receptor signaling complexes to identify new
Goethe University, he was a Group Leader at
treatments for autoimmunity and cancer? the Ludwig Institute for Cancer Research in
Uppsala (Sweden). He was trained as a medical
ID: We need to understand more details doctor in Zagreb, Croatia and obtained his PhD
about the spatiotemporal dynamics of the in molecular biology from the University of
Zagreb under the supervision of Joseph
ubiquitin system in vivo. Along these lines
Schlessinger at New York University Medical
we have recently developed specific engi- Center. Ivan’s research focuses on the role of
neered sensors (GFP-tagged versions of ubiquitin in the regulation of autophagy, DNA
ubiquitin binding domains) that can decode repair, inflammation, cancer, infection, receptor
specific ubiquitin chains and can be used to endocytosis, and proteasomal degradation. He
contributed to the identification of linear
detect specific ubiquitin signals on depolarize
ubiquitination, a signal that can regulate the
mitochondria or DNA damage foci in the NF-kB pathway, making a decision between cell
nucleus. I believe that by using the high- survival and death pathways. [Photo credit: Uwe Dettmar].
resolution microscopy we can better distin-
guish local ubiquitin signaling complexes, as
10 EMBO reports Vol 15 | No 1 | 2014 ª 2014 The Author
Published online: January 7, 2014
Interview Personal insights into the ubiquitin field EMBO reports
chosen it had I known that, but I found it very
Michael Rape is Professor of Cell and interesting. The sort of molecular mechanistic
Developmental Biology at the University of focus of the field was very attractive to me. I
California at Berkeley and Investigator of the
think there are still many open questions,
Howard Hughes Medical Institute, USA. He
obtained his PhD from the Max-Planck-Institute especially on the interplay between ubiquitin
of Biochemistry in Martinsried (Germany), after conjugation and other signaling systems, and
which he carried out postdoctoral research at so there is a lot to do. However, it is not easy
Harvard Medical School. In 2006, he joined the to enter the field from the biochemical side, as
faculty of the Department of Cell and
it is becoming technically quite sophisticated.
Developmental Biology at the University of
California at Berkeley, where he has held
You have to learn the technology, but there
various positions ever since. In 2013, he joined are courses to help people get to that level of
the Howard Hughes Medical Institute. He has sophistication, and that is useful.
won numerous accolades, including the NIH
Director’s New Innovator Award, the Vilcek
MR: Ubiquitin is a very supportive field, so I
Award for Creative Promise and the Curci
Foundation Award. Michael’s research is focused think it is a wonderful field to start to work
in understanding how proteins are modified in. I received a lot of support in my career
with ubiquitin, how processes in the cell are from more established people. The questions
regulated by ubiquitylation, and how to alter ubiquitylation to treat disease. [Photo credit: Daily that have been answered are very few com-
Californian]. pared to those we don’t know anything about.
We still have so much to learn, especially
from a biological perspective. It is also one of
the few fields where you can really combine
ubiquitin’s role in so many different aspects more young PIs, more people coming from
cell biology, biochemistry and mechanism. It
of biology. It is great to be part of that. different disciplines, with different ideas.
is established that this is the way it should be,
Because of the nature of the knowledge in
which can be a very fulfilling because you
WH: When I first started, I was in the cell the ubiquitin field, there was never a lack
can dip your hands in a lot of different areas.
cycle field, which was pretty contentious of topics to study, but a lack of people,
I would certainly choose it again.
for a long time; it is highly competitive. I because there is a lot to discover. At the
find that, overall, the ubiquitin field is end of the day, we sometimes compete,
RH: Yes, I would. In fact, I have worked in a
extremely collegial. People tend to share sometimes publish together, sometimes dis-
few different fields over the years, in DNA
reagents and ideas. That doesn’t mean that agree, but with time things are resolved sci-
replication and transcriptional regulation
it is not competitive, it is very competitive, entifically. This is the strength of the field.
mediated by NF-jB. I really enjoy the ubiqu-
but overall, I think the field is very posi-
itin field because it touches on many differ-
tive in its outlook and collaborative spirit. RH: I think it is a very collegial field and
ent biological problems, and so there is
there are a lot of new people coming into it.
really a wide interest.
ID: The ubiquitin field has a tradition of In most cases, people interact very well.
professional and friendly relations that was Over the last few years in Europe for
WH: Yes; it touches so many aspects of biology.
initiated by the pioneers in the field—like instance, we had quite a large consortia
funded by the EU and there was a very nice Every day there is something new to think
Aaron Ciechanover, Avram Herschko, Alex-
about and you can spend time going down
ander Varshavsky, and others—who trained spirit within that consortia. People inter-
acted well, they shared reagents, and in gen- one road or another road, and still have tons
an extremely high number of the people
to do.
who continued to develop the field to eral they were supportive of young people
where we are today. I think these standards establishing new areas.
have prevailed; the field is competitive, but EMBO reports thanks the participants of this
there is a very professional competitive Er: Would you choose the ubiquitin field multi-interview for their time and effort.
atmosphere. Friendships and competition now, if you were to start all over? The interviews were conducted and coordi-
go side by side and it is a real pleasure to nated by Nonia Pariente.
work in this field. The acceptance of new TS: For structural biology it has never been
PIs has been tremendous; we actually need easy. I’m not sure if 10 years ago I would have DOI 10.1002/embr.201338230
ª 2014 The Author EMBO reports Vol 15 | No 1 | 2014 11
Published online: January 7, 2014
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