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Posts Tagged ‘protein degradation’


Protein regulator of HIV replication

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

Updated 11/26/2015

 

Closing the loop on an HIV escape mechanism

University of Delaware

http://www.rdmag.com/news/2015/11/closing-loop-hiv-escape-mechanism

 

Tatyana Polenova, professor of chemistry and biochemistry at UD (background, left), with her UD research team involved in the HIV study. Next to her is Huilan Zhang. In the foreground, from left, are Guangjin Hou and Manman Lu.

http://www.rdmag.com/sites/rdmag.com/files/newsletter-ads/CHEM-Polenova_Research_Groups-111015-015.jpg

Tatyana Polenova, professor of chemistry and biochemistry at UD (background, left), with her UD research team involved in the HIV study. Next to her is Huilan Zhang. In the foreground, from left, are Guangjin Hou and Manman Lu.

 

Nearly 37 million people worldwide are living with HIV. When the virus destroys so many immune cells that the body can’t fight off infection, AIDS will develop. The disease took the lives of more than a million people last year.

For the past three and a half years, a team of researchers from six universities, led by the University of Delaware and funded by the National Institutes of Health and the National Science Foundation, has been working to uncover new information about a protein that regulates HIV’s capability to hijack a cell and start replicating. Their findings, reported recently in the Proceedings of the National Academy of Sciencespoint to a new avenue for developing potential strategies to thwart the virus.

The team included scientists from UD, the University of Pittsburgh School of Medicine, University of Illinois at Urbana-Champaign, Carnegie Mellon University, the National High Magnetic Field Laboratory at Florida State University and Vanderbilt University School of Medicine. They used a combination of high-tech tools and techniques, including magic-angle-spinning nuclear magnetic resonance (NMR) spectroscopy and computer simulations of molecules, to examine the interactions between HIV and the host-cell protein cyclophilin A (CypA), right down to the movement of individual atoms.

“In a nutshell, we found that the infectivity of HIV is regulated by the motions of these proteins,” says Tatyana Polenova, professor of chemistry and biochemistry at the University of Delaware, who led the study. “It’s a subtle regulation strategy that does not involve major structural changes in the virus.”

Sixty times smaller than a red blood cell, HIV contains a cone-shaped shell, or capsid, made of protein, which surrounds two strands of RNA and the enzymes the virus needs for replication. Like any virus, HIV can only produce copies of itself once it has invaded a host organism. Then it will begin directing certain host cells to begin producing the virus.

But how does HIV invade a cell? In humans, the protein CypA can either promote or inhibit viral infection through interactions with the HIV capsid, although the exact mechanism is not yet known. A portion of the HIV capsid protein, called the CypA loop, is responsible for binding to the CypA in the human host cell. Once this occurs, the virus typically becomes infectious.

However, a change of just one amino acid in the CypA loop can cause the virus to operate opposite from how it does normally, allowing the virus to become non-infectious when CypA is present, and to become infectious when there is no CypA present. Such changes are called “escape mutations,” Polenova says, because they allow the virus to “escape” from its dependence on CypA.

To home in on this escape mechanism, the research team examined assemblies of different variants of HIV capsid protein complexed with CypA. Using magic-angle-spinning NMR, they recorded the motions in these assemblies, atom by atom, on time scales ranging from nanoseconds to milliseconds, from a billionth of a second to a thousandth of a second.

The team found that a reduction in the naturally occurring motions in the binding region due to the mutations allowed the virus to escape from CypA dependence. Magic-angle-spinning NMR experiments provided a direct probe of these motions, recording the changes in the magnetic interactions between nuclei. Computer simulations allowed the team to visualize the motions.

Some portions of the capsid protein do not move at all or move only a little while other portions undergo large-amplitude motions distributed over a wide range of time scales, with the most dynamic region being the CypA loop. Polenova says it is rather surprising that such extensive motions are present in the assembled capsid, and that these dynamics could be detected by both NMR and computer simulations.

“It is the first time that quantitative agreement between experiment and computation was achieved in a dynamics study, and it’s particularly exciting that this was attained for such a complex system,” Polenova says. “We hope this work may guide the development of new therapeutic interventions, such as small molecules that would serve as interactors with the HIV capsid and inhibit these dynamics.”

Polenova says the diverse team of researchers, with expertise in HIV virology, structural biology, biophysics and biochemistry, was critical to the study’s success, along with access to national high-field NMR facilities through the National High Magnetic Field Laboratory. The team was assembled through the NIH-funded Pittsburgh Center for HIV Protein Interactions. Led by Prof. Angela Gronenborn, the center brings together high-caliber scientists and facilities to elucidate the interactions of HIV proteins with host cell factors.

 

Atomic-resolution structure of the CAP-Gly domain of dynactin on polymeric microtubules determined by magic angle spinning NMR spectroscopy

 

Significance

Microtubules and their associated proteins are central to most cellular functions. They have been extensively studied at multiple levels of resolution; however, significant knowledge gaps remain. Structures of microtubule-associated proteins bound to microtubules are not known at atomic resolution. We used magic angle spinning NMR to solve a structure of dynactin’s cytoskeleton-associated protein glycine-rich (CAP-Gly) domain bound to microtubules and to determine the intermolecular interface, the first example, to our knowledge, of the atomic-resolution structure of a microtubule-associated protein on polymeric microtubules. The results reveal remarkable structural plasticity of CAP-Gly, which enables CAP-Gly’s binding to microtubules and other binding partners. This approach offers atomic-resolution information of microtubule-binding proteins on microtubules and opens up the possibility to study critical parameters such as protonation states, strain, and dynamics on multiple time scales.

 

Microtubules and their associated proteins perform a broad array of essential physiological functions, including mitosis, polarization and differentiation, cell migration, and vesicle and organelle transport. As such, they have been extensively studied at multiple levels of resolution (e.g., from structural biology to cell biology). Despite these efforts, there remain significant gaps in our knowledge concerning how microtubule-binding proteins bind to microtubules, how dynamics connect different conformational states, and how these interactions and dynamics affect cellular processes. Structures of microtubule-associated proteins assembled on polymeric microtubules are not known at atomic resolution. Here, we report a structure of the cytoskeleton-associated protein glycine-rich (CAP-Gly) domain of dynactin motor on polymeric microtubules, solved by magic angle spinning NMR spectroscopy. We present the intermolecular interface of CAP-Gly with microtubules, derived by recording direct dipolar contacts between CAP-Gly and tubulin using double rotational echo double resonance (dREDOR)-filtered experiments. Our results indicate that the structure adopted by CAP-Gly varies, particularly around its loop regions, permitting its interaction with multiple binding partners and with the microtubules. To our knowledge, this study reports the first atomic-resolution structure of a microtubule-associated protein on polymeric microtubules. Our approach lays the foundation for atomic-resolution structural analysis of other microtubule-associated motors.

 

How Viruses Commandeer Human Proteins

http://www.technologynetworks.com/Proteomics/news.aspx?ID=185156

 

Researchers have produced the first image of an important human protein as it binds with ribonucleic acid (RNA), a discovery that could offer clues to how some viruses, including HIV, control expression of their genetic material.

 

RNA is one of three macromolecules — along with DNA and proteins — essential to all forms of life. By understanding how hnRNP A1 binds to RNA, the scientists may find ways to jam up components of the replication machinery when the protein is coopted by disease.

The team of scientists reveals the mechanism used by the protein, hnRNP A1 to link to the section of RNA, called the ‘hairpin loop.’

They found that hnRNP A1, a protein essential to cell function and virus replication, has a significantly different structure than its only previously known form: binding to DNA.

“We solved the three-dimensional structure of the protein bound to an RNA hairpin derived from the HIV virus,” said Blanton Tolbert, a chemistry professor at Case Western Reserve. “But because the hairpin loop is found in other viruses and throughout healthy cells, our findings may help explain how the protein connects to the other hairpin targets.”

Tolbert began this research six years ago, frustrated that the only information available was the structure of the protein bound to a synthetic DNA, which isn’t its natural target.

Proteins that bind hairpins sense both the structure and the sequence information presented in the loop. The structure of the DNA complex did not demonstrate the molecular recognition that must take place to bind RNA hairpins.

The process

To discover the structure bound to RNA, the researchers combined three techniques: X-ray crystallography, nuclear magnetic resonance spectroscopy and small angle x-ray scattering. Each technique yielded a piece of the puzzle.

To bind to RNA, hnRNP A1 has two domains, RRM1 and RRM2, which are akin to hands. Scientists already knew both hands are needed to connect to RNA.

But the researchers found that, instead of each domain grabbing a section of the loop, only RRM1 makes contact with the RNA. RRM2 acts as support, helping organize RRM1 into the structure needed to conform to a certain section of the loop.

To confirm that the structures are key to binding, the researchers inserted mutations by changing amino acids on the surface of the domains.

Surprisingly, mutations on the far side of RRM1 — the surface not in contact with the RNA but with the RRM2 — caused decoupling at that site and substantially weakened the affinity for RNA.

Without the normal connection between the two domains, RRM1 fails to adopt the geometric shape that conforms to the RNA hairpin loop.

The researchers are further investigating how the protein transmits the effects of RRM2 to RRM1 and bind. They are also exploring the development of antagonistic agents that would disrupt the interaction of the protein with viruses.

 

Natural defense protein against HIV discovered

HIV-1, ERManI, antiretroviral, defense protein

Earlier research had shown that it was possible to interfere with HIV spread but the exact molecular mechanisms had not been identified. For the first time, scientists have identified ERManI (Endoplasmic Reticulum Class I α-Mannosidase) as the essential host protein that slows the spread of HIV-1. Scientists investigated how the four ER-associated glycoside hydrolase family 47 (GH47) α-mannosidases, ERManI, and ER-degradation enhancing α-mannosidase-like (EDEM) proteins 1, 2, and 3, are involved in the HIV-1 envelope (Env) degradation process. Ectopic expression of these four α-mannosidases uncovered that only ERManI inhibited HIV-1 Env expression in a dose-dependent manner. Basically, ERManI is a host enzyme that adds sugars to proteins. The Env glycoprotein is targeted to the endoplasmic reticulum-associated protein degradation pathway for degradation after infecting cells. And ERManI was found to interact with the Env and initiate this degradation pathway.

With this discovery, ERManI has the potential as a new antiretroviral treatment option. Currently there is no cure for HIV-1 and once patients are infected, they have it for life. Current antiretroviral therapies can prolong life but cannot fully cure a patient. ERManI is different from current treatments in the sense that it can help the body protect itself.

 

ERManI (Endoplasmic Reticulum Class I α-Mannosidase) Is Required for HIV-1 Envelope Glycoprotein Degradation via Endoplasmic Reticulum-associated Protein Degradation Pathway (Sep 2015)

ERManI (Endoplasmic Reticulum Class I α-Mannosidase) Is Required for HIV-1 Envelope Glycoprotein Degradation via Endoplasmic Reticulum-associated Protein Degradation Pathway.

Previously, we reported that the mitochondrial translocator protein (TSPO) induces HIV-1 envelope (Env) degradation via the endoplasmic reticulum (ER)-associated protein degradation (ERAD) pathway, but the mechanism was not clear. Here we investigated how the four ER-associated glycoside hydrolase family 47 (GH47) α-mannosidases, ERManI, and ER-degradation enhancing α-mannosidase-like (EDEM) proteins 1, 2, and 3, are involved in the Env degradation process. Ectopic expression of these four α-mannosidases uncovers that only ERManI inhibits HIV-1 Env expression in a dose-dependent manner. In addition, genetic knock-out of the ERManI gene MAN1B1 using CRISPR/Cas9 technology disrupts the TSPO-mediated Env degradation. Biochemical studies show that HIV-1 Env interacts with ERManI, and between the ERManI cytoplasmic, transmembrane, lumenal stem, and lumenal catalytic domains, the catalytic domain plays a critical role in the Env-ERManI interaction. In addition, functional studies show that inactivation of the catalytic sites by site-directed mutagenesis disrupts the ERManI activity. These studies identify ERManI as a critical GH47 α-mannosidase in the ER-associated protein degradation pathway that initiates the Env degradation and suggests that its catalytic domain and enzymatic activity play an important role in this process.

 

T cell editing using CRISPR/Cas9 could revolutionize HIV therapeutics
September 15, 2015   

T cell therapy, HIV

Reinforcing the immune system by engineering lymphocytes to target and destroy viruses has the potential to be an effective therapy for many diseases. One potential approach to this strategy is to alter the genome of lymphocytes so that proteins that are typically hijacked by viruses are no longer present. While conceptually feasible, editing T cells has been challenging in practice; however, with the advent of mammalian cell editing using CRISPR/Cas9, T-cell editing is closer to becoming a reality.

How can CRISPR/Cas9 bring us closer to finding a cure for HIV?

In a study recently published in PNAS, scientists have optimized a protocol to introduce nucleotide replacements that would inhibit CXCR4 expression. The authors streamlined the CRISPR/Cas9 editing process by electroporating Cas9 ribonucleoproteins (RNPs) into CD4+ T cells. The RNPs, consisting of both a recombinant Cas9 enzyme and guide RNA, vastly improved editing efficiency, ultimately promoting knock-out of the CXCR4 cell-surface receptor. Taken together, these result suggest the potential of a new cell therapy approach for the fight against HIV.

Generation of knock-in primary human T cells using Cas9 ribonucleoproteins
Kathrin Schumann a , b , 1 Steven Lin c , 1 Eric Boyer a , b Dimitre R. Simeonov a , b , d Meena Subramaniam e , f Rachel E. Gate e , f , et al.  PNAS. 2015; 112(33): 10437-10442. http://dx.doi.org:/10.1073/pnas.1512503112

Significance

T-cell genome engineering holds great promise for cancer immunotherapies and cell-based therapies for HIV, primary immune deficiencies, and autoimmune diseases, but genetic manipulation of human T cells has been inefficient. We achieved efficient genome editing by delivering Cas9 protein pre-assembled with guide RNAs. These active Cas9 ribonucleoproteins (RNPs) enabled successful Cas9-mediated homology-directed repair in primary human T cells. Cas9 RNPs provide a programmable tool to replace specific nucleotide sequences in the genome of mature immune cells—a longstanding goal in the field. These studies establish Cas9 RNP technology for diverse experimental and therapeutic genome engineering applications in primary human T cells.

 

T-cell genome engineering holds great promise for cell-based therapies for cancer, HIV, primary immune deficiencies, and autoimmune diseases, but genetic manipulation of human T cells has been challenging. Improved tools are needed to efficiently “knock out” genes and “knock in” targeted genome modifications to modulate T-cell function and correct disease-associated mutations. CRISPR/Cas9 technology is facilitating genome engineering in many cell types, but in human T cells its efficiency has been limited and it has not yet proven useful for targeted nucleotide replacements. Here we report efficient genome engineering in human CD4+ T cells using Cas9:single-guide RNA ribonucleoproteins (Cas9 RNPs). Cas9 RNPs allowed ablation of CXCR4, a coreceptor for HIV entry. Cas9 RNP electroporation caused up to ∼40% of cells to lose high-level cell-surface expression of CXCR4, and edited cells could be enriched by sorting based on low CXCR4 expression. Importantly, Cas9 RNPs paired with homology-directed repair template oligonucleotides generated a high frequency of targeted genome modifications in primary T cells. Targeted nucleotide replacement was achieved in CXCR4 and PD-1 (PDCD1), a regulator of T-cell exhaustion that is a validated target for tumor immunotherapy. Deep sequencing of a target site confirmed that Cas9 RNPs generated knock-in genome modifications with up to ∼20% efficiency, which accounted for up to approximately one-third of total editing events. These results establish Cas9 RNP technology for diverse experimental and therapeutic genome engineering applications in primary human T cells.

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Ubiquitin researchers win Nobel

Larry H. Bernstein, MD, FCAP, Curator

 

Ciechanover, Hershko, and Rose awarded for discovery of ubiquitin-mediated proteolysis

http://www.the-scientist.com/?articles.view/articleNo/23111/title/Ubiquitin-researchers-win-Nobel/

Nature Cell Biology 2, E171 (2000) http://dx.doi.org:/10.1038/35036412

The Royal Swedish Academy of Sciences has decided to award the Nobel Prize in Chemistry for 2004 “for the discovery of ubiquitin-mediated protein degradation” jointly to

Aaron Ciechanover
Technion – Israel Institute of Technology, Haifa, Israel,

Avram Hershko
Technion – Israel Institute of Technology, Haifa, Israel and

Irwin Rose
University of California, Irvine, USA

 

Proteins labelled for destruction

Proteins build up all living things: plants, animals and therefore us humans. In the past few decades biochemistry has come a long way towards explaining how the cell produces all its various proteins. But as to thebreaking down of proteins, not so many researchers were interested. Aaron Ciechanover, Avram Hershko and Irwin Rose went against the stream and at the beginning of the 1980s discovered one of the cell’s most important cyclical processes, regulated protein degradation. For this, they are being rewarded with this year’s Nobel Prize in Chemistry.

Aaron Ciechanover, Avram Hershko and Irwin Rose have brought us to realise that the cell functions as a highly-efficient checking station where proteins are built up and broken down at a furious rate. The degradation is not indiscriminate but takes place through a process that is controlled in detail so that the proteins to be broken down at any given moment are given a molecular label, a ‘kiss of death’, to be dramatic. The labelled proteins are then fed into the cells’ “waste disposers”, the so called proteasomes, where they are chopped into small pieces and destroyed.

 

Avram Hershko is an Israeli biochemist and winner of the 2004 Nobel Prize for Chemistry.

Hershko (born December 31, 1937) was born as Hersko Ferenc in Karcag, Hungary. In 1950, Hershko and his family emigrated from Hungary to Israel, where he adopted the name Avram. Hershko received his M.D. and Ph.D. from the Hadassah Medical School of the Hebrew University. In 1965-67, Hershko worked as a physician in the Israel Defense Forces.

In 1969-72, Hershko was a postdoctoral fellow with the late Dr. Gordon Tomkins at the University of California, San Francisco.

In 1987, Hershko was awarded the Weizmann Prize for Sciences, an honor given to top Israeli scientists. In 1994, he won the Israeli Prize for his contributions to Israeli society through biochemistry and medicine.

In 2004, Hershko was awarded the Nobel Prize in Chemistry “for the discovery of ubiquitin-mediated protein degradation.”

Ciechanover was born in Haifa, a year before the establishment of Israel. He is the son of Bluma (Lubashevsky), a teacher of English, and Yitzhak Ciechanover, an office worker.[1] His family were Jewish immigrants from Poland before World War II.

He earned a master’s degree in science in 1971 and graduated from Hadassah Medical School in Jerusalem in 1974. He received his doctorate in biochemistry in 1981 from the Technion – Israel Institute of Technology in Haifa before conducting postdoctoral research in the laboratory of Harvey Lodish at the Whitehead Instituteat MIT from 1981-1984. He is currently a Technion Distinguished Research Professor in the Ruth and Bruce Rappaport Faculty of Medicine and Research Institute at the Technion.

Ciechanover is a member of the Israel Academy of Sciences and Humanities, the Pontifical Academy of Sciences, and is a foreign associate of the United States National Academy of Sciences.

As one of Israel’s first Nobel Laureates in Science, he is honored in playing a central role in the history of Israel and in the history of the Technion – Israel Institute of Technology

 

  • Ciechanover, A., Hod, Y. and Hershko, A. (1978). A Heat-stable Polypeptide Component of an ATP-dependent Proteolytic System from Reticulocytes. Biochem. Biophys. Res. Commun. 81, 1100–1105.
  • Ciechanover, A., Heller, H., Elias, S., Haas, A.L. and Hershko, A. (1980). ATP-dependent Conjugation of Reticulocyte Proteins with the Polypeptide Required for Protein Degradation. Proc. Natl. Acad. Sci. USA 77, 1365–1368.
  • Hershko, A. and Ciechanover, A. (1982). Mechanisms of intracellular protein breakdown. Annu. Rev. Biochem. 51, 335–364.

Interview Transcript

Transcript from an interview with the 2004 Nobel Laureates in Chemistry Aaron Ciechanover, Avram Hershko and Irwin Rose, on 9 December 2004. Interviewer is Joanna Rose, science writer.

Aaron Ciechanover, Avram Hershko and Irwin Rose during the interview

Dr Ciechanover, Dr Hershko and Dr Rose, my congratulations to the Nobel Prize and welcome to this interview. I know that you two started as medical doctors but you are in science now, and you get the prize for scientific research. How come you left medicine?

Avram Hershko: Well, I started out as a medical student, I wanted to be a doctor. And during my medical studies I studied biochemistry. That was one of the subjects that every medical student studies, so I liked it very much. I liked, you know, the whole concept of biochemistry, of looking for chemical processes in cells, so we had, we could take off one year from the studies to spend in research in the lab. I also found a very good teacher, Jacob Mager, and I wanted to spend it with him, so I did. That’s how I got involved in biochemistry. Afterwards, I finished my medical studies but already, I, after that one year, I knew that I will go to biochemistry and not to practical medicine. That’s how I started. So, it’s, it’s, like all things in life, it starts by some kind of accident or so, that was the accident, I met a subject during my studies that I liked.

And a good teacher.

Avram Hershko: And a very good teacher.

Was it also a topic, an issue that you were interested in?

Avram Hershko: No, no, not yet, not yet. Mager was interested in many subjects so that was … Actually, I continued with him after my army service as a doctor, and during the course of a couple of years I evolved in four completely different subjects, protein, synthesis, purine metabolism, and a certain disease called glucose-6-phosphate dehydrogenase deficiency, because he was interested in many things, so that gave me a very good background, a very, very, you know, very good basic background.

What about you, Dr Ciechanover?

I fell in love with biochemistry …

Aaron Ciechanover: Surely you can repeat the story verbatim. The same very story, I started in the same medical school, and after four years I decided to try and taste, I fell in love with biochemistry, too.

Like ten years later.

Aaron Ciechanover: Exactly ten years later, and I also decided to taste it, and at that time at medical school they let students take one year off for medical studies, try some research, so I went into biochemistry, same very story, different mentor. And, a wonderful mentor, and I studied lipids.

Also.

Aaron Ciechanover: Not proteins at all, and then exactly, made a decision, that that’s it. But I had, because of obligations to serve in Israel in the military as a physician. I completed my medical studies, went to serve in the army, but meanwhile, in between, I was looking already for a future mentor, in biochemistry, and Avram was at the time abroad, in the University of California in San Francisco, and I got rave recommendation, that he is a great teacher and a great biochemist, and I wrote him, and he was ready to accept me, and there started this story. More or less.

So did you go to the States?

Aaron Ciechanover: No, no, he came here. He returned to /- – -/ fellow, he started a new department in Haifa, which was a new medical school, I joined him, not initially on this project, on a different one because I still had to serve in the army. It’s a little bit complicated date-wise, but basically it’s the same very story, mentorship, the same footstep, without knowing where I am going.

You will never know.

Aaron Ciechanover: I never know, but it’s basically, ten years later the same very footsteps.

Oh, that’s funny. What about you, Dr Rose? How did you get …

Irwin Rose: I have an anomalist’s story. It doesn’t, there is no precedent for this. We moved from the east coast to the town of Spokane, Washington, when I was about 13 years old, and I did not adapt very well to the, to the style of the place, and I spent most of my time in the public library. And I enjoyed the company of the Journal of Biological Chemistry, because it was the book shaped thing, in those days, you know, it was the small journal …

Avram Hershko: At the age of 13?

Irwin Rose: No, you know, like a couple of years, you know, I was very unpopular with the other students, and so I read the Journal of Biological … the small, the small Journal of Biological Chemistry, and I found an article I thought I understood. And I read it and I thought I understood it to the point where I could make some suggestions as to how it would be, the experiment might work, and then I was very satisfied with that, and then I … I didn’t spend much time in science at that point. Went into the navy, got out of the navy, tried to go to the University of California at Berkeley, but due to the failure to find the bulletin board announcing the laboratory time of organic chemistry, I couldn’t do my organic chemistry there.

So I said OK, I’ll be a biochemist …

So I went back to the State College of Washington and there I was influenced, I would say, by the embryology teacher, who was a very strong personality in terms of academic research, he tried to encourage his students. Then I went to the University of Chicago and there was a big shock to learn all the new kinds of things that they were teaching there, in organic chemistry and that sort of stuff, and very attractive concepts, and things began to come together in my mind as to how chemistry worked and how I might be able to exploit some of the early kinds of techniques that were being used in organic chemistry into biochemistry, which was something I was attracted to, due to my reading of the Journal of Biological Chemistry. So at that point I signed up, there was a big gymnasium, and people were signing people up for which major you were going to go into. So I said OK, I’ll be a biochemist.

So I entered into the department of biochemistry, never saw the chairman of biochemistry because he was the appointed ambassador to Britain for the United States. So I floated around in the department of biochemistry and learned some interesting things, and then I began to … I never wanted to work with a mentor, because I always wanted to have my own reputation and be free to do what I wanted to do. So I worked with the weakest people in the department. Don’t make that public. No, I don’t mention the names, but … so I did that sort of thing and that way I came to learn some more independence, and once in a while I did a good experiment, and so I had more confidence that I could do research, and so that’s how it got started.

Avram Hershko: Can I mention the story that you did your PhD or eight counts per minute or …

Irwin Rose: Oh yes, well, in those days people weren’t counting, people counted on planchettes. And you …

Avram Hershko: Puckered.

Irwin Rose: Well, it could be, depends on they were flat.

Avram Hershko: You dried them, didn’t you?

Irwin Rose: Yes, you dried them out, depending … yes, that’s right. You had to dry them out, it depends on what the compound was, but if it was trillium you had to get an infinitely thin layer so that you wouldn’t get self-absorption.

Avram Hershko: It’s common, self-absorption on a planchette.

Irwin Rose: Did you guys do that, too?

Aaron Ciechanover: Yeah, yeah, yeah.

Avram Hershko: We had a counter with only three /- – -/ so we moved it like that …

Irwin Rose: Oh yeah, yeah.

Avram Hershko: … it was a big excitement.

Irwin Rose: So I wasn’t that primitive. You were doing these things in Israel, an advanced state.

Aaron Ciechanover: You came to our country.

Irwin Rose: I did. I came to Israel. But anyway, yes, so we did those things. And even if you had eight counts above background, if there were eight, there were eight. That’s right. So you could do some experiments. That’s how it worked out.

So how did you meet together?

Avram Hershko: Well, that’s another story. I got interested in protein degradation during my post-doc fellowship in San Francisco, and when I came back to Israel I continued with that, and at that time it was a very obscure field, you know. People, there were all kinds of, not too many people were interested in it. Those that were interested were not very good. So I looked for somebody, and so my first time I think I came up and I looked for somebody to spend a sabbatical with. I couldn’t find anybody that attracted me. So then I met Ernie at a meeting in 1976, one year before, before my sabbatical was due. And do you remember, we met in the breakfast, so I said can I, just began to talk …

Irwin Rose: It’s alright, I forgot.

… it turned out that he was interested in protein degradation. And that was a secret …

Avram Hershko: … breakfast table, so I knew who he was, he was very well known for his work on enzyme mechanism. That I knew, but then I asked him what are you interested in, in other things? So it turned out that he was interested in protein degradation. And that was a secret, it was a secret because he never published anything on it, and I asked him how come you never published anything, and so he said there is nothing worth publishing on protein degradation. So that’s what he said.

Irwin Rose: Yeah, that was my opinion. Well, because I hadn’t done anything, you don’t say it right.

Avram Hershko: OK. Well, that’s how I remember it. And anyhow, I liked that attitude very much, and asked, I asked him can I spend my sabbatical with you? And he said yes, so that’s how it started, and then Aaron, the same year he started his PhD with me, and after my sabbatical the following, the summer after my sabbatical, Aaron joined us, and then he joined us for a couple of summers afterwards, so that’s how, that’s how the whole connection started.

But how come you pick up an obscure field in science, to work on?

Irwin Rose: Well, I’ll tell you, because when I first worked at Yale, the guy who had a lab next to me had made the original observation that there was a protein, there was an energy dependent on protein breakdown. Now, nobody believed him, but he had made some pretty strong observations that if you …

Avram Hershko: Here, we could mention names.

Irwin Rose: Yes, Melvin Simpson. He made these important observations.

Aaron Ciechanover: He hardly believed himself, because when you go into discussion on the paper, you kind of come to a convoluted argument whether it’s a direct requirement or indirect. We can do the conclusion that it’s indirect.

When was it?

Avram Hershko: 1953, so …

Irwin Rose: So I didn’t read the paper, but I had this man in the laboratory next to me and he said, he made this observation and I got very interested in it. And worked on it for, on sabbatical, and when I went to England and when I went to Israel I got mice from Mager, it turned out the same guy, but he wasn’t there at the time, and … but I never found an energy dependence on the protein breakdown. And it turns out later on that a fellow named Art Haas who had been a post doc with me, made the observation that if you’re not careful when you break cells, there’s a lysosomal enzyme that degrades the ubiquitin. So I never would have found it, you know. Somebody else had to make the observation that you could make a self-resistent that … that would show an ATP dependence on protein breakdown. It was not for me, but I did work on it earlier, and that’s the, that’s why I told you that I’d never made any important observations.

But you three work together. How does it work, to do things together?

Irwin Rose: I don’t do anything.

You do nothing? Who is the worker?

Avram Hershko: Well, that’s, first of all, that’s not true. I remember that you made some ubiquitin preparation …

Irwin Rose: I did.

Avram Hershko: Yes, and it fell on the floor, and then you collected it up from the floor … yeah, yeah. That first step is to boil the extra, because ubiquitin is heat stable, so you boiled it but then it fell on the floor, but you picked it up and it was good, yeah.

Irwin Rose: It was good, nothing could destroy it.

Irwin Rose: It was a licence only enzyme.

Aaron Ciechanover: The /- – -/ can take it, but not the floor.

Avram Hershko: But, yeah, but when I came to his lab we already had his first step, which was the fractionation, well, the reticulocyte cell-free system system was actually established in the laboratory of somebody else, Alfred Goldberg in Harvard, but they didn’t …

Aaron Ciechanover: /Inaudible./

Avram Hershko: No, no, but, yeah, but he made it first, he made it first.

Aaron Ciechanover: The first publication was from Harvard, no doubt.

Avram Hershko: But then he didn’t progress, but then he didn’t do what he should have done, which is fractionation. It’s hard to purify right away, but ATP dependent enzyme, he never found it. And what we did was fractionation and constitution, so we already had this first step of separating it into two, two fractions, fraction one and fraction two.

… we didn’t really understand that it’s binding …

So during these two years between the beginning of ’77 when I write to your lab and December of ’79, when we made the breakthrough in your lab, we purified the component from fraction one, we found it a heat stable protein, and then you had a part in that, you also boiled ubiquitin, and then in Haifa we found that it gets … when we labelled it with iodine and we found it gets bound to proteins and ATP dependent reaction, but we didn’t really understand that it’s binding, its co-herent binding the substate until that summer in 1971 in the laboratory of Rose where you invited me, together with Aaron who was then my graduate student in /- – -/ who was there. 1979, 1979. So that is when, when the discovery that ubiquitin …

Irwin Rose: Shall I tell the story about the ubiquitin?

Avram Hershko: Yes. I think I have finished. So then, that’s how I remember it, and how …

Irwin Rose: OK, well, here they had a heat stable factor that was required, and they made the observation that the ubiquitin went on to proteins. And so one of my post docs went to a post doc of another student, of another faculty member at the Fox Chase Cancer Centre, and said, there was a conversation, and do you know of any examples of a protein covalently linked to a protein? And this post doctoral fellow said yes, there is in the nucleus, a protein called ubiquitin that’s covalently linked to histone. And so they rushed to look at the amino acid composition of that so-called ubiquitin, and they compared it to the amino acid composition which you had published, I guess …

Aaron Ciechanover: No, not yet.

Irwin Rose: Not yet published.

Aaron Ciechanover: But in the end it was published back to back with JBC.

Irwin Rose: No, no, no. But how did they know the conversation …

Aaron Ciechanover: No, because they knew, the end story is that the Wilkinson paper came back to back with ours on the /- – -/.

Avram Hershko: OK. Let’s not go into the detail.

Irwin Rose: Well, for some reason or other, they found confidence…

Avram Hershko: They knew that I published that.

Irwin Rose: Really, and I was not a leak.

Avram Hershko: No, no, you were not.

Aaron Ciechanover: No, he was in the lab, he was free and did this. We didn’t hide anything.

Irwin Rose: OK, you’re getting the inside story here. Now, wait a second.

I have a statement from your colleague. “At first nobody cared about your work, and those that knew something about it, they didn’t believe it.” Was it so …?

Irwin Rose: Who said that?

Avram Hershko: That was, that was Fred Goldberg, yeah.

Aaron Ciechanover: Let’s not mention names.

Avram Hershko: Oh! No, we didn’t mention names.

That citation is right.

Aaron Ciechanover: I’ll tell you, I’ll tell you a funny story. I left the lab in ’81, basically after my PhD was completed I submitted it and I went to Harvard, I went to MIT to do a post doc fellow, and Harvard carried out weekly seminars. And in this weekly seminar, one of the founders in the field of proteolysis, one of the originally, not the founder, but it doesn’t matter. A famous scientist in the field presented the weekly seminar at Harvard. I knew of him because he was our competitor for many years, and I went to hear the seminar, so I crossed the river by the bus, I took the shuttle bus that goes /- – -/ and I was sitting in the very back bench. And this was probably about two weeks before you came to visit, it was the very beginning of my, do you remember when I met you, I came to the airport to pick you up.

Avram Hershko: Yeah, yeah.

Aaron Ciechanover: And then, near me, was sitting a very famous scientist that I only later realised that his name is Arthur Dee, a very famous scientist, and after this presentation of the professor, this was only ’81 when we had like eight or nine papers already in the literature with a huge amount of information there. And he was a protein researcher and he raised his hand, I remember very well, and the other guy, when we were both  /- – -/ he said, you know, I have a question to ask you. There is a fellow in Haifa by the name of Hershko, and another one with a very complicated Polish name that I cannot even pronounce, that published a series of papers on a small protein that is attached to other proteins and marks them for degradation, can you comment on it? And he basically dismissed it as an artefact.

… it adds to our benefit, because they left us alone for seven successive years …

And I don’t, I don’t criticise him, all I’m telling you it was symbolic for me enough for after eight papers in the literature, this was the spirit in the field from people who worked in the field, and there were very few. As a matter of fact, it adds to our benefit, because they left us alone for seven successive years, even after I left the lab to work out basically the entire system. The next scientist to join the field was a scientist at MIT, Alex Varshavsky, who joined in ’84, ’83, but published in ’84, and given I was there and collaborated, so for seven successive years they let us lay the entire stone down in the literature so I don’t criticise him, actually I appreciate him tremendously for letting us do it. You know, in retrospect.

But I wonder, how do you survive as a scientist when nobody believes you somehow? Nobody’s interested. You become kind of non-visible.

Irwin Rose: You’re making observations, and the observations get published, so the observations are true. Whether anybody will say that belongs to a big story like it turns out to be is not predictable, but so you don’t make claims like that. You say that this is very interesting and so on and so on and so on, and you keep following it up, and it doesn’t necessarily become the centre of attention yet, until you build a big enough story. I think that’s the way it works.

We all survive because funding for research was generous in those days, you know. It’s been less generous now, and we have a peer review system which is more critical and so I think you have to, you have to add successively to the picture you’re trying to portray. It’s not sufficient to just provide data. So I think that’s part of it. But I agree that it’s important to be left alone for a sufficient amount of time in order to be able to do it, and not feel that you’re in the middle of a big activity already, so you know, you need to do that sort of thing.

So do you think you would get support today for such work, which was kind of apart?

Avram Hershko: Well, I hope the fund /- – -/ look up your website and will hear these things. Because it’s … yeah, Joe Goldstein, you know, a Nobel Laureate and a good one, wrote a nice article about this year’s Lasker Award, in which he compared science to a sculpture by this British sculptor who had his stone, it was a huge stone of two and a half ton, on which another stone, and another stone, and another stone, and at the end is a little stone, so he said that in science there are big stones and small stones. The important science is the opposite. When you have a little stone, and on top of it you put a bigger stone and then a bigger stone. If you throw out a big stone at the beginning so there’s a lot of publicity sometimes nothing comes out of it, and the scientist, to find his little stone, on which the other stones can be built. So I recommend to read his article.

Now you find the small stones, Dr Rose, in your kitchen, as I understand it. You have a small laboratory there?

Irwin Rose: You want to talk about my kitchen?

Yeah. Your laboratory, I would say.

Irwin Rose: Well, when I retired from Fox Chase I took my spectrophotometer and a lot of my chemicals, based on a sort of suggestion of Dr … his recommendation. So I took all my chemicals and my spectrophotometer and my constant temperature bath and so forth with me to Irvine, and when the person whose laboratory I was sitting decided to retire, I had to do something with the spectrophotometer and so I found a place in my kitchen for it. And this was very convenient because it saved me a lot of time. I didn’t have to go to work every day and if I had a little experiment to do I could do it in my kitchen. So that was very good, although I’ve got a lot of chemicals that I have no use for and I’d like to take them back.

Aaron Ciechanover: Send them over, send them over.

Irwin Rose: I’ll send them over. I’ll get a box.

Avram Hershko: But I worry that you don’t have an ice machine. You need an ice machine.

Irwin Rose: No, I don’t have an ice machine. But I have a freezer and I can make ice cubes and I can break them up.

It’s kind of worrying, in science. So you can work when everything’s /- – -/ ?

Irwin Rose: Yeah, that’s right, exactly.

So are you the kind of scientists that work all day and all night long, kind of nerd scientists?

So that’s my recommendation, do not retire. Do not retire fellas. …

Irwin Rose: I think we all work all day and all night long. I do. I don’t have any hobbies, you know, I’m very embarrassed when people ask me what are my hobbies, I don’t have any hobbies. I mean, it’s just enough to keep up with the things I’m trying to solve. You know, I used to work on little puzzles and so on and so forth. Each puzzle requires attention and, so you get an idea. You get your ideas at different times. Sometimes your wife makes a statement and you say: aha, maybe you’re right. And so you go off to your kitchen, and do a little experiment, so you try to, that’s the way you make progress, if you continue these things. So that’s my recommendation, do not retire. Do not retire fellas.

Avram Hershko: I won’t.

Aaron Ciechanover: I’m never going to.

You worked together in the beginning, you were the graduate student of Dr Hershko, how was it to separate from each other?

Aaron Ciechanover: Well, it’s the nature of science, I think, because you know, you graduate, you go your post doctorate fellowship, and Avram was gracious enough to bring me back, but now is independent and that’s the entire idea, if you bring a young scientist back, you give him a bench, start up funds, and then you tell him now in five years, come back in five years, and show the committees that you worked for something. So actually, you know, it would be unnatural if we would have continued to work together. So, each of us is independent. Now we’re in the same institute and that’s the whole idea of children that grow up, students that become their own, scientists on their own, I think that’s the way.

Do you compete with each other?

Avram Hershko: No, there is enough to do in the ubiquitin field, we don’t feel that we had to compete. There are different aspects of the ubiquitin field. I am working on cell cycle and he works on …

Aaron Ciechanover: /- – -/. Completely different.

How is it to live in a small country with big problems and to get funds for science?

Avram Hershko: It is not easy, it is not easy. You have to know the daily tension which is of course distractive. The funds are small, some funds for science are small. Graduate students have to go to serve in the army and things like that, so it’s more difficult than elsewhere, but it’s possible, it’s possible.

And now everybody’s happy. About the Nobel Prize. So thank you very much for sharing your thoughts with us, and being with us.

 

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26 min.

 

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MLA style: “Transcript from an interview with the 2004 Nobel Laureates in Chemistry Aaron Ciechanover, Avram Hershko and Irwin Rose, on 9 December 2004”. Nobelprize.org. Nobel Media AB 2014. Web. 5 Sep 2015. <http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2004/ciechanover-hershko-rose-interview-transcript.html>

 

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Summary of Proteomics

Author and Curator: Larry H. Bernstein, MD, FCAP 

 

We have completed a series of discussions on proteomics, a scientific endeavor that is essentially 15 years old.   It is quite remarkable what has been accomplished in that time.  The interest is abetted by the understanding of the limitations of the genomic venture that has preceded it.  The thorough, yet incomplete knowledge of the genome, has led to the clarification of its limits.  It is the coding for all that lives, but all that lives has evolved to meet a demanding and changing environment with respect to

  1. availability of nutrients
  2. salinity
  3. temperature
  4. radiation exposure
  5. toxicities in the air, water, and food
  6. stresses – both internal and external

We have seen how both transcription and translation of the code results in a protein, lipoprotein, or other complex than the initial transcript that was modeled from tRNA. What you see in the DNA is not what you get in the functioning cell, organ, or organism.  There are comparabilities as well as significant differences between plants, prokaryotes, and eukaryotes.  There is extensive variation.  The variation goes beyond genomic expression, and includes the functioning cell, organ type, and species.

Here, I return to the introductory discussion.  Proteomics is a goal directed, sophisticated science that uses a combination of methods to find the answers to biological questions. Graves PR and Haystead TAJ.  Molecular Biologist’s Guide to Proteomics.
Microbiol Mol Biol Rev. Mar 2002; 66(1): 39–63.  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC120780/

Peptide mass tag searching

Peptide mass tag searching

Peptide mass tag searching. Shown is a schematic of how information from an unknown peptide (top) is matched to a peptide sequence in a database (bottom) for protein identification. The partial amino acid sequence or “tag” obtained by MS/MS is combined with the peptide mass (parent mass), the mass of the peptide at the start of the sequence (mass tag 1), and the mass of the peptide at the end of the sequence (mass tag 2). The specificity of the protease used (trypsin is shown) can also be included in the search.

ICAT method for measuring differential protein expression

ICAT method for measuring differential protein expression

The ICAT method for measuring differential protein expression. (A) Structure of the ICAT reagent. ICAT consists of a biotin affinity group, a linker region that can incorporate heavy (deuterium) or light (hydrogen) atoms, and a thiol-reactive end group for linkage to cysteines. (B) ICAT strategy. Proteins are harvested from two different cell states and labeled on cysteine residues with either the light or heavy form of the ICAT reagent. Following labeling, the two protein samples are mixed and digested with a protease such as trypsin. Peptides labeled with the ICAT reagent can be purified by virtue of the biotin tag by using avidin chromatography. Following purification, ICAT-labeled peptides can be analyzed by MS to quantitate the peak ratios and proteins can be identified by sequencing the peptides with MS/MS.

Strategies for determination of phosphorylation sites in proteins

Strategies for determination of phosphorylation sites in proteins

Strategies for determination of phosphorylation sites in proteins. Proteins phosphorylated in vitro or in vivo can be isolated by protein electrophoresis and analyzed by MS. (A) Identification of phosphopeptides by peptide mass fingerprinting. In this method, phosphopeptides are identified by comparing the mass spectrum of an untreated sample to that of a sample treated with phosphatase. In the phosphatase-treated sample, potential phosphopeptides are identified by a decrease in mass due to loss of a phosphate group (80 Da). (B) Phosphorylation sites can be identified by peptide sequencing using MS/MS. (C) Edman degradation can be used to monitor the release of inorganic 32P to provide information about phosphorylation sites in peptides.

protein mining strategy

protein mining strategy

Proteome-mining strategy. Proteins are isolated on affinity column arrays from a cell line, organ, or animal source and purified to remove nonspecific adherents. Then, compound libraries are passed over the array and the proteins eluted are analyzed by protein electrophoresis. Protein information obtained by MS or Edman degradation is then used to search DNA and protein databases. If a relevant target is identified, a sublibrary of compounds can be evaluated to refine the lead. From this method a protein target and a drug lead can be simultaneously identified.

Although the technology for the analysis of proteins is rapidly progressing, it is still not feasible to study proteins on a scale equivalent to that of the nucleic acids. Most of proteomics relies on methods, such as protein purification or PAGE, that are not high-throughput methods. Even performing MS can require considerable time in either data acquisition or analysis. Although hundreds of proteins can be analyzed quickly and in an automated fashion by a MALDI-TOF mass spectrometer, the quality of data is sacrificed and many proteins cannot be identified. Much higher quality data can be obtained for protein identification by MS/MS, but this method requires considerable time in data interpretation. In our opinion, new computer algorithms are needed to allow more accurate interpretation of mass spectra without operator intervention. In addition, to access unannotated DNA databases across species, these algorithms should be error tolerant to allow for sequencing errors, polymorphisms, and conservative substitutions. New technologies will have to emerge before protein analysis on a large-scale (such as mapping the human proteome) becomes a reality.

Another major challenge for proteomics is the study of low-abundance proteins. In some eukaryotic cells, the amounts of the most abundant proteins can be 106-fold greater than those of the low-abundance proteins. Many important classes of proteins (that may be important drug targets) such as transcription factors, protein kinases, and regulatory proteins are low-copy proteins. These low-copy proteins will not be observed in the analysis of crude cell lysates without some purification. Therefore, new methods must be devised for subproteome isolation.

Tissue Proteomics for the Next Decade?  Towards a Molecular Dimension in Histology

R Longuespe´e, M Fle´ron, C Pottier, F Quesada-Calvo, Marie-Alice Meuwis, et al.
OMICS A Journal of Integrative Biology 2014; 18: 9.    http://dx.doi.org:/10.1089/omi.2014.0033

The concept of tissues appeared more than 200 years ago, since textures and attendant differences were described within the whole organism components. Instrumental developments in optics and biochemistry subsequently paved the way to transition from classical to molecular histology in order to decipher the molecular contexts associated with physiological or pathological development or function of a tissue. In 1941, Coons and colleagues performed the first systematic integrated examination of classical histology and biochemistry when his team localized pneumonia antigens in infected tissue sections. Most recently, in the early 21st century, mass spectrometry (MS) has progressively become one of the most valuable tools to analyze biomolecular compounds. Currently, sampling methods, biochemical procedures, and MS instrumentations
allow scientists to perform ‘‘in depth’’ analysis of the protein content of any type of tissue of interest. This article reviews the salient issues in proteomics analysis of tissues. We first outline technical and analytical considerations for sampling and biochemical processing of tissues and subsequently the instrumental possibilities for proteomics analysis such as shotgun proteomics in an anatomical context. Specific attention concerns formalin fixed and paraffin embedded (FFPE) tissues that are potential ‘‘gold mines’’ for histopathological investigations. In all, the matrix assisted laser desorption/ionization (MALDI) MS imaging, which allows for differential mapping of hundreds of compounds on a tissue section, is currently the most striking evidence of linkage and transition between ‘‘classical’’ and ‘‘molecular’’ histology. Tissue proteomics represents a veritable field of research and investment activity for modern biomarker discovery and development for the next decade.

Progressively, tissue analyses evolved towards the description of the whole molecular content of a given sample. Currently, mass spectrometry (MS) is the most versatile
analytical tool for protein identification and has proven its great potential for biological and clinical applications. ‘‘Omics’’ fields, and especially proteomics, are of particular
interest since they allow the analysis of a biomolecular picture associated with a given physiological or pathological state. Biochemical techniques were then adapted for an optimal extraction of several biocompounds classes from tissues of different natures.

Laser capture microdissection (LCM) is used to select and isolate tissue areas of interest for further analysis. The developments of MS instrumentations have then definitively transformed the scientific scene, pushing back more and more detection and identification limits. Since a few decades, new approaches of analyses appeared, involving the use of tissue sections dropped on glass slides as starting material. Two types of analyses can then be applied on tissue sections: shotgun proteomics and the very promising MS imaging (MSI) using Matrix Assisted Laser Desorption/Ionization (MALDI) sources. Also known as ‘‘molecular histology,’’ MSI is the most striking hyphen between histology and molecular analysis. In practice, this method allows visualization of the spatial distribution of proteins, peptides, drugs, or others analytes directly on tissue sections. This technique paved new ways of research, especially in the field of histopathology, since this approach appeared to be complementary to conventional histology.

Tissue processing workflows for molecular analyses

Tissue processing workflows for molecular analyses

Tissue processing workflows for molecular analyses. Tissues can either be processed in solution or directly on tissue sections. In solution, processing involves protein
extraction from tissue pieces in order to perform 2D gel separation and identification of proteins, shotgun proteomics, or MALDI analyses. Extracts can also be obtained from
tissues area selection and protein extraction after laser micro dissection or on-tissue processing. Imaging techniques are dedicated to the morphological characterization or molecular mapping of tissue sections. Histology can either be conducted by hematoxylin/eosin staining or by molecular mapping using antibodies with IHC. Finally, mass spectrometry imaging allows the cartography of numerous compounds in a single analysis. This approach is a modern form of ‘‘molecular histology’’ as it grafts, with the use of mathematical calculations, a molecular dimension to classical histology. (AR, antigen retrieval; FFPE, formalin fixed and paraffin embedded; fr/fr, fresh frozen; IHC, immunohistochemistry; LCM, laser capture microdissection; MALDI, matrix assisted laser desorption/ionization; MSI, mass spectrometry imaging; PTM, post translational modification.)

Analysis of tissue proteomes has greatly evolved with separation methods and mass spectrometry instrumentation. The choice of the workflow strongly depends on whether a bottom-up or a top-down analysis has to be performed downstream. In-gel or off-gel proteomics principally differentiates proteomic workflows. The almost simultaneous discoveries of the MS ionization sources (Nobel Prize awarded) MALDI (Hillenkamp and Karas, 1990; Tanaka et al., 1988) and electrospray ionization (ESI) (Fenn et al., 1989) have paved the way for analysis of intact proteins and peptides. Separation methods such as two-dimension electrophoresis (2DE) (Fey and Larsen, 2001) and nanoscale reverse phase liquid chromatography (nanoRP-LC) (Deterding et al., 1991) lead to efficient preparation of proteins for respectively topdown and bottom-up strategies. A huge panel of developments was then achieved mostly for LC-MS based proteomics in order to improve ion fragmentation approaches and peptide
identification throughput relying on database interrogation. Moreover, approaches were developed to analyze post translational modifications (PTM) such as phosphorylations (Ficarro et al., 2002; Oda et al., 2001; Zhou et al., 2001) or glycosylations (Zhang et al., 2003), proposing as well different quantification procedures. Regarding instrumentation, the most cutting edge improvements are the gain of mass accuracy for an optimal detection of the eluted peptides during LC-MS runs (Mann and Kelleher, 2008; Michalski et al., 2011) and the increase in scanning speed, for example with the use of Orbitrap analyzers (Hardman and Makarov, 2003; Makarov et al., 2006; Makarov et al., 2009; Olsen et al., 2009). Ion transfer efficiency was also drastically improved with the conception of ion funnels that homogenize the ion transmission
capacities through m/z ranges (Kelly et al., 2010; Kim et al., 2000; Page et al., 2006; Shaffer et al., 1998) or by performing electrospray ionization within low vacuum (Marginean et al., 2010; Page et al., 2008; Tang et al., 2011). Beside collision induced dissociation (CID) that is proposed for many applications (Li et al., 2009; Wells and McLuckey, 2005), new fragmentation methods were investigated, such as higher-energy collisional dissociation (HCD) especially for phosphoproteomic
applications (Nagaraj et al., 2010), and electron transfer dissociation (ETD) and electron capture dissociation (ECD) that are suited for phospho- and glycoproteomics (An
et al., 2009; Boersema et al., 2009; Wiesner et al., 2008). Methods for data-independent MS2 analysis based on peptide fragmentation in given m/z windows without precursor selection neither information knowledge, also improves identification throughput (Panchaud et al., 2009; Venable et al., 2004), especially with the use of MS instruments with high resolution and high mass accuracy specifications (Panchaud et al., 2011). Gas fractionation methods such as ion mobility (IM) can also be used as a supplementary separation dimension which enable more efficient peptide identifications (Masselon et al., 2000; Shvartsburg et al., 2013; Shvartsburg et al., 2011).

Microdissection relies on a laser ablation principle. The tissue section is dropped on a plastic membrane covering a glass slide. The preparation is then placed into a microscope
equipped with a laser. A highly focused beam will then be guided by the user at the external limit of the area of interest. This area composed by the plastic membrane, and the tissue section will then be ejected from the glass slide and collected into a tube cap for further processing. This mode of microdissection is the most widely used due to its ease of handling and the large panels of devices proposed by constructors. Indeed, Leica microsystem proposed the Leica LMD system (Kolble, 2000), Molecular Machine and Industries, the MMI laser microdissection system Microcut, which was used in combination with IHC (Buckanovich et al., 2006), Applied Biosystems developed the Arcturus
microdissection System, and Carl Zeiss patented P.A.L.M. MicroBeam technology (Braakman et al., 2011; Espina et al., 2006a; Espina et al., 2006b; Liu et al., 2012; Micke
et al., 2005). LCM represents a very adequate link between classical histology and sampling methods for molecular analyses as it is a simple customized microscope. Indeed,
optical lenses of different magnification can be used and the method is compatible with classical IHC (Buckanovich et al., 2006). Only the laser and the tube holder need to be
added to the instrumentation.

After microdissection, the tissue pieces can be processed for analyses using different available MS devices and strategies. The simplest one consists in the direct analysis of the
protein profiles by MALDI-TOF-MS (MALDI-time of flight-MS). The microdissected tissues are dropped on a MALDI target and directly covered by the MALDI matrix (Palmer-Toy et al., 2000; Xu et al., 2002). This approach was already used in order to classify breast cancer tumor types (Sanders et al., 2008), identify intestinal neoplasia protein biomarkers (Xu et al., 2009), and to determine differential profiles in glomerulosclerosis (Xu et al., 2005).

Currently the most common proteomic approach for LCM tissue analysis is LC-MS/MS. Label free LC-MS approaches have been used to study several cancers like head and neck squamous cell carcinomas (Baker et al., 2005), esophageal cancer (Hatakeyama et al., 2006), dysplasic cervical cells (Gu et al., 2007), breast carcinoma tumors (Hill et al., 2011; Johann et al., 2009), tamoxifen-resistant breast cancer cells (Umar et al., 2009), ER + / – breast cancer cells (Rezaul et al., 2010), Barretts esophagus (Stingl et al., 2011), and ovarian endometrioid cancer (Alkhas et al., 2011). Different isotope labeling methods have been used in order to compare proteins expression. ICAT was first used to investigate proteomes of hepatocellular carcinoma (Li et al., 2004; 2008). The O16/O18 isotopic labeling was then used for proteomic analysis of ductal carcinoma of the breast (Zang et al., 2004).

Currently, the lowest amount of collected cells for a relevant single analysis using fr/fr breast cancer tissues was 3000–4000 (Braakman et al., 2012; Liu et al., 2012; Umar et al., 2007). With a Q-Exactive (Thermo, Waltham) mass spectrometer coupled to LC, Braakman was able to identify up to 1800 proteins from 4000 cells. Processing
of FFPE microdissected tissues of limited sizes still remains an issue which is being addressed by our team.

Among direct tissue analyses modes, two categories of investigations can be done. MALDI profiling consists in the study of molecular localization of compounds and can be
combined with parallel shotgun proteomic methods. Imaging methods give less detailed molecular information, but is more focused on the accurate mapping of the detected compounds through tissue area. In 2007, a concept of direct tissue proteomics (DTP) was proposed for high-throughput examination of tissue microarray samples. However, contrary to the classical workflow, tissue section chemical treatment involved a first step of scrapping each FFPE tissue spot with a razor blade from the glass slide. The tissues were then transferred into a tube and processed with RIPA buffer and finally submitted to boiling as an AR step (Hwang et al., 2007). Afterward, several teams proved that it was possible to perform the AR directly on tissue sections. These applications were mainly dedicated to MALDI imaging analyses (Bonnel et al., 2011; Casadonte and Caprioli, 2011; Gustafsson et al., 2010). However, more recently, Longuespe´e used citric acid antigen retrieval (CAAR) before shotgun proteomics associated to global profiling proteomics (Longuespee et al., 2013).

MALDI imaging workflow

MALDI imaging workflow

MALDI imaging workflow. For MALDI imaging experiments, tissue sections are dropped on conductive glass slides. Sample preparations are then adapted depending on the nature of the tissue sample (FFPE or fr/fr). Then, matrix is uniformly deposited on the tissue section using dedicated devices. A laser beam subsequently irradiates the preparation following a given step length and a MALDI spectrum is acquired for each position. Using adapted software, the different detected ions are then mapped through the tissue section, in function of their differential intensities. The ‘‘molecular maps’’ are called images. (FFPE, formalin fixed and paraffin embedded; fr/fr, fresh frozen; MALDI, matrix assisted laser desorption ionization.)

Proteomics instrumentations, specific biochemical preparations, and sampling methods such as LCM altogether allow for the deep exploration and comparison of different proteomes between regions of interest in tissues with up to 104 detected proteins. MALDI MS imaging that allows for differential mapping of hundreds of compounds on a tissue section is currently the most striking illustration of association between ‘‘classical’’ and ‘‘molecular’’ histology.

Novel serum protein biomarker panel revealed by mass spectrometry and its prognostic value in breast cancer

L Chung, K Moore, L Phillips, FM Boyle, DJ Marsh and RC Baxter*  Breast Cancer Research 2014, 16:R63
http://breast-cancer-research.com/content/16/3/R63

Introduction: Serum profiling using proteomic techniques has great potential to detect biomarkers that might improve diagnosis and predict outcome for breast cancer patients (BC). This study used surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry (MS) to identify differentially expressed proteins in sera from BC and healthy volunteers (HV), with the goal of developing a new prognostic biomarker panel.
Methods: Training set serum samples from 99 BC and 51 HV subjects were applied to four adsorptive chip surfaces (anion-exchange, cation-exchange, hydrophobic, and metal affinity) and analyzed by time-of-flight MS. For validation, 100 independent BC serum samples and 70 HV samples were analyzed similarly. Cluster analysis of protein spectra was performed to identify protein patterns related to BC and HV groups. Univariate and multivariate statistical analyses were used to develop a protein panel to distinguish breast cancer sera from healthy sera, and its prognostic potential was evaluated.
Results: From 51 protein peaks that were significantly up- or downregulated in BC patients by univariate analysis, binary logistic regression yielded five protein peaks that together classified BC and HV with a receiver operating characteristic (ROC) area-under-the-curve value of 0.961. Validation on an independent patient cohort confirmed
the five-protein parameter (ROC value 0.939). The five-protein parameter showed positive association with large tumor size (P = 0.018) and lymph node involvement (P = 0.016). By matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS, immunoprecipitation and western blotting the proteins were identified as a fragment
of apolipoprotein H (ApoH), ApoCI, complement C3a, transthyretin, and ApoAI. Kaplan-Meier analysis on 181 subjects after median follow-up of >5 years demonstrated that the panel significantly predicted disease-free survival (P = 0.005), its efficacy apparently greater in women with estrogen receptor (ER)-negative tumors (n = 50, P = 0.003) compared to ER-positive (n = 131, P = 0.161), although the influence of ER status needs to be confirmed after longer follow-up.
Conclusions: Protein mass profiling by MS has revealed five serum proteins which, in combination, can distinguish between serum from women with breast cancer and healthy control subjects with high sensitivity and specificity. The five-protein panel significantly predicts recurrence-free survival in women with ER-negative tumors and may have value in the management of these patients.

Cellular prion protein is required for neuritogenesis: fine-tuning of multiple signaling pathways involved in focal adhesions and actin cytoskeleton dynamics

Aurélie Alleaume-Butaux, et al.   Cell Health and Cytoskeleton 2013:5 1–12

Neuritogenesis is a dynamic phenomenon associated with neuronal differentiation that allows a rather spherical neuronal stem cell to develop dendrites and axon, a prerequisite for the integration and transmission of signals. The acquisition of neuronal polarity occurs in three steps:

(1) neurite sprouting, which consists of the formation of buds emerging from the postmitotic neuronal soma;

(2) neurite outgrowth, which represents the conversion of buds into neurites, their elongation and evolution into axon or dendrites; and

(3) the stability and plasticity of neuronal polarity.

In neuronal stem cells, remodeling and activation of focal adhesions (FAs)

  • associated with deep modifications of the actin cytoskeleton is
  • a prerequisite for neurite sprouting and subsequent neurite outgrowth.

A multiple set of growth factors and interactors located in

  • the extracellular matrix and the plasma membrane orchestrate neuritogenesis
  • by acting on intracellular signaling effectors, notably small G proteins such as RhoA, Rac, and Cdc42,
  • which are involved in actin turnover and the dynamics of FAs.

The cellular prion protein (PrPC), a glycosylphosphatidylinositol (GPI)-anchored membrane protein

  • mainly known for its role in a group of fatal neurodegenerative diseases,
  • has emerged as a central player in neuritogenesis.

Here, we review the contribution of PrPC to neuronal polarization and

  • detail the current knowledge on the signaling pathways fine-tuned
  • by PrPC to promote neurite sprouting, outgrowth, and maintenance.

We emphasize that PrPC-dependent neurite sprouting is a process in which

  • PrPC governs the dynamics of FAs and the actin cytoskeleton via β1 integrin signaling.

The presence of PrPC is necessary to render neuronal stem cells

  • competent to respond to neuronal inducers and to develop neurites.

In differentiating neurons, PrPC exerts a facilitator role towards neurite elongation.

This function relies on the interaction of PrPC with a set of diverse partners such as

  1. elements of the extracellular matrix,
  2. plasma membrane receptors,
  3. adhesion molecules, and
  4. soluble factors that control actin cytoskeleton turnover
  • through Rho-GTPase signaling.

Once neurons have reached their terminal stage of differentiation and

  • acquired their polarized morphology,
  • PrPC also takes part in the maintenance of neurites.

By acting on tissue nonspecific alkaline phosphatase, or matrix metalloproteinase type 9,

  • PrPC stabilizes interactions between neurites and the extracellular matrix.

Fusion-pore expansion during syncytium formation is restricted by an actin network

Andrew Chen et al., Journal of Cell Science 121, 3619-3628. http://dx.doi.org:/10.1242/jcs.032169

Cell-cell fusion in animal development and in pathophysiology

  • involves expansion of nascent fusion pores formed by protein fusogens
  • to yield an open lumen of cell-size diameter.

Here we explored the enlargement of micron-scale pores in syncytium formation,

  • which was initiated by a well-characterized fusogen baculovirus gp64.

Radial expansion of a single or, more often, of multiple fusion pores

  • proceeds without loss of membrane material in the tight contact zone.

Pore growth requires cell metabolism and is

  • accompanied by a local disassembly of the actin cortex under the pores.

Effects of actin-modifying agents indicate that

  • the actin cortex slows down pore expansion.

We propose that the growth of the strongly bent fusion-pore rim

  1. is restricted by a dynamic resistance of the actin network and
  2. driven by membrane-bending proteins that are involved in
  3. the generation of highly curved intracellular membrane compartments.

Pak1 Is Required to Maintain Ventricular Ca2+ Homeostasis and Electrophysiological Stability Through SERCA2a Regulation in Mice

Yanwen Wang, et al.  Circ Arrhythm Electrophysiol. 2014;7:00-00.

Impaired sarcoplasmic reticular Ca2+ uptake resulting from

  • decreased sarcoplasmic reticulum Ca2+-ATPase type 2a (SERCA2a) expression or activity
  • is a characteristic of heart failure with its associated ventricular arrhythmias.

Recent attempts at gene therapy of these conditions explored strategies

  • enhancing SERCA2a expression and the activity as novel approaches to heart failure management.

We here explore the role of Pak1 in maintaining ventricular Ca2+ homeostasis and electrophysiological stability

  • under both normal physiological and acute and chronic β-adrenergic stress conditions.

Methods and Results—Mice with a cardiomyocyte-specific Pak1 deletion (Pak1cko), but not controls (Pak1f/f), showed

  • high incidences of ventricular arrhythmias and electrophysiological instability
  • during either acute β-adrenergic or chronic β-adrenergic stress leading to hypertrophy,
  • induced by isoproterenol.

Isolated Pak1cko ventricular myocytes correspondingly showed

  • aberrant cellular Ca2+ homeostasis.

Pak1cko hearts showed an associated impairment of SERCA2a function and

  • downregulation of SERCA2a mRNA and protein expression.

Further explorations of the mechanisms underlying the altered transcriptional regulation

  • demonstrated that exposure to control Ad-shC2 virus infection
  • increased SERCA2a protein and mRNA levels after
  • phenylephrine stress in cultured neonatal rat cardiomyocytes.

This was abolished by the

  • Pak1-knockdown in Ad-shPak1–infected neonatal rat cardiomyocytes and
  • increased by constitutive overexpression of active Pak1 (Ad-CAPak1).

We then implicated activation of serum response factor, a transcriptional factor well known for

  • its vital role in the regulation of cardiogenesis genes in the Pak1-dependent regulation of SERCA2a.

Conclusions—These findings indicate that

Pak1 is required to maintain ventricular Ca2+ homeostasis and electrophysiological stability

  • and implicate Pak1 as a novel regulator of cardiac SERCA2a through
  • a transcriptional mechanism

fusion in animal development and in pathophysiology involves expansion of nascent fusion pores

  • formed by protein fusogens to yield an open lumen of cell-size diameter.

Here we explored the enlargement of micron-scale pores in syncytium formation,

  • which was initiated by a well-characterized fusogen baculovirus gp64.

Radial expansion of a single or, more often, of multiple fusion pores proceeds

  • without loss of membrane material in the tight contact zone.

Pore growth requires cell metabolism and is accompanied by

  • a local disassembly of the actin cortex under the pores.

Effects of actin-modifying agents indicate that the actin cortex slows down pore expansion.

We propose that the growth of the strongly bent fusion-pore rim is restricted

  • by a dynamic resistance of the actin network and driven by
  • membrane-bending proteins that are involved in the generation of
  • highly curved intracellular membrane compartments.

Role of forkhead box protein A3 in age-associated metabolic decline

Xinran Maa,1, Lingyan Xua,1, Oksana Gavrilovab, and Elisabetta Muellera,2
PNAS Sep 30, 2014 | 111 | 39 | 14289–14294  http://pnas.org/cgi/doi/10.1073/pnas.1407640111

Significance
This paper reports that the transcription factor forkhead box protein A3 (Foxa3) is

  • directly involved in the development of age-associated obesity and insulin resistance.

Mice that lack the Foxa3 gene

  1. remodel their fat tissues,
  2. store less fat, and
  3. burn more energy as they age.

These mice also live significantly longer.

We show that Foxa3 suppresses a key metabolic cofactor, PGC1α,

  • which is involved in the gene programs that turn on energy expenditure in adipose tissues.

Overall, these findings suggest that Foxa3 contributes to the increased adiposity observed during aging,

  • and that it can be a possible target for the treatment of metabolic disorders.

Aging is associated with increased adiposity and diminished thermogenesis, but

  • the critical transcription factors influencing these metabolic changes late in life are poorly understood.

We recently demonstrated that the winged helix factor forkhead box protein A3 (Foxa3)

  • regulates the expansion of visceral adipose tissue in high-fat diet regimens; however,
  • whether Foxa3 also contributes to the increase in adiposity and the decrease in brown fat activity
  • observed during the normal aging process is currently unknown.

Here we report that during aging, levels of Foxa3 are significantly and selectively

  • up-regulated in brown and inguinal white fat depots, and that
  • midage Foxa3-null mice have increased white fat browning and thermogenic capacity,
  1. decreased adipose tissue expansion,
  2. improved insulin sensitivity, and
  3. increased longevity.

Foxa3 gain-of-function and loss-of-function studies in inguinal adipose depots demonstrated

  • a cell-autonomous function for Foxa3 in white fat tissue browning.

The mechanisms of Foxa3 modulation of brown fat gene programs involve

  • the suppression of peroxisome proliferator activated receptor γ coactivtor 1 α (PGC1α) levels
  • through interference with cAMP responsive element binding protein 1-mediated
  • transcriptional regulation of the PGC1α promoter.

Our data demonstrate a role for Foxa3 in energy expenditure and in age-associated metabolic disorders.

Control of Mitochondrial pH by Uncoupling Protein 4 in Astrocytes Promotes Neuronal Survival

HP Lambert, M Zenger, G Azarias, Jean-Yves Chatton, PJ. Magistretti,§, S Lengacher
JBC (in press) M114.570879  http://www.jbc.org/cgi/doi/10.1074/jbc.M114.570879

Background: Role of uncoupling proteins (UCP) in the brain is unclear.
Results: UCP, present in astrocytes, mediate the intra-mitochondrial acidification leading to a decrease in mitochondrial ATP production.
Conclusion: Astrocyte pH regulation promotes ATP synthesis by glycolysis whose final product, lactate, increases neuronal survival.
Significance: We describe a new role for a brain uncoupling protein.

Brain activity is energetically costly and requires a steady and

  • highly regulated flow of energy equivalents between neural cells.

It is believed that a substantial share of cerebral glucose, the major source of energy of the brain,

  • will preferentially be metabolized in astrocytes via aerobic glycolysis.

The aim of this study was to evaluate whether uncoupling proteins (UCPs),

  • located in the inner membrane of mitochondria,
  • play a role in setting up the metabolic response pattern of astrocytes.

UCPs are believed to mediate the transmembrane transfer of protons

  • resulting in the uncoupling of oxidative phosphorylation from ATP production.

UCPs are therefore potentially important regulators of energy fluxes. The main UCP isoforms

  • expressed in the brain are UCP2, UCP4, and UCP5.

We examined in particular the role of UCP4 in neuron-astrocyte metabolic coupling

  • and measured a range of functional metabolic parameters
  • including mitochondrial electrical potential and pH,
  1. reactive oxygen species production,
  2. NAD/NADH ratio,
  3. ATP/ADP ratio,
  4. CO2 and lactate production, and
  5. oxygen consumption rate (OCR).

In brief, we found that UCP4 regulates the intra-mitochondrial pH of astrocytes

  • which acidifies as a consequence of glutamate uptake,
  • with the main consequence of reducing efficiency of mitochondrial ATP production.
  • the diminished ATP production is effectively compensated by enhancement of glycolysis.
  • this non-oxidative production of energy is not associated with deleterious H2O2 production.

We show that astrocytes expressing more UCP4 produced more lactate,

  • used as energy source by neurons, and had the ability to enhance neuronal survival.

Jose Eduardo des Salles Roselino

The problem with genomics was it was set as explanation for everything. In fact, when something is genetic in nature the genomic reasoning works fine. However, this means whenever an inborn error is found and only in this case the genomic knowledge afterwards may indicate what is wrong and not the completely way to put biology upside down by reading everything in the DNA genetic as well as non-genetic problems.

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Ubiquinin-Proteosome pathway, autophagy, the mitochondrion, proteolysis and cell apoptosis


Original description - :Cartoon representation...

Original description – :Cartoon representation of ubiquitin protein, highlighting the secondary structure. α-helices are coloured in blue and the β-sheet in green. The normal attachment point for a further ubiquitin molecule in polyubiquitin chain formation, lysine 48, is shown in pink. :Image was created using PyMOL (Photo credit: Wikipedia)

Ubiquinin-Proteosome pathway, autophagy, the mitochondrion, proteolysis and cell apoptosis

Larry H Bernstein, MD, FACP, Curator, Reporter, AEW

The work reviewed follows a seminal contribution by two Israeli and an American molecular biologists who shared the Nobel Prize in Chemistry in 2004.

The Royal Swedish Academy of Sciences awarded the Nobel Prize in Chemistry for 2004 “for the discovery of ubiquitin-mediated protein degradation” jointly to Aaron Ciechanover Technion – Israel Institute of Technology, Haifa, Israel, Avram Hershko Technion – Israel Institute of Technology, Haifa, Israel and Irwin Rose – University of California, Irvine, USA.

Aaron Ciechanover, born 1947 (57 years) in Haifa, Israel (Israeli citizen) received a Doctor’s degree in medicine in 1975 at Hebrew University of Jerusalem, and in biology in 1982 at the Technion (Israel Institute of Technology), Haifa. He is a Distinguished Professor at the Center for Cancer and Vascular Biology, and the Rappaport Faculty of Medicine and Research Institute at the Technion, Haifa,
Israel.

Avram Hershko, born 1937 (67 years) in Karcag, Hungary (Israeli citizen) earned the Doctor’s degree in medicine in 1969 at the Hadassah and the Hebrew University Medical School, Jerusalem.  He is a Distinguished Professor at the Rappaport Family Institute for Research in Medical Sciences at the Technion (Israel Institute of Technology), Haifa, Israel.

Irwin Rose, born 1926 (78 years) in New York, USA (American citizen) achieved a Doctor’s degree in 1952 at the University of Chicago, USA. Specialist at the Department of Physiology and Biophysics, College of Medicine, University of California, Irvine, USA.

Proteins labelled for destruction
Proteins build up all living things: plants, animals and therefore us humans. In the past few decades biochemistry has come a long way towards explaining how the cell produces all its various proteins. But as to the breaking down of proteins, not so many researchers were interested. Aaron Ciechanover, Avram Hershko and Irwin Rose went against the stream and at the beginning of the 1980s discovered one of the cell’s most important cyclical processes, regulated protein degradation. For this, they are being rewarded
with the 2004 Nobel Prize in Chemistry.

The label consists of a molecule called ubiquitin. This fastens to the protein to be destroyed, accompanies it to the proteasome where it is recognised as the key in a lock, and signals that a protein is on the way for disassembly. Shortly before the protein is squeezed into the proteasome, its ubiquitin label is disconnected for re-use.

Aaron Ciechanover, Avram Hershko and Irwin Rose have brought us to realise that the cell functions as a highly-efficient checking station where proteins are built up and broken down at a furious rate. The degradation is not indiscriminate but takes place through a process that is controlled in detail so that the proteins to be broken down at any given moment are given a molecular label, a ‘kiss of death’, to be dramatic. The labelled proteins are then fed into the cells’ “waste disposers”, the so called proteasomes, where they are chopped into small pieces and destroyed.

Animation (Plug in requirement: Flash Player 6)

Thanks to the work of the three Laureates it is now possible to understand at  molecular level how the cell controls a number of central processes by breaking down certain proteins and not others. Examples of processes governed by ubiquitin-mediated protein degradation are cell division, DNA repair, quality control of newly-produced proteins, and important parts of the immune defence. When the degradation does not work correctly, we fall ill. Cervical cancer and cystic fibrosis are two examples. Knowledge of
ubiquitin-mediated protein degradation offers an opportunity to develop drugs against these diseases and others.

Aaron Ciechanover and Ronen Ben-Saadon. N-terminal ubiquitination: more protein substrates join in. TRENDS in Cell Biology 2004; 14 (3):103-106.

The ubiquitin–proteasome system (UPS) is involved in selective targeting of innumerable cellular proteins through a complex pathway that plays important roles in a broad array of processes. An important step in the proteolytic cascade is specific recognition of the substrate by one of many ubiquitin ligases, E3s, which is followed by generation of the polyubiquitin degradation signal. For most substrates, it is believed that the first ubiquitin moiety is conjugated, through its C-terminal Gly76 residue, to an 1-NH2 group of an internal Lys residue. Recent findings indicate that, for several proteins, the first ubiquitin moiety is fused linearly to the a-NH2 group of the N-terminal residue.

The ubiquitin–proteasome system (UPS). Ubiquitin is first activated to a high-energy intermediate by E1. It is then transferred to a member of the E2 family of enzymes. From E2 it can be transferred directly to the substrate (S, red) that is bound specifically to a member of the ubiquitin ligase family of proteins, E3

  • (a). This occurs when the E3 belongs to the RING finger family of ligases. In the case of a HECT-domain-containing ligase
  • (b), the activated ubiquitin is transferred first to the E3 before it is conjugated to the E3-bound substrate . Additional ubiquitin moieties are added successively to the previously conjugated moiety to generate a polyubiquitin chain.
  • The polyubiquitinated substrate binds to the 26S proteasome complex (comprising 19S and 20S sub-complexes): the substrate is degraded to short peptides, and free and reusable ubiquitin is released through the activity of de-ubiquitinating enzymes (DUBs).

Ubiquitination on an internal lysine and on the N-terminal residue of the target substrate.

  • (a) The first ubiquitin moiety is conjugated, through its C-terminal Gly76 residue, to the 1-NH2 group of an internal lysine residue of the target substrate (Kn).
  • (b) The first ubiquitin moiety is conjugated to a free a-NH2 group of the N-terminal residue, X.
  • In both cases, successive addition of activated ubiquitin moieties to internal Lys48 on the previously conjugated ubiquitin moiety leads to the synthesis of a  polyubiquitin chain that serves as the degradation signal for the 26S proteasome

 

A UPS Autophagy Review

Summary: This discussion is another in a series discussing mitochondrial metabolism, energetics and regulatory function, and dysfunction, and the process leading to apoptosis and a larger effect on disease, with a specific targeting of neurodegeneration. Why neurological and muscle damage are more sensitive than other organs is not explained easily, but recall in the article on mitochondrial oxidation-reduction reactions and repair that there are organ specific differences in the rates of organelle mutation errors and in the rates of repair. In addition, consider the effect of iron-binding in the function of the cell, and Ca2+ binding in the creation of the mechanic work or signal transmission carried out by the neuromuscular system. We target the previously mentioned role of ubiquitin-proteosome, and interaction with autophagy, mitophagy, and disease.

Keywords: autophagy, ubiquitin-proteosome, UPS, protein degradation, defective organelle removal, selective degradation, E3, neurodegenerative disease, mitochondria, mitophagy, proteolysis, ribosomes, apoptosis, Ca++, rapamycin, TORC1, atg1p kinase, ubiqitization, trafficking pathways, unfolded protein response (UPS), p52/sequestrome, IC3, nitrogen starvation, acetaldehyde dehydrogenase (Ald6p), Ut1hp, toxisomes, Pex3/14 proteins, Bax, E3 Ligase, TRAP1, TNF-a, NFkB.

Ubiquitin-Proteosome Pathway
Three recent papers, describing three apparently independent biological processes, highlight the role of the ubiquitin-proteasome system as a major, however selective, proteolytic and regulatory pathway. Using specific inhibitors to the proteasome, Rock et al. (1994) demonstrate a role for this protease in the degradation of the major bulk of cellular proteins. They also showed that antigen processing requires the ubiquitin-activating enzyme, El. This indicates that antigen processing is both ubiquitin dependent and proteasome dependent. Furthermore, inhibitors to the proteasome prevent tumor necrosis factor a (TNFa)-induced activation of mature NFKB and its entry into the nucleus. The two studies clearly demonstrate that the ubiquitin-proteasome system is involved not only in complete destruction of its protein substrates, but also in limited proteolysis and posttranslational processing in which biologically active peptides or fragments are generated. In addition, the unstable c-Jut but not the stable v-Jun, is multiubiquitinated and degraded. The escape of the oncogenic v-Jun from ubiquitin-dependent degradation suggests a novel route to malignant transformation. Presented here is a review of the components, mechanisms of action, and cellular physiology of the ubiquitin-proteasome pathway.

Experimental evidence implicates the ubiquitin system in the degradation of

  • mitotic cyclins,
  • oncoproteins,
  • the tumor suppressor protein p53,
  • several cell surface receptors,
  • transcriptional regulators, and
  • mutated and damaged proteins.

Some of the proteolytic processes occur throughout the cell cycle, whereas others are tightly programmed and occur following cell cycle-dependent posttranslational modifications of the components involved. Signaling and degradation of other proteins (cell surface receptors, for example) may occur only following structural changes or modification(s) in the target molecule that results from ligand binding. Cell cycle-and modification-dependent degradation, as well the ability of the system to destroy completely or only partially its protein substrates, reflects the complexity involved in regulated intracellular protein degradation.

Enzymes of the System
The reaction occurs in two distinct steps:

  1. signaling of the protein by covalent attachment of multiple ubiquitin molecules and
  2. degradation of the targeted protein with the release of free and reutilizable ubiquitin.

Conjugation of ubiquitin to proteins destined for degradation proceeds, in general, in a three-step mechanism.

  1. Initially, the C-terminal Gly of ubiquitin is activated by ATP to a high energy thiol ester intermediate in a reaction catalyzed by the ubiquitin-activating enzyme, El.
  2. Following activation, E2 (ubiquitin carrier protein or ubiquitin-conjugating enzyme [USC]) transfers ubiquitin from El to the substrate that is bound to a ubiquitin-protein ligase, E3.
  3. Here an isopeptide bond is formed between the activated C-terminal Gly of ubiquitin and an c-NH2 group of a Lys residue of the substrate.

As E3 enzymes specifically synthesized by processive transfer of ubiquitin moieties to Lys-48 of the previous (and already conjugated) ubiquitin molecule. In many cases, E2 transfers activated ubiquitin directly to the protein substrate. Thus, E2 enzymes also play an important role in substrate recognition, although, in most cases, this modification is of the monoubiquitin type.

The Ubiquitin-Mediated Proteolytic Pathway
(1) Activation of ubiquitin by El and E2.
(2) Binding of the protein substrate to E3.
(3) EP dependent but EM independent monoubiquitination.
(4) EP-dependent but EM independent polyubiquitination?
(5) Ed-dependent polyubiquitination.
(6) Degradation of ubiquitin-protein conjugate by the 26s protease.
(7) “Correction” function of C-terminal hydrolase(s).
(6) Release of ubiquitin from terminal proteolytic products by &terminal hydrolase(s).

It is essential for the system that ubiquitin recycles. This function is carried out by ubiquitin C-terminal hydrolases (isopeptidases). In protein degradation, hydrolase(s) is required to release ubiquitin from isopeptide linkage with Lys residues of the protein substrate at the final stage of the proteolytic process. A ubiquitin C-terminal hydrolytic activity is also required to disassemble polyubiquitin chains linked to the protein substrate, following or during the degradative process. A “proofreading” function has been proposed for hydrolases to release free protein from “incorrectly” ubiquitinated proteins. Another possibility is that ubiquitin C-terminal hydrolases are required for trimming polyubitin chains.

Hydrolases are probably required for the processing of biosynthetic precursors of ubiquitin, since most ubiquitin genes are arranged either in linear polyubiquitin arrays or are fused to ribosomal proteins. Yet another hydrolase may be required for the removal of extra amino acid residues that are encoded by certain genes at the C-termini of some polyubiquitin molecules. Ubiquitin C-terminal hydrolases may have other functions as well. High energy El-ubiquitin and E2-ubiquitin thiol esters may react with intracellular nucleophiles (such as glutathione or polyamines). Such reactions may lead to rapid depletion of free ubiquitin unless such side products are rapidly cleaved.

Recognition of Substrates
Short-lived proteins contain a region enriched with Pro, Glu, Ser, and Thr (PEST region). However, it has not been shown that this region indeed serves as a consensus proteolysis targeting signal. An interesting problem involves the evolution of the N-end rule pathway and its physiological roles. Proteins that are derived from processing of polyproteins (Sindbis virus RNA polymerase, for example) may contain destabilizing N-termini and thus are proteolyzed via the N-end rule pathway.

Using a “synthetic lethal” screen, Ota and Varshavsky attempted to isolate a mutant that requires the N-end rule pathway for viability. They characterized an extragenic suppressor of the mutation and found that it encodes a protein with a strong correlation to protein phosphotyrosine phosphatase. The target protein or the connection between dephosphorylation of phosphotyrosine and the N-end rule pathway is still obscure. In an additional study, these researchers have shown that a missense mutation in SLNI, a member of a two-component signal transduction system in yeast, is lethal in the absence, but not in the presence, of the N-end rule pathway. Further studies are required to isolate the target protein and identify the signal transduction pathway.

Two recent studies have shed light on the role of the ubiquitin system and the proteasome in the process. Michalek et al. (1993) have shown that a mutant cell that harbors a thermolabile El cannot present peptides derived from ovalbumin following inactivation of the enzyme. In contrast, presentation of a minigene-expressed antigene peptide or presentation of exogenous similar peptide was not perturbed at the nonpermissive temperature. The important conclusion of the researchers is that the processing of the protein to peptides requires the complete ubiquitin pathway. In a complementary study, Rock et al. (1994) have shown that inhibitors that block the chymotryptic activity of the proteasome also block antigen presentation, most probably by inhibiting proteolysis of the antigen (ovalbumin). Thus, it appears that processing of MHC restricted class I antigens requires both ubiquitination and subsequent degradation by the proteasome. It is likely that the proteasome catalyzes processing of these antigens as part of the 26s protease complex.
Ciechanover A. The Ubiquitin-Proteasome Proteolytic Pathway. Cell 1994; 79:13-21.
Regulation of autophagy
The protein content of the cell is determined by the balance between protein synthesis and protein degradation. At constant intracellular protein concentration, i.e. at steady state, rates of protein synthesis and degradation are equal. Although turnover of protein results in energy dissipation, regulation at the level of protein degradation effectively controls protein levels.
Intracellular proteins to be degraded in the lysosomes can get access to these organelles by the following processes:

  • macroautophagy,
  • microautophagy,
  • crinophagy and selective,
  • chaperonin mediated, direct uptake of proteins.

Overview of the involvement of signal transduction in the regulation of macroautophagic proteolysis by amino acids and cell swelling.

  1. Amino acids (AA) stimulate a protein kinase cascade via a plasma membrane receptor.
  2. Receptor activation results in activation of PtdIns 3-kinase (PI3K), possibly via a heterotrimeric Gái3 protein.
  3. followed by activation of PKC-æ, PKB/Akt, p70S6 kinase (p70S6k) and finally phosphorylation of ribosomal protein S6 (S6P).
  4. The GDP-bound form of Gái3 is required for autophagic sequestration, whereas the GTP-bound form is inhibitory.
  5. The constitutively formed phosphatidylinositol 3-phosphate (PI3P) is also required for autophagic sequestration. Therefore,

inhibition of PtdIns 3-kinase activity by

  • wortmannin (W),
  • LY294002 (LY) or
  • 3-methyladenine (3MA) prevents autophagic sequestration.

Activation of PKC-æ and PKB/Akt is mediated by the 3,4- and 3,4,5-phosphate forms of phosphatidylinositol (PI3,4P2 and PI3,4,5P3) that are produced upon activation of PtdIns 3-kinase.

As a result of this, the first step of the macroautophagic pathway is

  • inhibited by components of the cascade that are downstream of PtdIns 3-kinase.
  • inhibition of this downstream cascade by rapamycin (RAPA) accelerates autophagic sequestration.
  • cell swelling potentiates the effect of amino acids via a change in the receptor owing to membrane stretch.

Furthermore, the site of action of the different effectors of the cytoskeleton (okadaic acid, cytochalasin, nocodazole, vinblastin and colchicine) are indicated.

  • AVi,
  • initial autophagic vacuole;
  • AVd,
  • mature degradative autophagic vacuole,
  • ER, endoplasmic reticulum.

The rate of proteolysis , an important determinant of the intracellular protein content, and part of its degradation occurs in the lysosomes and is mediated by macroautophagy. In liver, macroautophagy is very active and almost completely accounts for starvation-induced proteolysis. Factors inhibiting this process include

  • amino acids,
  • cell swelling and
  • insulin.

In the mechanisms controlling macroautophagy, protein phosphorylation plays an important role.

  • Activation of a signal transduction pathway, ultimately
  • leading to phosphorylation of ribosomal protein S6,
  • accompanies Inhibition of macroautophagy.

Components of this pathway may include

  • a heterotrimeric Gi3-protein,
  • phosphatidylinositol 3-kinase and
  • p70S6 kinase.

Selectivity of Autophagy
It has been assumed for a long time that macroautophagy is a non-selective process, in which macromolecules are randomly degraded in the same ratio as they occur in the cytoplasm . However, recent observations strongly suggest that this may not always be the case, and that macroautophagy can be selective. Lysosomal protein degradation can selectively occur via ubiquitin-dependent and -independent pathways. In the perfused liver, although autophagic breakdown of protein and RNA (mainly ribosomal RNA) is sensitive to inhibition by amino acids and insulin, glucagon accelerates proteolysis but has no effect on RNA degradation.

Another example of selective autophagy is the degradation of superfluous peroxisomes in hepatocytes from clofibrate-treated rats. When hepatocytes from these rats, in which the number of peroxisomes is greatly increased, are incubated in the absence of amino acids to ensure maximal flux through the macroautophagic pathway, peroxisomes are degraded at a relative rate that exceeds that of any other component in the liver cell. The accelerated degradation of peroxisomes was sensitive to inhibition by 3-methyladenine, a specific autophagic sequestration inhibitor. Interestingly, the accelerated removal of peroxisomes was prevented by long-chain but not short-chain fatty acids. Since long-chain fatty acids are substrates for peroxisomal â-oxidation, this indicates that these organelles are removed by autophagy when they are functionally redundant.  Our hypothesis is that acylation (palmitoylation?) of a peroxisomal membrane protein protects the peroxisome against autophagic sequestration.

Under normal conditions macroautophagy may be largely unselective and serves, for example, to produce amino acids for gluconeogenesis and the synthesis of essential proteins in starvation. When cell structures are functionally redundant or when they become damaged, the autophagic system is able to recognize this and is able to degrade the structure concerned. As yet, nothing is known about the recognition signals. A possibility is that ubiquitination of membrane proteins is required to mark the structure to be degraded for autophagic sequestration.

Ubiquitin may be involved in macroautophagy
Ubiquitin not only contributes to extralysosomal proteolysis but is also involved in autophagic protein degradation. Thus, in fibroblasts ubiquitin–protein conjugates can be found in the lysosomes, as shown by immunohistochemistry and immunogold electron microscopy. Free ubiquitin can also be found inside lysosomes. Accumulations of ubiquitin–protein conjugates in filamentous, presumably lysosomal, structures are also found in a large number of neurodegenerative diseases. Mallory bodies in the liver of alcoholics also contain ubiquitin–protein conjugates.

This presence of ubiquitin–protein conjugates in filamentous inclusions in neurons and other cells can be caused by a defect in the extralysosomal ubiquitin-dependent proteolytic pathway. However, it is also possible that these filamentous inclusions represent an attempt of the cell to get rid of unwanted material (proteins, organelles) via autophagy. Direct evidence that ubiquitin may be involved in the control of macroautophagy came from experiments with CHO cells with a temperature-sensitive mutation in the ubiquitin-activating enzyme E1. Wild-type cells increased their rate of proteolysis in response to stress (amino acid depletion, increased temperature). This was prevented by the acidotropic agent ammonia or by the autophagic sequestration inhibitor 3-methyladenine, indicating that the accelerated proteolysis occurred by autophagy. In the mutant cells, there was no such increase in proteolysis in response to stress at the restrictive temperature.

Autophagy and carcinogenesis
In cancer development, cell growth is mainly induced by inhibition of protein degradation, since differences in the rate of protein synthesis between tumorigenic cells and their normal counterparts are rather small. A striking example of how reduced autophagic proteolysis can contribute to cell growth can be found in the development of liver carcinogenesis. This decrease in autophagic flux results from a decrease in the rate of autophagic sequestration and is already detectable in the early preneoplastic stage. Autophagic flux is then hardly inhibitable by amino acids nor is it inducible by catabolic stimuli
and declines in the more advanced stage of cancer development to a rate of less than 20% of that seen in normal hepatocytes. The fact that the addition of 3-methyladenine to hepatocytes from normal rats increased hepatocyte viability to the same level as observed for the tumour cells strongly suggests that the fall in autophagic proteolysis contributes to the rapid growth rate of these cells and gives them a selective advantage over the normal hepatocytes.

Underlying control mechanisms for autophagy are gradually being unravelled. It is perhaps not surprising that protein phosphorylation and signal transduction are key elements in these mechanisms. The discovery of an amino acid receptor in the plasma membrane of the hepatocyte with a signal transduction pathway coupled to it may have important repercussions, not only for the control of macroautophagy but also for the control of other pathways.

It remains to be seen whether the details of the mechanisms controlling the process in yeast are similar to those in mammalian cells. For example, it is not known whether amino acids are able to control the process as they do in mammalian cells.

Blommaart EFC, Luiken JJFP, Meijer AJ. Autophagic proteolysis: control and specificity. Histochemical Journal (1997); 29:365–385.
A Novel Type of Selective Autophagy
Eukaryotic cells use autophagy and the ubiquitin–proteasome system (UPS) as their major protein degradation pathways. Whereas the UPS is required for the rapid degradation of proteins when fast adaptation is needed, autophagy pathways selectively remove protein aggregates and damaged or excess organelles. However, little is known about the targets and mechanisms that provide specificity to this process. Here we show that mature ribosomes are rapidly degraded by autophagy upon nutrient starvation in Saccharomyces cerevisiae. Surprisingly, this degradation not only occurs by a nonselective mechanism, but also involves a novel type of selective autophagy, which we term ‘ribophagy’. A genetic screen revealed that selective degradation of ribosomes requires catalytic activity of the Ubp3p/Bre5p ubiquitin protease. Although Ubp3p and Bre5p cells strongly accumulate 60S ribosomal particles upon starvation, they are proficient in starvation sensing and in general trafficking and autophagy pathways. Moreover, ubiquitination of several ribosomal subunits and/or ribosome associated proteins was specifically enriched in Ubp3p cells, suggesting that the regulation of ribophagy by ubiquitination may be direct. Interestingly, Ubp3p cells are sensitive to rapamycin and nutrient starvation, implying that selective degradation of ribosomes is functionally important in vivo. Taken together, our results suggest a link between ubiquitination and the regulated degradation of mature ribosomes by autophagy.
Kraft C, Deplazes A, Sohrmann M,Peter M. Mature ribosomes are selectively degraded upon starvation by an autophagy pathway requiring the Ubp3p/Bre5p ubiquitin protease. Nature Cell Biology 2008; 10(5): 603-609. DOI: 10.1038/ncb1723.  www.nature.com/naturecellbiology

Mitochondrial Failure and Protein Degradation

Progressive mitochondrial failure is tightly associated with the the development of most age-related human diseases including neurodegenerative diseases, cancer, and type 2 diabetes.

This tight connection results from the double-edged sword of mitochondrial respiration, which is responsible for generating both ATP and ROS, as well as from risks that are inherent to mitochondrial biogenesis. To prevent and treat these diseases, a precise understanding of the mechanisms that maintain functional mitochondria is necessary. Mitochondrial protein quality control is one of the mechanisms that protect mitochondrial integrity, and increasing evidence implicates the cytosolic ubiquitin/proteasome system (UPS) as part of this surveillance network. In this review, we will discuss our current understanding of UPS-dependent mitochondrial protein degradation, its roles in diseases progression, and insights into future studies.

While mitochondria have their own genome, about 99% of the roughly 1000 mitochondrial proteins are encoded in the nuclear genome. Most mitochondrial proteins are therefore

  • synthesized in the cytoplasm,
  • unfolded,
  • transported across one or both mitochondrial membranes,
  • then refolded and/or assembled into complexes (Tatsuta, 2009).

Failure of this complex series of events generates unfolded or misfolded proteins within mitochondria, often disrupting critical functions.

Mitochondrial oxidative phosphorylation generates usable cellular energy in the form of ATP, but also produces reactive oxygen species (ROS) . ROS tend to react quickly, so their predominant sites of damage are mitochondrial macromolecules that are localized nearby the source of ROS production.

Exposure to oxidative stress facilitates misfolding and aggregation of these mitochondrial proteins, leading to disassembly of protein complexes and eventual loss of mitochondrial integrity.

The clearance of misfolded and aggregated proteins is constantly needed to maintain functional mitochondria.
There are several systems promoting this turnover.

  1. Mitophagy, a selective mitochondrial autophagy, mediates a bulk removal of damaged mitochondria.
  2. mitochondria intrinsically contain proteases in each of their compartments and these proteases recognize misfolded mitochondrial proteins and mediate their degradation.

Accumulating evidence shows that the ubiquitin proteasome system (UPS) plays an important role in mitochondrial protein degradation. At various cellular sites, the UPS is involved in protein degradation. With the help of ubiquitin E1–E2–E3 enzyme cascades, target proteins destined for destruction are marked by conjugation of K48-linked poly-ubiquitin chain. This poly-ubiquitinated protein is then targeted to the proteasome for degradation.

Cells treated with proteasome inhibitors exhibit elevated levels of ubiquitinated mitochondrial proteins, suggesting the potentially important roles of the proteasome on mitochondrial protein degradation. Studies have also identified mitochondrial substrates of the UPS.

  • Fzo1, an outer mitochondrial membrane (OMM) protein involved in mitochondrial fusion, is partially dependent on the proteasome for its degradation in yeast.
  • The F box protein Mdm30 mediates ubiquitination of Fzo1 by Skp1-Cullin-F-boxMdm30 ligase, which leads to proteasomal degradation.

The UPS has also been implicated in mitochondrial protein degradation in higher organisms. In mammals,

  • the OMM proteins mitofusin 1 and 2 (Mfn1/2; the mammalian orthologs of Fzo1) and Mcl1 are polyubiquitinated and degraded by the proteasome.
  • VDAC1, Tom20 and Tom70 were also suggested as targets of proteasomal degradation as they are stabilized by proteasome inhibition.
  •  inactivation of the proteasome also induces accumulation of intermembrane space (IMS) proteins and, consistent with this, the proteasome plays a role in degradation of the IMS protein, Endonuclease G.

Turnover of some inner mitochondrial membrane (IMM) proteins is also dependent upon the proteasome. Uncoupling proteins (UCPs) 2 and 3 exhibit an unusually short half-life compared with other IMM proteins, and Brand and colleagues showed that inactivation of the proteasome prevents their turnover in vivo and in a reconstituted in vitro system. Finally, mitochondrial matrix proteins can also be degraded by the proteasome.

Cdc48/p97 is involved in many cellular processes through its role in protein degradation and is targeted to different subcellular sites by adaptor proteins. For example, Cdc48/p97 is recruited to the endoplasmic reticulum with the help of two adaptor proteins, Npl4 and Ufd1. This implies the existence of specific adaptors that recruit Cdc48/p97 to mitochondria. Consistent with this notion, the authors recently identified a mitochondrial adaptor protein for Cdc48, which we named Vms1 (VCP/Cdc48-associated mitochondrial stress responsive 1). Vms1 interacts with Cdc48/p97 and Npl4, but not with Ufd1, which indicates that the Cdc48/p97–Npl4–Ufd1 complex functions in ER protein degradation while the Vms1–Cdc48/p97–Npl4 complex acts in mitochondria. In agreement with this notion, overexpression of Cdc48 or Npl4 rescues the Vms1 mutant phenotype while Ufd1 has no effect.

Normally, Vms1 is cytoplasmic. Upon mitochondrial stress, however, Vms1 recruits Cdc48 and Npl4 to mitochondria. In agreement with the role of Cdc48/p97 in OMM protein degradation, loss of the Vms1 system results in accumulation of ubiquitin-conjugated proteins in purified mitochondria as well as stabilization of Fzo1 under mitochondrial stress conditions. Accumulation of damaged and misfolded mitochondrial proteins disturbs the normal physiology of the mitochondria, leading to mitochondrial dysfunction. As expected, the Vms1 mutants progressively lose mitochondrial respiratory activity, eventually leading to cell death. The VMS1 gene is broadly conserved in eukaryotes, implying an important functional role in a wide range of organisms. The C. elegans Vms1 homolog exhibits a similar pattern of mitochondrial stress responsive translocation and is required for normal lifespan. Additionally, mammalian Vms1 also forms a stable complex with p97. Combining these observations, the authors conclude that Vms1 is a conserved component of the UPS-dependent mitochondrial protein quality control system.

The UPS regulates mitochondrial dynamics and initiation of mitophagy
The UPS regulates mitochondrial dynamics. Major proteins involved in mitochondrial fission or fusion (e.g. Mfn1/2, Drp1 and Fis1) are degraded by the UPS.  MITOL, a mitochondrial E3 ubiquitin ligase, is required for Drp1-dependent mitochondrial fission as depletion or inactivation of MITOL blocks mitochondrial fragmentation. Moreover, knockdown of USP30, an OMM-localized deubiquitinating enzyme, induces an elongated mitochondrial morphology, suggesting a defect in fission. Through this regulatory process, the UPS controls mitochondrial dynamics. Parkin, an E3 ligase involved in mitophagy, utilizes the UPS to enhance mitochondrial fission through degradation of components of the fusion machinery. By facilitating fragmentation of damaged mitochondria, which is essential for initiation of mitophagy, Parkin stimulates mitophagy. The underlying mechanisms linking the UPS to the regulation of mitochondrial dynamics remain unclear.

Accumulation of aberrant proteins and human diseases
In neurodegenerative diseases wherein aberrant pathological proteins accumulate throughout the cell, including sites in mitochondria. Amyloid precursor protein (APP), a protein associated with Alzheimer’s disease, accumulates within mitochondria and is implicated in blockade of mitochondrial protein import. A, a neurotoxic APP cleavage product, can also facilitate the formation of the mitochondrial permeability transition pore (mPTP) by binding to mPTP components VDAC1, CypD and ANT, which provokes cell death.
-Synuclein, a protein associated with the development of Parkinson’s disease, is targeted to the IMM where it binds to the mitochondrial respiratory complex I and impairs its function. -Synuclein interferes with mitochondrial dynamics as its unique interaction with the mitochondrial membrane disturbs the fusion process. Finally, in Huntington’s disease, increased association of the mutant huntingtin protein with mitochondria can impair mitochondrial trafficking. Moreover, accumulation of mutant huntingtin protein disrupts cristae structure and it facilitates mitochondrial fragmentation by activation of Drp1. These examples demonstrate the crucial importance of prompt removal of dysfunctional and/or aberrant proteins in maintaining functional mitochondria.

UPS-mediated mitochondrial protein degradation.
Misfolded and/or damaged mitochondrial proteins destined for proteasomal degradation in the cytosol are recruited to the outer mitochondrial membrane (OMM) from each mitochondrial compartment by unknown mechanisms. Upon reaching the OMM, these proteins are presented to the proteasome through a series of events. They are K48 polyubiquitinated by the cytoplasmic (e.g. Parkin) or mitochondrial ubiquitin E3 ligases. For proteasomal degradation, polyubiquitinated mitochondrial substrate proteins need to be retrotranslocated to the cytoplasm, probably, either by the proteasome per se or by the help of UPS components such as Vms1, Cdc48/p97 and Npl4. Following dislocation to the cytoplasm, these substrate proteins are degraded by the proteasome.

Treatment of diseases that arise from defects in protein quality control will depend on greater depth in our understanding of this process, which could contribute to the development of novel therapeutic approaches. For instance, both mutant SOD1, a misfolded mitochondrial protein associated with the onset of amyotrophic lateral sclerosis, and polyglutamine expanded ataxin-3, a pathogenic protein causing Machado-Joseph disease, are ubiquitinated by MITOL and then degraded by the proteasome. Facilitating the proteasomal degradation of these aberrant proteins might therefore efficiently control diseases progression and, eventually, cure the diseases. Answering these questions would partially unveil the mysterious physiology of mitochondria, which, in turn, would facilitate the development of therapeutics to prevent and cure devastating human diseases.

Heo JM, Rutter J. Ubiquitin-dependent mitochondrial protein degradation. The International Journal of Biochemistry & Cell Biology 2011; 43:1422– 1426. http://www.elsevier.com/locate/biocel
UPS Inhibitors and Apoptotic Machinery
Over the past decade, the promising results of UPSIs (UPS inhibitors) in eliciting apoptosis in various cancer cells, and the approval of the first UPSI (Bortezomib/Velcade/PS-341) for the treatment of multiple myeloma have raised interest in assessing the death program activated upon proteasomal blockage. Several reports indicate that UPSIs stimulate apoptosis in malignant cells by operating at multiple levels, possibly by inducing different types of cellular stress. Normally cellular stress signals converge on the core elements of the apoptotic machinery to trigger the cellular demise. In addition to eliciting multiple stresses, UPSIs can directly operate on the core elements of the apoptotic machinery to control their abundance. Alterations in the relative levels of anti and pro-apoptotic factors can render cancer cells more prone to die in response to other anti-cancer treatments. Aim of the present review is to discuss those core elements of the apoptotic machinery that are under the control of the UPS.

The UPS (Ubquitin-Proteasome System)
To fulfill the protein-degradation process two branches, operating at different levels, principally comprise the UPS.

  • The first branch is formed by the enzymatic activities responsible for delivering the substrate to the degradative machinery: the targeting branch.
  • The second branch is represented by the proteolytic machinery, which ultimately fragments the protein substrate into small oligopeptides.

Oligopeptides are further digested to single amino acids by cytosolic proteases.
It is important to remember that conjugation of ubiquitin to a specific protein is not sufficient to determine its degradation. In fact, mono-ubiquitination or poly-monoubiquitination and in certain cases also poly-ubiquitination of proteins are post-translational modifications related to various cellular functions including DNA repair or membrane trafficking . To deliver polypeptides for proteasomal degradation poly-ubiquitin chains of more than 4 ubiquitins must be assembled through lysine-48 linkages.

There are 3 catalytic sites for each polyubiquitin chain. These sites show specific requirements in terms of substrate specificities and catalytic activities, and they are identified as

  1. trypsin-like, which prefer to cleave after hydrophobic bonds, chymotrypsin-like, which cleave at basic residues and
  2. postglutamyl peptide hydrolase-like or
  3. caspase-like activities, which cut after acidic amino acid.

Each proteasome active site uses the side chain hydroxyl group of an NH2-terminal threonine as the catalytic nucleophile, a mechanism that distinguishes the proteasome from other cellular proteases. The presence of substrate proteolysis small size peptides ranging from 3 to 22 residues are generated. Alternative catalytic sites guarantees the efficient processing of several different substrates.

UPS Inhibitors
By UPS inhibitors (UPSI) we mean small molecules that share the ability to target and inhibit specific activities of the UPS, causing the accumulation of poly-ubiquitinated proteosomal substrates. UPSIs are heterogeneous compounds and among them bortezomib is the only one used in clinical practice.

PR-171, a modified peptide related to the natural product epoxomicin, is composed of two key elements:

  1. a peptide portion that selectively binds with high affinity in the substrate binding pocket(s) of the proteasome and
  2. an epoxyketone pharmacophore that stereospecifically interacts with the catalytic threonine residue and irreversibly inhibits enzyme activity.

In comparison to bortezomib, PR-171 exhibits equal potency, but greater selectivity, for the chymotrypsin-like activity of the proteasome. In cell culture PR-171 is more cytotoxic than bortezomib. In mice PR-171 is well tolerated and shows stronger anti-tumor activity when compared with bortezomib . Clinical studies are in progress to test the safety of PR-171 at different dose levels on some hematological cancers.

Cell Death by UPSI
In vitro experiments have unambiguously established that incubation of neoplastic cells with UPSIs including bortezomib triggers their death. Apoptosis or type I cell death relies on the timed activation of caspases, a group of cysteine proteases, which cleave selected cellular substrates after aspartic residues. Two main apoptotic pathways keep in check caspase activation.

The turnover of a large number of cellular proteins is under the control of the UPS. Thus in principle any proteosomal substrate could contribute directly or indirectly to the cell death phenotype. This is perfectly exemplified by two master regulators of cell life and death, p53 and NFkB.  UPSIs cause

  • NF-kB inhibition through reduced IkB degradation and,
  • in opposition; they promote stabilization and accumulation of p53.

c-FLIP is the most important element of the extrinsic pathway under the direct control of the UPS. Two different FLIP isoforms exist:

  1. c-FLIPL (Long) and
  2. c-FLIPS (Short).

c-FLIPL is highly homologus to caspase-8 and contains two tandem repeat Death Effector Domains (DED) and a catalytically inactive caspase-like domain. Both FLIPs can be degraded by the UPS; however they display distinct half-lives and the unique C terminus of c-FLIPS possesses a destabilizing function. The regulation of c-FLIP levels in response to UPSIs is rather controversial. Some reports indicate that UPSIs can reduce c-FLIP levels and in this manner synergize with TRAIL to promote apoptosis.

UPSIs activate multiple cellular responses and different stress signals that ultimately cause cell death. For this reason they represent broad inducers of apoptosis. In addition, since many of the available UPSIs alter the proteolytic activity of the proteasome, they represent non-specific modulators of the expression/activity of various components of the apoptotic machinery. Paradoxically they can simultaneously favor the accumulation of pro- and anti-apoptotic factors.
Brancolini C. Inhibitors of the Ubiquitin-Proteasome System and the Cell Death Machinery: How Many Pathways are Activated? Current Molecular Pharmacology, 2008; 1:24-37.

Mitochondrial Quality Control
The PINK1–Parkin pathway plays a critical role in mitochondrial quality control by selectively targeting damaged mitochondria for autophagy. The AAA-type ATPase p97 acts downstream of PINK1 and Parkin to segregate fusion-incompetent mitochondria for turnover. [Tanaka et al. (2010. J. Cell Biol. doi: 10.1083/jcb.201007013)]. p97 acts by targeting the mitochondrial fusion-promoting factor mitofusin for degradation through an endoplasmic reticulum–associated degradation (ERAD)-like mechanism.

Pallanck LJ. Culling sick mitochondria from the herd. J Cell Biol 2012;191(7):1225–1227. http://www.jcb.org/cgi/doi/10.1083/jcb.201011068

PINK1 and Parkin and Parkinson’s Disease

Studies of the familial Parkinson disease-related proteins PINK1 and Parkin have demonstrated that these factors promote the fragmentation and turnover of mitochondria following treatment of cultured cells with mitochondrial depolarizing agents. Whether PINK1 or Parkin influence mitochondrial quality control under normal physiological conditions in dopaminergic neurons, a principal cell type that degenerates in Parkinson disease, remains unclear. To address this matter, we developed a method to purify and characterize neural subtypes of interest from the adult Drosophila brain.

Using this method, we find that dopaminergic neurons from Drosophila parkin mutants accumulate enlarged, depolarized mitochondria, and that genetic perturbations that promote mitochondrial fragmentation and turnover rescue the mitochondrial depolarization and neurodegenerative phenotypes of parkin mutants. In contrast, cholinergic neurons from parkin mutants accumulate enlarged depolarized mitochondria to a lesser extent than dopaminergic neurons, suggesting that a higher rate of mitochondrial damage, or a deficiency in alternative mechanisms to repair or eliminate damaged mitochondria explains the selective vulnerability of dopaminergic neurons in Parkinson disease.

Our study validates key tenets of the model that PINK1 and Parkin promote the fragmentation and turnover of depolarized mitochondria in dopaminergic neurons. Moreover, our neural purification method provides a foundation to further explore the pathogenesis of Parkinson disease, and to address other neurobiological questions requiring the analysis of defined neural cell types.

Burmana JL, Yua S, Poole AC, Decala RB , Pallanck L. Analysis of neural subtypes reveals selective mitochondrial dysfunction in dopaminergic neurons from parkin mutants.

Autophagy in Parkinson’s Disease.
Parkinson’s disease is a common neurodegenerative disease in the elderly. To explore the specific role of autophagy and the ubiquitin-proteasome pathway in apoptosis, a specific proteasome inhibitor and macroautophagy inhibitor and stimulator were selected to investigate pheochromocytoma (PC12) cell lines transfected with human mutant (A30P) and wildtype (WT) -synuclein.

The apoptosis ratio was assessed by flow cytometry. LC3, heat shock protein 70 (hsp70) and caspase-3 expression in cell culture were determined by Western blot. The hallmarks of apoptosis and autophagy were assessed with transmission electron microscopy. Compared to the control group or the rapamycin (autophagy stimulator) group, the apoptosis ratio in A30P and WT cells was significantly higher after treatment with inhibitors of the proteasome and macroautophagy. The results of Western blots for caspase-3 expression were similar to those of flow cytometry; hsp70 protein was significantly higher in the proteasome inhibitor group than in control, but in the autophagy inhibitor and stimulator groups, hsp70 was similar to control. These findings show that inhibition of the proteasome and autophagy promotes apoptosis, and the macroautophagy stimulator rapamycin reduces the apoptosis ratio. And inhibiting or stimulating autophagy has less impact on hsp70 than the proteasome pathway.

In conclusion, either stimulation or inhibition of macroautophagy, has less impact on hsp70 than on the proteasome pathway. This study found that rapamycin decreased apoptotic cells in A30P cells independent of caspase-3 activity. Although several lines of evidence recently demonstrated crosstalk between autophagy and caspase-independent apoptosis, we could not confirm that autophagy activation protects cells from caspase-independent cell death. Undoubtedly, there are multiple connections between the apoptotic and autophagic processes.

Inhibition of autophagy may subvert the capacity of cells to remove damaged organelles or to remove misfolded proteins, which would favor apoptosis. However, proteasome inhibition activated macroautophagy and accelerated apoptosis. A likely explanation is inhibition of the proteasome favors oxidative reactions that trigger apoptosis, presumably through

1. a direct effect on mitochondria, and
2. the absence of NADPH2 and ATP

which may deinhibit the activation of caspase-2 or MOMP. Another possibility is that aggregated proteins induced by proteasome inhibition increase apoptosis.

Yang F, Yanga YP, Maoa CJ, Caoa BY, et al. Role of autophagy and proteasome degradation pathways in apoptosis of PC12 cells overexpressing human -synuclein. Neuroscience Letters 2009; 454:203–208. doi:10.1016/j.neulet.2009.03.027. http://www.elsevier.com/locate/neulet

Parkin-dependent Ubiquitination of Endogenous Bax 

Autosomal recessive loss-of-function mutations within the PARK2 gene functionally inactivate the E3 ubiquitin ligase parkin, resulting in neurodegeneration of catecholaminergic neurons and a familial form of Parkinson disease. Current evidence suggests both a mitochondrial function for parkin and a neuroprotective role, which may in fact be interrelated. The antiapoptotic effects of Parkin have been widely reported, and may involve fundamental changes in the threshold for apoptotic cytochrome c release, but the substrate(s) involved in Parkin dependent protection had not been identified. Here, we demonstrate the Parkin-dependent ubiquitination of endogenous Bax comparing primary cultured neurons from WT and Parkin KO mice and using multiple Parkin-overexpressing cell culture systems. The direct ubiquitination of purified Bax was also observed in vitro following incubation with recombinant parkin. The authors found that Parkin prevented basal and apoptotic stress induced translocation of Bax to the mitochondria. Moreover, an engineered ubiquitination-resistant form of Bax retained its apoptotic function, but Bax KO cells complemented with lysine-mutant Bax did not manifest the antiapoptotic effects of Parkin that were observed in cells expressing WT Bax. These data suggest that Bax is the primary substrate responsible for the antiapoptotic effects of Parkin, and provide mechanistic insight into at least a subset of the mitochondrial effects of Parkin.

Johnson BN, Berger AK, Cortese GP, and LaVoie MJ. The ubiquitin E3 ligase Parkin regulates the proapoptotic function of Bax. PNAS 2012, pp 6. http://www.pnas.org/cgi/doi/10.1073/pnas.1113248109
Parkin Promotes Mitochondrial Loss in Autophagy
Parkin, an E3 ubiquitin ligase implicated in Parkinson’s disease, promotes degradation of dysfunctional mitochondria by autophagy. Using proteomic and cellular approaches, we show that upon translocation to mitochondria, Parkin activates the ubiquitin–proteasome system (UPS) for widespread degradation of outer membrane proteins. This is evidenced by an increase in K48-linked polyubiquitin on mitochondria, recruitment of the 26S proteasome and rapid degradation of multiple outer membrane proteins. The degradation of proteins by the UPS occurs independently of the autophagy pathway, and inhibition of the 26S proteasome completely abrogates Parkin-mediated mitophagy in HeLa, SH-SY5Y and mouse cells. Although the mitofusins Mfn1 and Mfn2 are rapid degradation targets of Parkin, degradation of additional targets is essential for mitophagy. These results indicate that remodeling of the mitochondrial outer membrane proteome is important for mitophagy, and reveal a causal link between the UPS and autophagy, the major pathways for degradation of intracellular substrates.

Chan NC, Salazar AM, Pham AH, Sweredoski MJ, et al. Broad activation of the ubiquitin–proteasome system by Parkin is critical for mitophagy. Human Molecular Genetics 2011; 20(9): 1726–1737. doi:10.1093/hmg/ddr048.

TRAP1 and TBP7 Interaction in Refolding of Damaged Proteins
TRAP1 is a mitochondrial antiapoptotic heat shock protein. The information available on the TRAP1 pathway describes just a few well-characterized functions of this protein in mitochondria. However, our group’s use of mass spectrometry analysis identified TBP7, an AAA-ATPase of the 19S proteasomal subunit, as a putative TRAP1-interacting protein. Surprisingly, TRAP1 and TBP7 co-localize in the endoplasmic reticulum (ER), as demonstrated by biochemical and confocal/electron microscopy analyses, and directly interact, as confirmed by FRET analysis. This is the first demonstration of TRAP1 presence in this cellular compartment. TRAP1 silencing by shRNAs, in cells exposed to thapsigargin-induced ER stress, correlates with up-regulation of BiP/Grp78, thus suggesting a role of TRAP1 in the refolding of damaged proteins and in ER stress protection. Consistently, TRAP1 and/or TBP7 interference enhanced stress-induced cell death and increased intracellular protein ubiquitination. These experiments led us to hypothesize an involvement of TRAP1 in protein quality control for mistargeted/misfolded mitochondria-destined proteins, through interaction with the regulatory proteasome protein TBP7. Remarkably, the expression of specific mitochondrial proteins decreased upon TRAP1 interference as a consequence of increased ubiquitination. The proposed TRAP1 network has an impact in vivo, since it is conserved in human colorectal cancers, is controlled by ER-localized TRAP1 interacting with TBP7 and provides a novel model of ER-mitochondria crosstalk.

Amoroso MR, Matassa DS, Laudiero G, Egorova AV. TRAP1 AND THE PROTEASOME REGULATORY PARTICLE TBP7/Rpt3 INTERACT IN THE ENDOPLASMIC RETICULUM AND CONTROL CELLULAR UBIQUITINATION OF SPECIFIC MITOCHONDRIAL PROTEINS. Cell Death and Differentiation 2012; pp? DOI : 10.1038/cdd.2011.128

VMS1 and Mitochondrial Protein Degradation
We show that Ydr049 (renamed VCP/Cdc48-associated mitochondrial stress-responsive—Vms1), a member of an unstudied pan-eukaryotic protein family, translocates from the cytosol to mitochondria upon mitochondrial stress. Cells lacking Vms1 show progressive mitochondrial failure, hypersensitivity to oxidative stress, and decreased chronological life span. Both yeast and mammalian Vms1 stably interact with Cdc48/VCP/p97, a component of the ubiquitin/proteasome system with a well-defined role in endoplasmic reticulum-associated protein degradation (ERAD), wherein misfolded ER proteins are degraded in the cytosol. We show that oxidative stress triggers mitochondrial localization of Cdc48 and this is dependent on Vms1. When this system is impaired by mutation of Vms1,

  • ubiquitin-dependent mitochondrial protein degradation,
  • mitochondrial respiratory function,and
  • cell viability are compromised.

We demonstrate that Vms1 is a required component of an evolutionarily conserved system for mitochondrial protein degradation, which is
necessary to maintain

  • mitochondrial,
  • cellular, and
  • organismal viability.

Heo JM, Livnat-Levanon N, Taylor EB, Jones KT. A Stress-Responsive System
for Mitochondrial Protein Degradation. Molecular Cell 2010; 40:465–480.
DOI 10.1016/j.molcel.2010.10.021

Mitochondrial Protein Degradation
The biogenesis of mitochondria and the maintenance of mitochondrial functions depends on an autonomous proteolytic system in the organelle which is highly conserved throughout evolution. Components of this system include processing

  • peptidases and
  • ATP-dependent proteases, as well as
  • molecular chaperone proteins and
  • protein complexes with apparently regulatory functions.

While processing peptidases mediate maturation of nuclear-encoded mitochondrial preproteins, quality control within various subcompartments of mitochondria is ensured by ATP-dependent proteases which selectively remove non-assembled or misfolded polypeptides. Moreover, these proteases appear to control the activity- or steady-state levels of specific regulatory proteins and thereby ensure mitochondrial genome integrity, gene expression and protein assembly.

Kaser M and Langer T. Protein degradation in mitochondria. CELL & DEVELOPMENTAL BIOLOGY 2000; 11:181–190. doi: 10.1006/10.1006/scdb.2000.0166.

RING finger E3s

Ubiquitin-ligases or E3s are components of the ubiquitin proteasome system (UPS) that coordinate the transfer of ubiquitin to the target protein. A major class of ubiquitin-ligases consists of RING-finger domain proteins that include the substrate recognition sequences in the same polypeptide; these are known as single-subunit RING finger E3s. We are studying a particular family of RING finger E3s, named ATL, that contain a transmembrane domain and the RING-H2 finger domain; none of the member of the family contains any other previously described domain. Although the study of a few members in A. thaliana and O. sativa has been reported, the role of this family in the life cycle of a plant is still vague.

To provide tools to advance on the functional analysis of this family we have undertaken a phylogenetic analysis of ATLs in twenty-four plant genomes. ATLs were found in all the 24 plant species analyzed, in numbers ranging from 20–28 in two basal species to 162 in soybean. Analysis of ATLs arrayed in tandem indicates that sets of genes are expanding in a species-specific manner. To
get insights into the domain architecture of ATLs we generated 75 pHMM LOGOs from 1815 ATLs, and unraveled potential protein-protein interaction regions by means of yeast two-hybrid assays. Several ATLs were found to interact with DSK2a/ubiquilin through a region at the amino-terminal end, suggesting that this is a widespread interaction that may assist in the mode of action of ATLs; the region was traced to a distinct sequence LOGO. Our analysis provides significant observations on the evolution and expansion of the ATL family in addition to information on the domain structure of this class of ubiquitin-ligases that may be involved in plant adaptation to environmental stress.

Aguilar-Hernandez V, Aguilar-Henonin L, Guzman P. Diversity in the Architecture of ATLs, a Family of Plant Ubiquitin-Ligases, Leads to Recognition and Targeting of Substrates in Different Cellular Environments. PLoS ONE 2011; 6(8): e23934. doi:10.1371/journal.pone.0023934
UPS Proteolytic Function Inadequate in Proteinopathies
Proteinopathies are a family of human disease caused by toxic aggregation-prone proteins and featured by the presence of protein aggregates in the affected cells. The ubiquitin-proteasome system (UPS) and autophagy are two major intracellular protein degradation pathways. The UPS mediates the targeted degradation of most normal proteins after performing their normal functions as well as the removal of abnormal, soluble proteins. Autophagy is mainly responsible for degradation of defective organelles and the bulk degradation of cytoplasm during starvation. The collaboration between the UPS and autophagy appears to be essential to protein quality control in the cell.

UPS proteolytic function often becomes inadequate in proteinopathies which may lead to activation of autophagy, striving to remove abnormal proteins especially the aggregated forms. HADC6, p62, and FoxO3 may play an important role in mobilizing this proteolytic consortium. Benign measures to enhance proteasome function are currently lacking; however, enhancement of autophagy via pharmacological intervention and/or lifestyle change has shown great promise in alleviating bona fide proteinopathies in the cell and animal models. These pharmacological interventions are expected to be applied clinically to treat human proteinopathies in the near future.

Zheng Q, Li J, Wang X. Interplay between the ubiquitin-proteasome system and
autophagy in proteinopathies. Int J Physiol Pathophysiol Pharmacol 2009;1:127-142. http://www.ijppp.org/IJPPP904002

Ubiquitin-associated Protein-Protein Interactions

Applicability of in vitro biotinylated ubiquitin for evaluation of endogenous ubiquitin conjugation and analysis of ubiquitin-associated protein-protein interactions has been investigated. Incubation of rat brain mitochondria with biotinylated ubiquitin followed by affinity chromatography on avidin-agarose, intensive washing, tryptic digestion of proteins bound to the affinity sorbent and their mass spectrometry analysis resulted in reliable identification of 50 proteins belonging to mitochondrial and extramitochondrial compartments. Since all these proteins were bound to avidin-agarose only after preincubation of the mitochondrial fraction with biotinylated ubiquitin, they could therefore be referred to as specifically bound proteins. A search for specific
ubiquitination signature masses revealed several extramitochondrial and intramitochondrial ubiquitinated proteins representing about 20% of total number of proteins bound to avidin-agarose. The interactome analysis suggests that the identified non-ubiquitinated proteins obviously form tight complexes either with ubiquitinated proteins or with their partners and/or mitochondrial membrane components. Results of the present study demonstrate that the use of biotinylated ubiquitin may be considered as the method of choice for in vitro evaluation of endogenous ubiquitin-conjugating machinery in particular
subcellular organelles and changes in ubiquitin/organelle associated interactomes. This may be useful for evaluation of changes in interactomes induced by protein ubiquitination.

Buneeva OA, Medvedeva MV, Kopylov AT, Zgoda VG, Medvedev AE. Use of Biotinylated Ubiquitin for Analysis of Rat Brain Mitochondrial Proteome and Interactome. Int J Mol Sci 2012; 13: 11593-11609; doi:10.3390/ijms130911593
IL-6 regulation on mitochondrial remodeling/dysfunction

Muscle protein turnover regulation during cancer cachexia is being rapidly defined, and skeletal muscle mitochondria function appears coupled to processes regulating muscle wasting. Skeletal muscle oxidative capacity and the expression of proteins regulating mitochondrial biogenesis and dynamics are disrupted in severely cachectic ApcMin/+ mice. It has not been determined if these changes occur at the onset of cachexia and are necessary for the progression of muscle wasting. Exercise and anti-cytokine therapies have proven effective in preventing cachexia development in tumor bearing mice, while their effect on mitochondrial content, biogenesis and dynamics is not well understood.

The purposes of this study were to

1) determine IL-6 regulation on mitochondrial remodeling/dysfunction during the progression of cancer cachexia and
2) to determine if exercise training can attenuate mitochondrial dysfunction and the induction of proteolytic pathways during IL-6 induced cancer cachexia.

ApcMin/+ mice were examined during the progression of cachexia, after systemic interleukin (IL)-6r antibody treatment, or after IL-6 over-expression with or without exercise. Direct effects of IL-6 on mitochondrial remodeling were examined in cultured C2C12 myoblasts.

Mitochondrial content was not reduced during the initial development of cachexia, while muscle PGC-1α and fusion (Mfn1, Mfn2) protein expression was repressed.

With progressive weight loss mitochondrial content decreased, PGC-1α and fusion proteins were further suppressed, and fission protein (FIS1) was induced.

IL-6 receptor antibody administration after the onset of cachexia

  • improved mitochondrial content,
  • PGC-1α,
  • Mfn1/Mfn2 and
  • FIS1 protein expression.

IL-6 over-expression in pre-cachectic mice

  • accelerated body weight loss and muscle wasting, without reducing mitochondrial content,
  • while PGC-1α and Mfn1/Mfn2 protein expression was suppressed
  • and FIS1 protein expression induced.

Exercise normalized these IL-6 induced effects. C2C12 myotubes administered IL-6 had

  • increased FIS1 protein expression,
  • increased oxidative stress, and
  • reduced PGC-1α gene expression
  • without altered mitochondrial protein expression.

Altered expression of proteins regulating mitochondrial biogenesis and fusion are early events in the initiation of cachexia regulated by IL-6, which precede the loss of muscle mitochondrial content. Furthermore, IL-6 induced mitochondrial remodeling and proteolysis can be rescued with moderate exercise training even in the presence of high circulating IL-6 levels.

White JP, Puppa MJ, Sato S, Gao S. IL-6 regulation on skeletal muscle mitochondrial remodeling during cancer cachexia in the ApcMin/+ mouse. Skeletal Muscle 2012; 2:14-30.
http://www.skeletalmusclejournal.com/content/2/1/14

Starvation-induced Autophagy
Upon starvation cells undergo autophagy, a cellular degradation pathway important in the turnover of whole organelles and long lived proteins. Starvation-induced protein degradation has been regarded as an unspecific bulk degradation process. We studied global protein dynamics during amino acid starvation-induced autophagy by quantitative mass spectrometry and were able to record nearly 1500 protein profiles during 36 h of starvation. Cluster analysis of the recorded protein profiles revealed that cytosolic proteins were degraded rapidly, whereas proteins annotated to various complexes and organelles were degraded later at different time periods. Inhibition of protein degradation pathways identified the lysosomal/autophagosomal system as the main degradative route.

Thus, starvation induces degradation via autophagy, which appears to be selective and to degrade proteins in an ordered fashion and not completely arbitrarily as anticipated so far.

Kristensen AR, Schandorff S, Høyer-Hansen M, Nielsen MO, et al. Ordered Organelle Degradation during Starvation-induced Autophagy. Molecular & Cellular Proteomics 2008; 7:2419–2428.

Skeletal Muscle Macroautophagy
Skeletal muscles are the agent of motion and one of the most important tissues responsible for the control of metabolism. Coordinated movements are allowed by the highly organized structure of the cytosol of muscle fibers (or myofibers), the multinucleated and highly specialized cells of skeletal muscles involved in contraction. Contractile proteins are assembled into repetitive structures, the basal unit of which is the sarcomere, that are well packed into the myofiber cytosol. Myonuclei are located at the edge of the myofibers, whereas the various organelles such as mitochondria and sarcoplasmic reticulum are embedded among the myofibrils. Many different changes take place in the cytosol of myofibers during catabolic conditions:

  • proteins are mobilized
  • organelles networks are reorganized for energy needs
  • the setting of myonuclei can be modified.

Further,

  • strenuous physical activity,
  • improper dietary regimens and
  • aging

lead to mechanical and metabolic damages of myofiber organelles, especially mitochondria, and contractile proteins. During aging the protein turnover is slowed down, therefore it is easier to accumulate aggregates of dysfunctional proteins. Therefore, a highly dynamic tissue such as skeletal muscle requires a rapid and efficient system for the removal of altered organelles, the elimination of protein aggregates, and the disposal of toxic products.

The two major proteolytic systems in muscle are the ubiquitin-proteasome and the autophagy-lysosome pathways. The proteasome system requires

  • the transcription of the two ubiquitin ligases (atrogin-1 and MuRF1) and
  • the ubiquitination of the substrates.

Therefore, the ubiquitin-proteasome system can provide the rapid elimination of single proteins or small aggregates. Conversely, the autophagic system is able to degrade entire organelles and large proteins aggregates. In the autophagy-lysosome system, double-membrane vesicles named autophagosomes are able to engulf a portion of the cytosol and fuse with lysosomes, where their content is completely degraded by lytic enzymes.

The autophagy flux can be biochemicaly monitored following LC3 lipidation and p62 degradation. LC3 is the mammalian homolog of the yeast Atg8 gene, which is lipidated when recruited for the double-membrane commitment and growth. p62 (SQSTM-1) is a polyubiquitin-binding protein involved in the proteasome system and that can either reside free in the cytosol and nucleus or occur within autophagosomes and lysosomes. The GFP-LC3 transgenic mouse model allows easy detection of autophagosomes by simply monitoring the presence of bright GFP-positive puncta inside the myofibrils and beneath the plasma membrane of the myofibers, thus investigate the activation of autophagy in skeletal muscles with different contents of slow and fast-twitching myofibers and in response to stimuli such as fasting. For example, in the fast-twiching extensor digitorum longus muscle few GFP-LC3 dots were observed before starvation, while many small GFP-LC3 puncta appeared between myofibrils and in the perinuclear regions after 24 h starvation. Conversely, in the slow-twitching soleus muscle, autophagic puncta were almost absent in standard condition and scarcely induced after 24 h starvation.
Autophagy in Muscle Homeostasis
The autophagic flux was found to be increased during certain catabolic conditions, such as fasting, atrophy , and denervation , thus contributing to protein breakdown. Food deprivation is one of the strongest stimuli known to induce autophagy in muscle. Indeed skeletal muscle, after the liver, is the most responsive tissue to autophagy activation during food deprivation. Since muscles are the biggest reserve of amino acids in the body, during fasting autophagy has the vital role to maintain the amino acid pool by digesting muscular protein and organelles. In mammalian cells, mTORC1, which consists of

  • mTOR and
  • Raptor,

is the nutrient sensor that negatively regulates autophagy.

During atrophy, protein breakdown is mediated by atrogenes, which are under the forkhead box O (FoxO) transcription factors control, and activation of autophagy seems to aggravate muscle loss during atrophy. In vivo and in vitro studies demonstrated that several genes coding for components of the autophagic machinery, such as

  • LC3,
  • GABARAP,
  • Vps34,
  • Atg12 and
  • Bnip3,

are controlled by FoxO3 transcription factor. FoxO3 is able to regulate independently the ubiquitin-proteasome system and the autophagy-lysosome machinery in vivo and in vitro. Denervation is also able to induce autophagy in skeletal muscle, although at a slower rate than fasting. This effect is mediated by RUNX1, a transcription factor upregulated during autophagy; the lack of RUNX1 results in excessive autophagic flux in denervated muscle and leads to atrophy. The generation of Atg5 and Atg7 muscle-specific knockout mice have shown that with suppression of autophagy both models display muscle weakness and atrophy and a significant reduction of weight, which is correlated with the important loss of muscle tissue due to an atrophic condition. An unbalanced autophagy flux is highly detrimental for muscle, as too much induces atrophy whereas too little leads to muscle weakness and degeneration. Muscle wasting associated with autophagy inhibition becomes evident and symptomatic only after a number of altered proteins and dysfunctional organelles are accumulated, a condition that becomes evident after months or even years. On the other hand, the excessive increase of autophagy flux is able to induce a rapid loss of muscle mass (within days or weeks).
Alterations of autophagy are involved in the pathogenesis of several myopathies and dystrophies.

The maintenance of muscle homeostasis is finely regulated by the balance between catabolic and anabolic process. Macroautophagy (or autophagy) is a catabolic process that provides the degradation of protein aggregation and damaged organelles through the fusion between autophagosomes and lysosomes. Proper regulation of the autophagy flux is fundamental for the homeostasis of skeletal muscles during physiological situations and in response to stress. Defective as well as excessive autophagy is harmful for muscle health and has a pathogenic role in several forms of muscle diseases.
Grumati P, Bonaldo P. Autophagy in Skeletal Muscle Homeostasis and in Muscular Dystrophies. Cells 2012, 1, 325-345; doi:10.3390/cells1030325. ISSN 2073-4409. http://www.mdpi.com/journal/cells

Parkinson’s Disease Mutations
Mutations in parkin, a ubiquitin ligase, cause early-onset familial Parkinson’s disease (AR-JP). How Parkin suppresses Parkinsonism remains unknown. Parkin was recently shown to promote the clearance of impaired mitochondria by autophagy, termed mitophagy. Here, we show that Parkin promotes mitophagy by catalyzing mitochondrial ubiquitination, which in turn recruits ubiquitin-binding autophagic components, HDAC6 and p62, leading to mitochondrial clearance.

During the process, juxtanuclear mitochondrial aggregates resembling a protein aggregate-induced aggresome are formed. The formation of these “mito-aggresome” structures requires microtubule motor-dependent transport and is essential for efficient mitophagy. Importantly, we show that AR-JP–causing Parkin mutations are defective in supporting mitophagy due to distinct defects at

  • recognition,
  • transportation, or
  • ubiquitination of impaired mitochondria,

thereby implicating mitophagy defects in the development of Parkinsonism. Our results show that impaired mitochondria and protein aggregates are processed by common ubiquitin-selective autophagy machinery connected to the aggresomal pathway, thus identifying a mechanistic basis for the prevalence of these toxic entities in Parkinson’s disease.
Lee JY,Nagano Y, Taylor JP,Lim KL, and Yao TP. Disease-causing mutations in Parkin impair mitochondrial ubiquitination, aggregation, and HDAC6-dependent mitophagy. J Cell Biol 2010; 189(4):671-679. http://www.jcb.org/cgi/doi/10.1083/jcb.201001039

Drosophila Parkin Requires PINK1

Loss of the E3 ubiquitin ligase Parkin causes early onset Parkinson’s disease, a neurodegenerative disorder of unknown etiology. Parkin has been linked to multiple cellular processes including

  • protein degradation,
  • mitochondrial homeostasis, and
  • autophagy;

however, its precise role in pathogenesis is unclear. Recent evidence suggests that Parkin is recruited to damaged mitochondria, possibly affecting

  • mitochondrial fission and/or fusion,
  • to mediate their autophagic turnover.

The precise mechanism of recruitment and the ubiquitination target are unclear. Here we show in Drosophila cells that PINK1 is required to recruit Parkin to dysfunctional mitochondria and promote their degradation. Furthermore, PINK1 and Parkin mediate the ubiquitination of the profusion factor Mfn on the outer surface of mitochondria. Loss of Drosophila PINK1 or parkin causes an increase in Mfn abundance in vivo and concomitant elongation of mitochondria. These findings provide a molecular mechanism by which the PINK1/Parkin pathway affects mitochondrial fission/fusion as suggested by previous genetic interaction studies. We hypothesize that Mfn ubiquitination may provide a mechanism by which terminally damaged mitochondria are labeled and sequestered for degradation by autophagy.

Ziviani E, Tao RN, and Whitworth AJ. Drosophila Parkin requires PINK1 for mitochondrial translocation and ubiquitinates Mitofusin. PNAS 2010. Pp6 http://www.pnas.org/cgi/doi/10.1073/pnas.0913485107

Dynamin-related protein 1 (Drp1) in Parkinson’s
Mutations in Parkin, an E3 ubiquitin ligase that regulates protein turnover, represent one of the major causes of familial Parkinson’s disease (PD), a neurodegenerative disorder characterized by the loss of dopaminergic neurons and impaired mitochondrial functions. The underlying mechanism by which pathogenic parkin mutations induce mitochondrial abnormality is not fully understood. Here we demonstrate that Parkin interacts with and subsequently ubiquitinates dynamin-related protein 1 (Drp1), for promoting its proteasome-dependent degradation. Pathogenic mutation or knockdown of Parkin inhibits the ubiquitination and degradation of Drp1, leading to an increased level of Drp1 for mitochondrial fragmentation. These results identify Drp1 as a novel substrate of Parkin and suggest a potential mechanism linking abnormal Parkin expression to mitochondrial dysfunction in the pathogenesis of PD.

Wang H, Song P, Du L, Tian W. Parkin ubiquitinates Drp1 for proteasome-dependent degradation: implication of dysregulated mitochondrial dynamics in Parkinson’s disease.
JBC Papers in Press. Published on February 3, 2011 as Manuscript M110.144238. http://www.jbc.org/cgi/doi/10.1074/jbc.M110.144238

Pink1, Parkin, and DJ-1 Form a Complex
Mutations in the genes PTEN-induced putative kinase 1 (PINK1), PARKIN, and DJ-1 cause autosomal recessive forms of Parkinson disease (PD), and the Pink1/Parkin pathway regulates mitochondrial integrity and function. An important question is whether the proteins encoded by these genes function to regulate activities of other cellular compartments. A study in mice, reported by Xiong et al. in this issue of the JCI, demonstrates that Pink1, Parkin, and DJ-1 can form a complex in the cytoplasm, with Pink1 and DJ-1 promoting the E3 ubiquitin ligase activity of Parkin to degrade substrates via the proteasome (see the related article, doi:10.1172/ JCI37617).

This protein complex in the cytosol may or may not be related to the role of these proteins in regulating mitochondrial function or oxidative stress in vivo.
Three models for the role of the PPD complex. In this issue of the JCI, Xiong et al. report that Pink1, Parkin, and DJ-1 bind to each other and form a PPD E3 ligase complex in which Pink1 and DJ-1 modulate Parkin-dependent ubiquitination and subsequent degradation of substrates via the proteasome. Previous work suggests that the Pink1/Parkin pathway regulates mitochondrial integrity and promotes mitochondrial fission in Drosophila.

(A) Parkin and DJ-1 may be recruited to the mitochondrial outer membrane during stress and interact with Pink1. These interactions may facilitate the ligase activity of Parkin, thereby facilitating the turnover of molecules that regulate mitochondrial dynamics and mitophagy. The PPD complex may have other roles in the cytosol that result in degradative ubiquitination and/or relay information from mitochondria to other cellular compartments.
(B) Alternatively, Pink1 may be released from mitochondria after cleavage to interact with DJ-1 and Parkin in the cytosol.
A and B differ in the site of action of the PPD complex and the cleavage status of Pink1.
The complex forms on the mitochondrial outer membrane potentially containing full-length Pink1 in A, and in the cytosol with cleaved Pink1 in B.
Lack of DJ-1 function results in phenotypes that are distinct from the mitochondrial phenotypes observed in null mutants of Pink1 or Parkin in Drosophila. Thus, although the PPD complex is illustrated here as regulating mitochondrial fission, the role of DJ-1 in vivo remains to be clarified.
(C) It is also possible that the action occurs in the cytosol and is independent of the function of Pink1/Parkin in regulating mitochondrial integrity and function.

The Xiong et al. study offers an entry point for explorations of the role of Pink1, Parkin, and DJ-1 in the cytoplasm. It remains to be shown whether Parkin, in complex with Pink1 and DJ-1, carries out protein degradation in vivo.

Li H, and Guo M. Protein degradation in Parkinson disease revisited: it’s complex. commentaries. J Clin Invest.  doi:10.1172/JCI38619. http://www.jci.org

Xiong, H., et al. Parkin, PINK1, and DJ-1 form a ubiquitin E3 ligase complex promoting unfolded protein degradation. J. Clin. Invest. 2009; 119:650–660.

 Mitochondrial Ubiquitin Ligase, MITOL, protects neuronal cells

Nitric oxide (NO) is implicated in neuronal cell survival. However, excessive NO production mediates neuronal cell death, in part via mitochondrial dysfunction. Here, we report that the mitochondrial ubiquitin ligase, MITOL, protects neuronal cells from mitochondrial damage caused by accumulation of S-nitrosylated microtubule associated protein 1B-light chain 1 (LC1). S-nitrosylation of LC1 induces a conformational change that serves both to activate LC1 and to promote its ubiquination by MITOL, indicating that microtubule
stabilization by LC1 is regulated through its interaction with MITOL. Excessive NO production can inhibit MITOL, and MITOL inhibition resulted in accumulation of S-nitrosylated LC1 following stimulation of NO production by calcimycin and N-methyl-D-aspartate. LC1 accumulation under these conditions resulted in mitochondrial dysfunction and neuronal cell death. Thus, the balance between LC1 activation by S-nitrosylation and down-regulation by MITOL is critical for neuronal cell survival. Our findings may contribute significantly to an understanding of the mechanisms of neurological diseases caused by nitrosative stress-mediated mitochondrial dysfunction.

Yonashiro R, Kimijima Y, Shimura T, Kawaguchi K, et al. Mitochondrial ubiquitin ligase MITOL blocks S-nitrosylated MAP1B-light chain 1-mediated mitochondrial dysfunction and neuronal cell death. PNAS; 2012. pp 6. http://www.pnas.org/cgi/doi/10.1073/pnas.1114985109

Ubiquitin–Proteasome System in Neurodegeneration
A common histopathological hallmark of most neurodegenerative diseases is the presence of aberrant proteinaceous inclusions inside affected neurons. Because these protein aggregates are detected using antibodies against components of the ubiquitin–proteasome system (UPS), impairment of this machinery for regulated proteolysis has been suggested to be at the root of neurodegeneration. This hypothesis has been difficult to prove in vivo owing to the lack of appropriate tools. The recent report of transgenic mice with ubiquitous expression of a UPS-reporter protein should finally make it possible to test in vivo the role of the UPS in neurodegeneration.

Hernandez F, Dıaz-Hernandez M, Avila J and Lucas JJ. Testing the ubiquitin–proteasome hypothesis of neurodegeneration in vivo. TRENDS in Neurosciences 2004; 27(2): 66-68.

ALP in Parkinson’s
The ubiquitin-proteasome system (UPS) and autophagy-lysosome pathway (ALP) are the two most important mechanisms that normally repair or remove abnormal proteins. Alterations in the function of these systems to degrade misfolded and aggregated proteins are being increasingly recognized as playing a pivotal role in the pathogenesis of many neurodegenerative disorders such as Parkinson’s disease. Dysfunction of the UPS has been already strongly implicated in the pathogenesis of this disease and, more recently, growing interest has been shown in identifying the role of ALP in neurodegeneration. Mutations of a-synuclein and the increase of intracellular concentrations of non-mutant a-synuclein have been associated with Parkinson’s disease phenotype.

The demonstration that a-synuclein is degraded by both proteasome and autophagy indicates a possible linkage between the dysfunction of the UPS or ALP and the occurrence of this disorder.The fact that mutant a-synucleins inhibit ALP functioning by tightly binding to the receptor on the lysosomal membrane for autophagy pathway further supports the assumption that impairment of the ALP may be related to the development of Parkinson’s disease.

In this review, we summarize the recent findings related to this topic and discuss the unique role of the ALP in this neurogenerative disorder and the putative therapeutic potential through ALP enhancement.

Pan Y, Kondo S, Le W, Jankovic J. The role of autophagy-lysosome pathway in
neurodegeneration associated with Parkinson’s disease. Brain 2008; 131: 1969-1978. doi:10.1093/brain/awm318.

Ubiquitin-Proteasome System in Parkinson’s

There is growing evidence that dysfunction of the mitochondrial respiratory chain and failure of the cellular protein degradation machinery, specifically the ubiquitin-proteasome system, play an important role in the pathogenesis of Parkinson’s disease. We now show that the corresponding pathways of these two systems are linked at the transcriptomic level in Parkinsonian substantia nigra. We examined gene expression in medial and lateral substantia nigra (SN) as well as in frontal cortex using whole genome DNA oligonucleotide microarrays. In this study, we use a hypothesis-driven approach in analysing microarray data to describe the expression of mitochondrial and ubiquitin-proteasomal system (UPS) genes in Parkinson’s disease (PD).

Although a number of genes showed up-regulation, we found an overall decrease in expression affecting the majority of mitochondrial and UPS sequences. The down-regulated genes include genes that encode subunits of complex I and the Parkinson’s-disease-linked UCHL1. The observed changes in expression were very similar for both medial and lateral SN and also affected the PD cerebral cortex. As revealed by “gene shaving” clustering analysis, there was a very significant correlation between the transcriptomic profiles of both systems including in control brains.

Therefore, the mitochondria and the proteasome form a higher-order gene regulatory network that is severely perturbed in Parkinson’s disease. Our quantitative results also suggest that Parkinson’s disease is a disease of more than one cell class, i.e. that it goes beyond the catecholaminergic neuron and involves glia as well.

Duke DC, Moran LB, Kalaitzakis ME, Deprez M, et al. Transcriptome analysis reveals link between proteasomal and mitochondrial pathways in Parkinson’s disease. Neurogenetics 2006; 7:139-148.
Bax Degradation a Novel Mechanism for Survival in Bcl-2 overexpressed cancer cells
The authors previously reported that proteasome inhibitors were able to overcome Bcl-2-mediated protection from apoptosis, and now show that inhibition of the proteasome activity in Bcl-2-overexpressing cells accumulates the proapoptotic Bax protein to mitochondrial cytoplasm, where it interacts to Bcl-2 protein. This event was followed by release of mitochondrial cytochrome c into the cytosol and activation of caspase-mediated apoptosis. In contrast, proteasome inhibition did not induce any apparent changes in Bcl-2 protein levels. In addition, treatment with a proteasome inhibitor increased levels of ubiquitinated forms of Bax protein, without any effects on Bax mRNA expression. They also established a cell-free Bax degradation assay in which an in vitro-translated, 35S-labeled Bax protein can be degraded by a tumor cell protein extract, inhibitable by addition of a proteasome inhibitor or depletion of the proteasome or ATP. The Bax degradation activity can be reconstituted in the proteasome-depleted supernatant by addition of a purified 20S proteasome or proteasome-enriched fraction. Finally, by using tissue samples of human prostate adenocarcinoma, they demonstrated that increased levels of Bax degradation correlated well with decreased levels of Bax protein and increased Gleason scores of prostate cancer. These studies strongly suggest that ubiquitin-proteasome-mediated Bax degradation is a novel survival mechanism in human cancer cells and that selective targeting of this pathway should provide a unique approach for treatment of human cancers, especially those overexpressing Bcl-2.
In the current study, These investigators report that

  • (i) proteasome inhibition results in Bax accumulation before release of cytochrome c and induction of apoptosis, which is associated with the ability of proteasome inhibitors to overcome Bcl-2-mediated antiapoptotic function;
  • (ii) Bax is regulated by an ATP-ubiquitin-proteasome-dependent degradation pathway; and
  • (iii) decreased levels of Bax protein correlate with increased levels of Bax degradation in aggressive human prostate cancer.

Li B and Dou QP. Bax degradation by the ubiquitin-proteasome-dependent pathway: Involvement in tumor survival and progression. PNAS 2000; 97(8): 3851-3855. http://www.pnas.org

p97 and DBeQ, ATP-competitive p97 inhibitor
A major limitation to current studies on the biological functions of p97/Cdc48 is that there is no method to rapidly shut off its ATPase activity. Given the range of cellular processes in which Cdc48 participates, it is difficult to determine whether any particular phenotype observed in the existing mutants is due to a direct or indirect effect. Moreover, inhibition of p97 activity in animal cells by siRNA or expression of a dominant-negative version is challenged by its high abundance and is not suited to evaluating proximal phenotypic effects of p97 loss of function.

A specific small-molecule inhibitor of p97 would provide an important tool to investigate diverse functions of this essential ATPase associated with diverse cellular activities (AAA) ATPase and to evaluate its potential to be a therapeutic target in human disease. Cancer cells may be particularly sensitive to killing by suppression of protein degradation mechanisms, because they may exhibit a heightened dependency on these mechanisms to clear an elevated burden of quality-control substrates. For example, some cancers produce high levels of a specific protein that is a prominent quality-control substrate (e.g., Ig light chains in multiple myeloma) or produce high levels of reactive oxygen species, which can result in excessive protein damage via oxidation. Therefore, a specific p97 inhibitor would be a valuable research tool to investigate p97 function in cells.

We carried out a high-throughput screen to identify inhibitors of p97 ATPase activity. Dual-reporter cell lines that simultaneously express p97-dependent and p97-independent proteasome substrates were used to stratify inhibitors that emerged from the screen. N2,N4-dibenzylquinazoline-2,4-diamine (DBeQ) was identified as a selective,potent, reversible, and ATP-competitive p97 inhibitor.

DBeQ blocks multiple processes that have been shown by RNAi to depend on p97, including degradation of ubiquitin fusion degradation and endoplasmic reticulum-associated degradation pathway reporters, as well as autophagosome maturation. DBeQ also potently inhibits cancer cell growth and is more rapid than a proteasome inhibitor at mobilizing the executioner caspases-3 and -7.

Simultaneous inhibition of proteasome and histone deacetylase 6 (HDAC6) [which is required for autophagy results in synergistic killing of multiple myeloma cells]. Interestingly, more than one dozen human clinical trials (www.clinicaltrials.gov) combine bortezomib with the broad-spectrum HDAC inhibitor vorinostat, which is active toward HDAC6. Targeting p97
may provide an alternative route to achieving the same objective. Our results provide a rationale for targeting p97 in cancer therapy. Future work will provide molecular insight into how inhibition of p97 activity by DBeQ results in apoptosis and could strengthen the rationale for a p97-targeted cancer therapeutic.

Chou TF, Brown SJ, Minond D, Nordin BE, et al. Reversible inhibitor of p97, DBeQ, impairs both ubiquitin-dependent and autophagic protein clearance pathways. PNAS 2011; pp 6 http://www.pnas.org/cgi/doi/10.1073/pnas.1015312108

The causes of various neurodegenerative diseases, particularly sporadic cases, remain unknown, but increasing evidence suggests that these diseases may share similar molecular and cellular mechanisms of pathogenesis. One prominent feature common to most neurodegenerative diseases is the accumulation of misfolded proteins in the form of insoluble protein aggregates or inclusion bodies. Although these aggregates have different protein compositions, they all contain ubiquitin and proteasome subunits, implying a failure of the ubiquitin-proteasome system (UPS) in the removal of misfolded proteins.

A direct link between UPS dysfunction and neurodegeneration has been
provided by recent findings that genetic mutations in UPS components cause several rare, familial forms of neurodegenerative diseases. Furthermore, it is becoming increasingly clear that oxidative stress, which results from aging or exposure to environmental toxins, can directly damage UPS components, thereby contributing to the pathogenesis of sporadic forms of neurodegenerative diseases.

Aberrations in the UPS often result in defective proteasome-mediated protein degradation, leading to accumulation of toxic proteins and eventually to neuronal cell death. Interestingly, emerging evidence has begun to suggest that impairment in substrate-specific components of the UPS, such as E3 ubiquitin-protein ligases, may cause aberrant ubiquitination and neurodegeneration in a proteasome-independent manner. This provides an overview of the molecular components of the UPS and their impairment in familial and sporadic forms of neurodegenerative diseases, and summarizes present knowledge about the pathogenic mechanisms of UPS dysfunction in neurodegeneration.

Molecular mechanisms of protein ubiquitination and degradation by the UPS. Ubiquitination involves a highly specific enzyme cascade in which

  • ubiquitin (Ub) is first activated by the ubiquitinactivating enzyme (E1),
  • then transferred to an ubiquitin-conjugating enzyme (E2), and
  • finally covalently attached to the substrate by an ubiquitin-protein ligase (E3).

Ubiquitination is a reversible posttranslational modification in which the removal of Ub is mediated by a deubiquitinating enzyme (DUB).

  • Substrate proteins can be either monoubiquitinated or polyubiquitinated through successive conjugation of Ub moieties to an internal lysine residue in Ub.
  • K48-linked poly-Ub chains are recognized by the 26S proteasome, resulting in degradation of the substrate and recycling of Ub.
  • Monoubiquitination or K63-linked polyubiquitination plays a number of regulatory roles in cells that are proteasome-independent.

Parkin

Loss-of-function mutations in parkin, a 465-amino-acid RING-type E3 ligase, were first identified as the cause for autosomal recessive juvenile Parkinsonism (AR-JP) and subsequently found to account for ~50% of all recessively transmitted early-onset PD cases. Interestingly, patients with parkin mutations do not exhibit Lewy body pathology.

Possible pathogenic mechanisms by which impaired UPS components cause neurodegeneration. Genetic mutations or oxidative stress from aging and/or exposure to environmental toxins have been shown to impair the ubiquitination machinery (particularly E3 ubiquitin-protein ligases) and deubiquitinating enzymes (DUBs), resulting in abnormal ubiquitination. Depending on the type of ubiquitination affected, the impairment could cause neurodegeneration through two different mechanisms.

In the first model, aberrant K48-linked polyubiquitination resulting from impaired E3s or DUBs alters protein degradation by the proteasome, leading to accumulation of toxic proteins and subsequent neurodegeneration. The proteasomes could be directly damaged by oxidative stress or might be inhibited by protein aggregation, which exacerbates the neurotoxicity.

In the second model, aberrant monoubiquitination or K63-linked polyubiquitination resulting from impaired E3s or DUBs alters crucial non-proteasomal functions, such as gene transcription and protein trafficking, thereby causing neurodegeneration without protein aggregation.

These two models are not mutually exclusive because a single E3 or DUB enzyme, such as parkin or UCH-L1, could regulate more than one type of ubiquitination. In addition, abnormal ubiquitination and neurodegeneration could also result from mutation or oxidative stress-induced structural changes in the protein substrates that alter their recognition and degradation by the UPS.

Lian Li and Chin LS. IMPAIRMENT OF THE UBIQUITIN-PROTEASOME SYSTEM: A COMMON PATHOGENIC MECHANISM IN NEURODEGENERATIVE DISORDERS. In The Ubiquitin Proteasome System…Chapter 23. (Eds: Eds: Mario Di Napoli and Cezary Wojcik) 553-577 © 2007 Nova Science Publishers, Inc. ISBN 978-1-60021-749-4.

filedesc Schematic diagram of the ubiquitylati...

filedesc Schematic diagram of the ubiquitylation system. Created by Roger B. Dodd (Photo credit: Wikipedia)

 

Current Noteworthy Work

Nassif M and Hetz C.  Autophagy impairment: a crossroad between neurodegeneration and tauopathies.  BMC Biology 2012; 10:78. http://www.biomedcentral.com/1741-7007/10/78

Impairment of protein degradation pathways such as autophagy is emerging as a consistent and transversal pathological phenomenon in neurodegenerative diseases, including Alzheimer´s, Huntington´s, and Parkinson´s disease. Genetic inactivation of autophagy in mice has demonstrated a key role of the pathway in maintaining protein homeostasis in the brain, triggering massive neuronal loss and the accumulation of abnormal protein inclusions.  A paper in Molecular Neurodegeneration from Abeliovich´s group now suggests a role for phosphorylation of Tau and the activation of glycogen synthase kinase 3β (GSK3β) in driving neurodegeneration in autophagy-deficient neurons. We discuss the implications of this study for understanding the factors driving neurofibrillary tangle formation in Alzheimer´s disease and tauopathies.

Cajee UF, Hull R and Ntwasa M. Modification by Ubiquitin-Like Proteins: Significance in Apoptosis and Autophagy Pathways. Int. J. Mol. Sci. 2012, 13, 11804-11831; doi:10.3390/ijms130911804

Ubiquitin-like proteins (Ubls) confer diverse functions on their target proteins. The modified proteins are involved in various biological processes, including DNA replication, signal transduction, cell cycle control, embryogenesis, cytoskeletal regulation,
metabolism, stress response, homeostasis and mRNA processing. Modifiers such as SUMO, ATG12, ISG15, FAT10, URM1, and UFM have been shown to modify proteins thus conferring functions related to programmed cell death, autophagy and regulation of
the immune system. Putative modifiers such as Domain With No Name (DWNN) have been identified in recent times but not fully characterized. In this review, we focus on cellular processes involving human Ubls and their targets.

Aloy P. Shaping the future of interactome networks. (A report of the third Interactome Networks Conference, Hinxton, UK, 29 August-1 September 2007). Genome Biology 2007; 8:316 (doi:10.1186/gb-2007-8-10-316)

Complex systems are often networked, and biology is no exception. Following on from the genome sequencing projects,
experiments show that proteins in living organisms are highly connected, which helps to explain how such great complexity
can be achieved by a comparatively small set of gene products. At a recent conference on interactome networks held outside
Cambridge, UK, the most recent advances in research on cellular networks were discussed. This year’s conference focused on
identifying the strengths and weaknesses of currently resolved interaction networks and the techniques used to determine
them – reflecting the fact that the field of mapping interaction networks is maturing.

Peroutka RJ, Orcutt SJ, Strickler JE, and Butt TR. SUMO Fusion Technology for Enhanced Protein Expression and Purification in Prokaryotes and Eukaryotes. Chapter 2. in T.C. Evans, M.-Q. Xu (eds.), Heterologous Gene Expression in E. coli, Methods in Molecular Biology 705:15-29. DOI 10.1007/978-1-61737-967-3_2, © Springer Science+Business Media, LLC 2011

The preparation of sufficient amounts of high-quality protein samples is the major bottleneck for structural proteomics. The use of recombinant proteins has increased significantly during the past decades. The most commonly used host, Escherichia coli, presents many challenges including protein misfolding, protein degradation, and low solubility. A novel SUMO fusion technology appears to enhance protein expression and solubility (www.lifesensors.com). Efficient removal of the SUMO tag by SUMO protease in vitro facilitates the generation of target protein with a native N-terminus. In addition to its physiological relevance in eukaryotes, SUMO can be used as a powerful biotechnology tool for enhanced functional protein expression in prokaryotes and eukaryotes.

Juang YC, Landry MC, et al. OTUB1 Co-opts Lys48-Linked Ubiquitin Recognition to Suppress E2 Enzyme Function. Molecular Cell 2012; 45: 384–397. DOI 10.1016/j.molcel.2012.01.011

Ubiquitylation entails the concerted action of E1, E2, and E3 enzymes. We recently reported that OTUB1, a deubiquitylase, inhibits the DNA damage response independently of its isopeptidase activity. OTUB1 does so by blocking ubiquitin transfer by UBC13, the cognate E2 enzyme for RNF168. OTUB1 also inhibits E2s of the UBE2D and UBE2E families. Here we elucidate the structural mechanism by which OTUB1 binds E2s to inhibit ubiquitin transfer. OTUB1 recognizes ubiquitin-charged E2s through contacts with both donor ubiquitin and the E2 enzyme. Surprisingly, free ubiquitin associates with the canonical distal ubiquitin-binding site on OTUB1 to promote formation of the inhibited E2 complex. Lys48 of donor ubiquitin lies near the OTUB1 catalytic site and the C terminus of free ubiquitin, a configuration that mimics the products of Lys48-linked ubiquitin chain cleavage. OTUB1 therefore co-opts Lys48-linked ubiquitin chain recognition to suppress ubiquitin conjugation and the DNA damage response.

Hunter T. The Age of Crosstalk: Phosphorylation, Ubiquitination, and Beyond. Molecular Cell  2007; 28:730-738. DOI 10.1016/ j.molcel.2007.11.019.

Crosstalk between different types of posttranslational modification is an emerging theme in eukaryotic biology. Particularly prominent are the multiple connections between phosphorylation and ubiquitination, which act either positively or negatively in both directions to regulate these processes.

Tu Y, Chen C, et al. The Ubiquitin Proteasome Pathway (UPP) in the regulation of cell cycle control and DNA damage repair and its implication in tumorigenesis. Int J Clin Exp Pathol 2012;5(8):726-738. www.ijcep.com /ISSN:1936-2625/IJCEP1208018

Accumulated evidence supports that the ubiquitin proteasome pathway (UPP) plays a crucial role in protein
metabolism implicated in the regulation of many biological processes such as cell cycle control, DNA damage
response, apoptosis, and so on. Therefore, alterations for the ubiquitin proteasome signaling or functional impairments
for the ubiquitin proteasome components are involved in the etiology of many diseases, particularly in cancer
development.The authors discuss the ubiquitin proteasome pathway in the regulation of cell cycle control and DNA
damage response, the relevance for the altered regulation of these signaling pathways in tumorigenesis, and finally
assess and summarize the advancement for targeting the ubiquitin proteasome pathway in cancer therapy.

Cebollero E , Reggiori F  and Kraft C.  Ribophagy: Regulated Degradation of Protein Production Factories. Int J Cell Biol. 2012; 2012: 182834. doi:  10.1155/2012/182834 (online).

During autophagy, cytosol, protein aggregates, and organelles are sequestered into double-membrane vesicles called autophagosomes and delivered to the lysosome/vacuole for breakdown and recycling of their basic components. In all eukaryotes this pathway is important for adaptation to stress conditions such as nutrient deprivation, as well as to regulate intracellular homeostasis by adjusting organelle number and clearing damaged structures. For a long time, starvation-induced autophagy has been viewed as a nonselective transport pathway; however, recent studies have revealed that autophagy is able to selectively engulf specific structures, ranging from proteins to entire organelles. In this paper, we discuss recent findings on the mechanisms and physiological implications of two selective types of autophagy: ribophagy, the specific degradation of ribosomes, and reticulophagy, the selective elimination of portions of the ER.

Lee JH, Yu WH,…, Nixon RA.  Lysosomal Proteolysis and Autophagy Require Presenilin 1 and Are Disrupted by Alzheimer-Related PS1 Mutations. Cell 2010; 141, 1146–1158. DOI 10.1016/j.cell.2010.05.008.

Macroautophagy is a lysosomal degradative pathway essential for neuron survival. Here, we show that macroautophagy requires the Alzheimer’s disease (AD)-related protein presenilin-1 (PS1). In PS1 null blastocysts, neurons from mice hypomorphic for PS1 or
conditionally depleted of PS1, substrate proteolysis and autophagosome clearance during macroautophagy are prevented as a result of a selective impairment of autolysosome acidification and cathepsin activation. These deficits are caused by failed PS1-dependent
targeting of the v-ATPase V0a1 subunit to lysosomes. N-glycosylation of the V0a1 subunit, essential for its efficient ER-to-lysosome delivery, requires the selective binding of PS1 holoprotein to the unglycosylated subunit and the  sec61alpha/ oligosaccharyltransferase complex. PS1 mutations causing early-onset AD produce a similar lysosomal/autophagy phenotype in
fibroblasts from AD patients. PS1 is therefore essential for v-ATPase targeting to lysosomes, lysosome acidification, and proteolysis during autophagy. Defective lysosomal proteolysis represents a basis for pathogenic protein accumulations and neuronal cell death in AD and suggests previously unidentified therapeutic targets.

Pohl C and Jentsch S. Midbody ring disposal by autophagy is a post-abscission event of cytokinesis. nature cell biology 2009; 11 (1): 65-70.  DOI: 10.1038/ncb1813.

At the end of cytokinesis, the dividing cells are connected by an intercellular bridge, containing the midbody along with a single,
densely ubiquitylated, circular structure called the midbody ring (MR). Recent studies revealed that the MR serves as a target
site for membrane delivery and as a physical barrier between the prospective daughter cells. The MR materializes in telophase,
localizes to the intercellular bridge during cytokinesis, and moves asymmetrically into one cell after abscission. Daughter
cells rarely accumulate MRs of previous divisions, but how these large structures finally disappear remains unknown.
Here, we show that MRs are discarded by autophagy, which involves their sequestration into autophagosomes and delivery to
lysosomes for degradation. Notably, autophagy factors, such as the ubiquitin adaptor p62 and the ubiquitin-related protein Atg8 , associate with the MR during abscission, suggesting that autophagy is coupled to cytokinesis. Moreover, MRs accumulate in cells of patients with lysosomal storage disorders, indicating that defective MR disposal is characteristic of these diseases. Thus our findings suggest that autophagy has a broader role than previously assumed, and that cell renovation by clearing from superfluous large macromolecular assemblies, such as MRs, is an important autophagic function.

 

Hanai JI, Cao P, Tanksale P, Imamura S, et al. The muscle-specific ubiquitin ligase atrogin-1/MAFbx mediates statin-induced muscle toxicity. The Journal of Clinical Investigation  2007; 117(12):3930-3951.    http://www.jci.org

Statins inhibit HMG-CoA reductase, a key enzyme in cholesterol synthesis, and are widely used to treat hypercholesterolemia.
These drugs can lead to a number of side effects in muscle, including muscle fiber breakdown; however, the mechanisms of muscle injury by statins are poorly understood. We report that lovastatin induced the expression of atrogin-1, a key gene involved in skeletal muscle atrophy, in humans with statin myopathy, in zebrafish embryos, and in vitro in murine skeletal muscle cells. In cultured mouse myotubes, atrogin-1 induction following lovastatin treatment was accompanied by distinct morphological changes, largely absent in
atrogin-1 null cells. In zebrafish embryos, lovastatin promoted muscle fiber damage, an effect that was closely mimicked by knockdown of zebrafish HMG-CoA reductase. Moreover, atrogin-1 knockdown in zebrafish embryos prevented lovastatin-induced muscle injury. Finally, overexpression of PGC-1α, a transcriptional coactivator that induces mitochondrial biogenesis and protects against the development of muscle atrophy, dramatically prevented lovastatin-induced muscle damage and abrogated atrogin-1 induction both in fish and in cultured mouse myotubes. Collectively, our human, animal, and in vitro findings shed light on the molecular mechanism of statin-induced myopathy and suggest that atrogin-1 may be a critical mediator of the muscle
damage induced by statins.

Inami Y, Waguri S, Sakamoto A, Kouno T, et al.  Persistent activation of Nrf2 through p62 in hepatocellular carcinoma cells. J. Cell Biol. 2011; 193(2): 275–284. http://www.jcb.org/cgi/doi/10.1083/jcb.201102031

Macroautophagy (hereafter referred to as autophagy) is a cellular degradation system in which cytoplasmic components, including
organelles, are sequestered by double membrane structures called autophagosomes and the sequestered materials are
degraded by lysosomal hydrolases for supply of amino acids and for cellular homeostasis. Although autophagy has generally been considered nonselective, recent studies have shed light on another indispensable role for basal autophagy in cellular homeostasis, which is mediated by selective degradation of a specific substrate(s).  p62 is a ubiquitously expressed cellular protein that is conserved in metazoa but not in plants and fungi, and recently it has been known as one of the selective substrates for autophagy.
This protein is localized at the autophagosome formation site  and directly interacts with LC3, an autophagosome localizing protein . Subsequently, the p62 is incorporated into the autophagosome and then degraded. Therefore, impaired autophagy is accompanied by
accumulation of p62 followed by the formation of p62 and ubiquitinated protein aggregates because of the nature of both self- oligomerization and ubiquitin binding of p62.

 

Kima K, Khayrutdinov BI, Leeb CK, et al. Solution structure of the Zβ domain of human DNA-dependent activator of IFN-regulatory factors and its binding modes to B- and Z-DNAs. PNAS 2010; Early Edition ∣ pp 6. www.pnas.org/cgi/doi/10.1073/pnas.1014898107

The DNA-dependent activator of IFN-regulatory factors (DAI), also known as DLM-1/ZBP1, initiates an innate immune response by binding to foreign DNAs in the cytosol. For full activation of the immune response, three DNA binding domains at the N terminus are required: two Z-DNA binding domains (ZBDs), Zα and Zβ, and an adjacent putative B-DNA binding domain. The crystal structure of the Zβ domain of human DAI (hZβDAI) in complex with Z-DNA revealed structural features distinct from other known Z-DNA binding proteins, and it was classified as a group II ZBD. To gain structural insights into the DNA binding mechanism of hZβDAI, the solution structure of the free hZβDAI was solved, and its bindings to B- and Z-DNAs were analyzed by NMR spectroscopy. Compared to the Z-DNA–bound structure, the conformation of free hZβDAI has notable alterations in the α3 recognition helix, the “wing,” and Y145, which are critical in Z-DNA recognition. Unlike some other Zα domains, hZβDAI appears to have conformational flexibility, and structural adaptation is required for Z-DNA binding. Chemical-shift perturbation experiments revealed that hZβDAI also binds weakly to B-DNA via a different binding mode. The C-terminal domain of DAI is reported to undergo a conformational change on B-DNA binding; thus, it is possible that these changes are correlated. During the innate immune response, hZβDAI is likely to play an active role in binding to DNAs in both B and Z conformations in the recognition of foreign DNAs.

 

Epicrisis

This extensive review leaves little left unopened. We have seen the central role that the UPS system plays in normal organelle proteolysis in concert with autophagy. Impaired ubiquitination occurs from aging, and/or toxins, under oxidative stress involving E3s or DUBs.

This leads to altered gene transcripton, altered protein trafficking, and plays a role in neurodegenative disease, muscle malfunction, and cancer as well.

English: A cartoon representation of a lysine ...

English: A cartoon representation of a lysine 48-linked diubiquitin molecule. The two ubiquitin chains are shown as green cartoons with each chain labelled. The components of the linkage are indicated and shown as orange sticks. Image was created using PyMOL from PDB id 1aar. (Photo credit: Wikipedia)

Different forms of protein ubiquitylation

Different forms of protein ubiquitylation (Photo credit: Wikipedia)

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