Use It or Lose It

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3-D computer model of a fruit fly larva muscle fiber with multiple nuclei

 
Everyone knows that exercise can build muscle; without exercise, muscles quickly lose their strength and volume. These facts have been common knowledge for so long, it might come as a surprise to find that very little is known about the molecular mechanisms behind them. How indeed does physical activity cause muscles to strengthen?
 
Prof. Talila Volk
 
Weizmann Institute scientists have now proposed an explanation. Research conducted by the team of Prof. Talila Volk in the Molecular Genetics Department suggests that the long, cylinder-shaped muscle cells – the muscle fibers – contain proteins that function as biological “mechanosensors.” These spring-like, elastic proteins are connected to the cellular supporting structure – the cytoskeleton – on the one side, and on the other side, to the cell’s nucleus. Muscle contractions exert mechanical pressure on the cytoskeleton, which, in turn, puts pressure on these sensor proteins, causing them to transmit a signal to the nucleus.

This signal presumably alters the internal architecture of the chromosomes within the nucleus, changing gene expression – that is, the activity of genes – in the affected portion of the DNA. As a result, certain genes become activated, prompting the release of proteins that make up the filaments responsible for the contraction of the muscle fiber. In addition to contraction, the proteins fortify existing filaments and help produce new ones, building up muscle mass.
 
Muscle fibers of a fruit fly larva viewed under a confocal microscope: A normal fiber has normally-shaped, properly distributed nuclei (A), whereas the nuclei of fibers with mutated MSP-300 or its interacting proteins Klar and Klaroid are distorted and distributed abnormally (B, C and D)
 
 
In this manner, exercise triggers a strengthening of the muscle. But because muscle-building proteins have a high turnover, the signal for their production must be periodically repeated. If, in the absence of exercise, the muscle fails to contract for a while, the mechanosensors no longer send their signals to the nucleus, ultimately leading to a loss of muscle mass.

Evidence for this explanation comes from a series of studies that Volk and her team – including research students Hadas Elhanany-Tamir and Miri Shnayder, and postdoctoral fellow Dr. Shuoshuo Wang – conducted in fruit fly larvae. As reported in the Journal of Cell Biology, the scientists have identified a fruit fly protein, called MSP-300, whose shape and mechanical properties make it perfectly suited to serving as a mechanosensor. MSP-300 forms a ring around the nucleus, with numerous radial extensions connected to the cytoskeleton. It has elastic properties, as would be required from a mechanosensor; but on the other hand, it operates in close cooperation with two other proteins that help create rigid scaffolding around the nucleus, protecting it from muscle contractions. By introducing mutations into MSP-300, the scientists showed that it is indeed essential for maintaining muscle mass. The effect of the mutations on the fly’s muscles was devastating: The muscle fibers thinned out and their nuclei were deformed and clumped together abnormally. As a result, the muscles didn’t work properly, so the larvae couldn’t crawl and adult flies couldn’t fly.
 
The MSP-300 protein, viewed here under a confocal microscope, forms a ring (red in the left image, green on the right) around the muscle cell nucleus, with extensions to the cytoskeleton
 

Because human muscle cells contain proteins equivalent to MSP-300, suggesting they may also function as mechanosensors, these findings can shed new light on the connection between physical activity and a healthy build-up of muscle in humans. A better understanding of this connection may in the future lead to improved ways to prevent muscle loss resulting from aging, forced inactivity as in paralysis, or such disorders as muscular dystrophy.

Prof. Talila Volk's research is supported by Erica A. Drake and Robert Drake. Prof. Volk is the incumbent of the Sir Ernst B. Chain Professorial Chair.
 

 
Muscle fibers of a fruit fly larva viewed under a confocal microscope: A normal fiber has normally-shaped, properly distributed nuclei (A), whereas the nuclei of fibers with mutated MSP-300 or its interacting proteins Klar and Klaroid are distorted and distributed abnormally (B, C and D)
Life Sciences
English

Stopping the Stem Cell State

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Stem cell colony with cells in the process of differentiation; from the lab of Dr. Jacob Hanna
 
Scientists can now create cells that closely resemble embryonic stem cells in the lab. But what happens next? Because the use of these cells, called induced pluripotent stem (iPS) cells, to treat disease will ultimately depend on how we learn to direct their fate, we also need to figure out how they stop being stem cells – a process that naturally takes place right at the beginning of embryonic development. “The system must be shut off before differentiation into the various cell types can proceed,” says Dr. Jacob Hanna of the Weizmann Institute’s Molecular Genetics Department. “We have gotten somewhat proficient at getting the cells to revert, but very little is known about the termination of the iPS program.”

To investigate, Hanna and research student Shay Geula teamed up with Prof. Gideon Rechavi of Chaim Sheba Medical Center in Tel Aviv, and their findings recently appeared in Science. Hanna’s group is making strides in the field of iPS cell research; Rechavi’s group is one of the world’s leading experts in another little-known area, called RNA methylation.

Methylation is a basic biochemical process: A chemical “methyl” group gets attached to a genetic sequence, blocking it off from further use. In the better-known version, DNA methylation, the process is often described as a lock – hard to open again and relatively long-lasting. Some types of methylation can even be passed down to the next generation. So when Rechavi’s group and others noted that the short-lived genetic sequences of RNA can also be marked by methyl groups, it was unclear to what purpose.

The researchers identified an enzyme – Mettl3 – that attaches methyl groups to the RNA of mammalian cells. To see whether this action plays a role in undoing the stem-cell state, they silenced the gene for this enzyme in mouse embryos. The consequences were devastating: The embryos were not viable for more than a few days. Development didn’t progress as cell differentiation could not proceed properly.

A closer look at the actions of Mettl3 revealed that it attaches its methyl groups to the exact sequences that code for pluripotency – the capacity to become any cell type. Rather than simply locking these sequences, the methylation causes them to be broken down.

Hanna: “These findings showed that, on the one hand, RNA methylation plays a crucial role in embryonic development and, on the other, that it is not enough to reinstate the stem cell program. It must be turned off again, at the right time and in the right way, for the next step in cell differentiation to take place. RNA methylation is the dominant mechanism that safeguards adequate dismantling and decay of the stem cell state.”  
 
Dr. Jacob (Yaqub) Hanna
                               
 

Dr. Jacob Hanna's research is supported by Pascal and Ilana Mantoux, France/Israel; the Benoziyo Endowment Fund for the Advancement of Science; the Leona M. and Harry B. Helmsley Charitable Trust; the Sir Charles Clore Research Prize; Erica A. Drake and Robert Drake; the Abisch Frenkel Foundation for the Promotion of Life Sciences; the European Research Council; the Fritz Thyssen Stiftung; and the Alice and Jacob K. Rubin Charitable Remainder Unitrust. Dr. Hanna is the recipient of the Helen and Martin Kimmel Award for Innovative Investigation.
 

 
 
Stem cell colony with cells in the process of differentiation; from the lab of Dr. Jacob Hanna
Life Sciences
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Human Primordial Cells Created in the Lab

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Groups at the Weizmann Institute of Science and Cambridge University have jointly managed the feat of turning back the clock on human cells to create primordial germ cells – the embryonic cells that give rise to sperm and ova – in the lab. This is the first time that human cells have been programmed into this early developmental stage. The results of their study, which were published today in Cell, could help provide answers as to the causes of fertility problems, yield insight into the earliest stages of embryonic development and potentially, in the future, enable the development of new kinds of reproductive technology.


“Researchers have been attempting to create human primordial germ cells (PGCs) in the petri dish for years,” says Dr. Jacob Hanna of the Institute’s Molecular Genetics Department, who led the study together with research student Leehee Weinberger. PGCs arise within the early weeks of embryonic growth, as the embryonic stem cells in the fertilized egg begin to differentiate into the very basic cell types. Once these primordial cells become “specified,” they continue developing toward precursor sperm cells or ova “pretty much on autopilot,” says Hanna. The idea of creating these cells in the lab took off with the 2006 invention of induced pluripotent stem (iPS) cells – adult cells that are “reprogrammed” to look and act like embryonic stem cells, which can then differentiate into any cell type. Thus several years ago, when researchers in Japan created mouse iPS cells and then got them to differentiate into PGCs, scientists immediately set about trying to replicate the achievement in human cells. But until now, none had been successful.   
 
Previous research in Hanna’s lab pointed to new methods that could take human cells to the PGC state. That research had focused on the question of how human iPS cells and mouse embryonic cells differ: The mouse embryonic cells are easily kept in their stem cell state in the lab, while human iPS cells that have been reprogrammed – a technique that involves the insertion of four genes – have a strong drive to differentiate, and they often retain traces of “priming.”  Hanna and his group then created a method for tuning down the genetic pathway for differentiation, thus creating a new type of iPS cell that they dubbed “naïve cells.” These naïve cells appeared to rejuvenate iPS cells one step further, closer to the original embryonic state from which they can truly differentiate into any cell type. Since these naïve cells are more similar to their mouse counterparts, Hanna and his group thought they could be coaxed to differentiate into primordial germ cells.
 
Clusters of human embryonic stem cells that were differentiated to an early germ cell (PGC) state (colored cells). Each color reveals the expression of a different gene. (l-r) NANOS3, NANOG, OCT4 and, on the right, all three combined in a single image
 

 

 
Working with naïve human embryonic stem and iPS cells, and applying the techniques that had been successful in the mouse cell experiments, the research team managed to produce cells that, in both cases, appeared to be identical to human PGCs. Together with the lab group of Prof. Azim Surani of Cambridge University, the scientists further tested and refined the method jointly in both labs. By adding a glowing red fluorescent marker to the genes for PGCs, they were able to gauge how many of the cells had been programmed. Their results showed that quite a high rate – up to 40% – had become PGCs; this quantity enables easy analysis.

Hanna points out that PGCs are only the first step in creating human sperm and ova. A number of hurdles remain before labs will be able to complete the chain of events that move an adult cell through the cycle of embryonic stem cell and around to sperm or ova. For one, at some point in the process, these cells must learn to perform the neat trick of dividing their DNA in half before they can become viable reproductive cells. Still, he is confident that those hurdles will one day be overcome, raising the possibility, for example, of enabling women who have undergone chemotherapy or premature menopause to conceive.

In the meantime, the study has already yielded some interesting results that may have significant implications for further research on PGCs and possibly other early embryonic cells. The team managed to trace part of the genetic chain of events that directs a stem cell to differentiate into a primordial germ cell, and they discovered a master gene, Sox17, that regulates the process in humans, but not in mice. Because this gene network is quite different from the one that had been identified in mice, the researchers suspect that more than a few surprises may await scientists who study the process in humans.

Hanna: “Having the ability to create human PGCs in the petri dish will enable us to investigate the process of differentiation on the molecular level. For example, we found that only ‘fresh’ naïve cells can become PGCs; but after a week in conventional growth conditions they lose this capability once again. We want to know why this is. What is it about human stem cell states that makes them more or less competent? And what exactly drives the process of differentiation once a cell has been reprogrammed to its more naïve state? It is the answers to these basic questions that will, ultimately, advance iPS cell technology to the point of medical use.”
 
This collaborative project was made possible by a grant from BIRAX Britain Israel Research and Academic Exchange Partnership – Regenerative Medicine Initiative.

Dr. Jacob Hanna’s research is supported by Pascal and Ilana Mantoux, France/Israel; the New York Stem Cell Foundation, the Flight Attendant Medical Research Institute (FAMRI), the Israel Cancer Research Fund (ICRF), the Helen and Martin Kimmel Award for Innovative Investigation, the Benoziyo Endowment Fund for the Advancement of Science; the Leona M. and Harry B. Helmsley Charitable Trust; the Sir Charles Clore Research Prize; Erica A. Drake and Robert Drake; the Abisch Frenkel Foundation for the Promotion of Life Sciences; the European Research Council; the Israel Science Foundation, and the Fritz Thyssen Stiftung. Dr. Hanna is a New York Stem Cell Foundation-Robertson Investigator.
 
 
Clusters of human embryonic stem cells that were differentiated to an early germ cell (PGC) state (colored cells). Each color reveals the expression of a different gene. (l-r) NANOS3, NANOG, OCT4 and, on the right, all three combined in a single image
Life Sciences
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Cellular Signature Style

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To divide or not to divide: This is one of the most crucial decisions in the life of a cell. A new Weizmann Institute of Science study, conducted in collaboration with Danish researchers, has revealed a previously unknown mechanism that is involved in the control of such decisions in both healthy and cancerous cells. The findings, reported recently in Cell, provide an entirely new feature by which dividing and non-dividing cells can be told apart – a discovery that may, in the future, help advance the diagnosis, prognosis and perhaps even therapy of cancer.

The study focused on the presence of “synonyms” in the language of DNA: different three-letter portions of the genetic code that encode the same amino acid, a building block of proteins. For example, the two synonyms, GAA and GAG, differ chemically but produce the same amino acid. When the genetic code is translated into proteins – that is, when amino acids are manufactured on the basis of a particular DNA sequence – each synonym has its own messenger molecule, called transfer RNA (tRNA), which enables the translation. A tRNA is a two-headed molecular machine that on one end “reads” different synonyms of the code and on the other supplies the required amino acid for the synthesized protein.
 
Dr. Hila Gingold and Prof. Yitzhak Pilpel
 
Until now, the existence of more than 60 genetic three-letter synonyms, each having a corresponding tRNA, was not thought to have a major bearing on cell division. The ratios of different tRNAs were thought to be constant throughout the life of each cell, and in any event deviations or fluctuations in these ratios were not known to have particular biological significance.

Prof. Yitzhak Pilpel of the Weizmann Institute’s Molecular Genetics Department decided to look into the potential role played by the relative amounts of different tRNAs in the cell when he learned that Danish researchers had compiled an enormous database of genomic information from more than 400 people, including some 300 cancer patients, which contained a large volume of tRNA data. Pilpel’s intern Dr. Hila Gingold used DNA chip technology and mathematical algorithms to analyze the data, working together with Dr. Disa Tehler and other members from the team of Prof. Anders Lund of the University of Copenhagen, as well as other researchers from Denmark, the Netherlands, Switzerland and the United States.
 

Division signs


The results were so striking they surprised even the study authors themselves. The analysis revealed that two distinct subsets of tRNAs are present in the cell depending on whether it is dividing or not. For example, dividing cells tend to have large amounts of the tRNA that translates the GAG synonym, whereas non-dividing cells have a preference for the tRNA associated with the GAA synonym. As a result, dividing and non-dividing cells have discernible tRNA signatures – that is, characteristic amounts of all the different tRNAs.
 
Algorithm-generated comparisons among the genomes of cells from 450 tissue samples: The analysis revealed a striking similarity (red colors, upper right rectangle) in tRNA signatures among cancerous cells and healthy dividing cells, as well as a degree of similarity among the non-dividing cells (red colors, lower left rectangle), whereas no such similarity (blue) was found when dividing cells were compared with non-dividing ones
 

 

 
In other words, by measuring the relative amounts of tRNAs it’s possible to tell whether the cell is dividing, as is the case with cancerous cells, embryonic stem cells and other stem cells, or whether it’s a healthy cell that has stopped dividing after having specialized into a particular tissue type, such as a bone, blood or skin. In fact, all cancerous cells in the study were found to have characteristic tRNA signatures, which could be further classified by cancer type.
 

Changes in behavior

 
When the scientists examined the connection between tRNAs and different types of genes, they found, unsurprisingly, that the tRNAs more often present in dividing cells tended to be involved in the translation of genes that govern more “individualistic” cellular behavior – for example, rapid growth that doesn’t take neighboring cells into consideration – a feature typical of cancer. On the other hand, tRNAs present in non-dividing cells were associated with genes responsible for more “group-oriented” behaviors, such as cellular adhesion and communication, typical of healthy tissue.  

The scientists think the two tRNA signatures could have evolved as one of nature’s many ways of trying to block cancer. These signatures represent a mechanism that may add to cellular stability by keeping the two states, dividing and non-dividing, separate. When a normal non-dividing cell is on its way to becoming cancerous, it needs to alter its tRNA repertoire, a task that presents yet another hurdle it needs to overcome before it can start dividing uncontrollably: until this repertoire is changed, the translation of genes with cancerous potential may be less efficient.

Whatever their evolutionary significance, the analysis of tRNA signatures may in the future be developed into a tool for detecting or diagnosing cancer or for making a clinical prognosis of cancer development. An improved ability to distinguish between cancerous and healthy cells may also facilitate the design of therapies that will selectively target the tumor while sparing healthy tissue.
 
Prof. Yitzhak Pilpel's research is supported by the Sharon Zuckerman Laboratory for Research in Systems Biology; and the Braginsky Center for the Interface between Science and Humanities. Prof. Pilpel is the incumbent of the Ben May Professorial Chair.
 
Algorithm-generated comparisons among the genomes of cells from 450 tissue samples: The analysis revealed a striking similarity (red colors, upper right rectangle) in tRNA signatures among cancerous cells and healthy dividing cells, as well as a degree of similarity among the non-dividing cells (red colors, lower left rectangle), whereas no such similarity (blue) was found when dividing cells were compared with non-dividing ones
Life Sciences
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Pumping Zinc

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Why would a cell go to the trouble of destroying perfectly good, newly-minted proteins? New research at the Weizmann Institute and research centers in Germany, which was recently published in Molecular Cell, suggests that this unusual cellular mechanism may, among other things, be faulty in Alzheimer’s disease.  


Dr. Maya Schuldiner and research student Dr. Shai Fuchs of the Weizmann Institute’s Molecular Genetics Department, working in collaboration with Dr. Marius Lemberg and Dr. Donem Avci of Heidelberg University, looked into Presenilin, a human protein mutated in a familial form of early-onset Alzheimer’s.

To investigate the mechanism of this protein, the researchers looked to the ancestor of Presenilin, a yeast protein they identified as Ypf1 (for yeast presenilin fold1), which has been well-conserved throughout evolution. When they removed Ypf1 from the yeast cells, the result was excess quantities of a protein whose role is to pump zinc – an essential metal – into the cell. The puzzling thing was that, although there are two proteins for pumping zinc into the cell, only one was affected. The one increased is a “turbo,” or high affinity, pump; while the second, unaffected protein is more of a “workaday,” low affinity pump.  Like Presenilin, Ypf1 is a protease – a protein that degrades other proteins – so the researchers concluded that its function is to rid the cell of the “turbo” zinc transporters.
 
yeast proteins
 
In fact, they realized they were looking at a sort of two-pump system, which had first been described several years ago by the Weizmann Institute’s Prof. Naama Barkai. The low-affinity nutrient pumps may not be as efficient at bringing nutrients into the cell, but they are very sensitive to changes in those nutrients; when levels drop, they enable the activation of a back-up plan. High-affinity transporters can go into action to stockpile the nutrient in preparation for coming starvation, but these pumps can’t enable the back-up plan. In this scenario, healthy cells should work most of the time on the workaday pumps, only allowing the turbo pumps to reach their outer surfaces in times of need.     

The researchers asked how excess turbo pumping on the cell’s surface would affect its ability to prepare for scarcity. Indeed Ypf1-deficient cells were very slow to sense the nutrient’s lack, so they performed poorly during zinc starvation and took longer to recover. And more than zinc pumps are affected: The research showed that in the absence of Ypf1, high affinity transporters for many other nutrients are deregulated.   

 “Continually producing high-affinity transporters and then degrading them is a sort of double-safe mechanism that cells evolved to ensure that levels of vital nutrients like zinc remain as stable as possible within the cell,” says Fuchs. “Though we still don’t know exactly how the mechanism in humans is tied to Alzheimer’s, there is some interesting evidence that zinc transport in particular, and metal transport in general, could play a pivotal role in disease onset and progression.”
 
“We are excited that this new clue may open up fresh directions for thinking about the causes of Alzheimer’s disease, as these are still not well understood,” says Schuldiner.      

Dr. Maya Schuldiner’s research is supported by the Foundation Adelis; the Georges Lustgarten Cancer Research Fund; the Dora Yoachimowicz Endowed Fund for Research; the Berlin Family Foundation; Roberto and Renata Ruhman, Brazil; and Karen Siem, UK.
 
 
Fluorescent image of Baker's yeast cells showing that the yeast Presenilin-like protein, Ypf1 (green), is found in the same cellular area as Presenilin, around the nucleus
Life Sciences
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Where Two Paths Meet

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protein map
 
With modern maps, we can zoom out to a region’s entire road system or zoom in to distinguish the streets leading from one particular point to another. Somewhere in the middle of our zooming we might note the pattern of roads connecting neighboring cities that create interdependence between them. In the lab of Prof. Adi Kimchi of the Molecular Genetics Department, researchers creating such a map for two “cities” in the cell are coming to understand just how important the interactions created by such connecting roads might be for our body’s cells. Among other things, this arrangement may help prevent the growth of cancer.
 
The “cities” are molecular pathways that end in two different types of cell death. A pathway, in the language of molecular biology, is the set of proteins and the series of events they mobilize that lead to a particular end. Such pathways may comprise large networks of proteins and complex, multi-stage communications systems. Hundreds of proteins in each cell death pathway must talk to one another to opt for, initiate and orchestrate the process.
Prof. Adi Kimchi and Yuval Gilad
 
Cell death is so important to the body that it has at least three different pathways for accomplishing this: apoptosis, autophagy and necrosis. As opposed to the latter, which is a violent death generally due to wounds or infection, apoptosis is a considered and planned rapid suicide. It often comes into play during development, when the embryo is constantly being remodeled, or later, when damage to the DNA of a cell threatens to turn it cancerous. Autophagy, unlike necrosis or apoptosis, does not always lead to cell death: It can be a survival mechanism, shutting down parts of the cell’s functioning in stressful conditions and recycling nonessential proteins for emergency use. But when needed, this same mechanism can also recycle the cell out of existence.

Until recently, researchers had thought that apoptosis and autophagy were like independent walled cities, each with its own separate system of roads. But recent research in Kimchi’s lab reveals a more modern landscape, in which the two pathways veer into one another’s territory, interconnected by crisscrossing trails.

To map out the region where the two pathways meet, Kimchi and research student Yuval Gilad created an experimental system to check for interactions between the proteins in both pathways. Gilad did this by attaching pieces of a protein called luciferase – the molecule that makes bioluminescent plankton glow – to the pathway proteins. In the experiment, the luciferase emitted light when two proteins with matching halves met, thus reporting on a connection between these pairs. Each connection then added another line to the map. This new map was recently published in Cell Reports.
 
 
Mapping cell death: The protein-protein interactions discovered and mapped out in Prof. Adi Kimchi’s lab (red lines are newly-revealed interactions) divulge the wealth of interconnections between two major cell death pathways
 

 

 
 
All together, after testing thousands of possible pairs, Kimchi and Gilad identified 46 new interactions, “each with a story to tell,” says Kimchi. Next, they zoomed in on one particular location on the map, a protein known as DAP kinase 2 (DAPK2). DAP kinases, a family of proteins discovered nearly two decades ago in Kimchi’s lab, play a prominent role in apoptosis. But the six lines on the map leading to and from DAPK2 suggested that it is active in both pathways. Zooming in further, the researchers looked closely at one of its connections – an interaction with a protein known as 14-3-3. The protein 14-3-3 binds to a unique region on DAPK2, preventing it from assuming its active form. The discovery of this interaction revealed a new layer of regulation on DAPK2 activity. Since it’s activation can lead to cell death, says Kimchi, it will be interesting to look for treatments that activate DAPK2 in cancer cells by inhibiting its interaction with 14-3-3.
 
DAPK2 map
The new map reveals just how complex the business of cell death can be. The researchers believe that the interconnections between the pathways provide the cell with a backup in case one of them fails. This is especially important when a cell that could be cancerous needs to self-destruct; the growth of cancer usually involves a failure of the cell death pathways. Kimchi and Gilad say that this map and the method they used to create it could provide a valuable tool to both cancer researchers and drug developers. Not only has it revealed a rich new landscape of protein interactions, it can expose the stages at which these interactions occur. Since cancer cells tend to evade death, drug designers might attempt to target specific stages of the cell death process in order to encourage the cells to “commit suicide.” The new map can help highlight the better targets for drug screening and the reporters detected in the study can be used as tools for the identification of such drugs.

Prof. Adi Kimchi's research is supported by the Helen and Martin Kimmel Institute for Stem Cell Research; the EMET Prize sponsored by the A.M.N. Foundation for the Advancement of Science, Art and Culture in Israel; and the estate of Katherine and Ladislaus Braun.
 
 

 
 
 
 
Mapping cell death: The protein-protein interactions discovered and mapped out in Prof. Adi Kimchi’s lab (red lines are newly-revealed interactions) divulge the wealth of interconnections between two major cell death pathways
Life Sciences
English

Master Key

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Dr. Elik Chapnik, Natali Rivkin and Dr. Eran Hornstein
 
It takes only a tiny key to open a door wide or set large machinery in motion. Dr. Eran Hornstein of the Weizmann Institute’s Molecular Genetics Department and his team recently discovered such a key – one that unlocks the cellular machinery for producing mature blood cells. That key is a minuscule, hairpin-shaped RNA belonging to a class of RNA strands so small they had long been ignored. Even now, these so-called microRNAs are too often thought to be secondary to the cell’s major processes. The new findings suggest that microRNAs can also be master keys, putting several vital processes into motion at once.

In collaboration with Prof. Steffen Jung of the Immunology Department and his coworkers Dr. Elik Chapnik, Natali Rivkin and Dr. Alexander Mildner, Hornstein discovered that a microRNA called miR-142 was involved in the process by which the immature cells in the bone marrow give rise to all the types of blood cells, including immune cells and the oxygen-bearing red blood cells. In fact, an early hint for the importance of this microRNA had been documented years earlier, in 1989, as it plays a role in a type of B-cell leukemia. But back then, before the era of genomics and before the microRNA revolution, it was thought to be a protein-coding gene.

 

Wild type megakaryocyte
 
The Weizmann researchers looked at a broad lineage of myeloid cells – a group that includes the red blood cells and the platelets that make our blood clot. They were looking for cells in which miR-142 is instrumental, and that could provide a clear insight into its function. Their initial analysis pointed to megakaryocytes as the ideal experimental model.  

Megakaryocytes are very large cells in the bone marrow that generate platelets by budding off bits of their internal cytoplasm. The development of megakaryocytes and their ability to function as they mature depends on a strong, malleable internal structure – the cytoskeleton. In a series of experiments on mouse megakaryocytes, the researchers found that miR-142 is essential to the proper formation of the primary building material of the cytoskeleton – actin fibers. When miR-142 activity was halted, the production of actin was deregulated, and the megakaryocytes were not able to mature and produce platelets.
 
Megakaryocyte in which the microRNA mir-142 has been knocked out
 
Using a large array of techniques in their labs, the researchers were able to reveal the precise activities of miR-142. Their findings, which were recently published in eLife, show that miR-142 is, indeed, a master key that turns on and off a number of different cellular processes; these are crucial to actin production and regulation. To put it another way, microRNA-142 is a “hub” in the cellular network of pathways that keeps the cell growing, dividing, developing and functioning.  
 
According to Hornstein, the impact of microRNA-142 and its mechanism may even go all the way back to the first blood cells in the embryo. In addition, miR-142 malfunctions are likely to show up in certain clotting disorders; but the findings hint that the same miRNA gene may be involved in any number of other blood diseases. Hornstein: “This model for blood cell development is very informative and fruitful. Together with Jung we have already characterized four different cell types in which this miRNA is influential, which is very exciting.” 
 
The implications are clear for microRNA research, says Hornstein, helping cast microRNA in a new light: they can no longer be seen as mere helper molecules that “fine-tune” the cellular pathways; they are also key players with the power to direct the development of the cell.
 
 
 
 
Dr. Eran Hornstein’s research is supported by the Kekst Family Institute for Medical Genetics; the David and Fela Shapell Family Center for Genetic Disorders Research; the Crown Human Genome Center; the Yeda Sela Center; the Nella and Leon Benoziyo Center for Neurological Diseases; the Y. Leon Benoziyo Institute for Molecular Medicine; the Helen and Martin Kimmel Institute for Stem Cell Research; the Nathan, Shirley, Philip and Charlene Vener New Scientist Fund; the Julius and Ray Charlestein Foundation; the Celia Benattar Memorial Fund for Juvenile Diabetes; the Wolfson Family Charitable Trust; the Legacy Heritage Fund; the Adelis Foundation; the Minna-James-Heineman Stiftung; Dr. Sidney Brenner and Friends; Maria Halphen, France; and the estate of Fannie Sherr. Dr. Hornstein is the incumbent of the Helen and Milton A. Kimmelman Career Development Chair.

Prof. Steffen Jung’s research is supported by the Leir Charitable Foundations; the Leona M. and Harry B. Helmsley Charitable Trust; the Maurice and Vivienne Wohl Biology Endowment; the Adelis Foundation; Lord David Alliance, CBE; the Wolfson Family Charitable Trust; the estate of Olga Klein Astrachan; and the European Research Council.
 
Wild type megakaryocyte
Life Sciences
English

Backup

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(l-r) Idan Frumkin, Zohar Bloom-Ackerman, Prof. Tzachi Pilpel, Dr. Orna Dahan and Avihu Yona
 

 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Every cell has an entire legion of translators providing their crucial service. The work of these highly specialized molecules must be efficient yet accurate; research shows that they accomplish this partially through teamwork. When one is hurt or needs help, others provide backup. Research at the Weizmann Institute, which was recently reported in eLife, explains how the backup mechanism works, as well as revealing how evolution enables the cell to cope with change. That change may be an alteration in the cell’s environment that necessitates adaptation, or it could be a change in the cell, itself, that turns it cancerous and then induces further modifications in the protein manufacturing process so as to support the cancer growth.

Translation – the second step in the process of transforming the DNA code to protein – involves a conversation between two different chemical languages: the encoded nucleotide argot of the messenger RNA and the amino-acid vernacular of the proteins. The Rosetta Stone of cellular translation is a two-headed molecule called transfer RNA (tRNA). The side that “speaks” nucleotide is called an anticodon; it identifies a single triple-nucleotide sequence in the messenger RNA, called a codon, which encodes a specific amino acid. The other head on the molecule identifies that amino acid. Simple enough, but the translation team works with added layers of complexity. For example, each of the 20 amino acids can be encoded in a number a different codons, each with its own tRNA. And not all tRNA molecules are equal: Some are encoded in a single gene, and are thus rare in the tRNA legions, while others are found in multiple copies.
 
 
Yeast tRNA. Blue and gray are the anticodon end, purple translates to amino acid. Image: Yikrazuul via Wikimedia Commons
 
Prof. Tzachi Pilpel of the Molecular Genetics Department researches the translation system.  Several years ago, Zohar Bloom, then a research student in Pilpel’s group, created a “library” of mutated yeast cells, each containing a different mistake in one of the cell’s 274 tRNA genes (as well as some with multiple mutations). In particular, they wanted to see how the cell copes with these potentially damaging mutations, and whether it employs a good backup system.

Their research showed that such a backup does, indeed, exist – one that could be called tinkering. The cell patches together a chemical alteration on a similar tRNA molecule so that it can substitute for the missing one. This quick (and reversible) mechanism keeps the cell alive, but it is imperfect: The growth efficiency of yeast cells with a tRNA mutation was about 90% that of a normal cell.

As a quick fix, the chemical modification could be seen as a relative success, but over time, such yeast cells would lose out in the evolutionary fitness race. Can evolution provide a better, more permanent solution to the loss of a tRNA? Pilpel and his lab group, including research students Avihu Yona, Zohar Bloom-Ackerman, Idan Frumkin, Yoav Charpak-Amikam and research fellow Dr. Orna Dahan had a method to test this question in the lab: test-tube evolution. Yeast cells from the library's collection were grown in a robotic system over a period of weeks or months, allowing them to divide and accumulate further mutations. Continuous analysis of the yeast in this system enabled the researchers to track their evolution in real time.

After a month, one of their strains of yeast gave them a surprise: Its development had improved, and now rivaled that of normal yeast. As to why, the team members had two competing theories, and they began to place bets on the eventual outcome. The first theory stated that the solution to the missing tRNA was in another mutation. The second group thought that the recovery was too quick for a mutation of this sort to have taken effect, and the cell must have better tinkering skills to adapt on the similar molecule.
 

 

amino end
 

 

Common genes and rare ones

To settle the issue, the team sequenced all of the genes that coded for relevant tRNA molecules. The result: Those claiming a genetic mutation won the bet. The mutation was in the anticodon of the gene for a different tRNA that binds to the same amino acid, but with a different codon. This mutation was successful because it was in a gene for a common tRNA – there are normally 11 copies of it in the yeast cell. To exclude the possibility that another backup mechanism was at work, the scientists created yeast cells with two mutations – intentionally creating the mutation they had seen and removing the original tRNA. These yeast grew normally.
 
That the evolutionary change in these yeast was so rapid as to seem impossible, but a mathematical analysis showed it was actually not too fast to have occurred in a month of evolution. A likely explanation, says Pilpel, is that for these particular cells there is a large selection of available genes – 11. A mutation in any one of them would be sufficient to solve the problem. When the potential backup tRNA molecules are rare, there would be fewer opportunities for beneficial changes to occur.
 
This raises another question: Why are some tRNAs common and others rare? “Essentially, the question comes down to what the cell profits from having these rare tRNA molecules,” says Pilpel. “The answer we have proposed is that rareness functions as ‘punctuation’ – like a period at the end of a sentence that creates a pause in the flow.”  Such pauses are necessary because of protein folding – a process that takes place as translation proceeds. Slowing down translation at various points gives the tricky task of proper folding a chance to catch up. To demonstrate, the scientists added extra copies of these tRNAS to the yeast cells, so they were no longer rare. The result was a complete collapse of the protein folding process.  In other words, to work as a team, tRNA molecules need to be available to back up their friends, but also need to know when to make themselves scarce.
 
Prof. Yitzhak Pilpel's research is supported by the Sharon Zuckerman Laboratory for Research in Systems Biology; the Braginsky Center for the Interface between Science and Humanities; and the European Research Council. Prof. Pilpel is the incumbent of the Ben May Professorial Chair.
 
 
 
 

 

 
Yeast tRNA. Blue and gray are the anticodon end, purple translates to amino acid. Image: Yikrazuul via Wikimedia Commons
Life Sciences
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Chromosomes Show Off their Shapes

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Chromosomes – the 46 tightly-wrapped packages of genetic material in our cells – are iconically depicted as X-shaped formations. However, those neat X’s only appear when a cell is about to divide and the entire contents of its genome duplicated. Until now researchers have not been able to get a good picture of the way that our DNA – some two meters of strands all told – is neatly bundled into the nucleus while enabling day-to-day (non-dividing) gene activity. A combination of new techniques for sequencing DNA in individual chromosomes and analyzing data from thousands of measurements has given us a new picture of the 3-D structures of chromosomes. This method, the result of an international collaboration, which was recently reported in Nature, promises to help researchers understand the basic processes by which gene expression is regulated and genome stability maintained.


Prof. Amos Tanay of the Weizmann Institute’s Computer Science and Applied Mathematics and the Biological Regulation Departments develops advanced computer algorithms for analyzing genomic datasets, which can run to billions of bits of information. He and his team, including PhD students Yaniv Lubling and Eitan Yaffe, joined forces with Dr. Peter Fraser of the Babraham Institute, UK, in an attempt to resolve chromosomal architectures at an unprecedentedly high resolution. Rather than the traditional microscopy techniques, they harnessed the power of modern high-throughput DNA sequencing. Fraser and his team developed a sophisticated sequencing method for taking thousands of measurements of the contacts between genes inside single cells. While these techniques vastly improve upon approaches that average the conformations of millions of chromosomes, the data generated from just the few trillionths of a gram of DNA present within a single cell can only be interpreted by advanced statistical methods. Tanay and his team performed the complex computer analysis that turned millions of DNA sequences into reliable maps describing contacts between genes along individual chromosomes. Given these maps, the team, in collaboration with Dr. Ernest Laue of Cambridge University, UK, was able to produce 3-D models of individual chromosome structures.

Interestingly, the new high resolution depictions of chromosomal architecture indicate that the structure of the same DNA molecule can vary markedly between different cells. At the same time, the results point to some basic principles that underlie the genes’ organization. Their arrangement appears to be modular and based on the functions of the thousands of genes embedded within each chromosome. The data suggests that chromosomes expose the more active genes at their boundaries, possibly allowing these genes better access to the cellular machinery that regulates them.

Besides giving us a unique, surprising view of the structure of the chromosomes in our cells, the researchers believe that their method will present genetics research with a powerful new tool. For example, it may help uncover the variations in genetic activity between different types of cells, or promote understanding of the mechanisms determining gene activity or quiescence in various normal or disease conditions. The rapidly increasing power of massive DNA sequencing promises to make studies such as this even more powerful in the near future.
 

Video produced by BBSRC

Prof. Amos Tanay’s research is supported by the Helen and Martin Kimmel Award for Innovative Investigation; Pascal and Ilana Mantoux, Israel/France; the Wolfson Family Charitable Trust; the Rachel and Shaul Peles Fund for Hormone Research; and the estate of Evelyn Wellner.


 
Life Sciences
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Bacterial Booby Traps Revealed

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Growth of bacteria when only antitoxin is induced (left), only toxin is induced (middle), and both are induced together (right)

 

 

 
 
 
 
 
 
 
 
 
 
 
 
Bacteria can be veritable poison factories. In addition to those that harm humans, such as tetanus and botulism, or the toxins they produce to compete with other microorganisms, we now know that bacteria can produce poisons especially for committing suicide. Indeed, many bacteria carry around a sort of “suicide pill,” which comes with its own antidote. To do itself in, the bacterium simply does away with the antidote. Recent Weizmann Institute research revealed many novel versions of these suicide pills in bacteria and showed that they help the bacteria resist viral attacks.

Suicide is most often a last-ditch response to one of the viruses that invade bacterial cells. If the cell cannot overcome the infection, it may take its own life to prevent the virus from spreading to neighboring bacteria. Understanding how the suicide pill mechanism works may, on the one hand, help protect useful bacteria like those in yogurt cultures from viral assault and, on the other, lead to the development of new antibiotic drugs against harmful bacteria. In addition, it could yield new insights into treating such scourges as tuberculosis.
 
Drs. Rotem Sorek and Azita Leavitt
 
Dr. Rotem Sorek and his team in the Institute’s Molecular Genetics Department, working with Dr. Udi Qimron of Tel Aviv University, discovered the suicide mechanism using a method for identifying toxic bacterial genes that he had developed several years ago, when he realized that a drawback of a common technique for sequencing bacterial genomes could be a unique research tool in disguise. The technique of genome sequencing involves cutting up the bacterial genome and inserting the pieces into another bacterium – E. coli – for duplication and further sequencing. But this method always left gaps in the sequence. Sorek understood that the missing genes encoded toxins that killed the host E. coli cells. Building on this insight, he developed a computerized method for identifying these killer genes. Recently, together with his research team, he created an online database called PanDaTox containing some 40,000 sequences for genes encoding bacterial toxins.

But some instances of cell-killing genes seemed to be less than clear-cut: While many of the toxins killed the host E.coli cells outright, others seemed to be more sporadic – destroying them only part of the time. This led Sorek and his team to surmise that certain suicide mechanisms involve pairs of genes – one for a toxin, the other for an antitoxin.
 
Hila Sberro
         
In their study, which appeared recently in Molecular Cell, Sorek and research students Hila Sberro and Dr. Azita Leavitt went looking for toxin-antitoxin pairs. Their quest involved analyzing the results after inserting over a million genes from hundreds of microbial genomes into E. coli cells. When only the toxin gene was present, the E. coli cells died, but when both toxin and antitoxin were present, the genes for both were cloned in the cells. The researchers tentatively sorted into different families all of the toxin-antitoxin pairs they identified and explained how they function.

The team found that the toxin-antitoxin mechanism works something like a booby trap. The toxin molecule – which, as they discovered, can come in many different forms – is highly stable. The antitoxin that fits it, however, is a sort of hair-trigger component that is fragile and easily destroyed, so the supply must be constantly renewed. So when a virus takes over the cell and attempts to hijack its DNA production machinery, the frail antitoxin is destroyed, leaving the toxin free to kill the cell and the viruses along with it.
 
sorek infographic
 
 
Among other things, the study may yield some important insights into such hard-to-treat diseases as tuberculosis. Not only are new strains of TB appearing that are increasingly resistant to known antibiotics, but even the common forms of the disease require many months of treatment to rid the body of all the pathogens. The research helps explain why. TB-causing bacteria contain unusually large numbers of toxic genes, and the team identified some new ones. Their findings support the idea that some of those toxin-antitoxin mechanisms merely cause the cells to fake their own suicides: Though they appear to be dead, these cells are actually only dormant. Since only active cells are killed by the antibiotic drugs, these must be administered until all the bacteria have come out of dormancy. In the future, says Sorek, methods to prevent dormancy could shorten and improve TB treatment.

The findings have also yielded a number of new insights into the strategies that bacteria use in their evolutionary battle with viruses, and these, in turn, may have implications for industry as well as biomedical research. For instance, food industries that rely on bacterial cultures have already shown interest in new methods for boosting bacterial resistance to viral infection. The same findings might, in the future, lead to the development of novel antibiotic drugs based either on the new types of toxin molecules the team discovered or on substances that can interfere with the toxin-antitoxin mechanism.
 
 
 

Dr. Rotem Sorek’s research is supported by the Y. Leon Benoziyo Institute for Molecular Medicine; the Abisch Frenkel Foundation for the Promotion of Life Sciences; the European Research Council; the Leona M. and Harry B. Helmsley Charitable Trust; and the Hugo and Valerie Ramniceanu Foundation. Dr. Sorek is the incumbent of the Rowland and Sylvia Schaefer Career Development Chair in Perpetuity.

 
 
Life Sciences
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