Weizmann Institute Scientists discover: How an Injured Embryo Can Regenerate Itself and Keep its Organs in Relative Proportion

English

More than 80 years have passed since the German scientist Hans Spemann conducted his famous experiment that laid the foundations for the field of embryonic development. After dividing a salamander embryo in half, Spemann noticed that one half – specifically, the half that gives rise to the salamander’s 'belly'(ventral) starts to wither away.

 

However, the other 'back' (dorsal) half that develops into its head, brain and spinal cord, continues to grow, regenerating the missing belly half and develops into a complete, though be it smaller, fully functional embryo. Spemann then conducted another experiment, where this time, he removed a few cells from the back half of one embryo and transplanted them into the belly half of a different embryo.

 

To his surprise, this gave rise to a Siamese twin embryo where an extra head was generated from the transplanted cells. Moreover, although the resulting embryo was smaller than normal, all its tissues and organs developed in the right proportions irrespective of its size, and functioned properly. For this work, Spemann received the Nobel Prize in Physiology or Medicine in 1935.

 

But how does this happen? How exactly is the half embryo able to maintain its tissues and organs in the correct proportions despite being smaller than a normal sized embryo?

 

Despite many years of research, this question has remained unanswered – until now. More than 80 years since Spemann’s classic experiment, Profs. Naama Barkai, Benny Shilo and research student Danny Ben-Zvi of the Weizmann Institute of Science’s Molecular Genetics Department, together with Prof. Abraham Fainsod of the Hebrew University-Hadassah School of Medicine, Jerusalem, have finally discovered the mechanisms involved.

 

Previous studies have shown that the growth and development of cells and organs within the embryo is somehow linked to a special group of substances called morphogens. These morphogens are produced in one particular area within the embryo and then spread throughout the entire embryo in varying concentrations. Scientists then began to realize that the fate of embryo cells, that is to say, the type of tissue and organ they are eventually going to develop into, is determined by the concentration of morphogen that they come into contact with.

 

But this information does not answer the specific question as to how proportion is maintained between organs?

 

The idea for the present research came about when Weizmann Institute scientist Prof. Naama Barkai and her colleagues developed a mathematical model to describe interactions that occur within genetic networks of an embryo. The data ascertained from this model suggest that the way morphogens spread throughout the embryo in different concentrations is different than previously thought. The team predicts that an inhibitor molecule, which is secreted from a localized source at one side of the embryo and can bind the morphogen, acts as a type of ferry that 'shuttles' the morphogen to the other side. Therefore, the mathematical model suggests that it is the interactions between the two substances that enable the embryo to keep the relative proportion between organs constant, irrespective of its size. Indeed, these predictions have been validated by experiments conducted on frog embryos by the research team.

 

The importance of the role of these morphogenic substances, as well as their mechanism of action, is evident by the fact that they have been conserved throughout evolution, where different variants can be found to exist in species ranging from worms to fruit flies and up to higher species including humans. Therefore, understanding the processes that govern embryonic cell development could have many implications. For example, it may lead, in the future, to scientists being able to repair injured tissues.
        
Prof. Naama Barkai's research is supported by the Kahn Family Foundation for Humanitarian Support; the Helen and Martin Kimmel Award for Innovative Investigation; the Carolito Stiftung; the Minna James Heineman Stiftung; the PW-Iris Foundation; and the PW-Jani. M Research Fund.
      
Prof. Benny Shilo's research is supported by the Y. Leon Benoziyo Institute for Molecular Medicine; the Dr. Josef Cohn Minerva Center for Biomembrane Research; the J & R Center for Scientific Research; the Jeanne and Joseph Nissim Foundation for Life Sciences Research; and the Mary Ralph Designated Philanthropic Fund. Prof. Shilo is the incumbent of the Hilda and Cecil Lewis Professorial Chair in Molecular Genetics.


The Weizmann Institute of Science in Rehovot, Israel, is one of the world's top-ranking multidisciplinary research institutions. Noted for its wide-ranging exploration of the natural and exact sciences, the Institute is home to 2,600 scientists, students, technicians and supporting staff. Institute research efforts include the search for new ways of fighting disease and hunger, examining leading questions in mathematics and computer science, probing the physics of matter and the universe, creating novel materials and developing new strategies for protecting the environment.

 

Weizmann Institute news releases are posted on the World Wide Web at http://wis-wander.weizmann.ac.il/, and are also available at http://www.eurekalert.org/.

Space & Physics
English
  • Ben-Zion Shilo
  • Embryonic development
  • Naama Barkai
  • Organ repair
  • Transplant

Complex Channels

English

Weizmann Institute scientists discover how ion channels are organized to effectively control nerve cell communication

 

The messages passed in a neuronal network can target something like 100 billion nerve cells in the brain alone. These, in turn communicate with millions of other cells and organs in the body. How, then, do whole cascades of events trigger responses that are highly specific, quick and precisely timed? A team at the Weizmann Institute of Science has now shed light on this mysterious mechanism. Their discovery could have important implications for the future development of drugs for epilepsy and other nervous system diseases. These findings were recently published in the journal Neuron.

 

The secret is in the control over electrical signals generated by cells. These signals depend on ion channels – membrane proteins found in excitable cells, such as nerve cells – that allow them to generate electrical signals, depending on whether the channels are opened or closed. Prof. Eitan Reuveny, together with Ph.D. students Inbal Riven and Shachar Iwanir of the Weizmann Institute’s Biological Chemistry Department, studied channels that work on potassium ions and are coupled to a protein called the G protein, which when activated, causes the channel to open. Opening the channel inhibits the conductance of electrical signals, a fact that might be relevant, for example, in the control of seizures.

 

The G protein itself is activated by another protein, a receptor, which gets its cue to carry out its task from chemical messengers known as neurotransmitters. But neurotransmitters are general messengers – they can inhibit as well as excite, and the receptors can respond to either message. How, the scientists wanted to know, is the G protein targeted so quickly and precisely to activate the channel?

 

Reuveny and his team found that the receptor and G protein are physically bound together in a complex, allowing the process to be finely tuned. When the receptor receives a chemical message from the neurotransmitter, it is already hooked up to the correct G protein. After being activated by the receptor, the G protein changes shape, opening the ion channel. The evidence for this complex structure came from special technique called FRET (Fluorescence Resonance Energy Transfer) that can measure the distance between two molecules. The scientists observed that even without stimulation, there is a lot of energy transfer between the G protein and the potassium channel, suggesting that they are very close together.

 

Mutations in ion channels are likely to be involved in epilepsy, chronic pain, neurodegenerative diseases and muscular diseases, and ion channels are the target of many drugs. Understanding the basic biological phenomena behind the way proteins organize themselves and orchestrate biological processes may allow scientists to design better or more efficient drugs.  
  
Prof. Eitan Reuveny’s research is supported by the Y. Leon Benoziyo Institute for Molecular Medicine; the Clore Center for Biological Physics; and the Dr. Josef Cohn Minerva Center for Biomembrane Research.

Life Sciences
English
  • Biochemistry
  • Eitan Reuveny
  • Ion channel
  • Neuron
  • Neurotransmitter

Israeli Scientists Reveal the Plan of a Key Cellular Machine

English

The new study gives scientists insight into how the DNA code is turned into instructions for protein construction

 

A team of scientists from the Weizmann Institute of Science and the Hebrew University of Jerusalem has revealed the structure of a cellular editor that “cuts and pastes” the first draft of RNA straight after it is formed from its DNA template. Many diseases appear to be tied to mistakes in this process, and understanding the workings of the machinery involved may lead to the ability to correct or prevent them in the future.

 

Since the discovery, around 25 years ago, that the bits of DNA in the genes that code for protein formation are interspersed with “filler” segments that have no known function, scientists have worked to understand the process by which the right sequences are lifted out and strung together to make a coherent set of instructions. This act, referred to as “RNA splicing,” takes place in the “spliceosome” situated in the cell nucleus. A large complex of proteins and short strands of RNA, the spliceosome distinguishes the beginnings and ends of coded segments, precisely cutting and stitching them together. Alternative splicing, which underlies the huge diversity of proteins in the body by allowing segments of the genetic code to be strung together in different ways, takes place in the spliceosome as well. 

 

The team consisted of husband-and-wife scientists Prof. Ruth Sperling of the Genetics department of the Hebrew University and Prof. Joseph Sperling of the Organic Chemistry Department of the Weizmann Institute, Ruth’s graduate student Maia Azubel, and Sharon Wolf of the Chemical Research Support Department at the Institute. They produced the most detailed 3-D representation of the spliceosome’s structure to date with their study, published today in Molecular Cell. Rather than follow previous attempts to unravel the workings of the splicing mechanism by studying spliceosomes created in test tubes, they managed to take spliceosomes directly from living cells and examine them under an electron microscope. 

 

Their task was made difficult by the fact that spliceosomes in living cells are made up of four identical modules strung together like beads on a strand of RNA, each a miniature spliceosome capable of splicing on its own. The connections between the modules tend to be flexible, allowing the position of the units to vary in relation to each other. Thus pinning down a definitive shape and structure for the whole complex has been, until now, nearly impossible.

 

The team found a way to cut the RNA connections between the modules without harming the integral short strands of RNA that are essential to the splicing process, so they could study them individually. Split-second freezing at very low temperatures allowed the scientists to view the spliceosome units in as close to a natural state as possible. From thousands of images, each at a slightly different angle, a composite 3-D structure of the spliceosome was built up. 

 

The revealed structure has two distinct, unequal halves surrounding a tunnel. The larger part appears to contain proteins and the short segments of RNA, while the smaller half is made up of proteins alone. On one side, the tunnel opens up into a cavity, which the researchers think functions as a holding space for the fragile RNA waiting to be processed in the tunnel itself.

 

What they didn’t see may be as important as what they saw. Whereas researchers examining splicing in test tubes saw evidence of a complicated sequence of events in which the spliceosome machinery assembles itself anew for each splicing job, the team’s investigations of spliceosomes from live cells found splicing to take place in pre-formed machines. This fits in with what is known about the way cells optimize their workload.  “It’s much more efficient to have a machine on hand, ready to go, than to build a new one each time,” they noted.

 

Prof. Sperling's research is supported by the Joseph and Ceil Mazer Center for Structural Biology, the Helen and Milton A. Kimmelman Center for Biomolecular Structure and Assembly, the J. and R. Foundation, and Lois Zoller, Chicago, IL. He is the incumbent of the Hilda Pomeraniec Memorial Chair of Organic Chemistry.

 

A view of the spliceosome showing internal details

 

Front and side views of the spliceosome

(above) A view of the spliceosome showing internal details
(below) Front and side views of the spliceosome

 

Chemistry
English
  • 3-D structure
  • Electron microscopy
  • Joseph Sperling
  • Organic Chemistry
  • RNA splicing

New method tracking single atoms may lead to improved drug design

English
Until now, scientists studying the workings of ultra-microscopic forms have had to rely on the scientific equivalents of still photos, something like trying to fathom driving by looking at a photograph of a car. Now, Prof. Irit Sagi and her team, of the Structural Biology Department, are using new and innovative methods developed at the Weizmann Institute to see real time “video clips” of enzyme molecules at work. The resolution of these animated clips is so fine that the scientists are able to see the movements of individual atoms within the molecule.
 
The challenge facing the Weizmann team was to capture, step-by-step, the complex process (the whole of which takes place in a tiny fraction of a second) that an enzyme molecule goes through as it performs its work. Their pioneering method was published in Nature Structural Biology. It was hailed as the first of its kind, and a potentially important tool for biophysicists. 
 
To obtain the “live action” footage, Sagi and her team use a technique akin to stop-action photography, but on an infinitely smaller scale. They literally freeze the process at certain stages, using advanced methods of chemical analysis to determine the exact molecular layout at each stage. The most difficult part, says Sagi, was figuring out the correct time frames that would allow them to see each phase of enzyme activity clearly. She compares it to attempting to capture on film the swirling of syrup being mixed into cake batter – one has to gauge at what points individual stages of the process will be most visible.
 
Building an animated sequence from individual frames, the scientists are granted a rare peek into the intricate dance of life on the molecular level. “This method,” says Sagi, “represents more than a major breakthrough in the techniques used to understand enzyme activity. It changes the whole paradigm of drug formulation. Now we can precisely identify which parts of the molecule are the active regions (those which directly perform tasks), and the exact permutations of these molecular segments throughout the whole process. New, synthetic drugs can be designed to target specific actions or critical configurations.”
 
Sagi’s team is doing just that for one enzyme family known to play a role in cancer metastasis. Matrix metalloproteinases (MMPs), assist the cancer cells’ escape and entry into new tissues by breaking down the structural proteins that keep cells in place, a skill normally needed to clear out tissue in preparation for growth or repair. Using the knowledge gained by the new technique, the team designed a molecule to block MMPs at one crucial step in their dance. 
 
Prof. Irit Sagi’s research is supported by the Avron-Wilstatter Minerva Center; the Helen and Milton A. Kimmelman Center for Biomolecular Structure and Assembly; the Ceil and Joseph Mazer Center for Structural Biology; the Jakubskind-Cymerman Prize; the Laub Fund for Oncogene Research; Prof. Clotilde Pontecorvo, Italy; and Verband der Chemischen Industrie.
Chemistry
English
  • Enzyme›Enzyme
  • Irit Sagi
  • Structural Biology

Scientists Discover Enzymes Capable of Duplicating Damaged Genetic Material, Creating New Mutations

English

 

Genetic material (DNA) is damaged on a daily basis due to environmental factors, such as solar radiation and exposure to certain hazardous materials, as well as natural cell processes. This damage can leave chaos in its wake, scrambling or deleting the genetic 'letters' encoding an organism's traits. If left unchecked, the mutated DNA will continue to replicate, and may cause impaired protein production and disease.

 

Fortunately, all organisms employ various cellular DNA repair systems. In most cases, however, they perform on an 'all or nothing' basis: when unable to precisely correct the damage they stop operating, halting genetic replication entirely. The end result, even more severe than the initial damage, is that of cell death.

 

The key to life is therefore the cell's ability to 'compromise,' allowing DNA repair systems to operate with a certain 'sloppiness' that permits a small number of mutations. While this may pose a certain risk, it also ensures the cell's continued existence. Equally important, it increases genetic diversity allowing natural selection, the driving force behind evolution, to come into play.

 

Prof. Zvi Livneh of the Weizmann Institute's Biological Chemistry Department has discovered a group of enzymes that perform one such mechanism. His latest findings are reported in the Proceedings of the National Academy of Sciences (PNAS, USA).

 

Genetic material is constantly duplicated as an integral part of cell division and reproduction occurring in all living beings. In dividing, the cell unzips the DNA double helix (consisting of two winding strands linked together by matching base pairs) using each strand as a template to direct the formation of its companion strand. Overseeing this process is a unique enzyme known as DNA polymerase, that 'rides' on board the existing strand much like a train on a single track, reading its genetic sequence to form a matching strand. The result, generally achieved with remarkable precision, is two identical DNA molecules, each consisting of an original and a newly synthesized strand. Upon encountering damaged DNA, this duplicating enzyme usually stops in its tracks - which is where the specialized 'damage control' crews enter the scene.

 

Prof. Livneh has recently discovered one of these DNA repair mechanisms, based on a previously unknown group of polymerase enzymes. While these enzymes also duplicate genetic material, they usually do not stop when encountering damaged DNA. Instead, they duplicate the material, often creating new mutations.

 

According to Livneh, this family of enzymes, which is found in both humans and bacteria, is one of the most important factors preventing unnecessary cell destruction and driving the evolutionary process. The flip side, however, is that by enabling bacteria to rapidly evolve new genetic characteristics, these enzymes are also responsible for the increasing bacterial resistance to antibiotic drugs. The recent Weizmann Institute discovery of a particular member of this enzyme family, known as DNA polymerase R1, may open a new course of action against this growing health threat. By suppressing the activity of R1 and other similar DNA polymerases it may be possible to slow the spread of antibiotic-resistant bacteria.

 

Another potential application is the reconstruction of damaged DNA left at crime scenes, or ancient DNA found in the remains of prehistoric plants and animals. These two forms of DNA are often damaged (for instance, by cleaning detergents aimed at destroying the evidence left at a crime scene, or simply the ravages of time in the case of ancient DNA). 'Previous reconstruction attempts using known DNA polymerase agents were often hindered, since even localized DNA lesions can cause these enzymes to stop operating, dooming the entire reconstruction process,' explains Livneh. 'The 'sloppy' R1 duplicating enzyme may prove pivotal in this respect due to its ability to tolerate damaged genetic material.'

 

Prof. Zvi Livneh holds the Maxwell Ellis Professorial Chair in Biomedical Research. His research is supported by the Dolfi and Lola Ebner Center for Biomedical Research and the Minerva Foundation, Germany.

 

The Weizmann Institute of Science is a major center of scientific research and graduate study located in Rehovot, Israel. Its 2,500 scientists, students and support staff are engaged in more than 1,000 research projects across the spectrum of contemporary science.

Life Sciences
English
  • Antibiotics›Antibiotic resistance
  • Error-prone DNA repair
  • Zvi Livneh

Weizmann Institute Scientists Capture The First-Ever 3D Visualization Of How Molecules Break Apart When Exposed To X-Rays

English

 

'Vision is the art of seeing things invisible,' wrote master of fantasy, Jonathan Swift. His voyages to kingdoms of changing visual scales served to emphasize the potential insights to be gleaned from viewing the world through continuously fresh perspectives.


Weizmann Institute researchers have recently demonstrated this principle's applicability to the art of scientific discovery. A decision on their part to change an experimental focus resulted in their capturing the first ever time-resolved 'movie' demonstrating how molecules break apart when exposed to synchotron radiation. Their findings, published in the January 18th issue of the Proceedings of the National Academy of Science USA (PNAS) may pave the way to improved techniques for studying biological molecules, as well as to pharmacological measures for preventing high-dose radiation damage, a common cause of cancer and birth defects.


The Weizmann scientists participating in this study were Dr. Gitay Kryger, Dr. Michal Harel and Prof. Joel Sussman of the Structural Biology Department, together with Prof. Israel Silman of the Neurobiology Department. The team worked in close collaboration with Martin Weik, Maria Raves, Piet Gros, and Jan Kroon from Holland's Bijvoet Center for Biomolecular Research at Utrecht, as well as Raimond Ravelli and Sean McSweeney of the European Molecular Biology Laboratory Outstation at Grenoble, France.


Breaking the Bonds

'In science, it is quite common to seek answers to one question and find answers to entirely different ones,' says Dr. Kryger, providing the background to their discovery. 'While looking down one avenue, we were essentially sidetracked into an alley, with perhaps even broader applications.'


In the course of studying one of nature's most intriguing enzymes, acetylcholinesterase (AChE), which plays a pivotal role in brain function and memory, the team decided to examine its enzymatic reaction in 'real-time', using X-ray crystallography, based on exposing crystals of the enzyme to high intensity X-ray beams.


Since this enzyme's reaction proceeds within microseconds, the researchers hoped to record the process by taking an extremely rapid series of X-ray 'snapshots.' The results, in fact, indicated a time-dependent change. However, upon closer examination, the researchers realized that in their attempt to capture the enzymatic reaction, they had actually obtained the first-ever 3D recording of radiation-induced breakage of specific chemical bonds in the protein. 'The observation was stunning. While the time-series movie looks like a simulated animation of chemical processes, we knew that we were seeing a direct experimental observation - something that had never been seen before,' said Prof. Sussman.


Subsequent studies revealed that, contrary to the previously held belief, radiation damage could actually be highly specific. The team found that disulfide bonds (which often bridge protein polypeptide chains) and carboxyl acids (such as those found at the 'active site,' where enzymatic reactions are initiated) are particularly prone to radiation damage. They also found a cross-species similarity, suggesting a more general phenomenon. Highly similar results were obtained when working with AChE crystals derived from the Torpedo fish (one of the richest sources of this enzyme), humans, and the Drosophila fruit fly, as well as from a different enzyme entirely, hen egg white lysozyme.


Less may be More

These findings have direct implications for improving data collection using X-ray crystallography. This technology presents significant challenges. While providing a dramatic glimpse into heretofore inaccessible microscopic worlds, it simultaneously introduces radiation damage, thereby often destroying the experimental sample. The crystallographic community has traditionally walked a thin experimental line, trying to enhance information gathering via increased X-ray intensity, while mitigating radiation damage through various techniques, in particular cryo-crystallography (data collection at extremely cold temperatures).


According to Dr. Kryger, 'One of the most important 'take-home' lessons is that in the attempt to better understand biological molecules, less intensive radiation may provide more accurate results. The key is to avoid introducing inadvertent changes into experimental samples, such as those induced by radiation damage.'


A Diagnostic Tool

However, radiation damage and its prevention is a central issue which 'spills over' beyond laboratory walls. Organisms are constantly exposed to potentially detrimental radiation, whether from sunlight or radioactive materials. Such radiation, at high levels, is a common cause of cancer and birth defects. According to Prof. Sussman, 'The ability to visualize the specific damages caused by radiation on a 'test-tube' level offers an important diagnostic tool for developing pharmacological means to protect against radiation damage. These measures could be applied on a conventional or emergency situation basis, such as that which followed the Chernobyl nuclear power plant failure.' The Weizmann Institute team plans to collaborate with its European counterparts in examining the anti-radiation potential of various substances.


X-ray radiation from a synchrotron source can rapidly damage, in a very specific way, the structure of a protein, as seen by X-ray crystallography. The four images represent a series of electron density maps collected from the same protein crystal. Protein degradation is indicated by the disappearance of the disulfide bond (yellow bar, surrounded by empty blue cage) linking the carbon chains (white balls). These images represent the first-ever recording of experimentally-induced chemical bond breakage using X-ray crystallography.

 


This study was funded by the U.S. Army Medical and Materiel Command, The European Union 4th Framework Program in Biotechnology, the Kimmelman Center for Biomolecular Structure and Assembly (Rehovot, Israel), and the Dana Foundation. The generous support of Mrs. Tania Friedman is gratefully acknowledged. RBGR acknowledges support from the TMR Access to Large Scale Facilities to the EMBL Grenoble Outstation.


Prof. Israel Silman, a member of the Weizmann Institute's Neurobiology Department, holds the Bernstein-Mason Chair of Neurochemistry. Prof. Joel Sussman is a member of the Weizmann Institute Structural Biology Department and has a joint appointment at the Brookhaven National Laboratory in New York.


The Weizmann Institute of Science is a major scientific research graduate study located in Rehovot, Israel. Its 2,500 scientists, students and support staff are engaged in more than 1,000 research projects across the spectrum of contemporary science.
 

 
 
X-ray radiation from a synchrotron source can rapidly damage, in a very specific way, the structure of a protein, as seen by X-ray crystallography. The four images represent a series of electron density maps collected from the same protein crystal. Protein degradation is indicated by the disappearance of the disulfide bond (yellow bar, surrounded by empty blue cage) linking the carbon chains (white balls). These images represent the first-ever recording of experimentally-induced chemical bond breakage usin
Chemistry
English
  • AChE›AChE
  • Israel Silman
  • Joel Sussman
  • Neurobiology
  • Structural Biology
  • X-ray crystallography

Key Progress by Weizmann Scientists in the Race to Unravel Ribosomal Structure

English
A team of Weizmann Institute and Max-Planck Society scientists has determined the structure of the small ribosomal subunit at the highest resolution ever achieved, including the site where protein biosynthesis begins.

Ribosomes, the universal cellular organelles responsible for protein production, are essential to life. Receiving genetically encoded instructions from the cell nucleus, the ribosomal factory churns out proteins - the body's primary component and the basis of all enzymatic reactions. Understanding protein biosynthesis is therefore the gateway to grasping life itself, and it's darker side -- the emergence of disease when production goes haywire.

This explains why ribosomes have been the target of numerous biochemical, biophysical, and genetic studies. However, throughout nearly four decades of research, these pivotal biological units have stubbornly "resisted" scientific attempts to reveal their detailed functional design.
 
In order to examine microscopic structures scientists expose crystals of the material in question to high intensity x-ray beams - a method known as x-ray crystallography. However, the ribosome, a notoriously unstable giant protein complex, represents a daunting crystallographic challenge. To further complicate matters, it also lacks the internal symmetry and repetitions that eased the way to understanding the structure of other biological entities, such as viruses.
 
Nevertheless, using novel crystallographic techniques, Professor Ada Yonath of Weizmann's Department of Structural Biology and the Max-Planck Research Units for Ribosomal Structure in Hamburg and Berlin, has now overcome this obstacle. Her study, due to appear in the December issue of the Proceedings of the National Academy of Sciences (PNAS), introduces an electron density map of the small ribosomal subunit from bacterium Thermus thermophilus.
 
The uniqueness of Yonath's approach lies in phasing -- designing heavy atoms as markers that stand out like flares in the ribosomal map due to their high electron density. These markers significantly enhance the ability to pinpoint functional units within the ribosome. And the resultant image, constructed from twice the diffraction data than collected elsewhere, provides a far-reaching glimpse into the microscopic ribosomal world, revealing certain outstanding, heretofore unobserved features.
 

Opening the Ribosomal Gate

Ribosomes consist of two independent subunits of unequal size. It is on "30S", the smaller subunit, that Yonath set her sites. More specifically, she wanted to capture "snapshots" of 30S in its active form - during the precise moment that protein biosynthesis begins. To do so, her team had to first activate the ribosomal particles within the crystal lattice as well as trigger protein biosynthesis. Both tasks called for a creative stretch of scientific imagination.

 
Crystals limit molecular motion, thereby impeding conformational changes. Since controlled heating had previously been shown to enhance ribosomal activation, Yonath decided to take a chance at heating up the crystals despite concerns that this would cause their disintegration. Next, the team introduced an analogue of messenger RNA - a molecular "go-between" arriving from the nucleus, which triggers protein biosynthesis. "The messenger has to attach itself to a specific site in order to open the gate to protein production, which is essentially kept under lock and key," explains Yonath. Once activated and bound, it was time to record the 30S subunit "in the act" -- a feat accomplished by flash freezing the crystals through sudden exposure to cryo-temperature (-185 Celsius).
 
Yonath's findings are the result of almost twenty years of determined experimentation into largely uncharted territories. In the course of her pursuit, she became the first scientist to successfully create ribosomal crystals that diffract to high resolution, around 3 angstroms (1A = 10 -10 meter).
 
Her quest for durable crystals also gave rise to two novel approaches: the use of ribosomal material from hardy bacterial strains isolated from the Dead Sea and cryo-cystallography. This method, which later became standard research procedure in structural biology, is based on exposing crystals to cryo-temperature during x-ray measurements in order to minimize their disintegration.


Future Prospects

The achievements generated by Yonath's team indicate that the road to near-atomic resolution of ribosomal structures is closer than ever before. Their approach and procedures have recently been repeated by a growing contingent of international researchers - all racing to elucidate the mystery of ribosomal functioning. According to Yonath, this understanding should pave the way to improved antibiotics, targeting bacterial agents at the ribosomal level. Additionally, the enhanced understanding of normal protein biosynthesis may one day improve the ability to fight the pathogenic, uncontrolled protein production characteristic of cancer cells.


Prof. Ada Yonath holds the Martin S. Kimmel Professorial Chair. This research was funded by the Max-Planck Society, the US National Institutes of Health (NIH), the German Ministry for Science and Technology and the Kimmelman Center for Macromolecular Assembly at the Weizmann Institute
 
The Weizmann Institute of Science is a major center of scientific research and graduate study located in Rehovot, Israel. Its 2,500 scientists, students and support staff are engaged in more than 1,000 research projects across the spectrum of contemporary science
Space & Physics
English
  • Ada Yonath
  • Cryo-cystallography
  • Ribosome›Ribosome structure
  • Small ribosomal subunit

Protein 'Heroes' Block Genetic Mutations

English

REHOVOT, Israel - November 12, 1997 - Researchers at the Weizmann Institute of Science have discovered that two repair proteins perform a truly "heroic" act, stopping genetic mutations dead in their tracks. In a study reported in the November 14 issue of the Journal of Biological Chemistry , Institute researchers describe how these proteins "fling themselves" onto damaged genes, which, if replicated, lead to the formation of mutations.

 

Mutations are changes in DNA that can cause cancer by turning on cancer-causing genes or turning off the genes that suppress cancer. "If we can fully understand this and other natural DNA repair mechanisms, we may one day be able to turn them on as required in order to prevent cancer," says research team leader Prof. Zvi Livneh of the Weizmann Institute's Department of Biological Chemistry. He conducted the study with Dr. Tamar Paz-Elizur and doctoral student Yoav Barak.

 

Protein valor

DNA damage is a normal part of the life of a cell. Carcinogens, such as ultraviolet radiation or the chemicals in cigarette smoke, routinely damage DNA, leading to numerous mutations. Luckily, DNA can repair itself, relying on proteins known as repair enzymes. These enzymes literally cut out the damaged parts of the DNA and replace them with healthy DNA material. Without them, life on earth would be impossible because mutations would go haywire.

 

Sometimes, however, the damaged DNA escapes repair and a cascade of events leading to cancerous growth can begin. This is precisely where our two heroic proteins, known as Fpg and UvrA, step in. These proteins were previously known to play a role in cut-and-paste DNA repair jobs. But now Prof. Livneh's team has discovered that they are capable of a far more valiant task. By hurling themselves onto the damaged DNA and physically attaching themselves to it, these proteins can prevent the damaged site from multiplying and causing a mutation. According to the scientists, the two "heroic" proteins may be part of a larger family of DNA repair proteins that work on the same principle.

 

This mechanism provides a second line of defense against the mutation and gives the cell a crucial second chance at healthy growth. "The proteins block the road to replication like demonstrators throwing themselves down on the road to block traffic," says Prof. Livneh. "When a protein sits on the lesion and directly binds itself onto the site of the damage, the mutation cannot be formed." Only when this emergency defense mechanism fails, can malignant transformation begin.

 

Building up natural defenses

Weizmann scientists discovered the new role of the two proteins by analyzing E coli bacteria. They will follow up this research by analyzing human cells, Prof. Livneh says.

Every human body contains different kinds and quantities of repair proteins. In each individual they vary in their rate of repair. When scientists learn more about these proteins - determining, for example, which proteins repair what kinds of damage - they may be able to strengthen people's own natural defenses.

Scientists may also one day be able to identify people whose bodies aren't as effective as others at repairing DNA. For example, they may be able to warn people who are more prone to genetic defects induced by ultraviolet radiation to avoid excessive exposure to sunlight.

 

This research was funded in part by the Scheuer Research Foundation of the Israel Academy of Sciences and Humanities, the Israel Ministry of Science, and the Leo and Julia Forchheimer Center for Molecular Genetics at the Weizmann Institute.

 

The Weizmann Institute of Science is a major center of scientific research and graduate study located in Rehovot, Israel.

Space & Physics
English
  • Biological Chemistry
  • DNA damage and repair›DNA repair
  • Mutation
  • Zvi Livneh

Discovery Sheds Light on Increasing Bacterial Drug Resistance

English
REHOVOT, Israel -- April 1, 1997 -- In a study that throws new light on the alarming phenomenon of increasing bacterial drug resistance, researchers at the Weizmann Institute of Science have discovered a molecule that enables bacteria to resist an unusually wide range of drugs.

The finding, to be reported in the April issue of the Journal of Bacteriology, suggests it may become more and more difficult to design effective new medications for bacterial infections.

On the brighter side, the newly identified molecule, named MdfA, may serve as a model for the further study and understanding of multidrug resistance, aiding efforts to overcome this phenomenon in bacterial diseases.This research may also help clarify multidrug resistance in human cancers, which results in tumor cells expelling anti-cancer drugs, thus presenting serious obstacles to chemotherapy.

"The more sophisticated the drugs we develop, the more bacteria may emerge equipped with sophisticated ways to fight these drugs," says Dr. Eitan Bibi of the Institute's Biochemistry Department, who conducted the study with doctoral student Rotem Edgar. "This is an obvious challenge for antibacterial therapies that must be planned in anticipation of growing resistance mechanisms."


Dormant Potential to Survive

Cells of virtually all living organisms are known to contain molecules that enable them to resist a variety of substances. These molecules sit inside cell membranes and act as pumps, ejecting toxic compounds or other unwanted chemicals from the cell. However, the "unwanted" substances may include medications.
 

Previously, most of these versatile molecular "pumps" were known to be capable of recognizing and resisting certain classes of drugs with particular chemical properties, such as those with a positive charge and a propensity to attach to lipids (molecules that make up cell membranes).These chemical properties determine how a drug will be absorbed by a cell, and influence the drug's toxic effects on a target site inside the cell.
 
The newly identified multidrug resistance molecule, MdfA, allows bacterial cells to expel one of the widest ranges known of unrelated antibiotics and other drugs, with widely varying chemical properties. For example, it can resist both positively charged drugs and those with no charge at all, as well as drugs that attach to lipids and those that do not.

"Finding a molecule with such an extraordinarily broad spectrum of resistance in one species of bacteria means we are likely to find similar molecules in other bacteria," says Bibi. "This highlights the dormant potential of some bacteria to survive even complex antibiotic treatments, and presents a challenge for future therapies."


An Evolutionary Advantage

Bibi and Edgar identified the MdfA molecule while researching multidrug resistance in Escherichia coli, a species of bacteria commonly used in scientific research. (E. coli normally live in the human colon and aid digestion, but if certain strains of the bacteria enter other organs through contaminated drinking water or improper toilet hygiene, they can cause serious illnesses such as acute infant diarrhea and urinary tract infections.)


The scientists conducted experiments in which they attacked the bacteria with various drugs. They found that MdfA was present and functional in low levels in all the E. coli strains they studied, and could fight off drugs administered in low amounts.

Giving large amounts of combined drugs killed off most of the bacteria. But when bacteria contained more than the usual amount of the mdfA gene, resulting in their producing much greater quantities of the MdfA molecule than normally, they survived even these harsh treatments. This suggests that the MdfA molecule is capable of conferring a high level of resistance to many unrelated drugs.
 
Bibi says evolution, given a push by modern medicine, seems to have played a role in the appearance of such broad-spectrum resistance molecules. Although modern medicines have undoubted and obvious benefits, a few bacteria have unavoidably survived each new drug because of natural resistance, and these have had an evolutionary advantage that they have passed on to their descendants.

The result has been increasingly resistant bacteria, equipped with more versatile resistance mechanisms.

Dr. Eitan Bibi holds the Dr. Samuel O. Freedman Career Development Chair in the Life Sciences. Funding for this research came from the Israel Cancer Research Fund and from the Minerva Foundation of Munich, Germany.

The Weizmann Institute of Science is a major center of scientific research and graduate study located in Rehovot, Israel. Its 2,400 scientists, students and support staff are engaged in more than 850 research projects across the spectrum of contemporary science.
Space & Physics
English
  • Bacteria
  • Eitan Bibi
  • Multidrug resistance

A Sense of Size

English

 

Dr. Ida Rishal and Prof. Michael Fainzilber. Ping-Pong signals

 

How does a cell sense its own size? That question becomes especially significant when the cell is large: a human peripheral neuron, for example, which can grow extensions reaching up to a meter in length – some 20,000 times the cell body’s diameter. Without some basic information on the distance involved, just getting the building materials out to the growing end could be a logistical nightmare, exposing the cell to logjams in the supply line. These cells most probably assess their dimensions on an ongoing basis in order to direct further growth, but until now, no one was quite sure how they accomplished this feat.


Dr. Ida Rishal and Prof. Michael Fainzilber of the Weizmann Institute’s Biological Chemistry Department and their collaborators have now provided the answer for large cells such as neurons. Among other things, their findings may have relevance for understanding how to accelerate the repair of damaged nerves.
 

Fainzilber and Rishal, together with Dr. Naaman Kam and Rotem Ben-Tov Perry of the Biological Chemistry Department, Dr. Vera Shinder of the Chemical Research Support Department, Prof. Elizabeth Fisher of University College London and Prof. Giampietro Schiavo of Cancer Resesarch UK London Research Institute, thought the solution might lie in the motorized transport system that runs up and down the length of the nerve cell. This system consists of tracks called microtubules and two families of motors known as kinesin and dynein. One, the kinesin, travels only from the cell center to the end of the extension; the other, the dynein, goes only in the other direction, toward the center. Could these two, in addition to hauling cargo of various sorts up and down the tracks, be measuring distance?


The researchers began by constructing computer models of possible mechanisms by which these cellular motors might measure length. In the first model, dynein motors moving toward the cell center would carry signals that would gradually be lost along the way, like breadcrumbs dropping at a constant rate. The amount of signal left at the end of their journey would reveal the distance traveled. In this model, if the number of dynein motors was smaller than normal, the lowered signal would make the cell seem larger than it is, and thus the extensions would grow more slowly and end up shorter.


A second proposed mechanism involved a feedback loop between the two motors. When the signal on one motor reached the end of the line, it would activate a signal on the second, sending it back in the other direction. The second signal would then terminate the activity of the first at the opposite endpoint. The measurement in this case would be based on timing – more specifically, on the frequency of the interactions at the terminal points. This frequency is something like a game of Ping-Pong: When played in a small area close to the net, the “pings” are rapid; bounces off the table’s far edges, by contrast, produce longer pauses between hits. As opposed to the first model, this one predicted that reducing the levels of either motor would actually result in faster-growing, longer nerve cell extensions, because the signal frequency would drop more slowly.


The team then conducted experiments, first in nerve cells grown in culture and then in mice, in which the levels of the dynein motor were reduced. In all instances, the extensions grew longer than usual, ruling out the first model and supporting the second one.
 

Neurons from wild type (left) and dynein mutant (right) mice grown in culture. The mutant neurons with lower dynein levels show longer axon growth

 

Finally, the team asked whether this mechanism is specific to nerve cells, or whether other large cell types might use similar methods to sense their size. Repeating their experiment in connective tissue cells called fibroblasts, they again found evidence for motor-based frequency signals.


In addition to providing the answer to a long-standing question about size-sensing in large cells, these findings may be relevant to research on the regeneration of nerve cells. Cells in the peripheral nervous system can grow back after injury, but the process is extremely slow – sometimes taking years in the case of the longest nerve extensions. This is in part because once a growing nerve cell connects with its target – usually sometime during embryonic development – it stops elongating from the end and, instead, grows along with the body by stretching throughout its length. Understanding the precise signals the cell uses to not only measure itself but then to direct the embryonic growth process accordingly might point to new directions in boosting nerve regeneration.    

 

Prof. Michael Fainzilber's research is supported by the Sylvia Schaefer Alzheimer's Research Fund; the Kahn Family Research Center for Systems Biology of the Human Cell; the Dr. Miriam and Sheldon G. Adelson Medical Research Foundation; the Legacy Heritage Fund Program of the Israel Science Foundation; the Nella and Leon Benoziyo Center for Neurological Diseases; the Yeda-Sela Center for Basic Research; the estate of Raymond Lapon; the Irwin Green Alzheimer's Research Fund; and the estate of Florence Cuevas. Prof. Fainzilber is the incumbent of the Chaya Professorial Chair in Molecular Neuroscience.


 

 

 

Dr. Ida Rishal and Prof. Michael Fainzilber. Ping-Pong signals
Life Sciences
English
  • Axon
  • Biological Chemistry
  • Michael Fainzilber
  • Nerve cell

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