DNA Crystals Help Bacteria Respond to Stress

English
DNA becomes remarkably organized in bacteria that are subjected to various conditions of stress, Weizmann Institute scientists reported in the July 1 issue of Nature. The tightly packed structure promotes the ability of the cells to withstand extreme environmental assaults such as oxidating agents and starvation.

The finding may one day contribute to the development of more general methods against bacterial diseases. In addition, if a link is found between the mechanisms allowing bacteria to survive under stress, and those that render bacteria resistant against various chemical agents, chemotherapy could be efficiently used against pathological bacteria which have become resistant towards other methods.

The Weizmann team, headed by Prof. Avi Minsky of the Organic Chemistry Department, discovered that bacterial DNA forms a crystalline organization when bacteria are exposed to harsh conditions. They further revealed that this highly ordered structure is mediated by a protein called Dps which strongly binds DNA to form a very stable structure. The Dps protein, initially characterized by the group of Prof. Roberto Kolter at Harvard Medical School with which Prof. Minsky collaborates, is present in stressed cells at high levels. Within the ordered and tightly packed DNA-Dps structure, the DNA is very effectively protected against various assaults.

"In natural environments, bacterial life alternates between short periods of feast and long periods of famine and stress." says Prof. Minsky. "In order to survive, bacteria have evolved sophisticated mechanisms that allow them to protect themselves during starvation and stress, as well as to very rapidly resume growth when nutrients are again available. The ordered DNA structure may represent the ultimate mode of protection."

The scientists used X-ray and electron microscopy techniques. They are currently using these techniques to uncover the molecular structure of the complex between the Dps protein and the DNA, in order to better understand the mode of DNA protection. "We are currently investigating the actual signal that triggers the formation of the crystalline structure once subjected to starvation or stress and the signal that effects its fast disappearance once stress is eliminated," says Minsky.

Minsky: "Order is generally considered to be incompatible with life. However, in living systems exposed to severe environmental assaults, intracellular crystalline assemblies may confer an efficient means for wide range protection. Indeed, ribosomes in brain cells of people suffering from dementia were found to form crystalline organizations. Moreover, DNA in sperm cells is highly ordered. We have now found this to be true in bacterial DNA as well and are trying to understand how general and significant the correlation between order and survival is."

Accordingly, the Weizmann team has recently begun to study the correlation between the organization of DNA and fertility in human sperm cells.
 
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.
Space & Physics
English
  • Abraham Minsky
  • Bacteria
  • DNA
  • Electron microscopy
  • Organic Chemistry

'Plugs' For Drugs Promise Mightier Medicines

English
Whether it's one pill several times a day or a self-administered injection, taking medicine frequently can be a major nuisance. Now Weizmann Institute scientists have developed a new approach that may prolong the action of many drugs, making it possible to administer them at much greater intervals without jeopardizing their effectiveness. Immediately after it's taken, the medication's levels in the blood normally surge -- sometimes up to 100 times more than what is needed.
 
Such high levels often produce damaging side effects, but they are necessary to keep the drug in the blood long enough to do its job. Then, within minutes to several hours, the drug is cleared from the circulation, creating the need for a new dose. For several decades, scientists have exerted major efforts to invent a way of releasing drugs into the blood in a more balanced manner while prolonging the time a medication actively circulates in the body. Unfortunately, this goal has been achieved for only a very limited number of drugs.

Prof. Mati Fridkin of the Organic Chemistry Department and Prof. Yoram Shechter of the Biological Chemistry Department have designed a new technique that can affect how numerous categories of drugs, including antibiotics and cancer medications, are released into the body.  The technique is based on a molecular "plug" that attaches to and temporarily blocks the action of the drug. Once the medication enters the circulation, the "plug" is gradually disconnected. This, the scientists believe, releases relatively low but steady quantities of the drug into the patient's blood over a long period of time. This approach may make it possible to administer a drug less frequently in significantly larger doses than usual without causing side effects. Contributing to the drug's prolonged action is the fact that medications modified with the "plug" are less susceptible to breakdown by enzymes than their unmodified counterparts.
 
In an animal study to be published in Diabetes, the researchers, working with graduate student Eytan Gershonov, demonstrated that their approach works well for insulin, a drug used by diabetics to normalize their blood glucose levels. When diabetic rats were given insulin modified with the molecular "plug," a single injection kept glucose levels at a normal level for two days. In contrast, a single injection of unmodified insulin produced the same effect for only 6-12 hours. The new "plug" is a small organic molecule widely used in the production of organic compounds. In the test tube, it slowly disconnects from the drug under the temperature and pH conditions equivalent to those prevalent in human blood. The scientists can create different versions of the molecular plug that can be disconnected at different rates, so that the speed of the drug release into circulation can be precisely controlled.

Currently, the Institute scientists are exploring an additional potential advantage of this technology. Test-tube experiments suggest that the organic plug may improve drug absorption by the intestines. If these findings are supported by further studies, the plug technology, which is covered by a patent, may be used to convert injected drugs into oral medications.

To commercialize the new method, a start-up company, LAPID Pharmaceuticals Ltd., has recently been formed by Pamot Venture Capital Fund and Yeda Research and Development Co. Ltd, the Weizmann Institute's technology transfer arm. Prof. Fridkin holds the Lester B. Pearson Chair of Protein Research, and Prof. Shechter, the Charles H. Hollenberg Chair of Diabetes and Metabolic Research.

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

Space & Physics
English
  • Controlled release
  • Diabetes
  • Mati Fridkin
  • Yoram Shechter

Secrets of the SOS Repair Service

English
Some repair crews just do their job. Others go beyond the call of duty, leaving you better off than you were before the problem occurred. An emergency repair "service" that fixes DNA, the genetic material of cells, belongs to the second type.

Researchers at the Weizmann Institute of Science have now revealed the "trade secrets" of this molecular repair crew, demonstrating how a little genetic material patched into just the right place can save the DNA from a genetic disaster. And while averting a serious mutation, the repair squad leaves behind a surprising calling card: a "good" mutation, which can improve an organism's chance of survival.
 
DNA is regularly damaged by various factors in the environment, such as ultraviolet radiation. This damage is normally corrected with the help of special proteins known as repair enzymes. Sometimes, however, these enzymes fail to do their job.

Time to call the emergency repairmen. For more than 20 years, scientists have known that apart from the regular repair enzymes, DNA has a last-minute correction mechanism known as the SOS repair. In a study reported on August 28 in Molecular Cell (vol. 2, pp. 191-199),Prof. Zvi Livneh of the Weizmann Institute's Biological Chemistry Department, with graduate students Nina Reuven and Guy Tomer, reconstructed this mechanism in a test tube and revealed how the SOS squad does its job.

The scientists found that when damaged genetic material is not repaired, the defective section of the DNA - usually consisting of one or two "letters" of the genetic code - is simply deleted during replication, and the rest of the DNA molecule shifts to fill in the gap. The result is a disastrous mutation that scrambles the genetic script. This, in turn, leads to the production of defective proteins that can wreak havoc on cellular function. For example, such proteins can turn off the genes that suppress cancer, leading to the development of a tumor, or they can "kill" an essential protein, leading to cell death.

But when the SOS repair does kick in, it replaces damaged DNA with random genetic material. This material acts as a "spacer," keeping the DNA molecule in proper alignment. Similar to the way in which archaeologists fashion clay to fill the gaps between shards of an ancient pot, this "spacer" prevents the damaged genetic letters from being deleted and keeps the overall DNA structure intact.

The SOS repair does not just prevent a genetic catastrophe, it actually provides an "extra" benefit. By introducing random genetic material into the spaces previously inhabited by defective DNA, the SOS mechanism is creating a slightly mutated gene that is still functional and may work even better than the gene in its original form. In fact, such "mild" and beneficial mutations are the driving force behind evolution because they produce genetic diversity that serves as the basis of natural selection.

Understanding of this and other DNA repair mechanisms provides scientists with new insights into diseases such as cancer. Another potential application is in the area of treating bacterial infections. Because the SOS stress response is one of the strategies used by bacteria to resist medications, understanding of this mechanism throws light on the alarming phenomenon of bacterial resistance to antibiotics.

Prof. Livneh holds the Maxwell Ellis Professorial Chair in Biomedical Research. This study was supported by the U.S.-Israel Binational Science Foundation, the Israel Ministry of Science and the Weizmann Institute's Leo and Julia Forchheimer Center for Molecular Genetics.

The Weizmann Institute of Science is a major center of scientific research and graduate study located in Rehovot, Israel.
Space & Physics
English
  • DNA damage and repair›DNA repair
  • Zvi Livneh

Cellular Short Circuit Causes Insulin Resistance

English
Future treatments for diabetes may correct the underlying causes of this prevalent metabolic disorder rather than just treat its symptoms. An important step in this direction has been made by Prof. Yehiel Zick of the Weizmann Institute's Molecular Cell Biology Department.

In a study reported in the November 21 issue of the Journal of Biological Chemistry, Zick and colleagues provided a new insight into the molecular basis of insulin resistance, a condition that can lead to diabetes. In insulin resistance, cells no longer respond to ordinary levels of insulin. The scientists discovered that this may occur because some of the proteins that relay messages from the insulin receptor to the glucose uptake machinery in cells undergo excessive phosphorylation (a process in which they acquire phosphorus atoms). Such abnormal phosphorylation generates a "short circuit" that prevents the insulin receptors from communicating their "messages" to the cells' interior, making the cells resistant to insulin.

In addition, the new study may explain why diabetes is five times more common in obese people than in people of normal weight. According to Prof. Zick, a major culprit in enhancing the inappropriate phosphorylation is a molecule called TNF, which is secreted by fat cells. The excessive secretion of TNF by obese people may explain the link between obesity, insulin resistance and diabetes.

These findings may in the future lead to new treatments for diabetes that would be based on correcting insulin resistance.



Prof. Zick's team included Ph.D. student Keren Paz, Dr. Eytan Elhanany of the Israel Institute for Biological Research, Dr. Hannah Kanety, Prof. Avraham Karasik, and Rina Hemi of the Sheba Medical Center in Tel Hashomer and Dr. Derek LeRoith of the National Institutes of Health, Bethesda, MD. This work was supported by research grants from the Kekst Foundation, the Israel Ministry of Health, the Tolz Foundation, the Israel Cancer Research Fund, the Israel Cancer Association, the Israel Science Foundation, and the Juvenile Diabetes Foundation International.

The Weizmann Institute of Science is a major center of scientific research and graduate study located in Rehovot, Israel.
Space & Physics
English
  • Diabetes
  • Insulin›Insulin resistance
  • Metabolic disease
  • Molecular Cell Biology
  • TNF
  • Yehiel Zick

Resilience by Improvisation

English

Our cells can copy DNA even when it is severely damaged. Prof. Zvi Livneh and Ph.D. student Ayelet Maor-Shoshani of the Biological Chemistry Department inserted a foreign material - similar to that making up crude oil - into the DNA of the bacterium E. coli. To their surprise, the cell’s copying machinery was able to proceed unhindered.

The millions of cells that divide every day in the body do so by copying their DNA. This crucially important function, which enables the body to replace old cells and pass on genetic information from generation to generation, is performed by molecules called DNA polymerases. The new Weizmann Institute study shows that they are able to improvise to achieve their goal.

The scientists found that upon reaching the foreign material, the DNA polymerase stops working and a specialized DNA polymerase jumps in to rescue the stuck replication process. The latter is able to continue the copying process by inserting “nonsense” genetic components into the copy, much like a singer who forgets a few words and continues to sing by making up new ones. In other cases, the specialized DNA polymerase simply skipped over the foreign material or deleted it and was thus able to continue copying as usual.

These findings, published in Proceedings of the National Academy of Sciences (PNAS), USA, shed light on how the copying process is affected by damaged DNA. “They show the remarkable capacity of a cell to reproduce,” says Livneh, “and make one hopeful that even if extreme types of chemicals are accidentally introduced into our DNA, the body will be able to manage.” 

Prof. Livneh’s research is supported by the M.D. Moross Institute for Cancer Research; the Levine Institute of Applied Science; the Dr. Josef Cohn Minerva Center for Biomembrane Research; the Dolfi and Lola Ebner Center for Biomedical Research; and the J & R Center for Scientific Research. He is the incumbent of the Maxwell Ellis Professorial Chair in Biomedical Research.
Space & Physics
English
  • Biological Chemistry
  • Zvi Livneh

Nerves, Heal Thyselves

English

In a study published in Neuron, Weizmann scientists have now shown how neurons in the peripheral nervous system “raise the alarm” following injury, sparking a rescue process.

Nerves in the peripheral nervous system (any part of the body aside from the brain and spinal cord) are capable of regenerating, though they often do so poorly or slowly. A better understanding of how they regenerate could advance the treatment of injuries to the peripheral system (such as loss of sensation). It might also provide insights into fixing neurons in the central nervous system.

Nerve cells are uniquely shaped, consisting of a cell body and “arm-like” protrusions that transmit information to the cell (dendrites) and from it (axons). Axons can reach up to one meter in length in humans and are the main conduit for neural communication throughout the body.

Dr. Michael Fainzilber and Ph.D. students Shlomit Hanz and Eran Perlson of the Biological Chemistry Department found that a special protein called importin beta is produced in axons upon injury. This protein binds, among others, to components of a “healing message.” The whole group fastens itself to an “engine” called dynein that chugs along tracks leading from the axon to the nucleus. The group then enters the nucleus, alerting the cell to the problem and initiating nerve regeneration. 

Dr. Fainzilber’s research is supported by the Y. Leon Benoziyo Institute for Molecular Medicine; Mr. and Mrs. Alan Fischer, Larchmont, NY; the Abisch Frenkel Foundation for the Promotion of Life Sciences; the Irwin Green Alzheimer’s Research Fund; and the Buddy Taub Foundation. He is the incumbent of the Daniel E. Koshland Sr. Career Development Chair.
Space & Physics
English
  • Biological Chemistry
  • Michael Fainzilber
  • Nerve cell

First Glimpses of Folding Proteins

English
 
Proteins, it appears, have taken Frank Sinatra’s “I Did It My Way” to heart. A new study published in the Proceedings of the National Academy of Sciences (PNAS) reveals how single proteins, each a few nanometers (billionths of a meter) long, fold to assume their final shape. It shows that even proteins that end up with the same final shape take different routes to reach it.
 
Using a novel technology developed in their lab, Weizmann scientists headed by Dr. Gilad Haran of the Chemical Physics Department took the first glimpses ever of single proteins in the process of folding. Proteins, the fundamental components of all living cells, start out as randomly shaped chains and twist into a well-defined structure that determines their function. In some cases this process goes awry and can result in a wide variety of disorders.
 
For decades scientists have pondered how proteins go through this folding process, yet they were unable to follow individual folding proteins for more than a few milliseconds – the proteins were just too small and constantly on the go. Haran’s technology, which makes following single proteins possible, has provided an answer to a central question, showing that they differ in the routes taken to the same folded shape. The new technology might help clarify the reasons for protein misfolding and ensuing disease.
 
Dr. Gilad Haran is the incumbent of the  Benjamin H. Swig and Jack D. Weiler Career Development Chair. His research is supported by the Clore Center for Biological Physics; the Fritz Haber Center for Physical Chemistry; and the Avron-Wilstaetter Minerva Center for Research in Photosynthesis.
Space & Physics
English
  • Chemical Physics
  • Gilad Haran
  • Protein folding