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SECRET OF DEINOCOCCUS RADIODURANS FOR SURVIVAL

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SECRET OF DEINOCOCCUS RADIODURANS FOR SURVIVAL

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·         Uses common repair systems much more efficiently along with expanded systems involved in salvage.

·         When exposed to irradiation, approximately 60 genes are induced which prompt repair pathways to reassemble DNA accurately and repair it efficiently, preventing any further cellular division until all damage is fixed.

·         Used 4 types of repair mechanisms (TO FIX DOUBLE STRANDED BREAKS)

1.      Homologous recombination

§  Uses an intact copy of DNA (from another chromosomes/genome, as this microbe has several spare) as a template to fill in/fix the break/mutated section of DNA.

2.      Extended synthesis-dependent strand annealing

§  Uses an existing copy of DNA to connect and build DNA from fragments

3.      Single-strand annealing

§  Synthesizes missing sections on strand using another copy of DNA

4.      Non homologous end joining

§  Does not require another copy of DNA

§  The broken ends are recognized and proteins join the ends back together.

·         Contain thick cellular envelope along with the pigments contained in it

=      Protect against some of radiation damage

·         DNA is unusually densely packed

=      Prevent movement/loss of damaged fragments of DNA

·         Numerous copies of genome number

=      Aid in DNA repair (use as template to fix damaged sections)

·         High accumulation of manganese(Mn(II)), phosphate nucleosides, DNA bases, and peptides in its cytoplasm

=      Prevent protein oxidation under extremely high ionizing radiation levels

=      Mn(II) ions increases radiation tolerance and form complexes that protect proteins

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Can Deinococcus radiodurans survive in the outer space?

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Can Deinococcus radiodurans survive in the outer space?

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The Accidental (Space) Tourist :)

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Space Science News home

Humble microbe could become
"The Accidental (Space) Tourist"

Dec. 14, 1999: Like a muscle-bound movie hero, it withstands attacks from acid baths, high and low temperatures, and even radiation doses. Then, in a science fiction sequel, it dispenses lifesaving medications and reshapes a planet for new settlers.

Right: D. radiodurans growing on a nutrient agar plate. The red color is due to carotenoid pigment. Links to

. Credit: M. Daly, Uniformed Services University of the Health Sciences

And in true Hollywood fashion, the star of this epic had humble beginnings, living in cow patties and elephant dung, and coming to the attention of scientists when it refused to die in food sterilization tests.

You need a microscope to see this miniature future hero listed as Deinococcus radiodurans and known to its fans as Conan the Bacterium.

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" Deinococcus radiodurans beats most of the constraints for survival of life on Mars - radiation, cold, vacuum, dormancy, oxidative damage, and other factors," said Dr. Robert Richmond, a research biologist at NASA's Marshall Space Flight Center. With other scientists, he is investigating the possible utility of extremophiles to serve human exploration to inhospitable locations.

Humble origins
Richmond and his colleagues see D. radiodurans as playing the part of possible Martian microbes in simulations to help direct the search for life on Mars. Next, it could be genetically altered to produce medicines for astronauts in the short-term, rather than hauling an entire pharmacy along on the trip, and restructuring Mars for human habitation in the long-term.

Left: "Is anybody home?" The Sojourner Mars Rover nuzzles up to Yogi, a rock near the Mars Pathfinder lander, in preparation for a chemical assay of the rock. Future probes may be designed to turn over rocks in hopes of finding traces of microbial lifeforms. Credit: NASA and Jet Propulsion Laboratory.

With R. Sridhar of Howard University Medical Center in Washington, D.C. and Dr. Michael J. Daly of the Uniformed Services University of the Health Services in Bethesda, Md., Richmond presented a paper at the 1999 SPIE Conference in Denver on the "Physico-Chemical Survival Pattern for the Radiophile D. radiodurans: A Polyextremophile Model for Life on Mars."

Daly and his co-workers, in a recent article in Science magazine, announced that they had completed sequencing the genome of D. radiodurans. This opens the way for exploitation of its ability to integrate external genes selected to express products useful to explorers on Mars or other such places.

" Radiodurans' beginnings are thought to be from early Earth," Richmond said, and paralleled a time when the environment may have also approximated that existing on Mars for a few hundred million years. Given the presumed sharing of debris generated from meteorite impacts amongst the early planets, origins of D. radiodurans might even be accidentally common between Mars and Earth. "By nature, it is selected to survive radiation damage very well," D. radiodurans can withstand without loss of viability a dosage that is 3,000 times greater than what would kill a human. "The fact that you can genetically engineer these things is the key to the utility of this bug."

It's heady stuff for a primitive organism.

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But D. radiodurans has a feature that is considered all-important in aerospace: redundancy. Its genetic code repeats itself many times so that damage in one area can be recognized and quickly repaired. Coupled with its range of other survival characteristics, D. radiodurans has been dubbed a polyextremophile by Richmond, Sridhar, and Daly.

Extremophiles have been known to scientists for decades but often were regarded a laboratory oddity. The discovery of what appears to be nanobacteria (or nanobes, smaller than microbes) in a meteorite from Mars (Alan Hills 84001, or ALH84001) catapulted extremophiles into the spotlight as a model for possible lifeforms on Mars.

The debate over whether the ALH84001 forms ever were nanobes (or just non-living imitations) led to recent discoveries of probable nanobes living in such odd places as human kidney stones and in limestone 4 kilometers under the surface of the Earth.

A common link?
"We have a new door opening on the possibilities of lifeforms," Richmond said, "not just new species but whole new life forms that could connect to the origins of life on Earth and could be a common link to the possible beginnings of life on Mars."

Left: D. radiodurans photomicrograph showing the tetrad growth unit of this micrococcal eubacteria. Links to

. Credit: M. Daly, Uniformed Services University of the Health Sciences

Most extremophiles have optimized themselves for one or two extreme conditions and settled into wonderful ecological niches like the hot springs of Yosemite. Radiodurans has been dubbed a polyextremophile because it can endure many extremes, including the most dangerous space hazard, radiation.

"Radiation-induced DNA damage is an oxidizing type of damage," Richmond said. It happens when radiation energizes an atom enough to break a chemical bond and then act like an atom of oxygen and bind with another atom. Such free radicals have been implicated in a range of cancers and genetic mutations.

D. radiodurans, though, is hypothesized by Daly to resist such damage by virtue of repair specialized to utilize its redundant strands of DNA. This also means that it should resist damage from the chemistry of Mars, which chemical experiments done by the labs aboard the two Viking landers indicate may be highly oxidative.

D. radiodurans was discovered in the 1950s. Scientists experimenting with radiation to kill bacteria and preserve food for long periods found that something kept growing back after treatment.

Meet the Superbug. A Science News article (Dec. 12, 1998) describing D. radiodurans role in bioremediation.
The world's toughest bacterium. Web story at Pacific Northwest National Laboratory.
Abstract for Dr. M.J. Daly's grant to develop D. radiodurans for bioremediation.

It remained a laboratory oddity for several years until the arrival of genetic engineering, the science of altering an organism's basic biological code, sometimes by splicing into it portions of another organism's code. Daly's group is inserting specialized genes to help in eliminating dangerous chemicals from waste sites. An established example of the value of such genetic engineering is found with E. coli, the bacteria found in the human gut, that has been engineered to produce large quantities of human insulin, which once had to be refined from human cadavers.

"Daly has been active in developing D. radiodurans as a special model for bioremediation to clean radioactive supersites left over from the Cold War," Richmond explained. Some of those sites contain radioactive materials that are not easily removed by other microbes. While some other bacteria are being genetically engineered to thrive in toxic conditions while converting hazardous waste into reusable effluent, none can resist radiation the way D. radiodurans can.

Already, Daly and his colleagues have devised D. radiodurans variants that can clean up mercury, a deadly heavy metal, and toluene, a dangerous solvent. This work was sponsored by the U.S. Department of Energy.

The capability to insert genes also makes D. radiodurans a candidate for Mars pharmacists and to become "the plow that broke the plains" on Mars.

Left: The 200-meter-wide (660 ft) Nanedi Valles is one of several sites on Mars that show evidence that the planet once had running water. Recent images from the Mars Global Surveyor Orbiter, though, indicate that Mars never had a large ocean or sea, as scientists had hoped. Still, the presence of running water substantially increases the chances that life may have started and gotten a toehold. Credit: NASA and Jet Propulsion Laboratory.

But first, it may help search for life on Mars as a stand-in for Martian microbes in simulated Mars environments.

The changing face of Mars
Mars has gone through radical changes in our perception as a haven for life. After Sir Percival Lowell and a number of science fiction stories popularized Mars as a dying planet, U.S. space probes in the 1960s and 1970s rewrote the book to show Mars as long dead, perhaps never alive.

Then came the discoveries hidden inside ALH84001. Soon thereafter, images and data from the Mars Global Surveyor, Mars Pathfinder, and Sojourner Rover spacecraft showed Mars indeed has significant quantities of water, and once had running water.

While Mars has become more tantalizing, it is far from Eden. So the question is, if life was there, or is there, what are the best places to find it? Spacecraft surveying the planet to determine where water might survive beneath the surface, or where it once may have existed, are addressing this.

Even within those regions, you have to figure out which spots are best since a lander will have limited time and resources compared to the open wilds of Mars. One approach is to culture D. radiodurans in Mars simulations on Earth.

"We are restricted in the search for life right now to Earth-based microbes," Richmond explained. "We have to ask, What are the restraints on life that those microbes will have to surmount in order to plausibly exist on other planets?"

Extremophile habitats on Earth cover a range of conditions: temperatures near boiling or below freezing; a nearly total lack of water, or water that ranges from alkaline to acidic or salty; non-carbon foods; and a lack of oxygen. One of the tricks that less durable lifeforms use to survive such tough times is to hibernate as spores.

"The restraints become temporal, too," Richmond explained. "Dormancy has to carry on for thousands or millions of years" if a life form is to last until conditions on Mars become hospitable for growth, somewhat like the floral seeds waiting in the desert for the rare fall of rain.

And that's where radiation resistance comes in handy. While radiation issues are usually associated with nuclear power or exposure to the space environment, it is not commonly recognized as being inescapable. We are exposed through our entire lives to potassium-40, radon, carbon-14 and other radioactive sources. Living in the mountains or flying also increases exposure slightly.

Surviving a long winter's nap
But the total dosage from these is small during our lifespans, so the impact normally is insignificant. However, for an organism in hibernation for a million years or so, the cumulative exposure can be like sitting inside a reactor for several minutes.

That's why crawling under a rock to escape solar ultraviolet light on Mars is not a perfect strategy. The rock itself emits trace quantities of radiation over time.

"Within responsible imagination, no long-dormant lifeform can be expected on the surface of Mars due to combined build up of damage over time caused by both incoming space radiation plus the background radiation," Richmond said. The best hope is that life got started some billions of years ago when conditions were more hospitable, and that a few microbes adapted to extreme conditions or learned how to hibernate below the surface.

"But if they wake up too late, they run into the ultimate restriction, too much radiation damage that has accumulated if it's not repaired," Richmond said. "At that point, the population is dead."

Above: "Water, water, everywhere, and not a drop to drink." Mars Pathfinder landed in what was once a flood plain, as geologists deduce from the way rocks are arranged. Whatever water is left on Mars, though, is in polar ice caps and subsurface ice. Credit: NASA and Jet Propulsion Laboratory.

So even if something like D. radiodurans evolved on early Mars, it's possible that winter has lasted too long for any survivors to reawaken in the artificial spring of a petri dish.

Even so, D. radiodurans may yet travel to Mars as a Pharmacist's Mate First Class.

"Because of genetic engineering, you might do a lot with this bug to enhance the survivability of man in extraterrestrial environments," Richmond said. Altering the human genome to take on survival characteristics like D. radiodurans is far too complex a task (the human genome hasn't been completely sequenced, nor all of its 100,000+ genes decoded). But D. radiodurans could be altered to serve man.

"The interesting things about drugs we use is that about two-thirds are natural products or derived from natural products," Richmond said. "Anything that is a natural product ultimately comes down to a gene and can be genetically managed, in theory."

Living off the land - after you reshape it
Richmond, Sridhar, and Daly suggest that D. radiodurans can be genetically manipulated to produce various drugs that humans might need while exploring Mars, then put on ice during the mission. If someone became ill, treatment would start with drugs in from a small supply kept on hand, while the appropriate bugs were awakened to produce a regular supply. (This need was presaged this summer by the need to airdrop tamoxifen, a breast cancer chemotherapy agent, at the South Pole for a medical doctor who had diagnosed herself with breast cancer.) With such an approach, the issues of shelf life for drugs could also be circumvented. This would also reduce the weight that a spaceship would have to haul to Mars and back.

Right: With a little help from the tiniest of organisms, humans one day may explore and then colonize Mars. Credit: NASA/Johnson Space Center.

Radiodurans next might be drafted as a Seabee (Navy Construction Battalion, or C.B.) as humans set up camps and even homesteads on Mars. Other engineered versions of D. radiodurans could recycle wastes - producing clean water and oxygen - and perhaps even food supplements. "Its own food stock might even be Mars," Richmond suggested, giving new meaning to "living off the land." Again, the bug's genetic design might help ensure a renewable grocery store for explorers.

The ultimate step would be the popular notion of terraforming, reshaping the environment of Mars to make it more hospitable to humans. Terraforming was first performed by ancient lifeforms that converted Earth's environment from a carbon dioxide atmosphere and calcium-rich seas to the more hospitable world we have today. Because these early lifeforms spoiled their home, they now survive in what we consider to be extreme environments.

Mars, too, is considered to be an extreme environment. But with a little help from D. radiodurans, it may be made more accessible and, eventually, attractive. After all, a Seabee's motto is, "The difficult we do now. The impossible takes a little longer."

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Space Science News home Humble microbe could become "The Accidental (Space) Tourist" Dec. 14, 1999: Like a muscle-bound movie hero, it withstands attacks from acid baths, high and low temperatures, and even radiation doses. Then, in a science fiction sequel, it dispenses lifesaving medications and reshapes a planet for new settlers.

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Deinococcus radiodurans in Cell Survival and Radiation Tolerance

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Deinococcus radiodurans in Cell Survival and Radiation Tolerance

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0071651

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sorry guys, since we just using phone, i cannot take the picture properly and only some of us can see in the screen,

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take a look and have fun

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Dr. Michael Daly explains radioresistant bacteria

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Read more at: http://www.dcmilitary.com/article/20120726/NEWS11/707269939/worlds-toughest-microbe-helps-usu-scientists USU Pathology Professor Dr. Michael Daly has devoted more than 20 years to studying Deinococcus radiodurans, a microorganism the Guinness Book of World Records dubbed "the world's toughest bacterium."

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A simple intro to Deinococcus radiodurans

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hey guys, check this out. look how amazing our microbe is :D

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Figures

Citation: Cox MM, Keck JL, Battista JR (2010) Rising from the Ashes: DNA Repair in Deinococcus radiodurans. PLoS Genet 6(1): e1000815. https://doi.org/10.1371/journal.pgen.1000815

Editor: Susan M. Rosenberg, Baylor College of Medicine, United States of America

Published: January 15, 2010

Copyright: © 2010 Cox et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding: The authors received no specific funding for this work.

Competing interests: The authors have declared that no competing interests exist.

The extraordinary resistance of Deinococcus radiodurans to ionizing radiation (IR) and desiccation is slowly drawing more intense scrutiny. Relative to most other organisms, Deinococcus has a survival advantage measured in orders of magnitude. Exposure to 5 kGy of IR reduces the genome of any bacterium to hundreds of fragments. Deinococcus is no exception. However, Deinococcus seems to take this catastrophe in stride. Over a period of 3-4 hours, overlapping fragments are spliced together into complete chromosomes, and the cells soon resume normal growth. There is no measurable lethality. Attempts to understand the molecular basis of this phoenix-like capability has given rise to numerous hypotheses. Notable among them are proposals that the condensed nature of the Deinococcus genome [1] or an unusual capacity to avoid protein oxidation [2] are keys to radiation resistance.

Regardless of the physiological or metabolic adaptations that Deinococcus may employ to enhance survival, it is hard to explain extreme genome reconstitution without considering DNA repair. As originally defined by Daly and Minton [3], and reinforced more recently by Radman and colleagues [4],[5], genome reconstitution in Deinococcus proceeds in two phases. The first phase has been attributed to a process dubbed extended synthesis-dependent single-strand DNA annealing (ESDSA) [4],[5]. The second phase involves RecA protein-mediated double-strand break repair. Some initial studies suggested that the first phase of repair did not involve the Deinococcus RecA protein, but more recent work has documented a role for RecA in both phases [4],[5]. ESDSA involves considerable nuclease activity to generate single-stranded DNA, strand invasion mediated by the RecA and/or RadA proteins, and extensive DNA synthesis primed by the invading strands prior to the annealing steps [4],[5].

The emerging picture ( Figure 1) provides a useful framework, but one with many questions. Most of these involve enzymes and their roles. The generation of single-stranded DNA in ESDSA requires the function of at least one nuclease and helicase and perhaps several of both. Proteins are also needed to load RecA protein onto single-strand DNA binding protein (SSB)-coated single-stranded DNA. The most important pathway for double-strand break repair in Escherichia coli utilizes the RecBCD enzyme for all of these roles. However, Deinococcus encodes no homologue of RecB or RecC. Deinococcus does encode homologues of every protein involved in what is considered (in E. coli) an auxiliary pathway for recombinational DNA repair-the RecFOR pathway. In the RecFOR pathway, the RecJ and RecQ proteins take up the nuclease and helicase roles, respectively, while the RecFOR proteins function to load RecA protein onto the DNA. The absence of RecBC homologues in Deinococcus seems to imply that the RecFOR path is particularly important.

The first stage, extended synthesis-dependent single-strand annealing (ESDSA) is dominated by nuclease and DNA polymerase functions. The second stage is a more conventional RecA-mediated double-strand break repair process focused on the final splicing of large chromosomal segments.

In two important reports in this issue of PLoS Genetics, Sommer and colleagues convert much recent speculation into substance. In the first report [6], the Chandler and Sommer laboratories collaborate to explore the mechanism of transposition of element IS Dra2. This transposon is a member of a family of elements that transpose via single-stranded DNA intermediates. Transposition is activated by irradiation of Deinococcus. The work not only documents the transposition mechanism, it reinforces the proposition that extensive lengths of single-stranded genomic DNA are generated in the early stages of genome reconstitution in this bacterium. As a bonus, the work provides hope for the development of in vivo transposition as a tool for genetic manipulation of this genome.

The second report [7] clearly establishes the central role of the RecFOR pathway in genome reconstitution. Where the effects of RecFOR pathway gene deficiencies are generally modest in E. coli, they are dramatic in D. radiodurans. Sommer and colleagues demonstrate that cells lacking functional recF, recO, or recR genes are essentially as dysfunctional in genome reconstitution as recA mutants. Cells with these deficiencies are viable in the absence of extreme DNA damage, but grow much slower than wild type. Thus, the RecFOR pathway is important during normal replication, as well as during genome reconstitution. If the gene encoding the RecJ nuclease is inactivated, the cells are inviable. Surprisingly, cells lacking the RecQ helicase exhibit wild type resistance to IR. Instead, the helicase that appears to be critical is UvrD. In E. coli, the function of UvrD in recombinational DNA repair is to remove RecA filaments from the DNA [8],[9]. In Deinococcus, it almost certainly does more. In summary, Deinococcus now presents a unique opportunity to demonstrate what the RecFOR pathway can really do.

This RecFOR pathway may look a bit different from its cousin in E. coli. After irradiation, about 60 Deinococcus genes are induced, and quite a number of them have roles in genome reconstitution [10]. Many of these genes are novel. Knockouts do not have the dramatic effects of recAJFOR knockouts, but their cumulative effects can be significant. Some, like the DdrA protein (a distant homologue of the eukaryotic Rad52 protein [11]), and DdrB (a novel single-strand DNA binding protein [12]) must be worked into the schemes.

The work of Chandler and Sommer has a few more far-reaching implications. The spectacular feat of genome reconstitution after heavy irradiation does not require a completely new pathway for double-strand break repair, and no such pathway appears to be present. Instead, D. radiodurans relies heavily on a set of recombinational DNA repair functions that are recognizable in almost all species. In large measure, efficient genome reconstitution involves tweaking those repair proteins, providing a few novel augmentations, and perhaps modifying the environment in which all of these proteins function. However, the properties already noted that distinguish the RecFOR pathway in Deinococcus from the same process in E. coli bear reiteration. The roles that well-known repair proteins play in radioresistance are not perfectly predictable, based on what we understand about their function in E. coli. An orthologous relationship between proteins can inform speculation, but it must be subjected to experimental substantiation. Every DNA repair protein examined to date in D. radiodurans has provided one or more novel twists in our understanding of its function, structure, interaction with other proteins, and role in repair.

Last but not least, we may soon see a first in vitro reconstitution of a complete DNA double-strand break repair reaction. In this arena, D. radiodurans is gradually eclipsing E. coli as the most pliable bacterial model system. The proteins, or at least most of them, are in hand. Fortuitously, the enzymes from Deinococcus appear to be more amenable to structural determination than their E. coli cousins. The only structural information currently available about RecF, RecO, and RecR come from the Deinococcus enzymes [13]-[17]. Activities are being characterized, and more surprises are anticipated. Deinococcus simply does it better.

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Rising from the Ashes: DNA Repair in Deinococcus radiodurans

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Citation: Cox MM, Keck JL, Battista JR (2010) Rising from the Ashes: DNA Repair in Deinococcus radiodurans. PLoS Genet 6(1): e1000815. https://doi.org/10.1371/journal.pgen.1000815 Editor: Susan M. Rosenberg, Baylor College of Medicine, United States of America Published: January 15, 2010 Copyright: © 2010 Cox et al.

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The Deinococcus - a bacterial factory at your service