DNA repair and cancer II

I just wrote about this at some length, here.

It's funny, sometimes, how there are a bunch of results released in a short time period on the same topic. Usually it's because there's a big meeting that covers the topic, or else the editor of some journal wants several papers on the topic.

I've just come across three more papers on the topic and can't recall such a flurry of activity related to it. The papers were all published in different journals, and there doesn't appear to have just been a meeting on the topic, but it's understandably an active area of research.

The issue is whether or not variants of genes for DNA repair proteins make good biomarkers for cancer risk. As I discussed before, the recent meta-analysis suggests that in general this isn't as great a place to look for biomarkers as one might expect.

Compared to the most common allele of a DNA repair gene, less common alleles may correlate with either increased or decreased cancer risk, depending on the type of cancer and type of DNA repair involved.

In neither case can one automatically conclude that the common allele yields protection against cancer. By repairing DNA, the repair enzyme might actually help cancerous cells survive, offsetting any benefit from preventing further genome damage.

As a result, if one finds that a specific allele reduces cancer risk, it could be because the allele is actually less effective at repairing DNA. Conversely, if another allele increases cancer risk, it could be because the allele is too effective at repairing DNA.

Just looking at the situation from an anticancer perspective, when DNA damage is detected, the smart thing to do is to sacrifice the cell via apoptosis. But that's not the way nature looks at things. The type of damage involved may be so common that it's smarter to try to fix it, and then hope for the best cancer-wise. After all, most cancer depends on the presence of other, unrelated and probably very uncommon, kinds of genomic damage.

Research studies in this area really need to try to suss out what is actually happening, and that could be rather difficult. Basically, this is an evolutionary problem, with the outcome depending on what happens, statistically, in millions or billions of cells over a period of time. Which alleles will ultimately win out? The ones trying to fix DNA damage, or the others trying to exploit the damage? All the "players" in this game have different interests at stake.

Progress here may require some heavy-duty computer simulations trying to sort it all out. Cancer research could turn out to be a lot like climate modeling.

What would better understanding mean therapeutically? It could be possible to discover biomarkers – alleles that indicate significant cancer risk. Where serious risk is indicated to exist, then standard interventions like surgery or chemotherapy may be appropriate.

On the other hand, developing drugs that attempt to silence an allele which is found to predict significant cancer risk may not be very rewarding, for all the usual reasons that drugs may fail (e. g. side effects). That's what clinical trials are for – and trials are very expensive.

The first study we'll look at here involves fairly unique circumstances. It does not address many of the issues we'd like to know about, in particular concerning a direct mechanistic relationship between DNA repair and cancer.

But let's look at what it does say, with a view towards where further research could go. The study, first, determines that a specific type of DNA repair ("nucleotide excision repair") rises and falls substantially with the circadian clock. Second, it finds that levels of a specific repair-related protein (xeroderma pigmentosum A, or XPA) also rises and falls with the clock. Third, it shows levels of XPA are directly related to DNA repair activity.

Now, it's well known that certain types of chemotherapy have a circadian dependency. Quoting from the paper, there exists "empirical observation that circadian time of delivery of chemotherapeutic drugs such as cisplatin, whose major DNA lesions are cisplatin-d(GpG) and cisplatin-d(GpXpG) diadducts (6, 7), may be a significant contributing factor to the efficacy of the drug and the severity of its side effects (4, 5)." Thus it's at least plausible that circadian variability of the levels of repair-related proteins could account for this.

However, that hypothesis remains to be checked directly. It will be interesting to see how this develops.

Here's a press release:

Chemotherapy Most Effective At Time Of Day When Particular Enzyme At Lowest Level (1/13/09)

For years, research has hinted that the time of day that cancer patients receive chemotherapy can impact their chances of survival. But the lack of a clear scientific explanation for this finding has kept clinicians from considering timing as a factor in treatment.

Now, a new study from the University of North Carolina at Chapel Hill has suggested that treatment is most effective at certain times of day because that is when a particular enzyme system – one that can reverse the actions of chemotherapeutic drugs – is at its lowest levels in the body. ...

The study, published in the Proceedings of the National Academy of Sciences, provides the first solid evidence that the daily oscillations of the cell's repair machinery can affect the potency of cancer drugs.

Meta-observation: It's apparently difficult to pin down specific mechanisms at work here, so a fair amount of indirect inference is needed to draw conclusions. We'll see the same thing in two other recent studies (below).

Research paper:

Circadian oscillation of nucleotide excision repair in mammalian brain

T.-H. Kang, J. T. Reardon, M. Kemp, A. Sancar (2009). Circadian oscillation of nucleotide excision repair in mammalian brain Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0812638106

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Next up is a a case-control study that looked at nine single-nucleotide polymorphisms (SNPs) of seven DNA repair genes. The researchers were looking for correlations with the occurrence of pancreatic cancer. They studied 734 pancreatic cancer patients and 780 individuals without cancer. The strongest association was with a variant allele of one gene (LIG3), where individuals with the allele were 77% less likely than carriers of the normal gene to have cancer. The next strongest association was with a variant allele of another gene (ATM), carriers of which were in excess of 100% more likely to have cancer. (ATM also figures prominently in the third study, discussed below.)

Further investigation considered other cancer risk factors, such as smoking, heavy alcohol consumption, excess body weight, or diabetes – factors which might be responsible for excess DNA damage. The most significant factor turned out to be diabetes. In individuals with diabetes, carriers of an ATM allele were more than 200% likelier to have cancer, while carriers of a LIG4 allele were more than 100% likelier to have cancer.

So here's a study that successfully found several biomarkers, but involving only a few of the DNA genes studied.

Press release:

Abnormal DNA Repair Genes May Predict Pancreatic Cancer Risk (1/15/09)

Abnormalities in genes that repair mistakes in DNA replication may help identify people who are at high risk of developing pancreatic cancer, a research team from The University of Texas M. D. Anderson Cancer Center reports in the Jan. 15 issue of Clinical Cancer Research.

Defects in these critical DNA repair genes may act alone or in combination with traditional risk factors known to increase an individual's likelihood of being diagnosed with this very aggressive type of cancer. ...

With this in mind, [lead author Donghui] Li and her colleagues set out to identify DNA repair genes that could act as susceptibility markers to predict pancreatic cancer risk. In a case-control study of 734 patients with pancreatic cancer and 780 healthy individuals, they examined nine variants of seven DNA repair genes. The repair genes under investigation were: LIG3, LIG4, OGG1, ATM, POLB, RAD54L and RECQL.

The researchers looked for direct effects of the gene variants (also called single nucleotide polymorphisms) on pancreatic cancer risk as well as potential interactions between the gene variants and known risk factors for the disease, including family history of cancer, diabetes, heavy smoking, heavy alcohol consumption and being overweight.

Research abstract:

DNA Repair Gene Polymorphisms and Risk of Pancreatic Cancer

These observations suggest that genetic variations in DNA repair may act alone or in concert with other risk factors on modifying a patient's risk for pancreatic cancer.

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The last study we'll consider here is a little more tangential to the issue of DNA repair genes and cancer. It's primarily about how defects in DNA repair genes may be responsible for two related neurological diseases – ataxia telangiectasia-like disease (ATLD) and Nijmegen breakage syndrome (NBS).

The two diseases result from defects in the proteins Mre11 and Nbs1 (respectively), which are part of a protein complex called MRN (Mre11-Rad50-Nbs1). MRN is a part of a mechanism that repairs double-stranded DNA breaks.

The research used mouse models. Mice engineered to have an ATLD-like disease had defective genes for Mre11, while those with the NBS-like disease had defective genes for Nbs1. In both cases, DNA-damage stress was induced either by radiation or by knocking out another DNA repair enzyme. The idea was to trigger disease effects due to inadequate damage repair by MRN.

A further relevant fact is that part of the MRN damage-repair process invokes a protein kinase called ATM. Part of the role of ATM is to trigger apoptosis if the damaged DNA cannot be repaired.

For our purposes here, the relevant finding was that neurons of the ATLD mice were resistant to apoptosis, and consequently DNA-damaged neurons survived longer than they should, in view of their defects. The disease pathology results from the persistence of damaged neurons that cannot perform as required. However, neurons of the NBS mice were not unusually resistant to apoptosis, so the neurons died more rapidly, and pathology results from the excessive cell death.

How Defective DNA Repair Triggers Two Neurological Diseases (1/14/09)

To explore the differences between ATLD and NBS, the researchers used mice engineered to have defects in the causative genes, which produce two proteins that help form a critical component of the DNA repair machinery, called the MRN complex. The MRN complex zeroes in on broken DNA segments and attaches to them. It then recruits another important DNA repair protein, called ATM, to launch the repair process. However, if the damage is too severe, ATM may also trigger programmed cell death called apoptosis.

"It happens that defects in ATM also lead to a disease similar to ATLD, highlighting the connections between diseases resulting from defects in this DNA repair pathway," [senior author Peter] McKinnon said.

The mice engineered to mimic ATLD, like their human counterparts, had defective genes that produce a protein called Mre11; while NBS mice were engineered to have defects in the gene for the protein called Nbs1.

The key point may be this: when Mre11 is defective and ATM is then activated, it does not always trigger apoptosis when it should. But when Nbs1 is defective, ATM is able to do its job properly. In any event, when either Mre11 or Nbs1 is defective, MRN does not repair DNA damage as well as it should (in cells other than neurons). This may raise the risk of cancer due to randomly damaged DNA.

"There is a suspicion that people who carry these mutations may be predisposed to cancer and also more susceptible to chemotherapy agents or even to standard X-rays," McKinnon said. "Those agents induce the type of DNA damage that requires the MRN complex and ATM for repair. More generally, studies of the MRN complex and ATM are fundamental to understanding how to prevent changes to DNA that lead to cancer.

"Understanding more about how these proteins signal and interact, and how different cells in the body transduce the DNA damage signal, is of fundamental biological importance," McKinnon said. "This knowledge is necessary not only for understanding DNA repair diseases but for understanding the broader implications of maintaining of the stability of DNA."

Tags: cancer, DNA damage, DNA repair

DNA repair genes and cancer

DNA encodes genes needed for the production of essential proteins in a cell, and this DNA is vulnerable to damage in a number of ways. Perhaps the most common way is a consequence of inevitable errors that occur in the copying of all of a cell's DNA during cell division.

But there are a number of other ways that DNA damage can occur, such as damage due to reactive oxygen species or carcinogenic chemicals, ionizing radiation, or retroviruses, which insert their own DNA at random locations in the genome. (Technically, there's a distinction between DNA damage and DNA mutations, but we'll gloss over that for a moment.)

Most DNA damage affects only a single cell, and then, at most, only in the cell's ability to make certain proteins needed for normal cell function. Damage that occurs in DNA regions that don't affect protein production may have no effect at all. If important proteins are afffected, the cell may be unable to do its job properly, such as being a neuron or muscle cell. At worst, the cell dies, but its function is probably duplicated by billions of other cells in the same tissue or organ. Over a long enough period of time, of course, eventually a large percentage of cells will die due to DNA damage – and then the organism dies of "old age", if nothing more traumatic occurs first.

Against the relative improbability of one DNA damage event having serious consequences for a particular cell has to be weighed the frequency with which damage occurs. Most cells divide fewer than 100 times in their whole lifespan, though many errors can occur during each division. External factors like radiation, however, can cause millions of DNA damage events per day in a single cell. (Don't go sitting in front of an X-ray source all day! Or even under a source of UV radiation, like the Sun.) Internal factors, such as reactive oxygen species produced during normal metabolism, can cause many 1000s of mutations per cell per day, so DNA damage isn't something that cells can just ignore.

There are a couple of exceptions, when DNA damage can be an even more serious problem. One is in case the cell is an egg or sperm cell (a gamete), in a multicellular, sexually-reproducing organism, and the cell goes on to generate a new individual, which will inherit the damaged DNA. Since gametes are only a small proportion of all cells, and very few gametes are ever "lucky" enough to become new individuals, this is a fairly rare event. But it is how errors accumulate in genomes, over long periods of time. Such errors, being random events, are seldom beneficial to a species. But rarely they can be helpful and drive species evolution to adapt to a changing environment.

The other exception, which is much more consequential for the individual in which it occurs, is when the DNA damage affects one of the relatively small number of proteins responsible for keeping cell division and proliferation under control. Then you have a circumstance that can lead to cancer, even if only a single cell is affected to begin with. Clearly, it is in the best interest of the individual, and perhaps the whole species, for cells to have good mechanisms for dealing with the problems caused by DNA damage.

Apart from dealing with the original causes of DNA damage, cells have basically two ways of coping with damage after it occurs.

One sort of mechanism involves being able to detect the presence of DNA damage, and to initiate measures that limit or stop the cell's ability to proliferate, or even cause the cell to die. P53 is perhaps the best known protein involved in this type of mechanism. Compromised p53 production is found in more than half of all cancers. If a gene, in the same cell, that codes for a protein needed to implement one of these mechanisms has been damaged previously, the probability of cancerous proliferation will rise. Mechanisms of this kind are complex. There's a lot that can go wrong, and that's one reason cancer is as common as it is.

The other sort of mechanism is actual DNA repair. It's not so draconian. Such mechanisms attempt to actually correct the DNA damage, returning the DNA to its state before the damage occured. That's great. If it actually works, the cell can survive unharmed, and not pose any extra risk of becoming cancerous.

There are a variety of kinds of DNA damage, and hence a variety of repair mechanisms are needed. Individual bases attached to the nucleic acid backbone can be modified or deleted. The base sequence can be altered by faulty copying. The backbone itself can be broken or warped, preventing expression of some genes. Entire chromosomes, which carry DNA in a compact, packaged form, can be broken or improperly duplicated.

It's easier to recognize that damage has occurred than it is to repair it. Here the distinction between DNA mutations and other kinds of damage becomes relevant. A mutation exists when a base pair on the two strands of DNA is replaced with a different but otherwise normal base pair (i. e. adenine-thymine or guanine-cytosine). The resulting DNA is still technically undamaged, although the protein resulting from a gene with a mutation may not work as well as the unmodified version. In such a case, it is difficult or impossible for the problem to be recognized by DNA repair mechanisms. And it the problem can't be recognized, it certainly can't be repaired.

However, with most DNA damage, one or both strands of the DNA molecule is/are either distorted or broken. In that case, the DNA cannot be properly transcribed into RNA, or the DNA cannot be copied during cell division (or both). But for the same reason that these copying problems occur, it is also possible for appropriate enzymes to recognize that things are not right, and to activate a suitable repair mechanism (even if the repair cannot always succeed).

If, on the other hand, the damage is not repairable, other pathways can be activated to cause cell senescence or apoptosis. This more drastic situation may lead to cancer if there is already a problem with the senescence or apoptosis pathways. However, the research we're about to mention doesn't deal with this case. It's about problems in the repair mechanisms, due to DNA damage or mutations affecting those mechanisms, that lead to repair failure and that, consequently, lead to cancerous cell behavior.

The nature of repairable damage is varied, and the details of repair are quite technical, so we won't go into that here. Suffice it to say that there are effective damage repair mechanisms. What's not clear is whether malfunctions in those mechanisms (resulting from previous uncorrected errors or mutations) frequently result in cancer.

Researchers investigated genes that code for proteins involved in DNA repair. After statistical analysis of many relevant studies they found only two with a significant correlation to cancer:

Few DNA Repair Genes Maintain Association With Cancer In Field Synopsis (12/31/08)

Variants of numerous DNA repair genes initially appeared to be statistically significantly associated with cancer risk in epidemiological studies. When the data from individual studies are pooled, however, few DNA repair gene variants appear truly associated with increased cancer risk, according to a new field synopsis. ...

In the current study, John P. Ioannidis, M.D., of the University of Ioannina School of Medicine in Greece, and colleagues identified 241 previously reported associations between gene variants and the risk of cancer. The team pooled the data from 1,087 data sets and reexamined these associations.

Initially 31 of the 241 associations appeared to be statistically significantly associated with cancer risk in the meta-analysis. However, only two remained statistically significant after the researchers adjusted for multiple comparisons. An XRCC1 allele (-77 T>C) and an allele of ERCC2 (codon 751) were associated with lung cancer risk.

The conclusion of the meta-analysis is that either there's a problem with the way in which candidate genes were selected, or else problems in DNA repair mechanisms do not by themselves play a big role in carcinogenesis.

"The lack of many signals with strong credibility that emerged from our analysis, despite an enormous amount of work in this area over the years, needs careful consideration," the authors write. "The ability of the candidate gene approach to identify genetic risk factors may have been overestimated. Alternatively, the importance of the DNA repair pathway may have been exaggerated. However, there is increasing recognition that genetic risks of cancer conferred by single variants are almost always very modest. This means that even if the DNA repair pathway is essential for carcinogenesis, extremely large-scale evidence would be necessary to establish with high confidence the presence of specific associations."

Even though it seems that genomic studies have failed to turn up important oncogenes among genes that are involved in DNA repair, there is practical significance in these research findings.

For one thing, we should not expect to find useful biomarkers of cancer risk among alleles of DNA repair genes. Likewise, it's probably not worth exploring gene therapy approaches to compensating for malfunctioning DNA repair genes. Instead, what's more likely to succeed is a focus on alleles of genes involved in detection of DNA damage or of genes involved in senescence or apoptosis pathways.

Still, DNA repair genes remain very important. In many types of current cancer therapy, such as chemotherapy or radiotherapy, the intent is explicitly to cause DNA damage in order to bring about senescence or apoptosis. A problem with DNA repair in cancer cells cuts both ways. On one hand, faulty DNA repair leaves more errors uncorrected, exposing the cells to senescence or apoptosis as long as those pathways remain intact. That's good. But on the other hand, it can allow new errors to accumulate, making the cells more vulnerable to compromise of the senescence and apoptosis pathways, hence more likely to proliferate. That's bad.

Perhaps this ambivalence of DNA repair in the cancer process explains the apparent lack of strong correlation between faulty DNA repair and cancer.

Here's another way to think about the "right" way for an organism to defend itself from cancer. Cancer is a problem that's of concern only to multicellular organisms – communities of cells. While the integrity of each cell is certainly important, it's even more important to protect the whole community. A suitable analogy might be that it's more important to the community to have a good fire department as the last line of defense, than to rely on effective sprinkler systems to put out small fires in every separate location. If the fire department itself is compromised, and unable to combat a spreading conflagration, the community as a whole is in serious danger.

Here's the research abstract:

A Field Synopsis on Low-Penetrance Variants in DNA Repair Genes and Cancer Susceptibility

We have conducted meta-analyses of 241 associations between variants in DNA repair genes and cancer and have found sparse association signals with strong epidemiological credibility. This synopsis offers a model to survey the current status and gaps in evidence in the field of DNA repair genes and cancer susceptibility, may indicate potential pleiotropic activity of genes and gene pathways, and may offer mechanistic insights in carcinogenesis.

Update, 1/25/09: There's a significant follow-up on all this here.

Tags: cancer, DNA damage, DNA repair

Is DNA Repair A Substitute For Sex?

Yeah, it's a trick question. The answer is clearly "no" – unless you're a bdelloid rotifer.

What's interesting, of course, about these minute but multi-cellular animals is that they are completely asexual, and apparently have been for millions of years. There are no males, and females reproduce entirely by parthenogenesis. Although that might seem to imply a rather joyless existence, it hasn't stopped the bdelloids from persisting, and even diversifying into more than 370 species.

The conventional evolutionary reason for the invention and predominance of sexual reproduction – apart from the recreational aspect – is that it provides a mechanism for a species to cope with the inevitability of sustaining damage to its DNA. So why do the bdelloids seem to think they have a better way?

Is DNA Repair A Substitute For Sex?

These hardy creatures somehow escape the usual drawback of asexuality – extinction – and the MBL’s David Mark Welch, Matthew Meselson, and their colleagues are finding out how.

In two related papers published recently in Proceedings of the National Academy of Sciences (PNAS), the team proposes an interesting hypothesis: Bdelloid rotifers have been able to give up sex and survive because they have evolved an extraordinary efficient mechanism for repairing harmful mutations to their DNA. ...

In animals that do have sex, DNA repair is accomplished during meiosis, when chromosomes pair up (one from the father, one from the mother) and “fit” genes on one chromosome can serve as templates to repair damaged genes on the other chromosome. The bdelloid, though, always seems to reproduce asexually, by making a clone of itself. How then, does it cope with deleterious mutations?

Before we come to the hypothesized answer, it must be noted that the bdelloids' ability to repair their DNA is not merely adequate. It's spectacularly good:

MBL adjunct scientist Matthew Meselson and Eugene Gladyshev, both of Harvard University, demonstrate the enormous DNA repair capacity of bdelloid rotifers by zapping them with ionizing radiation (gamma rays), which has the effect of shattering its DNA into many pieces. “We kept exposing them to more and more radiation, and they didn’t die and they didn’t die and they didn’t die,” says Mark Welch. Even at five times the levels of radiation that all other animals are known to endure, the bdelloids were able to continue reproducing.

“Because there is no source of such intense ionizing radiation on Earth, except if we make it, there is no way these organisms could have evolved to be radiation resistant,” says Mark Welch. Instead, they propose that bdelloids’ DNA repair capacity evolved due to a different environmental adaptation – tolerance of extreme dryness.

Bdelloids, which live in ephemeral aquatic habitats such as temporary freshwater pools and on mosses, are able to survive complete desiccation (drying out) at any stage of their life cycle. They just curl up and go dormant for weeks, months, or years, and when water becomes available, they spring back to life. Mark Welch and his colleagues showed that desiccation, like ionizing radiation, breaks up the rotifers’ DNA into many pieces. Presumably, the same mechanisms they use to survive desiccation as part of their life cycle also protect them from ionizing radiation.

Hmmmm. That sounds oddly familiar. Where have we heard about that sort of thing before? Oh yes, this is apparently exactly the same thing found in a bacterium (Deinococcus radiodurans), as discussed here. And in the closely related bacterial species, Deinococcus geothermalis, as discussed here.

But what the bdelloids do is much more impressive, since they are multicellular eukaryotes, not simple prokaryotic bacteria. In any case, what't the trick for bdelloids?

One feature that may confer exceptional DNA repair capacity on the bdelloids is described in the team’s second PNAS paper. Here, they give evidence that the bdelloid rotifer, like most animals, originally had two copies of each chromosome. But at some point in its evolution, it underwent a “whole-genome duplication,” giving it four copies of each chromosome and hence of each gene. Normally, lineages that undergo whole-genome duplication lose the duplicate genes over time. The bdelloid, though, has kept most of its duplicate genes throughout its evolutionary history.

“We believe they have kept most of their duplicate genes because they are serving as templates for DNA repair,” says Mark Welch.

Another highly radiation-resistant bacterial species

Perhaps you recall that just about a year ago research identified some of the mechanism by which what was long thought to be unique species of bacterium – Deinococcus radiodurans – managed to survive extremes of exposure to radiation and dessication.

Now it turns out that the species isn't so unique, and a distant relative also has exceptional durability, despite significant genetic differences:

Second Extremely Resistant Bacteria Sequenced Is Surprisingly Different From First

Researchers have completed the whole-genome sequence of Deinococcus geothermalis, which is only the second extremely radiation- and desiccation-resistant bacterium to be sequenced.

The first was for the Guinness World Records-holder Deinococcus radiodurans, which for 50 years has been the subject of extensive investigations aimed at solving the mystery of how this microbe and its close relatives survive immense doses of x-rays and gamma-rays.

Most surprisingly, many of the unique D. radiodurans genes that were strongly implicated in resistance over the last decade have turned out to be unrelated to its survival, and are not present in D. geothermalis.

However, now that complete genome sequences are available, it turns out that the genes they have in common to account for their durability are surprisingly few:

Using computer-based systems to compare the D. geothermalis genome sequence with the sequence of D. radiodurans, a minimal set of genes which encode extreme resistance was defined. Far fewer genes than initially believed appear to be responsible for the extreme resistance trait.

Among other things, this finding apparently rules out one possible source of the durability:

The phenomenal resistance of Deinococcus bacteria has given rise to numerous descriptions of their origin, including that they evolved on Mars under harsh cosmic radiation. The present analysis firmly places the origin of Deinococcus bacteria on Earth, where the evolutionary steps that led to their survival mechanisms clearly occurred in their terrestrial ancestors - most likely in a desert near you.

Tags: microbiology, extremeophiles

Self-resurrecting bacteria

Who said resurrection is impossible? One species of bacterium, Deinococcus radiodurans, can do it — but it's the only case known.

Cheating DNA Death: How an Extremophile Repairs Shattered Chromosomes

Fifty years ago, scientists uncovered a microbe capable of withstanding radiation in canned meat that had been bombarded with gamma rays. Named Deinococcus radiodurans — or "strange berry that withstands radiation" — the microorganism can survive doses of radiation up to 500 times that which would kill a human. These doses shatter D. radiodurans's DNA — just as they would in a human — but the microbe can repair its broken DNA and spring back to life within hours, depending on the dose. Researchers in France have finally determined how the most durable of extremophiles manages this trick. "We have discovered the mechanism by which a clinically dead cell resurrects back to life," explains Miroslav Radman of INSERM, France's public biomedical research institution. "This extreme radiation resistance is but a by-product of its selection for resistance to desiccation."

It's taken microbiologists 50 years, but the details of how D. radiodurans accomplishes the feat of resurrection have finally been figured out. Well, almost all the details.

When any type of cell is exposed to enough toxic chemicals, oxidative damage, high levels of ionizing radiation, or dehydration, what kills the cell is the fragmentation of its DNA. Without intact DNA, a cell can't manufacture proteins required to sustain its life. What D. radiodurans seems uniquely capable of doing is putting all of its fragmented DNA back together, and in just the right order. Something that all the king's horses and all the king's men could not do for Humpty Dumpty.

It turns out there are two stages to this process. In the first stage, the short fragments of (single-stranded) DNA are gradually reassembled into longer and longer pieces, until they are complete again. This is possible at all only because of the unique structure of DNA — DNA segments will stick together only when they have precisely matching base sequences in common. The process is facilitated in bacterial DNA by an enzyme called DNA polymerase I. The enzyme is encoded by a gene known as polA, which is present in all prokaryotes. However, the DNA polymerase I found in D. radiodurans apparently performs its job much more efficiently than its analogue in other bacteria. This natural process is similar to the laboratory process known as polymerase chain reaction (PCR), which also uses a polymerase enzyme.

But it's the second stage that is really special in D. radiodurans, and which has just been elucidated in the latest research:

... single long strands of DNA do little to resurrect the microorganism until the second stage of the newly discovered process kicks in: the simple pairing discovered by Watson and Crick decades ago — adenine (A) bonds with thymine (T), and cytosine (C) bonds with guanine (G). By inserting a special version of the nucleotide thymine that only binds to single strands of DNA — known as 5-bromodeoxyuridine — the researchers could observe as the single strands bonded with complementary strands to form complete chromosomes. "Once the chromosome is functional, the synthesis of all cellular components starts, and the cellular life is back," Radman says.

Interesting questions remain unanswered. An obvious one is how this unique capability of D. radiodurans evolved. Of course, it's obvious that the capability is highly advantageous to the survival of any microbe that inhabits an extreme environment. But there are few, if any, environments on Earth that have the level of ionizing radiation in which D. radiodurans can survive. So there must have been some other extreme feature of the environment, like toxic chemicals or frequent dessication. But then, why don't many other kinds of bacteria have the same abilities as D. radiodurans? Perhaps something even stranger happened, and D. radiodurans evolved in an environment outside Earth, with much more radiation — like Mars — and later migrated to Earth on a meteorite.

Another important question is: what makes the form of DNA polymerase in D. radiodurans so special and efficient? Knowing this could be very useful, for instance if we wanted to endow other bacteria with the same kind of survivability in extreme environments. We might want to do that to create bacteria that could detoxify toxic wastes.

Eukaryotic cells (found in "higher" animals than bacteria) use a different type of DNA polymerase than what prokaryotes use, and they are much more complex in general than bacteria. But yet another interesting question is whether it is possible to endow eukaryotic cells with a more effective DNA repair capability.

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Further information:

Microbe probe -- announcement of earlier (2001) research on D. radiodurans

Radiation-resistant organism reveals its defense strategies -- announcement of earlier (2003) research on D. radiodurans

Deinococcus radiodurans -- History and summary of research on D. radiodurans

D. radiodurans -- links to more information on D. radiodurans

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Tags: biology, microbiology, extremeophiles