Science Is Sexy: Why Do NASA’s New Arsenic Bacteria Matter?

By Jimmy Rogers (@me)
Contributing Writer, [GAS]

Did you hear the news?  We’ve discovered alien life! We didn’t even have to go to another planet to find it…it was right here in our own back yard!  Ok, sure, we’re blowing things a little out of proportion, but even Mulder and Scully would agree that these arsenic-eating bacteria are “aliens.”

Here are the facts:

Last Thursday, NASA’s Astrobiology Institute announced at a press conference that they had discovered a new form of life, different from all previously discovered life-forms in one key way: it can live without phosphorous.  It has long been thought that all life on Earth required at least Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorous, and Sulfur, or “CHONPS”, to survive.  In this case, the new organism has found a way to replace phosphorous with arsenic.

The project was spearheaded by Dr. Felisa Wolfe-Simon, a geomicrobiologist and NASA Astrobiology researcher, who collected samples of bacteria from California’s famous Mono Lake.  The lake has high levels of naturally-accumulating arsenic and Wolfe-Simon hypothesized that some of the bacteria might have found a way to use the arsenic in place of phosphorous (As sits right below P on the periodic table).  They grew their sample (currently named GFAJ-1) on growth media with progressively less and less phosphorous, supplementing it with increasing levels of arsenic.  The real surprise came when they lowered the phosphorous levels below those thought to be required for any living cell. The bacteria still grew!

For you adventurous readers, Wolfe-Simon and her team published their findings in Science.  Here is the article and a short article about their work.  Also, if you want to follow the 32 year old scientist, she’s on Twitter.

Sooo, What’s the Big Deal?

As a microbiology grad student, I just about fell over when I heard about this discovery.  Then I looked around me and noticed nobody else had the same reaction.  I think there are a lot of reasons that non-microbiologists have to get excited about the new find, but maybe those reasons require a little explaining…

First off, any major change in a “dogmatic” science principle makes waves.  People rely on such principles when making scientific assumptions.  If you discovered a new planet but determined it had little phosphorous, you might safely assume it had no chance of life.  This new bacteria suggests that at least in the case of phosphorous, arsenic might work as a stand-in.  Beyond that, if nature teaches us anything, it’s that it never does something only once or one way.  Alternatives might exist for some or all of the other “required” elements as well.  Even Star Trek has played around with Silicon-based life forms a bit (in lieu of Carbon).

A Scanning Electron Micrograph (SEM) of the cells with low P and high As. (Science)

The next cool thing is that these bacteria were discovered here on our own planet.  If they developed, albeit in a fairly strange circumstance, what else might be lurking under our feet or in the oceans?  We generally assume that the vast majority of organisms on Earth are undiscovered by Man, so maybe we’ve yet to find even more bizarre microbes!

Lastly, studying extremophiles like GFAJ-1 can really pay off.  Ever seen CSI?  Almost all of the genetics they do (or pretend to do) are based on Polymerase Chain Reaction, or PCR.  The polymerase part is an enzyme that replicates DNA and is very heat-stable.  They found that enzyme while studying bacteria in the sulfur springs at Yellowstone National Park.  The thermophilic bacteria there can survive in almost boiling water, which is why they need such a heat-stable polymerase for replication.  We simply found a very lucrative use for it!

Are These Really Aliens Then?

I think by most people’s definition, these arsenophilic bacteria are NOT true aliens.  They developed on this planet and have probably been living here longer than we have.

That being said, there are a number of organisms on Earth that are so bizarre they really seem like aliens.  In fact, when Scully, on The X-Files, was trying to prove that the organisms in her lab were extraterrestrial, she looked at their DNA.  What she found was DNA with similar but significantly different chemistry (in that case, new nucleotides).  Believe it or not, the GFAJ-1 bacteria have almost the same phenomenon.  Because arsenic replaces the phosphorous throughout the cell, even the DNA backbone is made of arsenate instead of phosphate.  The differences extend beyond DNA into familiar molecules like ATP, too.

While they’re not from outer space, based on The X-Files, Mulder and Scully would certainly give these bugs the alien stamp of approval!

One more note:

Before I wrap up, I just want to clarify something I’ve heard a lot from non-scientists in response to this story.

“This is really cool, but they made these bacteria in the lab.  It’d be much cooler if they found these things in the wild.”

While laboratory conditions are not perfect replicas of a microbe’s natural habitat, rest assured that the scientists involved did not “make these bacteria capable of using arsenic.”  That ability developed over hundreds, thousands, or maybe even millions of years.  All the scientists did was give the bacteria what they needed to strut their stuff, so to speak.

Very cool stuff – this is one excited microbiology grad student!  Let me know what you think in the comments below or on Twitter!

Other installments in the “Science is Sexy” series:

[Mulder and Scully Image via Fox]

15 Responses to Science Is Sexy: Why Do NASA’s New Arsenic Bacteria Matter?

  1. Having studied quite a bit of chemical thermodynamics, my first thought after reading about the discovery was "I wonder how ATA compares with ATP for energy storage?"

    Would the larger size of the arsenic atoms increase charge separation and reduce the stored energy in ATA? Would the difference in acid dissociation constants be significant?

  2. Having studied quite a bit of chemical thermodynamics, my first thought after reading about the discovery was "I wonder how ATA compares with ATP for energy storage?"

    Would the larger size of the arsenic atoms increase charge separation and reduce the stored energy in ATA? Would the difference in acid dissociation constants be significant?

  3. Just fyi it's Yellowstone not Yellow Stone National Park. I should know, I work there. Very interesting tho. Just keeps proving the fact that we can't assume that the million times we've seen something do it's thing a certain way is the way it always does it.

  4. Replacing phosphorous with arsenic is just a regular adaptation — an extreme form of a regular adaptation, but regular none the less. I was more impressed by the discovery of the anaerobic, multicellular Loricifera that use hydrogenosomes instead of mitochondria.

    These bacteria that use arsenic are just that, bacteria and fit nicely into an existing domain. What would really be exciting is a life form that transcribes DNA so differently that it would indicate that they do not share a common ancestor with us, That would be life-as-we-do-not-know-it.

    • Agreed, this is the kind of thing we should actually EXPECT to see. That being said, we don't usually expect such things (even if they make sense), so it strikes us as sensational. Still, I think there are some neat possibilities that stem from this.

      Personally I'm interested in how the organism can deal with alternative forms of DNA (variable proteins or variable transcription??).

    • While I can't personally verify the criticisms in your link, there's probably some valid points. That being said, I don't think any of the points there COMPLETELY discredit the findings made in the paper. As Dr. Oremland said in his talk today at NASA (a very interesting presentation if you can find it somewhere), these are just the first results that point toward a very interesting conclusion. He openly invites a number of more rigorous tests to be conducted.

      I think one reason the paper seems kind of weird is that it was compiled by a lot of different people and none of them had a particularly clear idea of how the research should be conducted. Most papers are the result of a highly planned research project where the outcomes are much highly controlled. These guys were working without a net, it seems. I'm glad they stuck their necks out.

  5. I agree with Rflight79, you might want to actually read the article. Those who work on astrobiology are starting to worry that this type of shoddy science is actually going to be detrimental to obtaining funding.

  6. The recent announcement by NASA scientists and their collaborators that the GFAJ-1 strain of the Halomonadaceae bacteria provides hints into the potential biology of alien life-forms and the response of the media and scientific community to this claim have revealed several disturbing trends. These include the desperation of a government-funded science agency to generate publicity at a time when its financial support is in jeopardy; the inadequacy of the experiments by these researchers to support their conclusions; the relatively poor peer-review by one of the most prestigious of scientific journals; and the extra-hype added by the mass media. One rather positive aspect of this affair is the rapid response of the scientific community to question and challenge the most poorly supported and far reaching claims. It is likely that they will be disregarded much faster than the previous announcement by NASA of petrified Martian life in an Antarctic meteorite.

    A few of my colleagues as well as numerous bloggers have noted that the NASA publicity machine has been coincidently cranked up at a time when the next US budget, including the funding for NASA, is under question. The discovery of the model organism described in the Wolfe-Simon et al. paper in Science is actually not new. Since the mid-nineties, the ongoing study of various strains of Halomonadaceae bacteria and their respiration of arsenic at Mono Lake, the Aberjona Watershed and elsewhere has been reported by Dr. Ronald Oremland (the senior author of the Wolfe-Simon et al. paper) and independently by others.

    The central claim of the new Wolfe-Simon et al. study is that arsenic can substitute for phosphorus to sustain the growth of the GFAJ-1 bacterial strain, and some evidence is offered that the arsenic is incorporated into macromolecules such as nucleic acids and proteins. The GFAJ-1 cells were cultivated in the near absence of phosphorus in the growth media in the presence of arsenic. However, the media used in the study apparently had about 3 µM phosphorus, and one wonders whether phosphorus may have also been introduced with the culture plates that may have been pre-washed with phosphate-containing detergents. In any event, the cultured GFAJ-1 cells were still observed to contain phosphorus at about 1% of the levels seen in cells grown in the presence of high phosphorus. Even under these conditions, bathing in medium containing arsenic, these cells still featured 100-times more phosphorus than arsenic. Moreover, the levels of arsenic incorporated into the phosphorus-depleted bacteria was not that much different from phosphorus-supplemented GFAJ-1 cells grown without arsenic. Ideally, a synchrotron X-ray analysis of arsenic in biomolecules should have been undertaken for both the phosphorus-fed and starved populations of the bacteria rather than just the phosphorus-depleted cells as was performed in the study.

    Despite the speculations offered in the Wolfe-Simon et al. paper, no conclusive evidence was provided that any arsenic actually replaced phosphorus in the DNA backbone of the GFAJ-1 cells. To incorporate arsenic into nucleotides and proteins, the arsenic would have to be presented with the arsenic-containing equivalent of adenosine tri-phosphate (ATP), i.e. adenosine tri-arsenate (ATAs). No evidence was obtained for the presence of ATAs in the GFAJ-1 bacteria. In fact, I have been unable to find any reports of ATAs in any life-form from PubMed or Google searches.

    While arsenic and phosphorus are highly related in the periodic table of elements, the arsenic atom is slightly more than double the molecular mass of phosphorus. As atoms get larger, the electronic structure of the atom, particularly those parts that participate in chemical bonds, become increasingly diffuse. Consequently, arsenate esters are very unstable and hydrolyze markedly faster than phosphate esters. This instability of arsenate ester linkages really restricts their utility in the synthesis of macromolecules like DNA. Furthermore, the instability of arsenylation of proteins, would precludes it from effectively replacing protein phosphorylation. Protein phosphorylation appears to be the major post-translational regulatory mechanism for the emergence of eukaryotic organisms and seems to be required for the development of multi-cellular organisms.

    While the existence of stable ATAs is doubtful, it is more feasible that adenosine-diphosphate, mono-arsenate (ADPAs) might be produced that could fuel arsenylation reactions. Even if ADPAs exists, it is still difficult to reconcile the use of arsenate by a wide range of enzymes to replace all of the diverse metabolic and structural roles (e.g. nucleic acids, phospholipids, phosphoproteins) of phosphate in even bacteria. It is unlikely ADPAs would have a stable enough high energy bond between the gamma arsenic and oxygen atoms to serve as an efficient source of chemical energy. ATP is optimal in all biological systems on this planet with an intermediary position between the higher energy compounds from which ATP accepts phosphate and the lower-energy compounds from which it donates phosphate. Consequently, an organism that exclusively utilizes arsenic and not phosphorus would have a profoundly different metabolism with very different metabolites and macromolecules.

    As a member of the wide-spread Gammaproteobacteria, the Halomondadaceae bacteria clearly do not represent an alternatively evolved family of life-forms, but are well adapted to endure extreme conditions. These organisms are also commonly dispersed in environments in which “normal” microbes proliferate, which is most probably where they originated. The GFAJ-1 bacteria actually prospered better in the presence of phosphorus. Those grown in the presence of arsenic and near absence of phosphorus became bloated in size by approximately 60%. This was due to the appearance of large “empty” vacuoles in the bacteria. It seems that this organism functions optimally in phosphorus, but tolerates arsenic. This is not surprising, since the concentration of phosphorus in the Earth’s crust is around 1000 parts per million (ppm), which is about 500-times higher than measured for arsenic. Such a relative distribution of these two elements is likely to be universal, as more energy is required to forge arsenic atoms than phosphorus atoms.

    Many metals can poorly mimic each other as cofactors in enzyme-catalyzed reactions. This is why a few are highly toxic such as lead and mercury. The fidelity of enzymes for their optimal elements is not 100%, so it is not surprising if trace arsenic can replace phosphorus in the structures of small molecules and macromolecules. Many marine organisms, including clams and sea weeds can also accumulate arsenic. This is likely to be a protective response to reduce the threat of predation by animals that might try to consume them. Arsenic is particularly toxic in eukaryotic organisms, because amongst other many other problems, arsenic inhibits pyruvate dehydrogenase in the citric acid cycle and it uncouples oxidative phosphorylation in the mitochondria, both of which inhibit ATP synthesis. It seems probable that the Halomonadaceae bacteria have acquired the ability to tolerate arsenic, most likely to avoid being eaten. They may concentrate arsenic-containing compounds in vacuoles for this purpose, and they are known to excrete arsenic, presumably when it becomes too toxic for the bacteria themselves. This ability provides the opportunity for these bacteria to thrive in arsenic-rich environments where most other bacteria cannot.

    The lessons from all of this hype from a US government agency, a peer-reviewed scientific journal, and the popular press will likely go unheeded. Unfortunately, too many research institutions that depend on public funding through government agencies and charity will continue to feel pressured to over blow their latest scientific breakthroughs to justify the massive amounts of financial support that they have received. However, with the increasing ability of the wider scientific community to rapidly challenge these assertions in the Internet age, they do so at the peril of their credibility.