Here is my rather long analysis of the article. I've tried to write it so that non-chemists and non-biologists can understand it. If you're intimidated, you can skip to the last two paragraphs for a summary of my thoughts on the paper.
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Phosphorus is an extremely important element in biology. Found mostly in the form of phosphate (PO43-), phosphorus helps to form and stabilize the lipid membranes that structure the cell, plays important roles in transferring energy throughout the cell, acts as a reversible chemical switch to control many proteins inside the cell, and forms an integral part of the backbone of DNA. With so many diverse an important roles, it would be stunning to find an organism that could survive in the absence of phosphorus. Yet, in research published this week in Science, Felisa Wolfe-Simon and co-workers describe a bacterium that can do just that: live in the absence of phosphorus by using arsenic as a substitute. If true, this work represents a major discovery showing for the first time an organism with a genetic material chemically distinct from the genetic material of all other known terrestrial organisms. However, extraordinary claims require extraordinary evidence. While Wolfe-Simon and co-workers have done an excellent job identifying the arsenophilic bacterium and performing the initial characterization, more work must still be done to rigorously confirm the claims that the bacterium harbors functional arsenic-based biomolecules, in particular arsenic-containing DNA.
Arsenic sits below phosphorus in the periodic table and therefore shares many properties with phosphorus. Because of these similarities, arsenate (AsO43-) could possibly substitute for phosphate in organisms that live in environments rich in arsenate. In order to find such bacteria, the authors took samples from Mono Lake in California, an arsenic-rich lake in California where arsenic-metabolizing bacteria had previously been found. The authors then grew these samples media with no added phosphates and increasing amounts of arsenate over the course of 3 months. At the end of this process, the researchers obtained a bacterial strain, dubbed GFAJ-1, which seemed to incorporate arsenic in the place of phosphorus. This conclusion is based on five lines of evidence:
1) The bacteria exhibit arsenic-dependent growth. The bacteria grow well in the presence of phosphate and absence of arsenate (-As/+P), grow slightly less well in the presence of arsenate and absence of phosphate (+As/-P), and do not grow at all in the absence of both (-As/-P). The fact that the cells grow in +As/-P conditions but not -As/-P conditions suggests that arsenic is required for the cells to grow. It is important to note, however, that the –P samples actually do contain a trace amount of phosphate (3.1µM) compared to 1.5mM phosphate in the +P sample and 40mM arsenate in the +As sample. Because there are trace amounts of phosphate, it is possible that key components of the cell, such as DNA, can still be composed of phosphate. Furthermore, while the data do indicate that the cells require arsenic to grow, they do not pinpoint the exact roles of arsenic. It is completely possible that the bacteria require arsenic for, say lipids and proteins, but still retain phosphorus in their DNA.
2) The bacteria contain high amounts of arsenic and low amounts of phosphorus. The authors measured the amount of arsenic and phosphorus in the cells grown under the –As/+P and +As/-P conditions. Whereas the –As/+P bacteria contain 0.54% phosphorus, the +As/-P bacteria contain 0.02% phosphorus (versus 0.19% arsenic). However, since the authors estimate that ~4% of the phosphorus of the –As/+P bacteria is associated with the genome, the 0.02% phosphorus in the –As/+P bacteria would be sufficient to allow for a normal phosphorus-based DNA.
3) The bacteria incorporate arsenic into biomolecules. By growing the bacteria in a solution of radioactive arsenate, the researchers can track the incorporation of arsenic into biomolecules by following the radioactive signal. The researchers use standard biochemical techniques to perform a crude separation and obtain a fraction containing proteins and small molecular weight metabolites (e.g. ATP), a fraction containing lipids, and a fraction containing nucleic acids (RNA and DNA). They see radioactivity from all of the fractions indicating that arsenic is present in all of these types of biomolecules. The vast majority of the radioactive arsenic signal is present in the protein + small metabolite fraction, but the amount of radioactivity in the nucleic acid fraction is consistent with the amount expected if the DNA contained arsenic. However, it is well known that arsenate can substitute for phosphate; this substitution is the mechanism for arsenate toxicity. In human cells, our phosphate transporters cannot distinguish between arsenate and phosphate and therefore let arsenate into cells. Inside of the cell, some enzymes will substitute arsenate for phosphate, which gums up the cellular machinery eventually killing the cell. Obviously, the arsenate incorporation is not killing these bacteria and some of the arsenate-containing biomolecules are functional, but it is unclear which arsenate-containing molecules are functional and which ones are not, a distinction that cannot be made from the data presented in this paper.
4) Purified DNA from the bacteria contains arsenic. The purified DNA from bacteria grown in the +As/-P condition show more arsenic and much less phosphorus than purified DNA from bacteria grown in the –As/+P condition. However, for the +As/-P bacteria, the DNA still contains much more phosphorus than arsenic (the molar ratio of arsenic to phosphorus is 0.04), although this could be due to a high amount of background phosphate signal from the purification method. Better analyses, including steps to improve the DNA purification, are needed here.
5) X-ray spectroscopy of the arsenic gives signatures consistent with arsenate bound to biomolecules. I’m not very familiar with the technique, so I’ll trust these results at their face value. They give signatures consistent with arsenic incorporation into DNA and proteins, but these signatures are not proof of incorporation into DNA or protein as arsenic incorporation into other metabolites could give similar spectroscopic signatures.
In summary, Wolfe-Simon and colleagues have identified a strain of bacteria that can survive in high arsenic, low phosphorus environments. Surprisingly, this bacteria can use arsenic to replace some of the roles of phosphorus. More work needs to be done to elucidate exactly in which roles arsenic can replace phosphate and in which roles arsenic does not replace phosphate. While the evidence may be consistent with these bacteria containing arsenic-based DNA, the data do not offer irrefutable proof of this hypothesis. A lack of arsenic-based DNA would be expected because previous work by chemists suggests that arsenic-based DNA would be too unstable to exist inside a living cell (Westheimer (1987) Why Nature Chose Phosphates. Science 235: 1173. http://academic.evergreen.edu/curricular/m2o2006/seminar/westheimer.pdf ).
Nevertheless, Wolfe-Simon have made an important discovery identifying a bacterium where arsenic can replace some of the roles of phosphorus. The organism clearly has novel arsenic-based biochemistries that will be interesting to learn more about in the coming years. While it might be exciting to speculate that these bacteria represent a new form of life with a different type of genetic material than any other terrestrial organisms, we do not yet have enough evidence to say whether this is true or not.
