Tuesday, December 7, 2010

The Arsenic Bug: Updated!

The news today is full of the arsenic bug found in Mono Lake, and how it represents alien life. As a biogeochemist with a long interest, and dare I say some expertise, in arsenic, I find the story, while interesting, somewhat over-hyped. The bacteria is clearly identified as a member of a rather wide spread group, the gamma proteobacteria, a class which includes the human gut bacteria E. coli. How alien can that be?

The thing that apparently makes this bacterium very unusual is its ability to utilize arsenic (usually considered a toxic element) in place of phosphorus, a minor but essential element in all other known organisms. Arsenic is a step below phosphorus on the periodic table, and shares many of its chemical characteristics. For most organisms, arsenic in high concentrations is toxic because it interferes with the normal uses of phosphorus in the metabolism, because the enzymatic machinery of the cells cannot fully discriminate between the arsenic and the phosphorus. Thus, when arsenic concentrations are relatively high compared to the phosphorus, important cellular processes can be inhibited.

However, arsenic is not the rarest of elements and organisms have been evolving in its presence for a very long time, and many of them have evolved biochemical mechanisms for detoxifying arsenic, by combining it with organic molecules to make it less toxic, or allow it to be excreted (or both). For example, many varieties of seafood have rather high concentrations of total arsenic, because seawater has relatively high concentrations relative to phosphate. However, the vast majority of the arsenic in seafood is found in a number of organic compounds which are non toxic.

This bacterium seems to have evolved a different strategy for dealing with an excess of arsenic relative to phosphorus, use it. Rather than exclude it, its chemical metabolism has evolved to use arsenic in place of phosphorus in most or all functions including as a structural element in DNA. From the news accounts it's not clear whether it has evolved to the point that phosphorus is toxic to the organism for replacing, or whether it can use either phosphorus or arsenic depending up which is more abundant.

The route to a bacterium evolving in this direction is not hard to imagine. A bacterium which can survive and tolerate a minor amount of substitution of As for P will be at an advantage in certain environments where As is abundant, and the presence of environments where As is far more abundant than P often could push the bacteria to evolve in that direction.

I would note that I'm not the only skeptic:  http://blogs.discovermagazine.com/notrocketscience/2010/12/02/mono-lake-bacteria-build-their-dna-using-arsenic-and-no-this-isnt-about-aliens/


I read the paper and supplemental material today, and I have to say that while they might be right, I think there's plenty of room for reasonable doubt.  The article itself makes a pretty smooth case, but in the journal Science, unlike most other journals, the details are left out of the article and published separately as supplemental materials on the web.  The medium that they grew the bacteria in, while having no added P, had a pretty substantial contamination of P from the organic materials used as a growth medium.  Their conclusion that the DNA of the bacteria had to be based on As rather than P when grown without P is based largely on an assumption of the use of P in "normal" bacteria, of which this is clearly not one.

The answer to my question above is that the organism still clearly prefers P to As, and will not grow when both P and As are in sufficiently low supply, but will grow, and not as rapidly, if As is added back to the media.

An article in Slate by Carl Zimmer comes to as similar, but somewhat harsher conclusion, that the article should not have been published.  I'm fairly lenient in reviewing, but would suggest that the article be reworded to tone down the sense of breathless wonder, and that maybe a little follow up on the chemistry is warranted.

Hat tip to Chum for the Slate article.

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