Friday, December 03, 2010

Arsenic and New Microbes

Yesterday's announcement of a microbe which not only tolerates arsenic but actually appears to incorporate it in place of phosphorous has traveled a typical path for such a discovery: while it is quite a find, the media has generated more than a few ridiculous headlines. Yes, this potentially expands the definition of life, at least in an elemental sense, but it hardly suggests that such life forms exist elsewhere. A similar absurd atmosphere briefly reigned around a discovery of a potentially habitable world around a distant star -- the discoverer was quoted in at least one outlet that his find was guaranteed to have life. Given that we know very little about the probability of life starting, I always cringe when I hear someone announce that such events are either certain or certainly impossible; we simply can't calculate believable odds given our poor knowledge base. On the other end, suggestions have been raised as to this bug being a starting point for bioremediation of arsenic-contaminated aquifers; but really this discovery isn't a huge step in that direction beyond species already known to tolerate the stuff. It's also disappointing that none of the popular news items I've seen have pointed out how a periodic table can be read to show chemical similarity of phosphorous and arsenic.

That said, it is an intriguing discovery. The idea that all those phosphates on the metabolic diagrams might be substituted with arsenate is quite jarring. No reader of this space will be surprised to hear me advocate for immediate sequencing of this bug (if it hasn't already happened and just not yet reported). A microbial genome these days can be roughed out in well under a month (actually, sequence generation for Mycoplasma a decade ago took that long; clearly we can go faster now).

In order to interpret that genome, though, another whole line of experiments is needed. Assuming that the ability of this organism to incorporate arsenate in place of phosphate is confirmed, some of the precise enzymes capable of doing this trick need to be located. Simply finding arsenate-analogs of some key metabolites (such as phosphorylated intermediates in glycolysis) would point at a few enzymes, and then it would be valuable to demonstrate the purified enzymes pulling the trick. The next step then would be to test whether more conventional enzymes have this activity. Despite what many of us learned in various exposures to biochemistry from elementary school on up, enzymes aren't utterly specific for their substrates. Instead, there is a certain degree of promiscuity, though generally not with equal activity. So, to extend my analogy, if the new bug's triose phosphate isomerase can work on triose arsenates, then testing that activity in well-characterized TPIs would in order.

Assuming that such enzymes (from E.coli or human or yeast or what-not) do not have the activity, then crystal structures of the arsenate-lover would be an important next step. Of course, repeating this for the whole roster of enzymes in the bug would be quite an undertaking, but perhaps a number could be modeled to see if a consistent pattern of substitutions or other alterations emerges.

At one time, it was vogue to speculate on life forms which used silicon in place of carbon, given it's location one rung down on the periodic table. Did any author ever dare suggest arsenic for phosphate? I doubt it, but perhaps there was some mind playing with the possibilities who wrote it down somewhere (along with a large pile of other guesses that will not pan out).


Jonathan Badger said...

While I'm sure it wouldn't hurt sequencing this arsenic loving organism, what the media doesn't seem to get is that this bacterium, GFAJ-1, is not some member of some new branch of life akin to an alien creature whose genome would be truly a new finding.

It's just a Gammaproteobacterium -- the most studied and least exotic phylum of bacteria on Earth, containing such classic model organisms as E. coli and Salmonella typhimurium.

Keith Robison said...

Thanks for pointing that out -- I hadn't gotten to the tree in the supplemental figure yet (duh!).

Given that GFAJ-1 lumps very tightly in with other Halomonas, the question really does become is this really different from other Halomonads? If you take other strains & submit them to the same treatment, will they survive? And how many others were in the original sample and dropped out?

Anonymous said...

Yes I like the comment about the periodic table made above. If anything, they did not find extra terrestrial life but they succeeded in once again underscoring the paramount importance of the periodic table in modern science. It is a beautifully simple and hugely powerful concept.

For more info see the recent book,

Eric Scerri, The Periodic Table, Its Story & Its Significance, Oxford University press, 2007.

Marco said...

FWIW, in the movie "Evolution" with David Duchovny, it was suggested that because arsenic was poisonous to carbon-based life forms, that selenium could be used to destroy the nitrogen-based alien monster. They then proceed to douse the alien with Head & Shoulders shampoo and destroy it.

No real point here, it only reminded me of that line, which I found so ridiculous I think I actually walked out of the theater.