ZT:有关发现砷在细菌的蛋白和DNA里。 Arsenic found incoporated in DNA&protein

This blog explains in general terms to understand this new discovery of As incorporated in protein and DNA in an extremophile bacterium

Category: Evolution • Science
Posted on: December 2, 2010 5:28 PM, by PZ Myers

Oh, great. I get to be the wet blanket.

There's a lot of news going around right now about this NASA press release and paper in Science— before anyone had read the paper, there was some real crazy-eyedspeculation out there. I was even sent some rather loony odds from abookmaker that looked like this:

WHAT WILL NASA ANNOUNCE?

NASA HAS DISCOVERED A LIFE FORM ON MARS +200 33%
DISCOVERED EVIDENCE OF LIFE ON ONE OF SATURNS MOON +110 47%
ANNOUNCES A NEW MODEL FOR THE EXISTENCE OF LIFE -5000 98%
UNVEILS IMAGES OF A RECOVERED ALIEN SPACECRAFT +300 25%
CONFESSES THAT AREA 51 WAS USED FOR THE ALIEN STUDIES +500 16%

[The +/- Indicates the Return on the Wager. The percentage is thelikelihood that response will occur. For Example: Betting on thecandidate least likely to win would earn the most amount of money,should that happen.]

I think the bookie cleaned up on anyone goofy enough to make a bet on that.

Then the stories calmed down, and instead it was that they haddiscovered an earthly life form that used a radically differentchemistry. I was dubious, even at that. And then I finally got thepaper from Science, and I'm sorry to let you all down, but it'snone of the above. It's an extremophile bacterium that can be coaxedinto substiting arsenic for phosphorus in some of its basicbiochemistry. It's perfectly reasonable and interesting work in its ownright, but it's not radical, it's not particularly surprising, and it'sespecially not extraterrestrial. It's the kind of thing that will get asentence or three in biochemistry textbooks in the future.

Here's the story. Life on earth uses six elements heavily in itschemistry: carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur,also known as CHNOPS . There are other elements used in small amountsfor specialized functions, too: zinc, for instance, is incorporated asa catalyst in certain enzymes. We also use significant quantities ofsome ions, specifically of sodium, potassium, calcium, and chloride,for osmotic balance and they also play a role in nervous systemfunction and regulation; calcium, obviously, is heavily used in makingthe matrix of our skeletons. But for the most part, biochemistry is allabout CHNOPS.

Here's part of the periodic tablejust to remind you of where these atoms are. You should recall fromfreshman chemistry that the table isn't just an arbitrary arrangement —it actually is ordered by the properties of the elements, and, forinstance, atoms in a column exhibit similar properties. There's CHNOPS,and notice, just below phosphorous, there's another atom, arsenic.You'd predict just from looking at the table that arsenic ought to havesome chemical similarities to phosphorus, and you'd be right. Arseniccan substitute for phosphorus in many chemical reactions.

This is, in fact, one of the reasons arsenic is toxic. It's similar,but not identical, to phosphorus, and can take its place in chemicalreactions fundamental to life, for instance in the glycolytic pathwayof basic metabolism. That it's not identical, though, means that itactually gums up the process and brings it to a halt, blockingrespiration and killing the cell by starving it of ATP.

Got it? Arsenic already participates in earthly chemistry, badly.It's just off enough from phosphorus to bollix up the biology, so it'sgenerally bad for us to have it around.

What did the NASA paper do? Scientists started out the project withextremophile bacteria from Mono Lake in California. This is not apleasant place for most living creatures: it's an alkali lake with a pHof close to 10, and it also has high concentrations of arsenic (highbeing about 200 µM) dissolved in it. The bacteria living there werealready adapted to tolerate the presence of arsenic, and the mechanismof that would be really interesting to know…but this work didn'taddress that.

Next, what they did was culture the bacteria in the lab, andartificially jacked up the arsenic concentration, replacing all thephosphate (PO₄^3-) with arsenate (AsO₄^3-).The cells weren't happy, growing at a much slower rate on arsenate thanphosphate, but they still lived and they still grew. These are toughcritters.

They also look different in these conditions. Below, the bacteria in(C) were grown on arsenate with no phosphate, while those in (D) grewon phosphate with no arsenate. The arsenate bacteria are bigger, butthin sections through them reveal that they are actually bloated withlarge vacuoles. What are they doing building up these fluid-filledspaces inside them? We don't know, but it may be because somearsenate-containing molecules are less stable in water than theirphosphate analogs, so they're coping by generating internal partitionsthat exclude water.

What they also found, and this is the cool part, is that they incorporated the arsenate into familiar compounds^*.DNA has a backbone of sugars linked together by phosphate bonds, forinstance; in these baceria, some of those phosphates were replaced byarsenate. Some amino acids, serine, tyrosine, and threonine, can bemodified by phosphates, and arsenate was substituted there, too. Whatthis tells us is that the machinery of these cells is tolerant enoughof the differences between phosphate and arsenate that it can keep onworking to some degree no matter which one is present.

So what does it all mean? It means that researchers have found thatsome earthly bacteria that live in literally poisonous environments areadapted to find the presence of arsenic dramatically less lethal, andthat they can even incorporate arsenic into their routine, familiarchemistry.

It doesn't say a lot about evolutionary history, I'm afraid. Theseare derived forms of bacteria that are adapting to artificiallystringent environmental conditions, and they were found in ageologically young lake — so no, this is not the bacterium primeval.This lake also happens to be on Earth, not Saturn, although maybe beingin California gives them extra weirdness points, so I don't know thatit can even say much about extraterrestrial life. It does say that lifecan survive in a surprisingly broad range of conditions, but we alreadyknew that.

So it's nice work, a small piece of the story of life, but not quite the earthshaking news the bookmakers were predicting.

^*I've had it pointed out to me that they actuallydidn't fully demonstrate even this. What they showed was that, in thebacteria raised in arsenates, the proportion of arsenic rose and theproportion of phosphorus fell, which suggests indirectly that therecould have been a replacement of the phosphorus by arsenic.

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Wolfe-Simon F,Blum JS,Kulp TR,Gordon GW,Hoeft SE,Pett-Ridge J,Stolz JF,Webb SM,Weber PK,Davies PCW,Anbar AD, Oremland RS (2010) A Bacterium That Can Grow by Using ArsenicInstead of Phosphorus. Science DOI: 10.1126/science.1197258.