As exciting as this is, I have yet to see any actual technical information on it. All I’ve read is that it “eats” arsenic. I don’t find that particularly impressive. OTOH, they have said that it doesn’t use phosphorous, and it has very different DNA. That is much more impressive, but what does that mean technically?
I have had to assume then, that ATP is replaced by ATA. It’s really not so technical that the news couldn’t explicitly say that, so why don’t they? Also, I assume the phosphates in DNA have been replaced by arsenates. That is pretty impressive, but once again, the media has not explicitly said that.
What about beyond arsenic. Do the DNA codes match the rest of life on earth? Did it evolve completely separate from the rest of life on earth?
Yep that’s pretty much exactly what happens. This organism seems to prefer to use P for these purposes, but when there isn’t any phosphate around they can substitute in arsenic. The rest of the DNA is normal – same bases, etc.
It’s related to other bacteria which tolerate arsenic. In a sense it’s “just” another extremophile with an interesting metabolic trick.
It is an interesting finding, but a lot less exciting than it has been hyped up to be. And they have not even really shown for sure that the arsenic is going into the DNA. Even if it does, it will not affect the coding. The arsenic is replacing some of the phosphorus in the DNA (if it is) and the phosphorus is part of the molecule’s backbone, not of the bases strung along it that actually carry the coded information.
It’s fascinating to see phosphorous, one of the basic building elements of life, replaced by Arsenic, which is similar, but forms less stable compounds (hence its famed toxicity, celebrated here.)
There’s been an embargo on media coverage of the story until officially released. This has resulted in actual science journalists, who know a lot of the story and the background, not being able to write about it, but people who were willing to speculate wildly being able to say whatever they want, whether based on rumors that got out or not. It’ll be interesting to see the effect of the strange publicity approach on this story as we go. I think it has helped raise the profile of the story, although it’s opened the way for a lot of misunderstandings.
Yep. Phylogenetically, these critters are members of the Oceanospiralles (Oceanospirillales - Wikipedia) and as ladybratsche mentioned, it’s not a new form of life or separately evolved.
It turns out there may also be some reason to be skeptical of the claims in the paper - see this (http://scienceblogs.com/webeasties/2010/12/guest_post_arsenate-based_dna.php) blog post. Particularly disturbing is the lack of a negative control, but then I haven’t read the original paper - just some commentary about it.
I knew my skepticism was justified. Arsenic has some similarities to phosphorous but so foes nitrogen. Granted, without the d orbitals nitrogens a much different ball game, but I still don’t expect arsenic to replace phosphorous easily.
Basically, the bacteria are being fed a solution that contains no phosphorus, but contains arsenic. Yet, the bacteria are thriving. They have done some initial analysis, and it seems the arsenic is in the places you’d expect it to be if it was replacing phosphorus.
Phosphorus is considered one of the six basic elemental building blocks for life. No phosphorus, no life. So, if these bacteria are actually using arsenic instead of phosphorus, this would mean we can expect that there might be life forms out in the Universe that can do the same trick. Maybe whole planets of arsenic based life.
The problem is that they still haven’t shown that the arsenic is really replacing the phosphorus. All they can say is it appears the arsenic is being incorporated into the bacteria, and there is no source of phosphorus. It will take years of analysis to show that arsenic is actually being incorporated into the DNA, and that these bacteria are powering themselves via ATA instead of ATP.
But the solution does contain some phosphorus. They don’t add any as a separate ingredient, but it’s there in measurable amounts from the other stuff they put in.
I wouldn’t have thought so. It is routine, for example, to perform mass spec on DNA, nucleotides, etc., and these would easily confirm replacement of P by As.
I gave this example in the other thread and I’ll try find a cite for it if anyone is interested. Water that has been formed from oxygen and 2 deuterium atoms rather than hydrogen is poisonous. It has to do with the angle between the D2 atoms being off by 2 degrees or so.
So if the archaea is using arsenic for ANY purpose, it is impressive. A different element with the same valence will result in the compounds having a slightly different structure. That tiny difference is usually enough to throw off the rest of the cellular machinery.
So at the very least, this archaea has evolved to be extremely tolerant of conformational errors in DNA and other enzymes and proteins that might have a phosphorus atom. That alone is a big deal since we still don’t even understand how transcribed proteins get folded into their active form. This bug can not only seem to do it, but do it even when molecular bonds aren’t where they’re supposed to be.
If selenium is being incorporated into the DNA in any but trace amounts, it should fall quickly to mass spec.
If true, the little bug must have pretty robust methods of regulating gene expression.
I don’t see the point of your reference since the enzymes, etc that use it are designed to do so.
And I was making the same argument regarding robust mechanisms - “So at the very least, this archaea has evolved to be extremely tolerant of conformational errors in DNA and other enzymes and proteins that might have a phosphorus atom.”
As to the amount used as opposed to simply sequestered, they claim it is being incorporated but others say no
. We’ll see.
I tried to make this argument to myself and had trouble not running into potential technical issues. Since I’m not a biochemist, please correct if I’m wrong. For one thing, it is doubtful that they routinely rum MS on DNA without running PCR first to get a larger sample. That means you have to have enzymes that work in an arsenic environment on arsenic DNA. I do t know what techniques they may.have for isolating pure DNA from a sample, but one must be very careful not to accidentally introduce phosphorous or arsenic in this case. Also, when you look at DNA and the way it is likely to fragment in the MS, those phosphates and arsenates are going fly tight off. As a result, you may get an extremely high arsenate signal bring drowned out by the arsenate that is no doubt present in other forms in the solution. Similarly, in biochemistry, they often use soft ionization methods that allow non-covalent associations, so even if you find a m/z at Purine + ribose + arsenate + H, you can’t really prove that the arsenate was on the DNA.
Given those challenges, and others I have unforeseen, I can imagine that it may take two years to prove. I found similar issues with methods beyond mass spec.
I apologize for the typos. I wrote this on my iPhone.
Nothing is ‘designed’.
Things either work, or they are selected against.
If DNA incorporating arsenic works for these bacteria, that is the things live and reproduce, then all the mechanisms involved in gene expression and replication must also work +/- arsenic in the DNA.
Now having multiple processes continue to work after an elemental substitution would be impressive, but it’s not different, except in magnitude, from having an enzyme continue to work after an S gets replaced by an Se.
Except those enzymes EVOLVED (not designed) to work with selenocysteine - right? That’s what I got from the wiki article. But I assume your point is that the enzymes work with either? If so, then that that’s impressive as well.
As for the relative merits though, since an enzyme has an active site, unless the substitution is there . . . . hell, even if it is, if the valence is the same and it doesn’t screw up the re-folding when activated, meh, maybe it’s not a big deal.
But for other things that seem to require tight tolerances, I think it is still impressive - if for no other reason that the fact that its machinery is so robust.
