Planet Earth

Mono Lake bacteria build their DNA using arsenic (and no, this isn't about aliens)

Not Exactly Rocket ScienceBy Ed YongDec 2, 2010 11:28 PM


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Note: Serious concerns have been raised about the conclusions of this study. I've written a summary of the backlash in a separate post.

Arsenic isn’t exactly something you want to eat. It has a deserved reputation as a powerful poison. It has been used as a murder weapon and it contaminates the drinking water of millions of people. It’s about as antagonistic to life as a chemical can get. But in California’s Mono Lake, Felisa Wolfe-Simon has discovered bacteria that not only shrug off arsenic’s toxic effects, but positively thrive on it. They can even incorporate the poisonous element into their proteins and DNA, using it in place of phosphorus. Out of the hundred-plus elements in existence, life is mostly made up of just six: carbon, hydrogen, oxygen, nitrogen, sulphur and phosphorus. This elite clique is meant to be irreplaceable. But the Mono Lake bacteria may have broken their dependence on one of the group – phosphorus – by swapping it for arsenic. If that’s right, they would be the only known living things to do this. The discovery is amazing, but it’s easy to go overboard with it. For example, this breathlessly hyperbolic piece, published last year, suggests that finding such bacteria would be “one of the most significant scientific discoveries of all time”. It would imply that “Mono Lake was home to a form of life biologically distinct from all other known life on Earth” and “strongly suggest that life got started on our planet not once, but at least twice”. The results do nothing of the sort. For a start, the bacteria – a strain known as GFAJ-1 – don’t depend on arsenic. They still contain detectable levels of phosphorus in their molecules and they actually grow better on phosphorus if given the chance. It’s just that they might be able to do without this typically essential element – an extreme and impressive ability in itself. Nor do the bacteria belong to a second branch of life on Earth – the so-called “shadow biosphere” that Wolfe-Simon talked about a year ago. When she studied the genes of these arsenic-lovers, she found that they belong to a group called the Oceanospirillales. They are no stranger to difficult diets. Bacteria from the same order are munching away at the oil that was spilled into the Gulf of Mexico earlier this year. They aren’t a parallel branch of life; they’re very much part of the same tree that the rest of us belong to. That doesn’t, however, make them any less extraordinary. Phosphorus helps to form the backbone of DNA and it’s a crucial part of ATP, the molecule that acts as a cell’s energy currency. Arsenic sits just below phosphorus in the periodic table. The two elements have such similar properties that arsenic can usurp the place of phosphorus in many chemical reactions. But arsenic is a poor understudy – when it stands in for phosphorus, it produces similar but less stable products. This partially explains why the element is so toxic. But the bacteria of Mono Lake have clearly found a way to cope with this. They have every reason to do so. Mono Lake sits in a sealed basin close to California’s Yosemite National Park. With no outlet connecting it to other bodies of water, any chemicals flowing into the lake tend to stay there. As a result, the lake has built up some of the highest concentrations of arsenic on the planet. To survive here, bacteria have to be able to cope with the poison. In 2008, Ronald Oremland (who was also involved in the latest study) discovered bacteria in Mono Lake that can fuel themselves on arsenic. Like plants, they can photosynthesise, creating their own food using the power of the sun. But where plants use water in this reaction, the bacteria used arsenic. Wolfe-Simon has taken these discoveries a step further, by showing that the bacteria are actually incorporating arsenic into their most important of molecules. She took sediment from Mono Lake and added it to Petri dishes containing a soup of vitamins and other nutrients, but not a trace of phosphorus. She took samples from these dishes and added them to fresh ones, gradually diluting them to remove any phosphorus that might have stowed away onboard. And all the while, she added more and more arsenic. Amazingly, bacteria still grew in the dishes. Wolfe-Simon isolated one of these arsenic-lovers – a strain called GFAJ-1. Using an extremely sensitive technique called ICP-MS that measures the concentrations of different elements, she showed that the cells of these bacteria did indeed contain large amounts of arsenic. By giving the bacteria a mildly radioactive form of arsenic, Wolfe-Simon could also track where the element ended up in the cells. The answer: everywhere. There was arsenic in the bacteria’s proteins and in their fat molecules. It had replaced phosphorus in many important molecules including ATP and glucose (a sugar). It was even in their DNA, a conclusion that Wolfe-Simon backed up with a number of other techniques. All other life uses phosphorus to create the backbone of the famous double helix, but GFAJ-1’s DNA had a spine of arsenic. It’s an amazing result, but even here, there is room for doubt. As mentioned, Wolfe-Simon still found a smidgen of phosphorus in the bacteria by the end of the experiment. The levels were so low that the bacteria shouldn’t have been able to grow but it’s still not clear how important this phosphorus fraction is. Would the bacteria have genuinely been able to survive if there was no phosphorus at all? Nor is it clear if the arsenic-based molecules are part of the bacteria’s natural portfolio. Bear in mind that Wolfe-Simon cultured these extreme microbes using ever-increasing levels of arsenic. In doing so, she might have artificially selected for bacteria that can use arsenic in place of phosphorus, causing the denizens of Mono Lake to evolve new abilities (or overplay existing ones) under the extreme conditions of the experiment. Other species can cope with arsenic too. Some switch on genes that give them resistance to arsenic poisoning, while others can even “breathe” using arsenate. But GFAJ-1 uses the element to an even greater extent. How does it manage? Under the microscope, the bacteria become around 50% larger if they grow on arsenic compared to phosphorus, and they develop large internal compartments called vacuoles. These might be the key to their success. Wolfe-Simon thinks that the vacuoles could act as a safe haven for unstable arsenic-based molecules – they might contain chemicals that steady the molecules, and they might keep out water that would hasten their breakdown. These are questions for future research. In the mean time, the angle being used to sell the story is that this might have implications for alien life. Of course, the results have nothing to do with aliens. If anything, they expand the possibilities of what alien life might look like.If bacteria on Earth can exist using a biochemistry that’s very different to that of other microbes, it stands to reason that aliens could do the same. That hasn’t stopped the hype machine from rolling forward, fuelled by a public announcement from NASA, teasing a press conference about an “astrobiology discovery”. It’s a shame. In teasing their own press conference two days ahead of time, and refusing to budge on the embargo when the first information trickled in, NASA effectively muzzled everyone who knew about the actual story while allowing speculation to build to fever pitch. That may, of course, be their intention. However, I can’t help but feel that the result will be a lot of disappointed people, who’ve been robbed of an opportunity to be excited about a genuinely interesting discovery. Update: John Sutherland from the MRC Laboratory of Molecular Biology at Cambridge adds to the skepticism. He notes that arsenic-based compounds are "not sufficiently stable in water for the phosphorus to arsenic substitution implied in this paper to be functional" and the arsenic-phosphorus swap hasn't been demonstrated by the study's experiments in a "chemically rigorous manner". For Sutherland, the acid test would be actually synthesising a double helix of arsenic-based DNA and characterising its structure in detail. You could then use the data from that analysis "as a reference point" to examine the DNA from the Lake Mono bacteria. "This has not been done," he notes, and even if it were, the existing evidence suggests that the molecule would break apart when it's exposed to water. Update 2: Rosie Redfield has published a devastating critique of the paper, describing it as "lots of flim-flam, but very little reliable information." It's an incredibly technical post, recommended for everyone but probably only suitable for those with a scientific background. Likewise, Alex Bradley has a critique of his own. And David Dobbs asks if science journalists could have done better. I know I could have. Update 3: The updates are coming thick and fast on this story and I'm struggling to keep up with them. For the moment, check out the Guardian's story tracker for a comprehensive look at the coverage, responses, and counter-responses. Update 4: I've summarised the last week of responses to this study in a new post. Reference: Science

My other take on this story...

More on extreme bacteria:

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