Protocells YAY!

I’m briefly surfacing from the stress ocean that is paper writing to do a little dance of joy about the latest mind-blowing development in origin-of-life research.

(With my ability to go on endlessly about random scientific subjects, you’d think I’d love writing papers. No, no, no, hell no. I wish I could just upload my methods and figures to some database and be done with it. >.<)

My latest great squeal about abiogenesis research was due to an RNA enzyme that could copy long RNA strands. Well, that’s still bloody amazing, but maybe massive RNA enzymes are not how the thing we call life started. Jack Szostak’s group works witn a model of early life in which enzymes aren’t needed at all.

They’ve been working for years and years on their protocells (illustration above by Janet Iwasa via exploringorigins.org). These are basically little fat bubbles floating around in a watery solution, with a bit of nucleic acid inside. The fatty membranes of protocells are made of much simpler materials than modern cell membranes. Protocells haven’t got any proteins, and contain just a tiny “genome” that doesn’t encode anything meaningful. Yet they can, under the right circumstances, grow and divide and pass on that genome to their descendants through ordinary physical forces.

And now, they can also copy it.

The problem so far was magnesium. RNA can be replicated by an enzyme, or it can, to an extent, copy itself using base pairing. Magnesium is necessary for both kinds of replication. However, the Szostak group’s fatty protocells quickly fall apart in the presence of magnesium, spilling all their RNA content.

Adamala and Szostak (2013) tested a bunch of small molecules that bind magnesium to see if they could help. Many of them could protect the protocells, but only one, citrate, could do this without also stopping RNA replication. As a bonus, citrate prevented the degradation of RNA that, under normal circumstances, eventually happens at high magnesium levels.

Like other research toward RNA replication, this study isn’t quite there yet. For one thing, the “genomes” of these protocells are very limited – they are tiny, and they are just runs of a single RNA building block, so it’s hard to imagine how they could be precursors to more “meaningful” genomes. Also, although a lot of organic molecules just spontaneously show up when someone tries to recreate early Earth chemistry, citrate is not one of them.

Nonetheless, little by little we’re edging closer to a living RNA world. We may never know how life actually started, but the research on how it could have started looks more exciting by the day…

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Reference:

Adamala K & Szostak JW (2013) Nonenzymatic template-directed RNA synthesis inside model protocells. Science 342:1098-1100

Back to the warm little pond?

Oh, look, an abiogenesis post again! This time, of pure squee.

Back in olden days, a certain Charles Darwin wrote to a dear friend:

“It is often said that all the conditions for the first production of a living organism are now present, which could ever have been present. But if (and oh! what a big if!) we could conceive in some warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, &c., present, that a proteine compound was chemically formed ready to undergo stillmore complex changes, at the present day such matter would be instantly devoured or absorbed, which would not have been the case before living creatures were formed.”

The famous quote is obviously not a theory of abiogenesis as such; rather, it’s some (fairly obvious, in hindsight) reasoning as to why life doesn’t originate anew today. Still, the warm little pond has become something of a symbol for abiogenesis.

Ironically, it doesn’t seem to enjoy much popularity in the field itself.* The scientist favourites are more along volcanic lines – hydrothermal vents of some stripe, or cold seeps on the seafloor. The sea is a common theme with these… but volcanic environments spewing all kinds of useful chemicals are not limited to the sea. In fact, Mulkidjanian et al. (2012) argue, much more abiogenesis-friendly volcanic sites might be found on dry land.

Living cells, the reasoning goes, contain far higher concentrations of potassium, phosphate, zinc and some other ions than any ocean anywhere (and, most likely, anytime) on the planet. The most ancient proteins that are still present in living things today don’t simply tolerate these ions – they depend on them. However, the first cells would not yet have possessed the tightly insulating membranes and armada of ion-shuttling proteins modern cells use to maintain their special salt cocktail in all kinds of environments. Therefore, cells must have arisen in a salt solution similar to their interiors. (Note that this reasoning doesn’t necessarily apply to the origin of replicating molecules. We’re not talking about the very first steps towards life just yet.)

Where might one find such an environment? Not anywhere in the sea, the researchers argue. “[H]igh concentrations of transition metals, such as [zinc] and [manganese], are found only where extremely hot hydrothermal fluids leach metal ions from the crust and bring them to the surface,” they remind (pE823). Now, this also happens at deep sea vent systems – but deep sea vents don’t spill out much phosphate, so they only contain part of the “life cocktail”. Geothermal fields on land, on the other hand… Geothermal regions where the hot water boils and steams through the rock are also potassium-rich (again, unlike any place in the sea), bringing all the essential ingredients together. The steam either boils all the way to the surface and then condenses in pools, or reach the surface as a liquid and result in nice, bubbling mud pots.

These environments today are very acidic, which is not generally good for life – however, their acidity is the result of hydrogen sulphide reacting with oxygen. There was very little oxygen in the ancient atmosphere, so the first protocells forming in a primordial mud pot or hot volcanic pool wouldn’t have to contend with that little nuisance called sulphuric acid. What’s more, the silica carried by the rising steam would precipitate as silicate minerals of the exact sort that are thought to be conducive to the formation of all kinds of protocelly things including primordial lipid membranes and nucleic acids (Hanczyc et al., 2003)!

Swell! And there are other little gems scattered throughout Mulkidjanian et al. (2012). For example, some of the minerals that form in a geothermal environment without oxygen can catalyse the formation of various organic compounds, which the early protocells could eat. Inland geothermal fields also live much longer than deep sea vents, providing more time for life to get off the ground. What’s more, the rocks wetted by condensing geothermal vapours would dry out and then be re-wetted many times, which concentrates some of the organic chemicals thought to be most important for the origin of key life molecules like nucleic acids. Even better, geothermal vapours are full of borate, which can stabilise ribose – a component of RNA, thought to be the substance of the first genomes.

So, this study envisions a field of geysers, mud pots and warm pools fed by the runoff as the cradle of life. Probably not quite what Darwin had in mind, but hey, when Darwin thought up his warm little pond, people thought proteins were the substance of inheritance. I think we can give him a little slack here 😉

We’ll see what other abiogenesis researchers have to say about the idea, but for the time being, I rather like it!

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*Disclaimer: my reading on abiogenesis mostly consists of fangirling over interesting new ribozymes and cdk007’s Youtube videos. It’s not a field I would call myself well-versed in. So what “seems” to me might just be a nosy outsider’s distorted impression 😛 (Nonetheless, the paper seems to express the same impression, and the authors ain’t newbies to this field. Well, Eugene Koonin, the principal investigator, certainly isn’t.)

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References:

Darwin’s letter to Joseph Hooker is recorded in Darwin F (ed.) (1887) The life and letters of Charles Darwin, including an autobiographical chapter. London: John Murray. Volume 3.

Hanczyc MM et al. (2003) Experimental models of primitive cellular compartments: encapsulation, growth, and division. Science 302:618-622

Mulkidjanian AY et al. (2012) Origin of the first cells at terrestrial, anoxic geothermal fields. PNAS 109:E821-E830