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

This is when *I* need a good science blogger

Today you get to meet yet another of my random interests: the origin of life. (Is there a person with an interest in living things who isn’t fascinated by the origin of life?) And, since we sciencey types are very anxious about personal biases, I might as well start with a confession.

I love the RNA world hypothesis.

It was just one of those things that you learn at school/uni (I think it was 1st year molecular biology for me), and it’s so neat and elegant and compelling that you immediately fall in love. Sure, later, when you’re out of the inevitable simplicity of class, you learn about the nuances. The difficulties. But the evidence for still seems so convincing that you have no doubt that we’ll eventually solve the problems.

In case you aren’t familiar with it, the RNA world hypothesis is the leading solution to the chicken and egg problem that is the “central dogma” of molecular biology (diagram from Wikipedia):

DNA is great genetic hardware, but it’s nothing without proteins. Proteins are encoded in DNA, but the code is useless without proteins to read it. Making DNA requires proteins. But the proteins come from the DNA code. You see where this is going…

RNA takes the stage

The RNA world is an ingenious idea that elevates RNA from being merely the messenger between DNA and protein to centre stage. While its big brother DNA is a fairly stable and inert molecule, RNA is much more chemically active. It doesn’t like languishing in long, stable double helices – rather, it folds up into all kinds of odd shapes that can, surprisingly, catalyse a variety of chemical reactions. Just like proteins. Yet the “letters” of RNA can form complementary pairs, allowing for faithful copying. Just like DNA.

And, so the theory goes, there was a time when RNA was both the genome and the enzymes (enzymes made of RNA are called ribozymes). The right sort of RNA molecule could have copied itself without proteins [1], and performed whatever chemistry a primitive life form needed – also without proteins. Crucially, the right sort of RNA molecule could have invented proteins [2].

One of the key revelations to lend support to the RNA world hypothesis is that proteins in cells today are still made by RNA. Proteins are manufactured in ribosomes. A modern ribosome is a very complicated structure made of several folded-up RNA molecules and dozens of proteins. However, investigations of its structure (see Cech [2000] for a quick review) revealed that the place where amino acids are joined into a protein chain is all RNA – the proteins may support the RNA, but it seems to be the RNA that actually does the job.

Beautiful hypothesis vs. ugly facts?

So, everything is shiny and awesome and exciting. Ribozymes capable of all sorts of interesting chemistry [3] abound, and we have some very neat ideas regarding how RNA paved the way towards the modern protein-and-DNA world [2].

And then Harish and Caetano-Anollés (2012) come along, and I don’t know what to think.

A large part of the problem is that their methods go way over my head. I get the gist of their message. They figured out the relative ages of the RNA and protein components of the ribosome. The protein-synthesis parts – RNA and protein alike – turned out relatively new. They also found that the oldest protein parts interact with the oldest RNA parts – and seem to have coevolved. That, they say, would suggest that RNA and fairly large pieces of protein had a common history together before the future ribosome became capable of making proteins.

Yes, that means either that RNA didn’t invent proteins, or at the very least, that the “inventor” was not a precursor of the ribosome.

I really really don’t want to believe the former, and the latter possibility is a butchery of Occam’s razor without further evidence. But what else is left, if the study is correct?

One part of their results that I found intriguing is the structural similarity of the most ancient parts of ribosomal RNA to – you’d never guess – lab-evolved RNA-copying ribozymes. That is… oh, I don’t really know what it is, aside from “fascinating”. Did the ribosome start out as replication machinery, and turn into a protein factory only later? Or are the structures similar because reading the primitive genetic code required the same sort of molecular machine as copying RNA? Or is it even just coincidence?

And this is why I need a good science blogger. I need someone who deeply understands the paper and can translate it into something I can digest. Because at the moment, I can’t make heads or tails of this. I’m rather attached to the RNA world; it makes sense to me, and as far as scientific hypotheses go, it’s simply beautiful. Yet I can’t point to any obviously bullshit reasoning in the new study, other than where they seem to imply that because modern ribosomes need proteins to work, proteins must have been present in the ribosome from the start. (Which is a bit like every damn irreducible complexity argument advanced by creationists.) I just don’t have a good enough grasp on the methodology to tell whether it’s all solid or whether any of it is dodgy. Words fail to express how much that bugs me.

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Notes:

[1] Lincoln and Joyce (2009) and Wochner et al. (2011) came tantalisingly close to making/evolving the right sort of RNA molecule in the lab. The former’s pair of ribozymes can only copy each other by stitching together two half-ribozymes, but they can keep going at it forever and ever. Wochner et al.’s molecule can copy RNA using single letters as ingredients, but it runs out of steam after 90 or so of them. That’s several times better than the previous record, but still not long enough for the ribozyme to replicate its twice-as-long self.

[2] This excellent video describes one way it could have happened. When it comes to science education, cdk007 never fails to deliver!

[3] Including attaching amino acids to other RNA molecules (Turk et al., 2010) – look up tRNA if you don’t see why this is exciting 😉

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References:

Cech TR (2000) The ribosome is a ribozyme. Science 289:878-879

Harish A & Caetano-Anollés G (2012) Ribosomal history reveals origins of modern protein synthesis. PLoS ONE 7:e32776

Lincoln TA & Joyce GF (2009) Self-sustained replication of an RNA enzyme. Science 323:1229-1232

Turk RM et al. (2010) Multiple translational products from a five-nucleotide ribozyme. PNAS 107:4585-4589

Wochner A et al. (2011) Ribozyme-catalyzed transcription of an active ribozyme. Science 332:209-212