Feature: Origins of life

This feature appeared in the November/December 2009 issue of Australian Life Scientist. To subscribe to the magazine, go here.

Late on the morning of September 28, 1969, a piece of space rock sonic-boomed across the south-eastern Australia sky and broke up, scattering chunks of speckled, black rock across the rural landscape near the Victorian hamlet of Murchison. The famed Murchison meteorite, a rare carbonaceous chondrite, delivered to Earth a soup of organic ingredients, including proteogenic amino acids like glycine, alanine, and glutamic acid and uracil, one of the four bases that form RNA.

It’s from building blocks such as these that scientists, like David Penny, Professor of Theoretical Biology at Massey University’s Institute of Molecular Biosciences in Palmerston North, in New Zealand, believe led to the first self-replicating RNA molecules, They, in turn, begat all life on Earth. Proteins and DNA came later, when chance and natural selection colluded to add a second, template strand to the primal life code, greatly enhancing its stability and fidelity.

So while DNA has occupied centre stage in biological research for almost half a century, a research revolution in the past decade has made it clear that RNA rules. The true nature of the vast tracts of so-called ‘junk DNA’ within and between genes is revealed: many code for a host of small RNA molecules which collectively drive and coordinate the intricate machinery of the genome.

But as Penny observes, RNA “didn’t pop out of nowhere”. How, and under what physical conditions, did simple RNA oligonucleotides bootstrap themselves through the evolutionary process leading to complex, self- replicating RNA molecules with catalytic activity?

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Hot or cold start

Professor Penny and his biologist colleagues at the Institute of Molecular Bioscience have teamed up with physical chemists to investigate the conditions under which the first complex RNA molecules formed, and later acquired the two- and three-dimensional structures required to replicate themselves, and catalyse biochemical reactions. He will present his research group’s latest insights into this question in a public lecture talk at the University of Melbourne in November.

“The question is whether life got a cold start, or a hot start. Charles Darwin proposed that life began in a warm little pond somewhere. I wouldn’t make the pond too warm,” says Penny. To find out, he’s collaborating with a team of scientists to put the hot and cold start hypotheses to the test.

“There are two general approaches,” he says. “I come from the biological, top-down end; we biologists start with model organisms, and work backwards. Physicists and chemists start bottom-up, with simple molecules, and build upwards towards greater complexity. We’re building a tunnel from both ends, hoping to meet in the middle. One of the nice things about RNA is that it gives us both a clear target to aim for.

Penny and his colleagues are using a special high-pressure/high temperature reactor chamber, designed by the institute’s instrument-maker to be mounted inside a nuclear magnetic resonance (NMR) spectrometer. The apparatus allows them to explore various combinations of pressure and temperature to influence the assembly of short RNA molecules – oligonuleotides – from the four RNA bases – adenine, guanine, cytidine and uracil.

“We won’t have any real idea of how it will go, so the experiments will be illuminating,” says Penny. “For example, cytidine becomes unstable at high temperatures – at 90°C it has a half-life of only 19 hours, which is hardly conducive to a hot origin of life.

“But perhaps cytidine becomes more stable at high pressures. We want to know how pressure affects the stability of oligonucleotides, for example, whether cytidine becomes more stable at high pressures, which would support a hot start for life.”

Penny says the cell allows in-situ NMR analysis of the products of low-pressure synthesis and folding reactions at temperatures around O°C, on a substrate like sea ice. At the other end of the scale, it can reproduce the high-pressure, super-hot (200°C to 300°C) conditions that occur around the sulphide-rich outflows of ‘black smoker’ vents along mid-ocean rift zones.

The group’s physical chemists also use computer-based models to perform similar experiments in silico. The cross-referencing “keeps the computers honest” says Penny. “With computers, we can replicate any conditions. Our NMR experiments simulate real-world conditions, so we can constrain the computer modelling,” he says.

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Lazy RNA

“We have concluded that that it’s much easier for life to originate at low temperatures. We know that’s not the popular view – most people prefer the black smoker explanation. But if we compare the structure of water molecules in ice, liquid and steam, ice has a more ordered structure.

“But, until now, we have only been able to guess at how high pressures influence the formation of nucleotide dimers. If they reduce the volume in which the molecules react, it might help, but it’s possible that high pressures have no effect on volume, so they mightn’t help.

“We’ll use similar principles to study how linear RNA oligonucleotides form two-dimensional structures by base-pairing. We’re assuming that the transition from 2-D to 3-D structures involves similar processes. With proteins, people find it’s very easy for a linear peptide chain to adopt a three-dimensional structure. With molecules, there’s a huge saving in energy once you go to a 2-D structure.

“We have just finished collating our data, and it’s quite clear that RNA molecules are not nearly as good at catalysis as proteins. Of course, proteins are composed of up to 20 different amino acids, so they offer far more potential for bonding to form 3-D structures than four nucleotides.

“We’ve looked at the reasons why RNA catalysis is not as good as protein-mediated catalysis, and quite a few of our preliminary results fit with the idea that RNA tends to form quite a large number of different structures, rather than one unique structure, like the peptides chains that form proteins.

“The challenge is to determine the minimum free energy of the molecule, which produces the most stable structure. Protein molecules like enzymes make strong catalysts because they tend to adopt unique structures that retain lots of energy. RNA molecules make lazy enzymes, because they tend to adopt structures with very low levels of free energy.”

Penny says molecules with minimal free energy tend to become unstable when exposed to high levels of thermal energy – they are usually most stable at low temperatures. Proteins, for example, begin unfolding and denaturing as temperatures approach boiling point – which is why some people dislike the flavour of UHT milk pasteurised at high temperatures.

Where to next? “The main thing is to think very hard so that you can find simple little experiments that can be done successfully,” Penny said. “When the simple experiments work, that’s where progress comes from.”