Chemist Shows How RNA Can Be the Starting Point for Life

By NICHOLAS WADE

http://www.nytimes.com/2009/05/14/science/14rna.html

May 14, 2009

An English chemist has found the hidden gateway to the RNA world, the chemical milieu from which the first forms of life are thought to have emerged on earth some 3.8 billion years ago.

He has solved a problem that for 20 years has thwarted researchers trying to understand the origin of life - how the building blocks of RNA, called nucleotides, could have spontaneously assembled themselves in the conditions of the primitive earth.  The discovery, if correct, should set researchers on the right track to solving many other mysteries about the origin of life.  It will also mean that for the first time a plausible explanation exists for how an information-carrying biological molecule could have emerged through natural processes from chemicals on the primitive earth.

The author, John D. Sutherland, a chemist at the University of Manchester, likened his work to a crossword puzzle in which doing the first clues makes the others easier.  "Whether we've done one across is an open question," he said.  "Our worry is that it may not be right."

Other researchers say they believe he has made a major advance in prebiotic chemistry, the study of the natural chemical reactions that preceded the first living cells.  "It is precisely because this work opens up so many new directions for research that it will stand for years as one of the great advances in prebiotic chemistry," Jack Szostak of the Massachusetts General Hospital wrote in a commentary in Nature, where the work is being published on Thursday.

Scientists have long suspected that the first forms of life carried their biological information not in DNA but in RNA, its close chemical cousin.  Though DNA is better known because of its storage of genetic information, RNA performs many of the trickiest operations in living cells.  RNA seems to have delegated the chore of data storage to the chemically more stable DNA eons ago.  If the first forms of life were based on RNA, then the issue is to explain how the first RNA molecules were formed.

For more than 20 years researchers have been working on this problem.  The building blocks of RNA, known as nucleotides, each consist of a chemical base, a sugar molecule called ribose and a phosphate group.  Chemists quickly found plausible natural ways for each of these constituents to form from natural chemicals.  But there was no natural way for them all to join together.

The spontaneous appearance of such nucleotides on the primitive earth "would have been a near miracle," two leading researchers, Gerald Joyce and Leslie Orgel, wrote in 1999.  Others were so despairing that they believed some other molecule must have preceded RNA and started looking for a pre-RNA world.

The miracle seems now to have been explained.  In the article in Nature, Dr. Sutherland and his colleagues Matthew W. Powner and Béatrice Gerland report that they have taken the same starting chemicals used by others but have caused them to react in a different order and in different combinations than in previous experiments. they discovered their recipe, which is far from intuitive, after 10 years of working through every possible combination of starting chemicals.

Instead of making the starting chemicals form a sugar and a base, they mixed them in a different order, in which the chemicals naturally formed a compound that is half-sugar and half-base.  When another half-sugar and half-base are added, the RNA nucleotide called ribocytidine phosphate emerges.

A second nucleotide is created if ultraviolet light is shined on the mixture. Dr. Sutherland said he had not yet found natural ways to generate the other two types of nucleotides found in RNA molecules, but synthesis of the first two was thought to be harder to achieve.

If all four nucleotides formed naturally, they would zip together easily to form an RNA molecule with a backbone of alternating sugar and phosphate groups.  The bases attached to the sugar constitute a four-letter alphabet in which biological information can be represented.

"My assumption is that we are here on this planet as a fundamental consequence of organic chemistry," Dr. Sutherland said. "So it must be chemistry that wants to work."

The reactions he has described look convincing to most other chemists.  "The chemistry is very robust - all the yields are good and the chemistry is simple," said Dr. Joyce, an expert on the chemical origin of life at the Scripps Research Institute in La Jolla, Calif.

In Dr. Sutherland's reconstruction, phosphate plays a critical role not only as an ingredient but also as a catalyst and in regulating acidity.  Dr. Joyce said he was so impressed by the role of phosphate that "this makes me think of myself not as a carbon-based life form but as a phosphate-based life form."

Dr. Sutherland's proposal has not convinced everyone.  Dr. Robert Shapiro, a chemist at New York University, said the recipe "definitely does not meet my criteria for a plausible pathway to the RNA world."  He said that cyano-acetylene, one of Dr. Sutherland's assumed starting materials, is quickly destroyed by other chemicals and its appearance in pure form on the early earth "could be considered a fantasy."

Dr. Sutherland replied that the chemical is consumed fastest in the reaction he proposes, and that since it has been detected on Titan there is no reason it should not have been present on the early earth.

If Dr. Sutherland's proposal is correct it will set conditions that should help solve the many other problems in reconstructing the origin of life.  Darwin, in a famous letter of 1871 to the botanist Joseph Hooker, surmised that life began "in some warm little pond, with all sorts of ammonia and phosphoric salts."  But the warm little pond has given way in recent years to the belief that life began in some exotic environment like the fissures of a volcano or in the deep sea vents that line the ocean floor.

Dr. Sutherland's report supports Darwin.  His proposed chemical reaction take place at moderate temperatures, though one goes best at 60 degrees Celsius.  "It's consistent with a warm pond evaporating as the sun comes out," he said. His scenario would rule out deep sea vents as the place where life originated because it requires ultraviolet light.

A serious puzzle about the nature of life is that most of its molecules are right-handed or left-handed, whereas in nature mixtures of both forms exist.  Dr. Joyce said he had hoped an explanation for the one-handedness of biological molecules would emerge from prebiotic chemistry, but Dr. Sutherland's reactions do not supply any such explanation.  One is certainly required because of what is known to chemists as "original syn," referring to a chemical operation that can affect a molecule's handedness.

Dr. Sutherland said he was working on this problem and on others, including how to enclose the primitive RNA molecules in some kind of membrane as the precursor to the first living cell.

Did life begin with RNA?

RNA world easier to make

Ingenious chemistry shows how nucleotides may have formed in the primordial soup.

Richard Van Noorden

An elegant experiment has quashed a major objection to the theory that life on Earth originated with molecules of RNA.

John Sutherland and his colleagues from the University of Manchester, UK, created a ribonucleotide, a building block of RNA, from simple chemicals under conditions that might have existed on the early Earth.

The feat, never performed before, bolsters the 'RNA world' hypothesis, which suggests that life began when RNA, a polymer related to DNA that can duplicate itself and catalyse reactions, emerged from a prebiotic soup of chemicals.

"This is extremely strong evidence for the RNA world. We don't know if these chemical steps reflect what actually happened, but before this work there were large doubts that it could happen at all," says Donna Blackmond, a chemist at Imperial College London.

Molecular choreography

An RNA polymer is a string of ribonucleotides, each made up of three distinct parts: a ribose sugar, a phosphate group and a base — either cytosine or uracil, known as pyrimidines, or the purines guanine or adenine. Imagining how such a polymer might have formed spontaneously, chemists had thought the subunits would probably assemble themselves first, then join to form a ribonucleotide. But even in the controlled atmosphere of a laboratory, efforts to connect ribose and base together have met with frustrating failure.

The Manchester researchers have now managed to synthesise both pyrimidine ribonucleotides. Their remedy is to avoid producing separate ribose-sugar and base subunits. Instead, Sutherland's team makes a molecule whose scaffolding contains a bond that will turn out to be the key ribose-base connection. Further atoms are then added around this skeleton, which unfurls to create the ribonucleotide.

“We had a suspicion there was something good out there, but it took us 12 years to find it.”

John Sutherland

University of Manchester

The final connection is to add a phosphate group. But that phosphate, although only a reactant in the final stages of the sequence, influences the entire synthesis, Sutherland's team showed. By buffering acidity and acting as a catalyst, it guides small organic molecules into making the right connections.

"We had a suspicion there was something good out there, but it took us 12 years to find it," Sutherland says. "What we have ended up with is molecular choreography, where the molecules are unwitting choreographers." Next, he says, he expects to make purine ribonucleotides using a similar approach.

The start of something special?

Although Sutherland has shown that it is possible to build one part of RNA from small molecules, objectors to the RNA-world theory say the RNA molecule as a whole is too complex to be created using early-Earth geochemistry. "The flaw with this kind of research is not in the chemistry. The flaw is in the logic — that this experimental control by researchers in a modern laboratory could have been available on the early Earth," says Robert Shapiro, a chemist at New York University.

Sutherland points out that the sequence of steps he uses is consistent with early-Earth scenarios — those involving methods such as heating molecules in water, evaporating them and irradiating them with ultraviolet light. And breaking RNA's synthesis down into small, laboratory-controlled steps is merely a pragmatic starting point, he says, adding that his team also has results showing that they can string nucleotides together, once they have formed. "My ultimate goal is to get a living system (RNA) emerging from a one-pot experiment. We can pull this off. We just need to know what the constraints on the conditions are first."

Shapiro sides with supporters of another theory of life's origins – that because RNA is too complex to emerge from small molecules, simpler metabolic processes, which eventually catalysed the formation of RNA and DNA, were the first stirrings of life on Earth.

"They're perfectly entitled to disagree with us. But having got experimental results, we are on the high ground," says Sutherland.

"Ultimately, the challenge of prebiotic chemistry is that there is no way of validating historical hypotheses, however convincing an individual experiment," points out Steven Benner, who studies origin-of-life chemistry at the Foundation for Applied Molecular Evolution, a non-profit research centre in Gainesville, Florida.

Sutherland, though, hopes that ingenious organic chemistry might provide an RNA synthesis so convincing that it effectively serves as proof. "We might come up with something so coincidental that one would have to believe it," he says. "That is the goal of my career."

References

1. Powner, M. W., Gerland, B. & Sutherland, J. D. Nature 459, 239-242 2009 | Article |