Using the first living thing on Earth as a model

By William J. Cromie

Gazette Staff

Jack Szostak is trying to make a living organism out of nonliving chemicals.

It would be a modest creature, a microscopic bit of genetic material in a bubble of fat, capable of making copies of itself and evolving into a more efficient form of life. The creature would be modeled on the first, or one of the first, living things that appeared on Earth about 4 billion years ago.

"We're trying to imagine the simplest possible system that could get life started, then make it in our lab," said Szostak, a professor of genetics who works at Massachusetts General Hospital.

The best candidate for the first organism is a bit of ribonucleic acid (RNA) enclosed in a plain capsule. RNA can store information like a gene and reproduce itself. It makes up the genes of viruses.

"We're concentrating on making such an organism because, once it formed, most biologists agree that the first single-celled creature would follow," Szostak explains. Neither plant nor animal, such an organism would then give rise to creatures like bacteria, algae, and amoebas.

Much the same thing could have happened on Mars. Recently, NASA scientists announced that they may have found signs of life in a 4-billion-year-old meteor knocked to Earth from that planet. Szostak is skeptical about the finding, but he hopes that robots or astronauts may someday bring back samples of living Martian microbes.

If such primitive Martians have the same biology as early Earthlings, it would be "interesting, but relatively boring," Szostak thinks. "But if they have a fundamentally different biology, it would be fantastic! If life arose in different forms in different places, it would tell us that life could evolve in multiple forms all over the universe."

Good Progress Made

When Earth first formed about 4.5 million years ago, it was volcanic-hot and battered by rains of large meteorites. Most scientists believe life began shortly after the lethal impacts stopped, and the planet cooled enough to allow water to exist. Fossil evidence shows that primitive creatures, looking like today's bacteria, existed around 3.8-4 billion years ago.

For 10 years, Szostak has been trying to repeat hundreds of millions of years of evolution in his lab. He has not yet shouted: "Eureka, it's alive!" But he claims to have "learned a lot and made good progress."

A Nobel Prize-winning discovery by a colleague started him down the road to lab life. In 1982, Thomas Cech of the University of Colorado discovered that pieces of RNA living in a single-celled animal can splice themselves out of larger RNA molecules. That means RNA has the capability of doing chemistry on its own, specifically, the chemical reaction involved in splicing. From there, it's easy to assume that RNA can promote, or catalyze, other reactions, such as reproducing itself.

"That made it much easier to think about the origin of life," Szostak says. "Cech's discovery inspired me to think of ways of making RNAs that could catalyze their own replication."

At the time, he was working with yeast, studying how its genetic material reproduces itself when a cell divides to make two daughter cells from one parent. "The lab techniques that Cech used were not all that different from mine," he recalls. "I thought there'd be a few interesting experiments I could do. Five years later, my lab had completely changed focus from yeast to self-replicating RNA."

Today, he and his colleagues are close to an RNA catalyst, or enzyme, that copies other RNA molecules. If the molecule being copied is another copy of itself, then he will have an RNA enzyme that can be both the copier and the thing being copied.

"The way we do this is to harness the power of evolution," Szostak notes. "Since we don't know how to design better RNA, we have to evolve them. We're trying to evolve from an RNA that joins pieces of RNA to itself, to an RNA that copies itself and other RNA."

But evolving RNA like that on a newly formed planet is a huge problem. Szostak calls it "the biggest challenge left in our understanding of the origin of life."

RNA, like the DNA of which all modern genes are made, is put together from four chemical units, or bases, plus phosphate and a sugar. Some of these building blocks have been made in labs, using gases and other elements thought to be present at the beginning of Earth. But no one can figure out how to put these ingredients together to make long RNA molecules.

On the young Earth, the construction may have taken place in shallow coastal ponds that periodically dried up. That would allow the necessary chemicals to concentrate on particles of moist clay, or to be trapped in bubbles of fat.

One possible scenario cited by Szostak has some of the ingredients forming in volcanoes, then being washed down into ponds or shallow lakes by rain. The necessary compounds could also have been formed in the air with the help of lightning, or been bought to Earth by comets or meteorites.

Due to limitations of time and lab equipment, Szostak skips this part and starts with trillions of pieces of RNA in a solution. In living things, RNAs are made of varying sequences of the four bases; RNAs that do different jobs contain different sequences. "In our lab," he explains, "we start with lots of random sequences and try to find the rare ones that do something interesting, like catalyze a chemical reaction."

After selecting such promising RNAs out of the dilute soup, his team uses a system of directed evolution to make them work more efficiently. This involves putting in mutants, or changing the sequences slightly, then selecting the best sequences over and over until effective catalysts are found. Such evolution-in-glass yields molecules that fold up into three dimensions and serve as catalysts necessary for RNA copying.

Another life investigator, Gerald Joyce of Scripps Research Institute in California, worked out the same technique. Szostak and Joyce shared the 1994 National Academy of Sciences Monsanto Prize in Molecular Biology for this achievement.

With the help of this technique, Dave Bartel, a former student of Szostak's, succeeded in making an RNA enzyme that, under the best of conditions, joins together six RNA units or bases. "This really was a great breakthrough," Szostak comments.

Bartel, now at M.I.T.'s Whitehead Institute for Biomedical Research, showed for the first time that an RNA enzyme can do the same reaction done by proteins in more organized forms of life. "Now that this has been shown, all we have to do is use evolution to make it work better. By this means we should be able to get self-replication," says Szostak.

In today's world, protein enzymes assemble hundreds of thousands of chemical units into complex molecules needed for everything from growing a toe to thinking a thought. RNA enzymes have now been relegated to a minor role.

"The important point here is that protein enzymes came later because RNA-based cells evolved a way to make the first proteins," Szostak points out. "So one of the big projects in my lab is to evolve RNA enzymes that carry out all the steps needed for protein synthesis."

Putting It Together

A naked RNA molecule can't copy itself. It needs to be enclosed in a thin envelope, a bubble of fat, that keeps out harmful substances while letting in beneficial ones. Virtually every modern cell has such a protective covering, a soft armor of fat and protein complete with entry and exit ports. Surely, the first membranes were much simpler, but no one knows how and of what materials they were made.

"Surprisingly, few people are working on this problem," Szostak lamented. "Once protected by a membrane, RNA could evolve much more quickly."

Nature now constructs proteins from amino acids, small molecules made principally of carbon, hydrogen, oxygen, and nitrogen -- elements present when Earth first formed. Various researchers have created amino acids from combinations of these elements dissolved in sea water solutions. Stanley Miller at the University of California, San Diego, for example, passed electric discharges (to simulate lightning) through such mixtures and produced 13 of the 20 amino acids essential for building proteins.

Building on such experiments, Szostak has made an RNA molecule capable of bonding amino acids together. The next step is to link them together into so-called peptides. Put peptides together and you have proteins.

"It's an exciting advance," he says. "I'm sure we're not too far away from building small proteins with the help of RNA enzymes."

Down By the Sea

Szostak does not champion the idea that life began in hot springs on the ocean floor where a primitive one-celled creature, called an archeon, was recently discovered. Its genes show that it shares a common evolutionary heritage with us, but not with bacteria. The consensus is that both archeons and bacteria came from a common, even simpler creature. But even this one-celled organism is far more complicated than the first living thing.

"A lot of evolution had to occur before RNA, working alone, could have evolved into a cell like this, complete with genes and proteins," Szostak believes.

Viruses are the only organisms that now have genes made of RNA. DNA took over that vital function very early in evolution, even before the ancestors of archeons and bacteria.

"We believe life on Earth started with RNA molecules that stored genetic information and catalyzed the chemical reactions needed to make proteins," Szostak says. "Hundreds of millions of years later, the two functions became specialized. DNA now stores the genetic blueprints that make an organism an amoeba or a human. Proteins catalyze all of life's chemistry, including the replication of DNA that passes from parents to offspring."

Details of how Earth went from an RNA to a DNA world are lost forever in the natural record. All traces of the origin of life have long been destroyed by chemistry, geology, and the biology of more complex, more voracious creatures.

"Our only hope of reconstructing life is via laboratory experiments," Szostak says. "If we make something everyone agrees is alive, that would provide a plausible scenario for the great event. But, because the trail is billions of years cold, we'll never really know for sure if we're right."