Life from scratch: learning to make synthetic cells

Science News, Jan 12, 2008 by Patrick Barry

Maggots don't arise spontaneously out of dead, rotting meat. Aphids never materialize within drops of morning dew. Aristotle and others who believed in the spontaneous generation of life were dead wrong.

The only time life arose from nonlife, biologists believe, was almost 4 billion years ago, when simple living cells first appeared on Earth. But now, with the help of a microscopic parasite that infects people's genitals, researchers may rehabilitate the core of Aristotle's idea.

Scientists are on the verge of creating living cells by piecing together small molecules that are themselves not alive. The result would be the world's first human-made life forms, synthetic cells made more or less from scratch.

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The goal is to make cells that are as simple as possible, yet still able to grow, reproduce, and evolve--some of the defining traits of life.

"Simplicity has always been where we try to gain understanding," says John Glass of the J. Craig Venter Institute in Rockville, Md. "In a way, what we're doing is making a better platform for understanding what life is." It's a bit like learning the essentials of how a luxury car works by building a dune buggy from spare parts.

Some scientists, including Glass, hope to make such a minimal cell by whittling down the genome of an existing bacterium to its barest elements, and then synthesizing that minimal genome. In the lab, scientists can assemble the genomic DNA by piecing together chemicals called nucleotides, which constitute the individual letters of genetic code.

Other scientists, starting from long lists of molecules and genes, are devising plans to assemble these parts to make an entire cell, not just its genome, by hand.

Still other researchers take a radically different approach. Instead of trying to construct cells from the same proteins and DNA found in modern organisms, these investigators hope to assemble a cell from more-primitive molecules that better mimic the molecules probably involved in the origin of life. If successful, these scientists may uncover clues about how the original "spontaneous generation" of life occurred billions of years ago.

The first step, however, involves that irritating parasite.

STARTING SMALL Being a parasite has its perks. Living inside a mammalian host, a microbe enjoys a constant, comfy temperature and an endless supply of nutrients.

Because their living conditions are relatively cozy, parasitic microbes can get by with much smaller genetic toolkits. That's why one of the smallest known bacterial genomes belongs to Mycoplasma genitalium, a parasite that can infect the cervix and vagina of women and the urinary tracts of women and men.

While the human genome contains more than 3 billion letters of DNA code, M. genitalium has only about 580,000. This tiny genome encodes a mere 528 genes.

Even that's too many for Hamilton Smith, a Nobel laureate and Glass' colleague at the Venter Institute. For the past 9 years, Smith's team has been systematically removing single genes from M. genitalium to see which ones the bacterium can survive without. So far, the group has found about 100 genes that are dispensable when removed individually. Many of these genes help the microbe evade the human immune system, which isn't necessary in lab dishes.

However, "it's unlikely that all of the 100 could be removed simultaneously," Smith said last June at the Synthetic Biology 3.0 conference in Zurich. Some genes perform redundant functions, so if Smith's team removes one of these, the microbe can keep chugging along. But if the researchers take out all of the genes responsible for a crucial task, the organism will die.

With so many genes that might be expendable, testing every possible combination by hand would take years. So instead, the scientists produce thousands of combinations quickly and grow them in lab dishes to see which ones survive. "You let biological selection tell you what's necessary," Glass says.

Using this method, the team is homing in on a set of essential genes. With this minimal genome in hand, the researchers plan to build the DNA synthetically by stringing together individual nucleotides in the right sequence. Assembly of made-to-order DNA has become routine, but nobody has ever put together a single DNA molecule that's hundreds of thousands of nucleotides long.

To synthesize an entire minimal genome, Smith and his colleagues are stitching together medium-length segments of DNA using enzymes to join matching, overlapping regions capping the ends of each fragment. This way, the team can assemble the genome piecewise rather than trying to synthesize it all at once.

"We eventually want to make an organism called Mycoplasma laboratorium," Smith says. The more familiar name for this hypothetical cell is Synthia.

Glass says that the team is on the verge of making such a cell within the next few months. In the Aug. 3, 2007 Science, the researchers announced that they had transplanted the entire genome of one species of Mycoplasma into a related species. The recipient cells began using the foreign genome as if it was their own, showing that the receiving cells can "boot up" the newly inserted DNA (SN: 6/30/07, p. 403). All that remains is to finish piecing together a minimal, synthetic genome and then to insert it into a Mycoplasma bacterium by the same technique.