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Gene-swapping organisms muddle evolution's story


YOU CAN'T judge the book of life by its cover.

This book -- which contains recipes for living organisms written in the language of genes -- also tells the story of an organism's evolutionary history.

A quick read shows a straightforward story, a wholesome Walton's Mountain passage of gradual genetic changes to the next generation. But as scientists are getting closer looks at thousands of genes from dozens of life forms, they're finding that the tale of evolution is more like "Melrose Place."

Organisms don't always inherit genes only from their parents; they also can get them from their neighbors. It's a genetic block party.

Swapping genes "is the way of the world," said Carl Woese, a microbiologist at the University of Illinois at Urbana-Champaign. "Part and parcel of evolution is the import of new genes and maybe kicking out of others."

Besides filling in some key steps in the evolution of life, understanding how genes get donated from one species to another could help researchers predict what is ahead for certain organisms.

For example, most gene swapping discovered so far seems to have gone on between microscopic, one-celled organisms. So scientists interested in using microbes to clean up an industrial waste site need to know the likelihood that genes would be traded from their microbe to the ones already around.

Incompatible organisms

"You can think of organisms you wouldn't want to put together," said Claire Fraser, a biologist and president of The Institute for Genomic Research in Rockville, Md. "We don't understand all the intricacies of how it takes place."

And since gene-swapping, also known as lateral transfer, is so common among microbes, understanding it is key to understanding how the environment is responding to the stresses of civilization.

"Microorganisms are the base of the biosphere," said Mr. Woese. "Understanding lateral transfer is understanding the base of the biosphere."

It used to be that when scientists tried to place organisms in the story of evolution, they could go only by outward characteristics -- a person and a mouse, both with four limbs, would be put in a different group from plants, for example. Scientists also categorized creatures using characteristics they could see only with a microscope.

And then they got even more sophisticated, and started using organisms' genes. The more a particular gene from one organism looked like a gene from another, the closer the two species were depicted in evolution. The pattern that has emerged looks something like a tree, with similar organisms occupying branches near each other.

One part of the tree contains bacteria, single-celled microbes such as E. coli and salmonella. Another part contains people and other organisms whose cells show similar features. (People are on the same main part of the tree as amoebas, plants and molds.)

A third part of the tree contains a less-familiar type of organism called archaea. These microbes are also single-celled, and they tend to live in harsh environments.

The branching pattern is thought to represent the ancestry, or pedigree, for the world's life forms. But the new research is finding more and more examples where two far-apart branches on the tree really should be interconnected, because genes have been swapped between species.

"The recent insights are . . . that this is more rampant than we were led to believe," said Mitchell Sogin, an evolutionary biologist at the Marine Biological Laboratory in Woods Hole, Mass.

Tree of life

The standard tree of life is based on a gene that oversees production of a special molecule known as ribosomal RNA, or rRNA. Large numbers of these molecules form part of a cell's production facilities, helping guide the creation of important proteins needed for survival. Because every known organism has rRNA, the rRNA gene comes in handy to draw an evolutionary tree.

As evolution has progressed, the rRNA genes of different species have gradually changed -- to a point where a bacterium's rRNA is very different from a dog's, for instance. Over several decades of work, scientists have analyzed hundreds of different rRNA molecules and placed their owners on the evolutionary tree.

But now, scientists can easily learn about more than an organism's rRNA gene. In fact, for at least 20 organisms, researchers -- many at TIGR -- have deciphered the entire genetic blueprint. For the simplest organisms, bacteria and archaea, the number of genes can be a few hundred or thousand. For the most complex so far, a microscopic worm, the number of genes approaches 20,000.

Using computers to scrutinize these genes, scientists have found several instances in which genes (other than rRNA) from certain organisms would place those organisms in a different spot on the evolutionary tree than the rRNA gene would.

Ms. Fraser and her colleagues have found that about a quarter of the genes in the bacteria Thermotoga maritima are most similar to genes known so far only in archaea, an entirely different type of life.

Some of these, she suspects, were donated long ago from an archaeon.

Dieter Soll, a biochemist at Yale University in New Haven, Conn., and his colleagues have found that genes for crucial cell enzymes have been transferred from archaea to bacteria at two separate times during evolution.

And in what may be the most curious example of gene transfer, at least from a person's point of view, Mr. Sogin said his lab may have uncovered a case of a parasite picking up a gene from a mammal. Mr. Sogin and his colleagues are trying to decipher the genetic instructions from Giardia lamblia, the parasite that lives in mountain streams and causes intestinal distress.

The parasite's genetic blueprint is still only partly analyzed, but the scientists already have found a gene that closely resembles one found in rats and people.

Mr. Sogin said he can't say for sure who gave the gene to whom.

"That's the question," he said. "Did it come from giardia or did it get into giardia? My guess is that giardia got it" from some other organism.

Scientists don't know exactly how genes get passed between species.

In nature, if one cell bursts and its genes are released, other species might easily pick them up. Not every gene that gets picked up is likely to be permanently adopted, however. Some genes just might not work right in a new species, like a lawn mower engine that's not strong enough to move a car.

But by the luck of the draw, scientists say, sometimes a new gene will be just what an organism needs to survive in a different environment. Many researchers have suggested that donated genes help species exploit new environmental niches and are a big reason why life is so diverse.

And gene transfers shouldn't be that surprising. The class of cells that includes those now found in plants, people and fungi are thought to have arisen when an entire bacterium was engulfed by another type of cell. Today, the descendants of the bacteria are called mitochondria, and they serve as cells' energy-production plants. And bacteria that cause disease are well-known to swap genes that make them resistant to antibiotics.

While scientists have been able to pick out some cases of gene transfer, they say that other portions of the evolutionary record are inevitably lost through time.

But even though the rRNA evolutionary tree doesn't depict the details of the story, scientists believe it still represents the crux of life's pedigree. rRNA is crucial for life, Mr. Woese said, and tightly integrated into the inner workings of a cell.

"To define a grouping of organisms, you have to use the genes that are cemented into the structure of the organism," he said. "They are the basic fabric of the cell, and the other things are your luxury options."

Specific genes

In other words, rRNA and a few other genes are the framework of a cell's operations, but most of the genes are needed only in certain situations, so they exist only in certain species.

However, Mr. Sogin pointed out, scientists could theoretically find an organism whose rRNA gene was bacterial, for instance, but the rest of the genes were not. That type of organism would have a biological identity crisis.

"If we knew what the kernel set of genes were, but if it turned out that 99 percent of the genes were coming in and going out, what would that mean?" he asked. "Philosophically, it becomes tough."

Sue Goetinck writes for the Dallas Morning News.

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